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A

A - Variable in class edu.jhu.bme.smile.commons.math.L1LSCompressedSensing
 
a2fEdgeDirection - Static variable in class edu.jhu.cs.cisst.algorithms.geometry.surface.IsoSurfaceGenerator
a2fEdgeDirection lists the direction vector (vertex1-vertex0) for each edge in the cube.
a2fVertexOffset - Static variable in class edu.jhu.cs.cisst.algorithms.geometry.surface.IsoSurfaceGenerator
Lists the positions, relative to vertex 0, of each of the 8 vertices of a cube.
a2iEdgeConnection - Static variable in class edu.jhu.cs.cisst.algorithms.geometry.surface.IsoSurfaceGenerator
Lists the index of the endpoint vertices for each of the 12 edges of the cube.
a2iTetrahedronEdgeConnection - Static variable in class edu.jhu.cs.cisst.algorithms.geometry.surface.IsoSurfaceGenerator
Lists the index of the endpoint vertices for each of the 6 edges of the tetrahedron.
a2iTetrahedronsInACube - Static variable in class edu.jhu.cs.cisst.algorithms.geometry.surface.IsoSurfaceGenerator
Lists the index of verticies from a cube that made up each of the six tetrahedrons within the cube.
a2iTetrahedronTriangles - Static variable in class edu.jhu.cs.cisst.algorithms.geometry.surface.IsoSurfaceGenerator
For each of the possible vertex states listed in aiTetrahedronEdgeFlags there is a specific triangulation of the edge intersection points.
a2iTriangleConnectionTable - Static variable in class edu.jhu.cs.cisst.algorithms.geometry.surface.IsoSurfaceGenerator
For each of the possible vertex states listed in aiCubeEdgeFlags there is a specific triangulation of the edge intersection points.
aboutItem - Variable in class edu.jhu.ece.iacl.jist.pipeline.gui.PipelineLayoutTool
The paste item.
abs(float) - Static method in class edu.jhmi.rad.medic.utilities.NumericsPublic
 
abs(double) - Static method in class edu.jhmi.rad.medic.utilities.NumericsPublic
 
abs(int) - Static method in class edu.jhmi.rad.medic.utilities.NumericsPublic
 
AbstractCalculation - Class in edu.jhu.ece.iacl.jist.pipeline
Observable Calculation allows a calculation to be monitored.
AbstractCalculation() - Constructor for class edu.jhu.ece.iacl.jist.pipeline.AbstractCalculation
Default constructor.
AbstractCalculation(AbstractCalculation) - Constructor for class edu.jhu.ece.iacl.jist.pipeline.AbstractCalculation
Constructor with parent calculation.
accept(List<String>) - Method in class edu.jhu.ece.iacl.jist.io.FileExtensionFilter
Accept.
accept(File) - Method in class edu.jhu.ece.iacl.jist.io.FileExtensionFilter
 
accept(File) - Method in class edu.jhu.ece.iacl.jist.io.FileReaderWriter
Accept.
ace - Static variable in class edu.jhu.ece.iacl.algorithms.ReferencedPapers
 
action - Variable in class edu.jhu.ece.iacl.jist.pipeline.gui.PipeInternalFrame.EventRedirector
The action.
actionPerformed(ActionEvent) - Method in class edu.jhu.cs.cisst.vent.VisualizationApplication
 
actionPerformed(ActionEvent) - Method in class edu.jhu.ece.iacl.algorithms.dti.tractography.FACT.cPT
 
actionPerformed(ActionEvent) - Method in class edu.jhu.ece.iacl.jist.dialogs.JDialogSaveAll
 
actionPerformed(ActionEvent) - Method in class edu.jhu.ece.iacl.jist.pipeline.gui.GlobalPreferencePanel
 
actionPerformed(ActionEvent) - Method in class edu.jhu.ece.iacl.jist.pipeline.gui.LayoutPreferencePanel
 
actionPerformed(ActionEvent) - Method in class edu.jhu.ece.iacl.jist.pipeline.gui.PipeInternalFrame.EventRedirector
 
actionPerformed(ActionEvent) - Method in class edu.jhu.ece.iacl.jist.pipeline.gui.PipelineLayoutTool
 
actionPerformed(ActionEvent) - Method in class edu.jhu.ece.iacl.jist.pipeline.gui.PlugInSelector
Respond to if user presses Ok or Cancel.
actionPerformed(ActionEvent) - Method in class edu.jhu.ece.iacl.jist.pipeline.gui.PortComboBox
 
actionPerformed(ActionEvent) - Method in class edu.jhu.ece.iacl.jist.pipeline.gui.PortListBox
Action performed.
actionPerformed(ActionEvent) - Method in class edu.jhu.ece.iacl.jist.pipeline.gui.PortToggleButton
 
actionPerformed(ActionEvent) - Method in class edu.jhu.ece.iacl.jist.pipeline.gui.ProcessDebugInfoFrame
 
actionPerformed(ActionEvent) - Method in class edu.jhu.ece.iacl.jist.pipeline.gui.ProcessManager
 
actionPerformed(ActionEvent) - Method in class edu.jhu.ece.iacl.jist.pipeline.gui.ProcessManagerTable
 
actionPerformed(ActionEvent) - Method in class edu.jhu.ece.iacl.jist.pipeline.PipeScheduler.CleanAllDialog
 
actionPerformed(ActionEvent) - Method in class edu.jhu.ece.iacl.jist.pipeline.ProcessingDialog
Handle action events.
actionPerformed(ActionEvent) - Method in class edu.jhu.ece.iacl.jist.pipeline.view.input.AlgorithmInformationDialog
 
actionPerformed(ActionEvent) - Method in class edu.jhu.ece.iacl.jist.pipeline.view.input.AlgorithmInformationDialog.AuthorDialog
 
actionPerformed(ActionEvent) - Method in class edu.jhu.ece.iacl.jist.pipeline.view.input.AlgorithmInformationDialog.CitationDialog
 
actionPerformed(ActionEvent) - Method in class edu.jhu.ece.iacl.jist.pipeline.view.input.InformationListBox
Select files to load when the browse button is clicked.
actionPerformed(ActionEvent) - Method in class edu.jhu.ece.iacl.jist.pipeline.view.input.ParamColorInputView
 
actionPerformed(ActionEvent) - Method in class edu.jhu.ece.iacl.jist.pipeline.view.input.ParamDataLabelInputView
Open file dialog when load button is pressed.
actionPerformed(ActionEvent) - Method in class edu.jhu.ece.iacl.jist.pipeline.view.input.ParamFileCollectionInputView
Select files to load when the browse button is clicked.
actionPerformed(ActionEvent) - Method in class edu.jhu.ece.iacl.jist.pipeline.view.input.ParamFileInputView
Open file dialog box when browse button is pressed.
actionPerformed(ActionEvent) - Method in class edu.jhu.ece.iacl.jist.pipeline.view.input.ParamInformationInputView
Open file dialog box when browse button is pressed.
actionPerformed(ActionEvent) - Method in class edu.jhu.ece.iacl.jist.pipeline.view.input.ParamMatrixInputView
 
actionPerformed(ActionEvent) - Method in class edu.jhu.ece.iacl.jist.pipeline.view.input.ParamMipavDialogInputView
Display mipav dialog when user clicks view button.
actionPerformed(ActionEvent) - Method in class edu.jhu.ece.iacl.jist.pipeline.view.input.ParamNumberCollectionInputView
Select numbers to load when the browse button is clicked.
actionPerformed(ActionEvent) - Method in class edu.jhu.ece.iacl.jist.pipeline.view.input.ParamNumberTextInputView
 
actionPerformed(ActionEvent) - Method in class edu.jhu.ece.iacl.jist.pipeline.view.input.ParamOptionInputView
Update parameter with current selected option.
actionPerformed(ActionEvent) - Method in class edu.jhu.ece.iacl.jist.pipeline.view.input.ParamPointDoubleTextInputView
 
actionPerformed(ActionEvent) - Method in class edu.jhu.ece.iacl.jist.pipeline.view.input.ParamPointFloatTextInputView
 
actionPerformed(ActionEvent) - Method in class edu.jhu.ece.iacl.jist.pipeline.view.input.ParamTextInputView
 
actionPerformed(ActionEvent) - Method in class edu.jhu.ece.iacl.jist.pipeline.view.input.ParamURIInputView
Open file dialog box when browse button is pressed.
actionPerformed(ActionEvent) - Method in class edu.jhu.ece.iacl.jist.pipeline.view.input.ParamVolumeCollectionInputView
Select images to load when the browse button is clicked.
actionPerformed(ActionEvent) - Method in class edu.jhu.ece.iacl.jist.pipeline.view.input.ParamVolumeInputView
 
actionPerformed(ActionEvent) - Method in class edu.jhu.ece.iacl.jist.pipeline.view.input.ParamVolumeURICollectionInputView
Select files to load when the browse button is clicked.
actionPerformed(ActionEvent) - Method in class edu.jhu.ece.iacl.jist.pipeline.view.input.ParamVolumeURIInputView
 
actionPerformed(ActionEvent) - Method in class edu.jhu.ece.iacl.jist.pipeline.view.input.ParamWeightedVolumesInputView
Select images to load when the browse button is clicked.
actionPerformed(ActionEvent) - Method in class edu.jhu.ece.iacl.jist.pipeline.view.input.ParamWeightedVolumesURIInputView
Select images to load when the browse button is clicked.
actionPerformed(ActionEvent) - Method in class edu.jhu.ece.iacl.jist.pipeline.view.output.ParamSurfaceOutputView
 
actionPerformed(ActionEvent) - Method in class edu.jhu.ece.iacl.jist.pipeline.view.output.ParamVolumeOutputView
 
actionPerformed(ActionEvent) - Method in class license.JISTLicenseAbout
 
ActiveContourForce2D - Class in edu.jhu.cs.cisst.algorithms.segmentation.gac
The Class ActiveContourForce2D is an abstract class to represent level set forces.
ActiveContourForce2D(GridPoint2D[][], double) - Constructor for class edu.jhu.cs.cisst.algorithms.segmentation.gac.ActiveContourForce2D
Instantiates a new active contour force.
ActiveContourForce2D(GridPoint2D[][]) - Constructor for class edu.jhu.cs.cisst.algorithms.segmentation.gac.ActiveContourForce2D
Instantiates a new active contour force.
ActiveContourForce2D() - Constructor for class edu.jhu.cs.cisst.algorithms.segmentation.gac.ActiveContourForce2D
Instantiates a new active contour force.
activePoints - Variable in class edu.jhu.cs.cisst.algorithms.segmentation.gac.GeodesicActiveContour2D
The active points.
actualElapsed - Variable in class edu.jhu.ece.iacl.jist.pipeline.PerformanceSummary.TimeAndMemoryStamp
The actual elapsed time.
actuallySampleMatrix(int, int, int, int) - Method in class edu.jhu.cs.cisst.algorithms.optimize.fmg.pde.CachingPDE
sample the matrix A in a way that it can later be used by methods evaluate() and evaluateLHS() on a grid of the given size.
actuallySampleMatrix(int, int, int, int) - Method in class edu.jhu.cs.cisst.algorithms.segmentation.gac.VectorFieldDiffusion2D
implements method from CachingPDE.
actuallySampleRHS(int, int, int, int) - Method in class edu.jhu.cs.cisst.algorithms.optimize.fmg.pde.CachingPDE
sample the right hand side f on a cubic grid of the given size.
actuallySampleRHS(int, int, int, int) - Method in class edu.jhu.cs.cisst.algorithms.segmentation.gac.VectorFieldDiffusion2D
implements method from CachingPDE.
actualStart - Variable in class edu.jhu.ece.iacl.jist.pipeline.PerformanceSummary.TimeAndMemoryStamp
The actual start time.
actualStop - Variable in class edu.jhu.ece.iacl.jist.pipeline.PerformanceSummary.TimeAndMemoryStamp
The actual stop time.
actualTime - Variable in class edu.jhu.ece.iacl.jist.pipeline.ExecutionContext
Elapsed actual time in milliseconds.
add(Matrix, double) - Static method in class edu.jhu.bme.smile.commons.math.MatrixMath
 
add(ConstGrid) - Method in interface edu.jhu.cs.cisst.algorithms.optimize.fmg.grid.ConstGrid
create a new grid that is the sum of this grid and the given grid.
add(int, int, int, double) - Method in class edu.jhu.cs.cisst.algorithms.optimize.fmg.grid.Grid
add to the element at the specified position, which must be in the interior of the grid.
add(ConstGrid) - Method in class edu.jhu.cs.cisst.algorithms.optimize.fmg.grid.Grid
implements method from ConstGrid.
add(ActiveContourForce2D) - Method in class edu.jhu.cs.cisst.algorithms.segmentation.gac.GeodesicActiveContour2D
Adds the force.
add(ImageData) - Method in class edu.jhu.cs.cisst.vent.widgets.VisualizationImage
Adds the image.
add(EmbeddedSurface) - Method in class edu.jhu.cs.cisst.vent.widgets.VisualizationTriangleMesh
Adds the.
add(LabelImage, Integer) - Method in class edu.jhu.ece.iacl.algorithms.manual_label.LabelImageGroup
 
add(LabelImage, int) - Method in class edu.jhu.ece.iacl.algorithms.manual_label.LabelImageGroup
 
add(DocumentAllTests.Assertion) - Method in class edu.jhu.ece.iacl.doc.DocumentAllTests.TestCase
 
add(DocumentAllTests.ModuleDescription) - Method in class edu.jhu.ece.iacl.doc.DocumentAllTests.TestCase
 
add(AbstractCalculation) - Method in class edu.jhu.ece.iacl.jist.pipeline.AbstractCalculation
Add a child calculation to this calculation.
add(AlgorithmInformation.AlgorithmAuthor) - Method in class edu.jhu.ece.iacl.jist.pipeline.AlgorithmInformation
Adds the.
add(AlgorithmInformation.Citation) - Method in class edu.jhu.ece.iacl.jist.pipeline.AlgorithmInformation
Adds the.
add(T) - Method in interface edu.jhu.ece.iacl.jist.pipeline.parameter.ObjectCollection
Add item to collection.
add(Object) - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamCollection
Add object.
add(ParamModel) - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamCollection
Add parameter to children.
add(DataLabel) - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamDataLabel
Add data label to collection.
add(File) - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamFileCollection
Add file to collection.
add(Object) - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamFileCollection
Add a new value to the collection.
add(String) - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamMultiOption
Add string option.
add(Number) - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamNumberCollection
Add file to collection.
add(Object) - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamNumberCollection
Add a new value to the collection.
add(String) - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamOption
Add option to list.
add(Object) - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamSurfaceCollection
Add a new value to the collection.
add(Object) - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamVolumeCollection
Add a new value to the collection.
add(PipeAlgorithm) - Method in class edu.jhu.ece.iacl.jist.pipeline.PipeAlgorithmGroup
Add algorithm to collection.
add(PipeModule) - Method in class edu.jhu.ece.iacl.jist.pipeline.PipeLayout
Add module to layout.
add(Refreshable) - Method in class edu.jhu.ece.iacl.jist.pipeline.view.input.Refresher
add item to monitor.
add(Indexable) - Method in class edu.jhu.ece.iacl.jist.structures.data.BinaryMinFastHeap
Insert into the priority queue.
add(Indexable) - Method in class edu.jhu.ece.iacl.jist.structures.data.BinaryMinHeap
Insert into the priority queue.
add(Point3f) - Method in class edu.jhu.ece.iacl.jist.structures.geom.CurvePath
Adds the.
add(Triangle) - Method in class edu.jhu.ece.iacl.jist.structures.geom.Edge
Adds the.
add(Face) - Method in class edu.jhu.ece.iacl.jist.structures.geom.Surface
Adds the.
add(Edge) - Method in class edu.jhu.ece.iacl.jist.structures.geom.Vertex
Adds the.
add(ImageData) - Method in class edu.jhu.ece.iacl.jist.structures.image.ImageDataDouble
Adds the.
add(Voxel) - Method in class edu.jhu.ece.iacl.jist.structures.image.Voxel
Adds the.
add(Voxel) - Method in class edu.jhu.ece.iacl.jist.structures.image.VoxelBoolean
 
add(Voxel) - Method in class edu.jhu.ece.iacl.jist.structures.image.VoxelColor
 
add(Voxel) - Method in class edu.jhu.ece.iacl.jist.structures.image.VoxelDouble
 
add(Voxel) - Method in class edu.jhu.ece.iacl.jist.structures.image.VoxelFloat
 
add(Voxel) - Method in class edu.jhu.ece.iacl.jist.structures.image.VoxelIndexed
 
add(Voxel) - Method in class edu.jhu.ece.iacl.jist.structures.image.VoxelInt
 
add(Voxel) - Method in class edu.jhu.ece.iacl.jist.structures.image.VoxelMipav
 
add(Voxel) - Method in class edu.jhu.ece.iacl.jist.structures.image.VoxelShort
 
add(Voxel) - Method in class edu.jhu.ece.iacl.jist.structures.image.VoxelUByte
 
add(Voxel) - Method in class edu.jhu.ece.iacl.jist.structures.image.VoxelVector
 
add(double) - Method in class edu.jhu.ece.iacl.jist.structures.matrix.Matrix3
Adds the.
add(Matrix3) - Method in class edu.jhu.ece.iacl.jist.structures.matrix.Matrix3
Adds the.
add(double) - Method in class edu.jhu.ece.iacl.jist.structures.matrix.VectorMatrixX
Adds the.
add(VectorMatrixX) - Method in class edu.jhu.ece.iacl.jist.structures.matrix.VectorMatrixX
Adds the.
add(double) - Method in class edu.jhu.ece.iacl.jist.structures.vector.Vector2
 
add(VectorX) - Method in class edu.jhu.ece.iacl.jist.structures.vector.Vector2
 
add(double) - Method in class edu.jhu.ece.iacl.jist.structures.vector.Vector3
 
add(VectorX) - Method in class edu.jhu.ece.iacl.jist.structures.vector.Vector3
 
add(double) - Method in class edu.jhu.ece.iacl.jist.structures.vector.Vector4
 
add(VectorX) - Method in class edu.jhu.ece.iacl.jist.structures.vector.Vector4
 
add(double) - Method in class edu.jhu.ece.iacl.jist.structures.vector.VectorN
 
add(VectorX) - Method in class edu.jhu.ece.iacl.jist.structures.vector.VectorN
 
add(double) - Method in interface edu.jhu.ece.iacl.jist.structures.vector.VectorX
Adds the.
add(VectorX) - Method in interface edu.jhu.ece.iacl.jist.structures.vector.VectorX
Adds the.
addButton - Variable in class edu.jhu.ece.iacl.jist.pipeline.view.input.ParamVolumeCollectionInputView
The add button.
addChild(ExecutionContext) - Method in class edu.jhu.ece.iacl.jist.pipeline.ExecutionContext
Add child execution context that pulls data from this context.
addContextListener(ExecutionContext.ContextListener) - Method in class edu.jhu.ece.iacl.jist.pipeline.ExecutionContext
Add context listener.
addDependencyContexts(Vector<PipeAlgorithm>, int) - Method in class edu.jhu.ece.iacl.jist.pipeline.PipeScheduler
Create dependent contexts for specified parent contexts.
addEdge(Hashtable<Long, IsoContourGenerator.EdgeSplit>, LinkedList<IsoContourGenerator.Edge>, int, int, int, int, int, int, int, int) - Method in class edu.jhu.cs.cisst.algorithms.geometry.surface.IsoContourGenerator
Adds the edge.
addFileToHistory(File) - Method in class edu.jhu.ece.iacl.jist.pipeline.JistPreferences
Add file to history.
addFloatImage(ImageData, ImageData) - Static method in class edu.jhu.ece.iacl.structures.image.ImageDataMath
Adds the float image.
addFrame(String) - Method in class edu.jhu.ece.iacl.jist.pipeline.gui.LayoutPanel
Add frame with particular name.
AddingNoise - Class in edu.jhu.bme.smile.demo
 
AddingNoise() - Constructor for class edu.jhu.bme.smile.demo.AddingNoise
 
addItem() - Method in class edu.jhu.ece.iacl.jist.pipeline.view.input.AlgorithmInformationDialog.AuthorListBox
Add new author.
addItem() - Method in class edu.jhu.ece.iacl.jist.pipeline.view.input.AlgorithmInformationDialog.CitationListBox
Add new citation.
addItem() - Method in class edu.jhu.ece.iacl.jist.pipeline.view.input.InformationListBox
Called when "ADD" button is clicked.
addLayoutFrame() - Method in class edu.jhu.ece.iacl.jist.pipeline.gui.LayoutPanel
Add internal frame to desktop layout.
addListener(JistPreferences.PreferenceListener) - Method in class edu.jhu.ece.iacl.jist.pipeline.JistPreferences
Add listener.
addListener(PipeModule.PipeListener) - Method in class edu.jhu.ece.iacl.jist.pipeline.PipeModule
Add listener for this module.
addListener(PipePort.PortListener) - Method in class edu.jhu.ece.iacl.jist.pipeline.PipePort
Add listener.
addObserver(ParamViewObserver) - Method in class edu.jhu.ece.iacl.jist.pipeline.view.input.ParamInputView
Add observer to listen for changes to parameter values.
addOption(String, boolean, String) - Method in class edu.jhu.ece.iacl.jist.cli.JistCLI
 
addParent(ExecutionContext) - Method in class edu.jhu.ece.iacl.jist.pipeline.ExecutionContext
Add parent execution context that pushes data to this context.
addPicture(String) - Method in class edu.jhu.ece.iacl.doc.DocMediaWikiWriter
 
addRicianNoise(float, float) - Method in class edu.jhu.ece.iacl.pami.SimFramework
 
AddToFileCollection - Class in edu.jhu.ece.iacl.plugins.utilities.file
 
AddToFileCollection() - Constructor for class edu.jhu.ece.iacl.plugins.utilities.file.AddToFileCollection
 
addTotalUnits(long) - Method in class edu.jhu.ece.iacl.jist.pipeline.AbstractCalculation
Add extra computational units to the total computational units.
addVxToLookupTable(Map, int, char, char) - Method in class edu.jhu.ece.iacl.algorithms.dti.tractography.FACT.FACTfiber
 
addWeightedVolume() - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamWeightedVolumeCollection
 
adjacencies - Variable in class edu.jhu.ece.iacl.jist.structures.geom.EmbeddedPointSet
The adjacencies.
AdvectionForce2D - Class in edu.jhu.cs.cisst.algorithms.segmentation.gac
The Class AdvectionForce2D moves the zero level set in the direction of the force field.
AdvectionForce2D(float[][][]) - Constructor for class edu.jhu.cs.cisst.algorithms.segmentation.gac.AdvectionForce2D
Instantiates a new advection force.
affiliation - Variable in class edu.jhu.ece.iacl.jist.pipeline.AlgorithmInformation
The institute affiliation.
affiliation - Variable in class edu.jhu.ece.iacl.jist.pipeline.view.input.AlgorithmInformationDialog
The text fields.
affineTransformVertices(Matrix3f, Point3f) - Method in class edu.jhu.ece.iacl.jist.structures.geom.EmbeddedSurface
Affine transform vertices.
aiCubeEdgeFlags - Static variable in class edu.jhu.cs.cisst.algorithms.geometry.surface.IsoSurfaceGenerator
For any edge, if one vertex is inside of the surface and the other is outside of the surface then the edge intersects the surface For each of the 8 vertices of the cube can be two possible states : either inside or outside of the surface For any cube the are 2^8=256 possible sets of vertex states This table lists the edges intersected by the surface for all 256 possible vertex states There are 12 edges.
aiTetrahedronEdgeFlags - Static variable in class edu.jhu.cs.cisst.algorithms.geometry.surface.IsoSurfaceGenerator
For any edge, if one vertex is inside of the surface and the other is outside of the surface then the edge intersects the surface For each of the 4 vertices of the tetrahedron can be two possible states : either inside or outside of the surface For any tetrahedron the are 2^4=16 possible sets of vertex states This table lists the edges intersected by the surface for all 16 possible vertex states There are 6 edges.
algo - Variable in class edu.jhu.ece.iacl.jist.pipeline.ExecutionContext
Algorithm associated with this context.
algo - Variable in class edu.jhu.ece.iacl.jist.pipeline.gui.PlugInSelector
The algo.
algo - Variable in class edu.jhu.ece.iacl.jist.pipeline.PipeAlgorithm
processing algorithm.
algo - Variable in class edu.jhu.ece.iacl.jist.plugins.MedicAlgorithmExecutableAdapter
The algo.
algorithm - Variable in class edu.jhu.ece.iacl.jist.pipeline.ProcessingDialog
processing algorithm
algorithmClass - Variable in class edu.jhu.ece.iacl.jist.pipeline.AlgorithmInformation
The algorithm class.
AlgorithmComputeConnectivityMatrix - Class in edu.jhu.ece.iacl.plugins.dti.tractography
 
AlgorithmComputeConnectivityMatrix() - Constructor for class edu.jhu.ece.iacl.plugins.dti.tractography.AlgorithmComputeConnectivityMatrix
 
AlgorithmDWIMotionCorrection - Class in edu.jhu.ece.iacl.plugins.dti
 
AlgorithmDWIMotionCorrection() - Constructor for class edu.jhu.ece.iacl.plugins.dti.AlgorithmDWIMotionCorrection
 
AlgorithmGradientTableCorrection - Class in edu.jhu.ece.iacl.plugins.dti
 
AlgorithmGradientTableCorrection() - Constructor for class edu.jhu.ece.iacl.plugins.dti.AlgorithmGradientTableCorrection
 
AlgorithmInformation - Class in edu.jhu.ece.iacl.jist.pipeline
Information that describes the algorithm, including its authors, citations, and version information.
AlgorithmInformation(ProcessingAlgorithm) - Constructor for class edu.jhu.ece.iacl.jist.pipeline.AlgorithmInformation
Instantiates a new algorithm information.
AlgorithmInformation(String, String, String) - Constructor for class edu.jhu.ece.iacl.jist.pipeline.AlgorithmInformation
Instantiates a new algorithm information.
algorithmInformation - Variable in class edu.jhu.ece.iacl.jist.pipeline.ProcessingAlgorithm
Algorithm information associated with all algorithms.
AlgorithmInformation.AlgorithmAuthor - Class in edu.jhu.ece.iacl.jist.pipeline
The Class AlgorithmAuthor.
AlgorithmInformation.AlgorithmAuthor(String, String, String) - Constructor for class edu.jhu.ece.iacl.jist.pipeline.AlgorithmInformation.AlgorithmAuthor
Instantiates a new algorithm author.
AlgorithmInformation.Citation - Class in edu.jhu.ece.iacl.jist.pipeline
The Class Citation.
AlgorithmInformation.Citation(String) - Constructor for class edu.jhu.ece.iacl.jist.pipeline.AlgorithmInformation.Citation
Instantiates a new citation.
AlgorithmInformationDialog - Class in edu.jhu.ece.iacl.jist.pipeline.view.input
Dialog to view/edit information about the algorithm.
AlgorithmInformationDialog(Frame, AlgorithmInformation) - Constructor for class edu.jhu.ece.iacl.jist.pipeline.view.input.AlgorithmInformationDialog
Default constructor.
AlgorithmInformationDialog.AuthorDialog - Class in edu.jhu.ece.iacl.jist.pipeline.view.input
Author dialog allows user to edit author information.
AlgorithmInformationDialog.AuthorDialog(boolean) - Constructor for class edu.jhu.ece.iacl.jist.pipeline.view.input.AlgorithmInformationDialog.AuthorDialog
Default constructor.
AlgorithmInformationDialog.AuthorDialog(AlgorithmInformation.AlgorithmAuthor, boolean) - Constructor for class edu.jhu.ece.iacl.jist.pipeline.view.input.AlgorithmInformationDialog.AuthorDialog
Default constructor.
AlgorithmInformationDialog.AuthorListBox - Class in edu.jhu.ece.iacl.jist.pipeline.view.input
Author list box displays author information.
AlgorithmInformationDialog.AuthorListBox(boolean) - Constructor for class edu.jhu.ece.iacl.jist.pipeline.view.input.AlgorithmInformationDialog.AuthorListBox
Instantiates a new author list box.
AlgorithmInformationDialog.CitationDialog - Class in edu.jhu.ece.iacl.jist.pipeline.view.input
Citation dialog allows user to edge citation information.
AlgorithmInformationDialog.CitationDialog(boolean) - Constructor for class edu.jhu.ece.iacl.jist.pipeline.view.input.AlgorithmInformationDialog.CitationDialog
Instantiates a new citation dialog.
AlgorithmInformationDialog.CitationDialog(AlgorithmInformation.Citation, boolean) - Constructor for class edu.jhu.ece.iacl.jist.pipeline.view.input.AlgorithmInformationDialog.CitationDialog
Default constructor.
AlgorithmInformationDialog.CitationListBox - Class in edu.jhu.ece.iacl.jist.pipeline.view.input
Citation list box displays citations formated as HTML.
AlgorithmInformationDialog.CitationListBox(boolean) - Constructor for class edu.jhu.ece.iacl.jist.pipeline.view.input.AlgorithmInformationDialog.CitationListBox
Default constructor.
AlgorithmJointROIStats - Class in edu.jhu.ece.iacl.plugins.utilities.roi
 
AlgorithmJointROIStats() - Constructor for class edu.jhu.ece.iacl.plugins.utilities.roi.AlgorithmJointROIStats
 
AlgorithmLogOdds - Class in edu.jhu.ece.iacl.plugins.labeling.atlasing
 
AlgorithmLogOdds() - Constructor for class edu.jhu.ece.iacl.plugins.labeling.atlasing.AlgorithmLogOdds
 
algorithmPerformed(AlgorithmBase) - Method in class edu.jhu.ece.iacl.jist.dialogs.JDialogSaveAll
 
algorithmPerformed(AlgorithmBase) - Method in class edu.jhu.ece.iacl.jist.pipeline.ProcessingDialog
Handle the termination of the algorithm.
AlgorithmROIStats - Class in edu.jhu.ece.iacl.plugins.utilities.roi
 
AlgorithmROIStats() - Constructor for class edu.jhu.ece.iacl.plugins.utilities.roi.AlgorithmROIStats
 
AlgorithmRuntimeException - Exception in edu.jhu.ece.iacl.jist.pipeline
Algorithm Runtime Exception for error that occurs when running an algorithm.
AlgorithmRuntimeException(String) - Constructor for exception edu.jhu.ece.iacl.jist.pipeline.AlgorithmRuntimeException
Default constructor.
AlgorithmSimulateSurfaceRater - Class in edu.jhu.ece.iacl.plugins.labeling.simulation
 
AlgorithmSimulateSurfaceRater() - Constructor for class edu.jhu.ece.iacl.plugins.labeling.simulation.AlgorithmSimulateSurfaceRater
 
AlgorithmSimulateVolumeRater - Class in edu.jhu.ece.iacl.plugins.labeling.simulation
 
AlgorithmSimulateVolumeRater() - Constructor for class edu.jhu.ece.iacl.plugins.labeling.simulation.AlgorithmSimulateVolumeRater
 
AlgorithmVolumeFileCollectionTo3D - Class in edu.jhu.ece.iacl.plugins.utilities.volume
 
AlgorithmVolumeFileCollectionTo3D() - Constructor for class edu.jhu.ece.iacl.plugins.utilities.volume.AlgorithmVolumeFileCollectionTo3D
 
algoRoot - Variable in class edu.jhu.ece.iacl.jist.pipeline.ExecutionContext
Root directory for algorithm.
allComparisonHits - Variable in class edu.jhu.ece.iacl.algorithms.manual_label.LabelImage
 
allcontrasts(float[][][][], float[][][], float[][][], float[][][], float[][][], float[][][][], float[][][][], float[][][][], float[][][][]) - Static method in class edu.jhu.ece.iacl.algorithms.dti.ComputeTensorContrasts
 
allhits - Variable in class edu.jhu.ece.iacl.algorithms.manual_label.LabelImage
 
allhits - Variable in class edu.jhu.ece.iacl.algorithms.manual_label.LabelSurface
 
allocatedMemory - Variable in class edu.jhu.ece.iacl.jist.pipeline.ExecutionContext
Allocated memory in MB.
allocatedMemory - Variable in class edu.jhu.ece.iacl.jist.pipeline.PerformanceSummary.TimeAndMemoryStamp
Allocated memory in MB.
ALPHA - Variable in class edu.jhu.bme.smile.commons.math.L1LSCompressedSensing
 
AnalyzeDists - Class in edu.jhu.ece.iacl.algorithms.dti.tractography.FACT
 
AnalyzeDists() - Constructor for class edu.jhu.ece.iacl.algorithms.dti.tractography.FACT.AnalyzeDists
 
ancestorsPane - Variable in class edu.jhu.ece.iacl.jist.pipeline.gui.ProcessManager
The ancestors pane.
ancestorTop - Variable in class edu.jhu.ece.iacl.jist.pipeline.ExecutionContext
Root node for ancestors.
ancestorTree - Variable in class edu.jhu.ece.iacl.jist.pipeline.ExecutionContext
Tree representing context ancestors.
and(Voxel) - Method in class edu.jhu.ece.iacl.jist.structures.image.VoxelBoolean
And.
angle(Tuple3f, Tuple3f) - Static method in class edu.jhu.ece.iacl.jist.algorithms.graphics.GeomUtil
Angle.
angle(Tuple2d, Tuple2d) - Static method in class edu.jhu.ece.iacl.jist.algorithms.graphics.GeomUtil
Angle.
angle(Point3f, Point3f, Point3f) - Static method in class edu.jhu.ece.iacl.jist.algorithms.graphics.GeomUtil
Angle.
angleBisect(Point3f, Point3f, Point3f) - Static method in class edu.jhu.ece.iacl.jist.algorithms.graphics.GeomUtil
Angle bisect.
angulationCorrection(double[][]) - Method in class edu.jhu.ece.iacl.algorithms.dti.DTIGradientTableCreator
Before this - be sure we have the correct table.
anova - Static variable in class edu.jhu.ece.iacl.algorithms.ReferencedPapers
 
append(GradientTable) - Method in class edu.jhu.ece.iacl.algorithms.dti.GradientTable
Appends an input Gradient Table to this object.
appendName - Variable in class edu.jhu.ece.iacl.jist.pipeline.dest.PipeParamCopyDestination
The append name.
applet - Variable in class edu.jhu.cs.cisst.vent.renderer.processing.ImageRenderer
The applet.
applet - Variable in class edu.jhu.cs.cisst.vent.renderer.processing.SurfaceRenderer
The applet.
applet - Variable in class edu.jhu.cs.cisst.vent.renderer.processing.VectorField2DRenderer
The applet.
applet - Variable in class edu.jhu.cs.cisst.vent.renderer.processing.VolumeSliceRenderer
The applet.
applyAffine(FiberCollection, double[][]) - Static method in class edu.jhu.ece.iacl.algorithms.dti.tractography.FiberTransformation
 
applyCorrection(double[][]) - Method in class edu.jhu.ece.iacl.algorithms.dti.GradTableCorrection
 
applyCorrection() - Method in class edu.jhu.ece.iacl.algorithms.dti.GradTableCorrection
 
applyCorrection(double[], double[][]) - Method in class edu.jhu.ece.iacl.plugins.registration.MedicAlgorithmEfficientFileCollectionRegistration
 
applyDeformation(FiberCollection, ImageDataMipav) - Static method in class edu.jhu.ece.iacl.algorithms.dti.tractography.FiberTransformation
 
applyPortAttributes(double, double, PipePort) - Method in class edu.jhu.ece.iacl.jist.pipeline.graph.PipeModulePort
Create port attributes.
applyROINum(int) - Method in class edu.jhu.ece.iacl.algorithms.manual_label.ROI
 
applyRotation(double[][], double[][]) - Method in class edu.jhu.ece.iacl.algorithms.dti.DTIGradientTableCreator
 
argmax(float, float, float) - Static method in class edu.jhmi.rad.medic.utilities.NumericsPublic
gives the position of the highest value
argmax(double, double, double) - Static method in class edu.jhmi.rad.medic.utilities.NumericsPublic
gives the position of the highest value
argsOrder - Variable in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamArgsOrder
The args order.
ArithmeticSolver - Class in edu.jhu.cs.cisst.algorithms.optimize.fmg.solver
Solve a linear elliptic PDE at the coarsest level (level = 1), i.e.
ArithmeticSolver(PDE) - Constructor for class edu.jhu.cs.cisst.algorithms.optimize.fmg.solver.ArithmeticSolver
construct from the PDE.
ArrayDoubleDxReaderWriter - Class in edu.jhu.ece.iacl.jist.io
The Class ArrayDoubleDxReaderWriter.
ArrayDoubleDxReaderWriter() - Constructor for class edu.jhu.ece.iacl.jist.io.ArrayDoubleDxReaderWriter
Instantiates a new array double dx reader writer.
ArrayDoubleListTxtReaderWriter - Class in edu.jhu.ece.iacl.jist.io
The Class ArrayDoubleListTxtReaderWriter.
ArrayDoubleListTxtReaderWriter() - Constructor for class edu.jhu.ece.iacl.jist.io.ArrayDoubleListTxtReaderWriter
Instantiates a new array double list txt reader writer.
ArrayDoubleMtxReaderWriter - Class in edu.jhu.ece.iacl.jist.io
The Class ArrayDoubleMtxReaderWriter.
ArrayDoubleMtxReaderWriter() - Constructor for class edu.jhu.ece.iacl.jist.io.ArrayDoubleMtxReaderWriter
Instantiates a new array double mtx reader writer.
ArrayDoubleReaderWriter - Class in edu.jhu.ece.iacl.jist.io
The Class ArrayDoubleReaderWriter.
ArrayDoubleReaderWriter(FileExtensionFilter) - Constructor for class edu.jhu.ece.iacl.jist.io.ArrayDoubleReaderWriter
Instantiates a new array double reader writer.
ArrayDoubleReaderWriter() - Constructor for class edu.jhu.ece.iacl.jist.io.ArrayDoubleReaderWriter
Instantiates a new array double reader writer.
ArrayDoubleTxtReaderWriter - Class in edu.jhu.ece.iacl.jist.io
The Class ArrayDoubleTxtReaderWriter.
ArrayDoubleTxtReaderWriter() - Constructor for class edu.jhu.ece.iacl.jist.io.ArrayDoubleTxtReaderWriter
Instantiates a new array double txt reader writer.
ArrayIntegerDxReaderWriter - Class in edu.jhu.ece.iacl.jist.io
The Class ArrayIntegerDxReaderWriter.
ArrayIntegerDxReaderWriter() - Constructor for class edu.jhu.ece.iacl.jist.io.ArrayIntegerDxReaderWriter
Instantiates a new array integer dx reader writer.
ArrayIntegerReaderWriter - Class in edu.jhu.ece.iacl.jist.io
The Class ArrayIntegerReaderWriter.
ArrayIntegerReaderWriter(FileExtensionFilter) - Constructor for class edu.jhu.ece.iacl.jist.io.ArrayIntegerReaderWriter
Instantiates a new array integer reader writer.
ArrayIntegerReaderWriter() - Constructor for class edu.jhu.ece.iacl.jist.io.ArrayIntegerReaderWriter
Instantiates a new array integer reader writer.
ArrayIntegerTxtReaderWriter - Class in edu.jhu.ece.iacl.jist.io
The Class ArrayIntegerTxtReaderWriter.
ArrayIntegerTxtReaderWriter() - Constructor for class edu.jhu.ece.iacl.jist.io.ArrayIntegerTxtReaderWriter
Instantiates a new array integer txt reader writer.
ArrayObjectTxtReaderWriter - Class in edu.jhu.ece.iacl.jist.io
The Class ArrayObjectTxtReaderWriter.
ArrayObjectTxtReaderWriter() - Constructor for class edu.jhu.ece.iacl.jist.io.ArrayObjectTxtReaderWriter
Instantiates a new array object txt reader writer.
ArrayPrinter - Class in edu.jhu.ece.iacl.algorithms.dti.tractography.FACT
 
ArrayPrinter() - Constructor for class edu.jhu.ece.iacl.algorithms.dti.tractography.FACT.ArrayPrinter
 
arrowColor - Variable in class edu.jhu.cs.cisst.vent.renderer.processing.VectorField2DRenderer
The arrow color.
arrowColorParam - Variable in class edu.jhu.cs.cisst.vent.renderer.processing.VectorField2DRenderer
The arrow color param.
arrowHeadHeight - Variable in class edu.jhu.cs.cisst.vent.renderer.processing.VectorField2DRenderer
The arrow head height.
arrowHeadHeightParam - Variable in class edu.jhu.cs.cisst.vent.renderer.processing.VectorField2DRenderer
The arrow head height param.
arrowHeadWidth - Variable in class edu.jhu.cs.cisst.vent.renderer.processing.VectorField2DRenderer
The arrow head width.
arrowHeadWidthParam - Variable in class edu.jhu.cs.cisst.vent.renderer.processing.VectorField2DRenderer
The arrow head width param.
arrowWidth - Variable in class edu.jhu.cs.cisst.vent.renderer.processing.VectorField2DRenderer
The arrow width.
arrowWidthParam - Variable in class edu.jhu.cs.cisst.vent.renderer.processing.VectorField2DRenderer
The arrow width param.
askForAlgorithm(Frame) - Static method in class edu.jhu.ece.iacl.jist.pipeline.gui.PlugInSelector
Get selected module factory.
askForJavaExecutable(File) - Static method in class edu.jhu.ece.iacl.jist.pipeline.JistPreferences
Open file chooser to select directory.
askForLibraryDirectory(File) - Static method in class edu.jhu.ece.iacl.jist.pipeline.PipeLibrary
Open file chooser to select directory.
AssertionFailedException - Exception in edu.jhu.cs.cisst.algorithms.optimize.fmg.util
Exception class that is thrown if an assertion failed.
AssertionFailedException() - Constructor for exception edu.jhu.cs.cisst.algorithms.optimize.fmg.util.AssertionFailedException
construct with no particular message.
AssertionFailedException(String) - Constructor for exception edu.jhu.cs.cisst.algorithms.optimize.fmg.util.AssertionFailedException
construct with the given message.
assertions - Variable in class edu.jhu.ece.iacl.doc.DocumentAllTests.TestCase
 
assertTrue - Variable in class edu.jhu.ece.iacl.plugins.utilities.logic.MedicAlgorithmValueEquals
 
assertTrue - Variable in class edu.jhu.ece.iacl.plugins.utilities.logic.MedicAlgorithmValueGreaterThan
Output Parameters
assertTrue - Variable in class edu.jhu.ece.iacl.plugins.utilities.logic.MedicAlgorithmValueInRange
 
assertTrue - Variable in class edu.jhu.ece.iacl.plugins.utilities.logic.MedicAlgorithmValueLessThan
 
At - Variable in class edu.jhu.bme.smile.commons.math.L1LSCompressedSensing
 
AtA2 - Variable in class edu.jhu.bme.smile.commons.math.L1LSCompressedSensing
 
AtlasList - Class in edu.jhu.ece.iacl.utility
 
AtlasList() - Constructor for class edu.jhu.ece.iacl.utility.AtlasList
 
author - Variable in class edu.jhu.ece.iacl.jist.pipeline.AlgorithmInformation.AlgorithmAuthor
The author.
author - Variable in class edu.jhu.ece.iacl.jist.pipeline.view.input.AlgorithmInformationDialog.AuthorDialog
The website.
AUTHOR_TAG - Static variable in class edu.jhu.ece.iacl.jist.pipeline.parser.LoniPipeParser
The Constant AUTHOR_TAG.
authorList - Variable in class edu.jhu.ece.iacl.jist.pipeline.view.input.AlgorithmInformationDialog
The author list.
authors - Variable in class edu.jhu.ece.iacl.jist.pipeline.AlgorithmInformation
Algorithm authors.
AUTHORS_TAG - Static variable in class edu.jhu.ece.iacl.jist.pipeline.parser.LoniPipeParser
The Constant AUTHORS_TAG.
autoMinMax - Variable in class edu.jhu.bme.smile.commons.math.HistogramGenerator
 
autoMinMax - Variable in class edu.jhu.ece.iacl.plugins.utilities.surface.MedicAlgorithmSurfaceHistogram
 
autoMinMax - Variable in class edu.jhu.ece.iacl.plugins.utilities.volume.MedicAlgorithmVolumeHistogram
 
AvoidanceRouting - Class in edu.jhu.ece.iacl.jist.pipeline.graph
Algorithm for routing connectors so that they avoid intersecting graph modules.
AvoidanceRouting() - Constructor for class edu.jhu.ece.iacl.jist.pipeline.graph.AvoidanceRouting
 
avoidanceRouting - Static variable in class edu.jhu.ece.iacl.jist.pipeline.graph.PipeModuleEdge
The Constant avoidanceRouting.
AvoidanceRouting.Dir - Enum in edu.jhu.ece.iacl.jist.pipeline.graph
The Enum Dir.
axisLength - Variable in class edu.jhu.cs.cisst.vent.widgets.VisualizationTriangleMesh
The axis length.
axisOrientation - Variable in class edu.jhu.ece.iacl.jist.structures.image.ImageHeader
The axis orientation.
axisOrientationNames - Static variable in class edu.jhu.ece.iacl.jist.structures.image.ImageHeader
The Constant axisOrientationNames.

B

b - Variable in class edu.jhu.ece.iacl.algorithms.dti.tractography.FACT.RGB
 
b - Variable in class edu.jhu.ece.iacl.jist.structures.image.RGB
The b.
background - Variable in class edu.jhmi.rad.medic.utilities.CropParameters
The background.
BACKWARD - Static variable in class edu.jhu.ece.iacl.algorithms.dti.tractography.FiberTracker
 
BACKWARD - Static variable in class edu.jhu.ece.iacl.algorithms.dti.tractography.WildBootFiberTracker
 
baiYing - Static variable in class edu.jhu.ece.iacl.algorithms.CommonAuthors
 
baseInit(Matrix, double, double, double[], double[], double[]) - Method in class edu.jhu.ece.iacl.algorithms.dti.DTEMRLTensor
 
baseWeight - Variable in class edu.jhu.ece.iacl.algorithms.manual_label.staple.STAPLE
 
BASIS_TYPE - Enum in edu.jhu.ece.iacl.algorithms.hardi
 
bbox - Variable in class edu.jhu.cs.cisst.vent.renderer.processing.RendererProcessing3D
The bbox.
bbox - Variable in class edu.jhu.cs.cisst.vent.widgets.VisualizationTriangleMesh
The bounding box.
bennettLandman - Static variable in class edu.jhu.ece.iacl.algorithms.CommonAuthors
 
bestIndex(float[]) - Static method in class edu.jhmi.rad.medic.utilities.NumericsPublic
find the index of the largest values in val (>=0)
bestIndex(float[], int) - Static method in class edu.jhmi.rad.medic.utilities.NumericsPublic
find the indices of the num largest values in val (>=0)
bestIndex(byte[], float[], int) - Static method in class edu.jhmi.rad.medic.utilities.NumericsPublic
find the indices of the num largest values in val (>=0)
bestIndex(byte[], float[], float[], int) - Static method in class edu.jhmi.rad.medic.utilities.NumericsPublic
find the indices of the num largest values in val (any sign)
bestIndex(short[], float[], float[], int) - Static method in class edu.jhmi.rad.medic.utilities.NumericsPublic
find the indices of the num largest values in val (any sign)
bestIndex(byte[], float[], float[], int, byte) - Static method in class edu.jhmi.rad.medic.utilities.NumericsPublic
find the indices of the num largest values in val (>=0)
BETA - Variable in class edu.jhu.bme.smile.commons.math.L1LSCompressedSensing
 
beta - Variable in class edu.jhu.ece.iacl.algorithms.manual_label.staple.STAPLEgeneral
 
bgColor - Variable in class edu.jhu.cs.cisst.vent.widgets.VisualizationTriangleMesh
The bg color.
bgColorParam - Variable in class edu.jhu.cs.cisst.vent.widgets.VisualizationTriangleMesh
The bg color param.
BILINEAR - Static variable in class edu.jhu.cs.cisst.algorithms.optimize.fmg.interpolator.InterpolatorByStencil
 
bin(boolean) - Static method in class edu.jhmi.rad.medic.utilities.NumericsPublic
boolean to number value
BinaryMaxHeap<E extends java.lang.Comparable<? super E>> - Class in edu.jhu.ece.iacl.jist.structures.data
Binary Max Heap uses Java implemention with reverse comparator.
BinaryMaxHeap() - Constructor for class edu.jhu.ece.iacl.jist.structures.data.BinaryMaxHeap
Instantiates a new binary max heap.
BinaryMinFastHeap - Class in edu.jhu.ece.iacl.jist.structures.data
Implements a binary heap.
BinaryMinFastHeap(int, int, int, int) - Constructor for class edu.jhu.ece.iacl.jist.structures.data.BinaryMinFastHeap
Instantiates a new binary min fast heap.
BinaryMinFastHeap(Indexable[]) - Constructor for class edu.jhu.ece.iacl.jist.structures.data.BinaryMinFastHeap
Construct the binary heap from an array.
BinaryMinHeap - Class in edu.jhu.ece.iacl.jist.structures.data
Implements a binary heap.
BinaryMinHeap(int, int, int, int) - Constructor for class edu.jhu.ece.iacl.jist.structures.data.BinaryMinHeap
Instantiates a new binary min heap.
BinaryMinHeap(Indexable[]) - Constructor for class edu.jhu.ece.iacl.jist.structures.data.BinaryMinHeap
Construct the binary heap from an array.
bins - Variable in class edu.jhu.bme.smile.commons.math.HistogramGenerator
 
bins - Variable in class edu.jhu.ece.iacl.plugins.utilities.surface.MedicAlgorithmSurfaceHistogram
 
bins - Variable in class edu.jhu.ece.iacl.plugins.utilities.volume.MedicAlgorithmVolumeHistogram
 
blakeLucas - Static variable in class edu.jhu.ece.iacl.algorithms.CommonAuthors
 
blur(float[][], double) - Static method in class edu.jhu.cs.cisst.algorithms.util.DataOperations
Blur.
BndBox - Class in edu.jhu.ece.iacl.jist.structures.geom
Created by IntelliJ IDEA.
BndBox() - Constructor for class edu.jhu.ece.iacl.jist.structures.geom.BndBox
Instantiates a new bnd box.
BndBox(PT, PT) - Constructor for class edu.jhu.ece.iacl.jist.structures.geom.BndBox
Instantiates a new bnd box.
bndBox - Variable in class edu.jhu.ece.iacl.jist.structures.geom.Polygon
The bnd box.
bootstrap(PipeAlgorithm, File, File, boolean) - Static method in class edu.jhu.ece.iacl.jist.cli.runLayout
 
border - Variable in class edu.jhu.ece.iacl.jist.pipeline.graph.PipeEdgeEditor.DefaultSpinner
Border to use.
BORDER_SPACE - Static variable in class edu.jhu.ece.iacl.jist.pipeline.graph.AvoidanceRouting
The BORDE r_ space.
bottomFile - Variable in class edu.jhu.ece.iacl.jist.pipeline.gui.ProcessDebugInfoFrame.FileText
The bottom file.
bottomTextArea - Variable in class edu.jhu.ece.iacl.jist.pipeline.gui.ProcessDebugInfoFrame.FileText
The bottom text area.
BoundaryGrid - Class in edu.jhu.cs.cisst.algorithms.optimize.fmg.grid
An implementation of Grid where a boundary of some kind is supported.
BoundaryGrid(int, int, int, int, double) - Constructor for class edu.jhu.cs.cisst.algorithms.optimize.fmg.grid.BoundaryGrid
construct from size and initial value for all elements in the interior.
bounded(int, int, int) - Static method in class edu.jhmi.rad.medic.utilities.NumericsPublic
 
bounded(float, float, float) - Static method in class edu.jhmi.rad.medic.utilities.NumericsPublic
 
bounded(double, double, double) - Static method in class edu.jhmi.rad.medic.utilities.NumericsPublic
 
boundingBox - Variable in class edu.jhu.ece.iacl.algorithms.vabra.ImagePair
 
bounds - Variable in class edu.jhu.cs.cisst.vent.renderer.processing.RendererProcessing2D
The bounds.
bounds - Variable in class edu.jhu.ece.iacl.jist.pipeline.PipeModule
Size of module in graph.
bounds - Variable in class edu.jhu.ece.iacl.jist.pipeline.view.output.ParamSurfaceOutputView
The bounds.
bounds - Variable in class edu.jhu.ece.iacl.jist.structures.geom.CollisionDetection
The bounds.
bout - Variable in class edu.jhu.ece.iacl.pami.SimFramework
 
brainResultVol - Variable in class edu.jhu.ece.iacl.plugins.segmentation.CreateMask
 
BrentMethod1D - Class in edu.jhu.bme.smile.commons.optimize
Optimizes functions by using Brent's method.
BrentMethod1D() - Constructor for class edu.jhu.bme.smile.commons.optimize.BrentMethod1D
Default constructor.
BrentMethod1D(int) - Constructor for class edu.jhu.bme.smile.commons.optimize.BrentMethod1D
Constructor to set maximum number of iterations to run
BrentMethod1D() - Static method in class edu.jhu.bme.smile.commons.optimize.test.Test1DOptimizations
Brent's Method
BrentMethod1D() - Static method in class edu.jhu.bme.smile.commons.optimize.test.TestNDOptimizations
Line Search using Brent's Method
brightness - Variable in class edu.jhu.cs.cisst.vent.renderer.processing.ImageRenderer
The brightness.
brightness - Variable in class edu.jhu.cs.cisst.vent.renderer.processing.VectorField2DRenderer
The brightness.
brightness - Variable in class edu.jhu.cs.cisst.vent.renderer.processing.VolumeSliceRenderer
The brightness.
brightnessParam - Variable in class edu.jhu.cs.cisst.vent.renderer.processing.ImageRenderer
The brightness param.
brightnessParam - Variable in class edu.jhu.cs.cisst.vent.renderer.processing.VolumeSliceRenderer
The brightness param.
browseButton - Variable in class edu.jhu.ece.iacl.jist.pipeline.view.input.ParamVolumeInputView
The browse button.
browseButton - Variable in class edu.jhu.ece.iacl.jist.pipeline.view.input.ParamVolumeURIInputView
The browse button.
bryanWheeler - Static variable in class edu.jhu.ece.iacl.algorithms.CommonAuthors
 
buildAllTables() - Method in class edu.jhu.ece.iacl.jist.structures.geom.EmbeddedSurface
Builds the all tables.
buildButtonPanel() - Method in class edu.jhu.ece.iacl.jist.pipeline.view.input.AlgorithmInformationDialog
Build button panel to select action.
buildDescriptionBox() - Method in class edu.jhu.ece.iacl.jist.pipeline.view.input.AlgorithmInformationDialog
Build panel for description box.
buildEdgeHash(EmbeddedSurface.Edge[]) - Static method in class edu.jhu.ece.iacl.jist.structures.geom.EmbeddedSurface
Builds the edge hash.
buildEdgeTable(ModelTriangleMesh) - Static method in class edu.jhu.ece.iacl.jist.structures.geom.EmbeddedSurface
Builds the edge table.
buildFaceTable(ModelTriangleMesh, EmbeddedSurface.Edge[], Hashtable<Long, EmbeddedSurface.Edge>) - Static method in class edu.jhu.ece.iacl.jist.structures.geom.EmbeddedSurface
Builds the face table.
buildInputButtons() - Method in class edu.jhu.ece.iacl.jist.pipeline.ProcessingDialog
Build buttons that will appear on input pane.
buildLabel(String) - Method in class edu.jhu.ece.iacl.jist.pipeline.view.input.ParamInputView
Initialize label for parameter input.
buildLabelAndParam(JComponent) - Method in class edu.jhu.ece.iacl.jist.pipeline.view.input.ParamInputView
Build panel that contains the label and parameter formatted in a standard way.
buildListBoxPanel() - Method in class edu.jhu.ece.iacl.jist.pipeline.view.input.AlgorithmInformationDialog
Build panel for list boxes.
buildNeighborEdgeFaceTable(ModelTriangleMesh, EmbeddedSurface.Face[], Hashtable<Long, EmbeddedSurface.Edge>, EmbeddedSurface.Edge[]) - Static method in class edu.jhu.ece.iacl.jist.structures.geom.EmbeddedSurface
Builds the neighbor edge face table.
buildNeighborFaceFaceTable(ModelTriangleMesh, EmbeddedSurface.Face[], EmbeddedSurface.Face[][]) - Static method in class edu.jhu.ece.iacl.jist.structures.geom.EmbeddedSurface
Builds the neighbor face face table.
buildNeighborVertexEdgeTable(int[][], EmbeddedSurface.Edge[], Hashtable<Long, EmbeddedSurface.Edge>) - Static method in class edu.jhu.ece.iacl.jist.structures.geom.EmbeddedSurface
Builds the neighbor vertex edge table.
buildNeighborVertexFaceTable(EmbeddedSurface.Edge[][], EmbeddedSurface.Face[][]) - Static method in class edu.jhu.ece.iacl.jist.structures.geom.EmbeddedSurface
Builds the neighbor vertex face table.
buildNeighborVertexVertexTable(ModelTriangleMesh, EmbeddedSurface.Direction) - Static method in class edu.jhu.ece.iacl.jist.structures.geom.EmbeddedSurface
Construct a neighbor table ordered in a particular direction.
buildOutputButtons() - Method in class edu.jhu.ece.iacl.jist.pipeline.ProcessingDialog
Build buttons that will appear on output pane.
buildTextEntryPanel() - Method in class edu.jhu.ece.iacl.jist.pipeline.view.input.AlgorithmInformationDialog
Build panel to enter text fields.
buildTitlePanel() - Method in class edu.jhu.ece.iacl.jist.pipeline.view.input.AlgorithmInformationDialog
Build panel to display algorithm name.
button - Variable in class edu.jhu.ece.iacl.jist.pipeline.view.output.ParamVolumeOutputView
The button.
buttonPanel - Variable in class edu.jhu.ece.iacl.jist.pipeline.ProcessingDialog
Panel for pushing buttons.
bvals - Variable in class edu.jhu.ece.iacl.algorithms.dti.GTCparams
 
byteValue() - Method in class edu.jhu.ece.iacl.jist.structures.image.Voxel
 

C

c - Variable in class edu.jhu.ece.iacl.jist.pipeline.graph.PipeModuleFactory
The c.
cachedInputParams - Variable in class edu.jhu.ece.iacl.jist.pipeline.ExecutionContext
Cached parameters to compare against when checking for changes.
cachedParams - Variable in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamWeightedVolumeCollection
Cache of old weighted volumes
cacheFile - Variable in class edu.jhu.cs.cisst.vent.VisualizationApplication
The cache file.
CachingPDE - Class in edu.jhu.cs.cisst.algorithms.optimize.fmg.pde
An abstract class that has the same public interface as class PDE but adds caching for improved performance of classes that dervie from it.
CachingPDE() - Constructor for class edu.jhu.cs.cisst.algorithms.optimize.fmg.pde.CachingPDE
 
calcResidual(ConstBoundaryGrid, ConstNoBoundaryGrid) - Method in class edu.jhu.cs.cisst.algorithms.optimize.fmg.FMG
calculate the residual of an approximate solution to a PDE.
CalcResidualParallelizer - Class in edu.jhu.cs.cisst.algorithms.optimize.fmg
A helper class of class FMG that helps parallelizing method FMG.calcResidual().
CalcResidualParallelizer(FMG, NoBoundaryGrid, ConstBoundaryGrid, ConstNoBoundaryGrid) - Constructor for class edu.jhu.cs.cisst.algorithms.optimize.fmg.CalcResidualParallelizer
construct.
calcResidualProper(NoBoundaryGrid, ConstBoundaryGrid, ConstNoBoundaryGrid, int, int) - Method in class edu.jhu.cs.cisst.algorithms.optimize.fmg.FMG
implements the parallel part of calcResidual().
calculateBin(double, double, double) - Static method in class edu.jhu.ece.iacl.algorithms.registration.RegistrationUtilities
 
calculateMaxAndMinVals() - Method in class edu.jhu.ece.iacl.algorithms.vabra.ImagePairNMI
 
calculateMinAndMaxVals(ImageData, ImageData) - Method in class edu.jhu.ece.iacl.plugins.registration.MedicAlgorithmAtlasSelection
 
calculateMinAndMaxVals(ImageData, ImageData) - Method in class edu.jhu.ece.iacl.plugins.registration.MedicAlgorithmCreateSimilarityMetricVol
 
CalculationMonitor - Class in edu.jhu.ece.iacl.jist.pipeline
Monitor a calculation during its execution.
CalculationMonitor(ProcessingAlgorithm, ViewJProgressBar) - Constructor for class edu.jhu.ece.iacl.jist.pipeline.CalculationMonitor
Default constructor with algorithm and progress bar.
CalculationMonitor(ProcessingAlgorithm, ViewJProgressBar, AbstractCalculation) - Constructor for class edu.jhu.ece.iacl.jist.pipeline.CalculationMonitor
Default constructor with progress bar, observable calculation, and algorithm.
callAlgorithm() - Method in class edu.jhu.ece.iacl.jist.dialogs.JDialogSaveAll
 
callAlgorithm() - Method in class edu.jhu.ece.iacl.jist.pipeline.ProcessingDialog
Start the algorithm; but first, save the input parameters as defaults.
callers - Variable in class edu.jhu.ece.iacl.jist.pipeline.ExecutionContext
Execution contexts that forward to this context.
cancelButton - Variable in class edu.jhu.ece.iacl.jist.pipeline.view.input.AlgorithmInformationDialog.AuthorDialog
The cancel button.
cancelCellEditing() - Method in class edu.jhu.ece.iacl.jist.pipeline.graph.PipeEdgeRealEditor
Forwards the message from the CellEditor to the delegate.
cancelCellEditing() - Method in class edu.jhu.ece.iacl.jist.pipeline.graph.PipeEdgeRealEditor.EditorDelegate
Cancels editing.
caretUpdate(CaretEvent) - Method in class edu.jhu.ece.iacl.jist.pipeline.view.input.ParamFileInputView
Update parameter when text field is changed.
caretUpdate(CaretEvent) - Method in class edu.jhu.ece.iacl.jist.pipeline.view.input.ParamMatrixInputView
A change has occurred to the input field.
caretUpdate(CaretEvent) - Method in class edu.jhu.ece.iacl.jist.pipeline.view.input.ParamNumberTextInputView
A change has occurred to the input field.
caretUpdate(CaretEvent) - Method in class edu.jhu.ece.iacl.jist.pipeline.view.input.ParamPointDoubleTextInputView
A change has occurred to the input field.
caretUpdate(CaretEvent) - Method in class edu.jhu.ece.iacl.jist.pipeline.view.input.ParamPointFloatTextInputView
A change has occurred to the input field.
caretUpdate(CaretEvent) - Method in class edu.jhu.ece.iacl.jist.pipeline.view.input.ParamPointSpinnerInputView
A change has occurred to the input field.
caretUpdate(CaretEvent) - Method in class edu.jhu.ece.iacl.jist.pipeline.view.input.ParamTextInputView
A change has occurred to the input field.
caretUpdate(CaretEvent) - Method in class edu.jhu.ece.iacl.jist.pipeline.view.input.ParamURIInputView
Update parameter when text field is changed.
caretUpdate(CaretEvent) - Method in class edu.jhu.ece.iacl.jist.pipeline.view.input.ParamVolumeURIInputView
 
cart2sph(int, float[][]) - Static method in class edu.jhu.bme.smile.commons.math.specialFunctions.SphericalHarmonics
 
category - Variable in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamCollection
The Category
CATEGORY - Static variable in class PlugInJISTLayoutTool
The Constant CATEGORY.
CATEGORY - Static variable in class PlugInJISTPlugInSelector
The Constant CATEGORY.
CATEGORY - Static variable in class PlugInJISTProcessManager
The Constant CATEGORY.
ceil(float) - Static method in class edu.jhmi.rad.medic.utilities.NumericsPublic
 
ceil(double) - Static method in class edu.jhmi.rad.medic.utilities.NumericsPublic
 
cell - Variable in class edu.jhu.ece.iacl.jist.pipeline.PipeModule
Module cell to render on graph.
cellData - Variable in class edu.jhu.ece.iacl.jist.structures.geom.EmbeddedPointSet
The cell data.
cellData - Variable in class edu.jhu.ece.iacl.jist.structures.geom.EmbeddedSurface
The cell data.
center - Variable in class edu.jhu.cs.cisst.vent.widgets.VisualizationTriangleMesh
The center.
center - Variable in class edu.jhu.ece.iacl.jist.pipeline.view.output.ParamSurfaceOutputView
The center.
center - Variable in class edu.jhu.ece.iacl.jist.structures.geom.CollisionDetection
The center.
centerFreq(double[], double[]) - Method in class edu.jhu.ece.iacl.algorithms.spectro.MSWASSR
function centerFreq = MSWASSR(X,y) % Find point of maximum symmetry in graph of X and Y % w0= SPWASSR(X,y); yy=y-min(y); w0 = mean(X(find(yycenterParam - Variable in class edu.jhu.cs.cisst.vent.widgets.VisualizationTriangleMesh
The center param.
CESTAsymmetry - Class in edu.jhu.ece.iacl.plugins.spectro
 
CESTAsymmetry() - Constructor for class edu.jhu.ece.iacl.plugins.spectro.CESTAsymmetry
 
CESTAsymmetry.AlgorithmWrapper - Class in edu.jhu.ece.iacl.plugins.spectro
 
CESTAsymmetry.AlgorithmWrapper() - Constructor for class edu.jhu.ece.iacl.plugins.spectro.CESTAsymmetry.AlgorithmWrapper
 
CFARIBasisFunction - Class in edu.jhu.ece.iacl.algorithms.hardi
 
CFARIBasisFunction() - Constructor for class edu.jhu.ece.iacl.algorithms.hardi.CFARIBasisFunction
 
CFARIBasisSet - Class in edu.jhu.ece.iacl.algorithms.hardi
 
CFARIBasisSet() - Constructor for class edu.jhu.ece.iacl.algorithms.hardi.CFARIBasisSet
 
CFARIBasisTensor - Class in edu.jhu.ece.iacl.algorithms.hardi
 
CFARIBasisTensor(Matrix) - Constructor for class edu.jhu.ece.iacl.algorithms.hardi.CFARIBasisTensor
 
CFARIEstimation - Class in edu.jhu.ece.iacl.plugins.hardi
 
CFARIEstimation() - Constructor for class edu.jhu.ece.iacl.plugins.hardi.CFARIEstimation
 
CFARIEstimation2 - Class in edu.jhu.ece.iacl.plugins.hardi
 
CFARIEstimation2() - Constructor for class edu.jhu.ece.iacl.plugins.hardi.CFARIEstimation2
 
CFARIEstimation2.CFARIWrapper - Class in edu.jhu.ece.iacl.plugins.hardi
 
CFARIEstimation2.CFARIWrapper() - Constructor for class edu.jhu.ece.iacl.plugins.hardi.CFARIEstimation2.CFARIWrapper
 
CFARIEstimator - Class in edu.jhu.ece.iacl.algorithms.hardi
 
CFARIEstimator() - Constructor for class edu.jhu.ece.iacl.algorithms.hardi.CFARIEstimator
 
CFARIEstimator2 - Class in edu.jhu.ece.iacl.algorithms.hardi
Used to process each voxel and returns the results.
CFARIEstimator2() - Constructor for class edu.jhu.ece.iacl.algorithms.hardi.CFARIEstimator2
 
cgA - Variable in class edu.jhu.bme.smile.commons.math.L1LSCompressedSensing
 
CGOLD - Static variable in class edu.jhu.ece.iacl.algorithms.vabra.NumericalRecipes
 
change(int, int, int, Indexable) - Method in class edu.jhu.ece.iacl.jist.structures.data.BinaryMinFastHeap
Change.
change(Indexable, Comparable) - Method in class edu.jhu.ece.iacl.jist.structures.data.BinaryMinHeap
Change.
change(int, int, int, int, Comparable) - Method in class edu.jhu.ece.iacl.jist.structures.data.BinaryMinHeap
Change.
change(int, int, int, Indexable) - Method in class edu.jhu.ece.iacl.jist.structures.data.BinaryMinHeap
Change.
changeFunc() - Static method in class edu.jhu.bme.smile.commons.optimize.test.Test1DOptimizations
Changes the function to test.
changeFunc() - Static method in class edu.jhu.bme.smile.commons.optimize.test.TestNDOptimizations
Changes the function to optimize.
changeMinMax() - Static method in class edu.jhu.bme.smile.commons.optimize.test.Test1DOptimizations
Changes between finding minimum and maximum.
changeMinMax() - Static method in class edu.jhu.bme.smile.commons.optimize.test.TestNDOptimizations
Changes between finding the minimum and maximum.
ChebyShevFitting - Class in edu.jhu.bme.smile.demo
 
ChebyShevFitting() - Constructor for class edu.jhu.bme.smile.demo.ChebyShevFitting
 
checkInSync() - Method in class edu.jhu.ece.iacl.jist.pipeline.ExecutionContext
Check if two input files are in sync.
checkSlicerXMLoption() - Method in class edu.jhu.ece.iacl.jist.cli.JistCLI
 
chenyangXu - Static variable in class edu.jhu.ece.iacl.algorithms.CommonAuthors
 
childPort - Variable in class edu.jhu.ece.iacl.jist.pipeline.PipeSource
Port for child source.
children - Variable in class edu.jhu.ece.iacl.jist.pipeline.graph.PipeAlgorithmFactory.AlgorithmGroupCell
The children.
children - Variable in class edu.jhu.ece.iacl.jist.pipeline.PerformanceSummary
Children performance summaries.
citation - Variable in class edu.jhu.ece.iacl.jist.pipeline.AlgorithmInformation.Citation
The citation.
CITATION_TAG - Static variable in class edu.jhu.ece.iacl.jist.pipeline.parser.LoniPipeParser
The Constant CITATION_TAG.
citations - Variable in class edu.jhu.ece.iacl.jist.pipeline.AlgorithmInformation
The citations.
CITATIONS_TAG - Static variable in class edu.jhu.ece.iacl.jist.pipeline.parser.LoniPipeParser
The Constant CITATIONS_TAG.
citeList - Variable in class edu.jhu.ece.iacl.jist.pipeline.view.input.AlgorithmInformationDialog
The citation list.
clampColumn(int) - Method in class edu.jhu.cs.cisst.algorithms.geometry.surface.IsoSurfaceGenerator
Clamp column index.
clampRow(int) - Method in class edu.jhu.cs.cisst.algorithms.geometry.surface.IsoSurfaceGenerator
Clamp row.
clampSlice(int) - Method in class edu.jhu.cs.cisst.algorithms.geometry.surface.IsoSurfaceGenerator
Clamp slice.
className - Variable in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamHeader
Canonical calss name, which may or may not exist.
classpath - Static variable in class edu.jhu.ece.iacl.jist.pipeline.ExecutionContext
Java class path.
clean() - Method in class edu.jhu.ece.iacl.jist.pipeline.ExecutionContext
Remove the output directory and anything in it.
clean - Variable in class edu.jhu.ece.iacl.jist.pipeline.gui.ProcessManagerTable
The debug.
clean() - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamCollection
Clean collection and its children.
clean() - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamFile
 
clean() - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamFileCollection
 
clean() - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamModel
Clean resources that maybe out-of-date with the system
clean(PipeLayout) - Static method in class edu.jhu.ece.iacl.jist.pipeline.PipeLayout
Clean.
clean(Vector<ExecutionContext>, boolean) - Method in class edu.jhu.ece.iacl.jist.pipeline.PipeScheduler
Clean output directory for specified contexts.
clean() - Method in class edu.jhu.ece.iacl.jist.pipeline.PipeScheduler.CleanAllDialog
Clean.
clean() - Method in class edu.jhu.ece.iacl.jist.test.JistTestHarness
Clean.
cleanAll() - Method in class edu.jhu.ece.iacl.jist.pipeline.PipeScheduler
Clean all experiments in output directory
cleanAll(boolean) - Method in class edu.jhu.ece.iacl.jist.pipeline.PipeScheduler
 
cleanAllQuietly(PipeLayout) - Method in class edu.jhu.ece.iacl.jist.pipeline.gui.ProcessManager
 
cleanNow() - Method in class edu.jhu.ece.iacl.jist.pipeline.PipeScheduler.CleanAllDialog
Clean.
clear() - Method in class edu.jhu.ece.iacl.algorithms.manual_label.staple.PerformanceLevel
 
clear() - Method in interface edu.jhu.ece.iacl.jist.pipeline.parameter.ObjectCollection
Remove all values from collection.
clear() - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamCollection
Clear children.
clear() - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamFileCollection
Remove all files from collection.
clear() - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamNumberCollection
Remove all numbers from collection.
clear() - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamSurfaceCollection
Remove all files from collection.
clear() - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamVolume
Clear volume parameter.
clear() - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamVolumeCollection
Remove all files from collection.
clear() - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamWeightedVolumeCollection
Clear list and add members to cache
clearCache() - Method in class edu.jhu.cs.cisst.vent.renderer.processing.ImageRenderer
Clear cache.
clearCache() - Method in class edu.jhu.cs.cisst.vent.renderer.processing.VectorField2DRenderer
Clear cache.
clearCache() - Method in class edu.jhu.cs.cisst.vent.renderer.processing.VolumeSliceRenderer
Clear cache.
clearD() - Method in class edu.jhu.ece.iacl.algorithms.manual_label.staple.PerformanceLevel
 
clearF() - Method in class edu.jhu.ece.iacl.algorithms.manual_label.staple.PerformanceLevel
 
clickClose() - Method in class edu.jhu.ece.iacl.jist.pipeline.ProcessingDialog
Handle event when user clicks "Close".
clickClose() - Method in class edu.jhu.ece.iacl.jist.pipeline.ProcessingGroupDialog
Handle event when user clicks "Close".
clickCountToStart - Variable in class edu.jhu.ece.iacl.jist.pipeline.graph.PipeEdgeRealEditor
An integer specifying the number of clicks needed to start editing.
clickOk() - Method in class edu.jhu.ece.iacl.jist.pipeline.ProcessingDialog
Handle event when user clicks "OK".
clickOk() - Method in class edu.jhu.ece.iacl.jist.pipeline.ProcessingGroupDialog
Handle event when user clicks "OK".
clickOpen(File) - Method in class edu.jhu.ece.iacl.jist.pipeline.ProcessingDialog
Handle event when user clicks "Open".
clickOpen(File) - Method in class edu.jhu.ece.iacl.jist.pipeline.ProcessingGroupDialog
Handle event when user clicks "Open".
clickSaveAll(File) - Method in class edu.jhu.ece.iacl.jist.pipeline.ProcessingDialog
Handle event when user clicks "Save Parameters and Resources".
clickSaveAll(File) - Method in class edu.jhu.ece.iacl.jist.pipeline.ProcessingGroupDialog
Handle event when user clicks "Save Parameters and Resources".
clickSaveDefinition(File) - Method in class edu.jhu.ece.iacl.jist.pipeline.ProcessingDialog
Handle event when user clicks "Save As Module Definition".
clickSaveDefinition(File) - Method in class edu.jhu.ece.iacl.jist.pipeline.ProcessingGroupDialog
Handle event when user clicks "Save As Module Definition".
clickSaveInput(File) - Method in class edu.jhu.ece.iacl.jist.pipeline.ProcessingDialog
Handle event when user clicks "Save As Algorithm Input".
clickSaveInput(File) - Method in class edu.jhu.ece.iacl.jist.pipeline.ProcessingGroupDialog
Handle event when user clicks "Save As Algorithm Input".
cliTag - Variable in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamModel
 
clone() - Method in interface edu.jhu.cs.cisst.algorithms.optimize.fmg.grid.ConstGrid
clone this grid.
clone() - Method in class edu.jhu.cs.cisst.algorithms.optimize.fmg.grid.Grid
implements method from ConstGrid.
clone() - Method in class edu.jhu.ece.iacl.algorithms.vabra.VectorVolumeVabra
 
clone() - Method in class edu.jhu.ece.iacl.jist.pipeline.AlgorithmInformation.AlgorithmAuthor
Clone author information.
clone() - Method in class edu.jhu.ece.iacl.jist.pipeline.AlgorithmInformation.Citation
Clone citation.
clone() - Method in class edu.jhu.ece.iacl.jist.pipeline.AlgorithmInformation
Clone information.
clone() - Method in class edu.jhu.ece.iacl.jist.pipeline.graph.PipeAlgorithmFactory.AlgorithmCell
 
clone() - Method in class edu.jhu.ece.iacl.jist.pipeline.graph.PipeDestinationFactory.DestinationCell
 
clone() - Method in class edu.jhu.ece.iacl.jist.pipeline.graph.PipeModuleEdge
Create a clone of the cell.
clone() - Method in class edu.jhu.ece.iacl.jist.pipeline.graph.PipeModulePort
 
clone() - Method in class edu.jhu.ece.iacl.jist.pipeline.graph.PipeSourceFactory.SourceCell
 
clone() - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamArgsOrder
 
clone() - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamBoolean
Clone parameter.
clone() - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamCollection
Clone collections.
clone() - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamColor
 
clone() - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamDataLabel
Clone this object.
clone() - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamDouble
 
clone() - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamExecutable
Clone parameter.
clone() - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamFile
Clone object.
clone() - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamFileCollection
Clone object.
clone() - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamFloat
Clone parameter.
clone() - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamHeader
Clone object.
clone() - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamInformation
Clone object.
clone() - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamInteger
Clone object.
clone() - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamLong
Clone object.
clone() - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamMatrix
 
clone() - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamMipavDialog
Clone object.
clone() - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamModel
 
clone() - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamMultiOption
Clone object.
clone() - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamNumber
 
clone() - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamNumberCollection
Clone object.
clone() - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamObject
Clone object.
clone() - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamOption
Clone object.
clone() - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamPerformance
Clone object.
clone() - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamPointDouble
Clone object.
clone() - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamPointFloat
Clone object.
clone() - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamPointInteger
Clone object.
clone() - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamString
Clone object.
clone() - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamSurface
Clone object.
clone() - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamSurfaceCollection
Clone object.
clone() - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamSwitch
Clone object.
clone() - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamVolume
Clone object.
clone() - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamVolumeCollection
Clone object.
clone() - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamWeightedVolume
Clone object.
clone() - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamWeightedVolumeCollection
Clone object.
clone() - Method in class edu.jhu.ece.iacl.jist.pipeline.PerformanceSummary
Returns clone of performance summary.
clone() - Method in class edu.jhu.ece.iacl.jist.pipeline.PerformanceSummary.TimeAndMemoryStamp
Returns clone of time and memory stamp.
clone() - Method in class edu.jhu.ece.iacl.jist.pipeline.PipeAlgorithm
Clone algorithm by serializing and deserializing module.
clone() - Method in class edu.jhu.ece.iacl.jist.pipeline.PipeAlgorithmGroup
Return clone of this group.
clone() - Method in class edu.jhu.ece.iacl.jist.pipeline.PipeChildPort
Clone port.
clone() - Method in class edu.jhu.ece.iacl.jist.pipeline.PipeParentPort
Clone parent port.
clone() - Method in class edu.jhu.ece.iacl.jist.pipeline.PipePort
Clone parameter.
clone() - Method in class edu.jhu.ece.iacl.jist.structures.geom.EmbeddedSurface
 
clone(int[][]) - Static method in class edu.jhu.ece.iacl.jist.structures.image.ImageData
Clone.
clone(int[][][]) - Static method in class edu.jhu.ece.iacl.jist.structures.image.ImageData
Clone.
clone(int[][][][]) - Static method in class edu.jhu.ece.iacl.jist.structures.image.ImageData
Clone.
clone() - Method in class edu.jhu.ece.iacl.jist.structures.image.ImageData
 
clone() - Method in class edu.jhu.ece.iacl.jist.structures.image.ImageDataByte
 
clone() - Method in class edu.jhu.ece.iacl.jist.structures.image.ImageDataColor
 
clone() - Method in class edu.jhu.ece.iacl.jist.structures.image.ImageDataDouble
 
clone() - Method in class edu.jhu.ece.iacl.jist.structures.image.ImageDataFloat
 
clone() - Method in class edu.jhu.ece.iacl.jist.structures.image.ImageDataInt
 
clone() - Method in class edu.jhu.ece.iacl.jist.structures.image.ImageDataMipav
 
clone() - Method in class edu.jhu.ece.iacl.jist.structures.image.ImageDataUByte
 
clone() - Method in class edu.jhu.ece.iacl.jist.structures.image.ImageHeader
 
clone() - Method in class edu.jhu.ece.iacl.jist.structures.image.Voxel
 
clone() - Method in class edu.jhu.ece.iacl.jist.structures.image.VoxelBoolean
 
clone() - Method in class edu.jhu.ece.iacl.jist.structures.image.VoxelColor
 
clone() - Method in class edu.jhu.ece.iacl.jist.structures.image.VoxelDouble
 
clone() - Method in class edu.jhu.ece.iacl.jist.structures.image.VoxelFloat
 
clone() - Method in class edu.jhu.ece.iacl.jist.structures.image.VoxelIndexed
 
clone() - Method in class edu.jhu.ece.iacl.jist.structures.image.VoxelInt
 
clone() - Method in class edu.jhu.ece.iacl.jist.structures.image.VoxelMipav
 
clone() - Method in class edu.jhu.ece.iacl.jist.structures.image.VoxelShort
 
clone() - Method in class edu.jhu.ece.iacl.jist.structures.image.VoxelUByte
 
clone() - Method in class edu.jhu.ece.iacl.jist.structures.image.VoxelVector
 
clone() - Method in class edu.jhu.ece.iacl.jist.structures.matrix.Matrix3
 
clone() - Method in class edu.jhu.ece.iacl.jist.structures.matrix.VectorMatrixX
 
clone() - Method in class edu.jhu.ece.iacl.jist.structures.vector.Vector2
 
clone() - Method in class edu.jhu.ece.iacl.jist.structures.vector.Vector3
 
clone() - Method in class edu.jhu.ece.iacl.jist.structures.vector.Vector4
 
clone() - Method in class edu.jhu.ece.iacl.jist.structures.vector.VectorN
 
clone() - Method in interface edu.jhu.ece.iacl.jist.structures.vector.VectorX
Clone.
cloneCell(Object) - Method in class edu.jhu.ece.iacl.jist.pipeline.graph.PipeGraphModel
Creates a shallow copy of the cell including a copy of the user object.
cloneCells(Object[]) - Method in class edu.jhu.ece.iacl.jist.pipeline.graph.PipeGraphModel
 
clonePL() - Method in class edu.jhu.ece.iacl.algorithms.manual_label.staple.PerformanceLevel
 
cloneUserObject(Object) - Method in class edu.jhu.ece.iacl.jist.pipeline.graph.PipeGraphModel
 
close() - Method in class edu.jhu.ece.iacl.jist.io.LEFileWriter
Close.
close() - Method in class edu.jhu.ece.iacl.jist.pipeline.gui.PipeInternalFrame
Close current frame.
close() - Method in class edu.jhu.ece.iacl.jist.pipeline.gui.ProcessManager
Close process manager and clean up resources.
close() - Method in class edu.jhu.ece.iacl.jist.pipeline.PipeLayout
Ask user if they want to save before closing layout.
close() - Method in class edu.jhu.ece.iacl.jist.test.MipavTestHarness
Close.
closeSession(boolean) - Method in class edu.jhu.ece.iacl.jist.processcontrol.DispatchController
Close session.
cmap() - Method in class edu.jhu.ece.iacl.algorithms.dti.DiffusionTensor
 
cnt - Variable in class edu.jhu.ece.iacl.algorithms.dti.tractography.FiberTracker
 
cnt - Variable in class edu.jhu.ece.iacl.algorithms.dti.tractography.WildBootFiberTracker
 
coarseCostFunction(float[]) - Method in class edu.jhu.ece.iacl.algorithms.vabra.ImagePairRBF
 
coarseGradient(int[], double[]) - Method in class edu.jhu.ece.iacl.algorithms.vabra.ImagePair
 
coarseGradient(int[], double[]) - Method in class edu.jhu.ece.iacl.algorithms.vabra.ImagePairNMI
 
coarseGradient(int[], double[]) - Method in class edu.jhu.ece.iacl.algorithms.vabra.ImagePairRBF
 
coarseGradientParameters() - Method in class edu.jhu.ece.iacl.algorithms.vabra.ImagePair
 
coarseGradientParameters() - Method in class edu.jhu.ece.iacl.algorithms.vabra.ImagePairNMI
 
coarseGradientParameters() - Method in class edu.jhu.ece.iacl.algorithms.vabra.ImagePairRBF
 
coarseOptimize(int[], double[]) - Method in class edu.jhu.ece.iacl.algorithms.vabra.ImagePair
 
coarseOptimize(int[], double[]) - Method in class edu.jhu.ece.iacl.algorithms.vabra.ImagePairRBF
 
coarseSize - Variable in class edu.jhu.cs.cisst.algorithms.optimize.fmg.interpolator.InterpolatorByStencil
The coarse size.
coarsestLevelResolution - Variable in class edu.jhu.cs.cisst.algorithms.segmentation.gac.GradientVectorFlow2D
The coarsest level resolution.
collapse - Variable in class edu.jhu.ece.iacl.jist.pipeline.gui.PipeInternalFrame
The expand.
CollisionDetection - Class in edu.jhu.ece.iacl.jist.structures.geom
The Class CollisionDetection.
CollisionDetection(EmbeddedSurface, int, int, int, int) - Constructor for class edu.jhu.ece.iacl.jist.structures.geom.CollisionDetection
Instantiates a new collision detection.
CollisionDetection.Triangle - Class in edu.jhu.ece.iacl.jist.structures.geom
The Class Triangle.
CollisionDetection.Triangle(Point3d, Point3d, Point3d) - Constructor for class edu.jhu.ece.iacl.jist.structures.geom.CollisionDetection.Triangle
Instantiates a new triangle.
color - Variable in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamColor
The color.
cols - Variable in class edu.jhmi.rad.medic.utilities.CropParameters
The cols.
cols - Variable in class edu.jhu.cs.cisst.algorithms.geometry.surface.IsoContourGenerator
The cols.
cols - Variable in class edu.jhu.cs.cisst.algorithms.geometry.surface.IsoSurfaceGenerator
The slices.
cols - Variable in class edu.jhu.cs.cisst.algorithms.segmentation.gac.ActiveContourForce2D
The columns.
cols - Variable in class edu.jhu.cs.cisst.algorithms.segmentation.gac.GeodesicActiveContour2D
The columns.
cols - Variable in class edu.jhu.cs.cisst.algorithms.segmentation.gac.GradientVectorFlow2D
The cols.
cols - Variable in class edu.jhu.cs.cisst.plugins.segmentation.PlugInCircleLevelSet
 
cols - Variable in class edu.jhu.cs.cisst.vent.renderer.processing.ImageRenderer
The cols.
cols - Variable in class edu.jhu.cs.cisst.vent.renderer.processing.VectorField2DRenderer
The cols.
cols - Variable in class edu.jhu.cs.cisst.vent.renderer.processing.VolumeSliceRenderer
The slices.
cols - Variable in class edu.jhu.cs.cisst.vent.widgets.VisualizationImage
The columns.
cols - Variable in class edu.jhu.ece.iacl.algorithms.manual_label.staple.STAPLEmulti
 
cols - Variable in class edu.jhu.ece.iacl.algorithms.manual_label.staple.STAPLEmulti2
 
cols - Variable in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamMatrix
The cols.
cols - Variable in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamVolume
The cols.
cols - Variable in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamVolumeCollection
The cols.
cols - Variable in class edu.jhu.ece.iacl.jist.structures.image.ImageData
The cols.
cols - Variable in class edu.jhu.ece.iacl.plugins.utilities.math.MedicAlgorithmKLDivergence
 
cols - Variable in class edu.jhu.ece.iacl.plugins.utilities.surface.MedicAlgorithmSurfaceHistogram
 
cols - Variable in class edu.jhu.ece.iacl.plugins.utilities.volume.MedicAlgorithmVolumeHistogram
 
colSumNorm(Matrix) - Static method in class edu.jhu.bme.smile.commons.math.MatrixMath
 
columnClasses - Variable in class edu.jhu.ece.iacl.jist.pipeline.gui.ProcessManagerTable.ProcessTableModel
The column classes.
columnNames - Variable in class edu.jhu.ece.iacl.jist.pipeline.gui.ProcessManagerTable.ProcessTableModel
The column names.
combineAllRaterLabs() - Method in class edu.jhu.ece.iacl.algorithms.manual_label.staple.STAPLEgeneral
 
CombinedSlabCollectionToVolumeCollection - Class in edu.jhu.ece.iacl.plugins.utilities.volume
 
CombinedSlabCollectionToVolumeCollection() - Constructor for class edu.jhu.ece.iacl.plugins.utilities.volume.CombinedSlabCollectionToVolumeCollection
 
combineRaterLabels(double[][]) - Method in class edu.jhu.ece.iacl.algorithms.manual_label.staple.STAPLEgeneral
 
combo - Variable in class edu.jhu.ece.iacl.jist.pipeline.gui.PortComboBox
The combo.
commit() - Method in class edu.jhu.ece.iacl.jist.pipeline.gui.PortListBox
 
commit() - Method in class edu.jhu.ece.iacl.jist.pipeline.view.input.ParamBooleanInputView
Unimplemented.
commit() - Method in class edu.jhu.ece.iacl.jist.pipeline.view.input.ParamCollectionInputView
Commit changes to this view and its children.
commit() - Method in class edu.jhu.ece.iacl.jist.pipeline.view.input.ParamCollectionPipelineInputView
Commit changes to this parameter and its children.
commit() - Method in class edu.jhu.ece.iacl.jist.pipeline.view.input.ParamColorInputView
Commit changes to point.
commit() - Method in class edu.jhu.ece.iacl.jist.pipeline.view.input.ParamDoubleSliderInputView
Commit changes to this parameter.
commit() - Method in class edu.jhu.ece.iacl.jist.pipeline.view.input.ParamFileCollectionInputView
Commit changes to this parameter view.
commit() - Method in class edu.jhu.ece.iacl.jist.pipeline.view.input.ParamFileInputView
Commit changes to this parameter.
commit() - Method in class edu.jhu.ece.iacl.jist.pipeline.view.input.ParamHiddenInputView
Unimplemented.
commit() - Method in class edu.jhu.ece.iacl.jist.pipeline.view.input.ParamInformationInputView
Unimplemented.
commit() - Method in class edu.jhu.ece.iacl.jist.pipeline.view.input.ParamInputView
Force commitment of GUI input changes to parameter value.
commit() - Method in class edu.jhu.ece.iacl.jist.pipeline.view.input.ParamMatrixInputView
Commit changes to parameter.
commit() - Method in class edu.jhu.ece.iacl.jist.pipeline.view.input.ParamMipavDialogInputView
Unimplemented.
commit() - Method in class edu.jhu.ece.iacl.jist.pipeline.view.input.ParamMultiOptionInputView
Commit changes to this parameter.
commit() - Method in class edu.jhu.ece.iacl.jist.pipeline.view.input.ParamNumberCollectionInputView
Commit changes to this parameter view.
commit() - Method in class edu.jhu.ece.iacl.jist.pipeline.view.input.ParamNumberSliderInputView
Commit changes to this parameter.
commit() - Method in class edu.jhu.ece.iacl.jist.pipeline.view.input.ParamNumberSpinnerInputView
 
commit() - Method in class edu.jhu.ece.iacl.jist.pipeline.view.input.ParamNumberTextInputView
Commit changes to parameter.
commit() - Method in class edu.jhu.ece.iacl.jist.pipeline.view.input.ParamOptionCollectionInputView
Commit changes.
commit() - Method in class edu.jhu.ece.iacl.jist.pipeline.view.input.ParamOptionInputView
 
commit() - Method in class edu.jhu.ece.iacl.jist.pipeline.view.input.ParamPointDoubleTextInputView
Commit changes to this parameter.
commit() - Method in class edu.jhu.ece.iacl.jist.pipeline.view.input.ParamPointFloatTextInputView
Commit changes to this parameter.
commit() - Method in class edu.jhu.ece.iacl.jist.pipeline.view.input.ParamPointSpinnerInputView
Commit changes to point.
commit() - Method in class edu.jhu.ece.iacl.jist.pipeline.view.input.ParamTextInputView
Commit changes to text field.
commit() - Method in class edu.jhu.ece.iacl.jist.pipeline.view.input.ParamURIInputView
Commit changes to this parameter.
commit() - Method in class edu.jhu.ece.iacl.jist.pipeline.view.input.ParamVolumeCollectionInputView
Commit changes to list.
commit() - Method in class edu.jhu.ece.iacl.jist.pipeline.view.input.ParamVolumeInputView
Commit changes to parameter.
commit() - Method in class edu.jhu.ece.iacl.jist.pipeline.view.input.ParamVolumeURICollectionInputView
Commit changes to this parameter view.
commit() - Method in class edu.jhu.ece.iacl.jist.pipeline.view.input.ParamVolumeURIInputView
Commit changes to parameter.
commit() - Method in class edu.jhu.ece.iacl.jist.pipeline.view.input.ParamWeightedVolumesURIInputView
 
CommonAuthors - Class in edu.jhu.ece.iacl.algorithms
 
CommonAuthors() - Constructor for class edu.jhu.ece.iacl.algorithms.CommonAuthors
 
compare() - Method in class edu.jhu.ece.iacl.algorithms.volume.CompareVolumes
 
compare(PipeModuleFactory, PipeModuleFactory) - Method in class edu.jhu.ece.iacl.doc.DocumentAllModules.CompareFactories
 
compare(PipeModuleFactory, PipeModuleFactory) - Method in class edu.jhu.ece.iacl.jist.pipeline.PipeLibrary.CompareFactories
 
compare(File, File) - Method in class edu.jhu.ece.iacl.jist.pipeline.PipeLibrary.CompareFiles
 
compare(T, T) - Method in class edu.jhu.ece.iacl.jist.structures.data.ReverseComparator
 
CompareFibers - Class in edu.jhu.ece.iacl.algorithms.dti.tractography.FACT
 
CompareFibers() - Constructor for class edu.jhu.ece.iacl.algorithms.dti.tractography.FACT.CompareFibers
 
compareTo(GridPoint2D) - Method in class edu.jhu.cs.cisst.algorithms.segmentation.gac.GridPoint2D
 
compareTo(RegistrationUtilities.IndexedFloat) - Method in class edu.jhu.ece.iacl.algorithms.registration.RegistrationUtilities.IndexedFloat
 
compareTo(DocumentAllModules.ModuleDescription) - Method in class edu.jhu.ece.iacl.doc.DocumentAllModules.ModuleDescription
 
compareTo(DocumentAllTests.Assertion) - Method in class edu.jhu.ece.iacl.doc.DocumentAllTests.Assertion
Compare assertions by name.
compareTo(DocumentAllTests.ModuleDescription) - Method in class edu.jhu.ece.iacl.doc.DocumentAllTests.ModuleDescription
Compare modules by name.
compareTo(AlgorithmInformation) - Method in class edu.jhu.ece.iacl.jist.pipeline.AlgorithmInformation
Unimplemented.
compareTo(ExecutionContext) - Method in class edu.jhu.ece.iacl.jist.pipeline.ExecutionContext
Compare execution contexts by status for sorting purposes.
compareTo(ProcessManagerTable.MemoryStampWrapper) - Method in class edu.jhu.ece.iacl.jist.pipeline.gui.ProcessManagerTable.MemoryStampWrapper
 
compareTo(ProcessManagerTable.TimeStampWrapper) - Method in class edu.jhu.ece.iacl.jist.pipeline.gui.ProcessManagerTable.TimeStampWrapper
 
compareTo(DataLabel) - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.DataLabel
Compare data labels by intensity value.
compareTo(ParamModel) - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamArgsOrder
 
compareTo(ParamModel) - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamBoolean
Not restriction comparison needed for boolean values.
compareTo(ParamModel) - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamCollection
Compare the names of two collections to see if they are the same.
compareTo(ParamModel) - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamColor
Compare to.
compareTo(ParamModel) - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamDouble
Compare the min and max value restrictions of two parameters.
compareTo(ParamModel) - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamFile
Compare two parameters based on their dialog types, extensionFilters, and mandatory fields F *.
compareTo(ParamModel) - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamFileCollection
Compare restriction of one file collection to another.
compareTo(ParamModel) - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamFloat
Compare the min and max value restrictions of two parameters.
compareTo(ParamModel) - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamHeader
Compare values for compatibility.
compareTo(ParamModel) - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamInformation
Compare information.
compareTo(ParamModel) - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamInteger
Compare the min and max value restrictions of two parameters.
compareTo(ParamModel) - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamLong
Compare the min and max value restrictions of two parameters.
compareTo(ParamModel) - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamModel
Compare specificity of parameters.
compareTo(ParamModel) - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamMultiOption
Compare the options of one parameter to another to determine which list of options is more restrictive.
compareTo(ParamModel) - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamNumberCollection
Compare restriction of one file collection to another.
compareTo(ParamModel) - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamOption
Compare the options of one parameter to another to determine which list of options is more restrictive.
compareTo(ParamModel) - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamPerformance
Unimplemented.
compareTo(ParamModel) - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamPointDouble
 
compareTo(ParamModel) - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamPointFloat
 
compareTo(ParamModel) - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamPointInteger
 
compareTo(ParamModel) - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamString
 
compareTo(ParamModel) - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamSurface
 
compareTo(ParamModel) - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamSurfaceCollection
Compare restriction of one volume collection to another.
compareTo(ParamModel) - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamSwitch
 
compareTo(ParamModel) - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamVolume
Compare restrictions of parameters.
compareTo(ParamModel) - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamVolumeCollection
Compare restriction of one volume collection to another.
compareTo(ParamVolumeInputView.VolumeListBoxItem) - Method in class edu.jhu.ece.iacl.jist.pipeline.view.input.ParamVolumeInputView.VolumeListBoxItem
 
compareTo(ParamVolumeURIInputView.VolumeListBoxItem) - Method in class edu.jhu.ece.iacl.jist.pipeline.view.input.ParamVolumeURIInputView.VolumeListBoxItem
 
compareTo(Edge) - Method in class edu.jhu.ece.iacl.jist.structures.geom.Edge
 
compareTo(Double) - Method in class edu.jhu.ece.iacl.jist.structures.geom.EdgeIndexed
 
compareTo(EmbeddedSurface) - Method in class edu.jhu.ece.iacl.jist.structures.geom.EmbeddedSurface
 
compareTo(EmbeddedSurface.Edge) - Method in class edu.jhu.ece.iacl.jist.structures.geom.EmbeddedSurface.Edge
 
compareTo(Face) - Method in class edu.jhu.ece.iacl.jist.structures.geom.Face
 
compareTo(Object) - Method in class edu.jhu.ece.iacl.jist.structures.geom.GridPt
 
compareTo(Vertex) - Method in class edu.jhu.ece.iacl.jist.structures.geom.Vertex
 
compareTo(Double) - Method in class edu.jhu.ece.iacl.jist.structures.geom.VertexIndexed
 
compareTo(Voxel) - Method in class edu.jhu.ece.iacl.jist.structures.image.VoxelBoolean
 
compareTo(Voxel) - Method in class edu.jhu.ece.iacl.jist.structures.image.VoxelColor
 
compareTo(Voxel) - Method in class edu.jhu.ece.iacl.jist.structures.image.VoxelDouble
 
compareTo(Voxel) - Method in class edu.jhu.ece.iacl.jist.structures.image.VoxelFloat
 
compareTo(Voxel) - Method in class edu.jhu.ece.iacl.jist.structures.image.VoxelIndexed
 
compareTo(Voxel) - Method in class edu.jhu.ece.iacl.jist.structures.image.VoxelInt
 
compareTo(Voxel) - Method in class edu.jhu.ece.iacl.jist.structures.image.VoxelMipav
 
compareTo(Voxel) - Method in class edu.jhu.ece.iacl.jist.structures.image.VoxelShort
 
compareTo(Voxel) - Method in class edu.jhu.ece.iacl.jist.structures.image.VoxelUByte
 
compareTo(Voxel) - Method in class edu.jhu.ece.iacl.jist.structures.image.VoxelVector
 
compareTo(MedicAlgorithmSubsampleFibers.StaticCurve) - Method in class edu.jhu.ece.iacl.plugins.dti.MedicAlgorithmSubsampleFibers.StaticCurve
 
CompareVolumes - Class in edu.jhu.ece.iacl.algorithms.volume
Compare two volumes using a variety of different metrics.
CompareVolumes(ImageData, ImageData, double, double, int) - Constructor for class edu.jhu.ece.iacl.algorithms.volume.CompareVolumes
 
CompareVolumes(ImageData, ImageData, double, int) - Constructor for class edu.jhu.ece.iacl.algorithms.volume.CompareVolumes
 
CompatibilityChecker - Interface in edu.jhu.ece.iacl.jist.pipeline.parameter
Check for compatibility between ports.
compatibleColor - Static variable in class edu.jhu.ece.iacl.jist.pipeline.graph.PipePortView
The compatible color.
complete() - Method in class edu.jhu.ece.iacl.doc.DocumentAllTests
Complete.
complete() - Method in class edu.jhu.ece.iacl.jist.pipeline.dest.PipeDoubleCollectionExternalDestination
Clean up destination after iterating though all experiments.
complete() - Method in class edu.jhu.ece.iacl.jist.pipeline.dest.PipeDoubleExternalDestination
Clean up destination after iterating though all experiments.
complete() - Method in class edu.jhu.ece.iacl.jist.pipeline.dest.PipeExternalDestination
Clean up destination after iterating though all experiments.
complete() - Method in class edu.jhu.ece.iacl.jist.pipeline.dest.PipeFileCollectionExternalDestination
Clean up destination after iterating though all experiments.
complete() - Method in class edu.jhu.ece.iacl.jist.pipeline.dest.PipeFileExternalDestination
Clean up destination after iterating though all experiments.
complete() - Method in class edu.jhu.ece.iacl.jist.pipeline.dest.PipeIntegerCollectionExternalDestination
Clean up destination after iterating though all experiments.
complete() - Method in class edu.jhu.ece.iacl.jist.pipeline.dest.PipeIntegerExternalDestination
Clean up destination after iterating though all experiments.
complete() - Method in class edu.jhu.ece.iacl.jist.pipeline.dest.PipeParamCopyDestination
Clean up after copying files.
complete() - Method in class edu.jhu.ece.iacl.jist.pipeline.dest.PipeParamSummaryDestination
Clean up destination after iterating though all experiments.
complete() - Method in class edu.jhu.ece.iacl.jist.pipeline.dest.PipeSurfaceCollectionExternalDestination
Clean up destination after iterating though all experiments.
complete() - Method in class edu.jhu.ece.iacl.jist.pipeline.dest.PipeSurfaceExternalDestination
Clean up destination after iterating though all experiments.
complete() - Method in class edu.jhu.ece.iacl.jist.pipeline.dest.PipeVolumeCollectionExternalDestination
Clean up destination after iterating though all experiments.
complete() - Method in class edu.jhu.ece.iacl.jist.pipeline.dest.PipeVolumeExternalDestination
Clean up destination after iterating though all experiments.
complete() - Method in class edu.jhu.ece.iacl.jist.pipeline.PipeDestination
Execute after iterating is complete.
complete() - Method in class edu.jhu.ece.iacl.jist.test.JistTestHarness
Complete.
completed - Variable in class edu.jhu.ece.iacl.jist.pipeline.PipeScheduler
indicate that scheduler has completed running and processing destinations.
completedAssertions - Variable in class edu.jhu.ece.iacl.doc.DocumentAllTests.TestCase
 
completedQueue - Variable in class edu.jhu.ece.iacl.jist.pipeline.PipeScheduler
Queue to store completed contexts.
ComplexMatrix - Class in edu.jhu.bme.smile.commons.math.specialFunctions
 
ComplexMatrix(int, int) - Constructor for class edu.jhu.bme.smile.commons.math.specialFunctions.ComplexMatrix
 
ComplexVector - Class in edu.jhu.bme.smile.commons.math.specialFunctions
 
ComplexVector(ComplexMatrix) - Constructor for class edu.jhu.bme.smile.commons.math.specialFunctions.ComplexVector
 
component - Variable in class edu.jhu.cs.cisst.algorithms.geometry.surface.IsoContourGenerator
The component.
component - Variable in class edu.jhu.cs.cisst.vent.renderer.processing.VolumeSliceRenderer
The component.
componentHidden(ComponentEvent) - Method in class edu.jhu.ece.iacl.jist.pipeline.gui.PlugInSelector
 
componentHidden(ComponentEvent) - Method in class edu.jhu.ece.iacl.jist.pipeline.ProcessingDialog
 
componentHidden(ComponentEvent) - Method in class edu.jhu.ece.iacl.jist.pipeline.ProcessingGroupDialog
 
componentMoved(ComponentEvent) - Method in class edu.jhu.ece.iacl.jist.pipeline.gui.PlugInSelector
 
componentMoved(ComponentEvent) - Method in class edu.jhu.ece.iacl.jist.pipeline.ProcessingDialog
 
componentMoved(ComponentEvent) - Method in class edu.jhu.ece.iacl.jist.pipeline.ProcessingGroupDialog
 
componentParam - Variable in class edu.jhu.cs.cisst.vent.renderer.processing.VolumeSliceRenderer
The slice param.
componentResized(ComponentEvent) - Method in class edu.jhu.ece.iacl.jist.pipeline.gui.PlugInSelector
 
componentResized(ComponentEvent) - Method in class edu.jhu.ece.iacl.jist.pipeline.ProcessingDialog
Shameless hack to circumvent bug in linux implementation that prevents window from being resized.
componentResized(ComponentEvent) - Method in class edu.jhu.ece.iacl.jist.pipeline.ProcessingGroupDialog
Shameless hack to circumvent bug in linux implementation that prevents window from being resized.
components - Variable in class edu.jhmi.rad.medic.utilities.CropParameters
The components.
components - Variable in class edu.jhu.cs.cisst.vent.renderer.processing.VolumeSliceRenderer
The slices.
components - Variable in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamVolume
The components.
components - Variable in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamVolumeCollection
The components.
components - Variable in class edu.jhu.ece.iacl.jist.structures.image.ImageData
The components.
componentShown(ComponentEvent) - Method in class edu.jhu.ece.iacl.jist.pipeline.gui.PlugInSelector
 
componentShown(ComponentEvent) - Method in class edu.jhu.ece.iacl.jist.pipeline.ProcessingDialog
 
componentShown(ComponentEvent) - Method in class edu.jhu.ece.iacl.jist.pipeline.ProcessingGroupDialog
 
COMPRESSION_GZIP - Static variable in class edu.jhu.ece.iacl.jist.utility.FileUtil
The Constant COMPRESSION_GZIP.
COMPRESSION_NONE - Static variable in class edu.jhu.ece.iacl.jist.utility.FileUtil
The Constant COMPRESSION_NONE.
COMPRESSION_ZIP - Static variable in class edu.jhu.ece.iacl.jist.utility.FileUtil
The Constant COMPRESSION_ZIP.
compressionType - Variable in class edu.jhu.ece.iacl.jist.structures.image.ImageHeader
The compression type.
compute(List<double[]>, List<Point2i>, List<Integer>, byte) - Static method in class edu.jhu.ece.iacl.algorithms.dti.tractography.ConnectivityMatrix
This method organizes fiber data into a connectivity matrix.
computeBoundaryInformation() - Method in class edu.jhu.ece.iacl.algorithms.manual_label.simulation.SurfaceRater
Computes boundaries, and boundary vertices
computeBoundaryInformation() - Method in class edu.jhu.ece.iacl.algorithms.manual_label.simulation.VolumeRater
Computes boundaries, and boundary vertices
computeBounds(EmbeddedSurface) - Method in class edu.jhu.ece.iacl.jist.structures.geom.CollisionDetection
Compute bounds.
computeCoefficients(Point3f[], double[]) - Method in class edu.jhu.ece.iacl.jist.structures.geom.PolySpline
Compute coefficients.
computeConnectivityContrast() - Method in class edu.jhu.ece.iacl.algorithms.dti.tractography.FACT.DTIStudioReader
 
computeDirection() - Method in class edu.jhu.ece.iacl.algorithms.dti.tractography.FiberStatistics
 
computeEulerAngles() - Method in class edu.jhu.bme.smile.commons.math.RotationMatrix
 
computeGradient(float[][][], float[][][], float[][][], float[][][], int, int, int) - Static method in class edu.jhmi.rad.medic.libraries.ImageFunctionsPublic
simple gradient (central differences)
computeGradientHorn(float[][][], float[][][], float[][][], float[][][], int, int, int) - Static method in class edu.jhmi.rad.medic.libraries.ImageFunctionsPublic
Horn-like derivatives: use a 2x2 forward square as averaging the gradient images are passed from above
computeGSTeigenvalues(float[][][], float[][][][], int, int, int) - Static method in class edu.jhmi.rad.medic.libraries.ImageFunctionsPublic
gradient shape tensor: return the eigenvalues at each point
computeHardSeg() - Method in class edu.jhu.ece.iacl.algorithms.manual_label.staple.STAPLEmulti
 
computeHardSeg() - Method in class edu.jhu.ece.iacl.algorithms.manual_label.staple.STAPLEmulti2
 
computeHessian(float[][][], float[][][][], int, int, int) - Static method in class edu.jhmi.rad.medic.libraries.ImageFunctionsPublic
simple Hessian
computeHessianEigenvalues(float[][][], float[][][][], int, int, int) - Static method in class edu.jhmi.rad.medic.libraries.ImageFunctionsPublic
simple Hessian
computeLengths() - Method in class edu.jhu.ece.iacl.algorithms.dti.tractography.FiberStatistics
 
computeMap(float) - Method in class edu.jhu.ece.iacl.algorithms.manual_label.FastMarchingLabelExtension
 
computeMask(int) - Method in class edu.jhu.ece.iacl.algorithms.manual_label.ROI
 
ComputeMeanB0 - Class in edu.jhu.ece.iacl.plugins.dti
 
ComputeMeanB0() - Constructor for class edu.jhu.ece.iacl.plugins.dti.ComputeMeanB0
 
ComputeMeanB0.TensorEstimationWrapper - Class in edu.jhu.ece.iacl.plugins.dti
 
ComputeMeanB0.TensorEstimationWrapper() - Constructor for class edu.jhu.ece.iacl.plugins.dti.ComputeMeanB0.TensorEstimationWrapper
 
ComputeMeanDW - Class in edu.jhu.ece.iacl.plugins.dti
 
ComputeMeanDW() - Constructor for class edu.jhu.ece.iacl.plugins.dti.ComputeMeanDW
 
ComputeMeanDW.TensorEstimationWrapper - Class in edu.jhu.ece.iacl.plugins.dti
 
ComputeMeanDW.TensorEstimationWrapper() - Constructor for class edu.jhu.ece.iacl.plugins.dti.ComputeMeanDW.TensorEstimationWrapper
 
computeMinMax(float[][]) - Method in class edu.jhu.bme.smile.commons.math.HistogramGenerator
 
computeMinMax(double[][]) - Method in class edu.jhu.bme.smile.commons.math.HistogramGenerator
 
computeNumPts() - Method in class edu.jhu.ece.iacl.algorithms.dti.tractography.FiberStatistics
 
computeOrientationEncodedColormap(float[][][], float[][][][], Color[][][]) - Static method in class edu.jhu.ece.iacl.algorithms.dti.ComputeTensorContrasts
 
computeRobustMinMax(float[][]) - Method in class edu.jhu.bme.smile.commons.math.HistogramGenerator
 
computeRobustMinMax(double[][]) - Method in class edu.jhu.bme.smile.commons.math.HistogramGenerator
 
computeRoute(GraphLayoutCache, Point2D, Point2D, AvoidanceRouting.Dir) - Method in class edu.jhu.ece.iacl.jist.pipeline.graph.AvoidanceRouting
Compute avoidance route.
computeStatistics(LabelImage) - Method in class edu.jhu.ece.iacl.algorithms.manual_label.LabelImage
Computes a number of statistics between this LabelImage and another LabelImage {Dice Coefficient, Jaccard Coefficient, the containment of this object in A, the containment of A in this object, the Mountford Index, True Positive, True Negative, False Positive, and False Negative} for each label in this image.
computeStatistics(LabelSurface) - Method in class edu.jhu.ece.iacl.algorithms.manual_label.LabelSurface
 
ComputeTensorContrasts - Class in edu.jhu.ece.iacl.algorithms.dti
 
ComputeTensorContrasts() - Constructor for class edu.jhu.ece.iacl.algorithms.dti.ComputeTensorContrasts
 
computeVolumeAverage(ImageDataMipav) - Method in class edu.jhu.ece.iacl.algorithms.dti.tractography.FiberStatistics
 
concatinateColumns(Matrix, Matrix) - Static method in class edu.jhu.bme.smile.commons.math.MatrixMath
 
concatinateRows(Matrix, Matrix) - Static method in class edu.jhu.bme.smile.commons.math.MatrixMath
 
CONFIG - Static variable in class edu.jhu.ece.iacl.jist.utility.JistLogger
 
ConfusionMatrix - Class in edu.jhu.ece.iacl.algorithms.manual_label.simulation
 
ConfusionMatrix(int[]) - Constructor for class edu.jhu.ece.iacl.algorithms.manual_label.simulation.ConfusionMatrix
contructor with labels only
ConfusionMatrix(float[][]) - Constructor for class edu.jhu.ece.iacl.algorithms.manual_label.simulation.ConfusionMatrix
contructor - with default labels
ConfusionMatrix(float[][], int[]) - Constructor for class edu.jhu.ece.iacl.algorithms.manual_label.simulation.ConfusionMatrix
contructor with input labels
conn - Variable in class edu.jhu.ece.iacl.jist.structures.geom.GridPt
The conn.
connect(PipePort, PipePort) - Static method in class edu.jhu.ece.iacl.jist.pipeline.PipeConnector
Connect source port to destination.
connect(PipePort, PipePort, PipeModuleEdge) - Static method in class edu.jhu.ece.iacl.jist.pipeline.PipeConnector
Connect source port to destination.
connectAction(PipePort) - Method in class edu.jhu.ece.iacl.jist.pipeline.graph.PipeJGraph
 
connectAction(PipePort) - Method in class edu.jhu.ece.iacl.jist.pipeline.gui.ParameterPanel
Update input views when connection occurs.
connectAction(PipePort) - Method in class edu.jhu.ece.iacl.jist.pipeline.PipeModule
Listen for connection event to occur on a port.
connectAction(PipePort) - Method in interface edu.jhu.ece.iacl.jist.pipeline.PipePort.PortListener
Connect action.
connectAction(PipePort) - Method in class edu.jhu.ece.iacl.jist.pipeline.src.PipeSelectionExternalSource
Update selection options when a new connector is added.
connectAction(PipePort) - Method in class edu.jhu.ece.iacl.jist.pipeline.src.PipeSelectionListSource
 
connectAction(PipePort) - Method in class edu.jhu.ece.iacl.jist.pipeline.src.PipeSelectionSource
Update selection options when a new connector is added.
connectedColor - Static variable in class edu.jhu.ece.iacl.jist.pipeline.graph.PipePortView
The connected color.
connectible - Variable in class edu.jhu.ece.iacl.jist.pipeline.PipePort
Indicates if this port can be connected to.
CONNECTION_TAG - Static variable in class edu.jhu.ece.iacl.jist.pipeline.parser.LoniPipeParser
The Constant CONNECTION_TAG.
ConnectionEditor - Class in edu.jhu.ece.iacl.jist.pipeline.gui
Class for editing connections that have an identifying index.
ConnectionEditor(PipePort) - Constructor for class edu.jhu.ece.iacl.jist.pipeline.gui.ConnectionEditor
Constructor.
CONNECTIONS_TAG - Static variable in class edu.jhu.ece.iacl.jist.pipeline.parser.LoniPipeParser
The Constant CONNECTIONS_TAG.
ConnectivityMatrix - Class in edu.jhu.ece.iacl.algorithms.dti.tractography
This class organizes connectivity data into a connectivity matrix.
ConnectivityMatrix() - Constructor for class edu.jhu.ece.iacl.algorithms.dti.tractography.ConnectivityMatrix
 
connector - Variable in class edu.jhu.ece.iacl.jist.pipeline.graph.PipeModuleEdge
The connector.
ConnectorRenderer - Class in edu.jhu.ece.iacl.jist.pipeline.gui
Rendering class for connector with index.
ConnectorRenderer(PipePort) - Constructor for class edu.jhu.ece.iacl.jist.pipeline.gui.ConnectorRenderer
Constructor.
ConstBoundaryGrid - Interface in edu.jhu.cs.cisst.algorithms.optimize.fmg.grid
An interface to the constant methods of class BoundaryGrid.
ConstGrid - Interface in edu.jhu.cs.cisst.algorithms.optimize.fmg.grid
Interface to the constant methods of class Grid.
ConstNoBoundaryGrid - Interface in edu.jhu.cs.cisst.algorithms.optimize.fmg.grid
An interface to the constant methods of class NoBoundaryGrid.
constraints - Variable in class edu.jhu.ece.iacl.jist.pipeline.view.input.ParamInputView
The constraints.
constraints - Variable in class edu.jhu.ece.iacl.jist.pipeline.view.output.ParamOutputView
The constraints.
contains(double, double) - Method in class edu.jhu.cs.cisst.vent.renderer.processing.RendererProcessing2D
Contains.
contains(int) - Method in class edu.jhu.ece.iacl.jist.structures.geom.EmbeddedSurface.Edge
Contains.
contains(PT) - Method in class edu.jhu.ece.iacl.jist.structures.geom.Polyhedron
Contains.
contains(Vertex) - Method in class edu.jhu.ece.iacl.jist.structures.geom.Segment
Contains.
contains(Vertex, Vertex) - Method in class edu.jhu.ece.iacl.jist.structures.geom.Segment
Contains.
contains(PT) - Method in class edu.jhu.ece.iacl.jist.structures.geom.TriangleSigned
Contains.
contextId - Variable in class edu.jhu.ece.iacl.jist.pipeline.ExecutionContext
Identifying experiment number.
contextName - Variable in class edu.jhu.ece.iacl.jist.pipeline.ExecutionContext
The context name.
contextTable - Variable in class edu.jhu.ece.iacl.jist.pipeline.PipeScheduler
Table of dependent contexts for each scheduled context.
contextUpdate(ExecutionContext, ExecutionContext.Update) - Method in interface edu.jhu.ece.iacl.jist.pipeline.ExecutionContext.ContextListener
Fires when the statuedu.jhu.ece.iacl.jist.pipeline.PipeRunners or progress of an execution context changes.
contextUpdate(ExecutionContext, ExecutionContext.Update) - Method in class edu.jhu.ece.iacl.jist.pipeline.PipeScheduler
Update queues if a context's status changes.
contourColor - Variable in class edu.jhu.cs.cisst.vent.renderer.processing.VolumeIsoContourRenderer
The contour color.
contourColorParam - Variable in class edu.jhu.cs.cisst.vent.renderer.processing.VolumeIsoContourRenderer
The contour color param.
contourParam - Variable in class edu.jhu.cs.cisst.plugins.utilities.surface.PlugInIsoContourGenerator
 
contourWorker - Variable in class edu.jhu.cs.cisst.vent.renderer.processing.VolumeIsoContourRenderer
The contour worker.
Contract - Class in edu.jhu.cs.cisst.algorithms.optimize.fmg.util
Some minimal support for "design by contract".
Contract() - Constructor for class edu.jhu.cs.cisst.algorithms.optimize.fmg.util.Contract
 
contrast - Variable in class edu.jhu.cs.cisst.vent.renderer.processing.ImageRenderer
The contrast.
contrast - Variable in class edu.jhu.cs.cisst.vent.renderer.processing.VectorField2DRenderer
The contrast.
contrast - Variable in class edu.jhu.cs.cisst.vent.renderer.processing.VolumeSliceRenderer
The contrast.
contrastParam - Variable in class edu.jhu.cs.cisst.vent.renderer.processing.ImageRenderer
The contrast param.
contrastParam - Variable in class edu.jhu.cs.cisst.vent.renderer.processing.VolumeSliceRenderer
The contrast param.
controlJob(ProcessControlAction) - Method in interface edu.jhu.ece.iacl.jist.processcontrol.ProcessController
Control job.
controlJob(ProcessControlAction) - Method in class edu.jhu.ece.iacl.jist.processcontrol.ProcessControllerDRMAA
 
controlJob(ProcessControlAction) - Method in class edu.jhu.ece.iacl.jist.processcontrol.ProcessControllerNative
 
convergesum - Variable in class edu.jhu.ece.iacl.algorithms.manual_label.staple.STAPLE
 
convergesum - Variable in class edu.jhu.ece.iacl.algorithms.manual_label.staple.STAPLEgeneral
 
convergesum - Variable in class edu.jhu.ece.iacl.algorithms.manual_label.staple.STAPLEgeneralSingle
 
convergesum - Variable in class edu.jhu.ece.iacl.algorithms.manual_label.staple.STAPLEmulti
 
convergesum - Variable in class edu.jhu.ece.iacl.algorithms.manual_label.staple.STAPLEmulti2
 
convergesum - Variable in class edu.jhu.ece.iacl.algorithms.manual_label.staple.STAPLEsingle
 
convergesum - Variable in class edu.jhu.ece.iacl.algorithms.manual_label.staple.STAPLEsurf
 
convert(SourceType) - Method in interface edu.jhu.cs.cisst.vent.converter.Converter
Convert.
convert(ImageData) - Method in interface edu.jhu.cs.cisst.vent.converter.ConvertImageData
 
convert(EmbeddedSurface) - Method in class edu.jhu.cs.cisst.vent.converter.processing.ConvertEmbeddedSurfaceToPTriangleMesh
 
convert(ImageData) - Method in class edu.jhu.cs.cisst.vent.converter.processing.ConvertImageDataToPImage
 
convert(ImageData, int) - Method in class edu.jhu.cs.cisst.vent.converter.processing.ConvertImageDataToPImage
Convert.
convert(ImageData, int, double, double) - Method in class edu.jhu.cs.cisst.vent.converter.processing.ConvertImageDataToPImage
Convert.
convert(ImageData, int, int, double, double) - Method in class edu.jhu.cs.cisst.vent.converter.processing.ConvertImageDataToPImage
Convert.
convert(ImageData, int, int, double, double, double, double) - Method in class edu.jhu.cs.cisst.vent.converter.processing.ConvertImageDataToPImage
Convert.
convert(CurveCollection) - Method in class edu.jhu.cs.cisst.vent.converter.processing.CovertCurveCollectionToPCurveCollection
 
ConvertCurveCollection<DestinationType> - Interface in edu.jhu.cs.cisst.vent.converter
The Interface ConvertCurveCollection.
ConvertEmbeddedSurface<DestinationType> - Interface in edu.jhu.cs.cisst.vent.converter
The Interface ConvertEmbeddedSurface.
ConvertEmbeddedSurfaceToPTriangleMesh - Class in edu.jhu.cs.cisst.vent.converter.processing
The Class ConvertEmbeddedSurfaceToPTriangleMesh.
ConvertEmbeddedSurfaceToPTriangleMesh() - Constructor for class edu.jhu.cs.cisst.vent.converter.processing.ConvertEmbeddedSurfaceToPTriangleMesh
 
Converter<SourceType,DestinationType> - Interface in edu.jhu.cs.cisst.vent.converter
The Interface Converter.
ConvertImageData<DestinationType> - Interface in edu.jhu.cs.cisst.vent.converter
The Interface ConvertImageData.
ConvertImageDataToPImage - Class in edu.jhu.cs.cisst.vent.converter.processing
The Class ConvertImageDataToPImage.
ConvertImageDataToPImage() - Constructor for class edu.jhu.cs.cisst.vent.converter.processing.ConvertImageDataToPImage
 
convertToCartesian() - Method in class edu.jhu.ece.iacl.jist.structures.geom.EmbeddedSurface
Convert to cartesian.
convertToSpherical() - Method in class edu.jhu.ece.iacl.jist.structures.geom.EmbeddedSurface
Convert to spherical.
convolution(float[][][], int, int, int, float[][][], int, int, int) - Static method in class edu.jhmi.rad.medic.libraries.ImageFunctionsPublic
convolution
ConvolutionArrayKernel - Interface in edu.jhu.ece.iacl.jist.structures.image
Array kernel interface.
ConvolutionVolumeKernel - Interface in edu.jhu.ece.iacl.jist.structures.image
Volume kernel interface.
copy - Variable in class edu.jhu.ece.iacl.jist.pipeline.gui.PipeInternalFrame
The expand.
copyAllInfoTo(FileInfoBase) - Method in class edu.jhu.ece.iacl.jist.structures.image.ImageHeader
Copy all info to.
copyBasicInfoTo(FileInfoBase) - Method in class edu.jhu.ece.iacl.jist.structures.image.ImageHeader
Copy basic info to.
copyDataToModelImage(ImageData, ModelImage) - Static method in class edu.jhu.ece.iacl.jist.structures.image.ImageDataMipav
Copy data to model image.
copyFile(File, File) - Static method in class edu.jhu.ece.iacl.jist.pipeline.dest.PipeParamCopyDestination
Copy a file from source to destination.
copyGeometry(ImageHeader) - Method in class edu.jhu.ece.iacl.jist.structures.image.ImageHeader
Copy geometry from one image header into this one.
copyItem - Variable in class edu.jhu.ece.iacl.jist.pipeline.gui.PipelineLayoutTool
The paste item.
cor2ind(int, int) - Method in class edu.jhu.ece.iacl.algorithms.dti.tractography.FACT.cPT
 
corticalThicknessHeatKernelSmoothing - Static variable in class edu.jhu.ece.iacl.algorithms.ReferencedPapers
 
corticalThicknessPowerAnalysis - Static variable in class edu.jhu.ece.iacl.algorithms.ReferencedPapers
 
cosAngle(Vector3f, Vector3f) - Static method in class edu.jhu.ece.iacl.jist.algorithms.graphics.GeomUtil
Cos angle.
cosAngle(Vector2d, Vector2d) - Static method in class edu.jhu.ece.iacl.jist.algorithms.graphics.GeomUtil
Cos angle.
countLines() - Method in class edu.jhu.bme.smile.commons.textfiles.TextFileReader
 
CovertCurveCollectionToPCurveCollection - Class in edu.jhu.cs.cisst.vent.converter.processing
The Class CovertCurveCollectionToPCurveCollection.
CovertCurveCollectionToPCurveCollection() - Constructor for class edu.jhu.cs.cisst.vent.converter.processing.CovertCurveCollectionToPCurveCollection
 
cPT - Class in edu.jhu.ece.iacl.algorithms.dti.tractography.FACT
Created by IntelliJ IDEA.
cPT(float, float, float) - Constructor for class edu.jhu.ece.iacl.algorithms.dti.tractography.FACT.cPT
 
cpuTime - Variable in class edu.jhu.ece.iacl.jist.pipeline.ExecutionContext
Elapsed cpu time in milliseconds.
create() - Method in interface edu.jhu.cs.cisst.vent.Visualization
Creates the visualization and returns parameters used to control the visualziation.
create() - Method in class edu.jhu.cs.cisst.vent.VisualizationProcessing
Creates the.
create() - Method in class edu.jhu.cs.cisst.vent.widgets.VisualizationActiveContour2D
 
create() - Static method in class edu.jhu.ece.iacl.jist.pipeline.MipavViewUserInterface
Create view user interface.
create(Object) - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamFileCollection
Create a new ParamFile with the same restrictions as the collection and the specified value.
create(Object) - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamNumberCollection
Create a new ParamNumber with the same restrictions as the collection and the specified value.
create(Object) - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamSurfaceCollection
Create a new ParamSurface with the same restrictions as the collection and the specified value.
create(Object) - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamVolumeCollection
Create a new ParamVolume with the same restrictions as the collection and the specified value.
create(Object) - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamWeightedVolumeCollection
A new ParamWeightedVolume is created with the value set to the specified value.
createAlgorithm() - Method in class edu.jhu.ece.iacl.jist.pipeline.PipeAlgorithm
Create Processing Algorithm from the algorithm class.
createAlgorithm() - Method in class edu.jhu.ece.iacl.jist.pipeline.PipeAlgorithmGroup
Create Processing Algorithm from the algorithm class.
createAuthors(ProcessingAlgorithm) - Method in class edu.jhu.ece.iacl.doc.DocumentGenerator
 
createAuthors(ProcessingAlgorithm) - Method in class edu.jhu.ece.iacl.doc.DocumentGeneratorHTML
 
createCellAttributes() - Method in class edu.jhu.ece.iacl.jist.pipeline.graph.PipeModuleCell
Create cell attributes that are default with all cells.
createCitations(ProcessingAlgorithm) - Method in class edu.jhu.ece.iacl.doc.DocumentGenerator
 
createCitations(ProcessingAlgorithm) - Method in class edu.jhu.ece.iacl.doc.DocumentGeneratorHTML
 
createCpuTime(ExecutionContext) - Method in class edu.jhu.ece.iacl.jist.pipeline.gui.ProcessManagerTable.ProcessTableModel
Creates the cpu time.
CreateCrossingFiber - Class in edu.jhu.ece.iacl.pami
 
CreateCrossingFiber() - Constructor for class edu.jhu.ece.iacl.pami.CreateCrossingFiber
 
createDefaultGraphCell(DraggableNode) - Method in class edu.jhu.ece.iacl.jist.pipeline.graph.PipeJGraph
Creates the default graph cell.
createDefaultLabels() - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamDataLabel
Create default labels based on volume values.
createDocument(ProcessingAlgorithm) - Method in class edu.jhu.ece.iacl.doc.DocumentGenerator
 
createDocumentGenerator() - Method in class edu.jhu.ece.iacl.doc.DocumentAllModules
 
createEdgeAttributes() - Method in class edu.jhu.ece.iacl.jist.pipeline.graph.PipeModuleEdge
Creates the edge attributes.
createEdgeView(Object) - Method in class edu.jhu.ece.iacl.jist.pipeline.graph.PipeCellViewFactory
 
createFiber(FiberTracker.FACTfiber) - Method in class edu.jhu.ece.iacl.algorithms.dti.tractography.FiberTracker
 
createFiber(WildBootFiberTracker.WildBootFACTfiber) - Method in class edu.jhu.ece.iacl.algorithms.dti.tractography.WildBootFiberTracker
 
createFooter(ProcessingAlgorithm) - Method in class edu.jhu.ece.iacl.doc.DocumentGenerator
 
createFooter(ProcessingAlgorithm) - Method in class edu.jhu.ece.iacl.doc.DocumentGeneratorHTML
 
createGraph() - Method in class edu.jhu.ece.iacl.jist.pipeline.gui.PipeInternalFrame
Create graph and install listeners.
createGraphCell() - Method in class edu.jhu.ece.iacl.jist.pipeline.graph.PipeAlgorithmFactory
Create graph cell to represent algorithm.
createGraphCell() - Method in class edu.jhu.ece.iacl.jist.pipeline.graph.PipeDestinationFactory
 
createGraphCell() - Method in class edu.jhu.ece.iacl.jist.pipeline.graph.PipeModuleFactory
Create graph cell for internal frame.
createGraphCell() - Method in class edu.jhu.ece.iacl.jist.pipeline.graph.PipeSourceFactory
Create graph cell for source.
createGraphCellEditor() - Method in class edu.jhu.ece.iacl.jist.pipeline.graph.PipeEdgeEditor
This is invoked if a TreeCellEditor is not supplied in the constructor.
createGraphNode(PipeModule) - Method in class edu.jhu.ece.iacl.jist.pipeline.graph.PipeJGraph
Creates the graph node.
createHeader(ProcessingAlgorithm) - Method in class edu.jhu.ece.iacl.doc.DocumentGenerator
 
createHeader(ProcessingAlgorithm) - Method in class edu.jhu.ece.iacl.doc.DocumentGeneratorHTML
 
createInputDialog() - Method in class edu.jhu.ece.iacl.jist.pipeline.ProcessingDialog
Create input dialog frame from input parameters.
createInputDialog() - Method in class edu.jhu.ece.iacl.jist.pipeline.ProcessingGroupDialog
Create input dialog frame from input parameters.
createInputInformation(ProcessingAlgorithm) - Method in class edu.jhu.ece.iacl.doc.DocumentGenerator
 
createInputInformation(ProcessingAlgorithm) - Method in class edu.jhu.ece.iacl.doc.DocumentGeneratorHTML
 
createInputMenuBar() - Method in class edu.jhu.ece.iacl.jist.pipeline.ProcessingDialog
Create menubar for input pane.
createInputMenuBar() - Method in class edu.jhu.ece.iacl.jist.pipeline.ProcessingGroupDialog
Create menubar for input pane.
createInputParameters(ParamCollection) - Method in class edu.jhu.bme.smile.demo.AddingNoise
 
createInputParameters(ParamCollection) - Method in class edu.jhu.bme.smile.demo.ChebyShevFitting
 
createInputParameters(ParamCollection) - Method in class edu.jhu.bme.smile.demo.FirstPluginTest
 
createInputParameters(ParamCollection) - Method in class edu.jhu.bme.smile.demo.ImageAlgebra
 
createInputParameters(ParamCollection) - Method in class edu.jhu.bme.smile.demo.ImageArithmetic
 
createInputParameters(ParamCollection) - Method in class edu.jhu.bme.smile.demo.ImageCollectionAlgebra
 
createInputParameters(ParamCollection) - Method in class edu.jhu.bme.smile.demo.MemoryDemo
 
createInputParameters(ParamCollection) - Method in class edu.jhu.bme.smile.demo.RandomVol
Creates the input parameters.
createInputParameters(ParamCollection) - Method in class edu.jhu.bme.smile.demo.ScaleImageDemo
 
createInputParameters(ParamCollection) - Method in class edu.jhu.cs.cisst.plugins.classification.PlugInFuzzyMembershipThreshold2D
 
createInputParameters(ParamCollection) - Method in class edu.jhu.cs.cisst.plugins.segmentation.PlugInCircleLevelSet
 
createInputParameters(ParamCollection) - Method in class edu.jhu.cs.cisst.plugins.segmentation.PlugInGeodesicActiveContour2D
 
createInputParameters(ParamCollection) - Method in class edu.jhu.cs.cisst.plugins.segmentation.PlugInGradientVectorFlow2D
 
createInputParameters(ParamCollection) - Method in class edu.jhu.cs.cisst.plugins.utilities.file.PlugInTestDataSelector
 
createInputParameters(ParamCollection) - Method in class edu.jhu.cs.cisst.plugins.utilities.surface.PlugInIsoContourGenerator
 
createInputParameters(ParamCollection) - Method in class edu.jhu.cs.cisst.plugins.utilities.surface.PlugInIsoSurfaceGenerator
 
createInputParameters(ParamCollection) - Method in class edu.jhu.cs.cisst.plugins.visualization.PlugInVisualizeActiveContour2D
 
createInputParameters(ParamCollection) - Method in class edu.jhu.cs.cisst.plugins.visualization.PlugInVisualizeImage
 
createInputParameters(ParamCollection) - Method in class edu.jhu.cs.cisst.plugins.visualization.PlugInVisualizeSurface
 
createInputParameters(ParamCollection) - Method in class edu.jhu.ece.iacl.jist.pipeline.parser.MipavPluginParser
 
createInputParameters(ParamCollection) - Method in class edu.jhu.ece.iacl.jist.pipeline.ProcessingAlgorithm
Create input parameters.
createInputParameters(ParamCollection) - Method in class edu.jhu.ece.iacl.jist.plugins.MedicAlgorithmExecutableAdapter
 
createInputParameters(ParamCollection) - Method in class edu.jhu.ece.iacl.jist.plugins.MedicAlgorithmJistLayoutAdapter
 
createInputParameters(ParamCollection) - Method in class edu.jhu.ece.iacl.jist.plugins.MedicAlgorithmMipavAdapter
 
createInputParameters(ParamCollection) - Method in class edu.jhu.ece.iacl.jist.plugins.testing.MedicAlgorithmDemo
Create input parameters for this plug-in
createInputParameters(ParamCollection) - Method in class edu.jhu.ece.iacl.pami.CreateCrossingFiber
 
createInputParameters(ParamCollection) - Method in class edu.jhu.ece.iacl.pami.CreateTesselatedSurface
 
createInputParameters(ParamCollection) - Method in class edu.jhu.ece.iacl.pami.DivideReference
 
createInputParameters(ParamCollection) - Method in class edu.jhu.ece.iacl.pami.GenerateTensors
 
createInputParameters(ParamCollection) - Method in class edu.jhu.ece.iacl.pami.NameTest
 
createInputParameters(ParamCollection) - Method in class edu.jhu.ece.iacl.pami.SimFramework
 
createInputParameters(ParamCollection) - Method in class edu.jhu.ece.iacl.plugins.dti.AlgorithmDWIMotionCorrection
 
createInputParameters(ParamCollection) - Method in class edu.jhu.ece.iacl.plugins.dti.AlgorithmGradientTableCorrection
 
createInputParameters(ParamCollection) - Method in class edu.jhu.ece.iacl.plugins.dti.ComputeMeanB0
 
createInputParameters(ParamCollection) - Method in class edu.jhu.ece.iacl.plugins.dti.ComputeMeanDW
 
createInputParameters(ParamCollection) - Method in class edu.jhu.ece.iacl.plugins.dti.DWIBallStickEstCamino
 
createInputParameters(ParamCollection) - Method in class edu.jhu.ece.iacl.plugins.dti.DWIBallStickEstCaminoFileCollection
 
createInputParameters(ParamCollection) - Method in class edu.jhu.ece.iacl.plugins.dti.DWICombineBvalTables
 
createInputParameters(ParamCollection) - Method in class edu.jhu.ece.iacl.plugins.dti.DWICombineGradTables
 
createInputParameters(ParamCollection) - Method in class edu.jhu.ece.iacl.plugins.dti.DWIDefineCaminoScheme
 
createInputParameters(ParamCollection) - Method in class edu.jhu.ece.iacl.plugins.dti.DWITensorColorEncodedMap
 
createInputParameters(ParamCollection) - Method in class edu.jhu.ece.iacl.plugins.dti.DWITensorContrasts
 
createInputParameters(ParamCollection) - Method in class edu.jhu.ece.iacl.plugins.dti.DWITensorEstCamino
 
createInputParameters(ParamCollection) - Method in class edu.jhu.ece.iacl.plugins.dti.DWITensorEstCaminoFileCollection
 
createInputParameters(ParamCollection) - Method in class edu.jhu.ece.iacl.plugins.dti.DWITensorEstCaminoRESTOREVariableNoiseField
 
createInputParameters(ParamCollection) - Method in class edu.jhu.ece.iacl.plugins.dti.DWITensorEstLikelihood
 
createInputParameters(ParamCollection) - Method in class edu.jhu.ece.iacl.plugins.dti.DWITensorEstLLMSE
 
createInputParameters(ParamCollection) - Method in class edu.jhu.ece.iacl.plugins.dti.DWIThreeTensorEstCamino
 
createInputParameters(ParamCollection) - Method in class edu.jhu.ece.iacl.plugins.dti.DWIThreeTensorEstCaminoFileCollection
 
createInputParameters(ParamCollection) - Method in class edu.jhu.ece.iacl.plugins.dti.DWITwoTensorEstCamino
 
createInputParameters(ParamCollection) - Method in class edu.jhu.ece.iacl.plugins.dti.DWITwoTensorEstCaminoFileCollection
 
createInputParameters(ParamCollection) - Method in class edu.jhu.ece.iacl.plugins.dti.LocalNoiseEstimate
 
createInputParameters(ParamCollection) - Method in class edu.jhu.ece.iacl.plugins.dti.MedicAlgorithmFlipVectorTable
 
createInputParameters(ParamCollection) - Method in class edu.jhu.ece.iacl.plugins.dti.MedicAlgorithmFlipVectorVolume
 
createInputParameters(ParamCollection) - Method in class edu.jhu.ece.iacl.plugins.dti.MedicAlgorithmFormatVectorImage
 
createInputParameters(ParamCollection) - Method in class edu.jhu.ece.iacl.plugins.dti.MedicAlgorithmMultiGradientTableCreator
 
createInputParameters(ParamCollection) - Method in class edu.jhu.ece.iacl.plugins.dti.MedicAlgorithmMultiParV3Info
 
createInputParameters(ParamCollection) - Method in class edu.jhu.ece.iacl.plugins.dti.MedicAlgorithmMultiParV4Info
 
createInputParameters(ParamCollection) - Method in class edu.jhu.ece.iacl.plugins.dti.MedicAlgorithmSubsampleFibers
 
createInputParameters(ParamCollection) - Method in class edu.jhu.ece.iacl.plugins.dti.MedicAlgorithmTableFormat
 
createInputParameters(ParamCollection) - Method in class edu.jhu.ece.iacl.plugins.dti.MedicAlgorithmTensorFormatConvert
 
createInputParameters(ParamCollection) - Method in class edu.jhu.ece.iacl.plugins.dti.RegularizeNoiseField
 
createInputParameters(ParamCollection) - Method in class edu.jhu.ece.iacl.plugins.dti.tractography.AlgorithmComputeConnectivityMatrix
 
createInputParameters(ParamCollection) - Method in class edu.jhu.ece.iacl.plugins.dti.tractography.Fiber2Volume
 
createInputParameters(ParamCollection) - Method in class edu.jhu.ece.iacl.plugins.dti.tractography.MedicAlgorithmApplyFiberROI
 
createInputParameters(ParamCollection) - Method in class edu.jhu.ece.iacl.plugins.dti.tractography.MedicAlgorithmDeformFibers
 
createInputParameters(ParamCollection) - Method in class edu.jhu.ece.iacl.plugins.dti.tractography.MedicAlgorithmFiberComparison
 
createInputParameters(ParamCollection) - Method in class edu.jhu.ece.iacl.plugins.dti.tractography.MedicAlgorithmFibersFromSurfaceROI
 
createInputParameters(ParamCollection) - Method in class edu.jhu.ece.iacl.plugins.dti.tractography.MedicAlgorithmFiberTracker
 
createInputParameters(ParamCollection) - Method in class edu.jhu.ece.iacl.plugins.dti.tractography.MedicAlgorithmFiberVolumeStatistics
 
createInputParameters(ParamCollection) - Method in class edu.jhu.ece.iacl.plugins.dti.tractography.MedicAlgorithmTransformFibers
 
createInputParameters(ParamCollection) - Method in class edu.jhu.ece.iacl.plugins.dti.tractography.MedicAlgorithmWildBootTrac
 
createInputParameters(ParamCollection) - Method in class edu.jhu.ece.iacl.plugins.dti.tractography.SImageTractAnalysis
 
createInputParameters(ParamCollection) - Method in class edu.jhu.ece.iacl.plugins.dti.tractography.TractMapping
 
createInputParameters(ParamCollection) - Method in class edu.jhu.ece.iacl.plugins.hardi.CFARIEstimation
 
createInputParameters(ParamCollection) - Method in class edu.jhu.ece.iacl.plugins.hardi.CFARIEstimation2
 
createInputParameters(ParamCollection) - Method in class edu.jhu.ece.iacl.plugins.hardi.CreatePlatonicSolidSurface
 
createInputParameters(ParamCollection) - Method in class edu.jhu.ece.iacl.plugins.hardi.DefineCFARIScheme
 
createInputParameters(ParamCollection) - Method in class edu.jhu.ece.iacl.plugins.hardi.ExtractBvalGradFromPAR
 
createInputParameters(ParamCollection) - Method in class edu.jhu.ece.iacl.plugins.hardi.FunkRadonTransform
 
createInputParameters(ParamCollection) - Method in class edu.jhu.ece.iacl.plugins.hardi.GradToSurf
 
createInputParameters(ParamCollection) - Method in class edu.jhu.ece.iacl.plugins.hardi.NormalizeToUnitMagnitude
 
createInputParameters(ParamCollection) - Method in class edu.jhu.ece.iacl.plugins.hardi.Process3DMRIImages
 
createInputParameters(ParamCollection) - Method in class edu.jhu.ece.iacl.plugins.hardi.QBallEstimation
 
createInputParameters(ParamCollection) - Method in class edu.jhu.ece.iacl.plugins.hardi.QBallModifiedRealProjection
 
createInputParameters(ParamCollection) - Method in class edu.jhu.ece.iacl.plugins.hardi.QBallProjection
 
createInputParameters(ParamCollection) - Method in class edu.jhu.ece.iacl.plugins.hardi.SelectUniqueDiffusionDirections
 
createInputParameters(ParamCollection) - Method in class edu.jhu.ece.iacl.plugins.hardi.SurfToGrad
 
createInputParameters(ParamCollection) - Method in class edu.jhu.ece.iacl.plugins.hardi.TesselateSurface
 
createInputParameters(ParamCollection) - Method in class edu.jhu.ece.iacl.plugins.labeling.atlasing.AlgorithmLogOdds
 
createInputParameters(ParamCollection) - Method in class edu.jhu.ece.iacl.plugins.labeling.MedicAlgorithmCleanSurfLabels
 
createInputParameters(ParamCollection) - Method in class edu.jhu.ece.iacl.plugins.labeling.MedicAlgorithmFMLabelExtension
 
createInputParameters(ParamCollection) - Method in class edu.jhu.ece.iacl.plugins.labeling.MedicAlgorithmMultiAtlasLabeling
 
createInputParameters(ParamCollection) - Method in class edu.jhu.ece.iacl.plugins.labeling.MedicAlgorithmMultiAtlasSurfaceLabeling
 
createInputParameters(ParamCollection) - Method in class edu.jhu.ece.iacl.plugins.labeling.MedicAlgorithmVolumeToSurfaceLabeling
 
createInputParameters(ParamCollection) - Method in class edu.jhu.ece.iacl.plugins.labeling.simulation.AlgorithmSimulateSurfaceRater
 
createInputParameters(ParamCollection) - Method in class edu.jhu.ece.iacl.plugins.labeling.simulation.AlgorithmSimulateVolumeRater
 
createInputParameters(ParamCollection) - Method in class edu.jhu.ece.iacl.plugins.labeling.staple.MedicAlgorithmSTAPLE
 
createInputParameters(ParamCollection) - Method in class edu.jhu.ece.iacl.plugins.labeling.staple.MedicAlgorithmSTAPLEgeneral
 
createInputParameters(ParamCollection) - Method in class edu.jhu.ece.iacl.plugins.labeling.staple.MedicAlgorithmSTAPLEsurface
 
createInputParameters(ParamCollection) - Method in class edu.jhu.ece.iacl.plugins.quantitative.EstimateMTR
 
createInputParameters(ParamCollection) - Method in class edu.jhu.ece.iacl.plugins.quantitative.EstimateMTRseries
 
createInputParameters(ParamCollection) - Method in class edu.jhu.ece.iacl.plugins.quantitative.EstimateT1FromDoubleAngle
 
createInputParameters(ParamCollection) - Method in class edu.jhu.ece.iacl.plugins.quantitative.EstimateT2FromDualEcho
 
createInputParameters(ParamCollection) - Method in class edu.jhu.ece.iacl.plugins.registration.MedicAlgorithmAtlasSelection
 
createInputParameters(ParamCollection) - Method in class edu.jhu.ece.iacl.plugins.registration.MedicAlgorithmConstrainedFLIRT
 
createInputParameters(ParamCollection) - Method in class edu.jhu.ece.iacl.plugins.registration.MedicAlgorithmCreateSimilarityMetricVol
 
createInputParameters(ParamCollection) - Method in class edu.jhu.ece.iacl.plugins.registration.MedicAlgorithmEfficientFileCollectionRegistration
 
createInputParameters(ParamCollection) - Method in class edu.jhu.ece.iacl.plugins.registration.MedicAlgorithmFLIRT
 
createInputParameters(ParamCollection) - Method in class edu.jhu.ece.iacl.plugins.registration.MedicAlgorithmFLIRTCollection
 
createInputParameters(ParamCollection) - Method in class edu.jhu.ece.iacl.plugins.registration.MedicAlgorithmMultiAtlasReg
 
createInputParameters(ParamCollection) - Method in class edu.jhu.ece.iacl.plugins.registration.MedicAlgorithmMultiDeformVolume
 
createInputParameters(ParamCollection) - Method in class edu.jhu.ece.iacl.plugins.registration.MedicAlgorithmTransformVolume
 
createInputParameters(ParamCollection) - Method in class edu.jhu.ece.iacl.plugins.registration.MedicAlgorithmVABRA
 
createInputParameters(ParamCollection) - Method in class edu.jhu.ece.iacl.plugins.segmentation.CreateMask
 
createInputParameters(ParamCollection) - Method in class edu.jhu.ece.iacl.plugins.spectro.CESTAsymmetry
 
createInputParameters(ParamCollection) - Method in class edu.jhu.ece.iacl.plugins.spectro.JistMSWASSR
 
createInputParameters(ParamCollection) - Method in class edu.jhu.ece.iacl.plugins.utilities.file.AddToFileCollection
 
createInputParameters(ParamCollection) - Method in class edu.jhu.ece.iacl.plugins.utilities.file.FileCollectionToPins
 
createInputParameters(ParamCollection) - Method in class edu.jhu.ece.iacl.plugins.utilities.file.FileCollectionToVolumeCollection
 
createInputParameters(ParamCollection) - Method in class edu.jhu.ece.iacl.plugins.utilities.file.MedicAlgorithmChooseFileRegEx
 
createInputParameters(ParamCollection) - Method in class edu.jhu.ece.iacl.plugins.utilities.file.MedicAlgorithmChooseVolumeRegEx
 
createInputParameters(ParamCollection) - Method in class edu.jhu.ece.iacl.plugins.utilities.file.MedicAlgorithmConcatArrayDoubleTextLists
 
createInputParameters(ParamCollection) - Method in class edu.jhu.ece.iacl.plugins.utilities.file.MedicAlgorithmFibersToVtk
 
createInputParameters(ParamCollection) - Method in class edu.jhu.ece.iacl.plugins.utilities.file.MedicAlgorithmIdentifySubject
 
createInputParameters(ParamCollection) - Method in class edu.jhu.ece.iacl.plugins.utilities.file.MedicAlgorithmSurfaceConverter
 
createInputParameters(ParamCollection) - Method in class edu.jhu.ece.iacl.plugins.utilities.file.MedicAlgorithmVolumeConverter
 
createInputParameters(ParamCollection) - Method in class edu.jhu.ece.iacl.plugins.utilities.file.MedicAlgorithmVolumeConverter2
 
createInputParameters(ParamCollection) - Method in class edu.jhu.ece.iacl.plugins.utilities.file.MedicAlgorithmVolumeConverter4D
 
createInputParameters(ParamCollection) - Method in class edu.jhu.ece.iacl.plugins.utilities.file.MedicAlgorithmVolumeListOrganizer
 
createInputParameters(ParamCollection) - Method in class edu.jhu.ece.iacl.plugins.utilities.file.MedicAlgorithmZip
 
createInputParameters(ParamCollection) - Method in class edu.jhu.ece.iacl.plugins.utilities.file.VolumeDirectoryNoIter
 
createInputParameters(ParamCollection) - Method in class edu.jhu.ece.iacl.plugins.utilities.logic.MedicAlgorithmFloatsToPoint
 
createInputParameters(ParamCollection) - Method in class edu.jhu.ece.iacl.plugins.utilities.logic.MedicAlgorithmSerializeSurfaces
 
createInputParameters(ParamCollection) - Method in class edu.jhu.ece.iacl.plugins.utilities.logic.MedicAlgorithmSerializeVolumes
 
createInputParameters(ParamCollection) - Method in class edu.jhu.ece.iacl.plugins.utilities.logic.MedicAlgorithmSurfaceSplitter
 
createInputParameters(ParamCollection) - Method in class edu.jhu.ece.iacl.plugins.utilities.logic.MedicAlgorithmValueEquals
 
createInputParameters(ParamCollection) - Method in class edu.jhu.ece.iacl.plugins.utilities.logic.MedicAlgorithmValueGreaterThan
 
createInputParameters(ParamCollection) - Method in class edu.jhu.ece.iacl.plugins.utilities.logic.MedicAlgorithmValueInRange
 
createInputParameters(ParamCollection) - Method in class edu.jhu.ece.iacl.plugins.utilities.logic.MedicAlgorithmValueLessThan
 
createInputParameters(ParamCollection) - Method in class edu.jhu.ece.iacl.plugins.utilities.logic.MedicAlgorithmVolumeSplitter
 
createInputParameters(ParamCollection) - Method in class edu.jhu.ece.iacl.plugins.utilities.math.MedicAlgorithmArithmetic
 
createInputParameters(ParamCollection) - Method in class edu.jhu.ece.iacl.plugins.utilities.math.MedicAlgorithmImageCalculator
 
createInputParameters(ParamCollection) - Method in class edu.jhu.ece.iacl.plugins.utilities.math.MedicAlgorithmImageCalculatorBatch
 
createInputParameters(ParamCollection) - Method in class edu.jhu.ece.iacl.plugins.utilities.math.MedicAlgorithmImageCalculatorModified
 
createInputParameters(ParamCollection) - Method in class edu.jhu.ece.iacl.plugins.utilities.math.MedicAlgorithmImageMath
 
createInputParameters(ParamCollection) - Method in class edu.jhu.ece.iacl.plugins.utilities.math.MedicAlgorithmKLDivergence
 
createInputParameters(ParamCollection) - Method in class edu.jhu.ece.iacl.plugins.utilities.roi.AlgorithmJointROIStats
 
createInputParameters(ParamCollection) - Method in class edu.jhu.ece.iacl.plugins.utilities.roi.AlgorithmROIStats
 
createInputParameters(ParamCollection) - Method in class edu.jhu.ece.iacl.plugins.utilities.surface.MedicAlgorithmCombineSurfaceComponents
 
createInputParameters(ParamCollection) - Method in class edu.jhu.ece.iacl.plugins.utilities.surface.MedicAlgorithmCombineSurfaces
 
createInputParameters(ParamCollection) - Method in class edu.jhu.ece.iacl.plugins.utilities.surface.MedicAlgorithmCopyEmbeddedData
 
createInputParameters(ParamCollection) - Method in class edu.jhu.ece.iacl.plugins.utilities.surface.MedicAlgorithmEmbedSurface
 
createInputParameters(ParamCollection) - Method in class edu.jhu.ece.iacl.plugins.utilities.surface.MedicAlgorithmExtractSurfaceComponent
 
createInputParameters(ParamCollection) - Method in class edu.jhu.ece.iacl.plugins.utilities.surface.MedicAlgorithmReshapePoints
 
createInputParameters(ParamCollection) - Method in class edu.jhu.ece.iacl.plugins.utilities.surface.MedicAlgorithmReshapeSurface
 
createInputParameters(ParamCollection) - Method in class edu.jhu.ece.iacl.plugins.utilities.surface.MedicAlgorithmSurfaceHistogram
 
createInputParameters(ParamCollection) - Method in class edu.jhu.ece.iacl.plugins.utilities.surface.MedicAlgorithmSurfaceToVolumeConverter
 
createInputParameters(ParamCollection) - Method in class edu.jhu.ece.iacl.plugins.utilities.volume.AlgorithmVolumeFileCollectionTo3D
 
createInputParameters(ParamCollection) - Method in class edu.jhu.ece.iacl.plugins.utilities.volume.CombinedSlabCollectionToVolumeCollection
 
createInputParameters(ParamCollection) - Method in class edu.jhu.ece.iacl.plugins.utilities.volume.GetImageDimensions
 
createInputParameters(ParamCollection) - Method in class edu.jhu.ece.iacl.plugins.utilities.volume.MedicAlgorithmCombineVolumeComponents
 
createInputParameters(ParamCollection) - Method in class edu.jhu.ece.iacl.plugins.utilities.volume.MedicAlgorithmCrop
 
createInputParameters(ParamCollection) - Method in class edu.jhu.ece.iacl.plugins.utilities.volume.MedicAlgorithmDimensions
 
createInputParameters(ParamCollection) - Method in class edu.jhu.ece.iacl.plugins.utilities.volume.MedicAlgorithmExtractAllComponents
 
createInputParameters(ParamCollection) - Method in class edu.jhu.ece.iacl.plugins.utilities.volume.MedicAlgorithmExtractFileCollectionComponents
 
createInputParameters(ParamCollection) - Method in class edu.jhu.ece.iacl.plugins.utilities.volume.MedicAlgorithmExtractVolumeComponent
 
createInputParameters(ParamCollection) - Method in class edu.jhu.ece.iacl.plugins.utilities.volume.MedicAlgorithmFindEqualVolume
 
createInputParameters(ParamCollection) - Method in class edu.jhu.ece.iacl.plugins.utilities.volume.MedicAlgorithmIsotropicReslice
 
createInputParameters(ParamCollection) - Method in class edu.jhu.ece.iacl.plugins.utilities.volume.MedicAlgorithmMatchAllImages
 
createInputParameters(ParamCollection) - Method in class edu.jhu.ece.iacl.plugins.utilities.volume.MedicAlgorithmMipavReorient
 
createInputParameters(ParamCollection) - Method in class edu.jhu.ece.iacl.plugins.utilities.volume.MedicAlgorithmMultiCrop
 
createInputParameters(ParamCollection) - Method in class edu.jhu.ece.iacl.plugins.utilities.volume.MedicAlgorithmReverseComponents
 
createInputParameters(ParamCollection) - Method in class edu.jhu.ece.iacl.plugins.utilities.volume.MedicAlgorithmSetHeaders
 
createInputParameters(ParamCollection) - Method in class edu.jhu.ece.iacl.plugins.utilities.volume.MedicAlgorithmThreshold
 
createInputParameters(ParamCollection) - Method in class edu.jhu.ece.iacl.plugins.utilities.volume.MedicAlgorithmUncrop
 
createInputParameters(ParamCollection) - Method in class edu.jhu.ece.iacl.plugins.utilities.volume.MedicAlgorithmVolumeHistogram
 
createInputParameters(ParamCollection) - Method in class edu.jhu.ece.iacl.plugins.utilities.volume.VolumeCensorRange
 
createInputParameters(ParamCollection) - Method in class edu.jhu.ece.iacl.plugins.utilities.volume.VolumeCollectionToCombinedSlabCollection
 
createInputParameters(ParamCollection) - Method in class edu.vanderbilt.masi.plugins.utilities.volume.PluginCombineVolumes
 
createInputParams() - Method in class edu.jhu.ece.iacl.jist.pipeline.dest.PipeAssertionTestDestination
 
createInputParams() - Method in class edu.jhu.ece.iacl.jist.pipeline.dest.PipeDoubleCollectionExternalDestination
Create input parameters.
createInputParams() - Method in class edu.jhu.ece.iacl.jist.pipeline.dest.PipeDoubleExternalDestination
Create input parameters.
createInputParams() - Method in class edu.jhu.ece.iacl.jist.pipeline.dest.PipeFileCollectionExternalDestination
Create input parameters.
createInputParams() - Method in class edu.jhu.ece.iacl.jist.pipeline.dest.PipeFileExternalDestination
Create input parameters.
createInputParams() - Method in class edu.jhu.ece.iacl.jist.pipeline.dest.PipeIntegerCollectionExternalDestination
Create input parameters.
createInputParams() - Method in class edu.jhu.ece.iacl.jist.pipeline.dest.PipeIntegerExternalDestination
Create input parameters.
createInputParams() - Method in class edu.jhu.ece.iacl.jist.pipeline.dest.PipeParamCopyDestination
Create input parameters.
createInputParams() - Method in class edu.jhu.ece.iacl.jist.pipeline.dest.PipeParamSummaryDestination
Create input parameters.
createInputParams() - Method in class edu.jhu.ece.iacl.jist.pipeline.dest.PipeSurfaceCollectionExternalDestination
Create input parameters.
createInputParams() - Method in class edu.jhu.ece.iacl.jist.pipeline.dest.PipeSurfaceExternalDestination
Create input parameters.
createInputParams() - Method in class edu.jhu.ece.iacl.jist.pipeline.dest.PipeVolumeCollectionExternalDestination
Create input parameters.
createInputParams() - Method in class edu.jhu.ece.iacl.jist.pipeline.dest.PipeVolumeExternalDestination
Create input parameters.
createInputParams() - Method in class edu.jhu.ece.iacl.jist.pipeline.PipeDestination
Create input parameters for this destination.
createInputParams() - Method in class edu.jhu.ece.iacl.jist.pipeline.PipeSource
Create input parameters for this source.
createInputParams() - Method in class edu.jhu.ece.iacl.jist.pipeline.src.PipeDoubleCollectionExternalSource
 
createInputParams() - Method in class edu.jhu.ece.iacl.jist.pipeline.src.PipeDoubleCollectionListSource
Create input parameters.
createInputParams() - Method in class edu.jhu.ece.iacl.jist.pipeline.src.PipeDoubleExternalSource
 
createInputParams() - Method in class edu.jhu.ece.iacl.jist.pipeline.src.PipeDoubleListSource
Create input parameters.
createInputParams() - Method in class edu.jhu.ece.iacl.jist.pipeline.src.PipeDoubleSweepSource
Create input parameters.
createInputParams() - Method in class edu.jhu.ece.iacl.jist.pipeline.src.PipeFileCollectionExternalSource
 
createInputParams() - Method in class edu.jhu.ece.iacl.jist.pipeline.src.PipeFileCollectionListSource
 
createInputParams() - Method in class edu.jhu.ece.iacl.jist.pipeline.src.PipeFileCollectionSource
Create input parameters.
createInputParams() - Method in class edu.jhu.ece.iacl.jist.pipeline.src.PipeFileDirectorySource
Create input parameters.
createInputParams() - Method in class edu.jhu.ece.iacl.jist.pipeline.src.PipeFileExternalSource
 
createInputParams() - Method in class edu.jhu.ece.iacl.jist.pipeline.src.PipeFileListSource
Create input parameters.
createInputParams() - Method in class edu.jhu.ece.iacl.jist.pipeline.src.PipeIntegerCollectionExternalSource
 
createInputParams() - Method in class edu.jhu.ece.iacl.jist.pipeline.src.PipeIntegerCollectionListSource
Create input parameters.
createInputParams() - Method in class edu.jhu.ece.iacl.jist.pipeline.src.PipeIntegerExternalSource
 
createInputParams() - Method in class edu.jhu.ece.iacl.jist.pipeline.src.PipeIntegerListSource
Create input parameters.
createInputParams() - Method in class edu.jhu.ece.iacl.jist.pipeline.src.PipeIntegerSweepSource
 
createInputParams() - Method in class edu.jhu.ece.iacl.jist.pipeline.src.PipeListCollectionSource
Create input parameters.
createInputParams() - Method in class edu.jhu.ece.iacl.jist.pipeline.src.PipeListSource
Create input parameters.
createInputParams() - Method in class edu.jhu.ece.iacl.jist.pipeline.src.PipePointDoubleSweepSource
Create input parameters.
createInputParams() - Method in class edu.jhu.ece.iacl.jist.pipeline.src.PipePointListSource
Create Input Parameters.
createInputParams() - Method in class edu.jhu.ece.iacl.jist.pipeline.src.PipeSelectionExternalSource
Create input parameters.
createInputParams() - Method in class edu.jhu.ece.iacl.jist.pipeline.src.PipeSelectionListSource
 
createInputParams() - Method in class edu.jhu.ece.iacl.jist.pipeline.src.PipeSelectionSource
Create input parameters.
createInputParams() - Method in class edu.jhu.ece.iacl.jist.pipeline.src.PipeStringListSource
 
createInputParams() - Method in class edu.jhu.ece.iacl.jist.pipeline.src.PipeSurfaceCollectionExternalSource
 
createInputParams() - Method in class edu.jhu.ece.iacl.jist.pipeline.src.PipeSurfaceCollectionListSource
 
createInputParams() - Method in class edu.jhu.ece.iacl.jist.pipeline.src.PipeSurfaceCollectionSource
Create input parameters.
createInputParams() - Method in class edu.jhu.ece.iacl.jist.pipeline.src.PipeSurfaceDirectorySurface
 
createInputParams() - Method in class edu.jhu.ece.iacl.jist.pipeline.src.PipeSurfaceExternalSource
 
createInputParams() - Method in class edu.jhu.ece.iacl.jist.pipeline.src.PipeSurfaceListSource
Create input parameters.
createInputParams() - Method in class edu.jhu.ece.iacl.jist.pipeline.src.PipeToggleSource
Create input parameters.
createInputParams() - Method in class edu.jhu.ece.iacl.jist.pipeline.src.PipeVolumeCollectionExternalSource
 
createInputParams() - Method in class edu.jhu.ece.iacl.jist.pipeline.src.PipeVolumeCollectionListSource
 
createInputParams() - Method in class edu.jhu.ece.iacl.jist.pipeline.src.PipeVolumeCollectionSource
Create input parameters.
createInputParams() - Method in class edu.jhu.ece.iacl.jist.pipeline.src.PipeVolumeDirectoryCollectionSource
 
createInputParams() - Method in class edu.jhu.ece.iacl.jist.pipeline.src.PipeVolumeDirectorySource
 
createInputParams() - Method in class edu.jhu.ece.iacl.jist.pipeline.src.PipeVolumeExternalSource
 
createInputParams() - Method in class edu.jhu.ece.iacl.jist.pipeline.src.PipeVolumeListSource
Create input parameters.
createJob(boolean, List<String>) - Method in class edu.jhu.ece.iacl.jist.processcontrol.DispatchController
Creates the job.
createLM(int, int[][]) - Static method in class edu.jhu.bme.smile.commons.math.specialFunctions.SphericalHarmonics
 
createLongDescription(ProcessingAlgorithm) - Method in class edu.jhu.ece.iacl.doc.DocumentGenerator
 
createLongDescription(ProcessingAlgorithm) - Method in class edu.jhu.ece.iacl.doc.DocumentGeneratorHTML
 
CreateMask - Class in edu.jhu.ece.iacl.plugins.segmentation
 
CreateMask() - Constructor for class edu.jhu.ece.iacl.plugins.segmentation.CreateMask
 
createMemory(ExecutionContext) - Method in class edu.jhu.ece.iacl.jist.pipeline.gui.ProcessManagerTable.ProcessTableModel
Creates the memory.
createMenuBar() - Method in class edu.jhu.ece.iacl.jist.pipeline.gui.PipelineLayoutTool
Create menu items.
createMenuBar() - Method in class edu.jhu.ece.iacl.jist.pipeline.gui.PlugInSelector
Create menu bar for plug-ins.
createMenuBar() - Method in class edu.jhu.ece.iacl.jist.pipeline.gui.ProcessManager
Create menubar.
createMipavParameter(AlgorithmParameters) - Method in class edu.jhu.ece.iacl.jist.pipeline.factory.ParamBooleanFactory
 
createMipavParameter(AlgorithmParameters) - Method in class edu.jhu.ece.iacl.jist.pipeline.factory.ParamCollectionFactory
 
createMipavParameter(AlgorithmParameters) - Method in class edu.jhu.ece.iacl.jist.pipeline.factory.ParamColorFactory
 
createMipavParameter(AlgorithmParameters) - Method in class edu.jhu.ece.iacl.jist.pipeline.factory.ParamDoubleFactory
 
createMipavParameter(AlgorithmParameters) - Method in class edu.jhu.ece.iacl.jist.pipeline.factory.ParamFactory
Create Mipav parameter from MAPS parameter.
createMipavParameter(AlgorithmParameters) - Method in class edu.jhu.ece.iacl.jist.pipeline.factory.ParamFileCollectionFactory
 
createMipavParameter(AlgorithmParameters) - Method in class edu.jhu.ece.iacl.jist.pipeline.factory.ParamFileFactory
 
createMipavParameter(AlgorithmParameters) - Method in class edu.jhu.ece.iacl.jist.pipeline.factory.ParamFloatFactory
 
createMipavParameter(AlgorithmParameters) - Method in class edu.jhu.ece.iacl.jist.pipeline.factory.ParamHiddenFactory
 
createMipavParameter(AlgorithmParameters) - Method in class edu.jhu.ece.iacl.jist.pipeline.factory.ParamInformationFactory
 
createMipavParameter(AlgorithmParameters) - Method in class edu.jhu.ece.iacl.jist.pipeline.factory.ParamIntegerFactory
 
createMipavParameter(AlgorithmParameters) - Method in class edu.jhu.ece.iacl.jist.pipeline.factory.ParamLongFactory
 
createMipavParameter(AlgorithmParameters) - Method in class edu.jhu.ece.iacl.jist.pipeline.factory.ParamMatrixFactory
 
createMipavParameter(AlgorithmParameters) - Method in class edu.jhu.ece.iacl.jist.pipeline.factory.ParamMipavDialogFactory
 
createMipavParameter(AlgorithmParameters) - Method in class edu.jhu.ece.iacl.jist.pipeline.factory.ParamMultiOptionFactory
 
createMipavParameter(AlgorithmParameters) - Method in class edu.jhu.ece.iacl.jist.pipeline.factory.ParamNumberCollectionFactory
 
createMipavParameter(AlgorithmParameters) - Method in class edu.jhu.ece.iacl.jist.pipeline.factory.ParamOptionFactory
 
createMipavParameter(AlgorithmParameters) - Method in class edu.jhu.ece.iacl.jist.pipeline.factory.ParamPerformanceFactory
 
createMipavParameter(AlgorithmParameters) - Method in class edu.jhu.ece.iacl.jist.pipeline.factory.ParamPointDoubleFactory
 
createMipavParameter(AlgorithmParameters) - Method in class edu.jhu.ece.iacl.jist.pipeline.factory.ParamPointFloatFactory
 
createMipavParameter(AlgorithmParameters) - Method in class edu.jhu.ece.iacl.jist.pipeline.factory.ParamPointIntegerFactory
 
createMipavParameter(AlgorithmParameters) - Method in class edu.jhu.ece.iacl.jist.pipeline.factory.ParamStringFactory
 
createMipavParameter(AlgorithmParameters) - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamModel
Create MIPAV parameter that represents this parameter.
createModelImage(ImageData) - Static method in class edu.jhu.ece.iacl.jist.structures.image.ImageDataMipav
Creates the model image.
createModelImage(ImageData, ModelImage) - Static method in class edu.jhu.ece.iacl.jist.structures.image.ImageDataMipav
Creates the model image.
createModuleCell() - Method in class edu.jhu.ece.iacl.jist.pipeline.PipeAlgorithm
Create cell to render this module.
createModuleCell() - Method in class edu.jhu.ece.iacl.jist.pipeline.PipeAlgorithmGroup
Create cell to render this module.
createModuleCell() - Method in class edu.jhu.ece.iacl.jist.pipeline.PipeDestination
Create graph cell to render destination.
createModuleCell() - Method in class edu.jhu.ece.iacl.jist.pipeline.PipeModule
Create default graph cell representing this module.
createModuleCell() - Method in class edu.jhu.ece.iacl.jist.pipeline.PipeSource
Create new graph cell for this source.
createNewContext(PipeAlgorithm, int) - Method in class edu.jhu.ece.iacl.jist.pipeline.PipeScheduler
Create new context for specific algorithm.
createOutputInformation(ProcessingAlgorithm) - Method in class edu.jhu.ece.iacl.doc.DocumentGenerator
 
createOutputInformation(ProcessingAlgorithm) - Method in class edu.jhu.ece.iacl.doc.DocumentGeneratorHTML
 
createOutputParameters(ParamCollection) - Method in class edu.jhu.bme.smile.demo.AddingNoise
 
createOutputParameters(ParamCollection) - Method in class edu.jhu.bme.smile.demo.ChebyShevFitting
 
createOutputParameters(ParamCollection) - Method in class edu.jhu.bme.smile.demo.FirstPluginTest
 
createOutputParameters(ParamCollection) - Method in class edu.jhu.bme.smile.demo.ImageAlgebra
 
createOutputParameters(ParamCollection) - Method in class edu.jhu.bme.smile.demo.ImageArithmetic
 
createOutputParameters(ParamCollection) - Method in class edu.jhu.bme.smile.demo.ImageCollectionAlgebra
 
createOutputParameters(ParamCollection) - Method in class edu.jhu.bme.smile.demo.MemoryDemo
 
createOutputParameters(ParamCollection) - Method in class edu.jhu.bme.smile.demo.RandomVol
 
createOutputParameters(ParamCollection) - Method in class edu.jhu.bme.smile.demo.ScaleImageDemo
 
createOutputParameters(ParamCollection) - Method in class edu.jhu.cs.cisst.plugins.classification.PlugInFuzzyMembershipThreshold2D
 
createOutputParameters(ParamCollection) - Method in class edu.jhu.cs.cisst.plugins.segmentation.PlugInCircleLevelSet
 
createOutputParameters(ParamCollection) - Method in class edu.jhu.cs.cisst.plugins.segmentation.PlugInGeodesicActiveContour2D
 
createOutputParameters(ParamCollection) - Method in class edu.jhu.cs.cisst.plugins.segmentation.PlugInGradientVectorFlow2D
 
createOutputParameters(ParamCollection) - Method in class edu.jhu.cs.cisst.plugins.utilities.file.PlugInTestDataSelector
 
createOutputParameters(ParamCollection) - Method in class edu.jhu.cs.cisst.plugins.utilities.surface.PlugInIsoContourGenerator
 
createOutputParameters(ParamCollection) - Method in class edu.jhu.cs.cisst.plugins.utilities.surface.PlugInIsoSurfaceGenerator
 
createOutputParameters(ParamCollection) - Method in class edu.jhu.cs.cisst.plugins.visualization.PlugInVisualizeActiveContour2D
 
createOutputParameters(ParamCollection) - Method in class edu.jhu.cs.cisst.plugins.visualization.PlugInVisualizeImage
 
createOutputParameters(ParamCollection) - Method in class edu.jhu.cs.cisst.plugins.visualization.PlugInVisualizeSurface
 
createOutputParameters(ParamCollection) - Method in class edu.jhu.ece.iacl.jist.pipeline.parser.MipavPluginParser
 
createOutputParameters(ParamCollection) - Method in class edu.jhu.ece.iacl.jist.pipeline.ProcessingAlgorithm
Create output parameters.
createOutputParameters(ParamCollection) - Method in class edu.jhu.ece.iacl.jist.plugins.MedicAlgorithmExecutableAdapter
 
createOutputParameters(ParamCollection) - Method in class edu.jhu.ece.iacl.jist.plugins.MedicAlgorithmJistLayoutAdapter
 
createOutputParameters(ParamCollection) - Method in class edu.jhu.ece.iacl.jist.plugins.MedicAlgorithmMipavAdapter
 
createOutputParameters(ParamCollection) - Method in class edu.jhu.ece.iacl.jist.plugins.testing.MedicAlgorithmDemo
Create output parameters for this plug-in
createOutputParameters(ParamCollection) - Method in class edu.jhu.ece.iacl.pami.CreateCrossingFiber
 
createOutputParameters(ParamCollection) - Method in class edu.jhu.ece.iacl.pami.CreateTesselatedSurface
 
createOutputParameters(ParamCollection) - Method in class edu.jhu.ece.iacl.pami.DivideReference
 
createOutputParameters(ParamCollection) - Method in class edu.jhu.ece.iacl.pami.GenerateTensors
 
createOutputParameters(ParamCollection) - Method in class edu.jhu.ece.iacl.pami.NameTest
 
createOutputParameters(ParamCollection) - Method in class edu.jhu.ece.iacl.pami.SimFramework
 
createOutputParameters(ParamCollection) - Method in class edu.jhu.ece.iacl.plugins.dti.AlgorithmDWIMotionCorrection
 
createOutputParameters(ParamCollection) - Method in class edu.jhu.ece.iacl.plugins.dti.AlgorithmGradientTableCorrection
 
createOutputParameters(ParamCollection) - Method in class edu.jhu.ece.iacl.plugins.dti.ComputeMeanB0
 
createOutputParameters(ParamCollection) - Method in class edu.jhu.ece.iacl.plugins.dti.ComputeMeanDW
 
createOutputParameters(ParamCollection) - Method in class edu.jhu.ece.iacl.plugins.dti.DWIBallStickEstCamino
 
createOutputParameters(ParamCollection) - Method in class edu.jhu.ece.iacl.plugins.dti.DWIBallStickEstCaminoFileCollection
 
createOutputParameters(ParamCollection) - Method in class edu.jhu.ece.iacl.plugins.dti.DWICombineBvalTables
 
createOutputParameters(ParamCollection) - Method in class edu.jhu.ece.iacl.plugins.dti.DWICombineGradTables
 
createOutputParameters(ParamCollection) - Method in class edu.jhu.ece.iacl.plugins.dti.DWIDefineCaminoScheme
 
createOutputParameters(ParamCollection) - Method in class edu.jhu.ece.iacl.plugins.dti.DWITensorColorEncodedMap
 
createOutputParameters(ParamCollection) - Method in class edu.jhu.ece.iacl.plugins.dti.DWITensorContrasts
 
createOutputParameters(ParamCollection) - Method in class edu.jhu.ece.iacl.plugins.dti.DWITensorEstCamino
 
createOutputParameters(ParamCollection) - Method in class edu.jhu.ece.iacl.plugins.dti.DWITensorEstCaminoFileCollection
 
createOutputParameters(ParamCollection) - Method in class edu.jhu.ece.iacl.plugins.dti.DWITensorEstCaminoRESTOREVariableNoiseField
 
createOutputParameters(ParamCollection) - Method in class edu.jhu.ece.iacl.plugins.dti.DWITensorEstLikelihood
 
createOutputParameters(ParamCollection) - Method in class edu.jhu.ece.iacl.plugins.dti.DWITensorEstLLMSE
 
createOutputParameters(ParamCollection) - Method in class edu.jhu.ece.iacl.plugins.dti.DWIThreeTensorEstCamino
 
createOutputParameters(ParamCollection) - Method in class edu.jhu.ece.iacl.plugins.dti.DWIThreeTensorEstCaminoFileCollection
 
createOutputParameters(ParamCollection) - Method in class edu.jhu.ece.iacl.plugins.dti.DWITwoTensorEstCamino
 
createOutputParameters(ParamCollection) - Method in class edu.jhu.ece.iacl.plugins.dti.DWITwoTensorEstCaminoFileCollection
 
createOutputParameters(ParamCollection) - Method in class edu.jhu.ece.iacl.plugins.dti.LocalNoiseEstimate
 
createOutputParameters(ParamCollection) - Method in class edu.jhu.ece.iacl.plugins.dti.MedicAlgorithmFlipVectorTable
 
createOutputParameters(ParamCollection) - Method in class edu.jhu.ece.iacl.plugins.dti.MedicAlgorithmFlipVectorVolume
 
createOutputParameters(ParamCollection) - Method in class edu.jhu.ece.iacl.plugins.dti.MedicAlgorithmFormatVectorImage
 
createOutputParameters(ParamCollection) - Method in class edu.jhu.ece.iacl.plugins.dti.MedicAlgorithmMultiGradientTableCreator
 
createOutputParameters(ParamCollection) - Method in class edu.jhu.ece.iacl.plugins.dti.MedicAlgorithmMultiParV3Info
 
createOutputParameters(ParamCollection) - Method in class edu.jhu.ece.iacl.plugins.dti.MedicAlgorithmMultiParV4Info
 
createOutputParameters(ParamCollection) - Method in class edu.jhu.ece.iacl.plugins.dti.MedicAlgorithmSubsampleFibers
 
createOutputParameters(ParamCollection) - Method in class edu.jhu.ece.iacl.plugins.dti.MedicAlgorithmTableFormat
 
createOutputParameters(ParamCollection) - Method in class edu.jhu.ece.iacl.plugins.dti.MedicAlgorithmTensorFormatConvert
 
createOutputParameters(ParamCollection) - Method in class edu.jhu.ece.iacl.plugins.dti.RegularizeNoiseField
 
createOutputParameters(ParamCollection) - Method in class edu.jhu.ece.iacl.plugins.dti.tractography.AlgorithmComputeConnectivityMatrix
 
createOutputParameters(ParamCollection) - Method in class edu.jhu.ece.iacl.plugins.dti.tractography.Fiber2Volume
 
createOutputParameters(ParamCollection) - Method in class edu.jhu.ece.iacl.plugins.dti.tractography.MedicAlgorithmApplyFiberROI
 
createOutputParameters(ParamCollection) - Method in class edu.jhu.ece.iacl.plugins.dti.tractography.MedicAlgorithmDeformFibers
 
createOutputParameters(ParamCollection) - Method in class edu.jhu.ece.iacl.plugins.dti.tractography.MedicAlgorithmFiberComparison
 
createOutputParameters(ParamCollection) - Method in class edu.jhu.ece.iacl.plugins.dti.tractography.MedicAlgorithmFibersFromSurfaceROI
 
createOutputParameters(ParamCollection) - Method in class edu.jhu.ece.iacl.plugins.dti.tractography.MedicAlgorithmFiberTracker
 
createOutputParameters(ParamCollection) - Method in class edu.jhu.ece.iacl.plugins.dti.tractography.MedicAlgorithmFiberVolumeStatistics
 
createOutputParameters(ParamCollection) - Method in class edu.jhu.ece.iacl.plugins.dti.tractography.MedicAlgorithmTransformFibers
 
createOutputParameters(ParamCollection) - Method in class edu.jhu.ece.iacl.plugins.dti.tractography.MedicAlgorithmWildBootTrac
 
createOutputParameters(ParamCollection) - Method in class edu.jhu.ece.iacl.plugins.dti.tractography.SImageTractAnalysis
 
createOutputParameters(ParamCollection) - Method in class edu.jhu.ece.iacl.plugins.dti.tractography.TractMapping
 
createOutputParameters(ParamCollection) - Method in class edu.jhu.ece.iacl.plugins.hardi.CFARIEstimation
 
createOutputParameters(ParamCollection) - Method in class edu.jhu.ece.iacl.plugins.hardi.CFARIEstimation2
 
createOutputParameters(ParamCollection) - Method in class edu.jhu.ece.iacl.plugins.hardi.CreatePlatonicSolidSurface
 
createOutputParameters(ParamCollection) - Method in class edu.jhu.ece.iacl.plugins.hardi.DefineCFARIScheme
 
createOutputParameters(ParamCollection) - Method in class edu.jhu.ece.iacl.plugins.hardi.ExtractBvalGradFromPAR
 
createOutputParameters(ParamCollection) - Method in class edu.jhu.ece.iacl.plugins.hardi.FunkRadonTransform
 
createOutputParameters(ParamCollection) - Method in class edu.jhu.ece.iacl.plugins.hardi.GradToSurf
 
createOutputParameters(ParamCollection) - Method in class edu.jhu.ece.iacl.plugins.hardi.NormalizeToUnitMagnitude
 
createOutputParameters(ParamCollection) - Method in class edu.jhu.ece.iacl.plugins.hardi.Process3DMRIImages
 
createOutputParameters(ParamCollection) - Method in class edu.jhu.ece.iacl.plugins.hardi.QBallEstimation
 
createOutputParameters(ParamCollection) - Method in class edu.jhu.ece.iacl.plugins.hardi.QBallModifiedRealProjection
 
createOutputParameters(ParamCollection) - Method in class edu.jhu.ece.iacl.plugins.hardi.QBallProjection
 
createOutputParameters(ParamCollection) - Method in class edu.jhu.ece.iacl.plugins.hardi.SelectUniqueDiffusionDirections
 
createOutputParameters(ParamCollection) - Method in class edu.jhu.ece.iacl.plugins.hardi.SurfToGrad
 
createOutputParameters(ParamCollection) - Method in class edu.jhu.ece.iacl.plugins.hardi.TesselateSurface
 
createOutputParameters(ParamCollection) - Method in class edu.jhu.ece.iacl.plugins.labeling.atlasing.AlgorithmLogOdds
 
createOutputParameters(ParamCollection) - Method in class edu.jhu.ece.iacl.plugins.labeling.MedicAlgorithmCleanSurfLabels
 
createOutputParameters(ParamCollection) - Method in class edu.jhu.ece.iacl.plugins.labeling.MedicAlgorithmFMLabelExtension
 
createOutputParameters(ParamCollection) - Method in class edu.jhu.ece.iacl.plugins.labeling.MedicAlgorithmMultiAtlasLabeling
 
createOutputParameters(ParamCollection) - Method in class edu.jhu.ece.iacl.plugins.labeling.MedicAlgorithmMultiAtlasSurfaceLabeling
 
createOutputParameters(ParamCollection) - Method in class edu.jhu.ece.iacl.plugins.labeling.MedicAlgorithmVolumeToSurfaceLabeling
 
createOutputParameters(ParamCollection) - Method in class edu.jhu.ece.iacl.plugins.labeling.simulation.AlgorithmSimulateSurfaceRater
 
createOutputParameters(ParamCollection) - Method in class edu.jhu.ece.iacl.plugins.labeling.simulation.AlgorithmSimulateVolumeRater
 
createOutputParameters(ParamCollection) - Method in class edu.jhu.ece.iacl.plugins.labeling.staple.MedicAlgorithmSTAPLE
 
createOutputParameters(ParamCollection) - Method in class edu.jhu.ece.iacl.plugins.labeling.staple.MedicAlgorithmSTAPLEgeneral
 
createOutputParameters(ParamCollection) - Method in class edu.jhu.ece.iacl.plugins.labeling.staple.MedicAlgorithmSTAPLEsurface
 
createOutputParameters(ParamCollection) - Method in class edu.jhu.ece.iacl.plugins.quantitative.EstimateMTR
 
createOutputParameters(ParamCollection) - Method in class edu.jhu.ece.iacl.plugins.quantitative.EstimateMTRseries
 
createOutputParameters(ParamCollection) - Method in class edu.jhu.ece.iacl.plugins.quantitative.EstimateT1FromDoubleAngle
 
createOutputParameters(ParamCollection) - Method in class edu.jhu.ece.iacl.plugins.quantitative.EstimateT2FromDualEcho
 
createOutputParameters(ParamCollection) - Method in class edu.jhu.ece.iacl.plugins.registration.MedicAlgorithmAtlasSelection
 
createOutputParameters(ParamCollection) - Method in class edu.jhu.ece.iacl.plugins.registration.MedicAlgorithmConstrainedFLIRT
 
createOutputParameters(ParamCollection) - Method in class edu.jhu.ece.iacl.plugins.registration.MedicAlgorithmCreateSimilarityMetricVol
 
createOutputParameters(ParamCollection) - Method in class edu.jhu.ece.iacl.plugins.registration.MedicAlgorithmEfficientFileCollectionRegistration
 
createOutputParameters(ParamCollection) - Method in class edu.jhu.ece.iacl.plugins.registration.MedicAlgorithmFLIRT
 
createOutputParameters(ParamCollection) - Method in class edu.jhu.ece.iacl.plugins.registration.MedicAlgorithmFLIRTCollection
 
createOutputParameters(ParamCollection) - Method in class edu.jhu.ece.iacl.plugins.registration.MedicAlgorithmMultiAtlasReg
 
createOutputParameters(ParamCollection) - Method in class edu.jhu.ece.iacl.plugins.registration.MedicAlgorithmMultiDeformVolume
 
createOutputParameters(ParamCollection) - Method in class edu.jhu.ece.iacl.plugins.registration.MedicAlgorithmTransformVolume
 
createOutputParameters(ParamCollection) - Method in class edu.jhu.ece.iacl.plugins.registration.MedicAlgorithmVABRA
 
createOutputParameters(ParamCollection) - Method in class edu.jhu.ece.iacl.plugins.segmentation.CreateMask
 
createOutputParameters(ParamCollection) - Method in class edu.jhu.ece.iacl.plugins.spectro.CESTAsymmetry
 
createOutputParameters(ParamCollection) - Method in class edu.jhu.ece.iacl.plugins.spectro.JistMSWASSR
 
createOutputParameters(ParamCollection) - Method in class edu.jhu.ece.iacl.plugins.utilities.file.AddToFileCollection
 
createOutputParameters(ParamCollection) - Method in class edu.jhu.ece.iacl.plugins.utilities.file.FileCollectionToPins
 
createOutputParameters(ParamCollection) - Method in class edu.jhu.ece.iacl.plugins.utilities.file.FileCollectionToVolumeCollection
 
createOutputParameters(ParamCollection) - Method in class edu.jhu.ece.iacl.plugins.utilities.file.MedicAlgorithmChooseFileRegEx
 
createOutputParameters(ParamCollection) - Method in class edu.jhu.ece.iacl.plugins.utilities.file.MedicAlgorithmChooseVolumeRegEx
 
createOutputParameters(ParamCollection) - Method in class edu.jhu.ece.iacl.plugins.utilities.file.MedicAlgorithmConcatArrayDoubleTextLists
 
createOutputParameters(ParamCollection) - Method in class edu.jhu.ece.iacl.plugins.utilities.file.MedicAlgorithmFibersToVtk
 
createOutputParameters(ParamCollection) - Method in class edu.jhu.ece.iacl.plugins.utilities.file.MedicAlgorithmIdentifySubject
 
createOutputParameters(ParamCollection) - Method in class edu.jhu.ece.iacl.plugins.utilities.file.MedicAlgorithmSurfaceConverter
 
createOutputParameters(ParamCollection) - Method in class edu.jhu.ece.iacl.plugins.utilities.file.MedicAlgorithmVolumeConverter
 
createOutputParameters(ParamCollection) - Method in class edu.jhu.ece.iacl.plugins.utilities.file.MedicAlgorithmVolumeConverter2
 
createOutputParameters(ParamCollection) - Method in class edu.jhu.ece.iacl.plugins.utilities.file.MedicAlgorithmVolumeConverter4D
 
createOutputParameters(ParamCollection) - Method in class edu.jhu.ece.iacl.plugins.utilities.file.MedicAlgorithmVolumeListOrganizer
 
createOutputParameters(ParamCollection) - Method in class edu.jhu.ece.iacl.plugins.utilities.file.MedicAlgorithmZip
 
createOutputParameters(ParamCollection) - Method in class edu.jhu.ece.iacl.plugins.utilities.file.VolumeDirectoryNoIter
 
createOutputParameters(ParamCollection) - Method in class edu.jhu.ece.iacl.plugins.utilities.logic.MedicAlgorithmFloatsToPoint
 
createOutputParameters(ParamCollection) - Method in class edu.jhu.ece.iacl.plugins.utilities.logic.MedicAlgorithmSerializeSurfaces
 
createOutputParameters(ParamCollection) - Method in class edu.jhu.ece.iacl.plugins.utilities.logic.MedicAlgorithmSerializeVolumes
 
createOutputParameters(ParamCollection) - Method in class edu.jhu.ece.iacl.plugins.utilities.logic.MedicAlgorithmSurfaceSplitter
 
createOutputParameters(ParamCollection) - Method in class edu.jhu.ece.iacl.plugins.utilities.logic.MedicAlgorithmValueEquals
 
createOutputParameters(ParamCollection) - Method in class edu.jhu.ece.iacl.plugins.utilities.logic.MedicAlgorithmValueGreaterThan
 
createOutputParameters(ParamCollection) - Method in class edu.jhu.ece.iacl.plugins.utilities.logic.MedicAlgorithmValueInRange
 
createOutputParameters(ParamCollection) - Method in class edu.jhu.ece.iacl.plugins.utilities.logic.MedicAlgorithmValueLessThan
 
createOutputParameters(ParamCollection) - Method in class edu.jhu.ece.iacl.plugins.utilities.logic.MedicAlgorithmVolumeSplitter
 
createOutputParameters(ParamCollection) - Method in class edu.jhu.ece.iacl.plugins.utilities.math.MedicAlgorithmArithmetic
 
createOutputParameters(ParamCollection) - Method in class edu.jhu.ece.iacl.plugins.utilities.math.MedicAlgorithmImageCalculator
 
createOutputParameters(ParamCollection) - Method in class edu.jhu.ece.iacl.plugins.utilities.math.MedicAlgorithmImageCalculatorBatch
 
createOutputParameters(ParamCollection) - Method in class edu.jhu.ece.iacl.plugins.utilities.math.MedicAlgorithmImageCalculatorModified
 
createOutputParameters(ParamCollection) - Method in class edu.jhu.ece.iacl.plugins.utilities.math.MedicAlgorithmImageMath
 
createOutputParameters(ParamCollection) - Method in class edu.jhu.ece.iacl.plugins.utilities.math.MedicAlgorithmKLDivergence
 
createOutputParameters(ParamCollection) - Method in class edu.jhu.ece.iacl.plugins.utilities.roi.AlgorithmJointROIStats
 
createOutputParameters(ParamCollection) - Method in class edu.jhu.ece.iacl.plugins.utilities.roi.AlgorithmROIStats
 
createOutputParameters(ParamCollection) - Method in class edu.jhu.ece.iacl.plugins.utilities.surface.MedicAlgorithmCombineSurfaceComponents
 
createOutputParameters(ParamCollection) - Method in class edu.jhu.ece.iacl.plugins.utilities.surface.MedicAlgorithmCombineSurfaces
 
createOutputParameters(ParamCollection) - Method in class edu.jhu.ece.iacl.plugins.utilities.surface.MedicAlgorithmCopyEmbeddedData
 
createOutputParameters(ParamCollection) - Method in class edu.jhu.ece.iacl.plugins.utilities.surface.MedicAlgorithmEmbedSurface
 
createOutputParameters(ParamCollection) - Method in class edu.jhu.ece.iacl.plugins.utilities.surface.MedicAlgorithmExtractSurfaceComponent
 
createOutputParameters(ParamCollection) - Method in class edu.jhu.ece.iacl.plugins.utilities.surface.MedicAlgorithmReshapePoints
 
createOutputParameters(ParamCollection) - Method in class edu.jhu.ece.iacl.plugins.utilities.surface.MedicAlgorithmReshapeSurface
 
createOutputParameters(ParamCollection) - Method in class edu.jhu.ece.iacl.plugins.utilities.surface.MedicAlgorithmSurfaceHistogram
 
createOutputParameters(ParamCollection) - Method in class edu.jhu.ece.iacl.plugins.utilities.surface.MedicAlgorithmSurfaceToVolumeConverter
 
createOutputParameters(ParamCollection) - Method in class edu.jhu.ece.iacl.plugins.utilities.volume.AlgorithmVolumeFileCollectionTo3D
 
createOutputParameters(ParamCollection) - Method in class edu.jhu.ece.iacl.plugins.utilities.volume.CombinedSlabCollectionToVolumeCollection
 
createOutputParameters(ParamCollection) - Method in class edu.jhu.ece.iacl.plugins.utilities.volume.GetImageDimensions
 
createOutputParameters(ParamCollection) - Method in class edu.jhu.ece.iacl.plugins.utilities.volume.MedicAlgorithmCombineVolumeComponents
 
createOutputParameters(ParamCollection) - Method in class edu.jhu.ece.iacl.plugins.utilities.volume.MedicAlgorithmCrop
 
createOutputParameters(ParamCollection) - Method in class edu.jhu.ece.iacl.plugins.utilities.volume.MedicAlgorithmDimensions
 
createOutputParameters(ParamCollection) - Method in class edu.jhu.ece.iacl.plugins.utilities.volume.MedicAlgorithmExtractAllComponents
 
createOutputParameters(ParamCollection) - Method in class edu.jhu.ece.iacl.plugins.utilities.volume.MedicAlgorithmExtractFileCollectionComponents
 
createOutputParameters(ParamCollection) - Method in class edu.jhu.ece.iacl.plugins.utilities.volume.MedicAlgorithmExtractVolumeComponent
 
createOutputParameters(ParamCollection) - Method in class edu.jhu.ece.iacl.plugins.utilities.volume.MedicAlgorithmFindEqualVolume
 
createOutputParameters(ParamCollection) - Method in class edu.jhu.ece.iacl.plugins.utilities.volume.MedicAlgorithmIsotropicReslice
 
createOutputParameters(ParamCollection) - Method in class edu.jhu.ece.iacl.plugins.utilities.volume.MedicAlgorithmMatchAllImages
 
createOutputParameters(ParamCollection) - Method in class edu.jhu.ece.iacl.plugins.utilities.volume.MedicAlgorithmMipavReorient
 
createOutputParameters(ParamCollection) - Method in class edu.jhu.ece.iacl.plugins.utilities.volume.MedicAlgorithmMultiCrop
Create output parameters for Image Cropper: cubic volume and extents
createOutputParameters(ParamCollection) - Method in class edu.jhu.ece.iacl.plugins.utilities.volume.MedicAlgorithmReverseComponents
 
createOutputParameters(ParamCollection) - Method in class edu.jhu.ece.iacl.plugins.utilities.volume.MedicAlgorithmSetHeaders
 
createOutputParameters(ParamCollection) - Method in class edu.jhu.ece.iacl.plugins.utilities.volume.MedicAlgorithmThreshold
 
createOutputParameters(ParamCollection) - Method in class edu.jhu.ece.iacl.plugins.utilities.volume.MedicAlgorithmUncrop
 
createOutputParameters(ParamCollection) - Method in class edu.jhu.ece.iacl.plugins.utilities.volume.MedicAlgorithmVolumeHistogram
 
createOutputParameters(ParamCollection) - Method in class edu.jhu.ece.iacl.plugins.utilities.volume.VolumeCensorRange
 
createOutputParameters(ParamCollection) - Method in class edu.jhu.ece.iacl.plugins.utilities.volume.VolumeCollectionToCombinedSlabCollection
 
createOutputParameters(ParamCollection) - Method in class edu.vanderbilt.masi.plugins.utilities.volume.PluginCombineVolumes
 
createOutputParams() - Method in class edu.jhu.ece.iacl.jist.pipeline.dest.PipeDoubleCollectionExternalDestination
Create output parameters.
createOutputParams() - Method in class edu.jhu.ece.iacl.jist.pipeline.dest.PipeDoubleExternalDestination
Create output parameters.
createOutputParams() - Method in class edu.jhu.ece.iacl.jist.pipeline.dest.PipeExternalDestination
Create output parameters.
createOutputParams() - Method in class edu.jhu.ece.iacl.jist.pipeline.dest.PipeFileCollectionExternalDestination
Create output parameters.
createOutputParams() - Method in class edu.jhu.ece.iacl.jist.pipeline.dest.PipeFileExternalDestination
Create output parameters.
createOutputParams() - Method in class edu.jhu.ece.iacl.jist.pipeline.dest.PipeIntegerCollectionExternalDestination
Create output parameters.
createOutputParams() - Method in class edu.jhu.ece.iacl.jist.pipeline.dest.PipeIntegerExternalDestination
Create output parameters.
createOutputParams() - Method in class edu.jhu.ece.iacl.jist.pipeline.dest.PipeParamCopyDestination
Create output parameters.
createOutputParams() - Method in class edu.jhu.ece.iacl.jist.pipeline.dest.PipeParamSummaryDestination
Create output parameters.
createOutputParams() - Method in class edu.jhu.ece.iacl.jist.pipeline.dest.PipeSurfaceCollectionExternalDestination
Create output parameters.
createOutputParams() - Method in class edu.jhu.ece.iacl.jist.pipeline.dest.PipeSurfaceExternalDestination
Create output parameters.
createOutputParams() - Method in class edu.jhu.ece.iacl.jist.pipeline.dest.PipeVolumeCollectionExternalDestination
Create output parameters.
createOutputParams() - Method in class edu.jhu.ece.iacl.jist.pipeline.dest.PipeVolumeExternalDestination
Create output parameters.
createOutputParams() - Method in class edu.jhu.ece.iacl.jist.pipeline.PipeDestination
Create output parameters for this destination.
createOutputParams() - Method in class edu.jhu.ece.iacl.jist.pipeline.PipeSource
Create output parameters for this source.
createOutputParams() - Method in class edu.jhu.ece.iacl.jist.pipeline.src.PipeDoubleCollectionExternalSource
 
createOutputParams() - Method in class edu.jhu.ece.iacl.jist.pipeline.src.PipeDoubleCollectionListSource
Create output parameters.
createOutputParams() - Method in class edu.jhu.ece.iacl.jist.pipeline.src.PipeDoubleExternalSource
 
createOutputParams() - Method in class edu.jhu.ece.iacl.jist.pipeline.src.PipeDoubleListSource
Create output parameters.
createOutputParams() - Method in class edu.jhu.ece.iacl.jist.pipeline.src.PipeDoubleSweepSource
Create ouptut parameters.
createOutputParams() - Method in class edu.jhu.ece.iacl.jist.pipeline.src.PipeFileCollectionExternalSource
 
createOutputParams() - Method in class edu.jhu.ece.iacl.jist.pipeline.src.PipeFileCollectionListSource
 
createOutputParams() - Method in class edu.jhu.ece.iacl.jist.pipeline.src.PipeFileCollectionSource
Create output parameters.
createOutputParams() - Method in class edu.jhu.ece.iacl.jist.pipeline.src.PipeFileDirectorySource
Create output parameters.
createOutputParams() - Method in class edu.jhu.ece.iacl.jist.pipeline.src.PipeFileExternalSource
 
createOutputParams() - Method in class edu.jhu.ece.iacl.jist.pipeline.src.PipeFileListSource
Create output parameters.
createOutputParams() - Method in class edu.jhu.ece.iacl.jist.pipeline.src.PipeIntegerCollectionExternalSource
 
createOutputParams() - Method in class edu.jhu.ece.iacl.jist.pipeline.src.PipeIntegerCollectionListSource
Create output parameters.
createOutputParams() - Method in class edu.jhu.ece.iacl.jist.pipeline.src.PipeIntegerExternalSource
 
createOutputParams() - Method in class edu.jhu.ece.iacl.jist.pipeline.src.PipeIntegerListSource
Create output parameters.
createOutputParams() - Method in class edu.jhu.ece.iacl.jist.pipeline.src.PipeIntegerSweepSource
 
createOutputParams() - Method in class edu.jhu.ece.iacl.jist.pipeline.src.PipePointDoubleSweepSource
Create ouptut parameters.
createOutputParams() - Method in class edu.jhu.ece.iacl.jist.pipeline.src.PipePointListSource
Create output parameters.
createOutputParams() - Method in class edu.jhu.ece.iacl.jist.pipeline.src.PipeSelectionExternalSource
Create output parameters.
createOutputParams() - Method in class edu.jhu.ece.iacl.jist.pipeline.src.PipeSelectionListSource
 
createOutputParams() - Method in class edu.jhu.ece.iacl.jist.pipeline.src.PipeSelectionSource
Create output parameters.
createOutputParams() - Method in class edu.jhu.ece.iacl.jist.pipeline.src.PipeStringListSource
 
createOutputParams() - Method in class edu.jhu.ece.iacl.jist.pipeline.src.PipeSurfaceCollectionExternalSource
 
createOutputParams() - Method in class edu.jhu.ece.iacl.jist.pipeline.src.PipeSurfaceCollectionListSource
 
createOutputParams() - Method in class edu.jhu.ece.iacl.jist.pipeline.src.PipeSurfaceCollectionSource
Create output parameters.
createOutputParams() - Method in class edu.jhu.ece.iacl.jist.pipeline.src.PipeSurfaceDirectorySurface
 
createOutputParams() - Method in class edu.jhu.ece.iacl.jist.pipeline.src.PipeSurfaceExternalSource
 
createOutputParams() - Method in class edu.jhu.ece.iacl.jist.pipeline.src.PipeSurfaceListSource
Create input parameters.
createOutputParams() - Method in class edu.jhu.ece.iacl.jist.pipeline.src.PipeToggleSource
Create output parameters.
createOutputParams() - Method in class edu.jhu.ece.iacl.jist.pipeline.src.PipeVolumeCollectionExternalSource
 
createOutputParams() - Method in class edu.jhu.ece.iacl.jist.pipeline.src.PipeVolumeCollectionListSource
 
createOutputParams() - Method in class edu.jhu.ece.iacl.jist.pipeline.src.PipeVolumeCollectionSource
Create output parameters.
createOutputParams() - Method in class edu.jhu.ece.iacl.jist.pipeline.src.PipeVolumeDirectoryCollectionSource
 
createOutputParams() - Method in class edu.jhu.ece.iacl.jist.pipeline.src.PipeVolumeDirectorySource
 
createOutputParams() - Method in class edu.jhu.ece.iacl.jist.pipeline.src.PipeVolumeExternalSource
 
createOutputParams() - Method in class edu.jhu.ece.iacl.jist.pipeline.src.PipeVolumeListSource
Create input parameters.
createPane() - Method in class edu.jhu.ece.iacl.jist.pipeline.gui.GlobalPreferencePanel
Create panel to display preferences.
createPane() - Method in class edu.jhu.ece.iacl.jist.pipeline.gui.LayoutPreferencePanel
Create panel to display preferences.
createPanel() - Method in class edu.jhu.ece.iacl.jist.pipeline.gui.PlugInSelector
Create dialog panel.
createPanes() - Method in class edu.jhu.ece.iacl.jist.pipeline.gui.PipelineLayoutTool
Create split panes.
createPath(File, String) - Method in class edu.jhu.ece.iacl.doc.DocumentAllModules
 
createPath(File, String) - Method in class edu.jhu.ece.iacl.jist.pipeline.PipeLibrary
Creates the path.
createPipe() - Method in class edu.jhu.ece.iacl.jist.pipeline.graph.PipeAlgorithmFactory
Create module to represent algorithm.
createPipe() - Method in class edu.jhu.ece.iacl.jist.pipeline.graph.PipeDestinationFactory
Create module destination.
createPipe() - Method in class edu.jhu.ece.iacl.jist.pipeline.graph.PipeModuleFactory
Create pipe module to run algorithm.
createPipe() - Method in class edu.jhu.ece.iacl.jist.pipeline.graph.PipeSourceFactory
Crete pipe module for source.
createPipeView(ExecutionContext) - Method in class edu.jhu.ece.iacl.jist.pipeline.gui.ProcessManagerTable.ProcessTableModel
Creates the pipe view.
CreatePlatonicSolidSurface - Class in edu.jhu.ece.iacl.plugins.hardi
 
CreatePlatonicSolidSurface() - Constructor for class edu.jhu.ece.iacl.plugins.hardi.CreatePlatonicSolidSurface
 
createPopupMenu(Point, PipeAlgorithm, PipeAlgorithmFactory.AlgorithmCell) - Method in class edu.jhu.ece.iacl.jist.pipeline.graph.PipeMarqueeHandler
Creates the popup menu.
createPopupMenu(MouseEvent) - Method in class edu.jhu.ece.iacl.jist.pipeline.gui.ModuleTreePanel
Create popup menu to edit module.
createPopupMenu() - Method in class edu.jhu.ece.iacl.jist.pipeline.gui.ProcessManagerTable
Creates the popup menu.
createPorts() - Method in class edu.jhu.ece.iacl.jist.pipeline.graph.PipeDestinationFactory.DestinationCell
 
createPorts() - Method in class edu.jhu.ece.iacl.jist.pipeline.graph.PipeModuleCell
Create ports for module.
createPorts() - Method in class edu.jhu.ece.iacl.jist.pipeline.graph.PipeSourceFactory.SourceCell
 
createPortView(Object) - Method in class edu.jhu.ece.iacl.jist.pipeline.graph.PipeCellViewFactory
Create port view.
createProcessView(ExecutionContext) - Method in class edu.jhu.ece.iacl.jist.pipeline.gui.ProcessManagerTable.ProcessTableModel
Creates the process view.
createProgress(ExecutionContext) - Method in class edu.jhu.ece.iacl.jist.pipeline.gui.ProcessManagerTable.ProcessTableModel
Creates the progress.
createQueueView(ExecutionContext) - Method in class edu.jhu.ece.iacl.jist.pipeline.gui.ProcessManagerTable.ProcessTableModel
Creates the queue view.
createShape() - Method in class edu.jhu.ece.iacl.jist.pipeline.graph.PipePortView.ActivityRenderer
Creates the shape.
createShape() - Method in class edu.jhu.ece.iacl.jist.pipeline.graph.PortChildView.ActivityRenderer
 
createShape() - Method in class edu.jhu.ece.iacl.jist.pipeline.graph.PortInputView.ActivityRenderer
 
createShape() - Method in class edu.jhu.ece.iacl.jist.pipeline.graph.PortOutputView.ActivityRenderer
 
createShape() - Method in class edu.jhu.ece.iacl.jist.pipeline.graph.PortParentView.ActivityRenderer
 
createShortDescription(ProcessingAlgorithm) - Method in class edu.jhu.ece.iacl.doc.DocumentGenerator
 
createShortDescription(ProcessingAlgorithm) - Method in class edu.jhu.ece.iacl.doc.DocumentGeneratorHTML
 
createSplit(Hashtable<Long, IsoContourGenerator.EdgeSplit>, int, int, int, int) - Method in class edu.jhu.cs.cisst.algorithms.geometry.surface.IsoContourGenerator
Creates the split.
createStatus(ExecutionContext) - Method in class edu.jhu.ece.iacl.jist.pipeline.gui.ProcessManagerTable.ProcessTableModel
Creates the status.
createT() - Method in class edu.jhu.ece.iacl.algorithms.manual_label.staple.STAPLEmulti2
 
createTable() - Method in class edu.jhu.ece.iacl.jist.pipeline.gui.ProcessManagerTable
Create scroll pane table.
CreateTesselatedSurface - Class in edu.jhu.ece.iacl.pami
 
CreateTesselatedSurface() - Constructor for class edu.jhu.ece.iacl.pami.CreateTesselatedSurface
 
createToolBar() - Method in class edu.jhu.ece.iacl.jist.pipeline.gui.PipeInternalFrame
Create toolbar to manipulate graph.
createToolBar() - Method in class edu.jhu.ece.iacl.jist.pipeline.gui.ProcessManagerTable
Create toolbar to control execution.
createTreeNode() - Method in class edu.jhu.ece.iacl.jist.pipeline.factory.ParamCollectionFactory
 
createTreeNode() - Method in class edu.jhu.ece.iacl.jist.pipeline.factory.ParamFactory
Creates a new Param object.
createTreeNode() - Method in class edu.jhu.ece.iacl.jist.pipeline.graph.PipeAlgorithmFactory
Create tree node to represent algorithm.
createTreeNode() - Method in class edu.jhu.ece.iacl.jist.pipeline.graph.PipeDestinationFactory
Create tree node for destination.
createTreeNode() - Method in class edu.jhu.ece.iacl.jist.pipeline.graph.PipeModuleFactory
Create tree node for module panel.
createTreeNode() - Method in class edu.jhu.ece.iacl.jist.pipeline.graph.PipeSourceFactory
Create tree node for source.
createTreeNode() - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamModel
Create tree node that represents this parameter.
createTreeNodes(TreeSelectionListener) - Method in class edu.jhu.ece.iacl.jist.pipeline.ExecutionContext
Create ancestor and descendant tree and set the listener for those trees.
createTreePanel() - Method in class edu.jhu.ece.iacl.jist.pipeline.gui.PlugInSelector
Create tree to display modules.
createTypeView(ExecutionContext) - Method in class edu.jhu.ece.iacl.jist.pipeline.gui.ProcessManagerTable.ProcessTableModel
Creates the type view.
createUniqueName(PipeModule) - Method in class edu.jhu.ece.iacl.jist.pipeline.graph.PipeJGraph
Creates the unique name.
createUniqueName(ExecutionContext) - Method in class edu.jhu.ece.iacl.jist.pipeline.PipeScheduler
Create unique name for specified context.
createVertexView(Object) - Method in class edu.jhu.ece.iacl.jist.pipeline.graph.PipeCellViewFactory
Create cell view.
createVisualizationParameters(ParamCollection) - Method in class edu.jhu.cs.cisst.vent.renderer.processing.ImageRenderer
 
createVisualizationParameters(ParamCollection) - Method in class edu.jhu.cs.cisst.vent.renderer.processing.SurfaceRenderer
 
createVisualizationParameters(ParamCollection) - Method in class edu.jhu.cs.cisst.vent.renderer.processing.VectorField2DRenderer
Creates the visualization parameters.
createVisualizationParameters(ParamCollection) - Method in class edu.jhu.cs.cisst.vent.renderer.processing.VolumeIsoContourRenderer
Creates the visualization parameters.
createVisualizationParameters(ParamCollection) - Method in class edu.jhu.cs.cisst.vent.renderer.processing.VolumeSliceRenderer
Creates the visualization parameters.
createVisualizationParameters(ParamCollection) - Method in interface edu.jhu.cs.cisst.vent.VisualizationParameters
Creates the visualization parameters.
createVisualizationParameters(ParamCollection) - Method in class edu.jhu.cs.cisst.vent.VisualizationProcessing2D
Creates the visualization parameters.
createVisualizationParameters(ParamCollection) - Method in class edu.jhu.cs.cisst.vent.VisualizationProcessing3D
Creates the visualization parameters.
createVisualizationParameters(ParamCollection) - Method in class edu.jhu.cs.cisst.vent.widgets.VisualizationImage
Creates the visualization parameters.
createVisualizationParameters(ParamCollection) - Method in class edu.jhu.cs.cisst.vent.widgets.VisualizationTriangleMesh
Creates the visualization parameters.
createVolume() - Method in class edu.jhu.ece.iacl.jist.structures.matrix.Matrix3
Creates the volume.
createWeightParameter() - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamWeightedVolume
 
creationDate - Variable in class edu.jhu.ece.iacl.jist.pipeline.AlgorithmInformation
The creation date.
creationDate - Variable in class edu.jhu.ece.iacl.jist.pipeline.view.input.AlgorithmInformationDialog
The text fields.
crop(ImageData, CropParameters) - Method in class edu.jhmi.rad.medic.utilities.CubicVolumeCropper
This method make a cropped version of input image BECAUSE set(Number) is no longer supported, will not work for color volumes.
crop(ImageData, double, int) - Method in class edu.jhmi.rad.medic.utilities.CubicVolumeCropper
Crop.
crop(List<ImageData>, double, int) - Method in class edu.jhmi.rad.medic.utilities.CubicVolumeCropper
Crop.
CropParameters - Class in edu.jhmi.rad.medic.utilities
The Class CropParameters.
CropParameters(int, int, int, int, int, int, int, int, int, int, double) - Constructor for class edu.jhmi.rad.medic.utilities.CropParameters
Instantiates a new crop parameters.
cross(PT) - Method in class edu.jhu.ece.iacl.jist.structures.geom.PT
Cross.
crossProduct(Tuple2d, Tuple2d) - Static method in class edu.jhu.ece.iacl.jist.algorithms.graphics.GeomUtil
Cross product.
crossProductPoint(Point3f, Point3f) - Static method in class edu.jhu.bme.smile.commons.math.Point3fMath
 
cruise - Static variable in class edu.jhu.ece.iacl.algorithms.ReferencedPapers
 
cube() - Static method in class edu.jhu.ece.iacl.algorithms.hardi.SurfaceTools
 
cubicLagrangianInterpolation3D(float[][][], float[][], float, float, float, float, float, int, int, int) - Static method in class edu.jhmi.rad.medic.libraries.ImageFunctionsPublic
3D cubic Lagrangian function
cubicLagrangianInterpolation3D(float[][][], boolean[][][], float[][], float, float, float, float, float, int, int, int) - Static method in class edu.jhmi.rad.medic.libraries.ImageFunctionsPublic
3D cubic Lagrangian function
CubicVolumeCropper - Class in edu.jhmi.rad.medic.utilities
Utility for Cropping images.
CubicVolumeCropper() - Constructor for class edu.jhmi.rad.medic.utilities.CubicVolumeCropper
Instantiates a new cubic volume cropper.
curPanel - Variable in class edu.jhu.ece.iacl.jist.pipeline.view.input.ParamCollectionPipelineInputView
current displayed panel.
current - Variable in class edu.jhu.ece.iacl.jist.pipeline.graph.PipeMarqueeHandler
The current.
currentContext - Variable in class edu.jhu.ece.iacl.jist.pipeline.PipeModule
Execution context that represents this module.
currentDownSampleFactor - Variable in class edu.jhu.ece.iacl.algorithms.vabra.ImagePair
 
currentPort - Variable in class edu.jhu.ece.iacl.jist.pipeline.graph.PipeMarqueeHandler
The current port.
curvatureAnalysis - Static variable in class edu.jhu.ece.iacl.algorithms.ReferencedPapers
 
Curve - Interface in edu.jhu.ece.iacl.jist.structures.geom
The Interface Curve.
curve - Variable in class edu.jhu.ece.iacl.plugins.dti.MedicAlgorithmSubsampleFibers.StaticCurve
 
CurveCollection - Class in edu.jhu.ece.iacl.jist.structures.geom
The Class CurveCollection.
CurveCollection() - Constructor for class edu.jhu.ece.iacl.jist.structures.geom.CurveCollection
Instantiates a new curve collection.
CurvePath - Class in edu.jhu.ece.iacl.jist.structures.geom
The Class CurvePath.
CurvePath() - Constructor for class edu.jhu.ece.iacl.jist.structures.geom.CurvePath
Instantiates a new curve path.
curves - Variable in class edu.jhu.cs.cisst.vent.renderer.processing.VolumeIsoContourRenderer
The curves.
CurveVtkReaderWriter - Class in edu.jhu.ece.iacl.jist.io
The Class CurveVtkReaderWriter.
CurveVtkReaderWriter() - Constructor for class edu.jhu.ece.iacl.jist.io.CurveVtkReaderWriter
Instantiates a new curve vtk reader writer.
cut - Variable in class edu.jhu.ece.iacl.jist.pipeline.gui.PipeInternalFrame
The expand.
cutItem - Variable in class edu.jhu.ece.iacl.jist.pipeline.gui.PipelineLayoutTool
The paste item.

D

DampedJacobi - Class in edu.jhu.cs.cisst.algorithms.optimize.fmg.smoother
An implementation of the damped Jacobi method of relaxing (thereby smoothing) the solution of a linear elliptic PDE.
DampedJacobi(PDE, double) - Constructor for class edu.jhu.cs.cisst.algorithms.optimize.fmg.smoother.DampedJacobi
construct from PDE and weighting factor.
DampedJacobiSmoothParallelizer - Class in edu.jhu.cs.cisst.algorithms.optimize.fmg.smoother
A helper class of class DampedJacobi that implements method DampedJacobi.smooth() in a parallel manner.
DampedJacobiSmoothParallelizer(DampedJacobi, BoundaryGrid, ConstBoundaryGrid, ConstNoBoundaryGrid) - Constructor for class edu.jhu.cs.cisst.algorithms.optimize.fmg.smoother.DampedJacobiSmoothParallelizer
construct.
data - Variable in class edu.jhu.ece.iacl.algorithms.dti.tractography.FACT.DXFiberData
 
data - Variable in class edu.jhu.ece.iacl.algorithms.vabra.VectorVolumeVabra
 
data - Variable in class edu.jhu.ece.iacl.jist.pipeline.src.PipeListCollectionSource
The data.
data - Variable in class edu.jhu.ece.iacl.jist.pipeline.src.PipeListSource
The data.
data - Variable in class edu.jhu.ece.iacl.jist.structures.geom.GridPt
The data.
DATA_MODULE_TAG - Static variable in class edu.jhu.ece.iacl.jist.pipeline.parser.LoniPipeParser
The Constant DATA_MODULE_TAG.
DATA_TAG - Static variable in class edu.jhu.ece.iacl.jist.pipeline.parser.LoniPipeParser
The Constant DATA_TAG.
DataLabel - Class in edu.jhu.ece.iacl.jist.pipeline.parameter
Data label for TOADS.
DataLabel(float) - Constructor for class edu.jhu.ece.iacl.jist.pipeline.parameter.DataLabel
Default constructor.
DataLabelCollection - Class in edu.jhu.ece.iacl.jist.pipeline.parameter
Collection data labels.
DataLabelCollection() - Constructor for class edu.jhu.ece.iacl.jist.pipeline.parameter.DataLabelCollection
 
dataObjects - Variable in class edu.jhu.ece.iacl.jist.pipeline.dest.PipeParamCopyDestination
The data objects.
dataObjects - Variable in class edu.jhu.ece.iacl.jist.pipeline.dest.PipeParamSummaryDestination
The data objects.
DataOperations - Class in edu.jhu.cs.cisst.algorithms.util
The Class DataOperations defines basic operations to perform on raw data.
DataOperations() - Constructor for class edu.jhu.cs.cisst.algorithms.util.DataOperations
 
date - Variable in class edu.jhu.ece.iacl.algorithms.dti.GTCparams
 
debug - Variable in class edu.jhu.ece.iacl.jist.pipeline.gui.ProcessManagerTable
The debug.
debugLevel - Variable in class edu.jhu.ece.iacl.jist.pipeline.JistPreferences
Debug Level
debugLevels - Static variable in class edu.jhu.ece.iacl.jist.pipeline.JistPreferences
The debug level location.
decodeName(String) - Static method in class edu.jhu.ece.iacl.jist.pipeline.factory.ParamFactory
Decode name.
decodeValue(String) - Static method in class edu.jhu.ece.iacl.jist.pipeline.factory.ParamFactory
Decode value.
decrementCompletedUnits() - Method in class edu.jhu.ece.iacl.jist.pipeline.AbstractCalculation
Decrement the number of completed units.
decrementCompletedUnits(int) - Method in class edu.jhu.ece.iacl.jist.pipeline.AbstractCalculation
Decrement the number of completed units.
deepClone() - Method in class edu.jhu.ece.iacl.jist.structures.fiber.XYZ
Deep clone.
deepCloneTruth() - Method in class edu.jhu.ece.iacl.algorithms.manual_label.staple.STAPLEgeneral
 
DEFAULT_STEP - Static variable in class edu.jhu.bme.smile.commons.optimize.FunctionNumeric1DDifferentiation
 
DEFAULT_STEP - Static variable in class edu.jhu.bme.smile.commons.optimize.FunctionNumericND1DDifferentiation
 
defaultHeader - Variable in class edu.jhu.ece.iacl.jist.structures.image.ImageHeader
The default header.
defaultLabelDimension - Static variable in class edu.jhu.ece.iacl.jist.pipeline.view.input.ParamInputView
The Constant defaultLabelDimension.
defaultMaxProcesses - Variable in class edu.jhu.ece.iacl.jist.pipeline.JistPreferences
Default maximum number of simultaneous processes.
defaultMemory - Variable in class edu.jhu.ece.iacl.jist.pipeline.JistPreferences
Default maximum heap size.
defaultNumberFieldDimension - Static variable in class edu.jhu.ece.iacl.jist.pipeline.view.input.ParamInputView
The Constant defaultNumberFieldDimension.
defaultPointDimension - Static variable in class edu.jhu.ece.iacl.jist.pipeline.view.input.ParamColorInputView
The Constant defaultPointDimension.
defaultPointDimension - Static variable in class edu.jhu.ece.iacl.jist.pipeline.view.input.ParamPointDoubleTextInputView
The Constant defaultPointDimension.
defaultPointDimension - Static variable in class edu.jhu.ece.iacl.jist.pipeline.view.input.ParamPointFloatTextInputView
The Constant defaultPointDimension.
defaultPointDimension - Static variable in class edu.jhu.ece.iacl.jist.pipeline.view.input.ParamPointSpinnerInputView
The Constant defaultPointDimension.
defaultSize - Static variable in class edu.jhu.ece.iacl.jist.pipeline.graph.PipeModuleCell
The Constant defaultSize.
DefaultSolverResolutionLevels2D - Class in edu.jhu.cs.cisst.algorithms.optimize.fmg
The Class DefaultSolverResolutionLevels2D describes a set of solver resolutions.
DefaultSolverResolutionLevels2D(ConstGrid, int, int) - Constructor for class edu.jhu.cs.cisst.algorithms.optimize.fmg.DefaultSolverResolutionLevels2D
Instantiates a new solver resolutions.
DefaultSolverResolutionLevels3D - Class in edu.jhu.cs.cisst.algorithms.optimize.fmg
The Class DefaultSolverResolutionLevels3D describes a set of solver resolutions.
DefaultSolverResolutionLevels3D(ConstGrid, int, int) - Constructor for class edu.jhu.cs.cisst.algorithms.optimize.fmg.DefaultSolverResolutionLevels3D
Instantiates a new solver resolutions.
defaultTextFieldDimension - Static variable in class edu.jhu.ece.iacl.jist.pipeline.view.input.ParamInputView
The Constant defaultTextFieldDimension.
DefineCFARIScheme - Class in edu.jhu.ece.iacl.plugins.hardi
 
DefineCFARIScheme() - Constructor for class edu.jhu.ece.iacl.plugins.hardi.DefineCFARIScheme
 
deformationAnalysis - Static variable in class edu.jhu.ece.iacl.algorithms.ReferencedPapers
 
deformationField - Variable in class edu.jhu.ece.iacl.algorithms.vabra.VabraAlgorithm
 
DeformationFieldResample3DM(float[][][][], ImageDataFloat, int, int, int, int, int, int) - Static method in class edu.jhu.ece.iacl.algorithms.registration.RegistrationUtilities
 
deformedSubject - Variable in class edu.jhu.ece.iacl.algorithms.vabra.ImagePair
 
DeformImage3D(ImageData, ImageDataFloat, int) - Static method in class edu.jhu.ece.iacl.algorithms.registration.RegistrationUtilities
 
DeformImage3D(ImageData, ImageData, ImageDataFloat, int, int, int, int) - Static method in class edu.jhu.ece.iacl.algorithms.registration.RegistrationUtilities
 
DeformImageFloat3D(ImageData, ImageDataFloat) - Static method in class edu.jhu.ece.iacl.algorithms.registration.RegistrationUtilities
 
DegenerateIntersectionException - Exception in edu.jhu.ece.iacl.jist.structures.geom
Created by IntelliJ IDEA.
DegenerateIntersectionException(String) - Constructor for exception edu.jhu.ece.iacl.jist.structures.geom.DegenerateIntersectionException
Instantiates a new degenerate intersection exception.
delegate - Variable in class edu.jhu.ece.iacl.jist.pipeline.graph.PipeEdgeRealEditor
The delegate class which handles all methods sent from the CellEditor.
deleteDir(File, ProgressMonitor) - Static method in class edu.jhu.ece.iacl.jist.pipeline.ExecutionContext
Delete all contents in a directory.
demote() - Method in class edu.jhu.ece.iacl.jist.pipeline.ExecutionContext
Decrease context queue priority.
demote - Variable in class edu.jhu.ece.iacl.jist.pipeline.gui.ProcessManagerTable
The debug.
demote(Vector<ExecutionContext>) - Method in class edu.jhu.ece.iacl.jist.pipeline.PipeScheduler
Demote position of processes in queue.
dependents - Variable in class edu.jhu.ece.iacl.jist.pipeline.ExecutionContext
Execution contexts that are dependent on the output from this context.
DEPTH_LIMIT - Static variable in class edu.jhu.ece.iacl.jist.pipeline.graph.AvoidanceRouting
The DEPT h_ limit.
dequeue() - Method in class edu.jhu.ece.iacl.jist.pipeline.PipeScheduler
Remove and process context in waiting queue.
derivatives(double[][], double, double, double) - Method in class edu.jhu.bme.smile.commons.math.RotationMatrix
 
derivatives(double, double, double) - Method in class edu.jhu.bme.smile.commons.math.RotationMatrix
 
descendantsPane - Variable in class edu.jhu.ece.iacl.jist.pipeline.gui.ProcessManager
The descendants pane.
descendantTop - Variable in class edu.jhu.ece.iacl.jist.pipeline.ExecutionContext
Root node for descendants.
descendantTree - Variable in class edu.jhu.ece.iacl.jist.pipeline.ExecutionContext
Tree representing context descendants.
description - Variable in class edu.jhu.ece.iacl.jist.pipeline.AlgorithmInformation
The description.
description - Variable in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamModel
Description of parameter.
descriptionBox - Variable in class edu.jhu.ece.iacl.jist.pipeline.view.input.AlgorithmInformationDialog
The description box.
dest - Variable in class edu.jhu.ece.iacl.jist.pipeline.PipeConnector
destination port.
destroy() - Method in interface edu.jhu.ece.iacl.jist.processcontrol.ProcessController
Destroy.
destroy() - Method in class edu.jhu.ece.iacl.jist.processcontrol.ProcessControllerDRMAA
 
destroy() - Method in class edu.jhu.ece.iacl.jist.processcontrol.ProcessControllerNative
 
dests - Variable in class edu.jhu.ece.iacl.jist.pipeline.PipeScheduler
List of all destinations.
determinant(double, double, double, double, double, double, double, double, double, double, double, double, double, double, double, double) - Static method in class edu.jhu.ece.iacl.jist.algorithms.graphics.GeomUtil
Determinant.
determinant(double, double, double, double, double, double, double, double, double) - Static method in class edu.jhu.ece.iacl.jist.algorithms.graphics.GeomUtil
Determinant.
determinant3D(float[][]) - Static method in class edu.jhmi.rad.medic.utilities.NumericsPublic
Close-form 3D matrix determinant
determineRelease() - Method in class edu.jhu.ece.iacl.algorithms.dti.DTIGradientTableCreator
 
DevelopmentStatus - Enum in edu.jhu.ece.iacl.jist.pipeline
The Enum DevelopmentStatus.
devStatus - Variable in class edu.jhu.ece.iacl.jist.pipeline.AlgorithmInformation
The Category.
DF - Variable in class edu.jhu.ece.iacl.algorithms.vabra.ImagePair
 
diag(Matrix) - Static method in class edu.jhu.bme.smile.commons.math.MatrixMath
 
dialog - Variable in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamMipavDialog
The dialog.
dialogClass - Variable in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamMipavDialog
The dialog class.
dialogType - Variable in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamFile
The dialog type.
diceThreshold - Variable in class edu.jhu.cs.cisst.algorithms.segmentation.gac.GeodesicActiveContour2D
The dice threshold.
didAllTestsPass() - Method in class edu.jhu.ece.iacl.jist.pipeline.dest.PipeAssertionTestDestination
 
didTestPass() - Method in class edu.jhu.ece.iacl.doc.DocumentAllTests.Assertion
Did the assertion pass?
DIFF_3_POINT - Static variable in class edu.jhu.bme.smile.commons.optimize.FunctionNumeric1DDifferentiation
 
DIFF_3_POINT - Static variable in class edu.jhu.bme.smile.commons.optimize.FunctionNumericND1DDifferentiation
 
DIFF_5_POINT - Static variable in class edu.jhu.bme.smile.commons.optimize.FunctionNumeric1DDifferentiation
 
DIFF_5_POINT - Static variable in class edu.jhu.bme.smile.commons.optimize.FunctionNumericND1DDifferentiation
 
DIFF_7_POINT - Static variable in class edu.jhu.bme.smile.commons.optimize.FunctionNumeric1DDifferentiation
 
DIFF_7_POINT - Static variable in class edu.jhu.bme.smile.commons.optimize.FunctionNumericND1DDifferentiation
 
DIFF_9_POINT - Static variable in class edu.jhu.bme.smile.commons.optimize.FunctionNumeric1DDifferentiation
 
DIFF_9_POINT - Static variable in class edu.jhu.bme.smile.commons.optimize.FunctionNumericND1DDifferentiation
 
DIFF_BAC_EULER - Static variable in class edu.jhu.bme.smile.commons.optimize.FunctionNumeric1DDifferentiation
 
DIFF_BAC_EULER - Static variable in class edu.jhu.bme.smile.commons.optimize.FunctionNumericND1DDifferentiation
 
DIFF_FWD_EULER - Static variable in class edu.jhu.bme.smile.commons.optimize.FunctionNumeric1DDifferentiation
 
DIFF_FWD_EULER - Static variable in class edu.jhu.bme.smile.commons.optimize.FunctionNumericND1DDifferentiation
 
differentialSurfaceOperators - Static variable in class edu.jhu.ece.iacl.algorithms.ReferencedPapers
 
diffuseColor - Variable in class edu.jhu.cs.cisst.vent.renderer.processing.SurfaceRenderer
The diffuse color.
diffuseColorParam - Variable in class edu.jhu.cs.cisst.vent.renderer.processing.SurfaceRenderer
The diffuse color param.
DiffusionTensor - Class in edu.jhu.ece.iacl.algorithms.dti
 
DiffusionTensor(float[]) - Constructor for class edu.jhu.ece.iacl.algorithms.dti.DiffusionTensor
 
DiffusionTensor(double[]) - Constructor for class edu.jhu.ece.iacl.algorithms.dti.DiffusionTensor
 
diffusionWeight - Variable in class edu.jhu.cs.cisst.algorithms.segmentation.gac.GradientVectorFlow2D
The diffusion weight.
diffusionWeight - Variable in class edu.jhu.cs.cisst.algorithms.segmentation.gac.VectorFieldDiffusion2D
The diffusion weight.
dim - Variable in class edu.jhu.cs.cisst.algorithms.segmentation.gac.VectorFieldDiffusion2D
The dimension.
dim - Variable in class edu.jhu.ece.iacl.algorithms.manual_label.LabelImageGroup
 
dimensions - Variable in class edu.jhu.ece.iacl.jist.structures.fiber.FiberCollection
The dimensions.
dimResolutions - Variable in class edu.jhu.ece.iacl.jist.structures.image.ImageHeader
The dim resolutions.
dir - Variable in class edu.jhu.ece.iacl.algorithms.manual_label.staple.STAPLE
 
dir - Variable in class edu.jhu.ece.iacl.algorithms.manual_label.staple.STAPLEgeneral
 
dir - Variable in class edu.jhu.ece.iacl.algorithms.manual_label.staple.STAPLEgeneralSingle
 
dir - Variable in class edu.jhu.ece.iacl.algorithms.manual_label.staple.STAPLEmulti
 
dir - Variable in class edu.jhu.ece.iacl.algorithms.manual_label.staple.STAPLEmulti2
 
dir - Variable in class edu.jhu.ece.iacl.algorithms.manual_label.staple.STAPLEsingle
 
dir - Variable in class edu.jhu.ece.iacl.algorithms.manual_label.staple.STAPLEsurf
 
dir - Variable in class edu.jhu.ece.iacl.jist.pipeline.tree.PackageNode
The dir.
dirParam - Variable in class edu.jhu.ece.iacl.jist.pipeline.src.PipeFileDirectorySource
The dir param.
dirParam - Variable in class edu.jhu.ece.iacl.jist.pipeline.src.PipeVolumeDirectoryCollectionSource
The dir param.
dirParam - Variable in class edu.jhu.ece.iacl.plugins.utilities.file.VolumeDirectoryNoIter
The dir param.
dirty - Variable in class edu.jhu.ece.iacl.jist.pipeline.PipeLayout
flag to indicate whether the layout has changed and needs to be saved.
disable() - Method in class edu.jhu.ece.iacl.jist.pipeline.view.input.Refresher
 
disabled - Variable in class edu.jhu.ece.iacl.jist.pipeline.view.input.Refresher
 
disabledCount - Variable in class edu.jhu.ece.iacl.jist.pipeline.view.input.Refresher
 
disconnect() - Method in class edu.jhu.ece.iacl.jist.pipeline.PipeConnector
Remove this connection from the source and destination port.
disconnect() - Method in class edu.jhu.ece.iacl.jist.pipeline.PipeModule
Disconnect all incoming and outgoing ports for this module.
disconnect() - Method in class edu.jhu.ece.iacl.jist.pipeline.PipePort
Disconnect all incoming and outgoing connectors.
disconnect(int) - Method in class edu.jhu.ece.iacl.jist.pipeline.PipePort
Disconnect a specific connector.
disconnect(PipeConnector) - Method in class edu.jhu.ece.iacl.jist.pipeline.PipePort
Remove connector from this port.
disconnect(PipePort) - Method in class edu.jhu.ece.iacl.jist.pipeline.PipePort
Remove all connections between this port and the specified port.
disconnect() - Method in class edu.jhu.ece.iacl.jist.pipeline.PipeSource
Disconnect this module and all connections to this module.
disconnectAction(PipePort, PipePort, PipeConnector) - Method in class edu.jhu.ece.iacl.jist.pipeline.graph.PipeJGraph
 
disconnectAction(PipePort, PipePort, PipeConnector) - Method in class edu.jhu.ece.iacl.jist.pipeline.gui.ParameterPanel
Update input view when disconnection occurs.
disconnectAction(PipePort, PipePort, PipeConnector) - Method in class edu.jhu.ece.iacl.jist.pipeline.PipeModule
Listen for disconnect event to occur on a port.
disconnectAction(PipePort, PipePort, PipeConnector) - Method in interface edu.jhu.ece.iacl.jist.pipeline.PipePort.PortListener
Disconnect action.
disconnectAction(PipePort, PipePort, PipeConnector) - Method in class edu.jhu.ece.iacl.jist.pipeline.src.PipeSelectionExternalSource
Update selection options if connector is removed.
disconnectAction(PipePort, PipePort, PipeConnector) - Method in class edu.jhu.ece.iacl.jist.pipeline.src.PipeSelectionListSource
 
disconnectAction(PipePort, PipePort, PipeConnector) - Method in class edu.jhu.ece.iacl.jist.pipeline.src.PipeSelectionSource
Update selection options if connector is removed.
discover - Class in edu.jhu.ece.iacl.jist.cli
 
discover() - Constructor for class edu.jhu.ece.iacl.jist.cli.discover
 
discoverAllMapsAndLoniModules(ProgressMonitor) - Method in class edu.jhu.ece.iacl.jist.pipeline.PipeLibrary
Discover all MAPS and LONI files.
discoverAllModules(ProgressMonitor) - Method in class edu.jhu.ece.iacl.jist.pipeline.PipeLibrary
Discover all modules that can be loaded by MAPS.
discoverInternalMapsModules(ProgressMonitor) - Method in class edu.jhu.ece.iacl.jist.pipeline.PipeLibrary
Discover new algorithms along source path.
discoverLayouts(File) - Method in class edu.jhu.ece.iacl.doc.DocumentAllTests
Discover layouts.
discoverLayouts(File) - Method in class edu.jhu.ece.iacl.jist.test.JistTestHarness
Discover layouts.
DiscoverMipavJISTPlugins - Class in <Unnamed>
 
DiscoverMipavJISTPlugins() - Constructor for class DiscoverMipavJISTPlugins
 
discreteCurvatureOperators - Static variable in class edu.jhu.ece.iacl.algorithms.ReferencedPapers
 
discreteLabelsFromMemberships(List<ImageData>, float) - Static method in class edu.jhu.ece.iacl.algorithms.manual_label.LabelImage
 
discreteLabelsFromMemberships(List<ImageData>, List<Integer>, float) - Static method in class edu.jhu.ece.iacl.algorithms.manual_label.LabelImage
 
DispatchController - Class in edu.jhu.ece.iacl.jist.processcontrol
The Class DispatchController.
DispatchController() - Constructor for class edu.jhu.ece.iacl.jist.processcontrol.DispatchController
 
displayError(String) - Static method in class edu.jhmi.rad.medic.utilities.MedicUtilPublic
Display error.
displayError(String) - Static method in class edu.jhu.ece.iacl.jist.io.MipavController
Display error.
displayMessage(String) - Static method in class edu.jhmi.rad.medic.utilities.MedicUtilPublic
Display message.
displayMessage(String) - Static method in class edu.jhu.ece.iacl.jist.io.MipavController
Display message.
dispose() - Method in interface edu.jhu.cs.cisst.vent.Visualization
Dispose.
dispose() - Method in class edu.jhu.cs.cisst.vent.VisualizationProcessing
Dispose.
dispose() - Method in class edu.jhu.cs.cisst.vent.widgets.VisualizationImage
Dispose.
dispose() - Method in class edu.jhu.cs.cisst.vent.widgets.VisualizationTriangleMesh
 
dispose() - Method in class edu.jhu.ece.iacl.algorithms.vabra.ImagePair
 
dispose() - Method in class edu.jhu.ece.iacl.algorithms.vabra.ImagePairNMI
 
dispose() - Method in class edu.jhu.ece.iacl.algorithms.vabra.ImagePairRBF
 
dispose() - Method in class edu.jhu.ece.iacl.algorithms.vabra.VabraSolver
 
dispose() - Method in class edu.jhu.ece.iacl.jist.pipeline.graph.PipeJGraph
Dispose.
dispose() - Method in class edu.jhu.ece.iacl.jist.pipeline.graph.PipeMarqueeHandler
Dispose.
dispose() - Method in class edu.jhu.ece.iacl.jist.pipeline.gui.PipeInternalFrame
Dispose of graph.
dispose() - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamModel
Release as much memory as possible from this object without setting the entire object to null.
dispose() - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamVolume
Dispose of volume in memory.
dispose() - Method in class edu.jhu.ece.iacl.jist.pipeline.PipeLayoutRunner
Dispose.
dispose() - Method in class edu.jhu.ece.iacl.jist.pipeline.PipeScheduler
Dispose of scheduler by killing all current processes.
dispose() - Method in class edu.jhu.ece.iacl.jist.pipeline.ProcessingDialog
Dispose of dialog.
dispose() - Method in class edu.jhu.ece.iacl.jist.pipeline.ProcessingGroupDialog
Dispose of dialog.
dispose() - Method in class edu.jhu.ece.iacl.jist.structures.geom.CollisionDetection
Dispose.
dispose() - Method in class edu.jhu.ece.iacl.jist.structures.image.ImageData
Free any resources associated with an ImageData object.
dispose() - Method in class edu.jhu.ece.iacl.jist.structures.image.ImageDataByte
 
dispose() - Method in class edu.jhu.ece.iacl.jist.structures.image.ImageDataColor
 
dispose() - Method in class edu.jhu.ece.iacl.jist.structures.image.ImageDataDouble
 
dispose() - Method in class edu.jhu.ece.iacl.jist.structures.image.ImageDataFloat
 
dispose() - Method in class edu.jhu.ece.iacl.jist.structures.image.ImageDataInt
 
dispose() - Method in class edu.jhu.ece.iacl.jist.structures.image.ImageDataMipav
 
dispose() - Method in class edu.jhu.ece.iacl.jist.structures.image.ImageDataUByte
 
disposeAllTables() - Method in class edu.jhu.ece.iacl.jist.structures.geom.EmbeddedSurface
Dispose all tables.
distance(Tuple3f, Tuple3f) - Static method in class edu.jhu.ece.iacl.jist.algorithms.graphics.GeomUtil
Distance.
distance(Tuple3f, Tuple3d) - Static method in class edu.jhu.ece.iacl.jist.algorithms.graphics.GeomUtil
Distance.
distance(Tuple3d, Tuple3d) - Static method in class edu.jhu.ece.iacl.jist.algorithms.graphics.GeomUtil
Distance.
distance(XYZ) - Method in class edu.jhu.ece.iacl.jist.structures.fiber.XYZ
Distance.
distance(double, double, double) - Method in class edu.jhu.ece.iacl.jist.structures.geom.GridPt
Distance.
distance(GridPt) - Method in class edu.jhu.ece.iacl.jist.structures.geom.GridPt
Distance.
distance(GridPt, float, float, float) - Method in class edu.jhu.ece.iacl.jist.structures.geom.GridPt
Distance.
distance(XYZ) - Method in class edu.jhu.ece.iacl.jist.structures.geom.GridPt
Distance.
distance(double, double, double, double, double, double) - Static method in class edu.jhu.ece.iacl.jist.structures.geom.GridPt
Distance.
DistanceField - Class in edu.jhu.ece.iacl.algorithms.volume
Calculate distance field using Fast-marching method
DistanceField() - Constructor for class edu.jhu.ece.iacl.algorithms.volume.DistanceField
 
DistanceField(AbstractCalculation) - Constructor for class edu.jhu.ece.iacl.algorithms.volume.DistanceField
 
DistanceField2D - Class in edu.jhu.cs.cisst.algorithms.segmentation.gac
Calculate 2D distance field using the Fast-marching method.
DistanceField2D() - Constructor for class edu.jhu.cs.cisst.algorithms.segmentation.gac.DistanceField2D
Instantiates a new distance field2 d.
DistanceField2D(AbstractCalculation) - Constructor for class edu.jhu.cs.cisst.algorithms.segmentation.gac.DistanceField2D
Instantiates a new distance field2 d.
distField - Variable in class edu.jhu.cs.cisst.algorithms.segmentation.gac.GeodesicActiveContour2D
The distance field.
distFieldImage - Variable in class edu.jhu.cs.cisst.algorithms.segmentation.gac.GeodesicActiveContour2D
The distance field image.
distributeBeta() - Method in class edu.jhu.ece.iacl.algorithms.manual_label.staple.STAPLEmulti
 
distributeBeta() - Method in class edu.jhu.ece.iacl.algorithms.manual_label.staple.STAPLEmulti2
 
div(Voxel) - Method in class edu.jhu.ece.iacl.jist.structures.image.Voxel
Div.
div(Voxel) - Method in class edu.jhu.ece.iacl.jist.structures.image.VoxelBoolean
 
div(Voxel) - Method in class edu.jhu.ece.iacl.jist.structures.image.VoxelColor
 
div(Voxel) - Method in class edu.jhu.ece.iacl.jist.structures.image.VoxelDouble
 
div(Voxel) - Method in class edu.jhu.ece.iacl.jist.structures.image.VoxelFloat
 
div(Voxel) - Method in class edu.jhu.ece.iacl.jist.structures.image.VoxelIndexed
 
div(Voxel) - Method in class edu.jhu.ece.iacl.jist.structures.image.VoxelInt
 
div(Voxel) - Method in class edu.jhu.ece.iacl.jist.structures.image.VoxelMipav
 
div(Voxel) - Method in class edu.jhu.ece.iacl.jist.structures.image.VoxelShort
 
div(Voxel) - Method in class edu.jhu.ece.iacl.jist.structures.image.VoxelUByte
 
div(Voxel) - Method in class edu.jhu.ece.iacl.jist.structures.image.VoxelVector
 
div(double) - Method in class edu.jhu.ece.iacl.jist.structures.matrix.Matrix3
Div.
div(Matrix3) - Method in class edu.jhu.ece.iacl.jist.structures.matrix.Matrix3
Div.
div(double) - Method in class edu.jhu.ece.iacl.jist.structures.matrix.VectorMatrixX
Div.
div(VectorMatrixX) - Method in class edu.jhu.ece.iacl.jist.structures.matrix.VectorMatrixX
Div.
div(double) - Method in class edu.jhu.ece.iacl.jist.structures.vector.Vector2
 
div(VectorX) - Method in class edu.jhu.ece.iacl.jist.structures.vector.Vector2
 
div(double) - Method in class edu.jhu.ece.iacl.jist.structures.vector.Vector3
 
div(VectorX) - Method in class edu.jhu.ece.iacl.jist.structures.vector.Vector3
 
div(double) - Method in class edu.jhu.ece.iacl.jist.structures.vector.Vector4
 
div(VectorX) - Method in class edu.jhu.ece.iacl.jist.structures.vector.Vector4
 
div(double) - Method in class edu.jhu.ece.iacl.jist.structures.vector.VectorN
 
div(VectorX) - Method in class edu.jhu.ece.iacl.jist.structures.vector.VectorN
 
div(double) - Method in interface edu.jhu.ece.iacl.jist.structures.vector.VectorX
Div.
div(VectorX) - Method in interface edu.jhu.ece.iacl.jist.structures.vector.VectorX
Div.
divideByTots(int, float) - Method in class edu.jhu.ece.iacl.algorithms.manual_label.staple.PerformanceLevel
 
divideByTots(int, double) - Method in class edu.jhu.ece.iacl.algorithms.manual_label.staple.PerformanceLevel
 
DivideReference - Class in edu.jhu.ece.iacl.pami
 
DivideReference() - Constructor for class edu.jhu.ece.iacl.pami.DivideReference
 
dlinmind(double[], double[], int, double[], NumericalMethod, double[], int, double[]) - Method in class edu.jhu.ece.iacl.algorithms.vabra.NumericalRecipes
 
DocMediaWikiWriter - Class in edu.jhu.ece.iacl.doc
Class that writes module information in a mediawiki-text format
DocMediaWikiWriter(ProcessingAlgorithm) - Constructor for class edu.jhu.ece.iacl.doc.DocMediaWikiWriter
 
DocumentAllModules - Class in edu.jhu.ece.iacl.doc
Class automatically document module definitions
DocumentAllModules() - Constructor for class edu.jhu.ece.iacl.doc.DocumentAllModules
Default constructor.
DocumentAllModules(File) - Constructor for class edu.jhu.ece.iacl.doc.DocumentAllModules
 
DocumentAllModules.CompareFactories - Class in edu.jhu.ece.iacl.doc
The Class CompareFactories.
DocumentAllModules.CompareFactories() - Constructor for class edu.jhu.ece.iacl.doc.DocumentAllModules.CompareFactories
 
DocumentAllModules.ModuleDescription - Class in edu.jhu.ece.iacl.doc
 
DocumentAllModules.ModuleDescription(String, String, String, File, String) - Constructor for class edu.jhu.ece.iacl.doc.DocumentAllModules.ModuleDescription
 
DocumentAllTests - Class in edu.jhu.ece.iacl.doc
Automatically runs and documents all test cases
DocumentAllTests(File, File, File) - Constructor for class edu.jhu.ece.iacl.doc.DocumentAllTests
Instantiates a new jist test harness.
DocumentAllTests.Assertion - Class in edu.jhu.ece.iacl.doc
Assertion description
DocumentAllTests.Assertion(String, File, boolean) - Constructor for class edu.jhu.ece.iacl.doc.DocumentAllTests.Assertion
Constructor
DocumentAllTests.ModuleDescription - Class in edu.jhu.ece.iacl.doc
Module description.
DocumentAllTests.ModuleDescription(String, String) - Constructor for class edu.jhu.ece.iacl.doc.DocumentAllTests.ModuleDescription
Constructor
DocumentAllTests.TestCase - Class in edu.jhu.ece.iacl.doc
Test case description.
DocumentAllTests.TestCase(String, File) - Constructor for class edu.jhu.ece.iacl.doc.DocumentAllTests.TestCase
 
DocumentAllTests.TestCase.Status - Enum in edu.jhu.ece.iacl.doc
 
DocumentGenerator - Class in edu.jhu.ece.iacl.doc
 
DocumentGenerator() - Constructor for class edu.jhu.ece.iacl.doc.DocumentGenerator
 
DocumentGeneratorHTML - Class in edu.jhu.ece.iacl.doc
 
DocumentGeneratorHTML() - Constructor for class edu.jhu.ece.iacl.doc.DocumentGeneratorHTML
 
documentModules() - Method in class edu.jhu.ece.iacl.doc.DocumentAllModules
Searches for modules and writes documentation to file.
dodecahedron() - Static method in class edu.jhu.ece.iacl.algorithms.hardi.SurfaceTools
 
doesScenarioExist(PipeAlgorithm) - Method in class edu.jhu.ece.iacl.jist.pipeline.PipeScheduler
Find existing context with the same parameters as the algorithm module if one exists.
doInBackground() - Method in class edu.jhu.cs.cisst.vent.renderer.processing.VolumeIsoContourRenderer.IsoContourWorker
Do in background.
doInBackground() - Method in class edu.jhu.ece.iacl.jist.pipeline.gui.PipelineLayoutTool.InitializeLayout
 
doInBackground() - Method in class edu.jhu.ece.iacl.jist.pipeline.gui.ProcessDebugInfoFrame.FileReaderWorker
 
doInBackground() - Method in class edu.jhu.ece.iacl.jist.pipeline.gui.ProcessManager.LoadLayout
 
doInBackground() - Method in class edu.jhu.ece.iacl.jist.pipeline.PipeLibrary.InitializeTask
Load library in background.
doInBackground() - Method in class edu.jhu.ece.iacl.jist.pipeline.PipeLibrary.RebuildTask
Rebuild library in background.
doInBackground() - Method in class edu.jhu.ece.iacl.jist.pipeline.PipeScheduler.CleanAllDialog.DeleteDirectoriesWorker
Delete directories in the output directory in background with a process monitor
doInBackground() - Method in class edu.jhu.ece.iacl.jist.pipeline.PipeScheduler.DestinationProcessor
Process destinations in background.
done() - Method in class edu.jhu.ece.iacl.jist.pipeline.gui.ModuleTreePanel.InitializeWorker
Build tree from modules.
done() - Method in class edu.jhu.ece.iacl.jist.pipeline.gui.ModuleTreePanel.RebuildWorker
Remove existing tree and rebuild.
done() - Method in class edu.jhu.ece.iacl.jist.pipeline.gui.PipelineLayoutTool.InitializeLayout
 
done() - Method in class edu.jhu.ece.iacl.jist.pipeline.gui.PlugInSelector.InitializeWorker
Build tree from modules.
done() - Method in class edu.jhu.ece.iacl.jist.pipeline.gui.PlugInSelector.RebuildWorker
Rebuild tree from modules.
done() - Method in class edu.jhu.ece.iacl.jist.pipeline.PipeScheduler.CleanAllDialog.DeleteDirectoriesWorker
Close progress monitor.
done() - Method in class edu.jhu.ece.iacl.jist.pipeline.PipeScheduler.DestinationProcessor
Close progress monitor.
doPostAlgorithmActions() - Method in class edu.jhu.ece.iacl.jist.dialogs.JDialogSaveAll
 
doPostAlgorithmActions() - Method in class edu.jhu.ece.iacl.jist.pipeline.ProcessingDialog
Store result images in script runner.
doPostAlgorithmActions() - Method in class edu.jhu.ece.iacl.jist.pipeline.ProcessingGroupDialog
Store result images in script runner.
doSolve(ImageDataFloat, double) - Static method in class edu.jhu.cs.cisst.algorithms.segmentation.gac.DistanceField2D
Do solve.
doSolve(List<ImageData>, List<Number>, List<ImageData>, List<Number>, File) - Static method in class edu.jhu.ece.iacl.algorithms.vabra.VabraAlgorithm
 
doSolve(ImageDataFloat, double) - Static method in class edu.jhu.ece.iacl.algorithms.volume.DistanceField
 
dot(Tuple3d, Tuple3d) - Static method in class edu.jhu.ece.iacl.jist.algorithms.graphics.GeomUtil
Dot.
dot(Tuple3f, Tuple3f) - Static method in class edu.jhu.ece.iacl.jist.algorithms.graphics.GeomUtil
Dot.
dot(PT) - Method in class edu.jhu.ece.iacl.jist.structures.geom.PT
Dot.
dotProduct(Matrix, Matrix) - Static method in class edu.jhu.bme.smile.commons.math.MatrixMath
 
DoubleDistance(double, double, double, double, double, double) - Static method in class edu.jhu.ece.iacl.algorithms.registration.RegistrationUtilities
 
doubleFactorial(int) - Static method in class edu.jhu.bme.smile.commons.math.specialFunctions.SFunc
DoubleFactorial !! See: http://en.wikipedia.org/wiki/Factorial#Double_factorial
doubleParam - Variable in class edu.jhu.ece.iacl.jist.pipeline.src.PipeDoubleListSource
The double param.
doubleValue() - Method in class edu.jhu.ece.iacl.jist.structures.image.Voxel
 
downButton - Variable in class edu.jhu.ece.iacl.jist.pipeline.view.input.ParamVolumeCollectionInputView
The down button.
DownhillSimplex() - Static method in class edu.jhu.bme.smile.commons.optimize.test.TestNDOptimizations
Downhill Simplex
DownhillSimplexND - Class in edu.jhu.bme.smile.commons.optimize
This optimizer uses the Nelder-Mead downhill simplex method to optimize a function.
DownhillSimplexND() - Constructor for class edu.jhu.bme.smile.commons.optimize.DownhillSimplexND
Default constructor
DownhillSimplexND(int) - Constructor for class edu.jhu.bme.smile.commons.optimize.DownhillSimplexND
Constructor to set maximum number of iterations to run
dpl - Variable in class edu.jhu.ece.iacl.algorithms.manual_label.staple.PerformanceLevel
 
dragDropEnd(DragSourceDropEvent) - Method in class edu.jhu.ece.iacl.jist.pipeline.tree.DraggableJTree
DragSourceListener interface method.
dragEnter(DropTargetDragEvent) - Method in class edu.jhu.ece.iacl.jist.pipeline.graph.PipeJGraph
 
dragEnter(DragSourceDragEvent) - Method in class edu.jhu.ece.iacl.jist.pipeline.tree.DraggableJTree
DragSourceListener interface method.
dragEnter(DropTargetDragEvent) - Method in class edu.jhu.ece.iacl.jist.pipeline.tree.DraggableJTree
Accepts drag action on tree if destination is a package.
dragExit(DropTargetEvent) - Method in class edu.jhu.ece.iacl.jist.pipeline.graph.PipeJGraph
 
dragExit(DragSourceEvent) - Method in class edu.jhu.ece.iacl.jist.pipeline.tree.DraggableJTree
 
dragExit(DropTargetEvent) - Method in class edu.jhu.ece.iacl.jist.pipeline.tree.DraggableJTree
Unimplemented.
DraggableJTree - Class in edu.jhu.ece.iacl.jist.pipeline.tree
Tree that allows items to be dragged.
DraggableJTree(DefaultTreeModel, DefaultMutableTreeNode) - Constructor for class edu.jhu.ece.iacl.jist.pipeline.tree.DraggableJTree
Default constructor.
DraggableNode - Class in edu.jhu.ece.iacl.jist.pipeline.tree
A draggable node is a tree node that the user can drag.
DraggableNode() - Constructor for class edu.jhu.ece.iacl.jist.pipeline.tree.DraggableNode
Default constructor.
DraggableNode(PipeModuleFactory) - Constructor for class edu.jhu.ece.iacl.jist.pipeline.tree.DraggableNode
Default constructor.
dragGestureRecognized(DragGestureEvent) - Method in class edu.jhu.ece.iacl.jist.pipeline.tree.DraggableJTree
DragGestureListener interface method.
dragOver(DropTargetDragEvent) - Method in class edu.jhu.ece.iacl.jist.pipeline.graph.PipeJGraph
DropTaregetListener interface method.
dragOver(DragSourceDragEvent) - Method in class edu.jhu.ece.iacl.jist.pipeline.tree.DraggableJTree
DragSourceListener interface method.
dragOver(DropTargetDragEvent) - Method in class edu.jhu.ece.iacl.jist.pipeline.tree.DraggableJTree
Accepts drag action on tree if destination is package.
draw() - Method in class edu.jhu.cs.cisst.vent.renderer.processing.ImageRenderer
 
draw() - Method in class edu.jhu.cs.cisst.vent.renderer.processing.RendererProcessing
Draw.
draw() - Method in class edu.jhu.cs.cisst.vent.renderer.processing.SurfaceRenderer
 
draw() - Method in class edu.jhu.cs.cisst.vent.renderer.processing.VectorField2DRenderer
Draw.
draw(int, int, Vector3f) - Method in class edu.jhu.cs.cisst.vent.renderer.processing.VectorField2DRenderer
Draw.
draw() - Method in class edu.jhu.cs.cisst.vent.renderer.processing.VolumeIsoContourRenderer
(non-Javadoc).
draw() - Method in class edu.jhu.cs.cisst.vent.renderer.processing.VolumeSliceRenderer
Draw.
draw(PApplet, boolean, boolean) - Method in class edu.jhu.cs.cisst.vent.structures.processing.PTriangleMesh
Draw.
draw() - Method in class edu.jhu.cs.cisst.vent.VisualizationProcessing2D
Draw.
draw() - Method in class edu.jhu.cs.cisst.vent.VisualizationProcessing3D
Draw.
draw() - Method in class edu.jhu.cs.cisst.vent.widgets.VisualizationImage
Draw.
draw() - Method in class edu.jhu.cs.cisst.vent.widgets.VisualizationTriangleMesh
 
draw2D(PApplet) - Method in class edu.jhu.cs.cisst.vent.structures.processing.PCurveCollection
Draw in 2D
draw3D(PApplet) - Method in class edu.jhu.cs.cisst.vent.structures.processing.PCurveCollection
Draw in 3D
drawAxes() - Method in class edu.jhu.cs.cisst.vent.widgets.VisualizationTriangleMesh
Draw axes.
drawPortLabel(Graphics2D, PortView) - Method in class edu.jhu.ece.iacl.jist.pipeline.graph.PipeMarqueeHandler
Draw port label.
drawPortLabel(Graphics2D) - Method in class edu.jhu.ece.iacl.jist.pipeline.graph.PipePortView
Draw port label.
drop(DropTargetDropEvent) - Method in class edu.jhu.ece.iacl.jist.pipeline.graph.PipeJGraph
DropTargetListener interface method - What we do when drag is released.
drop(DropTargetDropEvent) - Method in class edu.jhu.ece.iacl.jist.pipeline.tree.DraggableJTree
Drop object on tree.
dropActionChanged(DropTargetDragEvent) - Method in class edu.jhu.ece.iacl.jist.pipeline.graph.PipeJGraph
 
dropActionChanged(DragSourceDragEvent) - Method in class edu.jhu.ece.iacl.jist.pipeline.tree.DraggableJTree
DragSourceListener interface method.
dropActionChanged(DropTargetDragEvent) - Method in class edu.jhu.ece.iacl.jist.pipeline.tree.DraggableJTree
Unimplemeted.
DTEMRLTensor - Class in edu.jhu.ece.iacl.algorithms.dti
This class is used to minimize the least likelihood estimator from data from diffusion weighted imaging.
DTEMRLTensor() - Constructor for class edu.jhu.ece.iacl.algorithms.dti.DTEMRLTensor
 
DTIGradientTableCreator - Class in edu.jhu.ece.iacl.algorithms.dti
 
DTIGradientTableCreator() - Constructor for class edu.jhu.ece.iacl.algorithms.dti.DTIGradientTableCreator
 
DTIGradientTableCreator(GTCparams) - Constructor for class edu.jhu.ece.iacl.algorithms.dti.DTIGradientTableCreator
 
DTIS2ITK(String) - Static method in class edu.jhu.ece.iacl.algorithms.dti.tractography.FACT.FiberConverter
 
DTISFiberWriter - Class in edu.jhu.ece.iacl.algorithms.dti.tractography.FACT
 
DTISFiberWriter() - Constructor for class edu.jhu.ece.iacl.algorithms.dti.tractography.FACT.DTISFiberWriter
 
DTIstudio - Variable in class edu.jhu.ece.iacl.algorithms.dti.GTCparams
 
DTIStudioHDR - Class in edu.jhu.ece.iacl.jist.structures.fiber
The Class DTIStudioHDR.
DTIStudioHDR() - Constructor for class edu.jhu.ece.iacl.jist.structures.fiber.DTIStudioHDR
Instantiates a new dTI studio hdr.
DTIStudioHDR(int[], float[]) - Constructor for class edu.jhu.ece.iacl.jist.structures.fiber.DTIStudioHDR
Instantiates a new dTI studio hdr.
DTIStudioReader - Class in edu.jhu.ece.iacl.algorithms.dti.tractography.FACT
Created by IntelliJ IDEA.
DTIStudioReader() - Constructor for class edu.jhu.ece.iacl.algorithms.dti.tractography.FACT.DTIStudioReader
 
DTIStudioStepSize - Static variable in class edu.jhu.ece.iacl.algorithms.dti.tractography.FiberTracker
 
DTIStudioStepSize - Static variable in class edu.jhu.ece.iacl.algorithms.dti.tractography.WildBootFiberTracker
 
DTISVecReader - Class in edu.jhu.ece.iacl.jist.io
The Class DTISVecReader.
DTISVecReader() - Constructor for class edu.jhu.ece.iacl.jist.io.DTISVecReader
 
DtisVsIacl - Class in edu.jhu.ece.iacl.algorithms.dti.tractography.FACT
 
DtisVsIacl() - Constructor for class edu.jhu.ece.iacl.algorithms.dti.tractography.FACT.DtisVsIacl
 
DtiVecMask - Class in edu.jhu.ece.iacl.algorithms.dti
 
DtiVecMask(AbstractCalculation) - Constructor for class edu.jhu.ece.iacl.algorithms.dti.DtiVecMask
 
DtiVecMask() - Constructor for class edu.jhu.ece.iacl.algorithms.dti.DtiVecMask
 
duyguTosun - Static variable in class edu.jhu.ece.iacl.algorithms.CommonAuthors
 
DWIBallStickEstCamino - Class in edu.jhu.ece.iacl.plugins.dti
 
DWIBallStickEstCamino() - Constructor for class edu.jhu.ece.iacl.plugins.dti.DWIBallStickEstCamino
 
DWIBallStickEstCaminoFileCollection - Class in edu.jhu.ece.iacl.plugins.dti
 
DWIBallStickEstCaminoFileCollection() - Constructor for class edu.jhu.ece.iacl.plugins.dti.DWIBallStickEstCaminoFileCollection
 
DWIBallStickEstCaminoFileCollection.TensorEstimationWrapper - Class in edu.jhu.ece.iacl.plugins.dti
 
DWIBallStickEstCaminoFileCollection.TensorEstimationWrapper() - Constructor for class edu.jhu.ece.iacl.plugins.dti.DWIBallStickEstCaminoFileCollection.TensorEstimationWrapper
 
DWICombineBvalTables - Class in edu.jhu.ece.iacl.plugins.dti
 
DWICombineBvalTables() - Constructor for class edu.jhu.ece.iacl.plugins.dti.DWICombineBvalTables
 
DWICombineGradTables - Class in edu.jhu.ece.iacl.plugins.dti
 
DWICombineGradTables() - Constructor for class edu.jhu.ece.iacl.plugins.dti.DWICombineGradTables
 
DWICoReg - Class in edu.jhu.ece.iacl.algorithms.dti
 
DWICoReg(ArrayList<ImageData>, ImageData, String, int[]) - Constructor for class edu.jhu.ece.iacl.algorithms.dti.DWICoReg
 
DWICoReg(ArrayList<ArrayList<ImageData>>, ImageData, String, int[], boolean) - Constructor for class edu.jhu.ece.iacl.algorithms.dti.DWICoReg
 
DWIDefineCaminoScheme - Class in edu.jhu.ece.iacl.plugins.dti
 
DWIDefineCaminoScheme() - Constructor for class edu.jhu.ece.iacl.plugins.dti.DWIDefineCaminoScheme
 
DWITensorColorEncodedMap - Class in edu.jhu.ece.iacl.plugins.dti
 
DWITensorColorEncodedMap() - Constructor for class edu.jhu.ece.iacl.plugins.dti.DWITensorColorEncodedMap
 
DWITensorColorEncodedMap.AlgorithmWrapper - Class in edu.jhu.ece.iacl.plugins.dti
 
DWITensorColorEncodedMap.AlgorithmWrapper() - Constructor for class edu.jhu.ece.iacl.plugins.dti.DWITensorColorEncodedMap.AlgorithmWrapper
 
DWITensorContrasts - Class in edu.jhu.ece.iacl.plugins.dti
 
DWITensorContrasts() - Constructor for class edu.jhu.ece.iacl.plugins.dti.DWITensorContrasts
 
DWITensorEstCamino - Class in edu.jhu.ece.iacl.plugins.dti
 
DWITensorEstCamino() - Constructor for class edu.jhu.ece.iacl.plugins.dti.DWITensorEstCamino
 
DWITensorEstCaminoFileCollection - Class in edu.jhu.ece.iacl.plugins.dti
 
DWITensorEstCaminoFileCollection() - Constructor for class edu.jhu.ece.iacl.plugins.dti.DWITensorEstCaminoFileCollection
 
DWITensorEstCaminoFileCollection.TensorEstimationWrapper - Class in edu.jhu.ece.iacl.plugins.dti
 
DWITensorEstCaminoFileCollection.TensorEstimationWrapper() - Constructor for class edu.jhu.ece.iacl.plugins.dti.DWITensorEstCaminoFileCollection.TensorEstimationWrapper
 
DWITensorEstCaminoRESTOREVariableNoiseField - Class in edu.jhu.ece.iacl.plugins.dti
 
DWITensorEstCaminoRESTOREVariableNoiseField() - Constructor for class edu.jhu.ece.iacl.plugins.dti.DWITensorEstCaminoRESTOREVariableNoiseField
 
DWITensorEstLikelihood - Class in edu.jhu.ece.iacl.plugins.dti
 
DWITensorEstLikelihood() - Constructor for class edu.jhu.ece.iacl.plugins.dti.DWITensorEstLikelihood
 
DWITensorEstLikelihood.TensorEstimationWrapper - Class in edu.jhu.ece.iacl.plugins.dti
 
DWITensorEstLikelihood.TensorEstimationWrapper() - Constructor for class edu.jhu.ece.iacl.plugins.dti.DWITensorEstLikelihood.TensorEstimationWrapper
 
DWITensorEstLLMSE - Class in edu.jhu.ece.iacl.plugins.dti
 
DWITensorEstLLMSE() - Constructor for class edu.jhu.ece.iacl.plugins.dti.DWITensorEstLLMSE
 
DWITensorEstLLMSE.TensorEstimationWrapper - Class in edu.jhu.ece.iacl.plugins.dti
 
DWITensorEstLLMSE.TensorEstimationWrapper() - Constructor for class edu.jhu.ece.iacl.plugins.dti.DWITensorEstLLMSE.TensorEstimationWrapper
 
DWIThreeTensorEstCamino - Class in edu.jhu.ece.iacl.plugins.dti
 
DWIThreeTensorEstCamino() - Constructor for class edu.jhu.ece.iacl.plugins.dti.DWIThreeTensorEstCamino
 
DWIThreeTensorEstCaminoFileCollection - Class in edu.jhu.ece.iacl.plugins.dti
 
DWIThreeTensorEstCaminoFileCollection() - Constructor for class edu.jhu.ece.iacl.plugins.dti.DWIThreeTensorEstCaminoFileCollection
 
DWIThreeTensorEstCaminoFileCollection.TensorEstimationWrapper - Class in edu.jhu.ece.iacl.plugins.dti
 
DWIThreeTensorEstCaminoFileCollection.TensorEstimationWrapper() - Constructor for class edu.jhu.ece.iacl.plugins.dti.DWIThreeTensorEstCaminoFileCollection.TensorEstimationWrapper
 
DWITwoTensorEstCamino - Class in edu.jhu.ece.iacl.plugins.dti
 
DWITwoTensorEstCamino() - Constructor for class edu.jhu.ece.iacl.plugins.dti.DWITwoTensorEstCamino
 
DWITwoTensorEstCaminoFileCollection - Class in edu.jhu.ece.iacl.plugins.dti
 
DWITwoTensorEstCaminoFileCollection() - Constructor for class edu.jhu.ece.iacl.plugins.dti.DWITwoTensorEstCaminoFileCollection
 
DWITwoTensorEstCaminoFileCollection.TensorEstimationWrapper - Class in edu.jhu.ece.iacl.plugins.dti
 
DWITwoTensorEstCaminoFileCollection.TensorEstimationWrapper() - Constructor for class edu.jhu.ece.iacl.plugins.dti.DWITwoTensorEstCaminoFileCollection.TensorEstimationWrapper
 
DxDataWriter - Class in edu.jhu.ece.iacl.algorithms.dti.tractography.FACT
 
DxDataWriter() - Constructor for class edu.jhu.ece.iacl.algorithms.dti.tractography.FACT.DxDataWriter
 
DxDataWriter - Class in edu.jhu.ece.iacl.jist.io
The Class DxDataWriter.
DxDataWriter() - Constructor for class edu.jhu.ece.iacl.jist.io.DxDataWriter
 
DXFiberData - Class in edu.jhu.ece.iacl.algorithms.dti.tractography.FACT
 
DXFiberData(Fiber[]) - Constructor for class edu.jhu.ece.iacl.algorithms.dti.tractography.FACT.DXFiberData
 
DXFiberData(Fiber[], Integer) - Constructor for class edu.jhu.ece.iacl.algorithms.dti.tractography.FACT.DXFiberData
 
DxFiberReaderWriter - Class in edu.jhu.ece.iacl.algorithms.dti.tractography.FACT
 
DxFiberReaderWriter() - Constructor for class edu.jhu.ece.iacl.algorithms.dti.tractography.FACT.DxFiberReaderWriter
 
DxReader - Class in edu.jhu.ece.iacl.jist.io
The Class DxReader.
DxReader() - Constructor for class edu.jhu.ece.iacl.jist.io.DxReader
 
DxSurfaceReader - Class in edu.jhu.ece.iacl.jist.io
The Class DxSurfaceReader.
DxSurfaceReader() - Constructor for class edu.jhu.ece.iacl.jist.io.DxSurfaceReader
 
DxSurfaceWriter - Class in edu.jhu.ece.iacl.jist.io
The Class DxSurfaceWriter.
DxSurfaceWriter() - Constructor for class edu.jhu.ece.iacl.jist.io.DxSurfaceWriter
 
DxWriter - Class in edu.jhu.ece.iacl.jist.io
The Class DxWriter.
DxWriter() - Constructor for class edu.jhu.ece.iacl.jist.io.DxWriter
 
dzungPham - Static variable in class edu.jhu.ece.iacl.algorithms.CommonAuthors
 

E

e1 - Variable in class edu.jhu.cs.cisst.algorithms.geometry.surface.IsoContourGenerator.EdgeSplit
The e2.
e1 - Variable in class edu.jhu.ece.iacl.jist.structures.geom.Triangle
The e3.
e2 - Variable in class edu.jhu.cs.cisst.algorithms.geometry.surface.IsoContourGenerator.EdgeSplit
The e2.
e2 - Variable in class edu.jhu.ece.iacl.jist.structures.geom.Triangle
The e3.
e3 - Variable in class edu.jhu.ece.iacl.jist.structures.geom.Triangle
The e3.
eauth - Variable in class edu.jhu.ece.iacl.jist.pipeline.view.input.AlgorithmInformationDialog.AuthorDialog
The author.
Edge - Class in edu.jhu.ece.iacl.jist.structures.geom
The Class Edge.
Edge(Vertex, Vertex) - Constructor for class edu.jhu.ece.iacl.jist.structures.geom.Edge
Instantiates a new edge.
EdgeIndexed - Class in edu.jhu.ece.iacl.jist.structures.geom
The Class EdgeIndexed.
EdgeIndexed(double) - Constructor for class edu.jhu.ece.iacl.jist.structures.geom.EdgeIndexed
Instantiates a new edge indexed.
edges - Variable in class edu.jhu.ece.iacl.jist.structures.geom.EmbeddedSurface
The edges.
edges - Variable in class edu.jhu.ece.iacl.jist.structures.geom.EmbeddedSurface.Face
The edges.
edges - Variable in class edu.jhu.ece.iacl.jist.structures.geom.Surface
The edges.
edges - Variable in class edu.jhu.ece.iacl.jist.structures.geom.Vertex
The edges.
edgeSelected - Variable in class edu.jhu.ece.iacl.jist.pipeline.graph.PipeMarqueeHandler
The edge selected.
edgeTable - Variable in class edu.jhu.ece.iacl.jist.structures.geom.EmbeddedSurface
The edge table.
editable - Variable in class edu.jhu.ece.iacl.jist.pipeline.AlgorithmInformation
Editable.
editable - Variable in class edu.jhu.ece.iacl.jist.pipeline.tree.PackageNode
The editable.
editable - Variable in class edu.jhu.ece.iacl.jist.pipeline.view.input.InformationListBox
Editable.
editItem(AlgorithmInformation.AlgorithmAuthor) - Method in class edu.jhu.ece.iacl.jist.pipeline.view.input.AlgorithmInformationDialog.AuthorListBox
Edge author.
editItem(AlgorithmInformation.Citation) - Method in class edu.jhu.ece.iacl.jist.pipeline.view.input.AlgorithmInformationDialog.CitationListBox
Edit citation.
editItem(T) - Method in class edu.jhu.ece.iacl.jist.pipeline.view.input.InformationListBox
Called when "EDIT" button is clicked.
editorComponent - Variable in class edu.jhu.ece.iacl.jist.pipeline.graph.PipeEdgeRealEditor
The Swing component being edited.
editorInsideCell - Static variable in class edu.jhu.ece.iacl.jist.pipeline.graph.PipeEdgeEditor
The editor inside cell.
edu.jhmi.rad.medic.libraries - package edu.jhmi.rad.medic.libraries
 
edu.jhmi.rad.medic.utilities - package edu.jhmi.rad.medic.utilities
Provides useful classes to perform simple operations.
edu.jhu.bme.smile.commons.math - package edu.jhu.bme.smile.commons.math
 
edu.jhu.bme.smile.commons.math.specialFunctions - package edu.jhu.bme.smile.commons.math.specialFunctions
 
edu.jhu.bme.smile.commons.optimize - package edu.jhu.bme.smile.commons.optimize
 
edu.jhu.bme.smile.commons.optimize.tensor - package edu.jhu.bme.smile.commons.optimize.tensor
 
edu.jhu.bme.smile.commons.optimize.test - package edu.jhu.bme.smile.commons.optimize.test
 
edu.jhu.bme.smile.commons.textfiles - package edu.jhu.bme.smile.commons.textfiles
 
edu.jhu.bme.smile.demo - package edu.jhu.bme.smile.demo
 
edu.jhu.cs.cisst.algorithms.geometry.surface - package edu.jhu.cs.cisst.algorithms.geometry.surface
 
edu.jhu.cs.cisst.algorithms.optimize.fmg - package edu.jhu.cs.cisst.algorithms.optimize.fmg
 
edu.jhu.cs.cisst.algorithms.optimize.fmg.grid - package edu.jhu.cs.cisst.algorithms.optimize.fmg.grid
 
edu.jhu.cs.cisst.algorithms.optimize.fmg.interpolator - package edu.jhu.cs.cisst.algorithms.optimize.fmg.interpolator
 
edu.jhu.cs.cisst.algorithms.optimize.fmg.parallel - package edu.jhu.cs.cisst.algorithms.optimize.fmg.parallel
 
edu.jhu.cs.cisst.algorithms.optimize.fmg.pde - package edu.jhu.cs.cisst.algorithms.optimize.fmg.pde
 
edu.jhu.cs.cisst.algorithms.optimize.fmg.restrictor - package edu.jhu.cs.cisst.algorithms.optimize.fmg.restrictor
 
edu.jhu.cs.cisst.algorithms.optimize.fmg.smoother - package edu.jhu.cs.cisst.algorithms.optimize.fmg.smoother
 
edu.jhu.cs.cisst.algorithms.optimize.fmg.solver - package edu.jhu.cs.cisst.algorithms.optimize.fmg.solver
 
edu.jhu.cs.cisst.algorithms.optimize.fmg.util - package edu.jhu.cs.cisst.algorithms.optimize.fmg.util
 
edu.jhu.cs.cisst.algorithms.segmentation.gac - package edu.jhu.cs.cisst.algorithms.segmentation.gac
 
edu.jhu.cs.cisst.algorithms.util - package edu.jhu.cs.cisst.algorithms.util
 
edu.jhu.cs.cisst.plugins.classification - package edu.jhu.cs.cisst.plugins.classification
 
edu.jhu.cs.cisst.plugins.segmentation - package edu.jhu.cs.cisst.plugins.segmentation
 
edu.jhu.cs.cisst.plugins.utilities.file - package edu.jhu.cs.cisst.plugins.utilities.file
 
edu.jhu.cs.cisst.plugins.utilities.surface - package edu.jhu.cs.cisst.plugins.utilities.surface
 
edu.jhu.cs.cisst.plugins.visualization - package edu.jhu.cs.cisst.plugins.visualization
 
edu.jhu.cs.cisst.test - package edu.jhu.cs.cisst.test
 
edu.jhu.cs.cisst.test.data - package edu.jhu.cs.cisst.test.data
 
edu.jhu.cs.cisst.vent - package edu.jhu.cs.cisst.vent
 
edu.jhu.cs.cisst.vent.converter - package edu.jhu.cs.cisst.vent.converter
 
edu.jhu.cs.cisst.vent.converter.processing - package edu.jhu.cs.cisst.vent.converter.processing
 
edu.jhu.cs.cisst.vent.renderer.processing - package edu.jhu.cs.cisst.vent.renderer.processing
 
edu.jhu.cs.cisst.vent.resources - package edu.jhu.cs.cisst.vent.resources
 
edu.jhu.cs.cisst.vent.structures.processing - package edu.jhu.cs.cisst.vent.structures.processing
 
edu.jhu.cs.cisst.vent.widgets - package edu.jhu.cs.cisst.vent.widgets
 
edu.jhu.ece.iacl.algorithms - package edu.jhu.ece.iacl.algorithms
 
edu.jhu.ece.iacl.algorithms.dti - package edu.jhu.ece.iacl.algorithms.dti
 
edu.jhu.ece.iacl.algorithms.dti.tractography - package edu.jhu.ece.iacl.algorithms.dti.tractography
 
edu.jhu.ece.iacl.algorithms.dti.tractography.FACT - package edu.jhu.ece.iacl.algorithms.dti.tractography.FACT
 
edu.jhu.ece.iacl.algorithms.hardi - package edu.jhu.ece.iacl.algorithms.hardi
 
edu.jhu.ece.iacl.algorithms.manual_label - package edu.jhu.ece.iacl.algorithms.manual_label
 
edu.jhu.ece.iacl.algorithms.manual_label.atlasing - package edu.jhu.ece.iacl.algorithms.manual_label.atlasing
 
edu.jhu.ece.iacl.algorithms.manual_label.simulation - package edu.jhu.ece.iacl.algorithms.manual_label.simulation
 
edu.jhu.ece.iacl.algorithms.manual_label.staple - package edu.jhu.ece.iacl.algorithms.manual_label.staple
 
edu.jhu.ece.iacl.algorithms.registration - package edu.jhu.ece.iacl.algorithms.registration
 
edu.jhu.ece.iacl.algorithms.spectro - package edu.jhu.ece.iacl.algorithms.spectro
 
edu.jhu.ece.iacl.algorithms.vabra - package edu.jhu.ece.iacl.algorithms.vabra
 
edu.jhu.ece.iacl.algorithms.volume - package edu.jhu.ece.iacl.algorithms.volume
 
edu.jhu.ece.iacl.doc - package edu.jhu.ece.iacl.doc
 
edu.jhu.ece.iacl.jist.algorithms.graphics - package edu.jhu.ece.iacl.jist.algorithms.graphics
Provides...
edu.jhu.ece.iacl.jist.cli - package edu.jhu.ece.iacl.jist.cli
 
edu.jhu.ece.iacl.jist.dialogs - package edu.jhu.ece.iacl.jist.dialogs
Provides...
edu.jhu.ece.iacl.jist.io - package edu.jhu.ece.iacl.jist.io
Provides...
edu.jhu.ece.iacl.jist.pipeline - package edu.jhu.ece.iacl.jist.pipeline
Contains components for the CRUISE Control Pipeline.
edu.jhu.ece.iacl.jist.pipeline.dest - package edu.jhu.ece.iacl.jist.pipeline.dest
Contains destinations to direct output of graph modules.
edu.jhu.ece.iacl.jist.pipeline.factory - package edu.jhu.ece.iacl.jist.pipeline.factory
Contains components for the CRUISE Control Pipeline.
edu.jhu.ece.iacl.jist.pipeline.graph - package edu.jhu.ece.iacl.jist.pipeline.graph
Contains customized extensions to JGraph's API for MAPS layout tool.
edu.jhu.ece.iacl.jist.pipeline.gui - package edu.jhu.ece.iacl.jist.pipeline.gui
Contains GUI applications for MAPS
edu.jhu.ece.iacl.jist.pipeline.gui.resources - package edu.jhu.ece.iacl.jist.pipeline.gui.resources
 
edu.jhu.ece.iacl.jist.pipeline.parameter - package edu.jhu.ece.iacl.jist.pipeline.parameter
Contains factories for manipulating parameter values.
edu.jhu.ece.iacl.jist.pipeline.parser - package edu.jhu.ece.iacl.jist.pipeline.parser
Contains parsers to read third party file types.
edu.jhu.ece.iacl.jist.pipeline.src - package edu.jhu.ece.iacl.jist.pipeline.src
Contains sources that generate multiple values to feed experiments that are run repeatedly with different values.
edu.jhu.ece.iacl.jist.pipeline.tree - package edu.jhu.ece.iacl.jist.pipeline.tree
Contains tree components to display in module panel.
edu.jhu.ece.iacl.jist.pipeline.view.input - package edu.jhu.ece.iacl.jist.pipeline.view.input
Contains GUI views to input parameter values.
edu.jhu.ece.iacl.jist.pipeline.view.output - package edu.jhu.ece.iacl.jist.pipeline.view.output
Contains GUI views to output parameter values.
edu.jhu.ece.iacl.jist.plugins - package edu.jhu.ece.iacl.jist.plugins
Provides...
edu.jhu.ece.iacl.jist.plugins.testing - package edu.jhu.ece.iacl.jist.plugins.testing
 
edu.jhu.ece.iacl.jist.processcontrol - package edu.jhu.ece.iacl.jist.processcontrol
Provides...
edu.jhu.ece.iacl.jist.structures.data - package edu.jhu.ece.iacl.jist.structures.data
Provides...
edu.jhu.ece.iacl.jist.structures.fiber - package edu.jhu.ece.iacl.jist.structures.fiber
Provides...
edu.jhu.ece.iacl.jist.structures.geom - package edu.jhu.ece.iacl.jist.structures.geom
Provides...
edu.jhu.ece.iacl.jist.structures.image - package edu.jhu.ece.iacl.jist.structures.image
Provides...
edu.jhu.ece.iacl.jist.structures.matrix - package edu.jhu.ece.iacl.jist.structures.matrix
Provides...
edu.jhu.ece.iacl.jist.structures.tensor - package edu.jhu.ece.iacl.jist.structures.tensor
Provides...
edu.jhu.ece.iacl.jist.structures.vector - package edu.jhu.ece.iacl.jist.structures.vector
Provides...
edu.jhu.ece.iacl.jist.test - package edu.jhu.ece.iacl.jist.test
Provides...
edu.jhu.ece.iacl.jist.utility - package edu.jhu.ece.iacl.jist.utility
Provides...
edu.jhu.ece.iacl.pami - package edu.jhu.ece.iacl.pami
 
edu.jhu.ece.iacl.plugins - package edu.jhu.ece.iacl.plugins
 
edu.jhu.ece.iacl.plugins.dti - package edu.jhu.ece.iacl.plugins.dti
 
edu.jhu.ece.iacl.plugins.dti.tractography - package edu.jhu.ece.iacl.plugins.dti.tractography
 
edu.jhu.ece.iacl.plugins.hardi - package edu.jhu.ece.iacl.plugins.hardi
 
edu.jhu.ece.iacl.plugins.labeling - package edu.jhu.ece.iacl.plugins.labeling
 
edu.jhu.ece.iacl.plugins.labeling.atlasing - package edu.jhu.ece.iacl.plugins.labeling.atlasing
 
edu.jhu.ece.iacl.plugins.labeling.simulation - package edu.jhu.ece.iacl.plugins.labeling.simulation
 
edu.jhu.ece.iacl.plugins.labeling.staple - package edu.jhu.ece.iacl.plugins.labeling.staple
 
edu.jhu.ece.iacl.plugins.quantitative - package edu.jhu.ece.iacl.plugins.quantitative
 
edu.jhu.ece.iacl.plugins.registration - package edu.jhu.ece.iacl.plugins.registration
 
edu.jhu.ece.iacl.plugins.segmentation - package edu.jhu.ece.iacl.plugins.segmentation
 
edu.jhu.ece.iacl.plugins.spectro - package edu.jhu.ece.iacl.plugins.spectro
 
edu.jhu.ece.iacl.plugins.utilities.file - package edu.jhu.ece.iacl.plugins.utilities.file
 
edu.jhu.ece.iacl.plugins.utilities.logic - package edu.jhu.ece.iacl.plugins.utilities.logic
 
edu.jhu.ece.iacl.plugins.utilities.math - package edu.jhu.ece.iacl.plugins.utilities.math
 
edu.jhu.ece.iacl.plugins.utilities.roi - package edu.jhu.ece.iacl.plugins.utilities.roi
 
edu.jhu.ece.iacl.plugins.utilities.surface - package edu.jhu.ece.iacl.plugins.utilities.surface
 
edu.jhu.ece.iacl.plugins.utilities.volume - package edu.jhu.ece.iacl.plugins.utilities.volume
 
edu.jhu.ece.iacl.structures.image - package edu.jhu.ece.iacl.structures.image
 
edu.jhu.ece.iacl.utility - package edu.jhu.ece.iacl.utility
 
edu.vanderbilt.masi.plugins.utilities.volume - package edu.vanderbilt.masi.plugins.utilities.volume
 
eigenvalues3D(float[][]) - Static method in class edu.jhmi.rad.medic.utilities.NumericsPublic
Close-form 3D matrix eigenvalues.
eigenvalues3D(double[][]) - Static method in class edu.jhmi.rad.medic.utilities.NumericsPublic
Close-form 3D matrix eigenvalues.
eigenvectors3D(float[][], float[]) - Static method in class edu.jhmi.rad.medic.utilities.NumericsPublic
Simple geometric technique to get eigenvectors of 3D matrices.
eigenvectors3D(double[][], double[]) - Static method in class edu.jhmi.rad.medic.utilities.NumericsPublic
Simple geometric technique to get eigenvectors of 3D matrices.
elapsed - Variable in class edu.jhu.ece.iacl.jist.pipeline.PerformanceSummary.TimeAndMemoryStamp
Elapsed time in milliseconds.
elementInverse(Matrix) - Static method in class edu.jhu.bme.smile.commons.math.MatrixMath
 
elementProduct(Matrix, Matrix) - Static method in class edu.jhu.bme.smile.commons.math.MatrixMath
 
email - Variable in class edu.jhu.ece.iacl.jist.pipeline.AlgorithmInformation.AlgorithmAuthor
The email.
email - Variable in class edu.jhu.ece.iacl.jist.pipeline.view.input.AlgorithmInformationDialog.AuthorDialog
The website.
EmbeddedCurvePath - Class in edu.jhu.ece.iacl.jist.structures.geom
The Class EmbeddedCurvePath.
EmbeddedCurvePath() - Constructor for class edu.jhu.ece.iacl.jist.structures.geom.EmbeddedCurvePath
Instantiates a new embedded curve path.
embeddedDataType - Variable in class edu.jhu.ece.iacl.plugins.utilities.surface.MedicAlgorithmSurfaceHistogram
 
EmbeddedPointSet - Class in edu.jhu.ece.iacl.jist.structures.geom
The Class EmbeddedPointSet.
EmbeddedPointSet() - Constructor for class edu.jhu.ece.iacl.jist.structures.geom.EmbeddedPointSet
Instantiates a new embedded point set.
EmbeddedPointSet(Point3f[]) - Constructor for class edu.jhu.ece.iacl.jist.structures.geom.EmbeddedPointSet
Instantiates a new embedded point set.
EmbeddedPointSet(Point3f[], int[]) - Constructor for class edu.jhu.ece.iacl.jist.structures.geom.EmbeddedPointSet
Instantiates a new embedded point set.
EmbeddedPointSet(Point3f[], int[], int[]) - Constructor for class edu.jhu.ece.iacl.jist.structures.geom.EmbeddedPointSet
Instantiates a new embedded point set.
EmbeddedPointSet.PointLocatorResult - Class in edu.jhu.ece.iacl.jist.structures.geom
The Class PointLocatorResult.
EmbeddedPointSet.PointLocatorResult() - Constructor for class edu.jhu.ece.iacl.jist.structures.geom.EmbeddedPointSet.PointLocatorResult
 
EmbeddedSurface - Class in edu.jhu.ece.iacl.jist.structures.geom
The Class EmbeddedSurface.
EmbeddedSurface(EmbeddedSurface) - Constructor for class edu.jhu.ece.iacl.jist.structures.geom.EmbeddedSurface
Instantiates a new embedded surface.
EmbeddedSurface(EmbeddedSurface, double[][]) - Constructor for class edu.jhu.ece.iacl.jist.structures.geom.EmbeddedSurface
Instantiates a new embedded surface.
EmbeddedSurface(ModelTriangleMesh) - Constructor for class edu.jhu.ece.iacl.jist.structures.geom.EmbeddedSurface
Instantiates a new embedded surface.
EmbeddedSurface(ModelTriangleMesh, double[][]) - Constructor for class edu.jhu.ece.iacl.jist.structures.geom.EmbeddedSurface
Instantiates a new embedded surface.
EmbeddedSurface(Point3f[], int[]) - Constructor for class edu.jhu.ece.iacl.jist.structures.geom.EmbeddedSurface
Instantiates a new embedded surface.
EmbeddedSurface(Point3f[], int[], double[][]) - Constructor for class edu.jhu.ece.iacl.jist.structures.geom.EmbeddedSurface
Instantiates a new embedded surface.
EmbeddedSurface(Point3f[], Vector3f[], Color3f[], int[]) - Constructor for class edu.jhu.ece.iacl.jist.structures.geom.EmbeddedSurface
Instantiates a new embedded surface.
EmbeddedSurface(Point3f[], Vector3f[], Color3f[], int[], double[][]) - Constructor for class edu.jhu.ece.iacl.jist.structures.geom.EmbeddedSurface
Instantiates a new embedded surface.
EmbeddedSurface(Point3f[], Vector3f[], Color4f[], int[]) - Constructor for class edu.jhu.ece.iacl.jist.structures.geom.EmbeddedSurface
Instantiates a new embedded surface.
EmbeddedSurface(Point3f[], Vector3f[], Color4f[], int[], double[][]) - Constructor for class edu.jhu.ece.iacl.jist.structures.geom.EmbeddedSurface
Instantiates a new embedded surface.
EmbeddedSurface(Point3f[], Vector3f[], int[]) - Constructor for class edu.jhu.ece.iacl.jist.structures.geom.EmbeddedSurface
Instantiates a new embedded surface.
EmbeddedSurface(Point3f[], Vector3f[], int[], double[][]) - Constructor for class edu.jhu.ece.iacl.jist.structures.geom.EmbeddedSurface
Instantiates a new embedded surface.
EmbeddedSurface.Direction - Enum in edu.jhu.ece.iacl.jist.structures.geom
The Enum Direction.
EmbeddedSurface.Edge - Class in edu.jhu.ece.iacl.jist.structures.geom
The Class Edge.
EmbeddedSurface.Edge(int, int, int) - Constructor for class edu.jhu.ece.iacl.jist.structures.geom.EmbeddedSurface.Edge
Instantiates a new edge.
EmbeddedSurface.EdgeSplit - Class in edu.jhu.ece.iacl.jist.structures.geom
The Class EdgeSplit.
EmbeddedSurface.EdgeSplit(EmbeddedSurface.Edge, int) - Constructor for class edu.jhu.ece.iacl.jist.structures.geom.EmbeddedSurface.EdgeSplit
Instantiates a new edge split.
EmbeddedSurface.EdgeSplit(int, int, int, int) - Constructor for class edu.jhu.ece.iacl.jist.structures.geom.EmbeddedSurface.EdgeSplit
Instantiates a new edge split.
EmbeddedSurface.Face - Class in edu.jhu.ece.iacl.jist.structures.geom
The Class Face.
EmbeddedSurface.Face(EmbeddedSurface.Edge, EmbeddedSurface.Edge, EmbeddedSurface.Edge, int) - Constructor for class edu.jhu.ece.iacl.jist.structures.geom.EmbeddedSurface.Face
Instantiates a new face.
EmbeddedSurface.Face(int) - Constructor for class edu.jhu.ece.iacl.jist.structures.geom.EmbeddedSurface.Face
Instantiates a new face.
EmbeddedSurface.Face(int, int, int, int) - Constructor for class edu.jhu.ece.iacl.jist.structures.geom.EmbeddedSurface.Face
Instantiates a new face.
enable() - Method in class edu.jhu.ece.iacl.jist.pipeline.view.input.Refresher
 
enableRelative(boolean) - Method in class edu.jhu.ece.iacl.jist.pipeline.gui.LayoutPreferencePanel
Enable relative.
encodeName(String) - Static method in class edu.jhu.ece.iacl.jist.pipeline.factory.ParamFactory
Encode name.
encodeValue(Object) - Static method in class edu.jhu.ece.iacl.jist.pipeline.factory.ParamFactory
Encode value.
encounteredParseError() - Method in class edu.jhu.ece.iacl.jist.cli.JistCLI
 
end - Variable in class edu.jhu.ece.iacl.jist.pipeline.src.PipeDoubleSweepSource
The end.
end - Variable in class edu.jhu.ece.iacl.jist.pipeline.src.PipeIntegerSweepSource
The end.
end - Variable in class edu.jhu.ece.iacl.jist.pipeline.src.PipePointDoubleSweepSource
The end.
end - Variable in class edu.jhu.ece.iacl.jist.pipeline.src.PipeToggleSource
The end.
endElement(String, String, String) - Method in class edu.jhu.ece.iacl.algorithms.vabra.VabraConfiguration
 
endEntry - Variable in class edu.jhu.ece.iacl.jist.pipeline.src.PipeListCollectionSource
The end entry.
endEntry - Variable in class edu.jhu.ece.iacl.jist.pipeline.src.PipeListSource
The end entry.
endianess - Variable in class edu.jhu.ece.iacl.jist.structures.image.ImageHeader
The endianess.
endParam - Variable in class edu.jhu.ece.iacl.jist.pipeline.src.PipeDoubleSweepSource
The val param.
endParam - Variable in class edu.jhu.ece.iacl.jist.pipeline.src.PipeIntegerSweepSource
The val param.
endParam - Variable in class edu.jhu.ece.iacl.jist.pipeline.src.PipePointDoubleSweepSource
The val param.
enqueue() - Method in class edu.jhu.ece.iacl.jist.pipeline.PipeScheduler
Enqueue all waiting processes.
enqueue(Vector<ExecutionContext>) - Method in class edu.jhu.ece.iacl.jist.pipeline.PipeScheduler
Enqueue processes in queue.
ENUMERATION_TAG - Static variable in class edu.jhu.ece.iacl.jist.pipeline.parser.LoniPipeParser
The Constant ENUMERATION_TAG.
eps - Variable in class edu.jhu.ece.iacl.algorithms.manual_label.staple.STAPLEgeneral
 
eps - Variable in class edu.jhu.ece.iacl.algorithms.manual_label.staple.STAPLEmulti
 
eps - Variable in class edu.jhu.ece.iacl.algorithms.manual_label.staple.STAPLEmulti2
 
eps - Variable in class edu.jhu.ece.iacl.algorithms.manual_label.staple.STAPLEsingle
 
eps - Variable in class edu.jhu.ece.iacl.algorithms.manual_label.staple.STAPLEsurf
 
EPS - Static variable in class edu.jhu.ece.iacl.jist.structures.geom.TriangleSigned
The EPS.
EPSILON - Static variable in class edu.jhu.ece.iacl.algorithms.dti.tractography.FACT.triangulate
 
equals(IsoContourGenerator.EdgeSplit) - Method in class edu.jhu.cs.cisst.algorithms.geometry.surface.IsoContourGenerator.EdgeSplit
Compare two edge splits.
equals(IsoSurfaceGenerator.EdgeSplit) - Method in class edu.jhu.cs.cisst.algorithms.geometry.surface.IsoSurfaceGenerator.EdgeSplit
Compare two edge splits.
equals(cPT) - Method in class edu.jhu.ece.iacl.algorithms.dti.tractography.FACT.cPT
 
equals(VEC) - Method in class edu.jhu.ece.iacl.algorithms.dti.tractography.FACT.VEC
 
equals(Object) - Method in class edu.jhu.ece.iacl.jist.io.FileExtensionFilter
 
equals(AlgorithmInformation) - Method in class edu.jhu.ece.iacl.jist.pipeline.AlgorithmInformation
Equals.
equals(Object) - Method in class edu.jhu.ece.iacl.jist.pipeline.ExecutionContext
Check if contexts are equal by comparing context names.
equals(Object) - Method in class edu.jhu.ece.iacl.jist.pipeline.factory.ParamCollectionFactory
 
equals(Object) - Method in class edu.jhu.ece.iacl.jist.pipeline.factory.ParamFactory
 
equals(Object) - Method in class edu.jhu.ece.iacl.jist.pipeline.factory.ParamFileCollectionFactory
 
equals(Object) - Method in class edu.jhu.ece.iacl.jist.pipeline.factory.ParamNumberCollectionFactory
 
equals(Object) - Method in class edu.jhu.ece.iacl.jist.pipeline.factory.ParamSurfaceCollectionFactory
 
equals(Object) - Method in class edu.jhu.ece.iacl.jist.pipeline.factory.ParamVolumeCollectionFactory
 
equals(Object) - Method in class edu.jhu.ece.iacl.jist.pipeline.factory.ParamVolumeFactory
 
equals(Object) - Method in class edu.jhu.ece.iacl.jist.pipeline.factory.ParamWeightedVolumeCollectionFactory
 
equals(Object) - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.DataLabel
Returns true if two data labels are equal.
equals(ParamModel<Boolean>) - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamBoolean
 
equals(ParamModel<Vector<ParamModel>>) - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamCollection
 
equals(ParamModel<Class>) - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamHeader
 
equals(ParamModel<AlgorithmInformation>) - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamInformation
 
equals(ParamModel<Matrix>) - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamMatrix
 
equals(ParamModel<T>) - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamModel
 
equals(ParamModel<Number>) - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamNumber
 
equals(Object) - Method in class edu.jhu.ece.iacl.jist.pipeline.view.input.ParamVolumeInputView.VolumeListBoxItem
 
equals(Object) - Method in class edu.jhu.ece.iacl.jist.pipeline.view.input.ParamVolumeURIInputView.VolumeListBoxItem
 
equals(Fiber) - Method in class edu.jhu.ece.iacl.jist.structures.fiber.Fiber
Equals.
equals(Object) - Method in class edu.jhu.ece.iacl.jist.structures.geom.Edge
 
equals(int, int) - Method in class edu.jhu.ece.iacl.jist.structures.geom.EmbeddedSurface.Edge
Equals.
equals(Object) - Method in class edu.jhu.ece.iacl.jist.structures.geom.EmbeddedSurface.Edge
 
equals(Object) - Method in class edu.jhu.ece.iacl.jist.structures.geom.Face
 
equals(GridPt) - Method in class edu.jhu.ece.iacl.jist.structures.geom.GridPt
Equals.
equals(PT) - Method in class edu.jhu.ece.iacl.jist.structures.geom.PT
Equals.
equals(Object) - Method in class edu.jhu.ece.iacl.jist.structures.geom.Triangle
 
equals(Object) - Method in class edu.jhu.ece.iacl.jist.structures.geom.TriangleFace
 
equals(Object) - Method in class edu.jhu.ece.iacl.jist.structures.geom.Vertex
 
equals(Object) - Method in class edu.jhu.ece.iacl.jist.structures.image.Voxel
 
equalVolume(Object) - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamVolume
Compare parameter volumes by model image names.
eraseCacheContext(ExecutionContext) - Method in class edu.jhu.ece.iacl.jist.pipeline.gui.ProcessInfoPanel
Erase cache storing last context.
error(SAXParseException) - Method in class edu.jhu.ece.iacl.jist.io.XMLErrorHandler
Handles parse exception errors by passing the parse exception up as a SAXException.
Estep() - Method in class edu.jhu.ece.iacl.algorithms.manual_label.staple.STAPLE
Estimate the true segmentation based on the rater segmentations and reliabilities using Equansions (14)-(16)
Estep() - Method in class edu.jhu.ece.iacl.algorithms.manual_label.staple.STAPLEgeneral
 
Estep() - Method in class edu.jhu.ece.iacl.algorithms.manual_label.staple.STAPLEgeneralSingle
 
Estep() - Method in class edu.jhu.ece.iacl.algorithms.manual_label.staple.STAPLEmulti
 
Estep() - Method in class edu.jhu.ece.iacl.algorithms.manual_label.staple.STAPLEmulti2
 
Estep() - Method in class edu.jhu.ece.iacl.algorithms.manual_label.staple.STAPLEsingle
 
Estep() - Method in class edu.jhu.ece.iacl.algorithms.manual_label.staple.STAPLEsurf
 
EstepEfficient() - Method in class edu.jhu.ece.iacl.algorithms.manual_label.staple.STAPLEmulti
 
EstepEfficient() - Method in class edu.jhu.ece.iacl.algorithms.manual_label.staple.STAPLEmulti2
 
estimate(float[][][][], float[][][], float[][][], float[][][][], float[], float[][], byte[][][], double[]) - Static method in class edu.jhu.ece.iacl.algorithms.dti.EstimateTensorLikelihood
 
estimate(float[][][][], float[], float[][], byte[][][], boolean) - Static method in class edu.jhu.ece.iacl.algorithms.dti.EstimateTensorLLMSE
estimate Use LLMSE to estimate tensors from DW imaging data on a voxel-wise basis.
estimateBallAndStickCamino(float[][][][], byte[][][], BallStickInversion, float[][][][], float[][][][], float[][][][], float[][][][], float[][][][]) - Static method in class edu.jhu.ece.iacl.algorithms.dti.EstimateTensorLLMSE
 
estimateCamino(float[][][][], byte[][][], DT_Inversion, float[][][][], float[][][][], float[][][][]) - Static method in class edu.jhu.ece.iacl.algorithms.dti.EstimateTensorLLMSE
 
estimateCaminoRESTORE(float[][][][], byte[][][], float[][][], float[][][][], float[][][][], float[][][][], Scheme) - Static method in class edu.jhu.ece.iacl.algorithms.dti.EstimateTensorLLMSE
 
estimateCaminoThreeTensor(float[][][][], byte[][][], ThreeTensorInversion, float[][][][], float[][][][], float[][][][], float[][][][], float[][][][], float[][][][], float[][][][], float[][][][]) - Static method in class edu.jhu.ece.iacl.algorithms.dti.EstimateTensorLLMSE
 
estimateCaminoTwoTensor(float[][][][], byte[][][], TwoTensorInversion, float[][][][], float[][][][], float[][][][], float[][][][], float[][][][], float[][][][]) - Static method in class edu.jhu.ece.iacl.algorithms.dti.EstimateTensorLLMSE
 
estimateCFARI(float[][][][], byte[][][], CFARIBasisSet, float[][][][], float[][][][], boolean, double) - Static method in class edu.jhu.ece.iacl.algorithms.hardi.CFARIEstimator
 
estimateCFARI(float[][][][], byte[][][], CFARIBasisSet, double, int[][][][], float[][][][], double, int[], int[], CFARIEstimation2.CFARIWrapper) - Static method in class edu.jhu.ece.iacl.algorithms.hardi.CFARIEstimator2
 
estimateCFARIList(float[][][][], byte[][][], CFARIBasisSet, double, int[][][][], float[][][][], double, int[], ArrayList<int[]>, CFARIEstimation2.CFARIWrapper) - Static method in class edu.jhu.ece.iacl.algorithms.hardi.CFARIEstimator2
 
estimateCFARIModel(L1LSCompressedSensing, double[], CFARIBasisSet, double, int[], float[], double, int[], CFARIEstimation2.CFARIWrapper) - Static method in class edu.jhu.ece.iacl.algorithms.hardi.CFARIEstimator2
 
EstimateMTR - Class in edu.jhu.ece.iacl.plugins.quantitative
 
EstimateMTR() - Constructor for class edu.jhu.ece.iacl.plugins.quantitative.EstimateMTR
 
EstimateMTR.AlgorithmWrapper - Class in edu.jhu.ece.iacl.plugins.quantitative
 
EstimateMTR.AlgorithmWrapper() - Constructor for class edu.jhu.ece.iacl.plugins.quantitative.EstimateMTR.AlgorithmWrapper
 
EstimateMTRseries - Class in edu.jhu.ece.iacl.plugins.quantitative
 
EstimateMTRseries() - Constructor for class edu.jhu.ece.iacl.plugins.quantitative.EstimateMTRseries
 
EstimateMTRseries.AlgorithmWrapper - Class in edu.jhu.ece.iacl.plugins.quantitative
 
EstimateMTRseries.AlgorithmWrapper() - Constructor for class edu.jhu.ece.iacl.plugins.quantitative.EstimateMTRseries.AlgorithmWrapper
 
estimateSphericalHarmonics(float[][][][], float[][][][], int[][], float[][][][], float[], float[][], byte[][][], int, float) - Static method in class edu.jhu.ece.iacl.algorithms.hardi.QBall
Proportional to b0
estimateSphericalHarmonicsADC(float[][][][], float[][][][], int[][], float[][][][], float[], float[][], byte[][][], int, float) - Static method in class edu.jhu.ece.iacl.algorithms.hardi.QBall
ADC: Apparent Diffusivity
estimateSphericalHarmonicsFRT(float[][][][], int[][], float[][][][], float[], float[][], byte[][][], int, float, float) - Static method in class edu.jhu.ece.iacl.algorithms.hardi.QBall
Funk-Radon Transform
EstimateT1FromDoubleAngle - Class in edu.jhu.ece.iacl.plugins.quantitative
 
EstimateT1FromDoubleAngle() - Constructor for class edu.jhu.ece.iacl.plugins.quantitative.EstimateT1FromDoubleAngle
 
EstimateT1FromDoubleAngle.AlgorithmWrapper - Class in edu.jhu.ece.iacl.plugins.quantitative
 
EstimateT1FromDoubleAngle.AlgorithmWrapper() - Constructor for class edu.jhu.ece.iacl.plugins.quantitative.EstimateT1FromDoubleAngle.AlgorithmWrapper
 
EstimateT2FromDualEcho - Class in edu.jhu.ece.iacl.plugins.quantitative
 
EstimateT2FromDualEcho() - Constructor for class edu.jhu.ece.iacl.plugins.quantitative.EstimateT2FromDualEcho
 
EstimateT2FromDualEcho.AlgorithmWrapper - Class in edu.jhu.ece.iacl.plugins.quantitative
 
EstimateT2FromDualEcho.AlgorithmWrapper() - Constructor for class edu.jhu.ece.iacl.plugins.quantitative.EstimateT2FromDualEcho.AlgorithmWrapper
 
EstimateTensorLikelihood - Class in edu.jhu.ece.iacl.algorithms.dti
 
EstimateTensorLikelihood() - Constructor for class edu.jhu.ece.iacl.algorithms.dti.EstimateTensorLikelihood
 
EstimateTensorLLMSE - Class in edu.jhu.ece.iacl.algorithms.dti
 
EstimateTensorLLMSE() - Constructor for class edu.jhu.ece.iacl.algorithms.dti.EstimateTensorLLMSE
 
eulerCharacteristicDensities - Static variable in class edu.jhu.ece.iacl.algorithms.ReferencedPapers
 
eulerLagrangeThickness - Static variable in class edu.jhu.ece.iacl.algorithms.ReferencedPapers
 
eulerThickness - Static variable in class edu.jhu.ece.iacl.algorithms.ReferencedPapers
 
evals() - Method in class edu.jhu.ece.iacl.algorithms.dti.DiffusionTensor
 
evaluate(ConstBoundaryGrid, ConstNoBoundaryGrid, int, int, int) - Method in interface edu.jhu.cs.cisst.algorithms.optimize.fmg.pde.PDE
evaluate the solution u of the PDE for a given interior grid element on a grid of a specific size.
evaluate(int, int) - Method in class edu.jhu.cs.cisst.algorithms.segmentation.gac.ActiveContourForce2D
Evaluate the force at a particular grid point position.
evaluate(int, int) - Method in class edu.jhu.cs.cisst.algorithms.segmentation.gac.AdvectionForce2D
 
evaluate(int, int) - Method in class edu.jhu.cs.cisst.algorithms.segmentation.gac.GaussianCurvatureForce2D
 
evaluate(int, int) - Method in class edu.jhu.cs.cisst.algorithms.segmentation.gac.MeanCurvatureForce2D
 
evaluate(int, int) - Method in class edu.jhu.cs.cisst.algorithms.segmentation.gac.PressureForce2D
 
evaluate(ConstBoundaryGrid, ConstNoBoundaryGrid, int, int, int) - Method in class edu.jhu.cs.cisst.algorithms.segmentation.gac.VectorFieldDiffusion2D
implements method from PDE.
evaluateLHS(ConstBoundaryGrid, ConstNoBoundaryGrid, int, int, int) - Method in interface edu.jhu.cs.cisst.algorithms.optimize.fmg.pde.PDE
evaluate the left hand side of the discretized PDE for a given interior grid element on a grid of a specific size.
evaluateLHS(ConstBoundaryGrid, ConstNoBoundaryGrid, int, int, int) - Method in class edu.jhu.cs.cisst.algorithms.segmentation.gac.VectorFieldDiffusion2D
implements method from PDE.
evenOrderTransform(int, double[], double[]) - Static method in class edu.jhu.bme.smile.commons.math.specialFunctions.SphericalHarmonics
 
evenOrderTransform(int, float[][]) - Static method in class edu.jhu.bme.smile.commons.math.specialFunctions.SphericalHarmonics
 
exclusiveMaskInterpolation(boolean[][][], float, float, float, int, int, int) - Static method in class edu.jhmi.rad.medic.libraries.ImageFunctionsPublic
interpolate a computation mask: where there is no data, the mask is set to false (generates a mask that is contained in the transformed image)
execute(CalculationMonitor) - Method in class edu.jhu.bme.smile.demo.AddingNoise
 
execute(CalculationMonitor) - Method in class edu.jhu.bme.smile.demo.ChebyShevFitting
 
execute(CalculationMonitor) - Method in class edu.jhu.bme.smile.demo.FirstPluginTest
 
execute(CalculationMonitor) - Method in class edu.jhu.bme.smile.demo.ImageAlgebra
 
execute(CalculationMonitor) - Method in class edu.jhu.bme.smile.demo.ImageArithmetic
 
execute(CalculationMonitor) - Method in class edu.jhu.bme.smile.demo.ImageCollectionAlgebra
 
execute(CalculationMonitor) - Method in class edu.jhu.bme.smile.demo.MemoryDemo
 
execute(CalculationMonitor) - Method in class edu.jhu.bme.smile.demo.RandomVol
 
execute(CalculationMonitor) - Method in class edu.jhu.bme.smile.demo.ScaleImageDemo
 
execute(CalculationMonitor) - Method in class edu.jhu.cs.cisst.plugins.classification.PlugInFuzzyMembershipThreshold2D
 
execute(CalculationMonitor) - Method in class edu.jhu.cs.cisst.plugins.segmentation.PlugInCircleLevelSet
 
execute(CalculationMonitor) - Method in class edu.jhu.cs.cisst.plugins.segmentation.PlugInGeodesicActiveContour2D
 
execute(CalculationMonitor) - Method in class edu.jhu.cs.cisst.plugins.segmentation.PlugInGradientVectorFlow2D
 
execute(CalculationMonitor) - Method in class edu.jhu.cs.cisst.plugins.utilities.file.PlugInTestDataSelector
 
execute(CalculationMonitor) - Method in class edu.jhu.cs.cisst.plugins.utilities.surface.PlugInIsoContourGenerator
 
execute(CalculationMonitor) - Method in class edu.jhu.cs.cisst.plugins.utilities.surface.PlugInIsoSurfaceGenerator
 
execute(CalculationMonitor) - Method in class edu.jhu.cs.cisst.plugins.visualization.PlugInVisualizeActiveContour2D
 
execute(CalculationMonitor) - Method in class edu.jhu.cs.cisst.plugins.visualization.PlugInVisualizeImage
 
execute(CalculationMonitor) - Method in class edu.jhu.cs.cisst.plugins.visualization.PlugInVisualizeSurface
 
execute() - Method in class edu.jhu.cs.cisst.vent.VisualizationApplication
Execute
execute(float[]) - Method in class edu.jhu.ece.iacl.algorithms.vabra.NumericalMethod
 
execute(double[]) - Method in class edu.jhu.ece.iacl.algorithms.vabra.NumericalMethod
 
execute(CalculationMonitor) - Method in class edu.jhu.ece.iacl.jist.pipeline.parser.MipavPluginParser
 
execute(ProcessingApplication, File, File) - Method in class edu.jhu.ece.iacl.jist.pipeline.PipeRunner
Execute a specified ProcessingApplication.
execute(CalculationMonitor) - Method in class edu.jhu.ece.iacl.jist.pipeline.ProcessingAlgorithm
Execute your algorithm.
execute(CalculationMonitor) - Method in class edu.jhu.ece.iacl.jist.plugins.MedicAlgorithmExecutableAdapter
 
execute(CalculationMonitor) - Method in class edu.jhu.ece.iacl.jist.plugins.MedicAlgorithmJistLayoutAdapter
 
execute(CalculationMonitor) - Method in class edu.jhu.ece.iacl.jist.plugins.MedicAlgorithmMipavAdapter
 
execute(CalculationMonitor) - Method in class edu.jhu.ece.iacl.jist.plugins.testing.MedicAlgorithmDemo
Execute algorithm
execute() - Method in class edu.jhu.ece.iacl.jist.plugins.testing.MedicAlgorithmDemo.MyAlgorithm
Call algorithm
execute(File, File) - Method in class edu.jhu.ece.iacl.jist.test.MipavTestHarness
Execute.
execute(CalculationMonitor) - Method in class edu.jhu.ece.iacl.pami.CreateCrossingFiber
 
execute(CalculationMonitor) - Method in class edu.jhu.ece.iacl.pami.CreateTesselatedSurface
 
execute(CalculationMonitor) - Method in class edu.jhu.ece.iacl.pami.DivideReference
 
execute(CalculationMonitor) - Method in class edu.jhu.ece.iacl.pami.GenerateTensors
 
execute(CalculationMonitor) - Method in class edu.jhu.ece.iacl.pami.NameTest
 
execute(CalculationMonitor) - Method in class edu.jhu.ece.iacl.pami.SimFramework
 
execute(CalculationMonitor) - Method in class edu.jhu.ece.iacl.plugins.dti.AlgorithmDWIMotionCorrection
 
execute(CalculationMonitor) - Method in class edu.jhu.ece.iacl.plugins.dti.AlgorithmGradientTableCorrection
 
execute(CalculationMonitor) - Method in class edu.jhu.ece.iacl.plugins.dti.ComputeMeanB0
 
execute() - Method in class edu.jhu.ece.iacl.plugins.dti.ComputeMeanB0.TensorEstimationWrapper
 
execute(CalculationMonitor) - Method in class edu.jhu.ece.iacl.plugins.dti.ComputeMeanDW
 
execute() - Method in class edu.jhu.ece.iacl.plugins.dti.ComputeMeanDW.TensorEstimationWrapper
 
execute(CalculationMonitor) - Method in class edu.jhu.ece.iacl.plugins.dti.DWIBallStickEstCamino
 
execute(CalculationMonitor) - Method in class edu.jhu.ece.iacl.plugins.dti.DWIBallStickEstCaminoFileCollection
 
execute(ProcessingAlgorithm) - Method in class edu.jhu.ece.iacl.plugins.dti.DWIBallStickEstCaminoFileCollection.TensorEstimationWrapper
 
execute(CalculationMonitor) - Method in class edu.jhu.ece.iacl.plugins.dti.DWICombineBvalTables
 
execute(CalculationMonitor) - Method in class edu.jhu.ece.iacl.plugins.dti.DWICombineGradTables
 
execute(CalculationMonitor) - Method in class edu.jhu.ece.iacl.plugins.dti.DWIDefineCaminoScheme
 
execute() - Method in class edu.jhu.ece.iacl.plugins.dti.DWITensorColorEncodedMap.AlgorithmWrapper
 
execute(CalculationMonitor) - Method in class edu.jhu.ece.iacl.plugins.dti.DWITensorColorEncodedMap
 
execute(CalculationMonitor) - Method in class edu.jhu.ece.iacl.plugins.dti.DWITensorContrasts
 
execute(CalculationMonitor) - Method in class edu.jhu.ece.iacl.plugins.dti.DWITensorEstCamino
 
execute(CalculationMonitor) - Method in class edu.jhu.ece.iacl.plugins.dti.DWITensorEstCaminoFileCollection
 
execute() - Method in class edu.jhu.ece.iacl.plugins.dti.DWITensorEstCaminoFileCollection.TensorEstimationWrapper
 
execute(CalculationMonitor) - Method in class edu.jhu.ece.iacl.plugins.dti.DWITensorEstCaminoRESTOREVariableNoiseField
 
execute(CalculationMonitor) - Method in class edu.jhu.ece.iacl.plugins.dti.DWITensorEstLikelihood
 
execute() - Method in class edu.jhu.ece.iacl.plugins.dti.DWITensorEstLikelihood.TensorEstimationWrapper
 
execute(CalculationMonitor) - Method in class edu.jhu.ece.iacl.plugins.dti.DWITensorEstLLMSE
 
execute() - Method in class edu.jhu.ece.iacl.plugins.dti.DWITensorEstLLMSE.TensorEstimationWrapper
 
execute(CalculationMonitor) - Method in class edu.jhu.ece.iacl.plugins.dti.DWIThreeTensorEstCamino
 
execute(CalculationMonitor) - Method in class edu.jhu.ece.iacl.plugins.dti.DWIThreeTensorEstCaminoFileCollection
 
execute() - Method in class edu.jhu.ece.iacl.plugins.dti.DWIThreeTensorEstCaminoFileCollection.TensorEstimationWrapper
 
execute(CalculationMonitor) - Method in class edu.jhu.ece.iacl.plugins.dti.DWITwoTensorEstCamino
 
execute(CalculationMonitor) - Method in class edu.jhu.ece.iacl.plugins.dti.DWITwoTensorEstCaminoFileCollection
 
execute() - Method in class edu.jhu.ece.iacl.plugins.dti.DWITwoTensorEstCaminoFileCollection.TensorEstimationWrapper
 
execute(CalculationMonitor) - Method in class edu.jhu.ece.iacl.plugins.dti.LocalNoiseEstimate
 
execute(CalculationMonitor) - Method in class edu.jhu.ece.iacl.plugins.dti.MedicAlgorithmFlipVectorTable
 
execute(CalculationMonitor) - Method in class edu.jhu.ece.iacl.plugins.dti.MedicAlgorithmFlipVectorVolume
 
execute(CalculationMonitor) - Method in class edu.jhu.ece.iacl.plugins.dti.MedicAlgorithmFormatVectorImage
 
execute(CalculationMonitor) - Method in class edu.jhu.ece.iacl.plugins.dti.MedicAlgorithmMultiGradientTableCreator
The execute algorithm that implements ProcessingAlgorithms's abstract method definition.
execute(CalculationMonitor) - Method in class edu.jhu.ece.iacl.plugins.dti.MedicAlgorithmMultiParV3Info
 
execute(CalculationMonitor) - Method in class edu.jhu.ece.iacl.plugins.dti.MedicAlgorithmMultiParV4Info
 
execute(CalculationMonitor) - Method in class edu.jhu.ece.iacl.plugins.dti.MedicAlgorithmSubsampleFibers
 
execute(CalculationMonitor) - Method in class edu.jhu.ece.iacl.plugins.dti.MedicAlgorithmTableFormat
 
execute(CalculationMonitor) - Method in class edu.jhu.ece.iacl.plugins.dti.MedicAlgorithmTensorFormatConvert
 
execute(CalculationMonitor) - Method in class edu.jhu.ece.iacl.plugins.dti.RegularizeNoiseField
 
execute(CalculationMonitor) - Method in class edu.jhu.ece.iacl.plugins.dti.tractography.AlgorithmComputeConnectivityMatrix
 
execute(CalculationMonitor) - Method in class edu.jhu.ece.iacl.plugins.dti.tractography.Fiber2Volume
 
execute(CalculationMonitor) - Method in class edu.jhu.ece.iacl.plugins.dti.tractography.MedicAlgorithmApplyFiberROI
 
execute(CalculationMonitor) - Method in class edu.jhu.ece.iacl.plugins.dti.tractography.MedicAlgorithmDeformFibers
 
execute(CalculationMonitor) - Method in class edu.jhu.ece.iacl.plugins.dti.tractography.MedicAlgorithmFiberComparison
 
execute(CalculationMonitor) - Method in class edu.jhu.ece.iacl.plugins.dti.tractography.MedicAlgorithmFibersFromSurfaceROI
 
execute(CalculationMonitor) - Method in class edu.jhu.ece.iacl.plugins.dti.tractography.MedicAlgorithmFiberTracker
 
execute(CalculationMonitor) - Method in class edu.jhu.ece.iacl.plugins.dti.tractography.MedicAlgorithmFiberVolumeStatistics
 
execute(CalculationMonitor) - Method in class edu.jhu.ece.iacl.plugins.dti.tractography.MedicAlgorithmTransformFibers
 
execute(CalculationMonitor) - Method in class edu.jhu.ece.iacl.plugins.dti.tractography.MedicAlgorithmWildBootTrac
 
execute(ProcessingAlgorithm) - Method in class edu.jhu.ece.iacl.plugins.dti.tractography.MedicAlgorithmWildBootTrac.ExecuteWrapper
 
execute(CalculationMonitor) - Method in class edu.jhu.ece.iacl.plugins.dti.tractography.SImageTractAnalysis
 
execute(CalculationMonitor) - Method in class edu.jhu.ece.iacl.plugins.dti.tractography.TractMapping
 
execute(CalculationMonitor) - Method in class edu.jhu.ece.iacl.plugins.hardi.CFARIEstimation
 
execute() - Method in class edu.jhu.ece.iacl.plugins.hardi.CFARIEstimation2.CFARIWrapper
 
execute(CalculationMonitor) - Method in class edu.jhu.ece.iacl.plugins.hardi.CFARIEstimation2
 
execute(CalculationMonitor) - Method in class edu.jhu.ece.iacl.plugins.hardi.CreatePlatonicSolidSurface
 
execute(CalculationMonitor) - Method in class edu.jhu.ece.iacl.plugins.hardi.DefineCFARIScheme
 
execute(CalculationMonitor) - Method in class edu.jhu.ece.iacl.plugins.hardi.ExtractBvalGradFromPAR
 
execute(CalculationMonitor) - Method in class edu.jhu.ece.iacl.plugins.hardi.FunkRadonTransform
 
execute(CalculationMonitor) - Method in class edu.jhu.ece.iacl.plugins.hardi.GradToSurf
 
execute(CalculationMonitor) - Method in class edu.jhu.ece.iacl.plugins.hardi.NormalizeToUnitMagnitude
 
execute(CalculationMonitor) - Method in class edu.jhu.ece.iacl.plugins.hardi.Process3DMRIImages
 
execute(CalculationMonitor) - Method in class edu.jhu.ece.iacl.plugins.hardi.QBallEstimation
 
execute(CalculationMonitor) - Method in class edu.jhu.ece.iacl.plugins.hardi.QBallModifiedRealProjection
 
execute(CalculationMonitor) - Method in class edu.jhu.ece.iacl.plugins.hardi.QBallProjection
 
execute(CalculationMonitor) - Method in class edu.jhu.ece.iacl.plugins.hardi.SelectUniqueDiffusionDirections
 
execute(CalculationMonitor) - Method in class edu.jhu.ece.iacl.plugins.hardi.SurfToGrad
 
execute(CalculationMonitor) - Method in class edu.jhu.ece.iacl.plugins.hardi.TesselateSurface
 
execute(CalculationMonitor) - Method in class edu.jhu.ece.iacl.plugins.labeling.atlasing.AlgorithmLogOdds
 
execute(CalculationMonitor) - Method in class edu.jhu.ece.iacl.plugins.labeling.MedicAlgorithmCleanSurfLabels
 
execute(CalculationMonitor) - Method in class edu.jhu.ece.iacl.plugins.labeling.MedicAlgorithmFMLabelExtension
 
execute(CalculationMonitor) - Method in class edu.jhu.ece.iacl.plugins.labeling.MedicAlgorithmMultiAtlasLabeling
 
execute(CalculationMonitor) - Method in class edu.jhu.ece.iacl.plugins.labeling.MedicAlgorithmMultiAtlasSurfaceLabeling
 
execute(MedicAlgorithmMultiAtlasSurfaceLabeling) - Method in class edu.jhu.ece.iacl.plugins.labeling.MedicAlgorithmMultiAtlasSurfaceLabeling.Wrapper
 
execute(CalculationMonitor) - Method in class edu.jhu.ece.iacl.plugins.labeling.MedicAlgorithmVolumeToSurfaceLabeling
 
execute(CalculationMonitor) - Method in class edu.jhu.ece.iacl.plugins.labeling.simulation.AlgorithmSimulateSurfaceRater
 
execute(CalculationMonitor) - Method in class edu.jhu.ece.iacl.plugins.labeling.simulation.AlgorithmSimulateVolumeRater
 
execute(CalculationMonitor) - Method in class edu.jhu.ece.iacl.plugins.labeling.staple.MedicAlgorithmSTAPLE
 
execute(CalculationMonitor) - Method in class edu.jhu.ece.iacl.plugins.labeling.staple.MedicAlgorithmSTAPLEgeneral
 
execute(CalculationMonitor) - Method in class edu.jhu.ece.iacl.plugins.labeling.staple.MedicAlgorithmSTAPLEsurface
 
execute() - Method in class edu.jhu.ece.iacl.plugins.quantitative.EstimateMTR.AlgorithmWrapper
 
execute(CalculationMonitor) - Method in class edu.jhu.ece.iacl.plugins.quantitative.EstimateMTR
 
execute() - Method in class edu.jhu.ece.iacl.plugins.quantitative.EstimateMTRseries.AlgorithmWrapper
 
execute(CalculationMonitor) - Method in class edu.jhu.ece.iacl.plugins.quantitative.EstimateMTRseries
 
execute() - Method in class edu.jhu.ece.iacl.plugins.quantitative.EstimateT1FromDoubleAngle.AlgorithmWrapper
 
execute(CalculationMonitor) - Method in class edu.jhu.ece.iacl.plugins.quantitative.EstimateT1FromDoubleAngle
 
execute() - Method in class edu.jhu.ece.iacl.plugins.quantitative.EstimateT2FromDualEcho.AlgorithmWrapper
 
execute(CalculationMonitor) - Method in class edu.jhu.ece.iacl.plugins.quantitative.EstimateT2FromDualEcho
 
execute(CalculationMonitor) - Method in class edu.jhu.ece.iacl.plugins.registration.MedicAlgorithmAtlasSelection
 
execute(CalculationMonitor) - Method in class edu.jhu.ece.iacl.plugins.registration.MedicAlgorithmConstrainedFLIRT
 
execute() - Method in class edu.jhu.ece.iacl.plugins.registration.MedicAlgorithmConstrainedFLIRT.FlirtWrapper
 
execute(CalculationMonitor) - Method in class edu.jhu.ece.iacl.plugins.registration.MedicAlgorithmCreateSimilarityMetricVol
 
execute(CalculationMonitor) - Method in class edu.jhu.ece.iacl.plugins.registration.MedicAlgorithmEfficientFileCollectionRegistration
 
execute(ImageData, ImageData) - Method in class edu.jhu.ece.iacl.plugins.registration.MedicAlgorithmEfficientFileCollectionRegistration.FlirtWrapper
 
execute(CalculationMonitor) - Method in class edu.jhu.ece.iacl.plugins.registration.MedicAlgorithmFLIRT
 
execute() - Method in class edu.jhu.ece.iacl.plugins.registration.MedicAlgorithmFLIRT.FlirtWrapper
 
execute(CalculationMonitor) - Method in class edu.jhu.ece.iacl.plugins.registration.MedicAlgorithmFLIRTCollection
 
execute() - Method in class edu.jhu.ece.iacl.plugins.registration.MedicAlgorithmFLIRTCollection.FlirtWrapper
 
execute(CalculationMonitor) - Method in class edu.jhu.ece.iacl.plugins.registration.MedicAlgorithmMultiAtlasReg
 
execute(CalculationMonitor) - Method in class edu.jhu.ece.iacl.plugins.registration.MedicAlgorithmMultiDeformVolume
 
execute(ProcessingAlgorithm) - Method in class edu.jhu.ece.iacl.plugins.registration.MedicAlgorithmMultiDeformVolume.ExecuteWrapper
 
execute(CalculationMonitor) - Method in class edu.jhu.ece.iacl.plugins.registration.MedicAlgorithmTransformVolume
 
execute(ProcessingAlgorithm) - Method in class edu.jhu.ece.iacl.plugins.registration.MedicAlgorithmTransformVolume.ExecuteWrapper
 
execute(CalculationMonitor) - Method in class edu.jhu.ece.iacl.plugins.registration.MedicAlgorithmVABRA
 
execute(CalculationMonitor) - Method in class edu.jhu.ece.iacl.plugins.segmentation.CreateMask
 
execute() - Method in class edu.jhu.ece.iacl.plugins.spectro.CESTAsymmetry.AlgorithmWrapper
 
execute(CalculationMonitor) - Method in class edu.jhu.ece.iacl.plugins.spectro.CESTAsymmetry
 
execute() - Method in class edu.jhu.ece.iacl.plugins.spectro.JistMSWASSR.AlgorithmWrapper
 
execute(CalculationMonitor) - Method in class edu.jhu.ece.iacl.plugins.spectro.JistMSWASSR
 
execute(CalculationMonitor) - Method in class edu.jhu.ece.iacl.plugins.utilities.file.AddToFileCollection
 
execute(CalculationMonitor) - Method in class edu.jhu.ece.iacl.plugins.utilities.file.FileCollectionToPins
 
execute(CalculationMonitor) - Method in class edu.jhu.ece.iacl.plugins.utilities.file.FileCollectionToVolumeCollection
 
execute(CalculationMonitor) - Method in class edu.jhu.ece.iacl.plugins.utilities.file.MedicAlgorithmChooseFileRegEx
 
execute(CalculationMonitor) - Method in class edu.jhu.ece.iacl.plugins.utilities.file.MedicAlgorithmChooseVolumeRegEx
 
execute(CalculationMonitor) - Method in class edu.jhu.ece.iacl.plugins.utilities.file.MedicAlgorithmConcatArrayDoubleTextLists
 
execute(CalculationMonitor) - Method in class edu.jhu.ece.iacl.plugins.utilities.file.MedicAlgorithmFibersToVtk
 
execute(CalculationMonitor) - Method in class edu.jhu.ece.iacl.plugins.utilities.file.MedicAlgorithmIdentifySubject
 
execute(CalculationMonitor) - Method in class edu.jhu.ece.iacl.plugins.utilities.file.MedicAlgorithmSurfaceConverter
 
execute(CalculationMonitor) - Method in class edu.jhu.ece.iacl.plugins.utilities.file.MedicAlgorithmVolumeConverter
 
execute(CalculationMonitor) - Method in class edu.jhu.ece.iacl.plugins.utilities.file.MedicAlgorithmVolumeConverter2
 
execute(CalculationMonitor) - Method in class edu.jhu.ece.iacl.plugins.utilities.file.MedicAlgorithmVolumeConverter4D
 
execute(CalculationMonitor) - Method in class edu.jhu.ece.iacl.plugins.utilities.file.MedicAlgorithmVolumeListOrganizer
 
execute(CalculationMonitor) - Method in class edu.jhu.ece.iacl.plugins.utilities.file.MedicAlgorithmZip
 
execute(CalculationMonitor) - Method in class edu.jhu.ece.iacl.plugins.utilities.file.VolumeDirectoryNoIter
 
execute(CalculationMonitor) - Method in class edu.jhu.ece.iacl.plugins.utilities.logic.MedicAlgorithmFloatsToPoint
 
execute(CalculationMonitor) - Method in class edu.jhu.ece.iacl.plugins.utilities.logic.MedicAlgorithmSerializeSurfaces
 
execute(CalculationMonitor) - Method in class edu.jhu.ece.iacl.plugins.utilities.logic.MedicAlgorithmSerializeVolumes
 
execute(CalculationMonitor) - Method in class edu.jhu.ece.iacl.plugins.utilities.logic.MedicAlgorithmSurfaceSplitter
 
execute(CalculationMonitor) - Method in class edu.jhu.ece.iacl.plugins.utilities.logic.MedicAlgorithmValueEquals
 
execute(CalculationMonitor) - Method in class edu.jhu.ece.iacl.plugins.utilities.logic.MedicAlgorithmValueGreaterThan
 
execute(CalculationMonitor) - Method in class edu.jhu.ece.iacl.plugins.utilities.logic.MedicAlgorithmValueInRange
 
execute(CalculationMonitor) - Method in class edu.jhu.ece.iacl.plugins.utilities.logic.MedicAlgorithmValueLessThan
 
execute(CalculationMonitor) - Method in class edu.jhu.ece.iacl.plugins.utilities.logic.MedicAlgorithmVolumeSplitter
 
execute(CalculationMonitor) - Method in class edu.jhu.ece.iacl.plugins.utilities.math.MedicAlgorithmArithmetic
 
execute(CalculationMonitor) - Method in class edu.jhu.ece.iacl.plugins.utilities.math.MedicAlgorithmImageCalculator
 
execute(CalculationMonitor) - Method in class edu.jhu.ece.iacl.plugins.utilities.math.MedicAlgorithmImageCalculatorBatch
 
execute(CalculationMonitor) - Method in class edu.jhu.ece.iacl.plugins.utilities.math.MedicAlgorithmImageCalculatorModified
 
execute(CalculationMonitor) - Method in class edu.jhu.ece.iacl.plugins.utilities.math.MedicAlgorithmImageMath
 
execute(CalculationMonitor) - Method in class edu.jhu.ece.iacl.plugins.utilities.math.MedicAlgorithmKLDivergence
 
execute(CalculationMonitor) - Method in class edu.jhu.ece.iacl.plugins.utilities.roi.AlgorithmJointROIStats
 
execute(CalculationMonitor) - Method in class edu.jhu.ece.iacl.plugins.utilities.roi.AlgorithmROIStats
 
execute(CalculationMonitor) - Method in class edu.jhu.ece.iacl.plugins.utilities.surface.MedicAlgorithmCombineSurfaceComponents
 
execute(CalculationMonitor) - Method in class edu.jhu.ece.iacl.plugins.utilities.surface.MedicAlgorithmCombineSurfaces
 
execute(CalculationMonitor) - Method in class edu.jhu.ece.iacl.plugins.utilities.surface.MedicAlgorithmCopyEmbeddedData
 
execute(CalculationMonitor) - Method in class edu.jhu.ece.iacl.plugins.utilities.surface.MedicAlgorithmEmbedSurface
 
execute(CalculationMonitor) - Method in class edu.jhu.ece.iacl.plugins.utilities.surface.MedicAlgorithmExtractSurfaceComponent
 
execute(CalculationMonitor) - Method in class edu.jhu.ece.iacl.plugins.utilities.surface.MedicAlgorithmReshapePoints
 
execute(CalculationMonitor) - Method in class edu.jhu.ece.iacl.plugins.utilities.surface.MedicAlgorithmReshapeSurface
 
execute(CalculationMonitor) - Method in class edu.jhu.ece.iacl.plugins.utilities.surface.MedicAlgorithmSurfaceHistogram
 
execute(CalculationMonitor) - Method in class edu.jhu.ece.iacl.plugins.utilities.surface.MedicAlgorithmSurfaceToVolumeConverter
 
execute(CalculationMonitor) - Method in class edu.jhu.ece.iacl.plugins.utilities.volume.AlgorithmVolumeFileCollectionTo3D
 
execute(CalculationMonitor) - Method in class edu.jhu.ece.iacl.plugins.utilities.volume.CombinedSlabCollectionToVolumeCollection
 
execute(CalculationMonitor) - Method in class edu.jhu.ece.iacl.plugins.utilities.volume.GetImageDimensions
 
execute(CalculationMonitor) - Method in class edu.jhu.ece.iacl.plugins.utilities.volume.MedicAlgorithmCombineVolumeComponents
 
execute(CalculationMonitor) - Method in class edu.jhu.ece.iacl.plugins.utilities.volume.MedicAlgorithmCrop
 
execute(CalculationMonitor) - Method in class edu.jhu.ece.iacl.plugins.utilities.volume.MedicAlgorithmDimensions
 
execute(CalculationMonitor) - Method in class edu.jhu.ece.iacl.plugins.utilities.volume.MedicAlgorithmExtractAllComponents
 
execute(CalculationMonitor) - Method in class edu.jhu.ece.iacl.plugins.utilities.volume.MedicAlgorithmExtractFileCollectionComponents
 
execute(CalculationMonitor) - Method in class edu.jhu.ece.iacl.plugins.utilities.volume.MedicAlgorithmExtractVolumeComponent
 
execute(CalculationMonitor) - Method in class edu.jhu.ece.iacl.plugins.utilities.volume.MedicAlgorithmFindEqualVolume
 
execute(CalculationMonitor) - Method in class edu.jhu.ece.iacl.plugins.utilities.volume.MedicAlgorithmIsotropicReslice
 
execute(CalculationMonitor) - Method in class edu.jhu.ece.iacl.plugins.utilities.volume.MedicAlgorithmMatchAllImages
 
execute(CalculationMonitor) - Method in class edu.jhu.ece.iacl.plugins.utilities.volume.MedicAlgorithmMipavReorient
 
execute() - Method in class edu.jhu.ece.iacl.plugins.utilities.volume.MedicAlgorithmMipavReorient.reorientWrapper
 
execute(CalculationMonitor) - Method in class edu.jhu.ece.iacl.plugins.utilities.volume.MedicAlgorithmMultiCrop
Execute Image Cropper
execute(CalculationMonitor) - Method in class edu.jhu.ece.iacl.plugins.utilities.volume.MedicAlgorithmReverseComponents
 
execute(CalculationMonitor) - Method in class edu.jhu.ece.iacl.plugins.utilities.volume.MedicAlgorithmSetHeaders
 
execute(CalculationMonitor) - Method in class edu.jhu.ece.iacl.plugins.utilities.volume.MedicAlgorithmThreshold
 
execute(CalculationMonitor) - Method in class edu.jhu.ece.iacl.plugins.utilities.volume.MedicAlgorithmUncrop
 
execute(CalculationMonitor) - Method in class edu.jhu.ece.iacl.plugins.utilities.volume.MedicAlgorithmVolumeHistogram
 
execute() - Method in class edu.jhu.ece.iacl.plugins.utilities.volume.VolumeCensorRange.AlgorithmWrapper
 
execute(CalculationMonitor) - Method in class edu.jhu.ece.iacl.plugins.utilities.volume.VolumeCensorRange
 
execute(CalculationMonitor) - Method in class edu.jhu.ece.iacl.plugins.utilities.volume.VolumeCollectionToCombinedSlabCollection
 
execute(CalculationMonitor) - Method in class edu.vanderbilt.masi.plugins.utilities.volume.PluginCombineVolumes
 
ExecutionContext - Class in edu.jhu.ece.iacl.jist.pipeline
An Execution Context provides threaded execution of a processing algorithm with a specified set of input parameters.
ExecutionContext(int, String, PipeLayout, PipeAlgorithm) - Constructor for class edu.jhu.ece.iacl.jist.pipeline.ExecutionContext
Construct a new execution context.
ExecutionContext.ContextListener - Interface in edu.jhu.ece.iacl.jist.pipeline
Listener to monitor for updates to an execution context.
ExecutionContext.ProcessStatusParser - Class in edu.jhu.ece.iacl.jist.pipeline
The Class ProcessStatusParser.
ExecutionContext.ProcessStatusParser(ProcessController) - Constructor for class edu.jhu.ece.iacl.jist.pipeline.ExecutionContext.ProcessStatusParser
Instantiates a new process status parser.
ExecutionContext.Status - Enum in edu.jhu.ece.iacl.jist.pipeline
The Enum Status.
ExecutionContext.Update - Enum in edu.jhu.ece.iacl.jist.pipeline
The Enum Update.
exit() - Method in class edu.jhu.ece.iacl.jist.pipeline.gui.PipelineLayoutTool
Close all frames and exit safely.
exitOnClose - Variable in class edu.jhu.ece.iacl.jist.pipeline.gui.ProcessManager
The exit on close.
expand - Variable in class edu.jhu.ece.iacl.jist.pipeline.gui.PipeInternalFrame
The expand.
extensionFilter - Variable in class edu.jhu.ece.iacl.jist.io.FileReaderWriter
The extension filter.
extensionFilter - Variable in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamFile
The extension filter.
extensionFilter - Variable in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamFileCollection
The extension filter.
extlabelsout - Variable in class edu.jhu.ece.iacl.plugins.labeling.MedicAlgorithmFMLabelExtension
 
extract3DVolume(ImageData, int) - Static method in class edu.jhu.ece.iacl.structures.image.ImageDataMath
 
ExtractBvalGradFromPAR - Class in edu.jhu.ece.iacl.plugins.hardi
 
ExtractBvalGradFromPAR() - Constructor for class edu.jhu.ece.iacl.plugins.hardi.ExtractBvalGradFromPAR
 
extractModelImage() - Method in class edu.jhu.ece.iacl.jist.structures.image.ImageDataMipav
 
ExtractPARGradientTable - Class in edu.jhu.ece.iacl.algorithms.hardi
 
ExtractPARGradientTable() - Constructor for class edu.jhu.ece.iacl.algorithms.hardi.ExtractPARGradientTable
 
ExtractPARGradientTable(String, Vector<Float>, Vector<Point3f>) - Static method in class edu.jhu.ece.iacl.algorithms.hardi.ExtractPARGradientTable
 

F

f1 - Variable in class edu.jhu.ece.iacl.jist.structures.geom.EmbeddedSurface.Edge
The f2.
f2 - Variable in class edu.jhu.ece.iacl.jist.structures.geom.EmbeddedSurface.Edge
The f2.
FA() - Method in class edu.jhu.ece.iacl.algorithms.dti.DiffusionTensor
 
Face - Class in edu.jhu.ece.iacl.jist.structures.geom
The Class Face.
Face() - Constructor for class edu.jhu.ece.iacl.jist.structures.geom.Face
 
faces - Variable in class edu.jhu.ece.iacl.jist.structures.geom.EmbeddedSurface
The faces.
faces - Variable in class edu.jhu.ece.iacl.jist.structures.geom.Surface
The faces.
FACT_INFACTcompare - Class in edu.jhu.ece.iacl.algorithms.dti.tractography.FACT
 
FACT_INFACTcompare() - Constructor for class edu.jhu.ece.iacl.algorithms.dti.tractography.FACT.FACT_INFACTcompare
 
FACTapi - Class in edu.jhu.ece.iacl.algorithms.dti.tractography.FACT
 
FACTapi() - Constructor for class edu.jhu.ece.iacl.algorithms.dti.tractography.FACT.FACTapi
 
FACTfiber - Class in edu.jhu.ece.iacl.algorithms.dti.tractography.FACT
Created by IntelliJ IDEA.
FACTfiber() - Constructor for class edu.jhu.ece.iacl.algorithms.dti.tractography.FACT.FACTfiber
 
factorial(int) - Static method in class edu.jhu.bme.smile.commons.math.specialFunctions.SFunc
 
factorialratio(int, int) - Static method in class edu.jhu.bme.smile.commons.math.specialFunctions.SFunc
 
factory - Variable in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamModel
The factory.
factory - Variable in class edu.jhu.ece.iacl.jist.pipeline.tree.DraggableNode
The factory.
FACTparameters - Class in edu.jhu.ece.iacl.algorithms.dti.tractography.FACT
Created by IntelliJ IDEA.
FACTparameters() - Constructor for class edu.jhu.ece.iacl.algorithms.dti.tractography.FACT.FACTparameters
 
faData - Variable in class edu.jhu.ece.iacl.algorithms.dti.tractography.FACT.FACTparameters
 
faData - Variable in class edu.jhu.ece.iacl.algorithms.dti.tractography.FiberTracker
 
faData - Variable in class edu.jhu.ece.iacl.algorithms.dti.tractography.WildBootFiberTracker
 
failedDir - Variable in class edu.jhu.ece.iacl.doc.DocumentAllTests
The failed dir.
failedDir - Variable in class edu.jhu.ece.iacl.jist.test.JistTestHarness
The failed dir.
failedFiles - Variable in class edu.jhu.ece.iacl.doc.DocumentAllTests
The failed files.
failedFiles - Variable in class edu.jhu.ece.iacl.jist.pipeline.PipeLayoutRunner
The failed files.
failedFiles - Variable in class edu.jhu.ece.iacl.jist.test.JistTestHarness
The failed files.
FastMarchingLabelExtension - Class in edu.jhu.ece.iacl.algorithms.manual_label
 
FastMarchingLabelExtension() - Constructor for class edu.jhu.ece.iacl.algorithms.manual_label.FastMarchingLabelExtension
 
FastMarchingLabelExtension(AbstractCalculation) - Constructor for class edu.jhu.ece.iacl.algorithms.manual_label.FastMarchingLabelExtension
 
fastMarchingMethods - Static variable in class edu.jhu.ece.iacl.algorithms.ReferencedPapers
 
fastMarchingSurfaceDistance - Static variable in class edu.jhu.ece.iacl.algorithms.ReferencedPapers
 
fastMarchingVolumeDistance - Static variable in class edu.jhu.ece.iacl.algorithms.ReferencedPapers
 
fatalError(SAXParseException) - Method in class edu.jhu.ece.iacl.jist.io.XMLErrorHandler
Handles parse exception fatal errors by passing the parse exception up as a SAXException.
fGetOffset(Point2i, Point2i) - Method in class edu.jhu.cs.cisst.algorithms.geometry.surface.IsoContourGenerator
Interpolate position along edge.
fGetOffset(Point3i, Point3i) - Method in class edu.jhu.cs.cisst.algorithms.geometry.surface.IsoSurfaceGenerator
Interpolate position along edge.
Fiber - Class in edu.jhu.ece.iacl.jist.structures.fiber
The Class Fiber.
Fiber() - Constructor for class edu.jhu.ece.iacl.jist.structures.fiber.Fiber
Instantiates a new fiber.
Fiber(XYZ[]) - Constructor for class edu.jhu.ece.iacl.jist.structures.fiber.Fiber
Instantiates a new fiber.
Fiber2Volume - Class in edu.jhu.ece.iacl.plugins.dti.tractography
 
Fiber2Volume() - Constructor for class edu.jhu.ece.iacl.plugins.dti.tractography.Fiber2Volume
 
FiberCollection - Class in edu.jhu.ece.iacl.jist.structures.fiber
The Class FiberCollection.
FiberCollection() - Constructor for class edu.jhu.ece.iacl.jist.structures.fiber.FiberCollection
Instantiates a new fiber collection.
FiberCollection(int) - Constructor for class edu.jhu.ece.iacl.jist.structures.fiber.FiberCollection
Instantiates a new fiber collection.
FiberCollectionReaderWriter - Class in edu.jhu.ece.iacl.jist.io
The Class FiberCollectionReaderWriter.
FiberCollectionReaderWriter() - Constructor for class edu.jhu.ece.iacl.jist.io.FiberCollectionReaderWriter
Instantiates a new fiber collection reader writer.
FiberComparator - Class in edu.jhu.ece.iacl.algorithms.dti.tractography
 
FiberComparator() - Constructor for class edu.jhu.ece.iacl.algorithms.dti.tractography.FiberComparator
 
FiberConverter - Class in edu.jhu.ece.iacl.algorithms.dti.tractography.FACT
 
FiberConverter() - Constructor for class edu.jhu.ece.iacl.algorithms.dti.tractography.FACT.FiberConverter
 
FiberLenMax - Variable in class edu.jhu.ece.iacl.jist.structures.fiber.DTIStudioHDR
The Fiber len max.
FiberLenMean - Variable in class edu.jhu.ece.iacl.jist.structures.fiber.DTIStudioHDR
The Fiber len mean.
FiberNR - Variable in class edu.jhu.ece.iacl.jist.structures.fiber.DTIStudioHDR
The Fiber nr.
fiberPoints - Variable in class edu.jhu.ece.iacl.algorithms.dti.tractography.FiberTracker.FACTfiber
 
fiberPoints - Variable in class edu.jhu.ece.iacl.algorithms.dti.tractography.WildBootFiberTracker.WildBootFACTfiber
 
fiberroi(FiberCollection, int, int) - Method in class edu.jhu.ece.iacl.algorithms.manual_label.ROI
A method to parcellate fibers based to DTIStudio like regions of interest ROIs
fibers2Volume(String, ImageData) - Method in class edu.jhu.ece.iacl.algorithms.dti.tractography.FiberStatistics
 
FiberScaler - Class in edu.jhu.ece.iacl.algorithms.dti.tractography.FACT
 
FiberScaler() - Constructor for class edu.jhu.ece.iacl.algorithms.dti.tractography.FACT.FiberScaler
 
FiberStatistics - Class in edu.jhu.ece.iacl.algorithms.dti.tractography
 
FiberStatistics() - Constructor for class edu.jhu.ece.iacl.algorithms.dti.tractography.FiberStatistics
 
FiberStatistics(Vector<Fiber>) - Constructor for class edu.jhu.ece.iacl.algorithms.dti.tractography.FiberStatistics
 
FiberStatistics(FiberCollection) - Constructor for class edu.jhu.ece.iacl.algorithms.dti.tractography.FiberStatistics
 
FiberTracker - Class in edu.jhu.ece.iacl.algorithms.dti.tractography
 
FiberTracker(AbstractCalculation, double, double, double, Point3f, ImageData, ImageData) - Constructor for class edu.jhu.ece.iacl.algorithms.dti.tractography.FiberTracker
 
FiberTracker(double, double, double, Point3f, ImageData, ImageData) - Constructor for class edu.jhu.ece.iacl.algorithms.dti.tractography.FiberTracker
 
FiberTracker.FACTfiber - Class in edu.jhu.ece.iacl.algorithms.dti.tractography
 
FiberTracker.FACTfiber() - Constructor for class edu.jhu.ece.iacl.algorithms.dti.tractography.FiberTracker.FACTfiber
 
FiberTransformation - Class in edu.jhu.ece.iacl.algorithms.dti.tractography
 
FiberTransformation() - Constructor for class edu.jhu.ece.iacl.algorithms.dti.tractography.FiberTransformation
 
field - Variable in class edu.jhu.ece.iacl.jist.pipeline.gui.PortListBox
The field.
field - Variable in class edu.jhu.ece.iacl.jist.pipeline.view.input.InformationListBox
The field.
field - Variable in class edu.jhu.ece.iacl.jist.pipeline.view.input.ParamFileCollectionInputView
The field.
field - Variable in class edu.jhu.ece.iacl.jist.pipeline.view.input.ParamMultiOptionInputView
The field.
field - Variable in class edu.jhu.ece.iacl.jist.pipeline.view.input.ParamNumberCollectionInputView
The field.
field - Variable in class edu.jhu.ece.iacl.jist.pipeline.view.input.ParamVolumeCollectionInputView
The field.
field - Variable in class edu.jhu.ece.iacl.jist.pipeline.view.input.ParamVolumeInputView
Field for selecting image input.
field - Variable in class edu.jhu.ece.iacl.jist.pipeline.view.input.ParamVolumeURIInputView
Field for selecting image input.
field - Variable in class edu.jhu.ece.iacl.jist.pipeline.view.output.ParamOutputView
The field.
fieldMat - Variable in class edu.jhu.cs.cisst.algorithms.geometry.surface.IsoContourGenerator
The field mat.
FieldRegularize - Class in edu.jhu.bme.smile.commons.math
public class FieldRegularize This class contains static methods to regularize (smooth) a 2d field using polynomial basis sets.
FieldRegularize() - Constructor for class edu.jhu.bme.smile.commons.math.FieldRegularize
 
file - Variable in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamFile
The file.
file - Variable in class edu.jhu.ece.iacl.jist.pipeline.PipeLayout
file location for this layout.
file - Variable in class edu.jhu.ece.iacl.jist.pipeline.view.input.ParamVolumeInputView.VolumeListBoxItem
The file.
file - Variable in class edu.jhu.ece.iacl.jist.pipeline.view.input.ParamVolumeURIInputView.VolumeListBoxItem
The file.
FILE_TYPE_TAG - Static variable in class edu.jhu.ece.iacl.jist.pipeline.parser.LoniPipeParser
The Constant FILE_TYPE_TAG.
FILE_TYPES_TAG - Static variable in class edu.jhu.ece.iacl.jist.pipeline.parser.LoniPipeParser
The Constant FILE_TYPES_TAG.
filecollection - Variable in class edu.jhu.ece.iacl.jist.pipeline.src.PipeFileCollectionSource
The filecollection.
FileCollectionToPins - Class in edu.jhu.ece.iacl.plugins.utilities.file
 
FileCollectionToPins() - Constructor for class edu.jhu.ece.iacl.plugins.utilities.file.FileCollectionToPins
 
FileCollectionToVolumeCollection - Class in edu.jhu.ece.iacl.plugins.utilities.file
 
FileCollectionToVolumeCollection() - Constructor for class edu.jhu.ece.iacl.plugins.utilities.file.FileCollectionToVolumeCollection
 
filecolParam - Variable in class edu.jhu.ece.iacl.jist.pipeline.src.PipeFileCollectionListSource
The volume collection param.
FileConverter - Class in edu.jhu.ece.iacl.jist.io
The Class FileConverter.
FileConverter() - Constructor for class edu.jhu.ece.iacl.jist.io.FileConverter
 
fileExtension - Variable in class edu.jhu.ece.iacl.jist.pipeline.src.PipeFileDirectorySource
The file extension.
fileExtension - Variable in class edu.jhu.ece.iacl.jist.pipeline.src.PipeVolumeDirectoryCollectionSource
The file extension.
FileExtensionFilter - Class in edu.jhu.ece.iacl.jist.io
File filter based on extensions.
FileExtensionFilter(String[]) - Constructor for class edu.jhu.ece.iacl.jist.io.FileExtensionFilter
Instantiates a new file extension filter.
FileExtensionFilter(Vector<String>) - Constructor for class edu.jhu.ece.iacl.jist.io.FileExtensionFilter
Instantiates a new file extension filter.
FileExtensionFilter() - Constructor for class edu.jhu.ece.iacl.jist.io.FileExtensionFilter
Instantiates a new file extension filter.
fileField - Variable in class edu.jhu.ece.iacl.jist.pipeline.view.input.ParamVolumeURICollectionInputView
The file field.
fileHistory - Variable in class edu.jhu.ece.iacl.jist.pipeline.JistPreferences
history of recent layout files.
fileList - Variable in class edu.jhu.ece.iacl.jist.pipeline.src.PipeFileDirectorySource
The images.
fileList - Variable in class edu.jhu.ece.iacl.jist.pipeline.src.PipeVolumeDirectoryCollectionSource
The images.
fileListBoxEntries - Variable in class edu.jhu.ece.iacl.jist.pipeline.view.input.ParamVolumeURICollectionInputView
The list box entries.
fileListPane - Variable in class edu.jhu.ece.iacl.jist.pipeline.view.input.ParamVolumeURICollectionInputView
The list pane.
fileName - Variable in class edu.jhu.ece.iacl.jist.io.FileReaderWriter
The file name.
fileName - Variable in class edu.jhu.ece.iacl.jist.pipeline.dest.PipeParamCopyDestination
The file name.
fileName - Variable in class edu.jhu.ece.iacl.jist.pipeline.dest.PipeParamSummaryDestination
The file name.
fileOutputDir - Variable in class edu.jhu.ece.iacl.jist.pipeline.dest.PipeParamCopyDestination
The file output dir.
fileParam - Variable in class edu.jhu.ece.iacl.jist.pipeline.src.PipeFileCollectionSource
The file param.
fileParam - Variable in class edu.jhu.ece.iacl.jist.pipeline.src.PipeFileDirectorySource
The file parameter
fileParam - Variable in class edu.jhu.ece.iacl.jist.pipeline.src.PipeListCollectionSource
The file param.
fileParam - Variable in class edu.jhu.ece.iacl.jist.pipeline.src.PipeListSource
The file param.
fileParam - Variable in class edu.jhu.ece.iacl.jist.pipeline.src.PipeSelectionListSource
The file param.
fileParam - Variable in class edu.jhu.ece.iacl.jist.pipeline.src.PipeVolumeDirectoryCollectionSource
The file parameter
fileParams - Variable in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamFileCollection
The file params.
FileReaderWriter<T> - Class in edu.jhu.ece.iacl.jist.io
FileReaderWriter is the abstract class for reading/writing various files Extensions exist for various object types (view type hierarchy) Every extension of FileReaderWriter should overwrite the following protected methods (1) readObject(File) (2) writeObject(T, File) (3) writeObjectToDirectory(T, File).
FileReaderWriter(FileExtensionFilter) - Constructor for class edu.jhu.ece.iacl.jist.io.FileReaderWriter
Instantiates a new file reader writer.
FileReaderWriter() - Constructor for class edu.jhu.ece.iacl.jist.io.FileReaderWriter
Instantiates a new file reader writer.
fileScrollPane - Variable in class edu.jhu.ece.iacl.jist.pipeline.view.input.ParamVolumeURICollectionInputView
The scroll pane.
filesParam - Variable in class edu.jhu.ece.iacl.jist.pipeline.src.PipeFileListSource
The files param.
fileToPatient(Vector3f, Vector3f, ModelStorageBase, int, boolean) - Static method in class edu.jhu.ece.iacl.jist.io.MipavFileVOI
File to patient.
fileToScanner(Vector3f, Vector3f, ModelImage) - Static method in class edu.jhu.ece.iacl.jist.io.MipavFileVOI
File to scanner.
fileType - Variable in class edu.jhu.ece.iacl.jist.pipeline.dest.PipeParamCopyDestination
The file type.
FileUtil - Class in edu.jhu.ece.iacl.jist.utility
The Class FileUtil.
FileUtil() - Constructor for class edu.jhu.ece.iacl.jist.utility.FileUtil
 
filterExpression - Variable in class edu.jhu.ece.iacl.jist.pipeline.src.PipeFileDirectorySource
The filter expression.
filterExpression - Variable in class edu.jhu.ece.iacl.jist.pipeline.src.PipeVolumeDirectoryCollectionSource
The filter expression.
filterExpression - Variable in class edu.jhu.ece.iacl.plugins.utilities.file.VolumeDirectoryNoIter
The filter expression.
filterRule - Variable in class edu.jhu.ece.iacl.jist.pipeline.src.PipeFileDirectorySource
The filter rule.
filterRule - Variable in class edu.jhu.ece.iacl.jist.pipeline.src.PipeVolumeDirectoryCollectionSource
The filter rule.
filterRule - Variable in class edu.jhu.ece.iacl.plugins.utilities.file.VolumeDirectoryNoIter
The filter rule.
filterTractByVolumeStatPercent() - Method in class edu.jhu.ece.iacl.algorithms.dti.tractography.FiberStatistics
 
filterTractByVolumeStatThresh(ImageDataMipav, double) - Method in class edu.jhu.ece.iacl.algorithms.dti.tractography.FiberStatistics
 
finalize() - Method in class edu.jhu.ece.iacl.algorithms.dti.tractography.FiberStatistics
 
finalize() - Method in class edu.jhu.ece.iacl.jist.structures.image.ImageDataFloat
 
finalize() - Method in class edu.jhu.ece.iacl.jist.structures.image.ImageDataMipav
 
finalize() - Method in class edu.jhu.ece.iacl.jist.structures.image.ImageDataMipavPointer
 
findBoundaries(EmbeddedSurface, int) - Static method in class edu.jhu.ece.iacl.algorithms.manual_label.simulation.SurfaceRater
Find all boundaries that exist on a surface.
findBoundaries(ImageData, GridPt.Connectivity) - Static method in class edu.jhu.ece.iacl.algorithms.manual_label.simulation.VolumeRater
Find all boundaries that exist in a volume.
findBoundaries() - Method in class edu.jhu.ece.iacl.algorithms.manual_label.simulation.VolumeRater
Find all boundaries that exist in a volume.
findBoundarySizes() - Method in class edu.jhu.ece.iacl.algorithms.manual_label.simulation.VolumeRater
Find the sizes of all boundaries that exist in a volume.
findClass(String) - Static method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamHeader
 
findCorrespondingFiberBySeed(int, Tract) - Method in class edu.jhu.ece.iacl.algorithms.dti.tractography.Tract
 
findCorrespondingFiberBySeed(Fiber, Tract) - Method in class edu.jhu.ece.iacl.algorithms.dti.tractography.Tract
 
findFibersByPoints(cPT[]) - Method in class edu.jhu.ece.iacl.algorithms.dti.tractography.FACT.FACTapi
 
findIntersect(PT, PT) - Method in class edu.jhu.ece.iacl.jist.structures.geom.TriangleSigned
Find intersect.
findIntersectPolygon(double[][], double[][], double) - Method in class edu.jhu.ece.iacl.algorithms.dti.tractography.FACT.DTIStudioReader
 
findIntersectPolygonDTIStudioCoordinates(double[][], double[][], double) - Method in class edu.jhu.ece.iacl.algorithms.dti.tractography.FACT.DTIStudioReader
 
findLabels() - Method in class edu.jhu.ece.iacl.algorithms.manual_label.staple.STAPLE
 
findLabels() - Method in class edu.jhu.ece.iacl.algorithms.manual_label.staple.STAPLEgeneral
 
findLabels() - Method in class edu.jhu.ece.iacl.algorithms.manual_label.staple.STAPLEmulti
 
findLabels() - Method in class edu.jhu.ece.iacl.algorithms.manual_label.staple.STAPLEmulti2
 
findLabels() - Method in class edu.jhu.ece.iacl.algorithms.manual_label.staple.STAPLEsurf
 
findMatchingFiles() - Method in class edu.jhu.ece.iacl.jist.pipeline.src.PipeFileDirectorySource
 
findMatchingFiles() - Method in class edu.jhu.ece.iacl.jist.pipeline.src.PipeVolumeDirectoryCollectionSource
 
findSeed(int) - Method in class edu.jhu.ece.iacl.algorithms.dti.tractography.Tract
 
findSeed(Fiber) - Method in class edu.jhu.ece.iacl.algorithms.dti.tractography.Tract
 
findSeedIndex(int) - Method in class edu.jhu.ece.iacl.algorithms.dti.tractography.Tract
 
findTractVolumeStats(ImageData) - Method in class edu.jhu.ece.iacl.algorithms.dti.tractography.FiberStatistics
 
FINE - Static variable in class edu.jhu.ece.iacl.jist.utility.JistLogger
 
fineGradient(int[][], int, double[]) - Method in class edu.jhu.ece.iacl.algorithms.vabra.ImagePairRBF
 
fineOptimize(int[][], double[]) - Method in class edu.jhu.ece.iacl.algorithms.vabra.ImagePair
 
fineOptimize(int[][], double[]) - Method in class edu.jhu.ece.iacl.algorithms.vabra.ImagePairRBF
 
FINER - Static variable in class edu.jhu.ece.iacl.jist.utility.JistLogger
 
fineSize - Variable in class edu.jhu.cs.cisst.algorithms.optimize.fmg.interpolator.InterpolatorByStencil
The fine size.
FINEST - Static variable in class edu.jhu.ece.iacl.jist.utility.JistLogger
 
finished() - Method in class edu.jhu.cs.cisst.algorithms.optimize.fmg.parallel.Parallelizer
called by the run() method of each thread as it finishes.
fireActionPerformed(Action) - Method in class edu.jhu.ece.iacl.jist.pipeline.gui.PipeInternalFrame
Fire action performed.
fireProgressStateChanged(int) - Method in class edu.jhu.ece.iacl.plugins.registration.MedicAlgorithmConstrainedFLIRT.AlgorithmConstrainedOAR3DWrapper
Notifies all listeners that have registered interest for notification on this event type.
fireProgressStateChanged(String, String) - Method in class edu.jhu.ece.iacl.plugins.registration.MedicAlgorithmConstrainedFLIRT.AlgorithmConstrainedOAR3DWrapper
Updates listeners of progress status.
fireProgressStateChanged(int) - Method in class edu.jhu.ece.iacl.plugins.registration.MedicAlgorithmFLIRT.AlgorithmRegOAR3DWrapper
Notifies all listeners that have registered interest for notification on this event type.
fireProgressStateChanged(String, String) - Method in class edu.jhu.ece.iacl.plugins.registration.MedicAlgorithmFLIRT.AlgorithmRegOAR3DWrapper
Updates listeners of progress status.
fireProgressStateChanged(int) - Method in class edu.jhu.ece.iacl.plugins.registration.MedicAlgorithmFLIRTCollection.AlgorithmRegOAR3DWrapper
Notifies all listeners that have registered interest for notification on this event type.
fireProgressStateChanged(String, String) - Method in class edu.jhu.ece.iacl.plugins.registration.MedicAlgorithmFLIRTCollection.AlgorithmRegOAR3DWrapper
Updates listeners of progress status.
firstIntersection(PT, PT) - Method in class edu.jhu.ece.iacl.jist.structures.geom.Polyhedron
First intersection.
FirstPluginTest - Class in edu.jhu.bme.smile.demo
 
FirstPluginTest() - Constructor for class edu.jhu.bme.smile.demo.FirstPluginTest
 
firstPort - Variable in class edu.jhu.ece.iacl.jist.pipeline.graph.PipeMarqueeHandler
The first port.
FixedBoundaryGrid - Class in edu.jhu.cs.cisst.algorithms.optimize.fmg.grid
An implementation of BoundaryGrid where all the boundary elements are set once at construction time to a single, common value and remain fixed thereafter.
FixedBoundaryGrid(int, int, int, int, double, double) - Constructor for class edu.jhu.cs.cisst.algorithms.optimize.fmg.grid.FixedBoundaryGrid
construct from size, initial value for all elements in the interior and initial value for all elements at the boundary.
flag - Variable in class edu.jhu.ece.iacl.algorithms.dti.GTCparams
 
fleissReliability(List<LabelImage>) - Static method in class edu.jhu.ece.iacl.algorithms.manual_label.LabelImage
 
flip() - Method in class edu.jhu.ece.iacl.jist.structures.geom.Segment
Flip.
flipComponents(double[][], boolean, boolean, boolean) - Static method in class edu.jhu.ece.iacl.algorithms.dti.GTCparams
 
flipNormals - Variable in class edu.jhu.cs.cisst.vent.renderer.processing.SurfaceRenderer
The flip normals.
flipNormalsParam - Variable in class edu.jhu.cs.cisst.vent.renderer.processing.SurfaceRenderer
The visible param.
FloatInterp - Class in edu.jhu.ece.iacl.algorithms.dti.tractography.FACT
Created by IntelliJ IDEA.
FloatInterp() - Constructor for class edu.jhu.ece.iacl.algorithms.dti.tractography.FACT.FloatInterp
 
floatParam - Variable in class edu.jhu.ece.iacl.jist.pipeline.src.PipeDoubleCollectionListSource
The float param.
floatValue() - Method in class edu.jhu.ece.iacl.jist.structures.image.Voxel
 
floor(float) - Static method in class edu.jhmi.rad.medic.utilities.NumericsPublic
 
floor(double) - Static method in class edu.jhmi.rad.medic.utilities.NumericsPublic
 
FMG - Class in edu.jhu.cs.cisst.algorithms.optimize.fmg
A class that implements the Full Multigrid (FMG) algorithm for the solution of a linear elliptic partial differential equation (PDE) on a regular cubic grid in 3D.
FMG(PDE, Smoother, Restrictor, Interpolator, Solver, ConstBoundaryGrid, ConstBoundaryGrid, SolverResolutionLevels) - Constructor for class edu.jhu.cs.cisst.algorithms.optimize.fmg.FMG
construct an FMG object that will be able to solve a linear elliptic PDE using the FMG algorithm on a regular cubic grid in 3D.
FMGAlreadyExecutingException - Exception in edu.jhu.cs.cisst.algorithms.optimize.fmg
Exception class that is thrown if FMG.fmg() is called while another instance of the method is already executing in its thread.
FMGAlreadyExecutingException() - Constructor for exception edu.jhu.cs.cisst.algorithms.optimize.fmg.FMGAlreadyExecutingException
construct with no particular message.
FMGAlreadyExecutingException(String) - Constructor for exception edu.jhu.cs.cisst.algorithms.optimize.fmg.FMGAlreadyExecutingException
construct with the given message.
FMGDefaultObserver - Class in edu.jhu.cs.cisst.algorithms.optimize.fmg
The default observer for observables of class FMG.
FMGDefaultObserver() - Constructor for class edu.jhu.cs.cisst.algorithms.optimize.fmg.FMGDefaultObserver
 
FMGNotExecutingException - Exception in edu.jhu.cs.cisst.algorithms.optimize.fmg
Exception class that is thrown if FMG.waitForResult() is called although the FMG algorithm is currently not executing in a thread.
FMGNotExecutingException() - Constructor for exception edu.jhu.cs.cisst.algorithms.optimize.fmg.FMGNotExecutingException
construct with no particular message.
FMGNotExecutingException(String) - Constructor for exception edu.jhu.cs.cisst.algorithms.optimize.fmg.FMGNotExecutingException
construct with the given message.
FMGThread - Class in edu.jhu.cs.cisst.algorithms.optimize.fmg
A helper class of class FMG that implements the run() method of class thread.
FMGThread(FMG, int, int, int, int) - Constructor for class edu.jhu.cs.cisst.algorithms.optimize.fmg.FMGThread
construct from target FMG object and from the parameters that will be passed on to method FMG.fmgProper() and immediately start the thread, i.e.
fo - Variable in class edu.jhu.ece.iacl.algorithms.dti.GTCparams
 
foldingManager - Variable in class edu.jhu.ece.iacl.jist.pipeline.gui.PipeInternalFrame
The folding manager.
forceInit() - Method in class edu.jhu.ece.iacl.jist.pipeline.gui.ModuleTreePanel
Force initialization even if the module tree already exists.
forceQuit() - Method in class edu.jhu.ece.iacl.jist.pipeline.gui.ProcessManager
 
forces - Variable in class edu.jhu.cs.cisst.algorithms.segmentation.gac.GeodesicActiveContour2D
The forces.
forceSafeFilename(String) - Static method in class edu.jhu.ece.iacl.jist.utility.FileUtil
Replace any potentially unsafe file system characters with "_".
FORMAT_TAG - Static variable in class edu.jhu.ece.iacl.jist.pipeline.parser.LoniPipeParser
The Constant FORMAT_TAG.
formatTime(long) - Static method in class edu.jhu.ece.iacl.jist.pipeline.PerformanceSummary
Format millisecond time to be in terms of days, hrs, minutes, and seconds.
FORWARD - Static variable in class edu.jhu.ece.iacl.algorithms.dti.tractography.FiberTracker
 
FORWARD - Static variable in class edu.jhu.ece.iacl.algorithms.dti.tractography.WildBootFiberTracker
 
forward(PipePort, PipePort) - Static method in class edu.jhu.ece.iacl.jist.pipeline.PipeModule
Forward information from the source port to destination port.
fractionalAnisotropy(Matrix) - Static method in class edu.jhu.ece.iacl.jist.algorithms.graphics.GeomUtil
Fractional anisotropy.
fractionalDistance - Variable in class edu.jhu.ece.iacl.jist.structures.geom.IntersectResult
The fractional distance.
frame - Variable in class edu.jhu.ece.iacl.jist.pipeline.view.output.ParamVolumeOutputView
The frame.
frames - Variable in class edu.jhu.ece.iacl.jist.pipeline.gui.LayoutPanel
The frames.
freeMem() - Method in class edu.jhu.ece.iacl.algorithms.dti.tractography.FACT.FloatInterp
 
FreeSurferAsciiReader - Class in edu.jhu.ece.iacl.jist.io
The Class FreeSurferAsciiReader.
FreeSurferAsciiReader() - Constructor for class edu.jhu.ece.iacl.jist.io.FreeSurferAsciiReader
 
FreeSurferAsciiWriter - Class in edu.jhu.ece.iacl.jist.io
The Class FreeSurferAsciiWriter.
FreeSurferAsciiWriter() - Constructor for class edu.jhu.ece.iacl.jist.io.FreeSurferAsciiWriter
 
FreeSurferReader - Class in edu.jhu.ece.iacl.jist.io
The Class FreeSurferReader.
FreeSurferReader() - Constructor for class edu.jhu.ece.iacl.jist.io.FreeSurferReader
 
FreeSurferWriter - Class in edu.jhu.ece.iacl.jist.io
The Class FreeSurferWriter.
FreeSurferWriter() - Constructor for class edu.jhu.ece.iacl.jist.io.FreeSurferWriter
 
from() - Method in class edu.jhu.cs.cisst.algorithms.optimize.fmg.util.IntRange1D
return lower boundary.
fromDxWriter(String[], String[], File, float, float, float) - Static method in class edu.jhu.ece.iacl.jist.io.FreeSurferAsciiWriter
From dx writer.
fromDxWriter(String[], String[], File, float, float, float) - Static method in class edu.jhu.ece.iacl.jist.io.MipavSurfaceXMLWriter
From dx writer.
fromFreeSurferWriter(String[], String[], File, float, float, float) - Static method in class edu.jhu.ece.iacl.jist.io.DxSurfaceWriter
From free surfer writer.
fromFreeSurferWriter(String[], String[], File, float, float, float) - Static method in class edu.jhu.ece.iacl.jist.io.MipavSurfaceXMLWriter
From free surfer writer.
fromMipavWriter(String[], String[], File, float, float, float) - Static method in class edu.jhu.ece.iacl.jist.io.DxSurfaceWriter
From mipav writer.
fromMipavWriter(String[], String[], File, float, float, float) - Static method in class edu.jhu.ece.iacl.jist.io.FreeSurferAsciiWriter
From mipav writer.
fromVector(Vector<Fiber>) - Static method in class edu.jhu.ece.iacl.jist.structures.fiber.Fiber
From vector.
fromXML(File) - Static method in class edu.jhu.ece.iacl.jist.pipeline.factory.ParamFactory
Read parameter from XML file.
fromXML(String) - Static method in class edu.jhu.ece.iacl.jist.pipeline.factory.ParamFactory
Reconstruct parameter from XML string.
fromXML(String) - Static method in class edu.jhu.ece.iacl.jist.pipeline.JistPreferences
Reconstruct algorithm from string.
fromXML(String) - Static method in class edu.jhu.ece.iacl.jist.pipeline.PipeAlgorithm
Reconstruct algorithm from string.
fromXML(String) - Static method in class edu.jhu.ece.iacl.jist.pipeline.PipeLayout
Reconstruct layout from string.
fs - Variable in class edu.jhu.ece.iacl.algorithms.dti.GTCparams
 
FULL_WEIGHTING - Static variable in class edu.jhu.cs.cisst.algorithms.optimize.fmg.restrictor.RestrictorByStencil
the stencil that characterises full weighting.
FULL_WEIGHTING_2D - Static variable in class edu.jhu.cs.cisst.algorithms.optimize.fmg.restrictor.RestrictorByStencil
The Constant FULL_WEIGHTING_2D.
funcInit() - Static method in class edu.jhu.bme.smile.commons.optimize.test.Test1DOptimizations
Initializes the function.
funcInit() - Static method in class edu.jhu.bme.smile.commons.optimize.test.TestNDOptimizations
Initializes the function.
FunctionExponential - Class in edu.jhu.bme.smile.commons.optimize.test
Test case to test 1D optimizers.
FunctionExponential() - Constructor for class edu.jhu.bme.smile.commons.optimize.test.FunctionExponential
Default constructor.
FunctionExponential(double, double) - Constructor for class edu.jhu.bme.smile.commons.optimize.test.FunctionExponential
Constructor to set the domain.
FunctionNegativeXSquared - Class in edu.jhu.bme.smile.commons.optimize.test
Test case to test 1D optimizers.
FunctionNegativeXSquared() - Constructor for class edu.jhu.bme.smile.commons.optimize.test.FunctionNegativeXSquared
Default constuctor.
FunctionNegativeXSquared(double, double, double) - Constructor for class edu.jhu.bme.smile.commons.optimize.test.FunctionNegativeXSquared
Constructor to specify extrema and domain.
FunctionNegativeXSquaredND - Class in edu.jhu.bme.smile.commons.optimize.test
Test case to test ND optimizers.
FunctionNegativeXSquaredND(int) - Constructor for class edu.jhu.bme.smile.commons.optimize.test.FunctionNegativeXSquaredND
Default constuctor.
FunctionNegativeXSquaredND(int, double[], double[], double[]) - Constructor for class edu.jhu.bme.smile.commons.optimize.test.FunctionNegativeXSquaredND
Constructor to specify extrema and domain.
FunctionNumeric1DDifferentiation - Class in edu.jhu.bme.smile.commons.optimize
This class does numeric differentiation in 1D.
FunctionNumeric1DDifferentiation(Optimizable1DContinuous) - Constructor for class edu.jhu.bme.smile.commons.optimize.FunctionNumeric1DDifferentiation
Constructor to create a 1D differentiable object.
FunctionNumeric1DDifferentiation(Optimizable1DContinuous, double, int) - Constructor for class edu.jhu.bme.smile.commons.optimize.FunctionNumeric1DDifferentiation
Constructor to create a 1D differentiable object.
FunctionNumericND1DDifferentiation - Class in edu.jhu.bme.smile.commons.optimize
A wrapper class used to facilitate getting derivatives of ND functions along each dimension individually
FunctionNumericND1DDifferentiation(OptimizableNDContinuous, int) - Constructor for class edu.jhu.bme.smile.commons.optimize.FunctionNumericND1DDifferentiation
Creates object to be used for getting a derivative of an ND function along 1-dimension, but contains the information to take more derivatives, along another other dimension as well.
FunctionNumericND1DDifferentiation(OptimizableNDContinuous, int, double, int) - Constructor for class edu.jhu.bme.smile.commons.optimize.FunctionNumericND1DDifferentiation
Creates object to be used for getting a derivative of an ND function along 1-dimension, but contains the information to take more derivatives, along another other dimension as well.
FunctionNumericNDDifferentiation - Class in edu.jhu.bme.smile.commons.optimize
This class does numeric differentiation in ND.
FunctionNumericNDDifferentiation(OptimizableNDContinuous) - Constructor for class edu.jhu.bme.smile.commons.optimize.FunctionNumericNDDifferentiation
Creates an object which can differentiate an ND function with default values.
FunctionNumericNDDifferentiation(OptimizableNDContinuous, double, int) - Constructor for class edu.jhu.bme.smile.commons.optimize.FunctionNumericNDDifferentiation
Creates an object which can differentiate an ND function in various ways.
FunctionRosenbrock - Class in edu.jhu.bme.smile.commons.optimize.test
Test case to test ND optimizers.
FunctionRosenbrock() - Constructor for class edu.jhu.bme.smile.commons.optimize.test.FunctionRosenbrock
Default constructor.
FunctionRosenbrock(double[], double[]) - Constructor for class edu.jhu.bme.smile.commons.optimize.test.FunctionRosenbrock
Constructor to set the domain.
FunctionXSquared - Class in edu.jhu.bme.smile.commons.optimize.test
Test case to test 1D optimizers.
FunctionXSquared() - Constructor for class edu.jhu.bme.smile.commons.optimize.test.FunctionXSquared
Default constuctor.
FunctionXSquared(double, double, double) - Constructor for class edu.jhu.bme.smile.commons.optimize.test.FunctionXSquared
Constructor to specify extrema and domain.
FunctionXSquaredND - Class in edu.jhu.bme.smile.commons.optimize.test
Test case to test ND optimizers.
FunctionXSquaredND(int) - Constructor for class edu.jhu.bme.smile.commons.optimize.test.FunctionXSquaredND
Default constuctor.
FunctionXSquaredND(int, double[], double[], double[]) - Constructor for class edu.jhu.bme.smile.commons.optimize.test.FunctionXSquaredND
Constructor to specify extrema and domain.
FunctionXXplusSinXX - Class in edu.jhu.bme.smile.commons.optimize.test
Test case to test 1D optimizers.
FunctionXXplusSinXX() - Constructor for class edu.jhu.bme.smile.commons.optimize.test.FunctionXXplusSinXX
Default constuctor.
FunctionXXplusSinXX(double, double, double) - Constructor for class edu.jhu.bme.smile.commons.optimize.test.FunctionXXplusSinXX
Constructor to specify extrema and domain.
FunctionXXplusSinXXND - Class in edu.jhu.bme.smile.commons.optimize.test
Test case to test ND optimizers.
FunctionXXplusSinXXND(int) - Constructor for class edu.jhu.bme.smile.commons.optimize.test.FunctionXXplusSinXXND
Default constuctor.
FunctionXXplusSinXXND(int, double[], double[], double[]) - Constructor for class edu.jhu.bme.smile.commons.optimize.test.FunctionXXplusSinXXND
Constructor to specify extrema and domain.
FunctionXXYYND - Class in edu.jhu.bme.smile.commons.optimize.test
Test case to test ND optimizers.
FunctionXXYYND(int) - Constructor for class edu.jhu.bme.smile.commons.optimize.test.FunctionXXYYND
Default constuctor.
FunctionXXYYND(int, double[], double[], double[]) - Constructor for class edu.jhu.bme.smile.commons.optimize.test.FunctionXXYYND
Constructor to specify extrema and domain.
FunkRadonTransform - Class in edu.jhu.ece.iacl.plugins.hardi
 
FunkRadonTransform() - Constructor for class edu.jhu.ece.iacl.plugins.hardi.FunkRadonTransform
 

G

g - Variable in class edu.jhu.cs.cisst.algorithms.optimize.fmg.grid.Grid
 
g - Variable in class edu.jhu.ece.iacl.algorithms.dti.tractography.FACT.RGB
 
g - Variable in class edu.jhu.ece.iacl.jist.structures.image.RGB
The b.
GaussianArrayKernel - Class in edu.jhu.ece.iacl.jist.structures.image
Create one-dimensional guassian kernel with specified sigma.
GaussianArrayKernel(double) - Constructor for class edu.jhu.ece.iacl.jist.structures.image.GaussianArrayKernel
Create gaussian kernel for specified sigma.
gaussianCurvature(float[][]) - Static method in class edu.jhu.cs.cisst.algorithms.util.DataOperations
Gaussian curvature.
GaussianCurvatureForce2D - Class in edu.jhu.cs.cisst.algorithms.segmentation.gac
The Class GaussianCurvatureForce2D moves the level set using Gaussian curvature, defined as the determinant of the second fundamental form divided by the determinant of the first fundamental form.
GaussianCurvatureForce2D() - Constructor for class edu.jhu.cs.cisst.algorithms.segmentation.gac.GaussianCurvatureForce2D
 
gaussianKernel(float, float, float) - Static method in class edu.jhmi.rad.medic.libraries.ImageFunctionsPublic
Gaussian kernel
GaussianVolumeKernel - Class in edu.jhu.ece.iacl.jist.structures.image
The Class GaussianVolumeKernel.
GaussianVolumeKernel(double, double, double) - Constructor for class edu.jhu.ece.iacl.jist.structures.image.GaussianVolumeKernel
Create gaussian kernel for convolution.
gedge - Variable in class edu.jhu.ece.iacl.jist.pipeline.PipeConnector
graph edge representing this connector.
genConfRaterSurface() - Method in class edu.jhu.ece.iacl.algorithms.manual_label.simulation.SurfaceRater
Calls genConfusionRater using this class's data
genConfRaterVolume() - Method in class edu.jhu.ece.iacl.algorithms.manual_label.simulation.VolumeRater
 
genConfusionRater(EmbeddedSurface, ConfusionMatrix, int, int[]) - Static method in class edu.jhu.ece.iacl.algorithms.manual_label.simulation.SurfaceRater
Returns a rater surface by passing the label at each vertex through a confusion matrix.
genConfusionRater(ImageData, ConfusionMatrix) - Static method in class edu.jhu.ece.iacl.algorithms.manual_label.simulation.VolumeRater
Returns a rater volume by passing the label at each point through a confusion matrix.
generalizedSurfaceFlows - Static variable in class edu.jhu.ece.iacl.algorithms.ReferencedPapers
 
generate(EmbeddedSurface) - Static method in class edu.jhu.ece.iacl.jist.structures.geom.NormalGenerator
Generate.
generate(Point3f[], int[]) - Static method in class edu.jhu.ece.iacl.jist.structures.geom.NormalGenerator
Generate.
generateMemoryReport() - Static method in class edu.jhu.ece.iacl.plugins.labeling.MedicAlgorithmMultiAtlasSurfaceLabeling
 
GenerateTensors - Class in edu.jhu.ece.iacl.pami
 
GenerateTensors() - Constructor for class edu.jhu.ece.iacl.pami.GenerateTensors
 
genNextLabel(int) - Method in class edu.jhu.ece.iacl.algorithms.manual_label.simulation.ConfusionMatrix
Given a true label, outputs this rater's label based on the confusion matrix
genNextLabelFromIndex(int) - Method in class edu.jhu.ece.iacl.algorithms.manual_label.simulation.ConfusionMatrix
Given a true label's index, outputs this rater's label based on the confusion matrix
genPerimRaterOld(EmbeddedSurface, float[], int[], float, int) - Static method in class edu.jhu.ece.iacl.algorithms.manual_label.simulation.SurfaceRater
Returns a rater surface by modifying boundary vertex labels until
genPerimRaterSurface() - Method in class edu.jhu.ece.iacl.algorithms.manual_label.simulation.SurfaceRater
Returns a simulated rater surface
genPerimRaterVolume() - Method in class edu.jhu.ece.iacl.algorithms.manual_label.simulation.VolumeRater
Returns a simulated rater volume
GeodesicActiveContour2D - Class in edu.jhu.cs.cisst.algorithms.segmentation.gac
The Class GeodesicActiveContour2D segments an image using the sparse matrix method.
GeodesicActiveContour2D(ImageData) - Constructor for class edu.jhu.cs.cisst.algorithms.segmentation.gac.GeodesicActiveContour2D
Instantiates a new geodesic active contour.
geometricTools - Static variable in class edu.jhu.ece.iacl.algorithms.ReferencedPapers
 
geometryDrivenOpticalFlow - Static variable in class edu.jhu.ece.iacl.algorithms.ReferencedPapers
 
GeomUtil - Class in edu.jhu.ece.iacl.jist.algorithms.graphics
The Class GeomUtil.
GeomUtil() - Constructor for class edu.jhu.ece.iacl.jist.algorithms.graphics.GeomUtil
 
get(int, int, int) - Method in interface edu.jhu.cs.cisst.algorithms.optimize.fmg.grid.ConstGrid
returns the element at the specified position.
get(int, int, int) - Method in class edu.jhu.cs.cisst.algorithms.optimize.fmg.grid.Grid
implements method from ConstGrid.
get(int, int, int) - Method in interface edu.jhu.cs.cisst.algorithms.optimize.fmg.Stencil
gets the element at the specified position.
get(int, int, int) - Method in class edu.jhu.cs.cisst.algorithms.optimize.fmg.StencilImpl
implements method from Stencil.
get(int, int, int) - Method in class edu.jhu.ece.iacl.algorithms.manual_label.staple.PerformanceLevel
 
get(int, int) - Method in class edu.jhu.ece.iacl.jist.structures.image.ImageData
Gets the.
get(int, int, int) - Method in class edu.jhu.ece.iacl.jist.structures.image.ImageData
Get voxel.
get(int, int, int, int) - Method in class edu.jhu.ece.iacl.jist.structures.image.ImageData
Get vector component for volume.
get(int, int, int, int) - Method in class edu.jhu.ece.iacl.jist.structures.image.ImageDataByte
 
get(int, int, int, int) - Method in class edu.jhu.ece.iacl.jist.structures.image.ImageDataColor
 
get(int, int, int, int) - Method in class edu.jhu.ece.iacl.jist.structures.image.ImageDataDouble
 
get(int, int, int, int) - Method in class edu.jhu.ece.iacl.jist.structures.image.ImageDataFloat
 
get(int, int, int, int) - Method in class edu.jhu.ece.iacl.jist.structures.image.ImageDataInt
 
get(int, int, int, int) - Method in class edu.jhu.ece.iacl.jist.structures.image.ImageDataMipav
 
get(int, int, int, int) - Method in class edu.jhu.ece.iacl.jist.structures.image.ImageDataNumber
 
get(int, int, int, int) - Method in class edu.jhu.ece.iacl.jist.structures.image.ImageDataUByte
 
get(int, int, int, int, ImageData) - Static method in class edu.jhu.ece.iacl.jist.structures.image.MaskVolume6
Gets the.
get(int, int, int) - Method in class edu.jhu.ece.iacl.jist.structures.matrix.Matrix3
Gets the.
get(int, int, int, int) - Method in class edu.jhu.ece.iacl.jist.structures.matrix.VectorMatrixX
Gets the.
get(int, int, int) - Method in class edu.jhu.ece.iacl.jist.structures.matrix.VectorMatrixX
Gets the.
get(int) - Method in class edu.jhu.ece.iacl.jist.structures.vector.Vector2
 
get(int) - Method in class edu.jhu.ece.iacl.jist.structures.vector.Vector3
 
get(int) - Method in class edu.jhu.ece.iacl.jist.structures.vector.Vector4
 
get(int) - Method in class edu.jhu.ece.iacl.jist.structures.vector.VectorN
 
get(int) - Method in interface edu.jhu.ece.iacl.jist.structures.vector.VectorX
Gets the.
get(int, int, int, int) - Method in class edu.jhu.ece.iacl.plugins.dti.MetaImageData4D
 
get2ndDerivative(double) - Method in class edu.jhu.bme.smile.commons.optimize.FunctionNumeric1DDifferentiation
Gets the second derivative
get2ndDerivative(double[], int, int) - Method in class edu.jhu.bme.smile.commons.optimize.FunctionNumericNDDifferentiation
Gets 2nd partial derivative for the dimensions given
get2ndDerivative(double[]) - Method in class edu.jhu.bme.smile.commons.optimize.FunctionNumericNDDifferentiation
Creates the hessian matrix
get2ndDerivative(double) - Method in class edu.jhu.bme.smile.commons.optimize.MinToMax1DDifferentiable
Gets the negated second derivative
get2ndDerivative(double[]) - Method in class edu.jhu.bme.smile.commons.optimize.MinToMaxNDDifferentiable
Gets the negated hessian
get2ndDerivative(double[], int, int) - Method in class edu.jhu.bme.smile.commons.optimize.MinToMaxNDDifferentiable
Gets the negated second derivative in a specific direction
get2ndDerivative(double) - Method in interface edu.jhu.bme.smile.commons.optimize.Optimizable1DContinuousDifferentiable
Gets the value of the 2nd derivative of the function.
get2ndDerivative(double[]) - Method in interface edu.jhu.bme.smile.commons.optimize.OptimizableNDContinuousDifferentiable
Gets the hessian of the function.
get2ndDerivative(double[], int, int) - Method in interface edu.jhu.bme.smile.commons.optimize.OptimizableNDContinuousDifferentiable
Gets the second derivative of the function in a specific direction
get2ndDerivative(double) - Method in class edu.jhu.bme.smile.commons.optimize.ProjectNDto1DOptimizableDifferentiable
Gets the second derivative at location x in the current dimension.
get2ndDerivative(double) - Method in class edu.jhu.bme.smile.commons.optimize.test.FunctionExponential
Gets the second derivative of the function.
get2ndDerivative(double, double, int) - Method in class edu.jhu.bme.smile.commons.optimize.test.FunctionExponential
Gets the second derivative of the function.
get2ndDerivative(double) - Method in class edu.jhu.bme.smile.commons.optimize.test.FunctionNegativeXSquared
Gets the second derivative of the function.
get2ndDerivative(double, double, int) - Method in class edu.jhu.bme.smile.commons.optimize.test.FunctionNegativeXSquared
Gets the second derivative of the function.
get2ndDerivative(double[]) - Method in class edu.jhu.bme.smile.commons.optimize.test.FunctionNegativeXSquaredND
Gets the hessian of the function.
get2ndDerivative(double[], double, int) - Method in class edu.jhu.bme.smile.commons.optimize.test.FunctionNegativeXSquaredND
Gets the hessian of the function.
get2ndDerivative(double[], int, int) - Method in class edu.jhu.bme.smile.commons.optimize.test.FunctionNegativeXSquaredND
Gets the 2nd derivative of the function in a specific direction.
get2ndDerivative(double[]) - Method in class edu.jhu.bme.smile.commons.optimize.test.FunctionRosenbrock
Gets the hessian of the function.
get2ndDerivative(double[], double, int) - Method in class edu.jhu.bme.smile.commons.optimize.test.FunctionRosenbrock
Gets the hessian of the function.
get2ndDerivative(double[], int, int) - Method in class edu.jhu.bme.smile.commons.optimize.test.FunctionRosenbrock
Gets the 2nd derivative of the function in a specific direction.
get2ndDerivative(double) - Method in class edu.jhu.bme.smile.commons.optimize.test.FunctionXSquared
Gets the second derivative of the function.
get2ndDerivative(double, double, int) - Method in class edu.jhu.bme.smile.commons.optimize.test.FunctionXSquared
Gets the second derivative of the function.
get2ndDerivative(double[]) - Method in class edu.jhu.bme.smile.commons.optimize.test.FunctionXSquaredND
Gets the hessian of the function.
get2ndDerivative(double[], double, int) - Method in class edu.jhu.bme.smile.commons.optimize.test.FunctionXSquaredND
Gets the hessian of the function.
get2ndDerivative(double[], int, int) - Method in class edu.jhu.bme.smile.commons.optimize.test.FunctionXSquaredND
Gets the 2nd derivative of the function in a specific direction.
get2ndDerivative(double) - Method in class edu.jhu.bme.smile.commons.optimize.test.FunctionXXplusSinXX
Gets the second derivative of the function.
get2ndDerivative(double, double, int) - Method in class edu.jhu.bme.smile.commons.optimize.test.FunctionXXplusSinXX
Gets the second derivative of the function.
get2ndDerivative(double[]) - Method in class edu.jhu.bme.smile.commons.optimize.test.FunctionXXplusSinXXND
Gets the hessian of the function.
get2ndDerivative(double[], double, int) - Method in class edu.jhu.bme.smile.commons.optimize.test.FunctionXXplusSinXXND
Gets the hessian of the function.
get2ndDerivative(double[], int, int) - Method in class edu.jhu.bme.smile.commons.optimize.test.FunctionXXplusSinXXND
Gets the 2nd derivative of the function in a specific direction.
get2ndDerivative(double[]) - Method in class edu.jhu.bme.smile.commons.optimize.test.FunctionXXYYND
Gets the hessian of the function.
get2ndDerivative(double[], double, int) - Method in class edu.jhu.bme.smile.commons.optimize.test.FunctionXXYYND
Gets the hessian of the function.
get2ndDerivative(double[], int, int) - Method in class edu.jhu.bme.smile.commons.optimize.test.FunctionXXYYND
Gets the 2nd derivative of the function in a specific direction.
get_version() - Static method in class edu.jhu.ece.iacl.algorithms.manual_label.FastMarchingLabelExtension
 
get_version() - Static method in class edu.jhu.ece.iacl.algorithms.manual_label.LabelImage
 
get_version() - Static method in class edu.jhu.ece.iacl.algorithms.manual_label.LabelSurface
 
getAboutFile() - Method in class edu.jhu.ece.iacl.jist.pipeline.ProcessingAlgorithm
Location of file that describes the algorithm.
getAbsoluteAverage() - Method in class edu.jhu.ece.iacl.algorithms.volume.CompareVolumes
 
getActiveFrame() - Method in class edu.jhu.ece.iacl.jist.pipeline.gui.LayoutPanel
Return currently selected frame.
getActualTime() - Method in class edu.jhu.ece.iacl.jist.pipeline.ExecutionContext
Gets the actual time.
getAdjacencies() - Method in class edu.jhu.ece.iacl.jist.structures.geom.EmbeddedPointSet
Gets the adjacencies.
getAffiliation() - Method in class edu.jhu.ece.iacl.jist.pipeline.AlgorithmInformation
Gets the affiliation.
getAlgorithm() - Method in class edu.jhu.ece.iacl.jist.pipeline.ExecutionContext
Get algorithm.
getAlgorithm() - Method in class edu.jhu.ece.iacl.jist.pipeline.PipeAlgorithm
Get Processing Algorithm wrapped by this pipe module.
getAlgorithm() - Method in class edu.jhu.ece.iacl.jist.pipeline.ProcessingApplication
Get the algorithm used by this processing module.
getAlgorithmClass() - Method in class edu.jhu.ece.iacl.jist.pipeline.AlgorithmInformation
Gets the algorithm class.
getAlgorithmClass() - Method in class edu.jhu.ece.iacl.jist.pipeline.PipeAlgorithm
Get the Processing Algorithm class from the input parameters.
getAlgorithmClass() - Method in class edu.jhu.ece.iacl.jist.pipeline.PipeAlgorithmGroup
Always returns null.
getAlgorithmClassName() - Method in class edu.jhu.ece.iacl.jist.pipeline.AlgorithmInformation
Gets the algorithm class name.
getAlgorithmInformation() - Method in class edu.jhu.ece.iacl.jist.pipeline.ProcessingAlgorithm
Get algorithm information for this algorithm.
getAlgorithmLabel() - Method in class edu.jhu.ece.iacl.jist.pipeline.ProcessingAlgorithm
Get algorithm label from input parameters.
getAlgorithmName() - Method in class edu.jhu.ece.iacl.jist.pipeline.ProcessingAlgorithm
Get algorithm name from input parameters.
getAllClasses(String[], Class) - Static method in class edu.jhu.ece.iacl.jist.cli.discover
 
getAllClasses(String) - Static method in class edu.jhu.ece.iacl.jist.pipeline.PipeLibrary
Gets the all classes.
getAllClasses(String, String) - Static method in class edu.jhu.ece.iacl.jist.pipeline.PipeLibrary
Get all classes starting from root package name.
getAllDescedants(boolean) - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamCollection
Get all descendants.
getAllDescendantModules() - Method in class edu.jhu.ece.iacl.jist.pipeline.PipeAlgorithmGroup
Get all descendant modules in group.
getAllDescendantPipes() - Method in class edu.jhu.ece.iacl.jist.pipeline.PipeLayout
Get all modules including parents and children.
getAllDescendants() - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamCollection
Get all children, including hidden ones.
getAllDescendantsByClass(Class, List<ParamModel>) - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamCollection
Get all descendants and append them to the list.
getAllDescendantsByClass(Class) - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamCollection
Get all descendants by class.
getAllElapsedActualTimes() - Method in class edu.jhu.ece.iacl.jist.pipeline.PerformanceSummary
Get list of elapsed times in msec.
getAllElapsedCPUTimes() - Method in class edu.jhu.ece.iacl.jist.pipeline.PerformanceSummary
Get list of elapsed times in msec.
getallFiberLengths(String) - Method in class edu.jhu.ece.iacl.algorithms.dti.tractography.FACT.DTIStudioReader
 
getAllLeafModules() - Method in class edu.jhu.ece.iacl.jist.pipeline.PipeAlgorithmGroup
Get all leaf modules.
getAllLeafPipes() - Method in class edu.jhu.ece.iacl.jist.pipeline.PipeLayout
Get all leaf modules.
getAllocatedMemory() - Method in class edu.jhu.ece.iacl.jist.pipeline.ExecutionContext
Get amount of allocated memory.
getAllTaskNames() - Method in class edu.jhu.ece.iacl.jist.pipeline.PerformanceSummary
Get list of task names.
getAllValues() - Method in class edu.jhu.ece.iacl.algorithms.manual_label.LabelSurface
 
getAllVisibleDescendants() - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamCollection
Get all visible descendants.
getAncestors() - Method in class edu.jhu.ece.iacl.jist.pipeline.PipeModule
Get all modules that may effect the input parameters to this module.
getAncestors(Vector<PipeModule>) - Method in class edu.jhu.ece.iacl.jist.pipeline.PipeModule
Get all ancestor modules and append them to the list.
getAncestorTree() - Method in class edu.jhu.ece.iacl.jist.pipeline.ExecutionContext
Get ancestor tree.
getArcSize(int, int) - Static method in class edu.jhu.ece.iacl.jist.pipeline.graph.PipeAlgorithmGroupView
getArcSize calculates an appropriate arc for the corners of the rectangle for boundary size cases of width and height.
getArcSize(int, int) - Static method in class edu.jhu.ece.iacl.jist.pipeline.graph.PipeAlgorithmView
getArcSize calculates an appropriate arc for the corners of the rectangle for boundary size cases of width and height.
getArea(EmbeddedSurface) - Method in class edu.jhu.ece.iacl.jist.structures.geom.EmbeddedSurface.Face
Gets the area.
getArray() - Method in interface edu.jhu.ece.iacl.jist.structures.image.ConvolutionArrayKernel
Gets the array.
getArray() - Method in class edu.jhu.ece.iacl.jist.structures.image.GaussianArrayKernel
 
getAssertions() - Method in class edu.jhu.ece.iacl.doc.DocumentAllTests.TestCase
 
getAuthor() - Method in class edu.jhu.ece.iacl.jist.pipeline.AlgorithmInformation.AlgorithmAuthor
Gets the author.
getAuthor() - Method in class edu.jhu.ece.iacl.jist.pipeline.view.input.AlgorithmInformationDialog.AuthorDialog
Gets the author.
getAuthors() - Method in class edu.jhu.ece.iacl.jist.pipeline.AlgorithmInformation
Gets the authors.
getAverage() - Method in class edu.jhu.ece.iacl.algorithms.volume.CompareVolumes
 
getAxisOrientation() - Method in class edu.jhu.ece.iacl.jist.structures.image.ImageHeader
Gets the axis orientation.
getB0() - Method in class edu.jhu.bme.smile.commons.optimize.tensor.MLTensor
Gets the value of b0
getB0() - Method in class edu.jhu.ece.iacl.algorithms.dti.DTEMRLTensor
Gets the value of b0
getb0() - Method in class edu.jhu.ece.iacl.algorithms.dti.DWICoReg
 
getBarycentrics(Point3f, int) - Method in class edu.jhu.ece.iacl.jist.structures.geom.EmbeddedPointSet
Gets the barycentrics.
getBasisSet() - Method in class edu.jhu.ece.iacl.algorithms.hardi.CFARIBasisSet
 
getBins() - Method in class edu.jhu.bme.smile.commons.math.HistogramGenerator
 
getBoolean(int, int) - Method in class edu.jhu.ece.iacl.jist.structures.image.ImageData
Gets the boolean.
getBoolean(int, int, int) - Method in class edu.jhu.ece.iacl.jist.structures.image.ImageData
Gets the boolean.
getBoolean(int, int, int, int) - Method in class edu.jhu.ece.iacl.jist.structures.image.ImageData
Gets the boolean.
getBoolean(int, int, int, int) - Method in class edu.jhu.ece.iacl.jist.structures.image.ImageDataByte
 
getBoolean(int, int, int, int) - Method in class edu.jhu.ece.iacl.jist.structures.image.ImageDataColor
 
getBoolean(int, int, int, int) - Method in class edu.jhu.ece.iacl.jist.structures.image.ImageDataDouble
 
getBoolean(int, int, int, int) - Method in class edu.jhu.ece.iacl.jist.structures.image.ImageDataFloat
 
getBoolean(int, int, int, int) - Method in class edu.jhu.ece.iacl.jist.structures.image.ImageDataInt
 
getBoolean(int, int, int, int) - Method in class edu.jhu.ece.iacl.jist.structures.image.ImageDataMipav
 
getBoolean(int, int, int, int) - Method in class edu.jhu.ece.iacl.jist.structures.image.ImageDataNumber
 
getBoolean(int, int, int, int) - Method in class edu.jhu.ece.iacl.jist.structures.image.ImageDataUByte
 
getBoolean() - Method in class edu.jhu.ece.iacl.jist.structures.image.Voxel
Gets the boolean.
getBoolean() - Method in class edu.jhu.ece.iacl.jist.structures.image.VoxelBoolean
 
getBoolean() - Method in class edu.jhu.ece.iacl.jist.structures.image.VoxelColor
 
getBoolean() - Method in class edu.jhu.ece.iacl.jist.structures.image.VoxelDouble
 
getBoolean() - Method in class edu.jhu.ece.iacl.jist.structures.image.VoxelFloat
 
getBoolean() - Method in class edu.jhu.ece.iacl.jist.structures.image.VoxelIndexed
 
getBoolean() - Method in class edu.jhu.ece.iacl.jist.structures.image.VoxelInt
 
getBoolean() - Method in class edu.jhu.ece.iacl.jist.structures.image.VoxelMipav
 
getBoolean() - Method in class edu.jhu.ece.iacl.jist.structures.image.VoxelShort
 
getBoolean() - Method in class edu.jhu.ece.iacl.jist.structures.image.VoxelUByte
 
getBoolean() - Method in class edu.jhu.ece.iacl.jist.structures.image.VoxelVector
 
getBorder() - Method in class edu.jhu.ece.iacl.jist.pipeline.graph.PipeEdgeEditor.DefaultSpinner
Overrides JComponent.getBorder to returns the current border.
getBoundary(int, int, int) - Method in class edu.jhu.cs.cisst.algorithms.optimize.fmg.grid.FixedBoundaryGrid
implements method from Grid.
getBoundary(int, int, int) - Method in class edu.jhu.cs.cisst.algorithms.optimize.fmg.grid.Grid
get an element from the boundary of the grid.
getBoundary(int, int, int) - Method in class edu.jhu.cs.cisst.algorithms.optimize.fmg.grid.NoBoundaryGrid
implements method from Grid.
getBoundary(int, int, int) - Method in class edu.jhu.cs.cisst.algorithms.optimize.fmg.grid.PeriodicBoundaryGrid
implements method from Grid.
getBoundary(int, int, int) - Method in class edu.jhu.cs.cisst.algorithms.optimize.fmg.grid.RepeatBoundaryGrid
implements method from Grid.
getBoundarySizes() - Method in class edu.jhu.ece.iacl.algorithms.manual_label.simulation.VolumeRater
 
getBoundingBox() - Method in class edu.jhu.cs.cisst.vent.renderer.processing.RendererProcessing3D
Gets the bounding box.
getBoundingBox() - Method in class edu.jhu.ece.iacl.algorithms.vabra.ImagePair
 
getBounds() - Method in class edu.jhu.ece.iacl.jist.pipeline.PipeModule
Rectangular bounds for graphical representation.
getBounds(ArrayList<CollisionDetection.Triangle>) - Static method in class edu.jhu.ece.iacl.jist.structures.geom.CollisionDetection.Triangle
Gets the bounds.
getbVals() - Method in class edu.jhu.ece.iacl.algorithms.dti.ParV3Info
 
getbVals() - Method in class edu.jhu.ece.iacl.algorithms.dti.ParV4Info
 
getbValues() - Method in class edu.jhu.ece.iacl.algorithms.dti.DTIGradientTableCreator
 
getByte(int, int) - Method in class edu.jhu.ece.iacl.jist.structures.image.ImageData
Gets the u byte.
getByte(int, int, int) - Method in class edu.jhu.ece.iacl.jist.structures.image.ImageData
Gets the u byte.
getByte(int, int, int, int) - Method in class edu.jhu.ece.iacl.jist.structures.image.ImageData
Gets the u byte.
getByte(int, int, int, int) - Method in class edu.jhu.ece.iacl.jist.structures.image.ImageDataByte
 
getByte(int, int, int, int) - Method in class edu.jhu.ece.iacl.jist.structures.image.ImageDataColor
 
getByte(int, int, int, int) - Method in class edu.jhu.ece.iacl.jist.structures.image.ImageDataDouble
 
getByte(int, int, int, int) - Method in class edu.jhu.ece.iacl.jist.structures.image.ImageDataFloat
 
getByte(int, int, int, int) - Method in class edu.jhu.ece.iacl.jist.structures.image.ImageDataInt
 
getByte(int, int, int, int) - Method in class edu.jhu.ece.iacl.jist.structures.image.ImageDataMipav
 
getByte(int, int, int, int) - Method in class edu.jhu.ece.iacl.jist.structures.image.ImageDataUByte
 
getCallers() - Method in class edu.jhu.ece.iacl.jist.pipeline.ExecutionContext
Get contexts that call this context.
getCategory() - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamCollection
 
getCategory() - Method in class edu.jhu.ece.iacl.jist.pipeline.PipeAlgorithm
Gets the category.
getCell() - Method in class edu.jhu.ece.iacl.jist.pipeline.graph.PipeAlgorithmGroupView
 
getCell() - Method in class edu.jhu.ece.iacl.jist.pipeline.graph.PipeAlgorithmView
 
getCellData() - Method in class edu.jhu.ece.iacl.jist.structures.geom.EmbeddedPointSet
Gets the cell data.
getCellData() - Method in class edu.jhu.ece.iacl.jist.structures.geom.EmbeddedSurface
 
getCellEditorValue() - Method in class edu.jhu.ece.iacl.jist.pipeline.graph.PipeEdgeRealEditor.EditorDelegate
Returns the value of this cell.
getCellEditorValue() - Method in class edu.jhu.ece.iacl.jist.pipeline.graph.PipeEdgeRealEditor
Forwards the message from the CellEditor to the delegate.
getCenterOfMass() - Method in class edu.jhu.ece.iacl.jist.structures.geom.EmbeddedSurface
Gets the center of mass.
getCentroid(int) - Method in class edu.jhu.ece.iacl.jist.structures.geom.EmbeddedSurface
Gets the centroid.
getCentroidAtOffset(int, int) - Method in class edu.jhu.ece.iacl.jist.structures.geom.EmbeddedSurface
Gets the centroid at offset.
getChain() - Method in class edu.jhu.ece.iacl.jist.structures.fiber.Fiber
Gets the chain.
getChainIndex() - Method in interface edu.jhu.ece.iacl.jist.structures.data.Indexable
Gets the chain index.
getChainIndex() - Method in class edu.jhu.ece.iacl.jist.structures.geom.EdgeIndexed
 
getChainIndex() - Method in class edu.jhu.ece.iacl.jist.structures.geom.VertexIndexed
 
getChainIndex() - Method in class edu.jhu.ece.iacl.jist.structures.image.VoxelIndexed
 
getChainIndex() - Method in class edu.jhu.ece.iacl.jist.structures.image.VoxelMipav
 
getChecker() - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamCollection
Get compatibility checker.
getChildPort() - Method in class edu.jhu.ece.iacl.jist.pipeline.PipeSource
Get port for child connection.
getChildren() - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamCollection
Get child parameters.
getChildren() - Method in class edu.jhu.ece.iacl.jist.pipeline.PipeModule
Get Pipe Modules that receive data from this module.
getChildrenCells() - Method in class edu.jhu.ece.iacl.jist.pipeline.graph.PipeAlgorithmFactory.AlgorithmGroupCell
Get children cells.
getChildrenHash() - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamCollection
Get hash that maps parameter names to parameters.
getCitation() - Method in class edu.jhu.ece.iacl.jist.pipeline.view.input.AlgorithmInformationDialog.CitationDialog
Gets the citation.
getCitations() - Method in class edu.jhu.ece.iacl.doc.DocMediaWikiWriter
 
getCitations() - Method in class edu.jhu.ece.iacl.jist.pipeline.AlgorithmInformation
Gets the citations.
getClassTag() - Method in interface edu.jhu.ece.iacl.jist.pipeline.parser.JISTDynamicPluginLookup
 
getClassTag() - Method in class edu.jhu.ece.iacl.jist.pipeline.parser.MipavPluginParser
 
getClickCountToStart() - Method in class edu.jhu.ece.iacl.jist.pipeline.graph.PipeEdgeRealEditor
Returns the number of clicks needed to start editing.
getCliTag() - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamModel
 
getCoeff(int, int, double, double) - Static method in class edu.jhu.bme.smile.commons.math.specialFunctions.SphericalHarmonics
% NOTE: It is very important to keep the various usages of THETA and PHI % straight.
getColor() - Method in class edu.jhu.ece.iacl.jist.structures.fiber.Fiber
Gets the color.
getColor(int, int) - Method in class edu.jhu.ece.iacl.jist.structures.image.ImageData
Gets the color.
getColor(int, int, int) - Method in class edu.jhu.ece.iacl.jist.structures.image.ImageData
Gets the color.
getColor(int, int, int, int) - Method in class edu.jhu.ece.iacl.jist.structures.image.ImageData
Gets the color.
getColor(int, int, int, int) - Method in class edu.jhu.ece.iacl.jist.structures.image.ImageDataByte
 
getColor(int, int, int, int) - Method in class edu.jhu.ece.iacl.jist.structures.image.ImageDataColor
 
getColor(int, int, int, int) - Method in class edu.jhu.ece.iacl.jist.structures.image.ImageDataDouble
 
getColor(int, int, int, int) - Method in class edu.jhu.ece.iacl.jist.structures.image.ImageDataFloat
 
getColor(int, int, int, int) - Method in class edu.jhu.ece.iacl.jist.structures.image.ImageDataInt
 
getColor(int, int, int, int) - Method in class edu.jhu.ece.iacl.jist.structures.image.ImageDataMipav
 
getColor(int, int, int, int) - Method in class edu.jhu.ece.iacl.jist.structures.image.ImageDataNumber
 
getColor(int, int, int, int) - Method in class edu.jhu.ece.iacl.jist.structures.image.ImageDataUByte
 
getColor() - Method in class edu.jhu.ece.iacl.jist.structures.image.Voxel
Gets the color.
getColor() - Method in class edu.jhu.ece.iacl.jist.structures.image.VoxelBoolean
 
getColor() - Method in class edu.jhu.ece.iacl.jist.structures.image.VoxelColor
 
getColor() - Method in class edu.jhu.ece.iacl.jist.structures.image.VoxelDouble
 
getColor() - Method in class edu.jhu.ece.iacl.jist.structures.image.VoxelFloat
 
getColor() - Method in class edu.jhu.ece.iacl.jist.structures.image.VoxelIndexed
 
getColor() - Method in class edu.jhu.ece.iacl.jist.structures.image.VoxelInt
 
getColor() - Method in class edu.jhu.ece.iacl.jist.structures.image.VoxelMipav
 
getColor() - Method in class edu.jhu.ece.iacl.jist.structures.image.VoxelShort
 
getColor() - Method in class edu.jhu.ece.iacl.jist.structures.image.VoxelUByte
 
getColor() - Method in class edu.jhu.ece.iacl.jist.structures.image.VoxelVector
 
getCols() - Method in interface edu.jhu.cs.cisst.algorithms.optimize.fmg.grid.ConstGrid
Gets the cols.
getCols() - Method in class edu.jhu.cs.cisst.algorithms.optimize.fmg.grid.Grid
implements method from ConstGrid.
getCols() - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamMatrix
Gets the cols.
getCols() - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamVolume
Get column restriction.
getCols() - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamVolumeCollection
Get column restriction.
getCols() - Method in class edu.jhu.ece.iacl.jist.structures.image.ImageData
Gets the cols.
getCols() - Method in class edu.jhu.ece.iacl.jist.structures.matrix.Matrix3
Gets the cols.
getCols() - Method in class edu.jhu.ece.iacl.jist.structures.matrix.VectorMatrixX
Gets the cols.
getCols() - Method in class edu.jhu.ece.iacl.plugins.dti.MetaImageData4D
 
getColumn() - Method in interface edu.jhu.ece.iacl.jist.structures.data.Indexable
Gets the column.
getColumn() - Method in class edu.jhu.ece.iacl.jist.structures.geom.EdgeIndexed
 
getColumn() - Method in class edu.jhu.ece.iacl.jist.structures.geom.VertexIndexed
 
getColumn() - Method in class edu.jhu.ece.iacl.jist.structures.image.VoxelIndexed
 
getColumn() - Method in class edu.jhu.ece.iacl.jist.structures.image.VoxelMipav
 
getColumnClass(int) - Method in class edu.jhu.ece.iacl.jist.pipeline.gui.ProcessManagerTable.ProcessTableModel
 
getColumnCount() - Method in class edu.jhu.ece.iacl.jist.pipeline.gui.ProcessManagerTable.ProcessTableModel
 
getColumnName(int) - Method in class edu.jhu.ece.iacl.jist.pipeline.gui.ProcessManagerTable.ProcessTableModel
 
getCombinedLabelList(List<LabelImage>) - Static method in class edu.jhu.ece.iacl.algorithms.manual_label.LabelImage
 
getCompatiblePorts(PipePort) - Static method in class edu.jhu.ece.iacl.jist.pipeline.view.input.ParamCollectionPipelineInputView
Get list of ports that are compatible with incoming port.
getCompletedCount() - Method in class edu.jhu.ece.iacl.jist.pipeline.PipeScheduler
Get the number of completed experiments.
getCompletedUnits() - Method in class edu.jhu.ece.iacl.jist.pipeline.AbstractCalculation
Completed computational units for the calculation.
getComponent() - Method in interface edu.jhu.cs.cisst.vent.Visualization
Gets the component used to display the visualization.
getComponent() - Method in class edu.jhu.cs.cisst.vent.VisualizationProcessing
Gets the component.
getComponent() - Method in class edu.jhu.ece.iacl.jist.pipeline.graph.PipeEdgeRealEditor
Returns a reference to the editor component.
getComponents() - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamVolume
Get component restriction.
getComponents() - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamVolumeCollection
Get component restriction.
getComponents() - Method in class edu.jhu.ece.iacl.jist.structures.image.ImageData
Gets the components.
getComponents() - Method in class edu.jhu.ece.iacl.jist.structures.matrix.VectorMatrixX
Gets the components.
getComponents() - Method in class edu.jhu.ece.iacl.plugins.dti.MetaImageData4D
 
getCompressionType() - Method in class edu.jhu.ece.iacl.jist.structures.image.ImageHeader
Gets the compression type.
getConnector() - Method in class edu.jhu.ece.iacl.jist.pipeline.graph.PipeModuleEdge
Get connector associated with edge.
getContainingTetrahedron(Point3f) - Method in class edu.jhu.ece.iacl.jist.structures.geom.EmbeddedPointSet
Gets the containing tetrahedron.
getContextId() - Method in class edu.jhu.ece.iacl.jist.pipeline.ExecutionContext
Get context id.
getContextInputParams() - Method in class edu.jhu.ece.iacl.jist.pipeline.ExecutionContext
Get context input parameters.
getContextName() - Method in class edu.jhu.ece.iacl.jist.pipeline.ExecutionContext
Get context name.
getContextShortName() - Method in class edu.jhu.ece.iacl.jist.pipeline.ExecutionContext
Get context name.
getCopy() - Method in class edu.jhu.ece.iacl.jist.pipeline.gui.PipeInternalFrame
Gets the copy.
getCorrectedTable() - Method in class edu.jhu.ece.iacl.algorithms.dti.DTIGradientTableCreator
 
getCorrectedTable() - Method in class edu.jhu.ece.iacl.algorithms.dti.GradTableCorrection
 
getCorrelationCoefficient() - Method in class edu.jhu.ece.iacl.algorithms.volume.CompareVolumes
 
getCpuTime() - Method in class edu.jhu.ece.iacl.jist.pipeline.ExecutionContext
Gets the cpu time.
getCreationDate() - Method in class edu.jhu.ece.iacl.jist.pipeline.AlgorithmInformation
Gets the creation date.
getCroppedCols() - Method in class edu.jhmi.rad.medic.utilities.CropParameters
Gets the cropped cols.
getCroppedRows() - Method in class edu.jhmi.rad.medic.utilities.CropParameters
Gets the cropped rows.
getCroppedSlices() - Method in class edu.jhmi.rad.medic.utilities.CropParameters
Gets the cropped slices.
getCurrentContext() - Method in class edu.jhu.ece.iacl.jist.pipeline.PipeModule
Get current context used to execute this module.
getCurrentLabel() - Method in class edu.jhu.ece.iacl.jist.pipeline.AbstractCalculation
Get current label of calculation including any child calculations in progress.
getCurrentLayout() - Method in class edu.jhu.ece.iacl.jist.pipeline.PipeDestination
Gets the current layout.
getCurrentLocation() - Method in class edu.jhu.ece.iacl.jist.pipeline.graph.PipeJGraph
Gets the current location.
getCurrentParentContexts() - Method in class edu.jhu.ece.iacl.jist.pipeline.PipeAlgorithm
Gets the current parent contexts.
getCurrentProgress() - Method in class edu.jhu.ece.iacl.jist.pipeline.AbstractCalculation
Return normalized progress of deepest child calculation.
getCurve() - Method in interface edu.jhu.ece.iacl.jist.structures.geom.Curve
Gets the curve.
getCurve() - Method in class edu.jhu.ece.iacl.jist.structures.geom.CurvePath
 
getCurve() - Method in class edu.jhu.ece.iacl.jist.structures.geom.PolySpline
 
getCurve(double) - Method in class edu.jhu.ece.iacl.jist.structures.geom.PolySpline
Gets the curve.
getCurve(int) - Method in class edu.jhu.ece.iacl.jist.structures.geom.PolySpline
Gets the curve.
getCurves() - Method in class edu.jhu.ece.iacl.jist.structures.geom.CurveCollection
Gets the curves.
getCut() - Method in class edu.jhu.ece.iacl.jist.pipeline.gui.PipeInternalFrame
Gets the cut.
getD() - Method in class edu.jhu.bme.smile.commons.optimize.tensor.MLTensor
Gets the D matrix
getD() - Method in class edu.jhu.ece.iacl.algorithms.dti.DTEMRLTensor
Gets the D matrix
getD(int, int, int) - Method in class edu.jhu.ece.iacl.algorithms.manual_label.staple.PerformanceLevel
 
getD(double[]) - Method in class edu.jhu.ece.iacl.pami.GenerateTensors
 
getData() - Method in class edu.jhu.ece.iacl.algorithms.dti.tractography.FACT.DXFiberData
 
getData() - Method in class edu.jhu.ece.iacl.algorithms.manual_label.ROI
 
getData() - Method in class edu.jhu.ece.iacl.jist.structures.geom.GridPt
Gets the data.
getDataLabels() - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamDataLabel
Get label collection.
getDate() - Method in class edu.jhu.ece.iacl.algorithms.dti.ParV3Info
 
getDate() - Method in class edu.jhu.ece.iacl.algorithms.dti.ParV4Info
 
getDebugLevel() - Method in class edu.jhu.ece.iacl.jist.pipeline.JistPreferences
Gets the preferred level for debug output: 0 = Error messages only 1 = Major events and warnings ...
getDefaultGroupMerges() - Method in class edu.jhu.ece.iacl.algorithms.manual_label.LabelImageGroup
 
getDefaultJVMArgs() - Method in class edu.jhu.ece.iacl.jist.pipeline.PipeAlgorithm
Gets the default jvm args for the algorithm unit that is encapsulated by this class
getDefaultJVMArgs() - Method in class edu.jhu.ece.iacl.jist.pipeline.ProcessingAlgorithm
Default JVM Arguments --- currently only the Sun VM is supported
getDefaultJVMArgs() - Method in class edu.jhu.ece.iacl.plugins.labeling.MedicAlgorithmMultiAtlasLabeling
 
getDefaultJVMArgs() - Method in class edu.jhu.ece.iacl.plugins.labeling.MedicAlgorithmMultiAtlasSurfaceLabeling
 
getDefaultJVMArgs() - Method in class edu.jhu.ece.iacl.plugins.registration.MedicAlgorithmAtlasSelection
 
getDefaultJVMArgs() - Method in class edu.jhu.ece.iacl.plugins.registration.MedicAlgorithmMultiAtlasReg
 
getDefaultJVMArgs() - Method in class edu.jhu.ece.iacl.plugins.registration.MedicAlgorithmVABRA
 
getDefaultLayoutExtension() - Static method in class edu.jhu.ece.iacl.jist.pipeline.JistPreferences
Gets the default layout extension.
getDefaultMaxProcesses() - Method in class edu.jhu.ece.iacl.jist.pipeline.JistPreferences
Get default maximum number of processes.
getDefaultMemory() - Method in class edu.jhu.ece.iacl.jist.pipeline.JistPreferences
Get default maximum heap size.
getDefaultModuleExtension() - Static method in class edu.jhu.ece.iacl.jist.pipeline.JistPreferences
Gets the default module extension.
getDefaultParam() - Method in class edu.jhu.ece.iacl.jist.pipeline.src.PipeExternalSource
 
getDefaultPreferencesFileName() - Static method in class edu.jhu.ece.iacl.jist.pipeline.JistPreferences
Gets the default preferences file name.
getDefaultWorkingDirectory() - Static method in class edu.jhu.ece.iacl.jist.io.MipavController
Gets the default working directory.
getDeformationField() - Method in class edu.jhu.ece.iacl.algorithms.vabra.VabraAlgorithm
 
getDeformationField() - Method in class edu.jhu.ece.iacl.algorithms.vabra.VabraSolver
 
getDeformedSubject() - Method in class edu.jhu.ece.iacl.algorithms.vabra.VabraSolver
 
getDependents() - Method in class edu.jhu.ece.iacl.jist.pipeline.ExecutionContext
Get contexts that depend on this context.
getDerivative(double) - Method in class edu.jhu.bme.smile.commons.optimize.FunctionNumeric1DDifferentiation
Gets the first derivative
getDerivative(double[]) - Method in class edu.jhu.bme.smile.commons.optimize.FunctionNumericND1DDifferentiation
Gets the first derivative.
getDerivative(double[]) - Method in class edu.jhu.bme.smile.commons.optimize.FunctionNumericNDDifferentiation
Gets the gradient
getDerivative(double) - Method in class edu.jhu.bme.smile.commons.optimize.MinToMax1DDifferentiable
Gets the negated derivative
getDerivative(double[]) - Method in class edu.jhu.bme.smile.commons.optimize.MinToMaxNDDifferentiable
Gets the negated gradient
getDerivative(double) - Method in interface edu.jhu.bme.smile.commons.optimize.Optimizable1DContinuousDifferentiable
Gets the value of the derivative of the function.
getDerivative(double[]) - Method in interface edu.jhu.bme.smile.commons.optimize.OptimizableNDContinuousDifferentiable
Gets the gradient of the function.
getDerivative(double) - Method in class edu.jhu.bme.smile.commons.optimize.ProjectNDto1DOptimizableDifferentiable
Gets the derivative at location x in the current dimension.
getDerivative(double) - Method in class edu.jhu.bme.smile.commons.optimize.test.FunctionExponential
Gets the first derivative of the function.
getDerivative(double, double, int) - Method in class edu.jhu.bme.smile.commons.optimize.test.FunctionExponential
Gets the first derivative of the function.
getDerivative(double) - Method in class edu.jhu.bme.smile.commons.optimize.test.FunctionNegativeXSquared
Gets the first derivative of the function.
getDerivative(double, double, int) - Method in class edu.jhu.bme.smile.commons.optimize.test.FunctionNegativeXSquared
Gets the first derivative of the function.
getDerivative(double[]) - Method in class edu.jhu.bme.smile.commons.optimize.test.FunctionNegativeXSquaredND
Gets the gradient of the function.
getDerivative(double[], double, int) - Method in class edu.jhu.bme.smile.commons.optimize.test.FunctionNegativeXSquaredND
Gets the gradient of the function.
getDerivative(double[]) - Method in class edu.jhu.bme.smile.commons.optimize.test.FunctionRosenbrock
Gets the gradient of the function.
getDerivative(double[], double, int) - Method in class edu.jhu.bme.smile.commons.optimize.test.FunctionRosenbrock
Gets the gradient of the function.
getDerivative(double) - Method in class edu.jhu.bme.smile.commons.optimize.test.FunctionXSquared
Gets the first derivative of the function.
getDerivative(double, double, int) - Method in class edu.jhu.bme.smile.commons.optimize.test.FunctionXSquared
Gets the first derivative of the function.
getDerivative(double[]) - Method in class edu.jhu.bme.smile.commons.optimize.test.FunctionXSquaredND
Gets the gradient of the function.
getDerivative(double[], double, int) - Method in class edu.jhu.bme.smile.commons.optimize.test.FunctionXSquaredND
Gets the gradient of the function.
getDerivative(double) - Method in class edu.jhu.bme.smile.commons.optimize.test.FunctionXXplusSinXX
Gets the first derivative of the function.
getDerivative(double, double, int) - Method in class edu.jhu.bme.smile.commons.optimize.test.FunctionXXplusSinXX
Gets the first derivative of the function.
getDerivative(double[]) - Method in class edu.jhu.bme.smile.commons.optimize.test.FunctionXXplusSinXXND
Gets the gradient of the function.
getDerivative(double[], double, int) - Method in class edu.jhu.bme.smile.commons.optimize.test.FunctionXXplusSinXXND
Gets the gradient of the function.
getDerivative(double[]) - Method in class edu.jhu.bme.smile.commons.optimize.test.FunctionXXYYND
Gets the gradient of the function.
getDerivative(double[], double, int) - Method in class edu.jhu.bme.smile.commons.optimize.test.FunctionXXYYND
Gets the gradient of the function.
getDescendantChildrenHash() - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamCollection
Get hash that maps parameter names to parameters.
getDescendants() - Method in class edu.jhu.ece.iacl.jist.pipeline.PipeModule
Get all modules that are effected by information outputted by this module.
getDescendants(Vector<PipeModule>) - Method in class edu.jhu.ece.iacl.jist.pipeline.PipeModule
Get all descendant modules and append them to the list.
getDescendantTree() - Method in class edu.jhu.ece.iacl.jist.pipeline.ExecutionContext
Get descendant tree.
getDescription() - Method in class edu.jhu.ece.iacl.doc.DocMediaWikiWriter
 
getDescription() - Method in class edu.jhu.ece.iacl.jist.io.FileExtensionFilter
 
getDescription() - Method in class edu.jhu.ece.iacl.jist.pipeline.AlgorithmInformation
Gets the description.
getDescription() - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamModel
 
getDescription() - Method in class edu.jhu.ece.iacl.jist.pipeline.PipePort
Get port description.
getDestination() - Method in class edu.jhu.ece.iacl.jist.pipeline.PipeConnector
Get destination port.
getDialog() - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamMipavDialog
Create dialog from class.
getDialog() - Method in class edu.jhu.ece.iacl.jist.pipeline.ProcessingApplication
Get the dialog used by this processing module.
getDialogType() - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamFile
Get dialog type.
getDice() - Method in class edu.jhu.ece.iacl.algorithms.volume.CompareVolumes
 
getDifferenceVolume() - Method in class edu.jhu.ece.iacl.algorithms.volume.CompareVolumes
 
getDiffusionWeight() - Method in class edu.jhu.cs.cisst.algorithms.segmentation.gac.GradientVectorFlow2D
Gets the diffusion weight.
getDimensions() - Method in class edu.jhu.ece.iacl.jist.structures.fiber.FiberCollection
Gets the dimensions.
getDimResolutions() - Method in class edu.jhu.ece.iacl.jist.structures.image.ImageHeader
Gets the dim resolutions.
getDims() - Method in class edu.jhu.ece.iacl.algorithms.manual_label.LabelImage
 
getDirectory() - Method in class edu.jhu.ece.iacl.jist.pipeline.tree.PackageNode
Get associated directory.
getdist(XYZ[], XYZ[]) - Static method in class edu.jhu.ece.iacl.algorithms.dti.tractography.FACT.DtisVsIacl
 
getDocument() - Method in class edu.jhu.ece.iacl.doc.DocMediaWikiWriter
 
getDomainMax() - Method in class edu.jhu.bme.smile.commons.optimize.FunctionNumeric1DDifferentiation
Gets the domain maximum
getDomainMax() - Method in class edu.jhu.bme.smile.commons.optimize.FunctionNumericND1DDifferentiation
Gets the domain maximum
getDomainMax() - Method in class edu.jhu.bme.smile.commons.optimize.FunctionNumericNDDifferentiation
Gets the domain maximum
getDomainMax() - Method in class edu.jhu.bme.smile.commons.optimize.MinToMax1D
Gets the domain maximum
getDomainMax() - Method in class edu.jhu.bme.smile.commons.optimize.MinToMax1DDifferentiable
Gets the domain maximum
getDomainMax() - Method in class edu.jhu.bme.smile.commons.optimize.MinToMaxND
Gets the domain maximum
getDomainMax() - Method in class edu.jhu.bme.smile.commons.optimize.MinToMaxNDDifferentiable
Gets the domain maximum
getDomainMax() - Method in interface edu.jhu.bme.smile.commons.optimize.Optimizable1DContinuous
Gets the maximum input of the function.
getDomainMax() - Method in interface edu.jhu.bme.smile.commons.optimize.OptimizableNDContinuous
Gets the maximum input of the function.
getDomainMax() - Method in class edu.jhu.bme.smile.commons.optimize.ProjectNDto1DOptimizable
Gets the domain maximum in the current dimension.
getDomainMax() - Method in class edu.jhu.bme.smile.commons.optimize.test.FunctionExponential
Gets the domain maximum
getDomainMax() - Method in class edu.jhu.bme.smile.commons.optimize.test.FunctionNegativeXSquared
Gets the domain maximum
getDomainMax() - Method in class edu.jhu.bme.smile.commons.optimize.test.FunctionNegativeXSquaredND
Gets the domain maximum.
getDomainMax() - Method in class edu.jhu.bme.smile.commons.optimize.test.FunctionRosenbrock
Gets the domain maximum.
getDomainMax() - Method in class edu.jhu.bme.smile.commons.optimize.test.FunctionXSquared
Gets the domain maximum
getDomainMax() - Method in class edu.jhu.bme.smile.commons.optimize.test.FunctionXSquaredND
Gets the domain maximum.
getDomainMax() - Method in class edu.jhu.bme.smile.commons.optimize.test.FunctionXXplusSinXX
Gets the domain maximum
getDomainMax() - Method in class edu.jhu.bme.smile.commons.optimize.test.FunctionXXplusSinXXND
Gets the domain maximum.
getDomainMax() - Method in class edu.jhu.bme.smile.commons.optimize.test.FunctionXXYYND
Gets the domain maximum.
getDomainMax() - Method in class edu.jhu.ece.iacl.algorithms.spectro.MSWASSR.Symscore
 
getDomainMin() - Method in class edu.jhu.bme.smile.commons.optimize.FunctionNumeric1DDifferentiation
Gets the domain minimum
getDomainMin() - Method in class edu.jhu.bme.smile.commons.optimize.FunctionNumericND1DDifferentiation
Gets the domain minimum
getDomainMin() - Method in class edu.jhu.bme.smile.commons.optimize.FunctionNumericNDDifferentiation
Gets the domain minimum
getDomainMin() - Method in class edu.jhu.bme.smile.commons.optimize.MinToMax1D
Gets the domain minimum
getDomainMin() - Method in class edu.jhu.bme.smile.commons.optimize.MinToMax1DDifferentiable
Gets the domain minimum
getDomainMin() - Method in class edu.jhu.bme.smile.commons.optimize.MinToMaxND
Gets the domain minimum
getDomainMin() - Method in class edu.jhu.bme.smile.commons.optimize.MinToMaxNDDifferentiable
Gets the domain minimum
getDomainMin() - Method in interface edu.jhu.bme.smile.commons.optimize.Optimizable1DContinuous
Gets the minimum input of the function.
getDomainMin() - Method in interface edu.jhu.bme.smile.commons.optimize.OptimizableNDContinuous
Gets the minimum input of the function.
getDomainMin() - Method in class edu.jhu.bme.smile.commons.optimize.ProjectNDto1DOptimizable
Gets the domain minimum in the current dimension.
getDomainMin() - Method in class edu.jhu.bme.smile.commons.optimize.test.FunctionExponential
Gets the domain minimum.
getDomainMin() - Method in class edu.jhu.bme.smile.commons.optimize.test.FunctionNegativeXSquared
Gets the domain minimum.
getDomainMin() - Method in class edu.jhu.bme.smile.commons.optimize.test.FunctionNegativeXSquaredND
Gets the domain minimum.
getDomainMin() - Method in class edu.jhu.bme.smile.commons.optimize.test.FunctionRosenbrock
Gets the domain minimum.
getDomainMin() - Method in class edu.jhu.bme.smile.commons.optimize.test.FunctionXSquared
Gets the domain minimum.
getDomainMin() - Method in class edu.jhu.bme.smile.commons.optimize.test.FunctionXSquaredND
Gets the domain minimum.
getDomainMin() - Method in class edu.jhu.bme.smile.commons.optimize.test.FunctionXXplusSinXX
Gets the domain minimum.
getDomainMin() - Method in class edu.jhu.bme.smile.commons.optimize.test.FunctionXXplusSinXXND
Gets the domain minimum.
getDomainMin() - Method in class edu.jhu.bme.smile.commons.optimize.test.FunctionXXYYND
Gets the domain minimum.
getDomainMin() - Method in class edu.jhu.ece.iacl.algorithms.spectro.MSWASSR.Symscore
 
getDomainTolerance() - Method in class edu.jhu.bme.smile.commons.optimize.FunctionNumeric1DDifferentiation
Gets the tolerance
getDomainTolerance() - Method in class edu.jhu.bme.smile.commons.optimize.FunctionNumericND1DDifferentiation
Gets the tolerance
getDomainTolerance() - Method in class edu.jhu.bme.smile.commons.optimize.FunctionNumericNDDifferentiation
Gets the tolerance
getDomainTolerance() - Method in class edu.jhu.bme.smile.commons.optimize.MinToMax1D
Gets the tolerance
getDomainTolerance() - Method in class edu.jhu.bme.smile.commons.optimize.MinToMax1DDifferentiable
Gets the tolerance
getDomainTolerance() - Method in class edu.jhu.bme.smile.commons.optimize.MinToMaxND
Gets the tolerance
getDomainTolerance() - Method in class edu.jhu.bme.smile.commons.optimize.MinToMaxNDDifferentiable
Gets the tolerance
getDomainTolerance() - Method in interface edu.jhu.bme.smile.commons.optimize.Optimizable1DContinuous
Gets the tolerance.
getDomainTolerance() - Method in interface edu.jhu.bme.smile.commons.optimize.OptimizableNDContinuous
Gets the tolerance
getDomainTolerance() - Method in class edu.jhu.bme.smile.commons.optimize.ProjectNDto1DOptimizable
Gets the tolerance.
getDomainTolerance() - Method in class edu.jhu.bme.smile.commons.optimize.test.FunctionExponential
Gets the tolerance.
getDomainTolerance() - Method in class edu.jhu.bme.smile.commons.optimize.test.FunctionNegativeXSquared
Gets the tolerance.
getDomainTolerance() - Method in class edu.jhu.bme.smile.commons.optimize.test.FunctionNegativeXSquaredND
Gets the tolerance.
getDomainTolerance() - Method in class edu.jhu.bme.smile.commons.optimize.test.FunctionRosenbrock
Gets the tolerance.
getDomainTolerance() - Method in class edu.jhu.bme.smile.commons.optimize.test.FunctionXSquared
Gets the tolerance.
getDomainTolerance() - Method in class edu.jhu.bme.smile.commons.optimize.test.FunctionXSquaredND
Gets the tolerance.
getDomainTolerance() - Method in class edu.jhu.bme.smile.commons.optimize.test.FunctionXXplusSinXX
Gets the tolerance.
getDomainTolerance() - Method in class edu.jhu.bme.smile.commons.optimize.test.FunctionXXplusSinXXND
Gets the tolerance.
getDomainTolerance() - Method in class edu.jhu.bme.smile.commons.optimize.test.FunctionXXYYND
Gets the tolerance.
getDomainTolerance() - Method in class edu.jhu.ece.iacl.algorithms.spectro.MSWASSR.Symscore
 
getDouble() - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamNumber
Get the number value as double.
getDouble(int, int) - Method in class edu.jhu.ece.iacl.jist.structures.image.ImageData
Gets the double.
getDouble(int, int, int) - Method in class edu.jhu.ece.iacl.jist.structures.image.ImageData
Gets the double.
getDouble(int, int, int, int) - Method in class edu.jhu.ece.iacl.jist.structures.image.ImageData
Gets the double.
getDouble(int, int, int, int) - Method in class edu.jhu.ece.iacl.jist.structures.image.ImageDataByte
 
getDouble(int, int, int, int) - Method in class edu.jhu.ece.iacl.jist.structures.image.ImageDataColor
 
getDouble(int, int, int, int) - Method in class edu.jhu.ece.iacl.jist.structures.image.ImageDataDouble
 
getDouble(int, int, int, int) - Method in class edu.jhu.ece.iacl.jist.structures.image.ImageDataFloat
 
getDouble(int, int, int, int) - Method in class edu.jhu.ece.iacl.jist.structures.image.ImageDataInt
 
getDouble(int, int, int, int) - Method in class edu.jhu.ece.iacl.jist.structures.image.ImageDataMipav
 
getDouble(int, int, int, int) - Method in class edu.jhu.ece.iacl.jist.structures.image.ImageDataNumber
 
getDouble(int, int, int, int) - Method in class edu.jhu.ece.iacl.jist.structures.image.ImageDataUByte
 
getDouble() - Method in class edu.jhu.ece.iacl.jist.structures.image.Voxel
Gets the double.
getDouble() - Method in class edu.jhu.ece.iacl.jist.structures.image.VoxelBoolean
 
getDouble() - Method in class edu.jhu.ece.iacl.jist.structures.image.VoxelColor
 
getDouble() - Method in class edu.jhu.ece.iacl.jist.structures.image.VoxelDouble
 
getDouble() - Method in class edu.jhu.ece.iacl.jist.structures.image.VoxelFloat
 
getDouble() - Method in class edu.jhu.ece.iacl.jist.structures.image.VoxelIndexed
 
getDouble() - Method in class edu.jhu.ece.iacl.jist.structures.image.VoxelInt
 
getDouble() - Method in class edu.jhu.ece.iacl.jist.structures.image.VoxelMipav
 
getDouble() - Method in class edu.jhu.ece.iacl.jist.structures.image.VoxelShort
 
getDouble() - Method in class edu.jhu.ece.iacl.jist.structures.image.VoxelUByte
 
getDouble() - Method in class edu.jhu.ece.iacl.jist.structures.image.VoxelVector
 
getDownSampleResolutions() - Method in class edu.jhu.ece.iacl.algorithms.vabra.VabraConfiguration
 
getDRMAASession() - Static method in class edu.jhu.ece.iacl.jist.processcontrol.DispatchController
Gets the dRMAA session.
getDWITransform() - Method in class edu.jhu.ece.iacl.algorithms.dti.DWICoReg
 
getDWScheme() - Method in class edu.jhu.ece.iacl.algorithms.hardi.CFARIBasisSet
 
getEdgeIndex() - Method in class edu.jhu.ece.iacl.jist.structures.geom.EdgeIndexed
Gets the edge index.
getEdges() - Method in class edu.jhu.ece.iacl.jist.structures.geom.EmbeddedSurface
Gets the edges.
getEdges() - Method in class edu.jhu.ece.iacl.jist.structures.geom.Face
Gets the edges.
getEdges() - Method in class edu.jhu.ece.iacl.jist.structures.geom.Surface
Gets the edges.
getEdges() - Method in class edu.jhu.ece.iacl.jist.structures.geom.TriangleFace
 
getEdgeTable() - Method in class edu.jhu.ece.iacl.jist.structures.geom.EmbeddedSurface
Gets the edge table.
getEditor() - Method in class edu.jhu.ece.iacl.jist.pipeline.graph.PipeEdgeView
 
getEditorComponent() - Method in class edu.jhu.ece.iacl.jist.pipeline.gui.ConnectionEditor
Get edit pane.
getElapsedActualTime() - Method in class edu.jhu.ece.iacl.jist.pipeline.PipeScheduler
Gets the elapsed actual time.
getElapsedCpuTime() - Method in class edu.jhu.ece.iacl.jist.pipeline.PipeScheduler
Gets the elapsed cpu time.
getElapsedTime() - Method in class edu.jhu.ece.iacl.doc.DocumentAllTests.TestCase
 
getElapsedTimeDescription() - Method in class edu.jhu.ece.iacl.jist.pipeline.ExecutionContext
Get elapsed cpu time in milliseconds.
getElapsedTimeString() - Method in class edu.jhu.ece.iacl.doc.DocumentAllTests.TestCase
 
getEmail() - Method in class edu.jhu.ece.iacl.jist.pipeline.AlgorithmInformation.AlgorithmAuthor
Gets the email.
getEmbeddedSphere(int, boolean) - Method in class edu.jhu.ece.iacl.jist.structures.geom.EmbeddedSurface
Gets the embedded sphere.
getEndianess() - Method in class edu.jhu.ece.iacl.jist.structures.image.ImageHeader
Gets the endianess.
getExitCode() - Method in interface edu.jhu.ece.iacl.jist.processcontrol.ProcessController
Gets the exit code.
getExitCode() - Method in class edu.jhu.ece.iacl.jist.processcontrol.ProcessControllerDRMAA
 
getExitCode() - Method in class edu.jhu.ece.iacl.jist.processcontrol.ProcessControllerNative
 
getExtensionFilter() - Method in class edu.jhu.ece.iacl.jist.io.FileReaderWriter
Gets the extension filter.
getExtensionFilter() - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamFile
Gets the extension filter.
getExtensionFilter() - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamFileCollection
Get extension filter.
getExtensions() - Method in class edu.jhu.ece.iacl.jist.io.FileExtensionFilter
Gets the extensions.
getExtrema() - Method in class edu.jhu.bme.smile.commons.optimize.BrentMethod1D
Gets the extrema that was found
getExtrema() - Method in class edu.jhu.bme.smile.commons.optimize.DownhillSimplexND
Gets the extrema that was found
getExtrema() - Method in class edu.jhu.bme.smile.commons.optimize.GoldenSectionSearch1D
Gets the extrema that was found
getExtrema() - Method in class edu.jhu.bme.smile.commons.optimize.LevenbergMarquardt
Gets the extrema that was found.
getExtrema() - Method in class edu.jhu.bme.smile.commons.optimize.LineSearchND
Gets the extrema that was found
getExtrema() - Method in class edu.jhu.bme.smile.commons.optimize.LineSearchNDDifferentiable
Gets the extrema that was found
getExtrema() - Method in class edu.jhu.bme.smile.commons.optimize.NewtonMethod1D
Gets the extrema that was found
getExtrema() - Method in interface edu.jhu.bme.smile.commons.optimize.Optimizer1DContinuous
Gets the optimized value.
getExtrema() - Method in interface edu.jhu.bme.smile.commons.optimize.Optimizer1DContinuousDifferentiable
Gets the optimized value.
getExtrema() - Method in interface edu.jhu.bme.smile.commons.optimize.OptimizerNDContinuous
Gets the optimized value.
getExtrema() - Method in interface edu.jhu.bme.smile.commons.optimize.OptimizerNDContinuousDifferentiable
Gets the optimized value.
getFaceArea(int) - Method in class edu.jhu.ece.iacl.jist.structures.geom.EmbeddedSurface
Gets the face area.
getFaceCount() - Method in class edu.jhu.ece.iacl.jist.structures.geom.EmbeddedSurface
Gets the face count.
getFacePoints(int) - Method in class edu.jhu.ece.iacl.jist.structures.geom.EmbeddedSurface
Gets the face points.
getFaces(File) - Static method in class edu.jhu.ece.iacl.jist.io.DxSurfaceReader
Gets the faces.
getFaces(File) - Static method in class edu.jhu.ece.iacl.jist.io.FreeSurferAsciiReader
Gets the faces.
getFaces(File) - Static method in class edu.jhu.ece.iacl.jist.io.FreeSurferReader
Gets the faces.
getFaces(File) - Static method in class edu.jhu.ece.iacl.jist.io.MipavSurfaceXMLReader
Gets the faces.
getFaces() - Method in class edu.jhu.ece.iacl.jist.structures.geom.EmbeddedSurface
Gets the faces.
getFaces() - Method in class edu.jhu.ece.iacl.jist.structures.geom.Surface
Gets the faces.
getFaceVertexIds(int) - Method in class edu.jhu.ece.iacl.jist.structures.geom.EmbeddedSurface
Gets the face vertex ids.
getFactory() - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamModel
Get parameter factory.
getFactory() - Method in class edu.jhu.ece.iacl.jist.pipeline.tree.DraggableNode
Get module factory.
getFailedCount() - Method in class edu.jhu.ece.iacl.jist.pipeline.PipeScheduler
Get number of failed experiments.
getFailedFiles() - Method in class edu.jhu.ece.iacl.jist.pipeline.PipeLayoutRunner
Gets the failed files.
getFiber(double) - Method in class edu.jhu.ece.iacl.algorithms.dti.tractography.FACT.DTIStudioReader
 
getFiberCollection() - Method in class edu.jhu.ece.iacl.algorithms.dti.tractography.Tract
 
getFiberColor(double) - Method in class edu.jhu.ece.iacl.algorithms.dti.tractography.FACT.DTIStudioReader
 
getFiberDataWithMax(Fiber, ImageData) - Static method in class edu.jhu.ece.iacl.algorithms.dti.tractography.FiberStatistics
 
getFiberLengths() - Method in class edu.jhu.ece.iacl.algorithms.dti.tractography.FiberStatistics
 
getFibers() - Method in class edu.jhu.ece.iacl.algorithms.dti.tractography.FACT.DTIStudioReader
 
getFibers() - Method in class edu.jhu.ece.iacl.algorithms.dti.tractography.FACT.FACTapi
 
getFiberXYZchain(int) - Method in class edu.jhu.ece.iacl.algorithms.dti.tractography.FACT.DTIStudioReader
 
getField() - Method in class edu.jhu.ece.iacl.jist.pipeline.gui.PortListBox
 
getField() - Method in class edu.jhu.ece.iacl.jist.pipeline.view.input.ParamBooleanInputView
Get field used to enter this value
getField() - Method in class edu.jhu.ece.iacl.jist.pipeline.view.input.ParamCollectionInputView
Get field used to enter this value
getField() - Method in class edu.jhu.ece.iacl.jist.pipeline.view.input.ParamCollectionPipelineInputView
Get field used to enter this value
getField() - Method in class edu.jhu.ece.iacl.jist.pipeline.view.input.ParamColorInputView
Get field used to enter this value.
getField() - Method in class edu.jhu.ece.iacl.jist.pipeline.view.input.ParamDoubleSliderInputView
Get field used to enter this value.
getField() - Method in class edu.jhu.ece.iacl.jist.pipeline.view.input.ParamFileCollectionInputView
Get field used to enter this value
getField() - Method in class edu.jhu.ece.iacl.jist.pipeline.view.input.ParamFileInputView
Get field used to enter this value
getField() - Method in class edu.jhu.ece.iacl.jist.pipeline.view.input.ParamHiddenInputView
Get field used to enter this value
getField() - Method in class edu.jhu.ece.iacl.jist.pipeline.view.input.ParamInformationInputView
Get field used to enter this value
getField() - Method in class edu.jhu.ece.iacl.jist.pipeline.view.input.ParamInputView
 
getField() - Method in class edu.jhu.ece.iacl.jist.pipeline.view.input.ParamMatrixInputView
Get field used to enter this value
getField() - Method in class edu.jhu.ece.iacl.jist.pipeline.view.input.ParamMipavDialogInputView
Get field used to enter this value
getField() - Method in class edu.jhu.ece.iacl.jist.pipeline.view.input.ParamMultiOptionInputView
Get field used to enter this value
getField() - Method in class edu.jhu.ece.iacl.jist.pipeline.view.input.ParamNumberCollectionInputView
Get field used to enter this value
getField() - Method in class edu.jhu.ece.iacl.jist.pipeline.view.input.ParamNumberSliderInputView
Get field used to enter this value
getField() - Method in class edu.jhu.ece.iacl.jist.pipeline.view.input.ParamNumberSpinnerInputView
Get field used to enter this value
getField() - Method in class edu.jhu.ece.iacl.jist.pipeline.view.input.ParamNumberTextInputView
Get field used to enter this value
getField() - Method in class edu.jhu.ece.iacl.jist.pipeline.view.input.ParamOptionCollectionInputView
Get field used to enter this value
getField() - Method in class edu.jhu.ece.iacl.jist.pipeline.view.input.ParamOptionInputView
Get field used to enter this value
getField() - Method in class edu.jhu.ece.iacl.jist.pipeline.view.input.ParamPointDoubleTextInputView
Get field used to enter this value
getField() - Method in class edu.jhu.ece.iacl.jist.pipeline.view.input.ParamPointFloatTextInputView
Get field used to enter this value
getField() - Method in class edu.jhu.ece.iacl.jist.pipeline.view.input.ParamPointSpinnerInputView
Get field used to enter this value
getField() - Method in class edu.jhu.ece.iacl.jist.pipeline.view.input.ParamTextInputView
Get field used to enter this value
getField() - Method in class edu.jhu.ece.iacl.jist.pipeline.view.input.ParamURIInputView
Get field used to enter this value
getField() - Method in class edu.jhu.ece.iacl.jist.pipeline.view.input.ParamVolumeCollectionInputView
Get field used to enter this value
getField() - Method in class edu.jhu.ece.iacl.jist.pipeline.view.input.ParamVolumeInputView
Get field used to enter this value
getField() - Method in class edu.jhu.ece.iacl.jist.pipeline.view.input.ParamVolumeURICollectionInputView
Get field used to enter this value
getField() - Method in class edu.jhu.ece.iacl.jist.pipeline.view.input.ParamVolumeURIInputView
Get field used to enter this value
getFile() - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.DataLabelCollection
Get location of XML file.
getFileExtension(File) - Static method in class edu.jhu.ece.iacl.jist.io.FileReaderWriter
Get file extension for file.
getFileExtension(String) - Static method in class edu.jhu.ece.iacl.jist.io.FileReaderWriter
Get file extension for file string.
getFileHistory() - Method in class edu.jhu.ece.iacl.jist.pipeline.JistPreferences
Get list of recently accessed files.
getFileList() - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamVolumeCollection
Get list of volume file locations.
getFileLocation() - Method in class edu.jhu.ece.iacl.jist.pipeline.PipeLayout
Returns file location for this layout.
getFileName(File) - Static method in class edu.jhu.ece.iacl.jist.io.FileReaderWriter
Get image name based on file name.
getFileName(String) - Static method in class edu.jhu.ece.iacl.jist.io.FileReaderWriter
Get image name from file name.
getFileName() - Method in class edu.jhu.ece.iacl.jist.io.FileReaderWriter
Gets the file name.
getFileNameWithoutExtension(String) - Static method in class edu.jhu.ece.iacl.plugins.dti.DWIDefineCaminoScheme
 
getFirstChildByClass(Class) - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamCollection
Get first child that is of the specified class type.
getFirstChildByLabel(String) - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamCollection
Get first child that has the specified label.
getFirstChildByName(String) - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamCollection
Get first child that has the specified name.
getFloat() - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamNumber
Get the number value as float.
getFloat(int, int) - Method in class edu.jhu.ece.iacl.jist.structures.image.ImageData
Gets the float.
getFloat(int, int, int) - Method in class edu.jhu.ece.iacl.jist.structures.image.ImageData
Gets the float.
getFloat(int, int, int, int) - Method in class edu.jhu.ece.iacl.jist.structures.image.ImageData
Gets the float.
getFloat(int, int, int, int) - Method in class edu.jhu.ece.iacl.jist.structures.image.ImageDataByte
 
getFloat(int, int, int, int) - Method in class edu.jhu.ece.iacl.jist.structures.image.ImageDataColor
 
getFloat(int, int, int, int) - Method in class edu.jhu.ece.iacl.jist.structures.image.ImageDataDouble
 
getFloat(int, int, int, int) - Method in class edu.jhu.ece.iacl.jist.structures.image.ImageDataFloat
 
getFloat(int, int, int, int) - Method in class edu.jhu.ece.iacl.jist.structures.image.ImageDataInt
 
getFloat(int, int, int, int) - Method in class edu.jhu.ece.iacl.jist.structures.image.ImageDataMipav
 
getFloat(int, int, int, int) - Method in class edu.jhu.ece.iacl.jist.structures.image.ImageDataNumber
 
getFloat(int, int, int, int) - Method in class edu.jhu.ece.iacl.jist.structures.image.ImageDataUByte
 
getFloat() - Method in class edu.jhu.ece.iacl.jist.structures.image.Voxel
Gets the float.
getFloat() - Method in class edu.jhu.ece.iacl.jist.structures.image.VoxelFloat
 
getFloat() - Method in class edu.jhu.ece.iacl.jist.structures.image.VoxelMipav
 
getFloat() - Method in class edu.jhu.ece.iacl.jist.structures.image.VoxelUByte
 
getFoldover() - Method in class edu.jhu.ece.iacl.algorithms.dti.ParV4Info
 
getFont() - Method in class edu.jhu.ece.iacl.jist.pipeline.graph.PipeEdgeEditor.DefaultSpinner
 
getForces() - Method in class edu.jhu.cs.cisst.algorithms.segmentation.gac.GeodesicActiveContour2D
Gets the forces.
getFrames() - Method in class edu.jhu.ece.iacl.jist.pipeline.gui.LayoutPanel
Return active frames.
getFromFiberArray(Fiber[]) - Method in class edu.jhu.ece.iacl.jist.structures.fiber.FiberCollection
Gets the from fiber array.
getFRTCoeff(int, int, double, double) - Static method in class edu.jhu.bme.smile.commons.math.specialFunctions.SphericalHarmonics
 
getFullFileName(ModelImage) - Static method in class edu.jhu.ece.iacl.jist.io.FileReaderWriter
Get the full file name of a model image.
getGenus(ModelTriangleMesh) - Static method in class edu.jhu.ece.iacl.jist.structures.geom.EmbeddedSurface
Gets the genus.
getGeometryArray() - Method in class edu.jhu.ece.iacl.jist.structures.geom.Surface
Gets the geometry array.
getGeometryArray() - Method in class edu.jhu.ece.iacl.jist.structures.geom.TriangleSurface
 
getGraph() - Method in class edu.jhu.ece.iacl.jist.pipeline.gui.PipeInternalFrame
Gets the graph.
getGraphCellEditorComponent(JGraph, Object, boolean) - Method in class edu.jhu.ece.iacl.jist.pipeline.graph.PipeEdgeRealEditor
 
getGraphEdge() - Method in class edu.jhu.ece.iacl.jist.pipeline.PipeConnector
Get graph edge.
getGraphPort() - Method in class edu.jhu.ece.iacl.jist.pipeline.PipePort
Get port to display on graph.
getGridPoint(int, int) - Method in class edu.jhu.cs.cisst.algorithms.segmentation.gac.ActiveContourForce2D
Gets the grid point.
getGridSpacing(int) - Method in class edu.jhu.cs.cisst.algorithms.optimize.fmg.DefaultSolverResolutionLevels2D
 
getGridSpacing(int) - Method in class edu.jhu.cs.cisst.algorithms.optimize.fmg.DefaultSolverResolutionLevels3D
 
getGridSpacing(int) - Method in interface edu.jhu.cs.cisst.algorithms.optimize.fmg.pde.PDE
return the grid spacing for a grid of the given size.
getGridSpacing(int) - Method in interface edu.jhu.cs.cisst.algorithms.optimize.fmg.SolverResolutionLevels
Gets the grid spacing.
getGridSpacing(int) - Method in class edu.jhu.cs.cisst.algorithms.segmentation.gac.VectorFieldDiffusion2D
implements method from PDE.
getGroupByFoldingHandle(JGraph, Point2D) - Static method in class edu.jhu.ece.iacl.jist.pipeline.graph.JGraphFoldingManager
Called when the mouse button is released to see if a collapse or expand request has been made.
getGroupModules() - Method in class edu.jhu.ece.iacl.jist.pipeline.PipeAlgorithmGroup
Get all modules in group.
getHardSeg() - Method in class edu.jhu.ece.iacl.algorithms.manual_label.staple.STAPLEgeneral
 
getHardSeg() - Method in class edu.jhu.ece.iacl.algorithms.manual_label.staple.STAPLEmulti
 
getHardSeg() - Method in class edu.jhu.ece.iacl.algorithms.manual_label.staple.STAPLEmulti2
 
getHardSeg() - Method in class edu.jhu.ece.iacl.algorithms.manual_label.staple.STAPLEsurf
 
getHardSegArray() - Method in class edu.jhu.ece.iacl.algorithms.manual_label.staple.STAPLEmulti
 
getHardSegArray() - Method in class edu.jhu.ece.iacl.algorithms.manual_label.staple.STAPLEmulti2
 
getHashKey() - Method in class edu.jhu.ece.iacl.jist.pipeline.ExecutionContext
Gets the hash key.
getHashKey(String, Class, ParamCollection) - Static method in class edu.jhu.ece.iacl.jist.pipeline.ExecutionContext
Gets the hash key.
getHDR() - Method in class edu.jhu.ece.iacl.algorithms.dti.tractography.FACT.DTIStudioReader
 
getHDRFiberNR() - Method in class edu.jhu.ece.iacl.algorithms.dti.tractography.FACT.DTIStudioReader
 
getHeader() - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamCollection
 
getHeader() - Method in class edu.jhu.ece.iacl.jist.structures.image.ImageData
Gets the header.
getHeader() - Method in class edu.jhu.ece.iacl.plugins.dti.MetaImageData4D
 
getHeight() - Method in class edu.jhu.cs.cisst.vent.renderer.processing.RendererProcessing2D
Gets the height.
getHierLinks() - Method in class edu.jhu.ece.iacl.doc.DocMediaWikiWriter
 
getHigh() - Static method in class edu.jhu.ece.iacl.algorithms.dti.GTCparams
 
getHighOP_24prev() - Static method in class edu.jhu.ece.iacl.algorithms.dti.GTCparams
 
getHighOP_25post() - Static method in class edu.jhu.ece.iacl.algorithms.dti.GTCparams
 
getHighOP_rel25() - Static method in class edu.jhu.ece.iacl.algorithms.dti.GTCparams
 
getHitIndex(int) - Method in class edu.jhu.ece.iacl.algorithms.manual_label.LabelImage
 
getHitIndex(int) - Method in class edu.jhu.ece.iacl.algorithms.manual_label.LabelSurface
 
getHostName() - Static method in class edu.jhu.ece.iacl.jist.pipeline.PipeLibrary
Gets the host name.
getHull() - Method in class edu.jhu.ece.iacl.jist.structures.geom.EmbeddedPointSet
Gets the hull.
getHumanReadableDataType() - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamArgsOrder
 
getHumanReadableDataType() - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamBoolean
 
getHumanReadableDataType() - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamCollection
 
getHumanReadableDataType() - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamColor
 
getHumanReadableDataType() - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamDouble
 
getHumanReadableDataType() - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamFile
 
getHumanReadableDataType() - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamFileCollection
 
getHumanReadableDataType() - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamFloat
 
getHumanReadableDataType() - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamHeader
 
getHumanReadableDataType() - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamInformation
 
getHumanReadableDataType() - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamInteger
 
getHumanReadableDataType() - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamLong
 
getHumanReadableDataType() - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamMatrix
 
getHumanReadableDataType() - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamMipavDialog
 
getHumanReadableDataType() - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamModel
 
getHumanReadableDataType() - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamMultiOption
 
getHumanReadableDataType() - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamNumberCollection
 
getHumanReadableDataType() - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamOption
 
getHumanReadableDataType() - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamPerformance
 
getHumanReadableDataType() - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamPointDouble
 
getHumanReadableDataType() - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamPointFloat
 
getHumanReadableDataType() - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamPointInteger
 
getHumanReadableDataType() - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamString
 
getHumanReadableDataType() - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamSwitch
 
getHumanReadableHelpMessage() - Method in class edu.jhu.ece.iacl.jist.cli.JistCLI
 
getIcon() - Method in class edu.jhu.ece.iacl.jist.pipeline.tree.DraggableNode
Gets the icon.
getId() - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.DataLabel
Get id.
getImag(int, int) - Method in class edu.jhu.bme.smile.commons.math.specialFunctions.ComplexMatrix
 
getImag() - Method in class edu.jhu.bme.smile.commons.math.specialFunctions.ComplexMatrix
 
getImag(int) - Method in class edu.jhu.bme.smile.commons.math.specialFunctions.ComplexVector
 
getImage(String, String, boolean, int, int) - Method in class edu.jhu.bme.smile.commons.math.HistogramGenerator
 
getImage(String, String, String, boolean, int, int) - Method in class edu.jhu.bme.smile.commons.math.KLDivergence
 
getImage() - Method in class edu.jhu.cs.cisst.vent.renderer.processing.ImageRenderer
Gets the image.
getImage(int) - Method in class edu.jhu.cs.cisst.vent.renderer.processing.VolumeSliceRenderer
Gets the image.
getImage() - Method in class edu.jhu.ece.iacl.jist.pipeline.view.output.ParamSurfaceOutputView
Get screenshot.
getImage() - Method in class edu.jhu.ece.iacl.jist.structures.geom.MipavVOI
Gets the image.
getImageByName(String) - Static method in class edu.jhu.ece.iacl.jist.io.MipavController
Select an image from the registry by image name.
getImageData() - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamVolume
Get the CubicVolume specified.
getImageData(boolean) - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamVolume
 
getImageDataList() - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamVolumeCollection
Get list of volumes.
GetImageDimensions - Class in edu.jhu.ece.iacl.plugins.utilities.volume
 
GetImageDimensions() - Constructor for class edu.jhu.ece.iacl.plugins.utilities.volume.GetImageDimensions
 
getImageNames() - Static method in class edu.jhu.ece.iacl.jist.io.MipavController
Get the names of all registered MIPAV images.
getImageNames() - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamVolumeCollection
Get list of model image names.
getImageOrientation() - Method in class edu.jhu.ece.iacl.jist.structures.image.ImageHeader
Gets the image orientation.
getImages() - Static method in class edu.jhu.ece.iacl.jist.io.MipavController
Get all registered MIPAV images.
getImageValue(float[][], int, int, int, int) - Static method in class edu.jhu.cs.cisst.algorithms.util.DataOperations
Gets the image value.
getImageVariableTable() - Static method in class edu.jhu.ece.iacl.jist.io.MipavController
Gets the image variable table.
getImagResult() - Method in class edu.jhu.bme.smile.commons.math.specialFunctions.ComplexVector
 
getImg() - Method in class edu.jhu.ece.iacl.algorithms.manual_label.LabelImage
 
getInBounds(ArrayList<CollisionDetection.Triangle>, BoundingBox) - Static method in class edu.jhu.ece.iacl.jist.structures.geom.CollisionDetection.Triangle
Gets the in bounds.
getIncomingConnector(PipePort) - Method in class edu.jhu.ece.iacl.jist.pipeline.PipePort
Get incoming connector for specified source.
getIncomingConnectors() - Method in class edu.jhu.ece.iacl.jist.pipeline.PipePort
Get input connections.
getIncomingPorts() - Method in class edu.jhu.ece.iacl.jist.pipeline.PipePort
Get all ports that are connected to this port.
getIndex() - Method in class edu.jhu.bme.smile.commons.math.HistogramGenerator
 
getIndex(int, int) - Method in class edu.jhu.cs.cisst.algorithms.segmentation.gac.GradientVectorFlow2D
Gets the index.
getIndex(int, int, int, int, int, int) - Method in class edu.jhu.cs.cisst.algorithms.segmentation.gac.GradientVectorFlow2D
Gets the index.
getIndex(int, int, int) - Static method in class edu.jhu.cs.cisst.algorithms.segmentation.gac.VectorFieldDiffusion2D
Gets the index.
getIndex(ArrayList<Number>, Number) - Method in class edu.jhu.ece.iacl.algorithms.manual_label.staple.STAPLEgeneral
 
getIndex(ArrayList<Integer>, Integer) - Method in class edu.jhu.ece.iacl.algorithms.manual_label.staple.STAPLEmulti
 
getIndex(int[], int) - Method in class edu.jhu.ece.iacl.algorithms.manual_label.staple.STAPLEmulti
 
getIndex(ArrayList<Integer>, Integer) - Method in class edu.jhu.ece.iacl.algorithms.manual_label.staple.STAPLEmulti2
 
getIndex(int[], int) - Method in class edu.jhu.ece.iacl.algorithms.manual_label.staple.STAPLEmulti2
 
getIndex(ArrayList<Number>, Number) - Method in class edu.jhu.ece.iacl.algorithms.manual_label.staple.STAPLEsurf
 
getIndex() - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamOption
Get selected option index.
getIndex() - Method in interface edu.jhu.ece.iacl.jist.structures.data.Indexable
Get heap index.
getIndex() - Method in class edu.jhu.ece.iacl.jist.structures.geom.EdgeIndexed
 
getIndex() - Method in class edu.jhu.ece.iacl.jist.structures.geom.VertexIndexed
 
getIndex() - Method in class edu.jhu.ece.iacl.jist.structures.image.VoxelIndexed
 
getIndex() - Method in class edu.jhu.ece.iacl.jist.structures.image.VoxelMipav
 
getIndexCount() - Method in class edu.jhu.ece.iacl.jist.structures.geom.EmbeddedPointSet
Gets the index count.
getIndexes() - Method in class edu.jhu.ece.iacl.jist.structures.geom.EmbeddedPointSet
Gets the indexes.
getIndexOf(String) - Method in class edu.jhu.ece.iacl.jist.pipeline.view.input.ParamMultiOptionInputView
Get index of list box entry.
getIndexOf(String) - Method in class edu.jhu.ece.iacl.jist.pipeline.view.input.ParamVolumeCollectionInputView
Get index of image name in list box entries.
getIndexOf(String) - Method in class edu.jhu.ece.iacl.jist.pipeline.view.input.ParamVolumeURICollectionInputView
Get index of image name in list box entries.
getInfo() - Method in class edu.jhu.ece.iacl.algorithms.dti.ParV3Info
The getInfo method parses the par file and sets the global variables.
getInfo() - Method in class edu.jhu.ece.iacl.algorithms.dti.ParV4Info
The getInfo method parses the par file and sets the global variables.
getInitializedCount() - Method in class edu.jhu.ece.iacl.jist.pipeline.PipeScheduler
Get the total number of initialized experiments.
getInitPath(TreeNode) - Method in class edu.jhu.ece.iacl.jist.pipeline.ExecutionContext
Get initial tree path by finding first child element.
getInnerPoint(int) - Method in class edu.jhu.ece.iacl.jist.structures.geom.EmbeddedSurface
Gets the inner point.
getInput() - Method in class edu.jhu.ece.iacl.jist.pipeline.ProcessingAlgorithm
Get input parameters.
getInputDirectory() - Method in class edu.jhu.ece.iacl.jist.pipeline.PipeLayout.RunParameters
Gets the input directory.
getInputHash() - Method in class edu.jhu.ece.iacl.jist.pipeline.PipeModule
Get input hash representing map from child parameter name to parameter.
getInputLocation() - Method in class edu.jhu.ece.iacl.jist.pipeline.ExecutionContext
Get directory where input parameters are located.
getInputParam() - Method in class edu.jhu.ece.iacl.jist.pipeline.dest.PipeDoubleCollectionExternalDestination
Get input parameter
getInputParam() - Method in class edu.jhu.ece.iacl.jist.pipeline.dest.PipeDoubleExternalDestination
Get input parameter
getInputParam() - Method in class edu.jhu.ece.iacl.jist.pipeline.dest.PipeFileCollectionExternalDestination
Get input parameter
getInputParam() - Method in class edu.jhu.ece.iacl.jist.pipeline.dest.PipeFileExternalDestination
Get input parameter
getInputParam() - Method in class edu.jhu.ece.iacl.jist.pipeline.dest.PipeIntegerCollectionExternalDestination
Get input parameter
getInputParam() - Method in class edu.jhu.ece.iacl.jist.pipeline.dest.PipeIntegerExternalDestination
Get input parameter
getInputParam() - Method in class edu.jhu.ece.iacl.jist.pipeline.dest.PipeParamCopyDestination
Get input parameter
getInputParam() - Method in class edu.jhu.ece.iacl.jist.pipeline.dest.PipeParamSummaryDestination
Get input parameter
getInputParam() - Method in class edu.jhu.ece.iacl.jist.pipeline.dest.PipeSurfaceCollectionExternalDestination
Get input parameter
getInputParam() - Method in class edu.jhu.ece.iacl.jist.pipeline.dest.PipeSurfaceExternalDestination
Get input parameter
getInputParam() - Method in class edu.jhu.ece.iacl.jist.pipeline.dest.PipeVolumeCollectionExternalDestination
Get input parameter
getInputParam() - Method in class edu.jhu.ece.iacl.jist.pipeline.dest.PipeVolumeExternalDestination
Get input parameter
getInputParam() - Method in class edu.jhu.ece.iacl.jist.pipeline.PipeDestination
Gets the input param.
getInputParams() - Method in class edu.jhu.ece.iacl.jist.pipeline.PipeModule
Get input parameters for this module.
getInputParamsFromFile() - Method in class edu.jhu.ece.iacl.jist.pipeline.ExecutionContext
Load parameters from file.
getInputPorts() - Method in class edu.jhu.ece.iacl.jist.pipeline.PipeModule
Get output parameters for this module.
getInputURI() - Method in class edu.jhu.ece.iacl.jist.pipeline.PipeLayout.RunParameters
Gets the input directory.
getInputView() - Method in class edu.jhu.ece.iacl.jist.pipeline.factory.ParamBooleanFactory
 
getInputView() - Method in class edu.jhu.ece.iacl.jist.pipeline.factory.ParamCollectionFactory
 
getInputView() - Method in class edu.jhu.ece.iacl.jist.pipeline.factory.ParamColorFactory
 
getInputView() - Method in class edu.jhu.ece.iacl.jist.pipeline.factory.ParamDataLabelFactory
 
getInputView() - Method in class edu.jhu.ece.iacl.jist.pipeline.factory.ParamDoubleFactory
 
getInputView() - Method in class edu.jhu.ece.iacl.jist.pipeline.factory.ParamFactory
Get the current input view.
getInputView() - Method in class edu.jhu.ece.iacl.jist.pipeline.factory.ParamFileCollectionFactory
 
getInputView() - Method in class edu.jhu.ece.iacl.jist.pipeline.factory.ParamFileFactory
Get parameter input view.
getInputView() - Method in class edu.jhu.ece.iacl.jist.pipeline.factory.ParamFloatFactory
 
getInputView() - Method in class edu.jhu.ece.iacl.jist.pipeline.factory.ParamHiddenFactory
 
getInputView() - Method in class edu.jhu.ece.iacl.jist.pipeline.factory.ParamInformationFactory
Get parameter input view.
getInputView() - Method in class edu.jhu.ece.iacl.jist.pipeline.factory.ParamIntegerFactory
 
getInputView() - Method in class edu.jhu.ece.iacl.jist.pipeline.factory.ParamLongFactory
 
getInputView() - Method in class edu.jhu.ece.iacl.jist.pipeline.factory.ParamMatrixFactory
 
getInputView() - Method in class edu.jhu.ece.iacl.jist.pipeline.factory.ParamMipavDialogFactory
Get parameter input view.
getInputView() - Method in class edu.jhu.ece.iacl.jist.pipeline.factory.ParamMultiOptionFactory
 
getInputView() - Method in class edu.jhu.ece.iacl.jist.pipeline.factory.ParamNumberCollectionFactory
 
getInputView() - Method in class edu.jhu.ece.iacl.jist.pipeline.factory.ParamObjectFactory
Get parameter input view.
getInputView() - Method in class edu.jhu.ece.iacl.jist.pipeline.factory.ParamOptionFactory
 
getInputView() - Method in class edu.jhu.ece.iacl.jist.pipeline.factory.ParamPerformanceFactory
 
getInputView() - Method in class edu.jhu.ece.iacl.jist.pipeline.factory.ParamPointDoubleFactory
 
getInputView() - Method in class edu.jhu.ece.iacl.jist.pipeline.factory.ParamPointFloatFactory
 
getInputView() - Method in class edu.jhu.ece.iacl.jist.pipeline.factory.ParamPointIntegerFactory
 
getInputView() - Method in class edu.jhu.ece.iacl.jist.pipeline.factory.ParamStringFactory
 
getInputView() - Method in class edu.jhu.ece.iacl.jist.pipeline.factory.ParamSurfaceCollectionFactory
 
getInputView() - Method in class edu.jhu.ece.iacl.jist.pipeline.factory.ParamSurfaceFactory
 
getInputView() - Method in class edu.jhu.ece.iacl.jist.pipeline.factory.ParamVolumeCollectionFactory
 
getInputView() - Method in class edu.jhu.ece.iacl.jist.pipeline.factory.ParamVolumeFactory
 
getInputView() - Method in class edu.jhu.ece.iacl.jist.pipeline.factory.ParamWeightedVolumeCollectionFactory
 
getInputView() - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamModel
Get the input view to specify the parameter value.
getInputView() - Method in class edu.jhu.ece.iacl.jist.pipeline.ProcessingDialog
Get input view.
getInputView() - Method in class edu.jhu.ece.iacl.jist.pipeline.ProcessingGroupDialog
Get input view.
getInstance() - Static method in class edu.jhu.ece.iacl.jist.io.ArrayDoubleDxReaderWriter
Gets the single instance of ArrayDoubleDxReaderWriter.
getInstance() - Static method in class edu.jhu.ece.iacl.jist.io.ArrayDoubleListTxtReaderWriter
Gets the single instance of ArrayDoubleListTxtReaderWriter.
getInstance() - Static method in class edu.jhu.ece.iacl.jist.io.ArrayDoubleMtxReaderWriter
Gets the single instance of ArrayDoubleMtxReaderWriter.
getInstance() - Static method in class edu.jhu.ece.iacl.jist.io.ArrayDoubleReaderWriter
Gets the single instance of ArrayDoubleReaderWriter.
getInstance() - Static method in class edu.jhu.ece.iacl.jist.io.ArrayDoubleTxtReaderWriter
Gets the single instance of ArrayDoubleTxtReaderWriter.
getInstance() - Static method in class edu.jhu.ece.iacl.jist.io.ArrayIntegerDxReaderWriter
Gets the single instance of ArrayIntegerDxReaderWriter.
getInstance() - Static method in class edu.jhu.ece.iacl.jist.io.ArrayIntegerReaderWriter
Gets the single instance of ArrayIntegerReaderWriter.
getInstance() - Static method in class edu.jhu.ece.iacl.jist.io.ArrayIntegerTxtReaderWriter
Gets the single instance of ArrayIntegerTxtReaderWriter.
getInstance() - Static method in class edu.jhu.ece.iacl.jist.io.ArrayObjectTxtReaderWriter
Gets the single instance of ArrayObjectTxtReaderWriter.
getInstance() - Static method in class edu.jhu.ece.iacl.jist.io.CurveVtkReaderWriter
Gets the single instance of CurveVtkReaderWriter.
getInstance() - Static method in class edu.jhu.ece.iacl.jist.io.FiberCollectionReaderWriter
Gets the single instance of FiberCollectionReaderWriter.
getInstance() - Static method in class edu.jhu.ece.iacl.jist.io.ImageDataReaderWriter
Gets the single instance of CubicVolumeReaderWriter.
getInstance() - Static method in class edu.jhu.ece.iacl.jist.io.ModelImageReaderWriter
Gets the single instance of ModelImageReaderWriter.
getInstance() - Static method in class edu.jhu.ece.iacl.jist.io.PointSetVtkReaderWriter
Gets the single instance of PointSetVtkReaderWriter.
getInstance() - Static method in class edu.jhu.ece.iacl.jist.io.RibbonVtkReaderWriter
Gets the single instance of RibbonVtkReaderWriter.
getInstance() - Static method in class edu.jhu.ece.iacl.jist.io.StringReaderWriter
Gets the single instance of StringReaderWriter.
getInstance() - Static method in class edu.jhu.ece.iacl.jist.io.SurfaceBrainSuiteReaderWriter
Gets the single instance of SurfaceBrainSuiteReaderWriter.
getInstance() - Static method in class edu.jhu.ece.iacl.jist.io.SurfaceDxReaderWriter
Gets the single instance of SurfaceDxReaderWriter.
getInstance() - Static method in class edu.jhu.ece.iacl.jist.io.SurfaceFreeSurferReaderWriter
Gets the single instance of SurfaceFreeSurferReaderWriter.
getInstance() - Static method in class edu.jhu.ece.iacl.jist.io.SurfaceMipavReaderWriter
Gets the single instance of SurfaceMipavReaderWriter.
getInstance() - Static method in class edu.jhu.ece.iacl.jist.io.SurfaceReaderWriter
Gets the single instance of SurfaceReaderWriter.
getInstance() - Static method in class edu.jhu.ece.iacl.jist.io.SurfaceVrmlReaderWriter
Gets the single instance of SurfaceVrmlReaderWriter.
getInstance() - Static method in class edu.jhu.ece.iacl.jist.io.SurfaceVtkReaderWriter
Gets the single instance of SurfaceVtkReaderWriter.
getInstance() - Static method in class edu.jhu.ece.iacl.jist.io.VertexDoubleDxReaderWriter
Gets the single instance of VertexDoubleDxReaderWriter.
getInstance() - Static method in class edu.jhu.ece.iacl.jist.io.VertexFloatDxReaderWriter
Gets the single instance of VertexFloatDxReaderWriter.
getInstance() - Static method in class edu.jhu.ece.iacl.jist.io.VolumeVtkReaderWriter
Gets the single instance of VolumeVtkReaderWriter.
getInstance() - Static method in class edu.jhu.ece.iacl.jist.io.ZipFileReaderWriter
Gets the single instance of ZipFileReaderWriter.
getInstance() - Static method in class edu.jhu.ece.iacl.jist.pipeline.gui.LayoutPanel
Gets the single instance of LayoutPanel.
getInstance() - Static method in class edu.jhu.ece.iacl.jist.pipeline.gui.ModuleTreePanel
Get singleton reference to tree panel.
getInstance() - Static method in class edu.jhu.ece.iacl.jist.pipeline.gui.ParameterPanel
Get singleton reference to parameter panel.
getInstance() - Static method in class edu.jhu.ece.iacl.jist.pipeline.gui.PipelineLayoutTool
Get singleton reference to layout tool.
getInstance() - Static method in class edu.jhu.ece.iacl.jist.pipeline.gui.ProcessManager
Get singleton reference.
getInstance() - Static method in class edu.jhu.ece.iacl.jist.pipeline.PipeLibrary
Get singleton reference to library.
getInstance() - Static method in class edu.jhu.ece.iacl.jist.pipeline.view.input.Refresher
Get singleton reference to constructor.
getInt() - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamNumber
Get the number value as int.
getInt(int, int) - Method in class edu.jhu.ece.iacl.jist.structures.image.ImageData
Gets the int.
getInt(int, int, int) - Method in class edu.jhu.ece.iacl.jist.structures.image.ImageData
Gets the int.
getInt(int, int, int, int) - Method in class edu.jhu.ece.iacl.jist.structures.image.ImageData
Gets the int.
getInt(int, int, int, int) - Method in class edu.jhu.ece.iacl.jist.structures.image.ImageDataByte
 
getInt(int, int, int, int) - Method in class edu.jhu.ece.iacl.jist.structures.image.ImageDataColor
 
getInt(int, int, int, int) - Method in class edu.jhu.ece.iacl.jist.structures.image.ImageDataDouble
 
getInt(int, int, int, int) - Method in class edu.jhu.ece.iacl.jist.structures.image.ImageDataFloat
 
getInt(int, int, int, int) - Method in class edu.jhu.ece.iacl.jist.structures.image.ImageDataInt
 
getInt(int, int, int, int) - Method in class edu.jhu.ece.iacl.jist.structures.image.ImageDataMipav
 
getInt(int, int, int, int) - Method in class edu.jhu.ece.iacl.jist.structures.image.ImageDataNumber
 
getInt(int, int, int, int) - Method in class edu.jhu.ece.iacl.jist.structures.image.ImageDataUByte
 
getInt() - Method in class edu.jhu.ece.iacl.jist.structures.image.Voxel
Gets the int.
getInt() - Method in class edu.jhu.ece.iacl.jist.structures.image.VoxelBoolean
 
getInt() - Method in class edu.jhu.ece.iacl.jist.structures.image.VoxelColor
 
getInt() - Method in class edu.jhu.ece.iacl.jist.structures.image.VoxelDouble
 
getInt() - Method in class edu.jhu.ece.iacl.jist.structures.image.VoxelFloat
 
getInt() - Method in class edu.jhu.ece.iacl.jist.structures.image.VoxelIndexed
 
getInt() - Method in class edu.jhu.ece.iacl.jist.structures.image.VoxelInt
 
getInt() - Method in class edu.jhu.ece.iacl.jist.structures.image.VoxelMipav
 
getInt() - Method in class edu.jhu.ece.iacl.jist.structures.image.VoxelShort
 
getInt() - Method in class edu.jhu.ece.iacl.jist.structures.image.VoxelUByte
 
getInt() - Method in class edu.jhu.ece.iacl.jist.structures.image.VoxelVector
 
getIntensity() - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.DataLabel
Get intensity.
getInternalFrames() - Method in class edu.jhu.ece.iacl.jist.pipeline.gui.LayoutPanel
Return all internal frames.
getItem() - Method in class edu.jhu.ece.iacl.jist.pipeline.gui.ConnectionEditor
Get selected item.
getIterations() - Method in class edu.jhu.bme.smile.commons.optimize.BrentMethod1D
Gets the number of iterations done.
getIterations() - Method in class edu.jhu.bme.smile.commons.optimize.DownhillSimplexND
Gets the number of iterations done.
getIterations() - Method in class edu.jhu.bme.smile.commons.optimize.GoldenSectionSearch1D
Gets the number of iterations done.
getIterations() - Method in class edu.jhu.bme.smile.commons.optimize.LevenbergMarquardt
Gets the number of iterations done.
getIterations() - Method in class edu.jhu.bme.smile.commons.optimize.LineSearchND
Gets the number of iterations done.
getIterations() - Method in class edu.jhu.bme.smile.commons.optimize.LineSearchNDDifferentiable
Gets the number of iterations done.
getIterations() - Method in class edu.jhu.bme.smile.commons.optimize.NewtonMethod1D
Gets the number of iterations done.
getIterations() - Method in interface edu.jhu.bme.smile.commons.optimize.Optimizer1DContinuous
Gets the number of iterations done.
getIterations() - Method in interface edu.jhu.bme.smile.commons.optimize.Optimizer1DContinuousDifferentiable
Gets the number of iterations done.
getIterations() - Method in interface edu.jhu.bme.smile.commons.optimize.OptimizerNDContinuous
Gets the number of iterations done.
getIterations() - Method in interface edu.jhu.bme.smile.commons.optimize.OptimizerNDContinuousDifferentiable
Gets the number of iterations done.
getIterations() - Method in class edu.jhu.bme.smile.commons.optimize.tensor.MLTensor
Gets the number of iterations required to calculate the result.
getIterations() - Method in class edu.jhu.ece.iacl.algorithms.dti.DTEMRLTensor
Gets the number of iterations required to calculate the result.
getJaccard() - Method in class edu.jhu.ece.iacl.algorithms.volume.CompareVolumes
 
getJobList() - Static method in class edu.jhu.ece.iacl.jist.processcontrol.DispatchController
Gets the job list.
getJones30() - Static method in class edu.jhu.ece.iacl.algorithms.dti.GTCparams
 
getJones30VMS() - Static method in class edu.jhu.ece.iacl.algorithms.dti.GTCparams
 
getJre() - Method in class edu.jhu.ece.iacl.jist.pipeline.JistPreferences
Get JRE executable.
getKurtosisExcess() - Method in class edu.jhu.ece.iacl.algorithms.volume.CompareVolumes
 
getL(int) - Method in class edu.jhu.bme.smile.commons.math.specialFunctions.SphericalHarmonics
 
getlabCM(int) - Method in class edu.jhu.ece.iacl.algorithms.manual_label.LabelImage
 
getLabel() - Method in class edu.jhu.ece.iacl.doc.DocumentAllTests.ModuleDescription
Get module label.
getLabel() - Method in class edu.jhu.ece.iacl.jist.pipeline.AbstractCalculation
Label for this computation.
getLabel() - Method in class edu.jhu.ece.iacl.jist.pipeline.AlgorithmInformation
Gets the label.
getLabel() - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamModel
Get the text label for this parameter.
getLabel() - Method in class edu.jhu.ece.iacl.jist.pipeline.PipeChildPort
Always returns "Child".
getLabel() - Method in class edu.jhu.ece.iacl.jist.pipeline.PipeModule
Get display label for this module.
getLabel() - Method in class edu.jhu.ece.iacl.jist.pipeline.PipeParentPort
Always returns "Parent".
getLabel() - Method in class edu.jhu.ece.iacl.jist.pipeline.PipePort
Get displayed label.
getLabelDat() - Method in class edu.jhu.ece.iacl.algorithms.manual_label.LabelSurface
 
getLabelFile() - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamDataLabel
Get location of label file.
getLabelImageList(List<ImageData>) - Static method in class edu.jhu.ece.iacl.algorithms.manual_label.LabelImage
 
getLabelList() - Method in class edu.jhu.ece.iacl.algorithms.manual_label.LabelImage
 
getLabelList(EmbeddedSurface, int) - Static method in class edu.jhu.ece.iacl.algorithms.manual_label.simulation.SurfaceRater
Gets a list of all of the labels (stored as an int array) that are present on an input surface
getLabelList(ImageData) - Static method in class edu.jhu.ece.iacl.algorithms.manual_label.simulation.VolumeRater
Gets a list of all of the labels (stored as an int array) that are present on an input volume
getLabels() - Method in class edu.jhu.ece.iacl.algorithms.manual_label.staple.STAPLEgeneral
 
getLabels() - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamCollection
Get all children labels.
getLabelVertexCount(int) - Method in class edu.jhu.ece.iacl.algorithms.manual_label.LabelSurface
 
getLabelVolume(int) - Method in class edu.jhu.ece.iacl.algorithms.manual_label.LabelImage
 
getlabset(int) - Method in class edu.jhu.ece.iacl.algorithms.manual_label.LabelImage
 
getlabset(double) - Method in class edu.jhu.ece.iacl.algorithms.manual_label.LabelSurface
 
getlabsetArray(int) - Method in class edu.jhu.ece.iacl.algorithms.manual_label.LabelImage
 
getlabsetArray(double) - Method in class edu.jhu.ece.iacl.algorithms.manual_label.LabelSurface
 
getLastComparisonHits() - Method in class edu.jhu.ece.iacl.algorithms.manual_label.LabelImage
 
getLastCropParams() - Method in class edu.jhmi.rad.medic.utilities.CubicVolumeCropper
Gets the last crop params.
getLastDirectory() - Method in class edu.jhu.ece.iacl.jist.pipeline.JistPreferences
Get last directory entered.
getLastModifiedTime() - Method in class edu.jhu.ece.iacl.jist.pipeline.PipeLayout
Gets the last modified time.
getLayout() - Method in class edu.jhu.ece.iacl.jist.pipeline.ExecutionContext
Get layout owner.
getLayoutConstraints() - Method in class edu.jhu.ece.iacl.jist.pipeline.view.input.ParamInputView
Get layout constraints.
getLayoutConstraints() - Method in class edu.jhu.ece.iacl.jist.pipeline.view.output.ParamOutputView
Get layout constraints.
getLayoutFile() - Method in class edu.jhu.ece.iacl.doc.DocumentAllTests.TestCase
 
getLength() - Method in class edu.jhu.ece.iacl.jist.structures.fiber.Fiber
Gets the length.
getLength() - Method in class edu.jhu.ece.iacl.jist.structures.geom.PolySpline
Gets the length.
getLevel() - Method in interface edu.jhu.cs.cisst.algorithms.optimize.fmg.grid.ConstGrid
Get the resolution level.
getLevel() - Method in class edu.jhu.cs.cisst.algorithms.optimize.fmg.grid.Grid
 
getLevels() - Method in class edu.jhu.ece.iacl.algorithms.vabra.VabraConfiguration
 
getLevelSet() - Method in class edu.jhu.cs.cisst.algorithms.segmentation.gac.GeodesicActiveContour2D
Gets the level set.
getLgFontSize() - Method in class edu.jhu.ece.iacl.jist.pipeline.JistPreferences
 
getLibraryPath() - Method in class edu.jhu.ece.iacl.jist.pipeline.PipeLibrary
Get location of library.
getLineData() - Method in class edu.jhu.ece.iacl.jist.structures.geom.CurveCollection
Gets the line data.
getList(List<T>) - Method in class edu.jhu.ece.iacl.jist.pipeline.view.input.InformationListBox
Copy list box entries into existing list.
getListCellRendererComponent(JList, Object, int, boolean, boolean) - Method in class edu.jhu.ece.iacl.jist.pipeline.gui.ConnectorRenderer
Render index as spinner box.
getListCellRendererComponent(JList, Object, int, boolean, boolean) - Method in class edu.jhu.ece.iacl.jist.pipeline.view.input.InformationListBox
Renderer for list box items.
getListCellRendererComponent(JList, Object, int, boolean, boolean) - Method in class edu.jhu.ece.iacl.jist.pipeline.view.input.ParamFileCollectionInputView
Use a custom cell renderer that can interpret ParamFiles.
getListCellRendererComponent(JList, Object, int, boolean, boolean) - Method in class edu.jhu.ece.iacl.jist.pipeline.view.input.ParamMultiOptionInputView
Use a custom cell renderer that can interpret option.
getListCellRendererComponent(JList, Object, int, boolean, boolean) - Method in class edu.jhu.ece.iacl.jist.pipeline.view.input.ParamNumberCollectionInputView
Use a custom cell renderer that can interpret number parameters.
getListCellRendererComponent(JList, Object, int, boolean, boolean) - Method in class edu.jhu.ece.iacl.jist.pipeline.view.input.ParamVolumeCollectionInputView
Use a custom cell renderer that can interpret ParamVolumes.
getListCellRendererComponent(JList, Object, int, boolean, boolean) - Method in class edu.jhu.ece.iacl.jist.pipeline.view.input.ParamVolumeURICollectionInputView
Use a custom cell renderer that can interpret ParamFiles.
getListCellRendererComponent(JList, Object, int, boolean, boolean) - Method in class edu.jhu.ece.iacl.jist.pipeline.view.input.ParamVolumeURIInputView
 
getListCellRendererComponent(JList, Object, int, boolean, boolean) - Method in class edu.jhu.ece.iacl.jist.pipeline.view.input.ParamWeightedVolumesInputView
Use custom render for list components so that they are the same size as the weight entry field.
getListCellRendererComponent(JList, Object, int, boolean, boolean) - Method in class edu.jhu.ece.iacl.jist.pipeline.view.input.ParamWeightedVolumesURIInputView
Use custom render for list components so that they are the same size as the weight entry field.
getListeners() - Method in class edu.jhu.ece.iacl.jist.pipeline.PipeModule
Get all listeners for this module.
getListeners() - Method in class edu.jhu.ece.iacl.jist.pipeline.PipePort
Get all listeners.
getLocation() - Method in class edu.jhu.ece.iacl.doc.DocumentAllTests.Assertion
Get location of assertion output.
getLocatorResult() - Method in class edu.jhu.ece.iacl.jist.structures.geom.EmbeddedPointSet
Gets the locator result.
getLog() - Method in class edu.jhu.bme.smile.commons.optimize.BrentMethod1D
Gets the logged data
getLog() - Method in class edu.jhu.bme.smile.commons.optimize.DownhillSimplexND
Gets the logged data
getLog() - Method in class edu.jhu.bme.smile.commons.optimize.GoldenSectionSearch1D
Gets the logged data
getLog() - Method in class edu.jhu.bme.smile.commons.optimize.LevenbergMarquardt
Gets the logged data
getLog() - Method in class edu.jhu.bme.smile.commons.optimize.LineSearchND
Gets the logged data
getLog() - Method in class edu.jhu.bme.smile.commons.optimize.LineSearchNDDifferentiable
Gets the logged data
getLog() - Method in class edu.jhu.bme.smile.commons.optimize.NewtonMethod1D
Gets the logged data
getLogScalingFactor() - Method in class edu.jhu.bme.smile.commons.math.HistogramGenerator
 
getLong() - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamNumber
Get the number value as long.
getLongDescription() - Method in class edu.jhu.ece.iacl.doc.DocMediaWikiWriter
 
getLongDescription() - Method in class edu.jhu.ece.iacl.jist.pipeline.AlgorithmInformation
Gets the Long description.
getLow() - Static method in class edu.jhu.ece.iacl.algorithms.dti.GTCparams
 
getLowOP() - Static method in class edu.jhu.ece.iacl.algorithms.dti.GTCparams
 
getLowOP2() - Static method in class edu.jhu.ece.iacl.algorithms.dti.GTCparams
 
getM(int) - Method in class edu.jhu.bme.smile.commons.math.specialFunctions.SphericalHarmonics
 
getMapFile() - Method in class edu.jhu.ece.iacl.jist.pipeline.graph.PipeAlgorithmFactory.AlgorithmNode
Gets the map file.
getMapFile() - Method in class edu.jhu.ece.iacl.jist.pipeline.graph.PipeAlgorithmFactory
Get module definition file.
getMapFile() - Method in class edu.jhu.ece.iacl.jist.pipeline.PipeAlgorithm
Get file that stores this algorithm.
getMapFile() - Method in class edu.jhu.ece.iacl.jist.pipeline.ProcessingAlgorithm
Get module definition file.
getMarker(int) - Method in class edu.jhu.ece.iacl.jist.structures.fiber.Fiber
Gets the marker.
getMaskedVol() - Method in class edu.jhu.ece.iacl.algorithms.manual_label.ROI
 
getMaskVolume() - Method in class edu.jhu.ece.iacl.algorithms.volume.CompareVolumes
 
getMatrix(int, int) - Method in class edu.jhu.bme.smile.commons.math.RotationMatrix
 
getMatrix() - Method in class edu.jhu.bme.smile.commons.math.RotationMatrix
 
getMatrix() - Method in class edu.jhu.bme.smile.commons.math.specialFunctions.ComplexVector
 
getMatrix2d() - Method in class edu.jhu.ece.iacl.jist.structures.matrix.Matrix3
Gets the matrix2d.
getMatrix2d(int) - Method in class edu.jhu.ece.iacl.jist.structures.matrix.Matrix3
Gets the matrix2d.
getMatrixArray() - Method in class edu.jhu.bme.smile.commons.math.RotationMatrix
 
getMatrixResult() - Method in class edu.jhu.bme.smile.commons.math.L1LSCompressedSensing
 
getMax() - Method in class edu.jhu.bme.smile.commons.math.HistogramGenerator
 
getMax() - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamNumber
Get maximum possible value.
getMax() - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamNumberCollection
Gets the max.
getMax() - Method in class edu.jhu.ece.iacl.jist.structures.geom.EmbeddedSurface
Gets the max.
getMax1() - Method in class edu.jhu.ece.iacl.algorithms.volume.CompareVolumes
 
getMax2() - Method in class edu.jhu.ece.iacl.algorithms.volume.CompareVolumes
 
getMaxAngle(int) - Method in class edu.jhu.ece.iacl.jist.structures.geom.EmbeddedSurface
Gets the max angle.
getMaxCurvatureForce() - Method in class edu.jhu.cs.cisst.algorithms.segmentation.gac.GaussianCurvatureForce2D
Gets the max curvature force.
getMaxCurvatureForce() - Method in class edu.jhu.cs.cisst.algorithms.segmentation.gac.MeanCurvatureForce2D
Gets the max curvature force.
getMaxError() - Method in class edu.jhu.ece.iacl.algorithms.volume.CompareVolumes
 
getMaxFromVolume() - Method in class edu.jhu.ece.iacl.algorithms.dti.tractography.FiberStatistics
 
getMaxHeap() - Method in class edu.jhu.ece.iacl.jist.pipeline.PipeLayout.RunParameters
Gets the max heap.
getMaxHistorySize() - Method in class edu.jhu.ece.iacl.jist.pipeline.JistPreferences
Get maximum history size.
getMaxIncoming() - Method in class edu.jhu.ece.iacl.jist.pipeline.PipePort
Maximum number of input ports.
getMaxIterations() - Method in class edu.jhu.cs.cisst.algorithms.segmentation.gac.GradientVectorFlow2D
Gets the max iterations.
getMaxOutgoing() - Method in class edu.jhu.ece.iacl.jist.pipeline.PipePort
Get maximum number of outgoing ports.
getMaxProcs() - Method in class edu.jhu.ece.iacl.jist.pipeline.PipeLayout.RunParameters
Gets the max processes.
getMdFontSize() - Method in class edu.jhu.ece.iacl.jist.pipeline.JistPreferences
 
getMean1() - Method in class edu.jhu.ece.iacl.algorithms.volume.CompareVolumes
 
getMean2() - Method in class edu.jhu.ece.iacl.algorithms.volume.CompareVolumes
 
getMeanFromVolume() - Method in class edu.jhu.ece.iacl.algorithms.dti.tractography.FiberStatistics
 
getMedianFromVolume() - Method in class edu.jhu.ece.iacl.algorithms.dti.tractography.FiberStatistics
 
getMedium() - Static method in class edu.jhu.ece.iacl.algorithms.dti.GTCparams
 
getMediumOP() - Static method in class edu.jhu.ece.iacl.algorithms.dti.GTCparams
 
getMediumOP2() - Static method in class edu.jhu.ece.iacl.algorithms.dti.GTCparams
 
getMessage() - Method in exception edu.jhu.ece.iacl.jist.pipeline.AlgorithmRuntimeException
Get error message.
getMessage() - Method in exception edu.jhu.ece.iacl.jist.pipeline.parameter.InvalidParameterException
 
getMethod() - Method in class edu.jhu.bme.smile.commons.optimize.FunctionNumeric1DDifferentiation
Gets the method
getMethod() - Method in class edu.jhu.bme.smile.commons.optimize.FunctionNumericNDDifferentiation
Gets the method used
getMin() - Method in class edu.jhu.bme.smile.commons.math.HistogramGenerator
 
getMin() - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamNumber
Get minimum possible value.
getMin() - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamNumberCollection
Gets the min.
getMin() - Method in class edu.jhu.ece.iacl.jist.structures.geom.EmbeddedSurface
Gets the min.
getMin1() - Method in class edu.jhu.ece.iacl.algorithms.volume.CompareVolumes
 
getMin2() - Method in class edu.jhu.ece.iacl.algorithms.volume.CompareVolumes
 
getMinAngle(int) - Method in class edu.jhu.ece.iacl.jist.structures.geom.EmbeddedSurface
Gets the min angle.
getMinError() - Method in class edu.jhu.ece.iacl.algorithms.volume.CompareVolumes
 
getMinFromVolume() - Method in class edu.jhu.ece.iacl.algorithms.dti.tractography.FiberStatistics
 
getMipavType(VoxelType) - Static method in class edu.jhu.ece.iacl.jist.structures.image.ImageDataMipav
Get MIPAV voxel type for specified voxel type MIPAV types are ambiguous because they use integers instead of enums This function is not reflexive for Vector types since MIPAV doesn't have a Vector type.
getModality() - Method in class edu.jhu.ece.iacl.jist.structures.image.ImageHeader
Gets the modality.
getModelImageCopy() - Method in class edu.jhu.ece.iacl.jist.structures.image.ImageData
Gets the model image.
getModelImageCopy() - Method in class edu.jhu.ece.iacl.jist.structures.image.ImageDataMipav
 
getModelImageDirect() - Method in class edu.jhu.ece.iacl.jist.structures.image.ImageDataMipav
 
getModule() - Method in class edu.jhu.ece.iacl.jist.cli.JistCLI
 
getModuleCell() - Method in class edu.jhu.ece.iacl.jist.pipeline.PipeModule
Get graph cell representing this module.
getModuleClass() - Method in class edu.jhu.ece.iacl.jist.pipeline.graph.PipeModuleCell
Module class that is stored in this cell.
getModuleClass() - Method in class edu.jhu.ece.iacl.jist.pipeline.graph.PipeModuleFactory
Get class that identifies the module which could be a PipeModule.
getModuleInputParam(String) - Method in class edu.jhu.ece.iacl.jist.pipeline.PipeLayout
Get input parameters for particular module by identifying name.
getModuleName() - Method in class edu.jhu.ece.iacl.jist.pipeline.graph.PipeModuleFactory
Get the module's name.
getModuleOutputParam(String) - Method in class edu.jhu.ece.iacl.jist.pipeline.PipeLayout
Get module output parameters.
getModulePanel() - Method in class edu.jhu.ece.iacl.jist.pipeline.gui.PipelineLayoutTool
 
getModules() - Method in class edu.jhu.ece.iacl.doc.DocumentAllTests.TestCase
 
getMutualInformation() - Method in class edu.jhu.ece.iacl.algorithms.volume.CompareVolumes
 
getName() - Method in interface edu.jhu.cs.cisst.vent.Visualization
Gets the name.
getName() - Method in class edu.jhu.cs.cisst.vent.VisualizationProcessing
Gets the name.
getName() - Method in class edu.jhu.ece.iacl.algorithms.manual_label.LabelImage
 
getName() - Method in class edu.jhu.ece.iacl.algorithms.manual_label.LabelSurface
 
getName() - Method in class edu.jhu.ece.iacl.doc.DocumentAllTests.Assertion
Get name of assertion.
getName() - Method in class edu.jhu.ece.iacl.doc.DocumentAllTests.ModuleDescription
Get module name.
getName() - Method in class edu.jhu.ece.iacl.doc.DocumentAllTests.TestCase
 
getName() - Method in class edu.jhu.ece.iacl.jist.pipeline.AlgorithmInformation
Gets the name.
getName() - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.DataLabel
Get name.
getName() - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamModel
Get the parameter's name, which should be unique.
getName() - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamVolume
 
getName() - Method in class edu.jhu.ece.iacl.jist.pipeline.PipeChildPort
Always returns "child".
getName() - Method in class edu.jhu.ece.iacl.jist.pipeline.PipeModule
Get unique name that identifies this parameter.
getName() - Method in class edu.jhu.ece.iacl.jist.pipeline.PipeParentPort
Always returns "parent".
getName() - Method in class edu.jhu.ece.iacl.jist.pipeline.PipePort
Get identifying name.
getName() - Method in class edu.jhu.ece.iacl.jist.pipeline.tree.DraggableNode
Get module name for this node.
getName() - Method in class edu.jhu.ece.iacl.jist.structures.fiber.FiberCollection
Gets the name.
getName() - Method in class edu.jhu.ece.iacl.jist.structures.geom.CurveCollection
Gets the name.
getName() - Method in class edu.jhu.ece.iacl.jist.structures.geom.EmbeddedPointSet
Gets the name.
getName() - Method in class edu.jhu.ece.iacl.jist.structures.image.ImageData
Gets the name.
getName() - Method in class edu.jhu.ece.iacl.jist.structures.image.ImageDataColor
 
getName() - Method in class edu.jhu.ece.iacl.jist.structures.image.ImageDataDouble
 
getName() - Method in class edu.jhu.ece.iacl.jist.structures.image.ImageDataFloat
 
getName() - Method in class edu.jhu.ece.iacl.jist.structures.image.ImageDataUByte
 
getName() - Method in class edu.jhu.ece.iacl.plugins.dti.MetaImageData4D
 
getNamingConvention() - Method in class edu.jhu.ece.iacl.jist.pipeline.JistPreferences
Gets the naming convention.
getNamingConvention() - Method in class edu.jhu.ece.iacl.jist.pipeline.PipeLayout.RunParameters
Gets the naming convention.
getNeighborEdgeFaceTable() - Method in class edu.jhu.ece.iacl.jist.structures.geom.EmbeddedSurface
Gets the neighbor edge face table.
getNeighborFaceFaceTable() - Method in class edu.jhu.ece.iacl.jist.structures.geom.EmbeddedSurface
Gets the neighbor face face table.
getNeighbors(int, int, int, GridPt.Connectivity, int, int, int) - Static method in class edu.jhu.ece.iacl.algorithms.manual_label.simulation.VolumeRater
 
getNeighbors(GridPt, GridPt.Connectivity, int, int, int) - Static method in class edu.jhu.ece.iacl.algorithms.manual_label.simulation.VolumeRater
 
getNeighbors(int, int, int) - Method in class edu.jhu.ece.iacl.algorithms.manual_label.staple.STAPLEmulti
 
getNeighbors(int, int, int) - Method in class edu.jhu.ece.iacl.algorithms.manual_label.staple.STAPLEmulti2
 
getNeighborsX() - Method in interface edu.jhu.ece.iacl.jist.structures.image.MaskVolume
Gets the neighbors x.
getNeighborsX() - Method in class edu.jhu.ece.iacl.jist.structures.image.MaskVolume18
 
getNeighborsX() - Method in class edu.jhu.ece.iacl.jist.structures.image.MaskVolume26
 
getNeighborsX() - Method in class edu.jhu.ece.iacl.jist.structures.image.MaskVolume6
 
getNeighborsY() - Method in interface edu.jhu.ece.iacl.jist.structures.image.MaskVolume
Gets the neighbors y.
getNeighborsY() - Method in class edu.jhu.ece.iacl.jist.structures.image.MaskVolume18
 
getNeighborsY() - Method in class edu.jhu.ece.iacl.jist.structures.image.MaskVolume26
 
getNeighborsY() - Method in class edu.jhu.ece.iacl.jist.structures.image.MaskVolume6
 
getNeighborsZ() - Method in interface edu.jhu.ece.iacl.jist.structures.image.MaskVolume
Gets the neighbors z.
getNeighborsZ() - Method in class edu.jhu.ece.iacl.jist.structures.image.MaskVolume18
 
getNeighborsZ() - Method in class edu.jhu.ece.iacl.jist.structures.image.MaskVolume26
 
getNeighborsZ() - Method in class edu.jhu.ece.iacl.jist.structures.image.MaskVolume6
 
getNeighborVertexEdgeTable() - Method in class edu.jhu.ece.iacl.jist.structures.geom.EmbeddedSurface
Gets the neighbor vertex edge table.
getNeighborVertexFaceTable() - Method in class edu.jhu.ece.iacl.jist.structures.geom.EmbeddedSurface
Gets the neighbor vertex face table.
getNeighborVertexVertexTable() - Method in class edu.jhu.ece.iacl.jist.structures.geom.EmbeddedSurface
Gets the neighbor vertex vertex table.
getNonNormalizedVector(int, int) - Static method in class edu.jhu.ece.iacl.algorithms.manual_label.atlasing.LogOdds
Helper method used in Logit and iLogit methods
getNormal(int) - Method in class edu.jhu.ece.iacl.jist.structures.geom.EmbeddedSurface
Gets the normal.
getNormal() - Method in class edu.jhu.ece.iacl.jist.structures.geom.TriangleFace
Gets the normal.
getNormals() - Method in class edu.jhu.cs.cisst.vent.structures.processing.PTriangleMesh
Gets the normals.
getNotReadyCount() - Method in class edu.jhu.ece.iacl.jist.pipeline.PipeScheduler
Get number of experiments that are not ready to run.
getNumberOfAddedConnections() - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamCollection
 
getNumberOfBasisFunctions() - Method in class edu.jhu.ece.iacl.algorithms.hardi.CFARIBasisSet
 
getNumberOfCoefficients(int) - Static method in class edu.jhu.ece.iacl.algorithms.hardi.QBall
 
getNumberOfDimensions() - Method in class edu.jhu.bme.smile.commons.optimize.FunctionNumericND1DDifferentiation
Gets the number of dimensions
getNumberOfDimensions() - Method in class edu.jhu.bme.smile.commons.optimize.FunctionNumericNDDifferentiation
Gets the number of dimensions
getNumberOfDimensions() - Method in class edu.jhu.bme.smile.commons.optimize.MinToMaxND
Gets the number of dimensions
getNumberOfDimensions() - Method in class edu.jhu.bme.smile.commons.optimize.MinToMaxNDDifferentiable
Gets the number of dimensions
getNumberOfDimensions() - Method in interface edu.jhu.bme.smile.commons.optimize.OptimizableNDContinuous
Gets the number of dimensions of the function.
getNumberOfDimensions() - Method in class edu.jhu.bme.smile.commons.optimize.ProjectNDto1DOptimizable
Gets the number of dimensions.
getNumberOfDimensions() - Method in class edu.jhu.bme.smile.commons.optimize.test.FunctionNegativeXSquaredND
Gets the number of dimensions.
getNumberOfDimensions() - Method in class edu.jhu.bme.smile.commons.optimize.test.FunctionRosenbrock
Gets the number of dimensions.
getNumberOfDimensions() - Method in class edu.jhu.bme.smile.commons.optimize.test.FunctionXSquaredND
Gets the number of dimensions.
getNumberOfDimensions() - Method in class edu.jhu.bme.smile.commons.optimize.test.FunctionXXplusSinXXND
Gets the number of dimensions.
getNumberOfDimensions() - Method in class edu.jhu.bme.smile.commons.optimize.test.FunctionXXYYND
Gets the number of dimensions.
getNumberOfHoles() - Method in class edu.jhu.ece.iacl.jist.structures.geom.EmbeddedSurface
Gets the number of holes.
getNumVolumes() - Method in class edu.jhu.ece.iacl.algorithms.dti.ParV3Info
 
getNumVolumes() - Method in class edu.jhu.ece.iacl.algorithms.dti.ParV4Info
 
getObject() - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamObject
Get object.
getObject() - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamSurface
Get Surface.
getObject() - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamVolume
Deprecated. 
getObservers() - Method in class edu.jhu.ece.iacl.jist.pipeline.view.input.ParamInputView
Get observers
getObstacles(GraphLayoutCache, Point2D, Point2D) - Method in class edu.jhu.ece.iacl.jist.pipeline.graph.AvoidanceRouting
Get list of rectangular obstacles in graph.
getOffCentre() - Method in class edu.jhu.ece.iacl.algorithms.dti.ParV3Info
 
getOffCentre() - Method in class edu.jhu.ece.iacl.algorithms.dti.ParV4Info
 
getOpposite(Vertex) - Method in class edu.jhu.ece.iacl.jist.structures.geom.Segment
Gets the opposite.
getOpposite(Vertex) - Method in class edu.jhu.ece.iacl.jist.structures.geom.Triangle
Gets the opposite.
getOpposite(Edge) - Method in class edu.jhu.ece.iacl.jist.structures.geom.Triangle
Gets the opposite.
getOptions() - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamMultiOption
Get list of possible options.
getOptions() - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamOption
Get list of possible options.
getOptionValue(String) - Method in class edu.jhu.ece.iacl.jist.cli.JistCLI
 
getOrderFromNumberOfCoeff(int) - Static method in class edu.jhu.ece.iacl.algorithms.hardi.QBall
 
getOrigin() - Method in class edu.jhu.ece.iacl.jist.structures.geom.EmbeddedSurface
Gets the origin.
getOrigin() - Method in class edu.jhu.ece.iacl.jist.structures.image.ImageHeader
Gets the origin.
getOrigTable() - Method in class edu.jhu.ece.iacl.algorithms.dti.DTIGradientTableCreator
 
getOutDir() - Method in class edu.jhu.ece.iacl.jist.cli.JistCLI
 
getOuterPoint(int) - Method in class edu.jhu.ece.iacl.jist.structures.geom.EmbeddedSurface
Gets the outer point.
getOutFile() - Method in class edu.jhu.ece.iacl.jist.cli.JistCLI
 
getOutFrame() - Method in class edu.jhu.ece.iacl.jist.pipeline.gui.ProcessManagerTable
Gets the out frame.
getOutgoingConnector(PipePort) - Method in class edu.jhu.ece.iacl.jist.pipeline.PipePort
Get outgoing connector for specified destination.
getOutgoingConnectors() - Method in class edu.jhu.ece.iacl.jist.pipeline.PipePort
Get output connections.
getOutgoingPorts() - Method in class edu.jhu.ece.iacl.jist.pipeline.PipePort
Get all ports that are connected to this port.
getOutput() - Method in class edu.jhu.ece.iacl.jist.pipeline.ProcessingAlgorithm
Get output parameters.
getOutputDirectory() - Method in class edu.jhu.ece.iacl.jist.pipeline.PipeLayout.RunParameters
Gets the output directory.
getOutputDirectory() - Method in class edu.jhu.ece.iacl.jist.pipeline.ProcessingAlgorithm
Get output directory.
getOutputHash() - Method in class edu.jhu.ece.iacl.jist.pipeline.PipeModule
Get output hash representing map from child parameter name to parameter.
getOutputLocation() - Method in class edu.jhu.ece.iacl.jist.pipeline.ExecutionContext
Get directory where output will be placed.
getOutputParam() - Method in class edu.jhu.ece.iacl.jist.pipeline.PipeSource
Get parameter representing the output to this source.
getOutputParam() - Method in class edu.jhu.ece.iacl.jist.pipeline.src.PipeDoubleCollectionListSource
Get output parameter.
getOutputParam() - Method in class edu.jhu.ece.iacl.jist.pipeline.src.PipeDoubleListSource
Get output parameters.
getOutputParam() - Method in class edu.jhu.ece.iacl.jist.pipeline.src.PipeDoubleSweepSource
Get output parameter.
getOutputParam() - Method in class edu.jhu.ece.iacl.jist.pipeline.src.PipeExternalSource
 
getOutputParam() - Method in class edu.jhu.ece.iacl.jist.pipeline.src.PipeFileCollectionListSource
 
getOutputParam() - Method in class edu.jhu.ece.iacl.jist.pipeline.src.PipeFileCollectionSource
Get output parameter.
getOutputParam() - Method in class edu.jhu.ece.iacl.jist.pipeline.src.PipeFileDirectorySource
Get file parameter.
getOutputParam() - Method in class edu.jhu.ece.iacl.jist.pipeline.src.PipeFileListSource
Get file parameters.
getOutputParam() - Method in class edu.jhu.ece.iacl.jist.pipeline.src.PipeIntegerCollectionListSource
Get output parameter.
getOutputParam() - Method in class edu.jhu.ece.iacl.jist.pipeline.src.PipeIntegerListSource
Get output parameter.
getOutputParam() - Method in class edu.jhu.ece.iacl.jist.pipeline.src.PipeIntegerSweepSource
 
getOutputParam() - Method in class edu.jhu.ece.iacl.jist.pipeline.src.PipePointDoubleSweepSource
Get output parameter.
getOutputParam() - Method in class edu.jhu.ece.iacl.jist.pipeline.src.PipePointListSource
Get parameter.
getOutputParam() - Method in class edu.jhu.ece.iacl.jist.pipeline.src.PipeSelectionExternalSource
Get output parameter.
getOutputParam() - Method in class edu.jhu.ece.iacl.jist.pipeline.src.PipeSelectionListSource
 
getOutputParam() - Method in class edu.jhu.ece.iacl.jist.pipeline.src.PipeSelectionSource
Get output parameter.
getOutputParam() - Method in class edu.jhu.ece.iacl.jist.pipeline.src.PipeStringListSource
 
getOutputParam() - Method in class edu.jhu.ece.iacl.jist.pipeline.src.PipeSurfaceCollectionListSource
 
getOutputParam() - Method in class edu.jhu.ece.iacl.jist.pipeline.src.PipeSurfaceDirectorySurface
 
getOutputParam() - Method in class edu.jhu.ece.iacl.jist.pipeline.src.PipeSurfaceListSource
Get output parameter.
getOutputParam() - Method in class edu.jhu.ece.iacl.jist.pipeline.src.PipeToggleSource
Get output parameter.
getOutputParam() - Method in class edu.jhu.ece.iacl.jist.pipeline.src.PipeVolumeCollectionListSource
 
getOutputParam() - Method in class edu.jhu.ece.iacl.jist.pipeline.src.PipeVolumeDirectoryCollectionSource
 
getOutputParam() - Method in class edu.jhu.ece.iacl.jist.pipeline.src.PipeVolumeDirectorySource
 
getOutputParam() - Method in class edu.jhu.ece.iacl.jist.pipeline.src.PipeVolumeListSource
Get output parameter.
getOutputParams() - Method in class edu.jhu.ece.iacl.jist.pipeline.PipeModule
Get input ports.
getOutputParamsFromFile() - Method in class edu.jhu.ece.iacl.jist.pipeline.ExecutionContext
Load output parameters from file.
getOutputPorts() - Method in class edu.jhu.ece.iacl.jist.pipeline.PipeModule
Get output ports.
getOutputURI() - Method in class edu.jhu.ece.iacl.jist.pipeline.PipeLayout.RunParameters
Gets the input directory.
getOutputView() - Method in class edu.jhu.ece.iacl.jist.pipeline.factory.ParamBooleanFactory
 
getOutputView() - Method in class edu.jhu.ece.iacl.jist.pipeline.factory.ParamCollectionFactory
 
getOutputView() - Method in class edu.jhu.ece.iacl.jist.pipeline.factory.ParamColorFactory
 
getOutputView() - Method in class edu.jhu.ece.iacl.jist.pipeline.factory.ParamDataLabelFactory
 
getOutputView() - Method in class edu.jhu.ece.iacl.jist.pipeline.factory.ParamDoubleFactory
 
getOutputView() - Method in class edu.jhu.ece.iacl.jist.pipeline.factory.ParamFactory
Get the current output view.
getOutputView() - Method in class edu.jhu.ece.iacl.jist.pipeline.factory.ParamFileCollectionFactory
 
getOutputView() - Method in class edu.jhu.ece.iacl.jist.pipeline.factory.ParamFileFactory
Get parameter output view.
getOutputView() - Method in class edu.jhu.ece.iacl.jist.pipeline.factory.ParamFloatFactory
 
getOutputView() - Method in class edu.jhu.ece.iacl.jist.pipeline.factory.ParamHiddenFactory
 
getOutputView() - Method in class edu.jhu.ece.iacl.jist.pipeline.factory.ParamInformationFactory
Get parameter output view.
getOutputView() - Method in class edu.jhu.ece.iacl.jist.pipeline.factory.ParamIntegerFactory
 
getOutputView() - Method in class edu.jhu.ece.iacl.jist.pipeline.factory.ParamLongFactory
 
getOutputView() - Method in class edu.jhu.ece.iacl.jist.pipeline.factory.ParamMatrixFactory
 
getOutputView() - Method in class edu.jhu.ece.iacl.jist.pipeline.factory.ParamMipavDialogFactory
Get parameter output view.
getOutputView() - Method in class edu.jhu.ece.iacl.jist.pipeline.factory.ParamMultiOptionFactory
 
getOutputView() - Method in class edu.jhu.ece.iacl.jist.pipeline.factory.ParamNumberCollectionFactory
 
getOutputView() - Method in class edu.jhu.ece.iacl.jist.pipeline.factory.ParamObjectFactory
Get parameter output view.
getOutputView() - Method in class edu.jhu.ece.iacl.jist.pipeline.factory.ParamOptionFactory
 
getOutputView() - Method in class edu.jhu.ece.iacl.jist.pipeline.factory.ParamPerformanceFactory
 
getOutputView() - Method in class edu.jhu.ece.iacl.jist.pipeline.factory.ParamPointDoubleFactory
 
getOutputView() - Method in class edu.jhu.ece.iacl.jist.pipeline.factory.ParamPointFloatFactory
 
getOutputView() - Method in class edu.jhu.ece.iacl.jist.pipeline.factory.ParamPointIntegerFactory
 
getOutputView() - Method in class edu.jhu.ece.iacl.jist.pipeline.factory.ParamStringFactory
 
getOutputView() - Method in class edu.jhu.ece.iacl.jist.pipeline.factory.ParamSurfaceCollectionFactory
 
getOutputView() - Method in class edu.jhu.ece.iacl.jist.pipeline.factory.ParamSurfaceFactory
 
getOutputView() - Method in class edu.jhu.ece.iacl.jist.pipeline.factory.ParamVolumeCollectionFactory
 
getOutputView() - Method in class edu.jhu.ece.iacl.jist.pipeline.factory.ParamVolumeFactory
 
getOutputView() - Method in class edu.jhu.ece.iacl.jist.pipeline.factory.ParamWeightedVolumeCollectionFactory
 
getOutputView() - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamModel
Get the output view to specify the output parameter.
getOutputView() - Method in class edu.jhu.ece.iacl.jist.pipeline.ProcessingDialog
Get output view.
getOutputView() - Method in class edu.jhu.ece.iacl.jist.pipeline.ProcessingGroupDialog
Get output view.
getOwner() - Method in class edu.jhu.ece.iacl.jist.pipeline.PipeChildPort
Get source module that owns this port.
getOwner() - Method in class edu.jhu.ece.iacl.jist.pipeline.PipeParentPort
Get source that owns this port.
getOwner() - Method in class edu.jhu.ece.iacl.jist.pipeline.PipePort
Module that owns this port.
getPackage() - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamCollection
 
getPackage() - Method in class edu.jhu.ece.iacl.jist.pipeline.PipeAlgorithm
Gets the package.
getParameter(int) - Method in class edu.jhu.bme.smile.commons.math.RotationMatrix
 
getParameter() - Method in class edu.jhu.ece.iacl.jist.pipeline.factory.ParamBooleanFactory
 
getParameter() - Method in class edu.jhu.ece.iacl.jist.pipeline.factory.ParamCollectionFactory
 
getParameter(String) - Method in class edu.jhu.ece.iacl.jist.pipeline.factory.ParamCollectionFactory
Gets the parameter.
getParameter() - Method in class edu.jhu.ece.iacl.jist.pipeline.factory.ParamColorFactory
 
getParameter() - Method in class edu.jhu.ece.iacl.jist.pipeline.factory.ParamDataLabelFactory
 
getParameter() - Method in class edu.jhu.ece.iacl.jist.pipeline.factory.ParamDoubleFactory
 
getParameter() - Method in class edu.jhu.ece.iacl.jist.pipeline.factory.ParamFactory
Get the parameter.
getParameter() - Method in class edu.jhu.ece.iacl.jist.pipeline.factory.ParamFileCollectionFactory
 
getParameter() - Method in class edu.jhu.ece.iacl.jist.pipeline.factory.ParamFileFactory
Get factory's parameter.
getParameter() - Method in class edu.jhu.ece.iacl.jist.pipeline.factory.ParamFloatFactory
 
getParameter() - Method in class edu.jhu.ece.iacl.jist.pipeline.factory.ParamHiddenFactory
 
getParameter() - Method in class edu.jhu.ece.iacl.jist.pipeline.factory.ParamInformationFactory
Get factory's parameter.
getParameter() - Method in class edu.jhu.ece.iacl.jist.pipeline.factory.ParamIntegerFactory
 
getParameter() - Method in class edu.jhu.ece.iacl.jist.pipeline.factory.ParamLongFactory
 
getParameter() - Method in class edu.jhu.ece.iacl.jist.pipeline.factory.ParamMatrixFactory
 
getParameter() - Method in class edu.jhu.ece.iacl.jist.pipeline.factory.ParamMipavDialogFactory
Get factory's parameter.
getParameter() - Method in class edu.jhu.ece.iacl.jist.pipeline.factory.ParamMultiOptionFactory
 
getParameter() - Method in class edu.jhu.ece.iacl.jist.pipeline.factory.ParamNumberCollectionFactory
 
getParameter() - Method in class edu.jhu.ece.iacl.jist.pipeline.factory.ParamObjectFactory
Get factory's parameter.
getParameter() - Method in class edu.jhu.ece.iacl.jist.pipeline.factory.ParamOptionFactory
 
getParameter() - Method in class edu.jhu.ece.iacl.jist.pipeline.factory.ParamPerformanceFactory
 
getParameter() - Method in class edu.jhu.ece.iacl.jist.pipeline.factory.ParamPointDoubleFactory
 
getParameter() - Method in class edu.jhu.ece.iacl.jist.pipeline.factory.ParamPointFloatFactory
 
getParameter() - Method in class edu.jhu.ece.iacl.jist.pipeline.factory.ParamPointIntegerFactory
 
getParameter() - Method in class edu.jhu.ece.iacl.jist.pipeline.factory.ParamStringFactory
 
getParameter() - Method in class edu.jhu.ece.iacl.jist.pipeline.factory.ParamSurfaceCollectionFactory
 
getParameter() - Method in class edu.jhu.ece.iacl.jist.pipeline.factory.ParamSurfaceFactory
 
getParameter() - Method in class edu.jhu.ece.iacl.jist.pipeline.factory.ParamVolumeCollectionFactory
 
getParameter() - Method in class edu.jhu.ece.iacl.jist.pipeline.factory.ParamVolumeFactory
 
getParameter() - Method in class edu.jhu.ece.iacl.jist.pipeline.factory.ParamWeightedVolumeCollectionFactory
 
getParameter() - Method in exception edu.jhu.ece.iacl.jist.pipeline.parameter.InvalidParameterException
Gets the parameter.
getParameter() - Method in class edu.jhu.ece.iacl.jist.pipeline.view.input.ParamBooleanInputView
Get boolean parameter.
getParameter() - Method in class edu.jhu.ece.iacl.jist.pipeline.view.input.ParamCollectionInputView
Get parameter collection.
getParameter() - Method in class edu.jhu.ece.iacl.jist.pipeline.view.input.ParamCollectionPipelineInputView
Get collection parameter.
getParameter() - Method in class edu.jhu.ece.iacl.jist.pipeline.view.input.ParamColorInputView
Gets the parameter.
getParameter() - Method in class edu.jhu.ece.iacl.jist.pipeline.view.input.ParamDataLabelInputView
 
getParameter() - Method in class edu.jhu.ece.iacl.jist.pipeline.view.input.ParamDoubleSliderInputView
Get number parameter.
getParameter() - Method in class edu.jhu.ece.iacl.jist.pipeline.view.input.ParamFileCollectionInputView
Get file parameter.
getParameter() - Method in class edu.jhu.ece.iacl.jist.pipeline.view.input.ParamFileInputView
Get file parameter.
getParameter() - Method in class edu.jhu.ece.iacl.jist.pipeline.view.input.ParamHiddenInputView
Get parameter.
getParameter() - Method in class edu.jhu.ece.iacl.jist.pipeline.view.input.ParamInformationInputView
Get information parameter.
getParameter() - Method in class edu.jhu.ece.iacl.jist.pipeline.view.input.ParamInputView
Get the parameter being viewed.
getParameter() - Method in class edu.jhu.ece.iacl.jist.pipeline.view.input.ParamMatrixInputView
Get number parameter.
getParameter() - Method in class edu.jhu.ece.iacl.jist.pipeline.view.input.ParamMipavDialogInputView
Get mipav dialog parameter.
getParameter() - Method in class edu.jhu.ece.iacl.jist.pipeline.view.input.ParamMultiOptionInputView
Get multi-option parameter.
getParameter() - Method in class edu.jhu.ece.iacl.jist.pipeline.view.input.ParamNumberCollectionInputView
Get file parameter.
getParameter() - Method in class edu.jhu.ece.iacl.jist.pipeline.view.input.ParamNumberSliderInputView
Get number parameter.
getParameter() - Method in class edu.jhu.ece.iacl.jist.pipeline.view.input.ParamNumberSpinnerInputView
 
getParameter() - Method in class edu.jhu.ece.iacl.jist.pipeline.view.input.ParamNumberTextInputView
Get number parameter.
getParameter() - Method in class edu.jhu.ece.iacl.jist.pipeline.view.input.ParamOptionInputView
 
getParameter() - Method in class edu.jhu.ece.iacl.jist.pipeline.view.input.ParamPointDoubleTextInputView
 
getParameter() - Method in class edu.jhu.ece.iacl.jist.pipeline.view.input.ParamPointFloatTextInputView
 
getParameter() - Method in class edu.jhu.ece.iacl.jist.pipeline.view.input.ParamPointSpinnerInputView
 
getParameter() - Method in class edu.jhu.ece.iacl.jist.pipeline.view.input.ParamTextInputView
 
getParameter() - Method in class edu.jhu.ece.iacl.jist.pipeline.view.input.ParamURIInputView
Get file parameter.
getParameter() - Method in class edu.jhu.ece.iacl.jist.pipeline.view.input.ParamVolumeCollectionInputView
 
getParameter() - Method in class edu.jhu.ece.iacl.jist.pipeline.view.input.ParamVolumeInputView
Get volume parameter.
getParameter() - Method in class edu.jhu.ece.iacl.jist.pipeline.view.input.ParamVolumeURICollectionInputView
Get file parameter.
getParameter() - Method in class edu.jhu.ece.iacl.jist.pipeline.view.input.ParamVolumeURIInputView
Get volume parameter.
getParameter() - Method in class edu.jhu.ece.iacl.jist.pipeline.view.input.ParamWeightedVolumesInputView
Get weighted volume parameter.
getParameter() - Method in class edu.jhu.ece.iacl.jist.pipeline.view.input.ParamWeightedVolumesURIInputView
Get weighted volume parameter.
getParameter() - Method in class edu.jhu.ece.iacl.jist.pipeline.view.output.ParamSurfaceOutputView
Get surface parameter.
getParameter() - Method in class edu.jhu.ece.iacl.jist.pipeline.view.output.ParamVolumeOutputView
Get volume parameter.
getParameterList() - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamNumberCollection
Get list of parameter numbers.
getParameters() - Method in class edu.jhu.bme.smile.commons.math.RotationMatrix
 
getParameters() - Method in class edu.jhu.ece.iacl.algorithms.dti.tractography.FACT.FACTapi
 
getParameters() - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamFileCollection
Get list of parameter files.
getParamInfo(List<ParamModel>, boolean) - Method in class edu.jhu.ece.iacl.doc.DocMediaWikiWriter
 
getParamVolume(int) - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamVolumeCollection
 
getParamVolumeList() - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamVolumeCollection
 
getParamX() - Method in interface edu.jhu.ece.iacl.jist.pipeline.parameter.ParamPoint
Get X coordinate parameter.
getParamX() - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamPointDouble
Get X coordinate parameter.
getParamX() - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamPointFloat
Get X coordinate.
getParamX() - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamPointInteger
Get X coordinate.
getParamY() - Method in interface edu.jhu.ece.iacl.jist.pipeline.parameter.ParamPoint
Get Y coordinate parameter.
getParamY() - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamPointDouble
Get Y coordinate parameter.
getParamY() - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamPointFloat
Get Y coordinate.
getParamY() - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamPointInteger
Get Y coordinate.
getParamZ() - Method in interface edu.jhu.ece.iacl.jist.pipeline.parameter.ParamPoint
Get Z coordinate parameter.
getParamZ() - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamPointDouble
Get Z coordinate parameter.
getParamZ() - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamPointFloat
Get Z coordinate.
getParamZ() - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamPointInteger
Get Z coordinate.
getParentFrame() - Method in class edu.jhu.ece.iacl.jist.pipeline.ProcessingDialog
Get parent frame for Mipav.
getParentFrame() - Method in class edu.jhu.ece.iacl.jist.pipeline.ProcessingGroupDialog
Get parent frame for Mipav.
getParentGroup() - Method in class edu.jhu.ece.iacl.jist.pipeline.PipeAlgorithm
Get parent module if this is a member of a group.
getParentPort() - Method in class edu.jhu.ece.iacl.jist.pipeline.PipeSource
Get port for parent connection.
getParents() - Method in class edu.jhu.ece.iacl.jist.pipeline.PipeModule
Get modules that provide information to this module.
getParseStatus() - Method in class edu.jhu.ece.iacl.jist.cli.JistCLI
 
getParVersion() - Method in class edu.jhu.ece.iacl.algorithms.dti.ParV3Info
 
getParVersion() - Method in class edu.jhu.ece.iacl.algorithms.dti.ParV4Info
 
getPassedFiles() - Method in class edu.jhu.ece.iacl.jist.pipeline.PipeLayoutRunner
Gets the passed files.
getPaste() - Method in class edu.jhu.ece.iacl.jist.pipeline.gui.PipeInternalFrame
Gets the paste.
getPathBounds(Point2D, Point2D) - Method in class edu.jhu.ece.iacl.jist.pipeline.graph.AvoidanceRouting
Get rectangular bounds around start and end locations.
getPatientOrientation() - Method in class edu.jhu.ece.iacl.algorithms.dti.ParV4Info
 
getPatientPosition() - Method in class edu.jhu.ece.iacl.algorithms.dti.ParV4Info
 
getPeakAllocatedMemory() - Method in class edu.jhu.ece.iacl.jist.pipeline.PerformanceSummary
Get peak allocated memory.
getPeakUsedMemory() - Method in class edu.jhu.ece.iacl.jist.pipeline.PerformanceSummary
Get peak used memory.
getPeformanceLevel() - Method in class edu.jhu.ece.iacl.algorithms.manual_label.staple.STAPLE
 
getPeformanceLevel() - Method in class edu.jhu.ece.iacl.algorithms.manual_label.staple.STAPLEgeneral
 
getPeformanceLevel() - Method in class edu.jhu.ece.iacl.algorithms.manual_label.staple.STAPLEgeneralSingle
 
getPeformanceLevel() - Method in class edu.jhu.ece.iacl.algorithms.manual_label.staple.STAPLEmulti
 
getPeformanceLevel() - Method in class edu.jhu.ece.iacl.algorithms.manual_label.staple.STAPLEmulti2
 
getPeformanceLevel() - Method in class edu.jhu.ece.iacl.algorithms.manual_label.staple.STAPLEsingle
 
getPeformanceLevel() - Method in class edu.jhu.ece.iacl.algorithms.manual_label.staple.STAPLEsurf
 
getPercent1Error() - Method in class edu.jhu.ece.iacl.algorithms.volume.CompareVolumes
 
getPercent2Error() - Method in class edu.jhu.ece.iacl.algorithms.volume.CompareVolumes
 
getPerformance() - Method in class edu.jhu.ece.iacl.algorithms.manual_label.staple.PerformanceLevel
 
getPerformance() - Method in class edu.jhu.ece.iacl.jist.pipeline.AbstractCalculation
Get performance summary.
getPerformance() - Method in class edu.jhu.ece.iacl.jist.pipeline.CalculationMonitor
Get summary of performance.
getPerformanceD() - Method in class edu.jhu.ece.iacl.algorithms.manual_label.staple.PerformanceLevel
 
getPerformanceLevels() - Method in class edu.jhu.ece.iacl.algorithms.manual_label.staple.STAPLE
 
getPerformanceLevels() - Method in class edu.jhu.ece.iacl.algorithms.manual_label.staple.STAPLEgeneral
 
getPerformanceLevels() - Method in class edu.jhu.ece.iacl.algorithms.manual_label.staple.STAPLEmulti
 
getPerformanceLevels() - Method in class edu.jhu.ece.iacl.algorithms.manual_label.staple.STAPLEmulti2
 
getPerformanceLevels() - Method in class edu.jhu.ece.iacl.algorithms.manual_label.staple.STAPLEsurf
 
getPerimeterPoint(EdgeView, Point2D, Point2D) - Method in class edu.jhu.ece.iacl.jist.pipeline.graph.PipeAlgorithmGroupView
Returns the intersection of the bounding rectangle and the straight line between the source and the specified point p.
getPipe() - Method in class edu.jhu.ece.iacl.jist.cli.JistCLI
 
getPipelineLayout() - Method in class edu.jhu.ece.iacl.jist.pipeline.graph.PipeJGraph
Gets the pipeline layout.
getPipelineLayout() - Method in class edu.jhu.ece.iacl.jist.pipeline.gui.LayoutPanel
Get the layout for the current active frame.
getPipelineLayout() - Method in class edu.jhu.ece.iacl.jist.pipeline.gui.PipeInternalFrame
Get layout for frame.
getPipeModule() - Method in class edu.jhu.ece.iacl.jist.pipeline.graph.PipeModuleCell
Get pipe module that is stored in this cell.
getPipes() - Method in class edu.jhu.ece.iacl.jist.pipeline.PipeLayout
Get all modules for this layout.
getPoint(int) - Method in class edu.jhu.ece.iacl.jist.structures.geom.EmbeddedPointSet
Gets the point.
getPointAtOffset(int, int) - Method in class edu.jhu.ece.iacl.jist.structures.geom.EmbeddedSurface
Gets the point at offset.
getPointCount() - Method in class edu.jhu.ece.iacl.jist.structures.geom.EmbeddedPointSet
Gets the point count.
getPointData() - Method in class edu.jhu.ece.iacl.jist.structures.geom.EmbeddedPointSet
Gets the point data.
getPointData(int) - Method in class edu.jhu.ece.iacl.jist.structures.geom.EmbeddedPointSet
Gets the point data.
getPointData(int, int) - Method in class edu.jhu.ece.iacl.jist.structures.geom.EmbeddedPointSet
Gets the point data.
getPointLocation(int) - Method in class edu.jhu.ece.iacl.jist.pipeline.graph.PipeEdgeView
 
getPoints() - Method in class edu.jhu.cs.cisst.vent.structures.processing.PTriangleMesh
Gets the points.
getPoints() - Method in class edu.jhu.ece.iacl.jist.structures.geom.CurvePath
Gets the points.
getPoints() - Method in class edu.jhu.ece.iacl.jist.structures.geom.EmbeddedPointSet
Gets the points.
getPort() - Method in class edu.jhu.ece.iacl.jist.pipeline.graph.PipeModulePort
Get pipe port for graph port.
getPortToCheck() - Method in class edu.jhu.ece.iacl.jist.pipeline.graph.PipeJGraph
Get port to check for compatibility.
getPortType() - Method in class edu.jhu.ece.iacl.jist.pipeline.PipePort
Get port type.
getPositionX() - Method in class edu.jhu.cs.cisst.vent.renderer.processing.RendererProcessing2D
Gets the position x.
getPositionY() - Method in class edu.jhu.cs.cisst.vent.renderer.processing.RendererProcessing2D
Gets the position y.
getPreferences() - Static method in class edu.jhu.ece.iacl.jist.pipeline.JistPreferences
Singleton method to get User Interface.
getPreferredExtension() - Method in class edu.jhu.ece.iacl.jist.io.FileExtensionFilter
Gets the preferred extension.
getPreferredExtension() - Method in class edu.jhu.ece.iacl.jist.pipeline.JistPreferences
Get preferred extension (for CubicVolumeReaderWriter).
getPreferredExtension() - Method in class edu.jhu.ece.iacl.jist.pipeline.PipeLayout.RunParameters
Gets the preferred extension.
getPreferredSize() - Method in class edu.jhu.ece.iacl.jist.pipeline.graph.PipeAlgorithmGroupView.ActivityRenderer
Return a slightly larger preferred size than for a rectangle.
getPreferredSize() - Method in class edu.jhu.ece.iacl.jist.pipeline.graph.PipeAlgorithmView.ActivityRenderer
Return a slightly larger preferred size than for a rectangle.
getPreferredSize() - Method in class edu.jhu.ece.iacl.jist.pipeline.graph.PipeDestinationView.ActivityRenderer
Return a slightly larger preferred size than for a rectangle.
getPreferredSize(int, int) - Static method in class edu.jhu.ece.iacl.jist.pipeline.graph.PipeModuleCell
Get preferred size for module as a function of the number of incoming and outgoing ports.
getPreferredSize(ParamCollection, ParamCollection) - Static method in class edu.jhu.ece.iacl.jist.pipeline.graph.PipeModuleCell
Get preferred size for module as a function of the input and output parameters.
getPreferredSize() - Method in class edu.jhu.ece.iacl.jist.pipeline.graph.PipeSourceView.ActivityRenderer
Return a slightly larger preferred size than for a rectangle.
getPreferredSize() - Method in class edu.jhu.ece.iacl.jist.pipeline.ProcessingAlgorithm
Get preferred size for algorithm The default is null.
getPresentWorkingDirectory() - Static method in class edu.jhu.ece.iacl.jist.test.MipavTestHarness
Gets the present working directory.
getPriority() - Method in class edu.jhu.ece.iacl.jist.pipeline.ExecutionContext
Get priority.
getPriorProb() - Method in class edu.jhu.ece.iacl.algorithms.manual_label.staple.STAPLE
 
getPriorProb() - Method in class edu.jhu.ece.iacl.algorithms.manual_label.staple.STAPLEgeneral
 
getPriorProb() - Method in class edu.jhu.ece.iacl.algorithms.manual_label.staple.STAPLEgeneralSingle
 
getPriorProb() - Method in class edu.jhu.ece.iacl.algorithms.manual_label.staple.STAPLEmulti
 
getPriorProb() - Method in class edu.jhu.ece.iacl.algorithms.manual_label.staple.STAPLEmulti2
 
getPriorProb() - Method in class edu.jhu.ece.iacl.algorithms.manual_label.staple.STAPLEsingle
 
getPriorProb() - Method in class edu.jhu.ece.iacl.algorithms.manual_label.staple.STAPLEsurf
 
getProcess() - Method in class edu.jhu.ece.iacl.jist.pipeline.ExecutionContext
Get running process.
getProcess() - Method in interface edu.jhu.ece.iacl.jist.processcontrol.ProcessController
Gets the process.
getProcess() - Method in class edu.jhu.ece.iacl.jist.processcontrol.ProcessControllerDRMAA
 
getProcess() - Method in class edu.jhu.ece.iacl.jist.processcontrol.ProcessControllerNative
 
getProcessingAlgorithmByClass(String) - Static method in class edu.jhu.ece.iacl.jist.cli.run
 
getProgress() - Method in class edu.jhu.ece.iacl.jist.pipeline.AbstractCalculation
Return normalized progress of this calculation.
getPrototype() - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamWeightedVolumeCollection
 
getPt(GridPt) - Method in class edu.jhu.ece.iacl.algorithms.manual_label.LabelImage
 
getQueuedCount() - Method in class edu.jhu.ece.iacl.jist.pipeline.PipeScheduler
Get number of queued waiting to run experiments.
getQueuePosition(ExecutionContext) - Method in class edu.jhu.ece.iacl.jist.pipeline.PipeScheduler
Return queue position based on status and priority.
getReaderWriter() - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamFileCollection
Get File reader writer.
getReaderWriter() - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamObject
Get reader and writer for object.
getReadyCount() - Method in class edu.jhu.ece.iacl.jist.pipeline.PipeScheduler
Get number of experiments that are ready to run.
getReal(int, int) - Method in class edu.jhu.bme.smile.commons.math.specialFunctions.ComplexMatrix
 
getReal() - Method in class edu.jhu.bme.smile.commons.math.specialFunctions.ComplexMatrix
 
getReal(int) - Method in class edu.jhu.bme.smile.commons.math.specialFunctions.ComplexVector
 
getRealResult() - Method in class edu.jhu.bme.smile.commons.math.specialFunctions.ComplexVector
 
getRecon() - Method in class edu.jhu.bme.smile.commons.math.specialFunctions.SphericalHarmonics
 
getReference() - Static method in class edu.jhu.ece.iacl.jist.pipeline.MipavViewUserInterface
Get a reference to the ViewUserInterface object.
getRefresher() - Method in class edu.jhu.ece.iacl.jist.pipeline.view.input.ParamMultiOptionInputView
Get refresher for this view.
getRefreshInterval() - Method in class edu.jhu.ece.iacl.jist.pipeline.view.input.Refresher
Get refreshing interval.
getRemove() - Method in class edu.jhu.ece.iacl.jist.pipeline.gui.PipeInternalFrame
Gets the remove.
getRenderer() - Method in class edu.jhu.ece.iacl.jist.pipeline.graph.PipeAlgorithmGroupView
 
getRenderer() - Method in class edu.jhu.ece.iacl.jist.pipeline.graph.PipeAlgorithmView
 
getRenderer() - Method in class edu.jhu.ece.iacl.jist.pipeline.graph.PipeDestinationView
 
getRenderer() - Method in class edu.jhu.ece.iacl.jist.pipeline.graph.PipeEdgeView
Returns a renderer for the class.
getRenderer() - Method in class edu.jhu.ece.iacl.jist.pipeline.graph.PipePortView
 
getRenderer() - Method in class edu.jhu.ece.iacl.jist.pipeline.graph.PipeSourceView
 
getRenderer() - Method in class edu.jhu.ece.iacl.jist.pipeline.graph.PortChildView
 
getRenderer() - Method in class edu.jhu.ece.iacl.jist.pipeline.graph.PortInputView
 
getRenderer() - Method in class edu.jhu.ece.iacl.jist.pipeline.graph.PortOutputView
 
getRenderer() - Method in class edu.jhu.ece.iacl.jist.pipeline.graph.PortParentView
 
getRendererComponent(JGraph, CellView, boolean, boolean, boolean) - Method in class edu.jhu.ece.iacl.jist.pipeline.graph.PipeAlgorithmGroupView.ActivityRenderer
Overrides the parent implementation to return the value component stored in the user object instead of this renderer if a value component exists.
getRes() - Method in class edu.jhu.ece.iacl.algorithms.dti.tractography.FiberStatistics
 
getResolution(int) - Method in class edu.jhu.cs.cisst.algorithms.optimize.fmg.DefaultSolverResolutionLevels2D
 
getResolution(int) - Method in class edu.jhu.cs.cisst.algorithms.optimize.fmg.DefaultSolverResolutionLevels3D
 
getResolution(int) - Method in interface edu.jhu.cs.cisst.algorithms.optimize.fmg.SolverResolutionLevels
Gets the resolution.
getResolutionCount() - Method in class edu.jhu.cs.cisst.algorithms.optimize.fmg.DefaultSolverResolutionLevels2D
 
getResolutionCount() - Method in class edu.jhu.cs.cisst.algorithms.optimize.fmg.DefaultSolverResolutionLevels3D
 
getResolutionCount() - Method in interface edu.jhu.cs.cisst.algorithms.optimize.fmg.SolverResolutionLevels
Gets the resolution count.
getResolutions() - Method in class edu.jhu.cs.cisst.algorithms.optimize.fmg.DefaultSolverResolutionLevels2D
 
getResolutions() - Method in class edu.jhu.cs.cisst.algorithms.optimize.fmg.DefaultSolverResolutionLevels3D
 
getResolutions() - Method in interface edu.jhu.cs.cisst.algorithms.optimize.fmg.SolverResolutionLevels
Gets the resolutions.
getResolutions() - Method in class edu.jhu.ece.iacl.jist.structures.fiber.FiberCollection
Gets the resolutions.
getResolutionSwitches() - Method in class edu.jhu.ece.iacl.algorithms.vabra.VabraConfiguration
 
getRestriction(VoxelType) - Static method in class edu.jhu.ece.iacl.jist.structures.image.Voxel
Determine restriction level for a particular Voxel Data Type The higher the value, the more restrictive.
getResult() - Method in class edu.jhu.bme.smile.commons.math.L1LSCompressedSensing
 
getResult() - Method in class edu.jhu.cs.cisst.algorithms.optimize.fmg.FMGDefaultObserver
return the result of the FMG algorithm that was or will be delivered to this object by calling update().
getROIdata(int) - Method in class edu.jhu.ece.iacl.algorithms.manual_label.ROI
 
getRoot() - Method in class edu.jhu.ece.iacl.jist.pipeline.PipeSource
Find the root source starting from this source.
getRow(int) - Method in class edu.jhu.ece.iacl.jist.pipeline.gui.ProcessManagerTable.ProcessTableModel
Gets the row.
getRow() - Method in interface edu.jhu.ece.iacl.jist.structures.data.Indexable
Gets the row.
getRow() - Method in class edu.jhu.ece.iacl.jist.structures.geom.EdgeIndexed
 
getRow() - Method in class edu.jhu.ece.iacl.jist.structures.geom.VertexIndexed
 
getRow() - Method in class edu.jhu.ece.iacl.jist.structures.image.VoxelIndexed
 
getRow() - Method in class edu.jhu.ece.iacl.jist.structures.image.VoxelMipav
 
getRowCount() - Method in class edu.jhu.ece.iacl.jist.pipeline.gui.ProcessManagerTable.ProcessTableModel
 
getRows() - Method in interface edu.jhu.cs.cisst.algorithms.optimize.fmg.grid.ConstGrid
Gets the rows.
getRows() - Method in class edu.jhu.cs.cisst.algorithms.optimize.fmg.grid.Grid
implements method from ConstGrid.
getRows() - Method in class edu.jhu.ece.iacl.jist.pipeline.gui.ProcessManagerTable.ProcessTableModel
Gets the rows.
getRows() - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamMatrix
Gets the rows.
getRows() - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamVolume
Get row restriction.
getRows() - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamVolumeCollection
Get row restriction.
getRows() - Method in class edu.jhu.ece.iacl.jist.structures.image.ImageData
Gets the rows.
getRows() - Method in class edu.jhu.ece.iacl.jist.structures.matrix.Matrix3
Gets the rows.
getRows() - Method in class edu.jhu.ece.iacl.jist.structures.matrix.VectorMatrixX
Gets the rows.
getRows() - Method in class edu.jhu.ece.iacl.plugins.dti.MetaImageData4D
 
getRunningCount() - Method in class edu.jhu.ece.iacl.jist.pipeline.PipeScheduler
Get number of running experiments.
getRunningQueue() - Method in class edu.jhu.ece.iacl.jist.pipeline.PipeScheduler
Get running queue for the scheduler.
getRunParameters() - Method in class edu.jhu.ece.iacl.jist.pipeline.PipeLayout
Runt.
getScale() - Method in class edu.jhu.ece.iacl.jist.structures.geom.EmbeddedSurface
Gets the scale.
getScenarioId() - Method in class edu.jhu.ece.iacl.jist.pipeline.ExecutionContext
Get scenario id.
getScheduler() - Method in class edu.jhu.ece.iacl.jist.pipeline.PipeLayout
Get scheduler.
getScreenshot() - Method in interface edu.jhu.cs.cisst.vent.Visualization
Gets the screenshot.
getScreenshot() - Method in class edu.jhu.cs.cisst.vent.VisualizationProcessing2D
 
getScreenshot() - Method in class edu.jhu.cs.cisst.vent.VisualizationProcessing3D
 
getSeeAlsos() - Method in class edu.jhu.ece.iacl.doc.DocMediaWikiWriter
 
getseedPointIndex() - Method in class edu.jhu.ece.iacl.jist.structures.fiber.Fiber
Gets the seed point index.
getseedPointIndex2() - Method in class edu.jhu.ece.iacl.jist.structures.fiber.Fiber
Gets the seed point index2.
getSelectedContexts() - Method in class edu.jhu.ece.iacl.jist.pipeline.gui.ProcessManagerTable
Set current selected contexts in table.
getSelectedFactory() - Method in class edu.jhu.ece.iacl.jist.pipeline.gui.PlugInSelector
Get selected module factory.
getSelectedNode() - Method in class edu.jhu.ece.iacl.jist.pipeline.tree.DraggableJTree
Returns The selected node.
getSelectedPort() - Method in class edu.jhu.ece.iacl.jist.pipeline.gui.PortComboBox
Get selected port.
getSelection() - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamMultiOption
Get selected option index.
getSensingMatrix() - Method in class edu.jhu.ece.iacl.algorithms.hardi.CFARIBasisSet
 
getShort(int, int) - Method in class edu.jhu.ece.iacl.jist.structures.image.ImageData
Gets the short.
getShort(int, int, int) - Method in class edu.jhu.ece.iacl.jist.structures.image.ImageData
Gets the short.
getShort(int, int, int, int) - Method in class edu.jhu.ece.iacl.jist.structures.image.ImageData
Gets the short.
getShort(int, int, int, int) - Method in class edu.jhu.ece.iacl.jist.structures.image.ImageDataByte
 
getShort(int, int, int, int) - Method in class edu.jhu.ece.iacl.jist.structures.image.ImageDataColor
 
getShort(int, int, int, int) - Method in class edu.jhu.ece.iacl.jist.structures.image.ImageDataDouble
 
getShort(int, int, int, int) - Method in class edu.jhu.ece.iacl.jist.structures.image.ImageDataFloat
 
getShort(int, int, int, int) - Method in class edu.jhu.ece.iacl.jist.structures.image.ImageDataInt
 
getShort(int, int, int, int) - Method in class edu.jhu.ece.iacl.jist.structures.image.ImageDataMipav
 
getShort(int, int, int, int) - Method in class edu.jhu.ece.iacl.jist.structures.image.ImageDataNumber
 
getShort(int, int, int, int) - Method in class edu.jhu.ece.iacl.jist.structures.image.ImageDataUByte
 
getShort() - Method in class edu.jhu.ece.iacl.jist.structures.image.Voxel
Gets the short.
getShort() - Method in class edu.jhu.ece.iacl.jist.structures.image.VoxelBoolean
 
getShort() - Method in class edu.jhu.ece.iacl.jist.structures.image.VoxelColor
 
getShort() - Method in class edu.jhu.ece.iacl.jist.structures.image.VoxelDouble
 
getShort() - Method in class edu.jhu.ece.iacl.jist.structures.image.VoxelFloat
 
getShort() - Method in class edu.jhu.ece.iacl.jist.structures.image.VoxelIndexed
 
getShort() - Method in class edu.jhu.ece.iacl.jist.structures.image.VoxelInt
 
getShort() - Method in class edu.jhu.ece.iacl.jist.structures.image.VoxelMipav
 
getShort() - Method in class edu.jhu.ece.iacl.jist.structures.image.VoxelShort
 
getShort() - Method in class edu.jhu.ece.iacl.jist.structures.image.VoxelUByte
 
getShort() - Method in class edu.jhu.ece.iacl.jist.structures.image.VoxelVector
 
getShortLabel() - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamModel
Get the short text label for this parameter.
getSigma() - Method in class edu.jhu.bme.smile.commons.optimize.tensor.MLTensor
Gets the value of sigma.
getSigma() - Method in class edu.jhu.ece.iacl.algorithms.dti.DTEMRLTensor
Gets the value of sigma.
getSkewness() - Method in class edu.jhu.ece.iacl.algorithms.volume.CompareVolumes
 
getSlice() - Method in interface edu.jhu.ece.iacl.jist.structures.data.Indexable
Gets the slice.
getSlice() - Method in class edu.jhu.ece.iacl.jist.structures.geom.EdgeIndexed
 
getSlice() - Method in class edu.jhu.ece.iacl.jist.structures.geom.VertexIndexed
 
getSlice() - Method in class edu.jhu.ece.iacl.jist.structures.image.VoxelIndexed
 
getSlice() - Method in class edu.jhu.ece.iacl.jist.structures.image.VoxelMipav
 
getSliceAngulation() - Method in class edu.jhu.ece.iacl.algorithms.dti.ParV3Info
 
getSliceAngulation() - Method in class edu.jhu.ece.iacl.algorithms.dti.ParV4Info
 
getSliceOrientation() - Method in class edu.jhu.ece.iacl.algorithms.dti.ParV3Info
 
getSliceOrientation() - Method in class edu.jhu.ece.iacl.algorithms.dti.ParV4Info
 
getSliceParameter() - Method in class edu.jhu.cs.cisst.vent.renderer.processing.VolumeSliceRenderer
 
getSlicerXML() - Method in class edu.jhu.ece.iacl.jist.cli.JistCLI
 
getSlices() - Method in interface edu.jhu.cs.cisst.algorithms.optimize.fmg.grid.ConstGrid
Gets the slices.
getSlices() - Method in class edu.jhu.cs.cisst.algorithms.optimize.fmg.grid.Grid
implements method from ConstGrid.
getSlices() - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamVolume
Get slice restriction.
getSlices() - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamVolumeCollection
Get slice restriction.
getSlices() - Method in class edu.jhu.ece.iacl.jist.structures.image.ImageData
Gets the slices.
getSlices() - Method in class edu.jhu.ece.iacl.jist.structures.matrix.Matrix3
Gets the slices.
getSlices() - Method in class edu.jhu.ece.iacl.jist.structures.matrix.VectorMatrixX
Gets the slices.
getSlices() - Method in class edu.jhu.ece.iacl.plugins.dti.MetaImageData4D
 
getSliceThickness() - Method in class edu.jhu.ece.iacl.jist.structures.image.ImageHeader
Gets the slice thickness.
getSmFontSize() - Method in class edu.jhu.ece.iacl.jist.pipeline.JistPreferences
 
getSource() - Method in class edu.jhu.ece.iacl.jist.pipeline.PipeConnector
Get source port.
getSourceIndex() - Method in class edu.jhu.ece.iacl.jist.pipeline.PipeConnector
Get source index if port accepts multiple connections.
getSourcePortAt(Point2D) - Method in class edu.jhu.ece.iacl.jist.pipeline.graph.PipeMarqueeHandler
Gets the source port at.
getStandardDeviation() - Method in class edu.jhu.cs.cisst.algorithms.segmentation.gac.GradientVectorFlow2D
Gets the standard deviation.
getStatistics(int) - Method in class edu.jhu.ece.iacl.jist.structures.geom.EmbeddedSurface
Gets the statistics.
getStats() - Method in class edu.jhu.ece.iacl.jist.structures.geom.EmbeddedSurface
Gets the stats.
getStatus() - Method in class edu.jhu.ece.iacl.doc.DocMediaWikiWriter
 
getStatus() - Method in class edu.jhu.ece.iacl.doc.DocumentAllTests.TestCase
 
getStatus() - Method in class edu.jhu.ece.iacl.jist.pipeline.AlgorithmInformation
Gets the status.
getStatus() - Method in class edu.jhu.ece.iacl.jist.pipeline.ExecutionContext
Get execution status.
getStatus() - Method in interface edu.jhu.ece.iacl.jist.processcontrol.ProcessController
Gets the status.
getStatus() - Method in class edu.jhu.ece.iacl.jist.processcontrol.ProcessControllerDRMAA
 
getStatus() - Method in class edu.jhu.ece.iacl.jist.processcontrol.ProcessControllerNative
 
getStatusBar() - Method in class edu.jhu.ece.iacl.jist.pipeline.ExecutionContext
Get progress bar.
getStatusString() - Method in class edu.jhu.ece.iacl.jist.pipeline.AlgorithmInformation
Gets the status string.
getStd1() - Method in class edu.jhu.ece.iacl.algorithms.volume.CompareVolumes
 
getStd2() - Method in class edu.jhu.ece.iacl.algorithms.volume.CompareVolumes
 
getStdDev() - Method in class edu.jhu.ece.iacl.algorithms.volume.CompareVolumes
 
getStderrFile() - Method in interface edu.jhu.ece.iacl.jist.processcontrol.ProcessController
Gets the stderr file.
getStderrFile() - Method in class edu.jhu.ece.iacl.jist.processcontrol.ProcessControllerDRMAA
 
getStderrFile() - Method in class edu.jhu.ece.iacl.jist.processcontrol.ProcessControllerNative
 
getStdoutFile() - Method in interface edu.jhu.ece.iacl.jist.processcontrol.ProcessController
Gets the stdout file.
getStdoutFile() - Method in class edu.jhu.ece.iacl.jist.processcontrol.ProcessControllerDRMAA
 
getStdoutFile() - Method in class edu.jhu.ece.iacl.jist.processcontrol.ProcessControllerNative
 
getStep() - Method in class edu.jhu.bme.smile.commons.optimize.FunctionNumericNDDifferentiation
Gets the step size used
getStruc() - Method in class edu.jhu.ece.iacl.algorithms.dti.DWICoReg
 
getStrucTransform() - Method in class edu.jhu.ece.iacl.algorithms.dti.DWICoReg
 
getSubmissionTime() - Method in interface edu.jhu.ece.iacl.jist.processcontrol.ProcessController
Gets the submission time.
getSubmissionTime() - Method in class edu.jhu.ece.iacl.jist.processcontrol.ProcessControllerDRMAA
 
getSubmissionTime() - Method in class edu.jhu.ece.iacl.jist.processcontrol.ProcessControllerNative
 
getSubsetArray(float[][][][], int[][][], int) - Method in class edu.jhu.ece.iacl.algorithms.dti.DtiVecMask
 
getSubsetDTISformat(ImageData, ImageData, Number) - Method in class edu.jhu.ece.iacl.algorithms.dti.DtiVecMask
 
getSubsetDTISformat(ImageData, ImageData, Number) - Method in class edu.jhu.ece.iacl.algorithms.manual_label.ROI
 
getSubsetMIPAVformat(ImageData, ImageData, Number) - Method in class edu.jhu.ece.iacl.algorithms.dti.DtiVecMask
 
getSubsetMIPAVformat(ImageData, ImageData, Number) - Method in class edu.jhu.ece.iacl.algorithms.manual_label.ROI
 
getSumFromVolume() - Method in class edu.jhu.ece.iacl.algorithms.dti.tractography.FiberStatistics
 
getSummary() - Method in class edu.jhu.ece.iacl.jist.pipeline.PerformanceSummary
Return long summary of elapsed time.
getSurface() - Method in class edu.jhu.ece.iacl.algorithms.manual_label.LabelSurface
 
getSurface() - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamSurface
Get surface.
getSurfaceList() - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamSurfaceCollection
Get surfaces.
getT2(double[], int) - Method in class edu.jhu.ece.iacl.pami.GenerateTensors
 
getT3(double[], double[], int) - Method in class edu.jhu.ece.iacl.pami.GenerateTensors
 
getTable() - Method in class edu.jhu.ece.iacl.algorithms.dti.GradientTable
This get method returns this object's gradient table.
getTable() - Method in class edu.jhu.ece.iacl.jist.pipeline.gui.ProcessManagerTable
Get table that stores execution contexts.
getTableCellEditorComponent(JTable, Object, boolean, int, int) - Method in class edu.jhu.ece.iacl.jist.pipeline.graph.PipeEdgeRealEditor
Implements the TableCellEditor interface.
getTableCellRendererComponent(JTable, Object, boolean, boolean, int, int) - Method in class edu.jhu.ece.iacl.jist.pipeline.gui.ProcessManagerTable.ClassRenderer
 
getTableCellRendererComponent(JTable, Object, boolean, boolean, int, int) - Method in class edu.jhu.ece.iacl.jist.pipeline.gui.ProcessManagerTable.ProgressRenderer
 
getTableCellRendererComponent(JTable, Object, boolean, boolean, int, int) - Method in class edu.jhu.ece.iacl.jist.pipeline.gui.ProcessManagerTable.StatusRenderer
 
getTableCellRendererComponent(JTable, Object, boolean, boolean, int, int) - Method in class edu.jhu.ece.iacl.jist.pipeline.gui.ProcessManagerTable.StringRenderer
 
getTableModel() - Method in class edu.jhu.ece.iacl.jist.pipeline.gui.ProcessManagerTable
Gets the table model.
getTableType() - Method in class edu.jhu.ece.iacl.algorithms.dti.GradientTable
This get method returns this object's table type.
getTargetPortAt(Point2D) - Method in class edu.jhu.ece.iacl.jist.pipeline.graph.PipeMarqueeHandler
Gets the target port at.
getTestResultsFile() - Method in class edu.jhu.ece.iacl.jist.pipeline.dest.PipeAssertionTestDestination
 
getTestVolume() - Method in class edu.jhu.ece.iacl.algorithms.manual_label.ROI
 
getTetrahedraCount() - Method in class edu.jhu.ece.iacl.jist.structures.geom.EmbeddedPointSet
Gets the tetrahedra count.
getTetrahedron(int) - Method in class edu.jhu.ece.iacl.jist.structures.geom.EmbeddedPointSet
Gets the tetrahedron.
getTetrahedron(int, int[]) - Method in class edu.jhu.ece.iacl.jist.structures.geom.EmbeddedPointSet
Gets the tetrahedron.
getText() - Method in class edu.jhu.ece.iacl.jist.pipeline.AlgorithmInformation.Citation
Gets the text.
getTextureCoordinates() - Method in class edu.jhu.ece.iacl.jist.structures.geom.EmbeddedSurface
Gets the texture coordinates.
getThickness(int) - Method in class edu.jhu.ece.iacl.jist.structures.geom.EmbeddedSurface
Gets the thickness.
getTimeStamp() - Method in class edu.jhu.ece.iacl.jist.pipeline.CalculationMonitor
Get time stamp in milliseconds.
getTimeStamp() - Method in class edu.jhu.ece.iacl.jist.pipeline.ProcessingAlgorithm
Get cpu timestamp for this thread in msec.
getTitle() - Method in class edu.jhu.ece.iacl.jist.pipeline.PipeLayout
Get title of layout.
getToback() - Method in class edu.jhu.ece.iacl.jist.pipeline.gui.PipeInternalFrame
Gets the toback.
getTofront() - Method in class edu.jhu.ece.iacl.jist.pipeline.gui.PipeInternalFrame
Gets the tofront.
getTotalElapsedActualTime() - Method in class edu.jhu.ece.iacl.jist.pipeline.PerformanceSummary
Get cumulative elapsed time for all tasks in msec.
getTotalElapsedCPUTime() - Method in class edu.jhu.ece.iacl.jist.pipeline.PerformanceSummary
Get cumulative elapsed time for all tasks in msec.
getTotalUnits() - Method in class edu.jhu.ece.iacl.jist.pipeline.AbstractCalculation
Total computational units for calculation.
getTractVoxSet() - Method in class edu.jhu.ece.iacl.algorithms.dti.tractography.FiberStatistics
 
getTransferData(DataFlavor) - Method in class edu.jhu.ece.iacl.jist.pipeline.tree.DraggableNode
implements Transferable interface.
getTransferData(DataFlavor) - Method in class edu.jhu.ece.iacl.jist.pipeline.tree.PackageNode
implements Transferable interface.
getTransferDataFlavors() - Method in class edu.jhu.ece.iacl.jist.pipeline.tree.DraggableNode
implements Transferable interface.
getTransferDataFlavors() - Method in class edu.jhu.ece.iacl.jist.pipeline.tree.PackageNode
implements Transferable interface.
getTreeCellEditorComponent(JTree, Object, boolean, boolean, boolean, int) - Method in class edu.jhu.ece.iacl.jist.pipeline.graph.PipeEdgeRealEditor
Implements the TreeCellEditor interface.
getTreeCellRendererComponent(JTree, Object, boolean, boolean, boolean, int, boolean) - Method in class edu.jhu.ece.iacl.jist.pipeline.gui.ModuleTreePanel.DraggableTreeCellRenderer
 
getTreeRoot() - Method in class edu.jhu.ece.iacl.jist.pipeline.PipeLibrary
Get tree representing algorithm factory hierarchy.
getTruth() - Method in class edu.jhu.ece.iacl.algorithms.manual_label.staple.STAPLE
 
getTruth() - Method in class edu.jhu.ece.iacl.algorithms.manual_label.staple.STAPLEgeneral
 
getTruth() - Method in class edu.jhu.ece.iacl.algorithms.manual_label.staple.STAPLEgeneralSingle
 
getTruth() - Method in class edu.jhu.ece.iacl.algorithms.manual_label.staple.STAPLEmulti
 
getTruth() - Method in class edu.jhu.ece.iacl.algorithms.manual_label.staple.STAPLEsingle
 
getTruth() - Method in class edu.jhu.ece.iacl.algorithms.manual_label.staple.STAPLEsurf
 
getTruthImage() - Method in class edu.jhu.ece.iacl.algorithms.manual_label.staple.STAPLE
 
getTruthImage() - Method in class edu.jhu.ece.iacl.algorithms.manual_label.staple.STAPLEmulti
 
getTruthImage() - Method in class edu.jhu.ece.iacl.algorithms.manual_label.staple.STAPLEsingle
 
getTruthImage() - Method in class edu.jhu.ece.iacl.algorithms.manual_label.staple.STAPLEsurf
 
getType() - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.DataLabel
Get object type.
getType() - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamVolumeCollection
Get voxel type restriction.
getType() - Method in class edu.jhu.ece.iacl.jist.structures.image.ImageData
Gets the type.
getType() - Method in class edu.jhu.ece.iacl.jist.structures.image.Voxel
Gets the type.
getType() - Method in class edu.jhu.ece.iacl.jist.structures.image.VoxelBoolean
 
getType() - Method in class edu.jhu.ece.iacl.jist.structures.image.VoxelColor
 
getType() - Method in class edu.jhu.ece.iacl.jist.structures.image.VoxelDouble
 
getType() - Method in class edu.jhu.ece.iacl.jist.structures.image.VoxelFloat
 
getType() - Method in class edu.jhu.ece.iacl.jist.structures.image.VoxelIndexed
 
getType() - Method in class edu.jhu.ece.iacl.jist.structures.image.VoxelInt
 
getType() - Method in class edu.jhu.ece.iacl.jist.structures.image.VoxelMipav
 
getType() - Method in class edu.jhu.ece.iacl.jist.structures.image.VoxelShort
 
getType() - Method in class edu.jhu.ece.iacl.jist.structures.image.VoxelUByte
 
getType() - Method in class edu.jhu.ece.iacl.jist.structures.image.VoxelVector
 
getUByte(int, int) - Method in class edu.jhu.ece.iacl.jist.structures.image.ImageData
Gets the u byte.
getUByte(int, int, int) - Method in class edu.jhu.ece.iacl.jist.structures.image.ImageData
Gets the u byte.
getUByte(int, int, int, int) - Method in class edu.jhu.ece.iacl.jist.structures.image.ImageData
Gets the u byte.
getUByte(int, int, int, int) - Method in class edu.jhu.ece.iacl.jist.structures.image.ImageDataByte
 
getUByte(int, int, int, int) - Method in class edu.jhu.ece.iacl.jist.structures.image.ImageDataColor
 
getUByte(int, int, int, int) - Method in class edu.jhu.ece.iacl.jist.structures.image.ImageDataDouble
 
getUByte(int, int, int, int) - Method in class edu.jhu.ece.iacl.jist.structures.image.ImageDataFloat
 
getUByte(int, int, int, int) - Method in class edu.jhu.ece.iacl.jist.structures.image.ImageDataInt
 
getUByte(int, int, int, int) - Method in class edu.jhu.ece.iacl.jist.structures.image.ImageDataMipav
 
getUByte(int, int, int, int) - Method in class edu.jhu.ece.iacl.jist.structures.image.ImageDataNumber
 
getUByte(int, int, int, int) - Method in class edu.jhu.ece.iacl.jist.structures.image.ImageDataUByte
 
getUByte() - Method in class edu.jhu.ece.iacl.jist.structures.image.Voxel
Gets the u byte.
getUByte() - Method in class edu.jhu.ece.iacl.jist.structures.image.VoxelMipav
 
getUByte() - Method in class edu.jhu.ece.iacl.jist.structures.image.VoxelUByte
 
getUI() - Static method in class edu.jhmi.rad.medic.utilities.MedicUtilPublic
Singleton method to get User Interface.
getUI() - Static method in class edu.jhu.ece.iacl.jist.io.MipavController
Singleton method to get User Interface.
getUnitsOfMeasure() - Method in class edu.jhu.ece.iacl.jist.structures.image.ImageHeader
Gets the units of measure.
getURI() - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamFile
Get uri location.
getUsageFile() - Method in class edu.jhu.ece.iacl.jist.pipeline.ProcessingAlgorithm
Location of file that describes how to use the algorithm.
getUsedMemory() - Method in class edu.jhu.ece.iacl.jist.pipeline.ExecutionContext
Get used memory.
getUShort(int, int) - Method in class edu.jhu.ece.iacl.jist.structures.image.ImageData
Gets the u short.
getUShort(int, int, int) - Method in class edu.jhu.ece.iacl.jist.structures.image.ImageData
Gets the u short.
getUShort(int, int, int, int) - Method in class edu.jhu.ece.iacl.jist.structures.image.ImageData
Gets the u short.
getUUID() - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamHeader
 
getUUID() - Method in class edu.jhu.ece.iacl.jist.pipeline.PipeScheduler
Gets the uUID.
getV1() - Method in class edu.jhu.ece.iacl.jist.structures.geom.EdgeIndexed
Gets the v1.
getV2() - Method in class edu.jhu.ece.iacl.jist.structures.geom.EdgeIndexed
Gets the v2.
getVal(int, int, int) - Method in class edu.jhu.ece.iacl.algorithms.manual_label.LabelImage
 
getVal(GridPt) - Method in class edu.jhu.ece.iacl.algorithms.manual_label.LabelImage
 
getVal(int) - Method in class edu.jhu.ece.iacl.algorithms.manual_label.LabelSurface
 
getValidModuleJavaPaths() - Method in class jist.modules.JistDefaultBase
 
getValidModuleJavaPaths() - Method in class jist.modules.JistDefaultPlugins
 
getValidModuleJavaPaths() - Method in interface jist.modules.JistModulesLocation
 
getValue(double) - Method in class edu.jhu.bme.smile.commons.optimize.FunctionNumeric1DDifferentiation
Gets the value
getValue(double[]) - Method in class edu.jhu.bme.smile.commons.optimize.FunctionNumericND1DDifferentiation
Same as getDerivative.
getValue(double[]) - Method in class edu.jhu.bme.smile.commons.optimize.FunctionNumericNDDifferentiation
Gets the value
getValue(double) - Method in class edu.jhu.bme.smile.commons.optimize.MinToMax1D
Gets the negated value
getValue(double) - Method in class edu.jhu.bme.smile.commons.optimize.MinToMax1DDifferentiable
Gets the negated value
getValue(double[]) - Method in class edu.jhu.bme.smile.commons.optimize.MinToMaxND
Gets the negated value
getValue(double[]) - Method in class edu.jhu.bme.smile.commons.optimize.MinToMaxNDDifferentiable
Gets the negated value
getValue(double) - Method in interface edu.jhu.bme.smile.commons.optimize.Optimizable1DContinuous
Gets the value of a function.
getValue(double[]) - Method in interface edu.jhu.bme.smile.commons.optimize.OptimizableNDContinuous
Gets the value of a function.
getValue(double) - Method in class edu.jhu.bme.smile.commons.optimize.ProjectNDto1DOptimizable
Gets the value of the function evaluated at the current dimension of x
getValue(double) - Method in class edu.jhu.bme.smile.commons.optimize.test.FunctionExponential
Evaluates the function.
getValue(double) - Method in class edu.jhu.bme.smile.commons.optimize.test.FunctionNegativeXSquared
Evaluates the function.
getValue(double[]) - Method in class edu.jhu.bme.smile.commons.optimize.test.FunctionNegativeXSquaredND
Evaluates the function at location x.
getValue(double[]) - Method in class edu.jhu.bme.smile.commons.optimize.test.FunctionRosenbrock
Evaluates the function at location x.
getValue(double) - Method in class edu.jhu.bme.smile.commons.optimize.test.FunctionXSquared
Evaluates the function.
getValue(double[]) - Method in class edu.jhu.bme.smile.commons.optimize.test.FunctionXSquaredND
Evaluates the function at location x.
getValue(double) - Method in class edu.jhu.bme.smile.commons.optimize.test.FunctionXXplusSinXX
Evaluates the function.
getValue(double[]) - Method in class edu.jhu.bme.smile.commons.optimize.test.FunctionXXplusSinXXND
Evaluates the function at location x.
getValue(double[]) - Method in class edu.jhu.bme.smile.commons.optimize.test.FunctionXXYYND
Evaluates the function at location x.
getValue(int, int) - Method in class edu.jhu.cs.cisst.algorithms.geometry.surface.IsoContourGenerator
Gets the value.
getValue(int, int, int, int, float[][]) - Static method in class edu.jhu.cs.cisst.algorithms.util.DataOperations
Gets the value.
getValue(double) - Method in class edu.jhu.ece.iacl.algorithms.spectro.MSWASSR.Symscore
 
getValue(int) - Method in interface edu.jhu.ece.iacl.jist.pipeline.parameter.ObjectCollection
Get value at specified index.
getValue() - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamArgsOrder
 
getValue() - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamBoolean
Get value.
getValue() - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamCollection
Get the parameter's children.
getValue(int) - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamCollection
Get child value.
getValue() - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamColor
 
getValue() - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamFile
Get file location.
getValue() - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamFileCollection
 
getValue(int) - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamFileCollection
 
getValue() - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamHeader
Get plug-in class.
getValue() - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamInformation
Get algorithm information.
getValue() - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamMatrix
 
getValue() - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamMipavDialog
Get mipav dialog class.
getValue() - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamModel
Get the value stored in the parameter.
getValue() - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamMultiOption
Get selected option name.
getValue() - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamNumber
Get the number value.
getValue() - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamNumberCollection
 
getValue(int) - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamNumberCollection
 
getValue() - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamOption
Get selected option name.
getValue() - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamPerformance
Get algorithm performance.
getValue() - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamPointDouble
Get point value.
getValue() - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamPointFloat
Get float point.
getValue() - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamPointInteger
Get integer point.
getValue() - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamString
Get string.
getValue() - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamSwitch
Get switch string.
getValue() - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamVolume
Get file location of Model Image if it exists.
getValue() - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamVolumeCollection
Get list of volume files.
getValue(int) - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamVolumeCollection
Get file.
getValue() - Method in class edu.jhu.ece.iacl.jist.pipeline.PipeChildPort
Unimplemented.
getValue() - Method in class edu.jhu.ece.iacl.jist.pipeline.PipeParentPort
Get value from associated parameter.
getValue() - Method in class edu.jhu.ece.iacl.jist.pipeline.PipePort
Value associated with this port.
getValue(int) - Method in class edu.jhu.ece.iacl.jist.pipeline.src.PipeDoubleCollectionListSource
Get value.
getValue(int) - Method in class edu.jhu.ece.iacl.jist.pipeline.src.PipeDoubleListSource
Get double value.
getValue(int) - Method in class edu.jhu.ece.iacl.jist.pipeline.src.PipeFileCollectionListSource
 
getValue(int) - Method in class edu.jhu.ece.iacl.jist.pipeline.src.PipeFileListSource
Get File value.
getValue(int) - Method in class edu.jhu.ece.iacl.jist.pipeline.src.PipeIntegerCollectionListSource
Get value.
getValue(int) - Method in class edu.jhu.ece.iacl.jist.pipeline.src.PipeIntegerListSource
Get value.
getValue(int) - Method in class edu.jhu.ece.iacl.jist.pipeline.src.PipeListCollectionSource
Get list value.
getValue(int) - Method in class edu.jhu.ece.iacl.jist.pipeline.src.PipeListSource
Get list value.
getValue(int) - Method in class edu.jhu.ece.iacl.jist.pipeline.src.PipePointListSource
Get value.
getValue(int) - Method in class edu.jhu.ece.iacl.jist.pipeline.src.PipeSelectionListSource
 
getValue(int) - Method in class edu.jhu.ece.iacl.jist.pipeline.src.PipeStringListSource
 
getValue(int) - Method in class edu.jhu.ece.iacl.jist.pipeline.src.PipeSurfaceCollectionListSource
 
getValue(int) - Method in class edu.jhu.ece.iacl.jist.pipeline.src.PipeSurfaceListSource
Get value.
getValue(int) - Method in class edu.jhu.ece.iacl.jist.pipeline.src.PipeVolumeCollectionListSource
 
getValue(int) - Method in class edu.jhu.ece.iacl.jist.pipeline.src.PipeVolumeListSource
Get value.
getValue() - Method in interface edu.jhu.ece.iacl.jist.structures.data.Indexable
Gets the value.
getValue() - Method in interface edu.jhu.ece.iacl.jist.structures.geom.Curve
Gets the value.
getValue() - Method in class edu.jhu.ece.iacl.jist.structures.geom.CurvePath
 
getValue() - Method in class edu.jhu.ece.iacl.jist.structures.geom.EdgeIndexed
 
getValue() - Method in class edu.jhu.ece.iacl.jist.structures.geom.EmbeddedCurvePath
 
getValue() - Method in class edu.jhu.ece.iacl.jist.structures.geom.PolySpline
 
getValue() - Method in class edu.jhu.ece.iacl.jist.structures.geom.VertexIndexed
 
getValue() - Method in class edu.jhu.ece.iacl.jist.structures.image.VoxelIndexed
 
getValue() - Method in class edu.jhu.ece.iacl.jist.structures.image.VoxelMipav
 
getValueAt(int, int) - Method in class edu.jhu.ece.iacl.jist.pipeline.gui.ProcessManagerTable.ProcessTableModel
 
getValuesForAllImages(GridPt) - Method in class edu.jhu.ece.iacl.algorithms.manual_label.LabelImageGroup
 
getVector(EmbeddedSurface) - Method in class edu.jhu.ece.iacl.jist.structures.geom.EmbeddedSurface.Edge
Gets the vector.
getVector() - Method in class edu.jhu.ece.iacl.jist.structures.geom.Segment
Gets the vector.
getVector(int, int, int) - Method in class edu.jhu.ece.iacl.jist.structures.image.ImageDataColor
Gets the vector.
getVector() - Method in class edu.jhu.ece.iacl.jist.structures.image.Voxel
Gets the vector.
getVector() - Method in class edu.jhu.ece.iacl.jist.structures.image.VoxelVector
 
getVectorAtOffset(int, int) - Method in class edu.jhu.ece.iacl.jist.structures.geom.EmbeddedSurface
Gets the vector at offset.
getVectorField() - Method in class edu.jhu.cs.cisst.vent.renderer.processing.VectorField2DRenderer
Gets the vector field.
getVersion() - Static method in class edu.jhu.cs.cisst.algorithms.geometry.surface.IsoContourGenerator
Gets the version.
getVersion() - Static method in class edu.jhu.cs.cisst.algorithms.geometry.surface.IsoSurfaceGenerator
 
getVersion() - Static method in class edu.jhu.cs.cisst.algorithms.segmentation.gac.DistanceField2D
Gets the version.
getVersion() - Static method in class edu.jhu.cs.cisst.algorithms.segmentation.gac.GeodesicActiveContour2D
Gets the version.
getVersion() - Static method in class edu.jhu.cs.cisst.algorithms.segmentation.gac.GradientVectorFlow2D
Gets the version.
getVersion() - Static method in class edu.jhu.cs.cisst.vent.widgets.VisualizationActiveContour2D
Gets the version.
getVersion() - Static method in class edu.jhu.cs.cisst.vent.widgets.VisualizationImage
Gets the version.
getVersion() - Static method in class edu.jhu.cs.cisst.vent.widgets.VisualizationTriangleMesh
Gets the version.
getVersion() - Static method in class edu.jhu.ece.iacl.algorithms.registration.RegistrationUtilities
 
getVersion() - Static method in class edu.jhu.ece.iacl.algorithms.vabra.VabraAlgorithm
 
getVersion() - Static method in class edu.jhu.ece.iacl.algorithms.volume.CompareVolumes
 
getVersion() - Static method in class edu.jhu.ece.iacl.algorithms.volume.DistanceField
 
getVersion() - Method in class edu.jhu.ece.iacl.jist.pipeline.AlgorithmInformation
Gets the version.
getVersion() - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamHeader
Get MAPS version number.
getVertex(int) - Method in class edu.jhu.ece.iacl.jist.structures.geom.EmbeddedSurface
Gets the vertex.
getVertexData() - Method in class edu.jhu.ece.iacl.jist.structures.geom.EmbeddedSurface
 
getVertexData(int) - Method in class edu.jhu.ece.iacl.jist.structures.geom.EmbeddedSurface
 
getVertexDataAtOffset(int, int) - Method in class edu.jhu.ece.iacl.jist.structures.geom.EmbeddedSurface
Gets the vertex data at offset.
getVertexDoubleCopy() - Method in class edu.jhu.ece.iacl.jist.structures.geom.EmbeddedSurface
Gets the vertex double copy.
getVertexes() - Method in class edu.jhu.ece.iacl.jist.structures.geom.EmbeddedSurface.Face
Gets the vertexes.
getVertexId() - Method in class edu.jhu.ece.iacl.jist.structures.geom.VertexIndexed
Gets the vertex id.
getVertices(File) - Static method in class edu.jhu.ece.iacl.jist.io.DxSurfaceReader
Gets the vertices.
getVertices(File) - Static method in class edu.jhu.ece.iacl.jist.io.FreeSurferAsciiReader
Gets the vertices.
getVertices(File) - Static method in class edu.jhu.ece.iacl.jist.io.FreeSurferReader
Gets the vertices.
getVertices(File) - Static method in class edu.jhu.ece.iacl.jist.io.MipavSurfaceXMLReader
Gets the vertices.
getVertices() - Method in class edu.jhu.ece.iacl.jist.structures.geom.Face
Gets the vertices.
getVertices() - Method in class edu.jhu.ece.iacl.jist.structures.geom.Surface
Gets the vertices.
getVertices() - Method in class edu.jhu.ece.iacl.jist.structures.geom.TriangleFace
 
getVideoFrames() - Method in interface edu.jhu.cs.cisst.vent.Visualization
Gets the video frames.
getVideoFrames() - Method in class edu.jhu.cs.cisst.vent.VisualizationProcessing
 
getView() - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamModel
Get panel that represents this parameter, depending on whether it is an input or output parameter.
getView() - Method in class edu.jhu.ece.iacl.jist.pipeline.PipeChildPort
Unimplemented.
getView() - Method in class edu.jhu.ece.iacl.jist.pipeline.PipeParentPort
Unimplemented.
getView() - Method in class edu.jhu.ece.iacl.jist.pipeline.PipePort
Get panel to render user input to this port.
getVolume() - Method in class edu.jhu.ece.iacl.jist.structures.geom.EmbeddedPointSet
Gets the volume.
getVolume(int) - Method in class edu.jhu.ece.iacl.jist.structures.geom.EmbeddedPointSet
Gets the volume.
getVolume() - Method in interface edu.jhu.ece.iacl.jist.structures.image.ConvolutionVolumeKernel
Gets the volume.
getVolume() - Method in class edu.jhu.ece.iacl.jist.structures.image.GaussianVolumeKernel
 
getVoxelType() - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamVolume
Get voxel type restriction.
getVoxelType(int) - Static method in class edu.jhu.ece.iacl.jist.structures.image.ImageDataMipav
Get voxel type for specified MIPAV voxel type MIPAV types are ambiguous because they use integers instead of enums.
getW() - Method in class edu.jhu.ece.iacl.jist.structures.vector.Vector2
 
getW() - Method in class edu.jhu.ece.iacl.jist.structures.vector.Vector3
 
getW() - Method in class edu.jhu.ece.iacl.jist.structures.vector.Vector4
 
getW() - Method in class edu.jhu.ece.iacl.jist.structures.vector.VectorN
 
getW() - Method in interface edu.jhu.ece.iacl.jist.structures.vector.VectorX
Gets the w.
getWaitingCount() - Method in class edu.jhu.ece.iacl.jist.pipeline.PipeScheduler
Get number of waiting to run experiments.
getWebsite() - Method in class edu.jhu.ece.iacl.jist.pipeline.AlgorithmInformation.AlgorithmAuthor
Gets the website.
getWebsite() - Method in class edu.jhu.ece.iacl.jist.pipeline.AlgorithmInformation
Gets the website.
getWeight() - Method in class edu.jhu.cs.cisst.algorithms.segmentation.gac.ActiveContourForce2D
Gets the weight.
getWeight() - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamWeightedVolume
Get weight.
getWeight(int) - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamWeightedVolumeCollection
Get the volume weight for the specified volume index.
getWeightedImage(int) - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamWeightedVolumeCollection
Construct a new weighted volume collection with specified restrictions.
getWeightList() - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamWeightedVolumeCollection
Get list of weights
getWeightParameter() - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamWeightedVolume
 
getWidth() - Method in class edu.jhu.cs.cisst.vent.renderer.processing.RendererProcessing2D
Gets the width.
getX() - Method in class edu.jhu.ece.iacl.jist.structures.vector.Vector2
 
getX() - Method in class edu.jhu.ece.iacl.jist.structures.vector.Vector3
 
getX() - Method in class edu.jhu.ece.iacl.jist.structures.vector.Vector4
 
getX() - Method in class edu.jhu.ece.iacl.jist.structures.vector.VectorN
 
getX() - Method in interface edu.jhu.ece.iacl.jist.structures.vector.VectorX
Gets the x.
getXMLValue() - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamArgsOrder
 
getXMLValue() - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamBoolean
 
getXMLValue() - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamCollection
 
getXMLValue() - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamColor
 
getXMLValue() - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamDouble
 
getXMLValue() - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamFile
 
getXMLValue() - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamFileCollection
 
getXMLValue() - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamFloat
 
getXMLValue() - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamHeader
 
getXMLValue() - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamInformation
 
getXMLValue() - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamInteger
 
getXMLValue() - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamLong
 
getXMLValue() - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamMatrix
 
getXMLValue() - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamMipavDialog
 
getXMLValue() - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamModel
 
getXMLValue() - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamMultiOption
 
getXMLValue() - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamNumberCollection
 
getXMLValue() - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamOption
 
getXMLValue() - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamPerformance
 
getXMLValue() - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamPointDouble
 
getXMLValue() - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamPointFloat
 
getXMLValue() - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamPointInteger
 
getXMLValue() - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamString
 
getXMLValue() - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamSwitch
 
getXMLValue() - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamWeightedVolume
 
getXMLValue() - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamWeightedVolumeCollection
 
getXN() - Method in class edu.jhu.ece.iacl.algorithms.vabra.VectorVolumeVabra
 
getXYZChain() - Method in class edu.jhu.ece.iacl.jist.structures.fiber.Fiber
Gets the xYZ chain.
getY() - Method in class edu.jhu.ece.iacl.jist.structures.vector.Vector2
 
getY() - Method in class edu.jhu.ece.iacl.jist.structures.vector.Vector3
 
getY() - Method in class edu.jhu.ece.iacl.jist.structures.vector.Vector4
 
getY() - Method in class edu.jhu.ece.iacl.jist.structures.vector.VectorN
 
getY() - Method in interface edu.jhu.ece.iacl.jist.structures.vector.VectorX
Gets the y.
getYN() - Method in class edu.jhu.ece.iacl.algorithms.vabra.VectorVolumeVabra
 
getZ() - Method in class edu.jhu.ece.iacl.jist.structures.vector.Vector2
 
getZ() - Method in class edu.jhu.ece.iacl.jist.structures.vector.Vector3
 
getZ() - Method in class edu.jhu.ece.iacl.jist.structures.vector.Vector4
 
getZ() - Method in class edu.jhu.ece.iacl.jist.structures.vector.VectorN
 
getZ() - Method in interface edu.jhu.ece.iacl.jist.structures.vector.VectorX
Gets the z.
GLIMIT - Static variable in class edu.jhu.ece.iacl.algorithms.vabra.NumericalRecipes
 
globalParameterizationSurvey - Static variable in class edu.jhu.ece.iacl.algorithms.ReferencedPapers
 
GlobalPreferencePanel - Class in edu.jhu.ece.iacl.jist.pipeline.gui
 
GlobalPreferencePanel(JistPreferences) - Constructor for class edu.jhu.ece.iacl.jist.pipeline.gui.GlobalPreferencePanel
 
GOLD - Static variable in class edu.jhu.ece.iacl.algorithms.vabra.NumericalRecipes
 
GoldenSectionSearch() - Static method in class edu.jhu.bme.smile.commons.optimize.test.TestNDOptimizations
Line Search using Golden Section Search
GoldenSectionSearch1D - Class in edu.jhu.bme.smile.commons.optimize
Class GoldenSectionSearch1D Uses the gold section search algorithm to find the minima of a 1D function
GoldenSectionSearch1D() - Constructor for class edu.jhu.bme.smile.commons.optimize.GoldenSectionSearch1D
Default constructor Sets iterations to 1000
GoldenSectionSearch1D(int) - Constructor for class edu.jhu.bme.smile.commons.optimize.GoldenSectionSearch1D
Constructor that allows setting the maximum number of iterations.
GoldenSectionSearch1D() - Static method in class edu.jhu.bme.smile.commons.optimize.test.Test1DOptimizations
Golden Section Search
gouraud - Variable in class edu.jhu.cs.cisst.vent.renderer.processing.SurfaceRenderer
The gouraud.
gouraudParam - Variable in class edu.jhu.cs.cisst.vent.renderer.processing.SurfaceRenderer
The visible param.
gout - Variable in class edu.jhu.ece.iacl.pami.SimFramework
 
gport - Variable in class edu.jhu.ece.iacl.jist.pipeline.PipePort
Rendering port component.
grad_choice - Variable in class edu.jhu.ece.iacl.algorithms.dti.GTCparams
 
gradient(float[][], boolean) - Static method in class edu.jhu.cs.cisst.algorithms.util.DataOperations
Gradient.
gradientPyramid - Variable in class edu.jhu.cs.cisst.algorithms.segmentation.gac.VectorFieldDiffusion2D
The gradient pyramid.
GradientTable - Class in edu.jhu.ece.iacl.algorithms.dti
The GradientTable class represents a GradientTable used for DWMRI as a 2D double array.
GradientTable() - Constructor for class edu.jhu.ece.iacl.algorithms.dti.GradientTable
Default constructor.
GradientTable(double[][]) - Constructor for class edu.jhu.ece.iacl.algorithms.dti.GradientTable
Constructor that accepts a double array representation.
GradientVectorFlow2D - Class in edu.jhu.cs.cisst.algorithms.segmentation.gac
The Class GradientVectorFlowField2D extends a gradient field using vector field diffusion.
GradientVectorFlow2D() - Constructor for class edu.jhu.cs.cisst.algorithms.segmentation.gac.GradientVectorFlow2D
Instantiates a new gradient vector flow field2 d.
GradientVectorFlow2D(double, double, boolean) - Constructor for class edu.jhu.cs.cisst.algorithms.segmentation.gac.GradientVectorFlow2D
Instantiates a new gradient vector flow field2 d.
GradientVectorFlow2D.Method - Enum in edu.jhu.cs.cisst.algorithms.segmentation.gac
The Enum Method.
GradTableCorrection - Class in edu.jhu.ece.iacl.algorithms.dti
 
GradTableCorrection(String, ArrayList<double[][]>) - Constructor for class edu.jhu.ece.iacl.algorithms.dti.GradTableCorrection
 
GradTableCorrection(File, ArrayList<double[][]>) - Constructor for class edu.jhu.ece.iacl.algorithms.dti.GradTableCorrection
 
GradTableCorrection(List<File>, ArrayList<double[][]>) - Constructor for class edu.jhu.ece.iacl.algorithms.dti.GradTableCorrection
 
GradTableCorrection(double[][], ArrayList<double[][]>) - Constructor for class edu.jhu.ece.iacl.algorithms.dti.GradTableCorrection
 
GradToSurf - Class in edu.jhu.ece.iacl.plugins.hardi
 
GradToSurf() - Constructor for class edu.jhu.ece.iacl.plugins.hardi.GradToSurf
 
graph - Variable in class edu.jhu.ece.iacl.jist.pipeline.graph.PipeCellViewFactory
The graph.
graph - Variable in class edu.jhu.ece.iacl.jist.pipeline.graph.PipePortView
The graph.
graph - Variable in class edu.jhu.ece.iacl.jist.pipeline.gui.PipeInternalFrame
The graph.
graphChanged(GraphModelEvent) - Method in class edu.jhu.ece.iacl.jist.pipeline.graph.PipeJGraph
 
graphForeground - Variable in class edu.jhu.ece.iacl.jist.pipeline.graph.PipeAlgorithmGroupView.ActivityRenderer
Holds the background and foreground of the graph.
graphForeground - Variable in class edu.jhu.ece.iacl.jist.pipeline.graph.PipeAlgorithmView.ActivityRenderer
Holds the background and foreground of the graph.
Grid - Class in edu.jhu.cs.cisst.algorithms.optimize.fmg.grid
A grid in 3D whose elements are alterable doubles.
Grid(int, int, int, int, double) - Constructor for class edu.jhu.cs.cisst.algorithms.optimize.fmg.grid.Grid
construct from size and initial value for all elements.
GridPoint2D - Class in edu.jhu.cs.cisst.algorithms.segmentation.gac
The Class GridPoint2D stores information about a narrow band node.
GridPoint2D(int, int, int, float) - Constructor for class edu.jhu.cs.cisst.algorithms.segmentation.gac.GridPoint2D
Instantiates a new grid point.
GridPoint2D(int, int, int) - Constructor for class edu.jhu.cs.cisst.algorithms.segmentation.gac.GridPoint2D
Instantiates a new grid point.
gridPoints - Variable in class edu.jhu.cs.cisst.algorithms.segmentation.gac.ActiveContourForce2D
The grid points.
gridPoints - Variable in class edu.jhu.cs.cisst.algorithms.segmentation.gac.GeodesicActiveContour2D
The grid points.
GridPt - Class in edu.jhu.ece.iacl.jist.structures.geom
The Class GridPt.
GridPt(int, int, int) - Constructor for class edu.jhu.ece.iacl.jist.structures.geom.GridPt
Instantiates a new grid pt.
GridPt(int, int, int, double) - Constructor for class edu.jhu.ece.iacl.jist.structures.geom.GridPt
Instantiates a new grid pt.
GridPt(Point3f) - Constructor for class edu.jhu.ece.iacl.jist.structures.geom.GridPt
Instantiates a new grid pt.
GridPt(Point3f, double) - Constructor for class edu.jhu.ece.iacl.jist.structures.geom.GridPt
Instantiates a new grid pt.
GridPt.Connectivity - Enum in edu.jhu.ece.iacl.jist.structures.geom
The Enum Connectivity.
gridSizes - Variable in class edu.jhu.cs.cisst.algorithms.optimize.fmg.DefaultSolverResolutionLevels2D
The grid sizes.
gridSizes - Variable in class edu.jhu.cs.cisst.algorithms.optimize.fmg.DefaultSolverResolutionLevels3D
The grid sizes.
group - Variable in class edu.jhu.ece.iacl.jist.pipeline.gui.PipeInternalFrame
The expand.
group(Object[]) - Method in class edu.jhu.ece.iacl.jist.pipeline.gui.PipeInternalFrame
Group cells together.
groups - Variable in class edu.jhu.ece.iacl.algorithms.manual_label.LabelImageGroup
 
GTCparams - Class in edu.jhu.ece.iacl.algorithms.dti
 
GTCparams() - Constructor for class edu.jhu.ece.iacl.algorithms.dti.GTCparams
 
gvf - Static variable in class edu.jhu.ece.iacl.algorithms.ReferencedPapers
 
gvfFieldParam - Variable in class edu.jhu.cs.cisst.plugins.visualization.PlugInVisualizeActiveContour2D
 
gyrificationIndex - Static variable in class edu.jhu.ece.iacl.algorithms.ReferencedPapers
 

H

HALF_WEIGHTING - Static variable in class edu.jhu.cs.cisst.algorithms.optimize.fmg.restrictor.RestrictorByStencil
the stencil that characterises half weighting which is halfway between full weighting and straigh injection.
handle - Static variable in class edu.jhu.ece.iacl.jist.pipeline.graph.PipeAlgorithmGroupView.ActivityRenderer
Default handle bounds for renderer, '+' or '-'.
handle - Static variable in class edu.jhu.ece.iacl.jist.pipeline.graph.PipeAlgorithmView.ActivityRenderer
Default handle bounds for renderer, '+' or '-'.
handleColor - Variable in class edu.jhu.ece.iacl.jist.pipeline.graph.PipeAlgorithmGroupView.ActivityRenderer
Holds the background and foreground of the graph.
handleColor - Variable in class edu.jhu.ece.iacl.jist.pipeline.graph.PipeAlgorithmView.ActivityRenderer
Holds the background and foreground of the graph.
hardseg - Variable in class edu.jhu.ece.iacl.algorithms.manual_label.staple.STAPLEmulti
 
hardseg - Variable in class edu.jhu.ece.iacl.algorithms.manual_label.staple.STAPLEmulti2
 
hasComparableGeometry(ImageHeader) - Method in class edu.jhu.ece.iacl.jist.structures.image.ImageHeader
NOTE: This method is a stub.
hasEmbeddedData() - Method in class edu.jhu.ece.iacl.jist.structures.geom.EmbeddedSurface
Checks for embedded data.
hash(int, int, int, int) - Method in class edu.jhu.ece.iacl.jist.structures.data.BinaryMinFastHeap
Hash.
hashCode() - Method in class edu.jhu.ece.iacl.jist.structures.geom.Vertex
 
hashCodeLong(int, int) - Static method in class edu.jhu.ece.iacl.jist.structures.geom.EmbeddedSurface.Edge
Hash code long.
hashCodeLong() - Method in class edu.jhu.ece.iacl.jist.structures.geom.EmbeddedSurface.Edge
Hash code long.
hashValue() - Method in class edu.jhu.cs.cisst.algorithms.geometry.surface.IsoContourGenerator.EdgeSplit
Hash value that uniquely identifies edge split.
hashValue(Point2i) - Method in class edu.jhu.cs.cisst.algorithms.geometry.surface.IsoContourGenerator.EdgeSplit
Generate hash value for grid point.
hashValue() - Method in class edu.jhu.cs.cisst.algorithms.geometry.surface.IsoSurfaceGenerator.EdgeSplit
Hash value that uniquely identifies edge split.
hashValue(Point3i) - Method in class edu.jhu.cs.cisst.algorithms.geometry.surface.IsoSurfaceGenerator.EdgeSplit
Generate hash value for grid point
hasNext() - Method in class edu.jhu.ece.iacl.jist.pipeline.PipeScheduler
Returns true if sources have move elements.
hasNext() - Method in class edu.jhu.ece.iacl.jist.pipeline.PipeSource
Returns true if there are more parameter values.
hasNext() - Method in class edu.jhu.ece.iacl.jist.pipeline.src.PipeDoubleSweepSource
Return true if iterator has more elements.
hasNext() - Method in class edu.jhu.ece.iacl.jist.pipeline.src.PipeExternalSource
 
hasNext() - Method in class edu.jhu.ece.iacl.jist.pipeline.src.PipeFileCollectionSource
Returns true if iterator has more elements.
hasNext() - Method in class edu.jhu.ece.iacl.jist.pipeline.src.PipeFileDirectorySource
Returns true if iterator has more elements.
hasNext() - Method in class edu.jhu.ece.iacl.jist.pipeline.src.PipeIntegerSweepSource
 
hasNext() - Method in class edu.jhu.ece.iacl.jist.pipeline.src.PipeListCollectionSource
Returns true if iterator has more values.
hasNext() - Method in class edu.jhu.ece.iacl.jist.pipeline.src.PipeListSource
Returns true if iterator has more values.
hasNext() - Method in class edu.jhu.ece.iacl.jist.pipeline.src.PipePointDoubleSweepSource
Return true if iterator has more elements.
hasNext() - Method in class edu.jhu.ece.iacl.jist.pipeline.src.PipeSelectionSource
Returns true if iterator has more elements.
hasNext() - Method in class edu.jhu.ece.iacl.jist.pipeline.src.PipeToggleSource
Returns true if iterator has more elements.
hasNext() - Method in class edu.jhu.ece.iacl.jist.pipeline.src.PipeVolumeDirectoryCollectionSource
Returns true if iterator has more elements.
hasPreferences() - Static method in class edu.jhu.ece.iacl.jist.pipeline.JistPreferences
Returns true if MAPS has preferences already.
hasRunningQueue() - Method in class edu.jhu.ece.iacl.jist.pipeline.PipeScheduler
Checks for running queue.
heatDiffusion(float[][][], float, int, float, int, int, int) - Static method in class edu.jhmi.rad.medic.libraries.ImageFunctionsPublic
GVF-style diffusion on scalar images
heatDiffusion(float[][][], float, float, int, float, int, int, int) - Static method in class edu.jhmi.rad.medic.libraries.ImageFunctionsPublic
GVF-style diffusion on scalar images
height - Variable in class edu.jhu.cs.cisst.vent.VisualizationProcessing2D
The height.
height - Variable in class edu.jhu.cs.cisst.vent.VisualizationProcessing3D
The height.
hello() - Method in class edu.jhu.ece.iacl.algorithms.dti.tractography.FACT.FACTapi
 
hidden - Variable in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamModel
The hidden.
hide() - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamModel
Hide this parameter.
hideVolumeInputs() - Method in class edu.jhu.ece.iacl.plugins.registration.MedicAlgorithmVABRA
 
hist - Variable in class edu.jhu.bme.smile.commons.math.HistogramGenerator
 
hist2string(double[][]) - Static method in class edu.jhu.bme.smile.commons.math.StatisticsDouble
 
histImg - Variable in class edu.jhu.ece.iacl.plugins.utilities.math.MedicAlgorithmKLDivergence
 
histImg - Variable in class edu.jhu.ece.iacl.plugins.utilities.surface.MedicAlgorithmSurfaceHistogram
 
histImg - Variable in class edu.jhu.ece.iacl.plugins.utilities.volume.MedicAlgorithmVolumeHistogram
 
histogram(double[], int) - Static method in class edu.jhu.bme.smile.commons.math.StatisticsDouble
Computes the histogram using equally spaced bins.
histogram(double[], double[]) - Static method in class edu.jhu.bme.smile.commons.math.StatisticsDouble
Computes the histogram using the specified bins The first column of the output array is the lower bounds for each bin The second column of the output array is the count in that bin.
histogram - Variable in class edu.jhu.ece.iacl.plugins.utilities.surface.MedicAlgorithmSurfaceHistogram
 
histogram - Variable in class edu.jhu.ece.iacl.plugins.utilities.volume.MedicAlgorithmVolumeHistogram
 
Histogram3D(ImageData, int, int[], int[]) - Static method in class edu.jhu.ece.iacl.algorithms.registration.RegistrationUtilities
 
Histogram3D(ImageData[], int, int, int[], int[][]) - Static method in class edu.jhu.ece.iacl.algorithms.registration.RegistrationUtilities
 
HistogramGenerator - Class in edu.jhu.bme.smile.commons.math
 
HistogramGenerator() - Constructor for class edu.jhu.bme.smile.commons.math.HistogramGenerator
 
historyChange(JistPreferences) - Method in class edu.jhu.ece.iacl.jist.io.ImageDataReaderWriter
 
historyChange(JistPreferences) - Method in class edu.jhu.ece.iacl.jist.pipeline.gui.PipelineLayoutTool
Change menu to reflect changes to history.
historyChange(JistPreferences) - Method in class edu.jhu.ece.iacl.jist.pipeline.gui.ProcessManager
Update menus if history changed.
historyChange(JistPreferences) - Method in interface edu.jhu.ece.iacl.jist.pipeline.JistPreferences.PreferenceListener
History change.
histX - Variable in class edu.jhu.ece.iacl.plugins.utilities.math.MedicAlgorithmKLDivergence
 
histY - Variable in class edu.jhu.ece.iacl.plugins.utilities.math.MedicAlgorithmKLDivergence
 
hspace - Static variable in class edu.jhu.ece.iacl.jist.pipeline.graph.PipeModuleCell
The Constant hspace.

I

icon - Variable in class edu.jhu.ece.iacl.jist.pipeline.tree.DraggableNode
The icon.
id - Variable in class edu.jhu.ece.iacl.jist.structures.geom.EmbeddedSurface.Edge
The id.
id - Variable in class edu.jhu.ece.iacl.jist.structures.geom.EmbeddedSurface.Face
The id.
IDEAL_WEIGHTING_FACTOR - Static variable in class edu.jhu.cs.cisst.algorithms.optimize.fmg.smoother.DampedJacobi
in theory the ideal weighting factor, i.e.
ignoreRefresh - Variable in class edu.jhu.ece.iacl.jist.pipeline.gui.ParameterPanel
The ignore refresh.
image - Variable in class edu.jhu.cs.cisst.algorithms.segmentation.gac.GeodesicActiveContour2D
The reference image.
image - Variable in class edu.jhu.cs.cisst.vent.renderer.processing.ImageRenderer
The image.
image - Variable in class edu.jhu.cs.cisst.vent.renderer.processing.VectorField2DRenderer
The image.
image - Variable in class edu.jhu.cs.cisst.vent.renderer.processing.VolumeSliceRenderer
The image.
ImageAlgebra - Class in edu.jhu.bme.smile.demo
 
ImageAlgebra() - Constructor for class edu.jhu.bme.smile.demo.ImageAlgebra
 
ImageArithmetic - Class in edu.jhu.bme.smile.demo
 
ImageArithmetic() - Constructor for class edu.jhu.bme.smile.demo.ImageArithmetic
 
ImageCollectionAlgebra - Class in edu.jhu.bme.smile.demo
 
ImageCollectionAlgebra() - Constructor for class edu.jhu.bme.smile.demo.ImageCollectionAlgebra
 
ImageData - Class in edu.jhu.ece.iacl.jist.structures.image
Structure used for storing all volumetric data.
ImageData() - Constructor for class edu.jhu.ece.iacl.jist.structures.image.ImageData
 
ImageDataByte - Class in edu.jhu.ece.iacl.jist.structures.image
The Class ImageDataInt.
ImageDataByte(ImageData) - Constructor for class edu.jhu.ece.iacl.jist.structures.image.ImageDataByte
Instantiates a new image data int.
ImageDataByte(int, int) - Constructor for class edu.jhu.ece.iacl.jist.structures.image.ImageDataByte
Instantiates a new image data int.
ImageDataByte(int, int, int) - Constructor for class edu.jhu.ece.iacl.jist.structures.image.ImageDataByte
Instantiates a new image data int.
ImageDataByte(String, int, int) - Constructor for class edu.jhu.ece.iacl.jist.structures.image.ImageDataByte
Instantiates a new image data int.
ImageDataByte(String, int, int, int) - Constructor for class edu.jhu.ece.iacl.jist.structures.image.ImageDataByte
Instantiates a new image data int.
ImageDataByte(String, int, int, int, int) - Constructor for class edu.jhu.ece.iacl.jist.structures.image.ImageDataByte
Instantiates a new image data int.
ImageDataByte(int, int, int, int) - Constructor for class edu.jhu.ece.iacl.jist.structures.image.ImageDataByte
Instantiates a new image data int.
ImageDataByte(byte[][]) - Constructor for class edu.jhu.ece.iacl.jist.structures.image.ImageDataByte
Instantiates a new image data int.
ImageDataByte(byte[][][]) - Constructor for class edu.jhu.ece.iacl.jist.structures.image.ImageDataByte
Instantiates a new image data int.
ImageDataByte(byte[][][][]) - Constructor for class edu.jhu.ece.iacl.jist.structures.image.ImageDataByte
Instantiates a new image data int.
ImageDataColor - Class in edu.jhu.ece.iacl.jist.structures.image
The Class ImageDataColor.
ImageDataColor(Color[][]) - Constructor for class edu.jhu.ece.iacl.jist.structures.image.ImageDataColor
Instantiates a new image data color.
ImageDataColor(Color[][][]) - Constructor for class edu.jhu.ece.iacl.jist.structures.image.ImageDataColor
Instantiates a new image data color.
ImageDataColor(Color[][][][]) - Constructor for class edu.jhu.ece.iacl.jist.structures.image.ImageDataColor
Instantiates a new image data color.
ImageDataColor(ImageData) - Constructor for class edu.jhu.ece.iacl.jist.structures.image.ImageDataColor
Instantiates a new image data color.
ImageDataColor(VoxelType, int, int) - Constructor for class edu.jhu.ece.iacl.jist.structures.image.ImageDataColor
Instantiates a new image data color.
ImageDataColor(VoxelType, int, int, int) - Constructor for class edu.jhu.ece.iacl.jist.structures.image.ImageDataColor
Instantiates a new image data color.
ImageDataColor(VoxelType, int, int, int, int) - Constructor for class edu.jhu.ece.iacl.jist.structures.image.ImageDataColor
Instantiates a new image data color.
ImageDataDouble - Class in edu.jhu.ece.iacl.jist.structures.image
The Class ImageDataDouble.
ImageDataDouble(ImageData) - Constructor for class edu.jhu.ece.iacl.jist.structures.image.ImageDataDouble
Instantiates a new image data double.
ImageDataDouble(double[][]) - Constructor for class edu.jhu.ece.iacl.jist.structures.image.ImageDataDouble
Instantiates a new image data double.
ImageDataDouble(double[][][]) - Constructor for class edu.jhu.ece.iacl.jist.structures.image.ImageDataDouble
Instantiates a new image data double.
ImageDataDouble(double[][][][]) - Constructor for class edu.jhu.ece.iacl.jist.structures.image.ImageDataDouble
Instantiates a new image data double.
ImageDataDouble(int, int) - Constructor for class edu.jhu.ece.iacl.jist.structures.image.ImageDataDouble
Instantiates a new image data double.
ImageDataDouble(int, int, int) - Constructor for class edu.jhu.ece.iacl.jist.structures.image.ImageDataDouble
Instantiates a new image data double.
ImageDataDouble(int, int, int, int) - Constructor for class edu.jhu.ece.iacl.jist.structures.image.ImageDataDouble
Instantiates a new image data double.
ImageDataFloat - Class in edu.jhu.ece.iacl.jist.structures.image
The Class ImageDataFloat.
ImageDataFloat(ImageData) - Constructor for class edu.jhu.ece.iacl.jist.structures.image.ImageDataFloat
Instantiates a new image data float.
ImageDataFloat(float[][][]) - Constructor for class edu.jhu.ece.iacl.jist.structures.image.ImageDataFloat
Instantiates a new image data float.
ImageDataFloat(float[][][][]) - Constructor for class edu.jhu.ece.iacl.jist.structures.image.ImageDataFloat
Instantiates a new image data float.
ImageDataFloat(int, int) - Constructor for class edu.jhu.ece.iacl.jist.structures.image.ImageDataFloat
Instantiates a new image data float.
ImageDataFloat(int, int, int) - Constructor for class edu.jhu.ece.iacl.jist.structures.image.ImageDataFloat
Instantiates a new image data float.
ImageDataFloat(int, int, int, int) - Constructor for class edu.jhu.ece.iacl.jist.structures.image.ImageDataFloat
 
ImageDataFloat(String, int, int) - Constructor for class edu.jhu.ece.iacl.jist.structures.image.ImageDataFloat
Instantiates a new image data float.
ImageDataFloat(String, int, int, int) - Constructor for class edu.jhu.ece.iacl.jist.structures.image.ImageDataFloat
Instantiates a new image data float.
ImageDataFloat(String, int, int, int, int) - Constructor for class edu.jhu.ece.iacl.jist.structures.image.ImageDataFloat
Instantiates a new image data float.
ImageDataInt - Class in edu.jhu.ece.iacl.jist.structures.image
The Class ImageDataInt.
ImageDataInt(ImageData) - Constructor for class edu.jhu.ece.iacl.jist.structures.image.ImageDataInt
Instantiates a new image data int.
ImageDataInt(int, int) - Constructor for class edu.jhu.ece.iacl.jist.structures.image.ImageDataInt
Instantiates a new image data int.
ImageDataInt(int, int, int) - Constructor for class edu.jhu.ece.iacl.jist.structures.image.ImageDataInt
Instantiates a new image data int.
ImageDataInt(String, int, int) - Constructor for class edu.jhu.ece.iacl.jist.structures.image.ImageDataInt
Instantiates a new image data int.
ImageDataInt(String, int, int, int) - Constructor for class edu.jhu.ece.iacl.jist.structures.image.ImageDataInt
Instantiates a new image data int.
ImageDataInt(String, int, int, int, int) - Constructor for class edu.jhu.ece.iacl.jist.structures.image.ImageDataInt
Instantiates a new image data int.
ImageDataInt(int, int, int, int) - Constructor for class edu.jhu.ece.iacl.jist.structures.image.ImageDataInt
Instantiates a new image data int.
ImageDataInt(int[][]) - Constructor for class edu.jhu.ece.iacl.jist.structures.image.ImageDataInt
Instantiates a new image data int.
ImageDataInt(int[][][]) - Constructor for class edu.jhu.ece.iacl.jist.structures.image.ImageDataInt
Instantiates a new image data int.
ImageDataInt(int[][][][]) - Constructor for class edu.jhu.ece.iacl.jist.structures.image.ImageDataInt
Instantiates a new image data int.
ImageDataMath - Class in edu.jhu.ece.iacl.structures.image
The Class ImageDataMath.
ImageDataMath() - Constructor for class edu.jhu.ece.iacl.structures.image.ImageDataMath
 
ImageDataMipav - Class in edu.jhu.ece.iacl.jist.structures.image
Cubic volume adapter to MIPAV ModelImage type.
ImageDataMipav(ImageData) - Constructor for class edu.jhu.ece.iacl.jist.structures.image.ImageDataMipav
Instantiates a new image data mipav.
ImageDataMipav(ModelImage) - Constructor for class edu.jhu.ece.iacl.jist.structures.image.ImageDataMipav
 
ImageDataMipav(String, int, int) - Constructor for class edu.jhu.ece.iacl.jist.structures.image.ImageDataMipav
Instantiates a new image data mipav.
ImageDataMipav(String, int, int, int) - Constructor for class edu.jhu.ece.iacl.jist.structures.image.ImageDataMipav
Instantiates a new image data mipav.
ImageDataMipav(String, int, int, int, int) - Constructor for class edu.jhu.ece.iacl.jist.structures.image.ImageDataMipav
Instantiates a new image data mipav.
ImageDataMipav(String, VoxelType, int, int, int) - Constructor for class edu.jhu.ece.iacl.jist.structures.image.ImageDataMipav
Instantiates a new image data mipav.
ImageDataMipav(String, VoxelType, int, int, int, int) - Constructor for class edu.jhu.ece.iacl.jist.structures.image.ImageDataMipav
Instantiates a new image data mipav.
ImageDataMipav() - Constructor for class edu.jhu.ece.iacl.jist.structures.image.ImageDataMipav
 
ImageDataMipavPointer - Class in edu.jhu.ece.iacl.jist.structures.image
 
ImageDataMipavPointer(ModelImage) - Constructor for class edu.jhu.ece.iacl.jist.structures.image.ImageDataMipavPointer
 
ImageDataMipavPrivate(ModelImage) - Method in class edu.jhu.ece.iacl.jist.structures.image.ImageDataMipav
Instantiates a new image data mipav.
ImageDataMipavWrapper - Class in edu.jhu.ece.iacl.jist.structures.image
 
ImageDataMipavWrapper(ModelImage) - Constructor for class edu.jhu.ece.iacl.jist.structures.image.ImageDataMipavWrapper
 
ImageDataNumber - Class in edu.jhu.ece.iacl.jist.structures.image
The Class ImageDataNumber.
ImageDataNumber(ImageData) - Constructor for class edu.jhu.ece.iacl.jist.structures.image.ImageDataNumber
Instantiates a new image data number.
ImageDataNumber(int, int) - Constructor for class edu.jhu.ece.iacl.jist.structures.image.ImageDataNumber
Instantiates a new image data number.
ImageDataNumber(int, int, int) - Constructor for class edu.jhu.ece.iacl.jist.structures.image.ImageDataNumber
Instantiates a new image data number.
ImageDataNumber(int, int, int, int) - Constructor for class edu.jhu.ece.iacl.jist.structures.image.ImageDataNumber
Instantiates a new image data number.
ImageDataNumber(Number[][]) - Constructor for class edu.jhu.ece.iacl.jist.structures.image.ImageDataNumber
Instantiates a new image data number.
ImageDataNumber(Number[][][]) - Constructor for class edu.jhu.ece.iacl.jist.structures.image.ImageDataNumber
Instantiates a new image data number.
ImageDataNumber(Number[][][][]) - Constructor for class edu.jhu.ece.iacl.jist.structures.image.ImageDataNumber
Instantiates a new image data number.
ImageDataNumber(String, VoxelType, int, int, int, int) - Constructor for class edu.jhu.ece.iacl.jist.structures.image.ImageDataNumber
Instantiates a new image data number.
ImageDataNumber(VoxelType, int, int, int, int) - Constructor for class edu.jhu.ece.iacl.jist.structures.image.ImageDataNumber
Instantiates a new image data number.
ImageDataReaderWriter - Class in edu.jhu.ece.iacl.jist.io
The Class CubicVolumeReaderWriter.
ImageDataReaderWriter() - Constructor for class edu.jhu.ece.iacl.jist.io.ImageDataReaderWriter
Instantiates a new cubic volume reader writer.
ImageDataUByte - Class in edu.jhu.ece.iacl.jist.structures.image
The Class ImageDataUByte.
ImageDataUByte(byte[][]) - Constructor for class edu.jhu.ece.iacl.jist.structures.image.ImageDataUByte
Instantiates a new image data u byte.
ImageDataUByte(byte[][][]) - Constructor for class edu.jhu.ece.iacl.jist.structures.image.ImageDataUByte
Instantiates a new image data u byte.
ImageDataUByte(byte[][][][]) - Constructor for class edu.jhu.ece.iacl.jist.structures.image.ImageDataUByte
Instantiates a new image data u byte.
ImageDataUByte(ImageData) - Constructor for class edu.jhu.ece.iacl.jist.structures.image.ImageDataUByte
Instantiates a new image data u byte.
ImageDataUByte(int, int) - Constructor for class edu.jhu.ece.iacl.jist.structures.image.ImageDataUByte
Instantiates a new image data u byte.
ImageDataUByte(int, int, int) - Constructor for class edu.jhu.ece.iacl.jist.structures.image.ImageDataUByte
Instantiates a new image data u byte.
ImageDataUByte(int, int, int, int) - Constructor for class edu.jhu.ece.iacl.jist.structures.image.ImageDataUByte
Instantiates a new image data u byte.
imageField - Variable in class edu.jhu.ece.iacl.jist.pipeline.view.input.ParamVolumeURICollectionInputView
The file field.
ImageFunctionsPublic - Class in edu.jhmi.rad.medic.libraries
This class computes various basic image functions, e.g.
ImageFunctionsPublic() - Constructor for class edu.jhmi.rad.medic.libraries.ImageFunctionsPublic
 
imageHeader - Variable in class edu.jhu.ece.iacl.jist.structures.image.ImageData
The image header.
ImageHeader - Class in edu.jhu.ece.iacl.jist.structures.image
The Class ImageHeader.
ImageHeader() - Constructor for class edu.jhu.ece.iacl.jist.structures.image.ImageHeader
Instantiates a new image header.
ImageHeader(FileInfoBase) - Constructor for class edu.jhu.ece.iacl.jist.structures.image.ImageHeader
Instantiates a new image header.
ImageHeader.AxisOrientation - Enum in edu.jhu.ece.iacl.jist.structures.image
The Enum AxisOrientation.
ImageHeader.Compression - Enum in edu.jhu.ece.iacl.jist.structures.image
The Enum Compression.
ImageHeader.Endianess - Enum in edu.jhu.ece.iacl.jist.structures.image
The Enum Endianess.
ImageHeader.ImageModality - Enum in edu.jhu.ece.iacl.jist.structures.image
The Enum ImageModality.
ImageHeader.ImageOrientation - Enum in edu.jhu.ece.iacl.jist.structures.image
The Enum ImageOrientation.
ImageHeader.MeasurementUnit - Enum in edu.jhu.ece.iacl.jist.structures.image
The Enum MeasurementUnit.
imageListBoxEntries - Variable in class edu.jhu.ece.iacl.jist.pipeline.view.input.ParamVolumeURICollectionInputView
The list box entries.
imageListPane - Variable in class edu.jhu.ece.iacl.jist.pipeline.view.input.ParamVolumeURICollectionInputView
The list pane.
imageListSize - Variable in class edu.jhu.ece.iacl.jist.pipeline.view.input.ParamFileCollectionInputView
The image list size.
imageListSize - Variable in class edu.jhu.ece.iacl.jist.pipeline.view.input.ParamNumberCollectionInputView
The image list size.
imageListSize - Variable in class edu.jhu.ece.iacl.jist.pipeline.view.input.ParamVolumeCollectionInputView
The image list size.
imageListSize - Variable in class edu.jhu.ece.iacl.jist.pipeline.view.input.ParamVolumeInputView
The image list size.
imageListSize - Variable in class edu.jhu.ece.iacl.jist.pipeline.view.input.ParamVolumeURICollectionInputView
The image list size.
imageListSize - Variable in class edu.jhu.ece.iacl.jist.pipeline.view.input.ParamVolumeURIInputView
The image list size.
imageOrientation - Variable in class edu.jhu.ece.iacl.jist.structures.image.ImageHeader
The image orientation.
imageOrientationNames - Static variable in class edu.jhu.ece.iacl.jist.structures.image.ImageHeader
The Constant imageOrientationNames.
ImagePair - Class in edu.jhu.ece.iacl.algorithms.vabra
 
ImagePair() - Constructor for class edu.jhu.ece.iacl.algorithms.vabra.ImagePair
 
ImagePairNMI - Class in edu.jhu.ece.iacl.algorithms.vabra
 
ImagePairNMI(List<ImageData>, List<Number>, List<ImageData>, List<Number>, AbstractCalculation, float, float, int, int[]) - Constructor for class edu.jhu.ece.iacl.algorithms.vabra.ImagePairNMI
 
ImagePairNMI(List<ImageData>, List<Number>, List<ImageData>, List<Number>, AbstractCalculation, int[]) - Constructor for class edu.jhu.ece.iacl.algorithms.vabra.ImagePairNMI
 
ImagePairRBF - Class in edu.jhu.ece.iacl.algorithms.vabra
 
ImagePairRBF(List<ImageData>, List<Number>, List<ImageData>, List<Number>, AbstractCalculation, int[]) - Constructor for class edu.jhu.ece.iacl.algorithms.vabra.ImagePairRBF
 
ImagePairRBF(List<ImageData>, List<Number>, List<ImageData>, List<Number>, AbstractCalculation, float, float, int, int[]) - Constructor for class edu.jhu.ece.iacl.algorithms.vabra.ImagePairRBF
 
ImageRenderer - Class in edu.jhu.cs.cisst.vent.renderer.processing
The Class ImageRenderer.
ImageRenderer(ImageData, VisualizationProcessing) - Constructor for class edu.jhu.cs.cisst.vent.renderer.processing.ImageRenderer
Instantiates a new image renderer.
images - Variable in class edu.jhu.cs.cisst.vent.renderer.processing.ImageRenderer
The images.
images - Variable in class edu.jhu.cs.cisst.vent.renderer.processing.VolumeSliceRenderer
The images.
images - Variable in class edu.jhu.ece.iacl.algorithms.manual_label.staple.STAPLEmulti
 
images - Variable in class edu.jhu.ece.iacl.plugins.utilities.file.VolumeDirectoryNoIter
The images.
imagesArray - Variable in class edu.jhu.ece.iacl.algorithms.manual_label.staple.STAPLEmulti
 
imagesArray - Variable in class edu.jhu.ece.iacl.algorithms.manual_label.staple.STAPLEmulti2
 
imagesArrayFloat - Variable in class edu.jhu.ece.iacl.algorithms.manual_label.staple.STAPLEmulti
 
imagesArrayFloat - Variable in class edu.jhu.ece.iacl.algorithms.manual_label.staple.STAPLEmulti2
 
imageScrollPane - Variable in class edu.jhu.ece.iacl.jist.pipeline.view.input.ParamVolumeURICollectionInputView
The scroll pane.
ImageSize - Variable in class edu.jhu.ece.iacl.jist.structures.fiber.DTIStudioHDR
The Image size.
ImageUtil - Class in edu.jhu.ece.iacl.jist.utility
The Class ImageUtil.
ImageUtil() - Constructor for class edu.jhu.ece.iacl.jist.utility.ImageUtil
 
img - Variable in class edu.jhu.ece.iacl.algorithms.manual_label.LabelImage
 
img - Variable in class edu.jhu.ece.iacl.jist.structures.geom.MipavVOI
The img.
img - Variable in class edu.jhu.ece.iacl.jist.structures.image.ImageDataMipav
The img.
imgMat - Variable in class edu.jhu.cs.cisst.algorithms.geometry.surface.IsoContourGenerator
The img mat.
implicitFairing - Static variable in class edu.jhu.ece.iacl.algorithms.ReferencedPapers
 
importMipavParameter(ParameterTable) - Method in class edu.jhu.ece.iacl.jist.pipeline.factory.ParamBooleanFactory
 
importMipavParameter(ParameterTable) - Method in class edu.jhu.ece.iacl.jist.pipeline.factory.ParamCollectionFactory
 
importMipavParameter(ParameterTable) - Method in class edu.jhu.ece.iacl.jist.pipeline.factory.ParamColorFactory
 
importMipavParameter(ParameterTable) - Method in class edu.jhu.ece.iacl.jist.pipeline.factory.ParamDoubleFactory
 
importMipavParameter(ParameterTable) - Method in class edu.jhu.ece.iacl.jist.pipeline.factory.ParamFactory
Import Mipav parameter into this parameter.
importMipavParameter(ParameterTable) - Method in class edu.jhu.ece.iacl.jist.pipeline.factory.ParamFileCollectionFactory
 
importMipavParameter(ParameterTable) - Method in class edu.jhu.ece.iacl.jist.pipeline.factory.ParamFileFactory
 
importMipavParameter(ParameterTable) - Method in class edu.jhu.ece.iacl.jist.pipeline.factory.ParamFloatFactory
 
importMipavParameter(ParameterTable) - Method in class edu.jhu.ece.iacl.jist.pipeline.factory.ParamHiddenFactory
 
importMipavParameter(ParameterTable) - Method in class edu.jhu.ece.iacl.jist.pipeline.factory.ParamInformationFactory
 
importMipavParameter(ParameterTable) - Method in class edu.jhu.ece.iacl.jist.pipeline.factory.ParamIntegerFactory
 
importMipavParameter(ParameterTable) - Method in class edu.jhu.ece.iacl.jist.pipeline.factory.ParamLongFactory
 
importMipavParameter(ParameterTable) - Method in class edu.jhu.ece.iacl.jist.pipeline.factory.ParamMatrixFactory
 
importMipavParameter(ParameterTable) - Method in class edu.jhu.ece.iacl.jist.pipeline.factory.ParamMipavDialogFactory
 
importMipavParameter(ParameterTable) - Method in class edu.jhu.ece.iacl.jist.pipeline.factory.ParamMultiOptionFactory
 
importMipavParameter(ParameterTable) - Method in class edu.jhu.ece.iacl.jist.pipeline.factory.ParamNumberCollectionFactory
 
importMipavParameter(ParameterTable) - Method in class edu.jhu.ece.iacl.jist.pipeline.factory.ParamOptionFactory
 
importMipavParameter(ParameterTable) - Method in class edu.jhu.ece.iacl.jist.pipeline.factory.ParamPerformanceFactory
 
importMipavParameter(ParameterTable) - Method in class edu.jhu.ece.iacl.jist.pipeline.factory.ParamPointDoubleFactory
 
importMipavParameter(ParameterTable) - Method in class edu.jhu.ece.iacl.jist.pipeline.factory.ParamPointFloatFactory
 
importMipavParameter(ParameterTable) - Method in class edu.jhu.ece.iacl.jist.pipeline.factory.ParamPointIntegerFactory
 
importMipavParameter(ParameterTable) - Method in class edu.jhu.ece.iacl.jist.pipeline.factory.ParamStringFactory
 
importMipavParameter(ParameterTable) - Method in class edu.jhu.ece.iacl.jist.pipeline.factory.ParamVolumeCollectionFactory
 
importMipavParameter(ParameterTable) - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamModel
Import value from MIPAV script parameter.
importParameter(ParamModel) - Method in class edu.jhu.ece.iacl.jist.pipeline.factory.ParamCollectionFactory
 
importParameter(ParamModel) - Method in class edu.jhu.ece.iacl.jist.pipeline.factory.ParamDataLabelFactory
Import model image and label file location from foreign parameter.
importParameter(ParamModel) - Method in class edu.jhu.ece.iacl.jist.pipeline.factory.ParamFactory
Import parameter into existing parameter as long as parameter is not more restrictive than this parameter.
importParameter(ParamModel) - Method in class edu.jhu.ece.iacl.jist.pipeline.factory.ParamHeaderFactory
 
importParameter(ParamModel) - Method in class edu.jhu.ece.iacl.jist.pipeline.factory.ParamWeightedVolumeCollectionFactory
 
importParameter(ParamModel) - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamModel
Import the contents of a foreign parameter into this parameter.
importVolume(ParamVolume, int) - Method in class edu.jhu.ece.iacl.algorithms.vabra.ImagePair
 
importVolumes(List<ImageData>, List<Number>, int[]) - Method in class edu.jhu.ece.iacl.algorithms.vabra.ImagePair
 
inBounds(BoundingBox) - Method in class edu.jhu.ece.iacl.jist.structures.geom.CollisionDetection.Triangle
In bounds.
inc - Variable in class edu.jhu.ece.iacl.jist.pipeline.src.PipeDoubleSweepSource
The inc.
inc - Variable in class edu.jhu.ece.iacl.jist.pipeline.src.PipeIntegerSweepSource
The inc.
inc - Variable in class edu.jhu.ece.iacl.jist.pipeline.src.PipePointDoubleSweepSource
The inc.
inc - Variable in class edu.jhu.ece.iacl.jist.pipeline.src.PipeToggleSource
The inc.
includeParam - Variable in class edu.jhu.ece.iacl.jist.pipeline.src.PipeFileDirectorySource
The include param.
includeParam - Variable in class edu.jhu.ece.iacl.jist.pipeline.src.PipeVolumeDirectoryCollectionSource
The include param.
includeParam - Variable in class edu.jhu.ece.iacl.plugins.utilities.file.VolumeDirectoryNoIter
The include param.
inclusive - Variable in class edu.jhu.ece.iacl.plugins.utilities.logic.MedicAlgorithmValueGreaterThan
 
inclusive - Variable in class edu.jhu.ece.iacl.plugins.utilities.logic.MedicAlgorithmValueInRange
 
inclusive - Variable in class edu.jhu.ece.iacl.plugins.utilities.logic.MedicAlgorithmValueLessThan
 
inclusiveMaskInterpolation(boolean[][][], float, float, float, int, int, int) - Static method in class edu.jhmi.rad.medic.libraries.ImageFunctionsPublic
interpolate a computation mask: where there is some data, the mask is set to true (generates a mask that contain the transformed image)
incomingConnectors - Variable in class edu.jhu.ece.iacl.jist.pipeline.PipePort
incoming connectors attached to this port.
incParam - Variable in class edu.jhu.ece.iacl.jist.pipeline.src.PipeDoubleSweepSource
The val param.
incParam - Variable in class edu.jhu.ece.iacl.jist.pipeline.src.PipeIntegerSweepSource
The val param.
incParam - Variable in class edu.jhu.ece.iacl.jist.pipeline.src.PipePointDoubleSweepSource
The val param.
incrementCompletedUnits() - Method in class edu.jhu.ece.iacl.jist.pipeline.AbstractCalculation
Increment the number of completed units.
incrementCompletedUnits(int) - Method in class edu.jhu.ece.iacl.jist.pipeline.AbstractCalculation
Increment the number of completed units.
index - Variable in class edu.jhu.bme.smile.commons.math.HistogramGenerator
 
index - Variable in class edu.jhu.ece.iacl.algorithms.registration.RegistrationUtilities.IndexedFloat
 
index - Variable in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamOption
The index.
index - Variable in class edu.jhu.ece.iacl.jist.pipeline.src.PipeFileCollectionSource
The index.
index - Variable in class edu.jhu.ece.iacl.jist.pipeline.src.PipeFileDirectorySource
The index.
index - Variable in class edu.jhu.ece.iacl.jist.pipeline.src.PipeListCollectionSource
The index.
index - Variable in class edu.jhu.ece.iacl.jist.pipeline.src.PipeListSource
The index.
index - Variable in class edu.jhu.ece.iacl.jist.pipeline.src.PipeSelectionExternalSource
The index.
index - Variable in class edu.jhu.ece.iacl.jist.pipeline.src.PipeSelectionSource
The index.
index - Variable in class edu.jhu.ece.iacl.jist.pipeline.src.PipeVolumeDirectoryCollectionSource
The index.
index - Variable in class edu.jhu.ece.iacl.jist.structures.geom.Vertex
The index.
index - Variable in class edu.jhu.ece.iacl.plugins.utilities.file.VolumeDirectoryNoIter
The index.
index - Variable in class edu.jhu.ece.iacl.plugins.utilities.surface.MedicAlgorithmSurfaceHistogram
 
Indexable<E extends java.lang.Comparable<? super E>> - Interface in edu.jhu.ece.iacl.jist.structures.data
Indexable object used for heap.
indexes - Variable in class edu.jhu.cs.cisst.vent.structures.processing.PTriangleMesh
The indexes.
indexes - Variable in class edu.jhu.ece.iacl.jist.structures.geom.EmbeddedPointSet
The indexes.
INF - Static variable in class edu.jhmi.rad.medic.utilities.NumericsPublic
mathematical constants
info - Variable in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamInformation
The info.
info - Variable in class edu.jhu.ece.iacl.jist.pipeline.view.input.AlgorithmInformationDialog
The algorithm information.
INFO - Static variable in class edu.jhu.ece.iacl.jist.utility.JistLogger
 
InformationListBox<T> - Class in edu.jhu.ece.iacl.jist.pipeline.view.input
A customized list box for displaying and editing algorithm information.
InformationListBox(String, boolean) - Constructor for class edu.jhu.ece.iacl.jist.pipeline.view.input.InformationListBox
Default constructor.
inHitRegion(Point2D) - Method in class edu.jhu.ece.iacl.jist.pipeline.graph.PipeAlgorithmGroupView.ActivityRenderer
Detect whether or not a point has hit the group/ungroup image.
init(Matrix, double, double, double, double[], double[]) - Method in class edu.jhu.bme.smile.commons.optimize.tensor.MLTensor
Initializes MLTensor with these parameters
init(ImageData) - Method in class edu.jhu.cs.cisst.algorithms.segmentation.gac.GeodesicActiveContour2D
Initializes the solver.
init() - Method in class edu.jhu.cs.cisst.vent.VisualizationApplication
Inits the.
init(Matrix, double, double, double[], double[], double[], double[]) - Method in class edu.jhu.ece.iacl.algorithms.dti.DTEMRLTensor
Initializes MLTensor with these parameters
init(Matrix, double, double, double[], double[], float[], double[]) - Method in class edu.jhu.ece.iacl.algorithms.dti.DTEMRLTensor
 
init(double[], double[]) - Method in class edu.jhu.ece.iacl.algorithms.dti.tractography.FACT.FloatInterp
 
init - Variable in class edu.jhu.ece.iacl.algorithms.manual_label.staple.STAPLEgeneral
 
init() - Method in class edu.jhu.ece.iacl.doc.DocumentAllTests
Inits the.
init() - Static method in class edu.jhu.ece.iacl.jist.io.MipavController
Inits the.
init(ProcessingAlgorithm) - Method in class edu.jhu.ece.iacl.jist.pipeline.AlgorithmInformation
Initialize the information from the algorithm.
init(PipeJGraph) - Method in class edu.jhu.ece.iacl.jist.pipeline.dest.PipeParamCopyDestination
Initialize module cell.
init(JistPreferences) - Method in class edu.jhu.ece.iacl.jist.pipeline.gui.GlobalPreferencePanel
Initialize preference panel for layout.
init(PipeLayout) - Method in class edu.jhu.ece.iacl.jist.pipeline.gui.LayoutPreferencePanel
Initialize preference panel for layout.
init() - Method in class edu.jhu.ece.iacl.jist.pipeline.gui.ModuleTreePanel
Initialize module panel by loading library.
init() - Method in class edu.jhu.ece.iacl.jist.pipeline.gui.PipelineLayoutTool
Initialize layout tool.
init() - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamArgsOrder
 
init() - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamBoolean
Initialize parameter.
init() - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamCollection
Initialize parameter.
init() - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamColor
Initialize parameter.
init() - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamDataLabel
Initialize parameter.
init() - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamDouble
Initialize this object.
init() - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamExecutable
Initialize parameter.
init() - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamFile
 
init() - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamFileCollection
Initialize parameter.
init() - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamFloat
Initialize this object.
init() - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamHeader
Initialize parameter.
init() - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamHidden
Initialize parameter.
init() - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamInformation
Initialize parameter.
init() - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamInteger
 
init() - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamLong
 
init() - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamMatrix
 
init() - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamMipavDialog
Initialize parameter.
init() - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamMultiOption
 
init() - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamNumberCollection
Initialize parameter.
init() - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamObject
Initialize parameter.
init() - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamOption
Initialize parameter.
init() - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamPerformance
Initialize parameter.
init() - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamPointDouble
Initialize parameter.
init() - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamPointFloat
Initialize parameter.
init() - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamPointInteger
Initialize parameter.
init() - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamString
Initialize parameter.
init() - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamSurface
Initialize parameter.
init() - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamSwitch
Initialize parameter.
init() - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamVolume
Initialize parameter.
init() - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamVolumeCollection
Initialize parameter.
init() - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamWeightedVolumeCollection
Initialize parameter.
init(String) - Method in interface edu.jhu.ece.iacl.jist.pipeline.parser.JISTDynamicPluginLookup
 
init(PipeJGraph) - Method in class edu.jhu.ece.iacl.jist.pipeline.PipeAlgorithm
Initialize transient fields that could not be deserialized.
init(PipeJGraph) - Method in class edu.jhu.ece.iacl.jist.pipeline.PipeAlgorithmGroup
Initialize transient fields that could not be deserialized.
init() - Method in class edu.jhu.ece.iacl.jist.pipeline.PipeChildPort
Initialize child port as always an input port.
init(PipeJGraph) - Method in class edu.jhu.ece.iacl.jist.pipeline.PipeDestination
Initialize destination and create graph cell.
init() - Method in class edu.jhu.ece.iacl.jist.pipeline.PipeLayout
Initialize transient fields that could not be deserialized.
init(PipeJGraph, ProgressMonitor) - Method in class edu.jhu.ece.iacl.jist.pipeline.PipeLayout
Initialize transient fields that could not be deserialized.
init() - Method in class edu.jhu.ece.iacl.jist.pipeline.PipeLayoutRunner
Inits the.
init(PipeJGraph) - Method in class edu.jhu.ece.iacl.jist.pipeline.PipeModule
Initialize all transient data that could not be deserialized.
init() - Method in class edu.jhu.ece.iacl.jist.pipeline.PipeParentPort
Initialize port to always be a parent port.
init() - Method in class edu.jhu.ece.iacl.jist.pipeline.PipePort
Initialized data that could not be deserialized.
init() - Method in class edu.jhu.ece.iacl.jist.pipeline.PipeScheduler.CleanAllDialog
Inits the.
init() - Method in class edu.jhu.ece.iacl.jist.pipeline.PipeScheduler
Generate list of contexts parsed on sources.
init(PipeJGraph) - Method in class edu.jhu.ece.iacl.jist.pipeline.PipeSource
Initialize fields that could not be deserialized.
init(File) - Method in class edu.jhu.ece.iacl.jist.pipeline.ProcessingAlgorithm
Initialize parameters and algorithm.
init(PipeAlgorithm) - Method in class edu.jhu.ece.iacl.jist.pipeline.ProcessingAlgorithm
Initialize parameters and algorithm.
init(File) - Method in class edu.jhu.ece.iacl.jist.pipeline.ProcessingDialog
Initialize parameters and algorithm from file.
init(PipeAlgorithm) - Method in class edu.jhu.ece.iacl.jist.pipeline.ProcessingDialog
Initialize parameter and algorithm from existing algorithm.
init(File) - Method in class edu.jhu.ece.iacl.jist.pipeline.ProcessingGroupDialog
Initialize parameters and algorithm from file.
init(PipeAlgorithm) - Method in class edu.jhu.ece.iacl.jist.pipeline.ProcessingGroupDialog
Initialize parameter and algorithm from existing algorithm.
init() - Method in class edu.jhu.ece.iacl.jist.pipeline.view.input.ParamCollectionInputView
Initialize view with custom layout.
init(ParamCollection, LayoutManager) - Method in class edu.jhu.ece.iacl.jist.pipeline.view.input.ParamCollectionInputView
Initialize view.
init() - Method in class edu.jhu.ece.iacl.jist.pipeline.view.input.ParamCollectionPipelineInputView
Initialize input view.
init(File) - Method in class edu.jhu.ece.iacl.jist.plugins.MedicAlgorithmExecutableAdapter
Initialize parameters and algorithm.
init(PipeAlgorithm) - Method in class edu.jhu.ece.iacl.jist.plugins.MedicAlgorithmExecutableAdapter
Initialize parameters and algorithm.
init(File) - Method in class edu.jhu.ece.iacl.jist.plugins.MedicAlgorithmJistLayoutAdapter
Initialize parameters and algorithm.
init(PipeAlgorithm) - Method in class edu.jhu.ece.iacl.jist.plugins.MedicAlgorithmJistLayoutAdapter
Initialize parameters and algorithm.
init(File) - Method in class edu.jhu.ece.iacl.jist.plugins.MedicAlgorithmMipavAdapter
Initialize parameters and algorithm.
init(PipeAlgorithm) - Method in class edu.jhu.ece.iacl.jist.plugins.MedicAlgorithmMipavAdapter
Initialize parameters and algorithm.
init(EmbeddedSurface) - Method in class edu.jhu.ece.iacl.jist.structures.geom.CollisionDetection
Inits the.
init() - Method in class edu.jhu.ece.iacl.jist.test.JistTestHarness
Inits the.
initDRMAASession() - Method in class edu.jhu.ece.iacl.jist.processcontrol.DispatchController
Inits the drmaa session.
initialize(Optimizable1DContinuous) - Method in class edu.jhu.bme.smile.commons.optimize.BrentMethod1D
Initialize the optimizer with the 1D function.
initialize(OptimizableNDContinuous, double[], double) - Method in class edu.jhu.bme.smile.commons.optimize.DownhillSimplexND
Initializes the optimizer with a function and an initial guess.
initialize(OptimizableNDContinuous) - Method in class edu.jhu.bme.smile.commons.optimize.DownhillSimplexND
Default initialize method.
initialize(Optimizable1DContinuous) - Method in class edu.jhu.bme.smile.commons.optimize.GoldenSectionSearch1D
Sets up the optimization.
initialize(OptimizableNDContinuousDifferentiable, double[]) - Method in class edu.jhu.bme.smile.commons.optimize.LevenbergMarquardt
Initializes the optimizer with a differentiable ND function.
initialize(OptimizableNDContinuousDifferentiable) - Method in class edu.jhu.bme.smile.commons.optimize.LevenbergMarquardt
Initializes the optimizer with a differentiable ND function.
initialize(OptimizableNDContinuous) - Method in class edu.jhu.bme.smile.commons.optimize.LineSearchND
Initialize the optimizer with the ND function.
initialize(OptimizableNDContinuous, double[]) - Method in class edu.jhu.bme.smile.commons.optimize.LineSearchND
Initialize the optimizer with the ND function.
initialize(OptimizableNDContinuousDifferentiable) - Method in class edu.jhu.bme.smile.commons.optimize.LineSearchNDDifferentiable
Initialize the optimizer with the Differentiable ND function
initialize(OptimizableNDContinuousDifferentiable, double[]) - Method in class edu.jhu.bme.smile.commons.optimize.LineSearchNDDifferentiable
Initialize the optimizer with the ND Differentiable function.
initialize(Optimizable1DContinuousDifferentiable) - Method in class edu.jhu.bme.smile.commons.optimize.NewtonMethod1D
Initialize the optimizer with the Differentiable 1D function.
initialize(Optimizable1DContinuousDifferentiable, double) - Method in class edu.jhu.bme.smile.commons.optimize.NewtonMethod1D
Initialize the optimizer with the Differentiable 1D function.
initialize(Optimizable1DContinuous) - Method in interface edu.jhu.bme.smile.commons.optimize.Optimizer1DContinuous
Initializes an Optimizable1DContinuous function.
initialize(Optimizable1DContinuousDifferentiable) - Method in interface edu.jhu.bme.smile.commons.optimize.Optimizer1DContinuousDifferentiable
Initializes an Optimizable1DContinuousDifferentiable function.
initialize(OptimizableNDContinuous) - Method in interface edu.jhu.bme.smile.commons.optimize.OptimizerNDContinuous
Initializes an OptimizableNDContinuous function.
initialize(OptimizableNDContinuousDifferentiable) - Method in interface edu.jhu.bme.smile.commons.optimize.OptimizerNDContinuousDifferentiable
Initializes an OptimizableNDContinuousDifferentiable function.
initialize(float) - Method in class edu.jhu.ece.iacl.algorithms.manual_label.staple.PerformanceLevel
Initialize all performance levels the the same value.
initialize(double) - Method in class edu.jhu.ece.iacl.algorithms.manual_label.staple.PerformanceLevel
 
initialize() - Method in class edu.jhu.ece.iacl.algorithms.manual_label.staple.STAPLE
 
initialize() - Method in class edu.jhu.ece.iacl.algorithms.manual_label.staple.STAPLEgeneral
 
initialize() - Method in class edu.jhu.ece.iacl.algorithms.manual_label.staple.STAPLEgeneralSingle
 
initialize() - Method in class edu.jhu.ece.iacl.algorithms.manual_label.staple.STAPLEmulti
 
initialize() - Method in class edu.jhu.ece.iacl.algorithms.manual_label.staple.STAPLEmulti2
 
initialize() - Method in class edu.jhu.ece.iacl.algorithms.manual_label.staple.STAPLEsingle
 
initialize() - Method in class edu.jhu.ece.iacl.algorithms.manual_label.staple.STAPLEsurf
 
initialize2(float) - Method in class edu.jhu.ece.iacl.algorithms.manual_label.staple.PerformanceLevel
 
initialize2(double) - Method in class edu.jhu.ece.iacl.algorithms.manual_label.staple.PerformanceLevel
 
initializeBoundary(float) - Method in class edu.jhu.ece.iacl.algorithms.manual_label.FastMarchingLabelExtension
 
initializedCount - Variable in class edu.jhu.ece.iacl.jist.pipeline.PipeScheduler
Counter to indicate the number of initialized experiments.
initializeHistograms() - Method in class edu.jhu.ece.iacl.algorithms.vabra.ImagePairNMI
 
initializeSingle() - Method in class edu.jhu.ece.iacl.algorithms.manual_label.staple.STAPLE
 
initializing - Variable in class edu.jhu.ece.iacl.jist.pipeline.PipeLayout
flag indicating that layout is initializing and should not be edited.
initializing - Variable in class edu.jhu.ece.iacl.jist.pipeline.PipeScheduler
Flag indicating the scheduler is initializing.
initModules(ProgressMonitor) - Method in class edu.jhu.ece.iacl.jist.pipeline.PipeLibrary
Find and initialize modules from library directory.
initNarrowBand(ImageDataFloat) - Method in class edu.jhu.cs.cisst.algorithms.segmentation.gac.GeodesicActiveContour2D
Initializes the narrow band.
initScheduler(PipeLayout) - Method in class edu.jhu.ece.iacl.jist.pipeline.gui.ProcessManager
Initlaize manager.
initTransforms1() - Method in class edu.jhu.ece.iacl.algorithms.dti.DWICoReg
 
initTransforms2() - Method in class edu.jhu.ece.iacl.algorithms.dti.DWICoReg
 
initType - Variable in class edu.jhu.ece.iacl.algorithms.manual_label.staple.STAPLEmulti
 
initType - Variable in class edu.jhu.ece.iacl.algorithms.manual_label.staple.STAPLEmulti2
 
initType - Variable in class edu.jhu.ece.iacl.algorithms.manual_label.staple.STAPLEsurf
 
innerIterations - Variable in class edu.jhu.cs.cisst.algorithms.segmentation.gac.GeodesicActiveContour2D
The inner iterations.
input - Static variable in class DiscoverMipavJISTPlugins
 
INPUT_TAG - Static variable in class edu.jhu.ece.iacl.jist.pipeline.parser.LoniPipeParser
The Constant INPUT_TAG.
inputAliases - Variable in class edu.jhu.ece.iacl.jist.pipeline.parser.LoniPipeParser
The input aliases.
inputFile - Variable in class edu.jhu.ece.iacl.jist.pipeline.ExecutionContext
The input file.
inputHash - Variable in class edu.jhu.ece.iacl.jist.pipeline.PipeModule
Input hash representing map from child parameter name to parameter.
inputParams - Variable in class edu.jhu.ece.iacl.jist.pipeline.ExecutionContext
The input parameters.
inputParams - Variable in class edu.jhu.ece.iacl.jist.pipeline.PipeModule
Input parameters, some of which may not be visible.
inputParams - Variable in class edu.jhu.ece.iacl.jist.pipeline.ProcessingAlgorithm
The input parameters.
inputPorts - Variable in class edu.jhu.ece.iacl.jist.pipeline.PipeModule
Input and output ports for module.
inputView - Variable in class edu.jhu.ece.iacl.jist.pipeline.factory.ParamFactory
Input view for parameter.
inputView - Variable in class edu.jhu.ece.iacl.jist.pipeline.ProcessingDialog
View for input parameters.
insert(DraggableNode, Point) - Method in class edu.jhu.ece.iacl.jist.pipeline.graph.PipeJGraph
Insert.
insert(DraggableNode) - Method in class edu.jhu.ece.iacl.jist.pipeline.gui.PipeInternalFrame
Insert draggable node into graph.
insert(DraggableNode, Point) - Method in class edu.jhu.ece.iacl.jist.pipeline.gui.PipeInternalFrame
Insert node into graph.
insertIntoPath(DefaultMutableTreeNode, String, DefaultMutableTreeNode) - Method in class edu.jhu.ece.iacl.jist.pipeline.gui.ModuleTreePanel
 
insertIntoProperQueue(ExecutionContext) - Method in class edu.jhu.ece.iacl.jist.pipeline.PipeScheduler
Insert experiment into proper queue based on experiment status.
inside(PT) - Method in class edu.jhu.ece.iacl.jist.structures.geom.BndBox
Inside.
insideCount - Variable in class edu.jhu.cs.cisst.algorithms.segmentation.gac.GeodesicActiveContour2D
The inside point count.
insidePoints - Variable in class edu.jhu.cs.cisst.algorithms.segmentation.gac.GeodesicActiveContour2D
The inside points.
installListeners(JGraph) - Method in class edu.jhu.ece.iacl.jist.pipeline.gui.PipeInternalFrame
Install listeners.
integerParam - Variable in class edu.jhu.ece.iacl.jist.pipeline.src.PipeIntegerCollectionListSource
The integer param.
integerParam - Variable in class edu.jhu.ece.iacl.jist.pipeline.src.PipeIntegerListSource
The integer param.
integrate() - Method in class edu.jhu.bme.smile.commons.math.Spline
 
INTENSIVE_I - Static variable in class edu.jhu.ece.iacl.jist.utility.JistLogger
 
INTENSIVE_II - Static variable in class edu.jhu.ece.iacl.jist.utility.JistLogger
 
INTENSIVE_III - Static variable in class edu.jhu.ece.iacl.jist.utility.JistLogger
 
internalFrameActivated(InternalFrameEvent) - Method in class edu.jhu.ece.iacl.jist.pipeline.gui.LayoutPanel
 
internalFrameActivated(InternalFrameEvent) - Method in class edu.jhu.ece.iacl.jist.pipeline.gui.PipeInternalFrame
Internal frame activated.
internalFrameClosed(InternalFrameEvent) - Method in class edu.jhu.ece.iacl.jist.pipeline.gui.LayoutPanel
Remove frame from list if frame is closed.
internalFrameClosing(InternalFrameEvent) - Method in class edu.jhu.ece.iacl.jist.pipeline.gui.LayoutPanel
Close frame if possible.
internalFrameDeactivated(InternalFrameEvent) - Method in class edu.jhu.ece.iacl.jist.pipeline.gui.LayoutPanel
 
internalFrameDeiconified(InternalFrameEvent) - Method in class edu.jhu.ece.iacl.jist.pipeline.gui.LayoutPanel
 
internalFrameIconified(InternalFrameEvent) - Method in class edu.jhu.ece.iacl.jist.pipeline.gui.LayoutPanel
 
internalFrameOpened(InternalFrameEvent) - Method in class edu.jhu.ece.iacl.jist.pipeline.gui.LayoutPanel
 
interp(Tuple3f, Tuple3f, double) - Static method in class edu.jhu.ece.iacl.jist.algorithms.graphics.GeomUtil
Interp.
interpolate(ConstBoundaryGrid, SolverResolutionLevels) - Method in interface edu.jhu.cs.cisst.algorithms.optimize.fmg.interpolator.Interpolator
interpolates a function sampled on a specific grid to the next finer grid
interpolate(ConstBoundaryGrid, SolverResolutionLevels) - Method in class edu.jhu.cs.cisst.algorithms.optimize.fmg.interpolator.InterpolatorByStencil
implements method from Interpolator.
interpolate(double, double, float[][], int, int) - Static method in class edu.jhu.cs.cisst.algorithms.util.DataOperations
Interpolate.
interpolate(double, double, double, float[][][], int, int, int) - Static method in class edu.jhu.cs.cisst.algorithms.util.DataOperations
Interpolate.
interpolate(double, double, double, ConstGrid, int, int, int) - Static method in class edu.jhu.cs.cisst.algorithms.util.DataOperations
Interpolate.
interpolate(double) - Method in class edu.jhu.ece.iacl.jist.structures.geom.PolySpline
Interpolate.
interpolateProper(BoundaryGrid, ConstBoundaryGrid, int, int) - Method in class edu.jhu.cs.cisst.algorithms.optimize.fmg.interpolator.InterpolatorByStencil
implements the parallel part of interpolate().
interpolateTriliear(double[], double[], double[]) - Method in class edu.jhu.ece.iacl.algorithms.dti.tractography.FACT.FloatInterp
 
Interpolation(ImageData[], int, int, int, int, double, double, double, double[], int[]) - Static method in class edu.jhu.ece.iacl.algorithms.registration.RegistrationUtilities
 
Interpolation(ImageData, int, int, int, double, double, double, int) - Static method in class edu.jhu.ece.iacl.algorithms.registration.RegistrationUtilities
 
interpolation - Variable in class edu.jhu.ece.iacl.plugins.utilities.volume.MedicAlgorithmMipavReorient
 
Interpolator - Interface in edu.jhu.cs.cisst.algorithms.optimize.fmg.interpolator
This interface defines the interpolate() method which produces a fine grid from the next coarser grid by interpolation.
InterpolatorByStencil - Class in edu.jhu.cs.cisst.algorithms.optimize.fmg.interpolator
An interpolator that operates according to an interpolation stencil.
InterpolatorByStencil(Stencil) - Constructor for class edu.jhu.cs.cisst.algorithms.optimize.fmg.interpolator.InterpolatorByStencil
construct from interpolation stencil.
InterpType - Variable in class edu.jhu.ece.iacl.algorithms.vabra.VectorVolumeVabra
 
interpVec(Point3f) - Method in class edu.jhu.ece.iacl.algorithms.dti.tractography.FACT.FACTparameters
 
intersect(BndBox) - Method in class edu.jhu.ece.iacl.jist.structures.geom.BndBox
Intersect.
intersect(PT, PT) - Method in class edu.jhu.ece.iacl.jist.structures.geom.Polygon
Intersect.
intersect(PT, PT) - Method in class edu.jhu.ece.iacl.jist.structures.geom.TriangleSigned
Intersect.
intersectHistory - Variable in class edu.jhu.ece.iacl.jist.structures.geom.EmbeddedPointSet.PointLocatorResult
The intersect history.
intersectionAngle(Vector3f, Vector3f, Vector3f, Vector3f) - Static method in class edu.jhu.ece.iacl.jist.algorithms.graphics.GeomUtil
Intersection angle.
intersectionNormal - Variable in class edu.jhu.ece.iacl.jist.structures.geom.IntersectResult
The intersection normal.
intersectionPoint - Variable in class edu.jhu.ece.iacl.jist.structures.geom.IntersectResult
The intersection point.
intersectionTime(Tuple2d, Tuple2d, Tuple2d, Tuple2d) - Static method in class edu.jhu.ece.iacl.jist.algorithms.graphics.GeomUtil
Intersection time.
intersectRayDistance(Point3d, Vector3d) - Method in class edu.jhu.ece.iacl.jist.structures.geom.CollisionDetection
Intersect ray distance.
intersectRayPoint(Point3d, Vector3d) - Method in class edu.jhu.ece.iacl.jist.structures.geom.CollisionDetection
Intersect ray point.
intersectRayPoint(Point3f, Vector3f) - Method in class edu.jhu.ece.iacl.jist.structures.geom.CollisionDetection
Intersect ray point.
IntersectResult - Class in edu.jhu.ece.iacl.jist.structures.geom
Created by IntelliJ IDEA.
IntersectResult(PT, float, PT) - Constructor for class edu.jhu.ece.iacl.jist.structures.geom.IntersectResult
Instantiates a new intersect result.
IntersectResult(char, PT) - Constructor for class edu.jhu.ece.iacl.jist.structures.geom.IntersectResult
Instantiates a new intersect result.
intersects(Polygon) - Method in class edu.jhu.ece.iacl.jist.structures.fiber.Fiber
Intersects.
intersectSegmentDistance(Point3d, Point3d) - Method in class edu.jhu.ece.iacl.jist.structures.geom.CollisionDetection
Intersect segment distance.
intersectSegmentPoint(Point3d, Point3d) - Method in class edu.jhu.ece.iacl.jist.structures.geom.CollisionDetection
Intersect segment point.
intersectSegmentPoint(Point3f, Point3f) - Method in class edu.jhu.ece.iacl.jist.structures.geom.CollisionDetection
Intersect segment point.
interSurfaceMapping - Static variable in class edu.jhu.ece.iacl.algorithms.ReferencedPapers
 
IntRange1D - Class in edu.jhu.cs.cisst.algorithms.optimize.fmg.util
A class to represent a one-diensional range of integer values.
IntRange1D(int, int) - Constructor for class edu.jhu.cs.cisst.algorithms.optimize.fmg.util.IntRange1D
construct from lower and upper boundary.
intrinsicParameterization - Static variable in class edu.jhu.ece.iacl.algorithms.ReferencedPapers
 
intValue() - Method in class edu.jhu.ece.iacl.jist.structures.image.Voxel
 
InvalidParameterException - Exception in edu.jhu.ece.iacl.jist.pipeline.parameter
Invalid Parameter Exception is thrown when a parameter value does not validate.
InvalidParameterException(PipePort) - Constructor for exception edu.jhu.ece.iacl.jist.pipeline.parameter.InvalidParameterException
Default constructor.
InvalidParameterException(PipePort, String) - Constructor for exception edu.jhu.ece.iacl.jist.pipeline.parameter.InvalidParameterException
Defautl constructor.
InvalidParameterValueException - Exception in edu.jhu.ece.iacl.jist.pipeline.parameter
Invalid Parameter Value Exception is thrown when the setValue() method is used for an invalid data type.
InvalidParameterValueException(ParamModel, Object) - Constructor for exception edu.jhu.ece.iacl.jist.pipeline.parameter.InvalidParameterValueException
Instantiates a new invalid parameter value exception.
inverse() - Method in class edu.jhu.bme.smile.commons.math.specialFunctions.ComplexMatrix
 
inverseTransform(SphericalHarmonicRepresentation) - Method in class edu.jhu.bme.smile.commons.math.specialFunctions.SphericalHarmonics
 
inverseTransform(double[]) - Method in class edu.jhu.bme.smile.commons.math.specialFunctions.SphericalHarmonics
 
inverseTransform(double[], double[]) - Method in class edu.jhu.bme.smile.commons.math.specialFunctions.SphericalHarmonics
 
invert3Dmatrix(float[][]) - Static method in class edu.jhmi.rad.medic.utilities.NumericsPublic
Close-form 3D matrix inversion
invertMatrix(float[][], float[][], int) - Static method in class edu.jhmi.rad.medic.utilities.NumericsPublic
This method compute the inverse of a matrix
invertTable(double[][]) - Static method in class edu.jhu.ece.iacl.algorithms.dti.GTCparams
 
InvLogit(float[][][][], int, boolean) - Static method in class edu.jhu.ece.iacl.algorithms.manual_label.atlasing.LogOdds
Computes the probability map corresponding to a point in Log-Odds space The probabilities for each label should be stored in the 4th dimension of the input array.
InvLogit(ImageData, int, boolean, String) - Static method in class edu.jhu.ece.iacl.algorithms.manual_label.atlasing.LogOdds
Computes the probability map corresponding to a point in Log-Odds space The probabilities for each label should be stored in the 4th dimension of the input array.
invoke(File, File) - Method in class edu.jhu.ece.iacl.jist.pipeline.PipeLayoutRunner
Invoke.
invoke(File, File, File) - Method in class edu.jhu.ece.iacl.jist.pipeline.PipeLayoutRunner
Invoke.
invoke(File, File) - Method in class edu.jhu.ece.iacl.jist.pipeline.PipeRunner
Invoke parameter file and save output to specified directory.
invoke(ProcessingAlgorithm) - Method in class edu.jhu.ece.iacl.jist.pipeline.PipeRunner
Invoke processing application.
invoke(ProcessingApplication) - Method in class edu.jhu.ece.iacl.jist.pipeline.PipeRunner
Invoke plug-in by calling run algorithm.
invoke(ProcessingAlgorithm) - Method in class edu.jhu.ece.iacl.jist.test.MipavTestHarness
Invoke.
invoke(ProcessingApplication) - Method in class edu.jhu.ece.iacl.jist.test.MipavTestHarness
Invoke.
invoke(File, File) - Method in class edu.jhu.ece.iacl.jist.test.MipavTestHarness
Invoke.
isAncestorOf(PipeModule) - Method in class edu.jhu.ece.iacl.jist.pipeline.PipeModule
Returns true if this is an ancestor of the specified module.
isAppFrameVisible() - Method in class edu.jhu.ece.iacl.jist.pipeline.MipavViewUserInterface
Accessor to check whether the application frame visible or not.
isAttemptingToConnect() - Method in class edu.jhu.ece.iacl.jist.pipeline.graph.PipePortView.ActivityRenderer
Checks if is attempting to connect.
isAutoMinMax() - Method in class edu.jhu.bme.smile.commons.math.HistogramGenerator
 
isBoundary(int, int, int) - Method in interface edu.jhu.cs.cisst.algorithms.optimize.fmg.grid.ConstGrid
determines if the specified element is at the boundary of the grid.
isBoundary(int, int, int) - Method in class edu.jhu.cs.cisst.algorithms.optimize.fmg.grid.Grid
implements method from ConstGrid.
isCellEditable(EventObject) - Method in class edu.jhu.ece.iacl.jist.pipeline.graph.PipeEdgeRealEditor.EditorDelegate
Returns true if anEvent is not a MouseEvent.
isCellEditable(EventObject) - Method in class edu.jhu.ece.iacl.jist.pipeline.graph.PipeEdgeRealEditor
Forwards the message from the CellEditor to the delegate.
isComparable() - Method in class edu.jhu.ece.iacl.algorithms.volume.CompareVolumes
 
isComparable(ImageData, ImageData) - Method in class edu.jhu.ece.iacl.algorithms.volume.CompareVolumes
 
isCompatible(FileExtensionFilter) - Method in class edu.jhu.ece.iacl.jist.io.FileExtensionFilter
Checks if is compatible.
isCompatible(ParamModel) - Method in class edu.jhu.ece.iacl.jist.pipeline.factory.ParamFactory
Import parameter into existing parameter as long as parameter is not more restrictive than this parameter.
isCompatible() - Method in class edu.jhu.ece.iacl.jist.pipeline.graph.PipePortView.ActivityRenderer
Checks if is compatible.
isCompatible() - Method in class edu.jhu.ece.iacl.jist.pipeline.graph.PortChildView.ActivityRenderer
 
isCompatible() - Method in class edu.jhu.ece.iacl.jist.pipeline.graph.PortInputView.ActivityRenderer
 
isCompatible() - Method in class edu.jhu.ece.iacl.jist.pipeline.graph.PortOutputView.ActivityRenderer
 
isCompatible() - Method in class edu.jhu.ece.iacl.jist.pipeline.graph.PortParentView.ActivityRenderer
 
isCompatible(PipePort) - Method in interface edu.jhu.ece.iacl.jist.pipeline.parameter.CompatibilityChecker
Returns true if two ports are compatible.
isCompatible(PipePort) - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamCollection
Check for compatibility between parameters.
isCompatible(PipePort) - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamColor
Checks if is compatible.
isCompatible(PipePort) - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamExecutable
Always returns false.
isCompatible(PipePort) - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamFile
Returns true if port is compatible with this parameter's extension filter.
isCompatible(PipePort) - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamFileCollection
Returns true if port is compatible with this parameter's extension filter.
isCompatible(PipePort) - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamMatrix
Check compatibility between parameters.
isCompatible(PipePort) - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamModel
Check for compatibility between parameters.
isCompatible(PipePort) - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamNumber
Check compatiblity between parameters.
isCompatible(PipePort) - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamNumberCollection
Returns true if port is compatible with this parameter's extension filter.
isCompatible(PipePort) - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamPointDouble
 
isCompatible(PipePort) - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamPointFloat
 
isCompatible(PipePort) - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamPointInteger
 
isCompatible(PipePort) - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamSurface
 
isCompatible(PipePort) - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamSurfaceCollection
 
isCompatible(PipePort) - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamVolume
 
isCompatible(PipePort) - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamVolumeCollection
 
isCompatible(PipePort) - Method in class edu.jhu.ece.iacl.jist.pipeline.PipeChildPort
Only allow child ports to connect to parent ports.
isCompatible(PipePort, PipePort) - Static method in class edu.jhu.ece.iacl.jist.pipeline.PipeConnector
Returns true if source port can be safely connected to destination port and the connection will not create loops in the graph.
isCompatible(PipePort) - Method in class edu.jhu.ece.iacl.jist.pipeline.PipeParentPort
Return true if other port is child port.
isCompatible(PipePort) - Method in class edu.jhu.ece.iacl.jist.pipeline.PipePort
Check if port is compatible with other port.
isCompleted() - Method in class edu.jhu.ece.iacl.jist.pipeline.AbstractCalculation
True if completed units equals total computational units.
isCompleted() - Method in class edu.jhu.ece.iacl.jist.pipeline.ExecutionContext
Check if algorithm has completed by checking if the output file exists.
isCompleted() - Method in class edu.jhu.ece.iacl.jist.pipeline.PipeScheduler
Checks if is completed.
isConnected() - Method in class edu.jhu.ece.iacl.jist.pipeline.graph.PipePortView.ActivityRenderer
Checks if is connected.
isConnected() - Method in class edu.jhu.ece.iacl.jist.pipeline.PipePort
Returns true if this port is connected to another port.
isConnectedTo(PipePort) - Method in class edu.jhu.ece.iacl.jist.pipeline.PipePort
Returns true if this port is connected to the specified port.
isConnectible() - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamModel
returns true if connector can connect to this parameter.
isConnectible() - Method in class edu.jhu.ece.iacl.jist.pipeline.PipePort
Returns true if this port is connectible.
isConvereged() - Method in class edu.jhu.bme.smile.commons.math.L1LSCompressedSensing
 
isCurrent() - Method in class edu.jhu.ece.iacl.jist.pipeline.PipeLayout
Detect if current version of layout is most current.
isDataFlavorSupported(DataFlavor) - Method in class edu.jhu.ece.iacl.jist.pipeline.tree.DraggableNode
Returns true if data flavor is module type.
isDataFlavorSupported(DataFlavor) - Method in class edu.jhu.ece.iacl.jist.pipeline.tree.PackageNode
Returns true if the data flavor is package type.
isDefaultHeader() - Method in class edu.jhu.ece.iacl.jist.structures.image.ImageHeader
Checks if is default header.
isDescendantOf(PipeModule) - Method in class edu.jhu.ece.iacl.jist.pipeline.PipeModule
Returns true if this is a descendant of the specified module.
isDirty() - Method in class edu.jhu.ece.iacl.jist.pipeline.PipeLayout
Returns true if layout has changed since last save.
isEditable() - Method in class edu.jhu.ece.iacl.jist.pipeline.AlgorithmInformation
Returns true if editable.
isEditable() - Method in class edu.jhu.ece.iacl.jist.pipeline.tree.PackageNode
Returns true if package name is editable.
isEmpty() - Method in class edu.jhu.ece.iacl.jist.structures.data.BinaryMinFastHeap
Test if the priority queue is logically empty.
isEmpty() - Method in class edu.jhu.ece.iacl.jist.structures.data.BinaryMinHeap
Test if the priority queue is logically empty.
isFinite(float) - Static method in class edu.jhu.bme.smile.commons.math.FieldRegularize
 
isForceMarqueeEvent(MouseEvent) - Method in class edu.jhu.ece.iacl.jist.pipeline.graph.PipeMarqueeHandler
 
isGroup - Variable in class edu.jhu.ece.iacl.jist.pipeline.graph.PipeAlgorithmGroupView.ActivityRenderer
Specifies whether the current view is a rich text value, and if the image should be stretched.
isGroup - Variable in class edu.jhu.ece.iacl.jist.pipeline.graph.PipeAlgorithmView.ActivityRenderer
Specifies whether the current view is a rich text value, and if the image should be stretched.
isHidden() - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamHidden
Always returns false.
isHidden() - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamModel
Returns true if parameter is hidden.
isIgnoreRefresh() - Method in class edu.jhu.ece.iacl.jist.pipeline.gui.ParameterPanel
Returns true if panel is currently ignoring refreshing.
isinBounds(GridPt) - Method in class edu.jhu.ece.iacl.algorithms.manual_label.LabelImage
 
isInitialized() - Static method in class edu.jhu.ece.iacl.jist.pipeline.gui.PipelineLayoutTool
 
isInitializing() - Method in class edu.jhu.ece.iacl.jist.pipeline.PipeLayout
Returns true if layout is initializing and should not be edited.
isInitializing() - Method in class edu.jhu.ece.iacl.jist.pipeline.PipeScheduler
Indicates the scheduler is initializing.
isInputPort() - Method in class edu.jhu.ece.iacl.jist.pipeline.PipePort
Returns true if this is an input port.
isInside(Point3d) - Method in class edu.jhu.ece.iacl.jist.structures.geom.CollisionDetection
Checks if is inside.
isInterior(int, int, int) - Method in interface edu.jhu.cs.cisst.algorithms.optimize.fmg.grid.ConstGrid
determines if the specified element is in the interior of the grid.
isInterior(int, int, int) - Method in class edu.jhu.cs.cisst.algorithms.optimize.fmg.grid.Grid
implements method from ConstGrid.
isLogScale() - Method in class edu.jhu.bme.smile.commons.math.HistogramGenerator
 
isMandatory() - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamFileCollection
File field is mandatory.
isMandatory() - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamModel
File field is mandatory.
isMandatory() - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamNumberCollection
Number field is mandatory.
isNotAvailable() - Method in class edu.jhu.ece.iacl.jist.structures.image.ImageData
 
isNotAvailable() - Method in class edu.jhu.ece.iacl.jist.structures.image.ImageDataByte
 
isNotAvailable() - Method in class edu.jhu.ece.iacl.jist.structures.image.ImageDataColor
 
isNotAvailable() - Method in class edu.jhu.ece.iacl.jist.structures.image.ImageDataDouble
 
isNotAvailable() - Method in class edu.jhu.ece.iacl.jist.structures.image.ImageDataFloat
 
isNotAvailable() - Method in class edu.jhu.ece.iacl.jist.structures.image.ImageDataInt
 
isNotAvailable() - Method in class edu.jhu.ece.iacl.jist.structures.image.ImageDataMipav
 
isNotAvailable() - Method in class edu.jhu.ece.iacl.jist.structures.image.ImageDataNumber
 
isNotAvailable() - Method in class edu.jhu.ece.iacl.jist.structures.image.ImageDataUByte
 
IsoContourGenerator - Class in edu.jhu.cs.cisst.algorithms.geometry.surface
The Iso-Contour generator generates 2D curves representing closed contours.
IsoContourGenerator() - Constructor for class edu.jhu.cs.cisst.algorithms.geometry.surface.IsoContourGenerator
Instantiates a new iso contour generator.
IsoContourGenerator(AbstractCalculation) - Constructor for class edu.jhu.cs.cisst.algorithms.geometry.surface.IsoContourGenerator
Instantiates a new iso contour generator.
IsoContourGenerator.Edge - Class in edu.jhu.cs.cisst.algorithms.geometry.surface
The Class Edge stores vertex ids.
IsoContourGenerator.Edge() - Constructor for class edu.jhu.cs.cisst.algorithms.geometry.surface.IsoContourGenerator.Edge
Instantiates a new edge.
IsoContourGenerator.Edge(int, int) - Constructor for class edu.jhu.cs.cisst.algorithms.geometry.surface.IsoContourGenerator.Edge
Instantiates a new edge.
IsoContourGenerator.EdgeSplit - Class in edu.jhu.cs.cisst.algorithms.geometry.surface
The Class EdgeSplit is a container to describe a level set crossing point.
IsoContourGenerator.EdgeSplit(Point2i, Point2i) - Constructor for class edu.jhu.cs.cisst.algorithms.geometry.surface.IsoContourGenerator.EdgeSplit
Instantiates a new edge split.
IsoContourGenerator.Winding - Enum in edu.jhu.cs.cisst.algorithms.geometry.surface
The winding order for triangle vertices.
isoLevel - Variable in class edu.jhu.cs.cisst.algorithms.geometry.surface.IsoContourGenerator
The iso level.
isoLevel - Variable in class edu.jhu.cs.cisst.algorithms.geometry.surface.IsoSurfaceGenerator
The target iso-level.
isoLevel - Variable in class edu.jhu.cs.cisst.vent.renderer.processing.VolumeIsoContourRenderer
The iso level.
isoLevelParam - Variable in class edu.jhu.cs.cisst.plugins.utilities.surface.PlugInIsoContourGenerator
 
isoLevelParam - Variable in class edu.jhu.cs.cisst.plugins.utilities.surface.PlugInIsoSurfaceGenerator
 
isolevelParam - Variable in class edu.jhu.cs.cisst.vent.renderer.processing.VolumeIsoContourRenderer
The iso-level parameter.
IsoSurfaceGenerator - Class in edu.jhu.cs.cisst.algorithms.geometry.surface
The IsoSurface Generator generates an iso-surface using either the marching-cubes or marching-tetrahedral algorithm.
IsoSurfaceGenerator() - Constructor for class edu.jhu.cs.cisst.algorithms.geometry.surface.IsoSurfaceGenerator
Instantiates a new iso surface generator.
IsoSurfaceGenerator(AbstractCalculation) - Constructor for class edu.jhu.cs.cisst.algorithms.geometry.surface.IsoSurfaceGenerator
Instantiates a new iso surface generator.
IsoSurfaceGenerator.EdgeSplit - Class in edu.jhu.cs.cisst.algorithms.geometry.surface
The Class EdgeSplit is a container to describe a level set crossing point.
IsoSurfaceGenerator.EdgeSplit(Point3i, Point3i) - Constructor for class edu.jhu.cs.cisst.algorithms.geometry.surface.IsoSurfaceGenerator.EdgeSplit
Instantiates a new edge split.
IsoSurfaceGenerator.Method - Enum in edu.jhu.cs.cisst.algorithms.geometry.surface
The Iso-surface generation method
IsoSurfaceGenerator.Triangle - Class in edu.jhu.cs.cisst.algorithms.geometry.surface
The Class Triangle stores vertex ids.
IsoSurfaceGenerator.Triangle() - Constructor for class edu.jhu.cs.cisst.algorithms.geometry.surface.IsoSurfaceGenerator.Triangle
Instantiates a new triangle.
IsoSurfaceGenerator.Winding - Enum in edu.jhu.cs.cisst.algorithms.geometry.surface
The winding order for triangle vertices.
IsotropicResample - Class in edu.jhu.ece.iacl.algorithms.volume
 
IsotropicResample() - Constructor for class edu.jhu.ece.iacl.algorithms.volume.IsotropicResample
 
IsotropicResample.InterpolationMethod - Enum in edu.jhu.ece.iacl.algorithms.volume
 
isOutOfSync() - Method in class edu.jhu.ece.iacl.jist.pipeline.ExecutionContext
Return true if file is out of sync.
isOutputPort() - Method in class edu.jhu.ece.iacl.jist.pipeline.PipePort
Returns true if this is an output port.
isPlugInFrameVisible() - Method in class edu.jhu.ece.iacl.jist.pipeline.MipavViewUserInterface
Accessor to see if a stand-alone plugin frame is visible (not app frame).
isProbability() - Method in class edu.jhu.bme.smile.commons.math.HistogramGenerator
 
isPtinBounds(GridPt) - Method in class edu.jhu.ece.iacl.algorithms.manual_label.LabelImage
 
isPtinBounds(int[][][], GridPt) - Static method in class edu.jhu.ece.iacl.algorithms.manual_label.LabelImage
 
isQuiet() - Static method in class edu.jhmi.rad.medic.utilities.MedicUtilPublic
Checks if is quiet.
isQuiet() - Static method in class edu.jhu.ece.iacl.jist.io.MipavController
Checks if is quiet.
isReady() - Method in class edu.jhu.ece.iacl.jist.pipeline.ExecutionContext
Check if algorithm is ready to run by validating the input parameters for this context that are read from an input file.
isReset - Variable in class edu.jhu.ece.iacl.jist.pipeline.PipeSource
Flag for source is reset after iterating through all parameter values.
isRobustMinMax() - Method in class edu.jhu.bme.smile.commons.math.HistogramGenerator
 
isRoot() - Method in class edu.jhu.ece.iacl.jist.pipeline.PipeAlgorithm
Return true if this module doesn't have any parents who are Processing Algorithms.
isRoot() - Method in class edu.jhu.ece.iacl.jist.pipeline.PipeModule
Returns true if this module has no incoming connections.
isRoot() - Method in class edu.jhu.ece.iacl.jist.pipeline.PipeSource
Returns true if this source is a root.
isRunning() - Method in class edu.jhu.ece.iacl.jist.pipeline.PipeScheduler
Indicates that the scheduler is running.
isRunningInSeparateProcess() - Method in class edu.jhu.ece.iacl.jist.pipeline.ProcessingAlgorithm
Checks if is running in separate process.
isSameOrientation(ImageHeader) - Method in class edu.jhu.ece.iacl.jist.structures.image.ImageHeader
Compares the orientation of this header with another header.
isSameResolution(ImageHeader) - Method in class edu.jhu.ece.iacl.jist.structures.image.ImageHeader
Compares the resolution of this header with another header.
isSegment() - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.DataLabel
Returns true if segmented.
isSwitchSpaced() - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamSwitch
Returns true if there is a space after the switch.
isUseGridEngine() - Method in class edu.jhu.ece.iacl.jist.pipeline.JistPreferences
Checks if is use grid engine.
isUseGridEngine() - Method in class edu.jhu.ece.iacl.jist.pipeline.PipeLayout.RunParameters
Checks if is use grid engine.
isUsingWorker() - Method in class edu.jhu.ece.iacl.jist.pipeline.gui.ProcessManager
 
isUsingWorker() - Method in class edu.jhu.ece.iacl.jist.pipeline.PipeScheduler
Checks if is using worker.
isValid() - Method in class edu.jhu.ece.iacl.jist.pipeline.graph.PipePortView.ActivityRenderer
 
item - Variable in class edu.jhu.ece.iacl.jist.pipeline.gui.PipeInternalFrame.EventRedirector
The item.
iterate() - Method in class edu.jhu.ece.iacl.algorithms.manual_label.staple.STAPLE
 
iterate() - Method in class edu.jhu.ece.iacl.algorithms.manual_label.staple.STAPLEgeneral
 
iterate() - Method in class edu.jhu.ece.iacl.algorithms.manual_label.staple.STAPLEgeneralSingle
 
iterate() - Method in class edu.jhu.ece.iacl.algorithms.manual_label.staple.STAPLEmulti
 
iterate() - Method in class edu.jhu.ece.iacl.algorithms.manual_label.staple.STAPLEmulti2
 
iterate() - Method in class edu.jhu.ece.iacl.algorithms.manual_label.staple.STAPLEsingle
 
iterate() - Method in class edu.jhu.ece.iacl.algorithms.manual_label.staple.STAPLEsurf
 
iterate(ProgressMonitor) - Method in class edu.jhu.ece.iacl.jist.pipeline.dest.PipeAssertionTestDestination
 
iterate(ProgressMonitor) - Method in class edu.jhu.ece.iacl.jist.pipeline.dest.PipeDoubleCollectionExternalDestination
Iterate through objects.
iterate(ProgressMonitor) - Method in class edu.jhu.ece.iacl.jist.pipeline.dest.PipeDoubleExternalDestination
Iterate through objects.
iterate(ProgressMonitor) - Method in class edu.jhu.ece.iacl.jist.pipeline.dest.PipeExternalDestination
Iterate through objects.
iterate(ProgressMonitor) - Method in class edu.jhu.ece.iacl.jist.pipeline.dest.PipeFileCollectionExternalDestination
Iterate through objects.
iterate(ProgressMonitor) - Method in class edu.jhu.ece.iacl.jist.pipeline.dest.PipeFileExternalDestination
Iterate through objects.
iterate(ProgressMonitor) - Method in class edu.jhu.ece.iacl.jist.pipeline.dest.PipeIntegerCollectionExternalDestination
Iterate through objects.
iterate(ProgressMonitor) - Method in class edu.jhu.ece.iacl.jist.pipeline.dest.PipeIntegerExternalDestination
Iterate through objects.
iterate(ProgressMonitor) - Method in class edu.jhu.ece.iacl.jist.pipeline.dest.PipeParamCopyDestination
Iterate through all active experiments and the save the output of each to a specified location.
iterate(ProgressMonitor) - Method in class edu.jhu.ece.iacl.jist.pipeline.dest.PipeParamSummaryDestination
Iterate through objects.
iterate(ProgressMonitor) - Method in class edu.jhu.ece.iacl.jist.pipeline.dest.PipeSurfaceCollectionExternalDestination
Iterate through objects.
iterate(ProgressMonitor) - Method in class edu.jhu.ece.iacl.jist.pipeline.dest.PipeSurfaceExternalDestination
Iterate through objects.
iterate(ProgressMonitor) - Method in class edu.jhu.ece.iacl.jist.pipeline.dest.PipeVolumeCollectionExternalDestination
Iterate through objects.
iterate(ProgressMonitor) - Method in class edu.jhu.ece.iacl.jist.pipeline.dest.PipeVolumeExternalDestination
Iterate through objects.
iterate(ProgressMonitor) - Method in class edu.jhu.ece.iacl.jist.pipeline.PipeDestination
Iterate through destination values.
iterate(Vector<PipeSource>) - Method in class edu.jhu.ece.iacl.jist.pipeline.PipeScheduler
Iterate through all values for sources.
iterate() - Method in class edu.jhu.ece.iacl.jist.pipeline.PipeSource
Iterate through all parameter values and all child parameter values.
iterate() - Method in class edu.jhu.ece.iacl.jist.pipeline.src.PipeDoubleSweepSource
Iterate through double values.
iterate() - Method in class edu.jhu.ece.iacl.jist.pipeline.src.PipeExternalSource
 
iterate() - Method in class edu.jhu.ece.iacl.jist.pipeline.src.PipeFileCollectionSource
Iterate through files.
iterate() - Method in class edu.jhu.ece.iacl.jist.pipeline.src.PipeFileDirectorySource
Iterate through files.
iterate() - Method in class edu.jhu.ece.iacl.jist.pipeline.src.PipeIntegerSweepSource
 
iterate() - Method in class edu.jhu.ece.iacl.jist.pipeline.src.PipeListCollectionSource
Iterate.
iterate() - Method in class edu.jhu.ece.iacl.jist.pipeline.src.PipeListSource
Iterate.
iterate() - Method in class edu.jhu.ece.iacl.jist.pipeline.src.PipePointDoubleSweepSource
Iterate through double values.
iterate() - Method in class edu.jhu.ece.iacl.jist.pipeline.src.PipeSelectionSource
Iterate.
iterate() - Method in class edu.jhu.ece.iacl.jist.pipeline.src.PipeToggleSource
Iterate.
iterate() - Method in class edu.jhu.ece.iacl.jist.pipeline.src.PipeVolumeDirectoryCollectionSource
 
iterations - Static variable in class edu.jhu.bme.smile.commons.optimize.test.Test1DOptimizations
 
iterations - Static variable in class edu.jhu.bme.smile.commons.optimize.test.TestNDOptimizations
 
ITMAX - Static variable in class edu.jhu.ece.iacl.algorithms.vabra.NumericalRecipes
 

J

jacobianCartesianToSphere(Point3f, Point3f, Point3d, Point2d, Point2d, Point2d, Point2d) - Static method in class edu.jhu.ece.iacl.jist.algorithms.graphics.GeomUtil
Jacobian cartesian to sphere.
jacobianCartesianToStereo(Point3f, Point3f, Point3d, Point2d, Point2d, Point2d) - Static method in class edu.jhu.ece.iacl.jist.algorithms.graphics.GeomUtil
Jacobian cartesian to stereo.
jacobianSphereToStereo(Point2d) - Static method in class edu.jhu.ece.iacl.jist.algorithms.graphics.GeomUtil
Jacobian sphere to stereo.
jacobianStereoToCartesian(Point3f, Point3f, Point3d, Point2d, Point2d, Point2d) - Static method in class edu.jhu.ece.iacl.jist.algorithms.graphics.GeomUtil
Jacobian stereo to cartesian.
jacobianStereoToSphere(Point2d) - Static method in class edu.jhu.ece.iacl.jist.algorithms.graphics.GeomUtil
Jacobian stereo to sphere.
JDialogSaveAll - Class in edu.jhu.ece.iacl.jist.dialogs
The Class JDialogSaveAll.
JDialogSaveAll() - Constructor for class edu.jhu.ece.iacl.jist.dialogs.JDialogSaveAll
Instantiates a new j dialog save all.
jerryPrince - Static variable in class edu.jhu.ece.iacl.algorithms.CommonAuthors
 
JGraphFoldingManager - Class in edu.jhu.ece.iacl.jist.pipeline.graph
Manages the folding and unfolding of groups.
JGraphFoldingManager() - Constructor for class edu.jhu.ece.iacl.jist.pipeline.graph.JGraphFoldingManager
 
jingWan - Static variable in class edu.jhu.ece.iacl.algorithms.CommonAuthors
 
jist.modules - package jist.modules
 
JIST_VERSION - Static variable in class edu.jhu.ece.iacl.jist.pipeline.ProcessingAlgorithm
The Constant MAPS version.
JIST_VERSION_ID - Static variable in class edu.jhu.ece.iacl.jist.pipeline.JistPreferences
Numeric revision for algorithm compatibility
JistCLI - Class in edu.jhu.ece.iacl.jist.cli
 
JistCLI(ProcessingAlgorithm) - Constructor for class edu.jhu.ece.iacl.jist.cli.JistCLI
 
JistCLI(PipeAlgorithm) - Constructor for class edu.jhu.ece.iacl.jist.cli.JistCLI
 
JistDefaultBase - Class in jist.modules
 
JistDefaultBase() - Constructor for class jist.modules.JistDefaultBase
 
JistDefaultPlugins - Class in jist.modules
 
JistDefaultPlugins() - Constructor for class jist.modules.JistDefaultPlugins
 
JISTDynamicPluginLookup - Interface in edu.jhu.ece.iacl.jist.pipeline.parser
 
JISTInternalParam - Interface in edu.jhu.ece.iacl.jist.pipeline.parameter
Interface used to flag options which are strictly internal to the JIST system.
JistLayoutParser - Class in edu.jhu.ece.iacl.jist.pipeline.parser
 
JistLayoutParser() - Constructor for class edu.jhu.ece.iacl.jist.pipeline.parser.JistLayoutParser
 
JistLayoutReaderWriter - Class in edu.jhu.ece.iacl.jist.io
The Class JistLayoutReaderWriter.
JistLayoutReaderWriter() - Constructor for class edu.jhu.ece.iacl.jist.io.JistLayoutReaderWriter
Instantiates a new jist layout reader writer.
JISTLicenseAbout - Class in license
 
JISTLicenseAbout() - Constructor for class license.JISTLicenseAbout
 
JistLogger - Class in edu.jhu.ece.iacl.jist.utility
 
JistLogger() - Constructor for class edu.jhu.ece.iacl.jist.utility.JistLogger
 
JistModulesLocation - Interface in jist.modules
 
JistMSWASSR - Class in edu.jhu.ece.iacl.plugins.spectro
 
JistMSWASSR() - Constructor for class edu.jhu.ece.iacl.plugins.spectro.JistMSWASSR
 
JistMSWASSR.AlgorithmWrapper - Class in edu.jhu.ece.iacl.plugins.spectro
 
JistMSWASSR.AlgorithmWrapper() - Constructor for class edu.jhu.ece.iacl.plugins.spectro.JistMSWASSR.AlgorithmWrapper
 
JistPluginUtil - Class in edu.jhu.ece.iacl.plugins
 
JistPluginUtil() - Constructor for class edu.jhu.ece.iacl.plugins.JistPluginUtil
 
JistPreferences - Class in edu.jhu.ece.iacl.jist.pipeline
MAPS preferences.
JistPreferences() - Constructor for class edu.jhu.ece.iacl.jist.pipeline.JistPreferences
Default constructor.
JistPreferences.NamingConvention - Enum in edu.jhu.ece.iacl.jist.pipeline
The Enum NamingConvention.
JistPreferences.PreferenceListener - Interface in edu.jhu.ece.iacl.jist.pipeline
Listens for changes in preferences.
JistTestHarness - Class in edu.jhu.ece.iacl.jist.test
The Class JistTestHarness.
JistTestHarness(File) - Constructor for class edu.jhu.ece.iacl.jist.test.JistTestHarness
Instantiates a new jist test harness.
johnBogovic - Static variable in class edu.jhu.ece.iacl.algorithms.CommonAuthors
 
jointhistogram(double[], double[], int) - Static method in class edu.jhu.bme.smile.commons.math.StatisticsDouble
Computes the joint histogram using equally spaced bins.
JointHistogram3D(ImageData, ImageData, int, int[], int[][]) - Static method in class edu.jhu.ece.iacl.algorithms.registration.RegistrationUtilities
 
JointHistogram3D(ImageData[], ImageData[], int, int, int[], int[][][]) - Static method in class edu.jhu.ece.iacl.algorithms.registration.RegistrationUtilities
 
jre - Variable in class edu.jhu.ece.iacl.jist.pipeline.JistPreferences
location of java executable.

K

kernelSize - Variable in class edu.jhu.ece.iacl.plugins.utilities.math.MedicAlgorithmKLDivergence
 
keyPressed() - Method in class edu.jhu.cs.cisst.vent.widgets.VisualizationTriangleMesh
Mouse dragged.
keyPressed(KeyEvent) - Method in class edu.jhu.ece.iacl.jist.pipeline.gui.PipeInternalFrame
 
keyReleased(KeyEvent) - Method in class edu.jhu.ece.iacl.jist.pipeline.gui.PipeInternalFrame
 
keySet() - Method in class edu.jhu.ece.iacl.algorithms.manual_label.LabelImageGroup
 
keyTyped(KeyEvent) - Method in class edu.jhu.ece.iacl.jist.pipeline.gui.PipeInternalFrame
 
killAll() - Method in class edu.jhu.ece.iacl.jist.pipeline.PipeScheduler
Kill all running processes.
kld - Variable in class edu.jhu.ece.iacl.plugins.utilities.math.MedicAlgorithmKLDivergence
 
KLDivergence - Class in edu.jhu.bme.smile.commons.math
 
KLDivergence() - Constructor for class edu.jhu.bme.smile.commons.math.KLDivergence
 
KLdivergence(double[][], double[][], double) - Method in class edu.jhu.bme.smile.commons.math.KLDivergence
 
KLdivergence(double[], double[], int) - Static method in class edu.jhu.bme.smile.commons.math.StatisticsDouble
Computes the Kullbach-Liebler divergence between two data sets x and y

L

L - Variable in class edu.jhu.bme.smile.commons.math.specialFunctions.SphericalHarmonics
 
L1LSCompressedSensing - Class in edu.jhu.bme.smile.commons.math
 
L1LSCompressedSensing(double[][]) - Constructor for class edu.jhu.bme.smile.commons.math.L1LSCompressedSensing
 
L1LSCompressedSensing(Matrix) - Constructor for class edu.jhu.bme.smile.commons.math.L1LSCompressedSensing
 
L1LSCompressedSensingNonNeg - Class in edu.jhu.bme.smile.commons.math
Positively constrained least squares solver
L1LSCompressedSensingNonNeg(double[][]) - Constructor for class edu.jhu.bme.smile.commons.math.L1LSCompressedSensingNonNeg
 
L1LSCompressedSensingNonNeg(Matrix) - Constructor for class edu.jhu.bme.smile.commons.math.L1LSCompressedSensingNonNeg
 
L1LSCompressedSensingUnconstrained - Class in edu.jhu.bme.smile.commons.math
 
L1LSCompressedSensingUnconstrained(double[][]) - Constructor for class edu.jhu.bme.smile.commons.math.L1LSCompressedSensingUnconstrained
 
L1LSCompressedSensingUnconstrained(Matrix) - Constructor for class edu.jhu.bme.smile.commons.math.L1LSCompressedSensingUnconstrained
 
label - Variable in class edu.jhu.ece.iacl.jist.pipeline.AlgorithmInformation
name and label for parameter.
label - Variable in class edu.jhu.ece.iacl.jist.pipeline.gui.PortListBox
The label.
label - Variable in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamModel
The label.
label - Variable in class edu.jhu.ece.iacl.jist.pipeline.PipeModule
Label to display for this parameter.
label - Variable in class edu.jhu.ece.iacl.jist.pipeline.view.output.ParamOutputView
The label.
labelDimension - Static variable in class edu.jhu.ece.iacl.jist.pipeline.view.output.ParamOutputView
The Constant labelDimension.
labelFile - Variable in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamDataLabel
The label file.
LabelImage - Class in edu.jhu.ece.iacl.algorithms.manual_label
 
LabelImage() - Constructor for class edu.jhu.ece.iacl.algorithms.manual_label.LabelImage
 
LabelImage(ImageData) - Constructor for class edu.jhu.ece.iacl.algorithms.manual_label.LabelImage
 
LabelImage(List<ImageData>) - Constructor for class edu.jhu.ece.iacl.algorithms.manual_label.LabelImage
 
LabelImageGroup - Class in edu.jhu.ece.iacl.algorithms.manual_label
 
LabelImageGroup() - Constructor for class edu.jhu.ece.iacl.algorithms.manual_label.LabelImageGroup
 
labels - Variable in class edu.jhu.ece.iacl.algorithms.manual_label.LabelSurface
 
labels - Variable in class edu.jhu.ece.iacl.algorithms.manual_label.staple.STAPLE
 
labels - Variable in class edu.jhu.ece.iacl.algorithms.manual_label.staple.STAPLEgeneral
 
labels - Variable in class edu.jhu.ece.iacl.algorithms.manual_label.staple.STAPLEgeneralSingle
 
labels - Variable in class edu.jhu.ece.iacl.algorithms.manual_label.staple.STAPLEmulti
 
labels - Variable in class edu.jhu.ece.iacl.algorithms.manual_label.staple.STAPLEmulti2
 
labels - Variable in class edu.jhu.ece.iacl.algorithms.manual_label.staple.STAPLEsingle
 
labels - Variable in class edu.jhu.ece.iacl.algorithms.manual_label.staple.STAPLEsurf
 
labels - Variable in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamDataLabel
The labels.
labelsin - Variable in class edu.jhu.ece.iacl.plugins.labeling.MedicAlgorithmFMLabelExtension
 
labelSize - Variable in class edu.jhu.ece.iacl.algorithms.manual_label.staple.STAPLEmulti2
 
labelSize - Variable in class edu.jhu.ece.iacl.jist.pipeline.graph.PipePortView
The label size.
labelstoindex - Variable in class edu.jhu.ece.iacl.algorithms.manual_label.staple.STAPLEmulti
 
labelstoindex - Variable in class edu.jhu.ece.iacl.algorithms.manual_label.staple.STAPLEmulti2
 
LabelSurface - Class in edu.jhu.ece.iacl.algorithms.manual_label
 
LabelSurface() - Constructor for class edu.jhu.ece.iacl.algorithms.manual_label.LabelSurface
 
LabelSurface(EmbeddedSurface) - Constructor for class edu.jhu.ece.iacl.algorithms.manual_label.LabelSurface
 
lairdWareLME - Static variable in class edu.jhu.ece.iacl.algorithms.ReferencedPapers
 
laplaceBeltramiSurfaceFlattening - Static variable in class edu.jhu.ece.iacl.algorithms.ReferencedPapers
 
laplaceThickness - Static variable in class edu.jhu.ece.iacl.algorithms.ReferencedPapers
 
lastCell - Variable in class edu.jhu.ece.iacl.jist.pipeline.PipeAlgorithm
graph cell to represent algorithm.
lastDirectory - Variable in class edu.jhu.ece.iacl.jist.pipeline.JistPreferences
last directory inspected.
lastFaceOpposite - Variable in class edu.jhu.ece.iacl.jist.structures.geom.EmbeddedPointSet.PointLocatorResult
The last face opposite.
lastFaceOppositeIndex - Variable in class edu.jhu.ece.iacl.jist.structures.geom.EmbeddedPointSet.PointLocatorResult
The last face opposite index.
lastFaceV0 - Variable in class edu.jhu.ece.iacl.jist.structures.geom.EmbeddedPointSet.PointLocatorResult
The last face v0.
lastFaceV1 - Variable in class edu.jhu.ece.iacl.jist.structures.geom.EmbeddedPointSet.PointLocatorResult
The last face v1.
lastFaceV2 - Variable in class edu.jhu.ece.iacl.jist.structures.geom.EmbeddedPointSet.PointLocatorResult
The last face v2.
lastModified - Variable in class edu.jhu.ece.iacl.jist.pipeline.PipeLayout
Time for when the file was last modified.
lastModifiedLayoutTime - Variable in class edu.jhu.ece.iacl.jist.pipeline.gui.ProcessManager
 
lastModifiedLock - Variable in class edu.jhu.ece.iacl.jist.pipeline.gui.ProcessManager
 
lastPort - Variable in class edu.jhu.ece.iacl.jist.pipeline.gui.PortComboBox
The last port.
layout - Variable in class edu.jhu.ece.iacl.jist.pipeline.ExecutionContext
Layout process associated with this context.
layout - Variable in class edu.jhu.ece.iacl.jist.pipeline.PipeScheduler
pipeline layout to schedule.
layout - Variable in class edu.jhu.ece.iacl.jist.pipeline.view.input.ParamCollectionInputView
Customized layout for this collection.
layoutFile - Variable in class edu.jhu.ece.iacl.doc.DocumentAllTests.TestCase
 
layoutFiles - Variable in class edu.jhu.ece.iacl.doc.DocumentAllTests
The layout files.
layoutFiles - Variable in class edu.jhu.ece.iacl.jist.test.JistTestHarness
The layout files.
LayoutPanel - Class in edu.jhu.ece.iacl.jist.pipeline.gui
Desktop pane for pipe layouts.
LayoutPanel() - Constructor for class edu.jhu.ece.iacl.jist.pipeline.gui.LayoutPanel
Default constructor.
LayoutPreferencePanel - Class in edu.jhu.ece.iacl.jist.pipeline.gui
Preference panel.
LayoutPreferencePanel(PipeLayout) - Constructor for class edu.jhu.ece.iacl.jist.pipeline.gui.LayoutPreferencePanel
Constructor.
LEFileReader - Class in edu.jhu.ece.iacl.jist.io
Created by IntelliJ IDEA.
LEFileReader(String) - Constructor for class edu.jhu.ece.iacl.jist.io.LEFileReader
Instantiates a new lE file reader.
LEFileWriter - Class in edu.jhu.ece.iacl.jist.io
The Class LEFileWriter.
LEFileWriter(String) - Constructor for class edu.jhu.ece.iacl.jist.io.LEFileWriter
Instantiates a new lE file writer.
Legendre - Class in edu.jhu.bme.smile.commons.math.specialFunctions
 
Legendre() - Constructor for class edu.jhu.bme.smile.commons.math.specialFunctions.Legendre
 
len - Variable in class edu.jhu.ece.iacl.algorithms.dti.tractography.FiberTracker
 
len - Variable in class edu.jhu.ece.iacl.algorithms.dti.tractography.WildBootFiberTracker
 
len - Variable in class edu.jhu.ece.iacl.plugins.dti.MedicAlgorithmSubsampleFibers.StaticCurve
 
length() - Method in class edu.jhu.bme.smile.commons.math.specialFunctions.ComplexVector
 
length(Tuple3f) - Static method in class edu.jhu.ece.iacl.jist.algorithms.graphics.GeomUtil
Length.
length(Tuple3d) - Static method in class edu.jhu.ece.iacl.jist.algorithms.graphics.GeomUtil
Length.
length(double, double, double) - Method in class edu.jhu.ece.iacl.jist.structures.fiber.Fiber
Length.
length() - Method in class edu.jhu.ece.iacl.jist.structures.geom.PT
Length.
length - Static variable in class edu.jhu.ece.iacl.jist.structures.image.MaskVolume18
The Constant length.
length - Static variable in class edu.jhu.ece.iacl.jist.structures.image.MaskVolume26
The Constant length.
length - Static variable in class edu.jhu.ece.iacl.jist.structures.image.MaskVolume6
The Constant length.
lengthDiffMM(Fiber, Fiber, double, double, double) - Static method in class edu.jhu.ece.iacl.algorithms.dti.tractography.FiberComparator
 
lengthDiffPt(Fiber, Fiber) - Static method in class edu.jhu.ece.iacl.algorithms.dti.tractography.FiberComparator
 
level - Variable in class edu.jhu.cs.cisst.algorithms.optimize.fmg.grid.Grid
 
levels - Variable in class edu.jhu.cs.cisst.algorithms.segmentation.gac.VectorFieldDiffusion2D
The resolution levels.
levelSetParam - Variable in class edu.jhu.cs.cisst.plugins.utilities.surface.PlugInIsoContourGenerator
 
levelSetParam - Variable in class edu.jhu.cs.cisst.plugins.utilities.surface.PlugInIsoSurfaceGenerator
 
levelSetParam - Variable in class edu.jhu.cs.cisst.plugins.visualization.PlugInVisualizeActiveContour2D
 
LevenbergMarquardt - Class in edu.jhu.bme.smile.commons.optimize
This optimizer uses the Levenberg Marquardt method in order to find the minimum of a function.
LevenbergMarquardt() - Constructor for class edu.jhu.bme.smile.commons.optimize.LevenbergMarquardt
Default constructor for LM.
LevenbergMarquardt(int) - Constructor for class edu.jhu.bme.smile.commons.optimize.LevenbergMarquardt
Constructor to let you set the maximum number of iterations.
levenbergMarquardt - Static variable in class edu.jhu.ece.iacl.algorithms.ReferencedPapers
 
lgFontSize - Static variable in class edu.jhu.ece.iacl.jist.pipeline.JistPreferences
 
library - Variable in class edu.jhu.ece.iacl.jist.pipeline.gui.PlugInSelector
The library.
library - Static variable in class edu.jhu.ece.iacl.jist.pipeline.PipeLibrary
Singleton reference to library.
license - package license
Provides...
lilliesTest - Static variable in class edu.jhu.ece.iacl.algorithms.ReferencedPapers
 
limits - Variable in class edu.jhu.ece.iacl.jist.pipeline.view.output.ParamSurfaceOutputView
The limits.
limits - Variable in class edu.jhu.ece.iacl.jist.structures.geom.CollisionDetection
The limits.
lindstromBatesLME - Static variable in class edu.jhu.ece.iacl.algorithms.ReferencedPapers
 
linearDistanceInterpolation(float[][][], float, float, float, float, int, int, int) - Static method in class edu.jhmi.rad.medic.libraries.ImageFunctionsPublic
linear interpolation, with distance to boundary outside image
linearGradientInterpolation(float[][][], float, int, float, float, float, int, int, int) - Static method in class edu.jhmi.rad.medic.libraries.ImageFunctionsPublic
linear interpolation, with +/- value outside the image useful for interpolating gradients (suppose the gradient is +value away from the image)
linearInterpolation(float[][][], float, float, float, int, int, int) - Static method in class edu.jhmi.rad.medic.libraries.ImageFunctionsPublic
linear interpolation, with 0 outside the image
linearInterpolation(float[][][], float, float, float, float, int, int, int) - Static method in class edu.jhmi.rad.medic.libraries.ImageFunctionsPublic
linear interpolation, with value outside the image
linearInterpolation(float[], float, float, float, float, int, int, int) - Static method in class edu.jhmi.rad.medic.libraries.ImageFunctionsPublic
linear interpolation, with value outside the image
linearInterpolation(float[][][], boolean[][][], float, float, float, float, int, int, int) - Static method in class edu.jhmi.rad.medic.libraries.ImageFunctionsPublic
linear interpolation, with value outside the image and mask
linearInterpolationXderivative(float[][][], float, float, float, int, int, int) - Static method in class edu.jhmi.rad.medic.libraries.ImageFunctionsPublic
exact derivatives of linear interpolation
linearInterpolationXderivative(float[], float, float, float, int, int, int) - Static method in class edu.jhmi.rad.medic.libraries.ImageFunctionsPublic
exact derivatives of linear interpolation
linearInterpolationYderivative(float[][][], float, float, float, int, int, int) - Static method in class edu.jhmi.rad.medic.libraries.ImageFunctionsPublic
exact derivatives of linear interpolation
linearInterpolationYderivative(float[], float, float, float, int, int, int) - Static method in class edu.jhmi.rad.medic.libraries.ImageFunctionsPublic
exact derivatives of linear interpolation
linearInterpolationZderivative(float[][][], float, float, float, int, int, int) - Static method in class edu.jhmi.rad.medic.libraries.ImageFunctionsPublic
exact derivatives of linear interpolation
linearInterpolationZderivative(float[], float, float, float, int, int, int) - Static method in class edu.jhmi.rad.medic.libraries.ImageFunctionsPublic
exact derivatives of linear interpolation
linearMaskInterpolation(boolean[][][], float, float, float, int, int, int) - Static method in class edu.jhmi.rad.medic.libraries.ImageFunctionsPublic
interpolate a computation mask: the mask is true if the linear interpolant is above 0.5
linearMaskInterpolationValue(boolean[][][], float, float, float, int, int, int) - Static method in class edu.jhmi.rad.medic.libraries.ImageFunctionsPublic
interpolate a computation mask: returns the linearly interpolated value in [0,1]
lineData - Variable in class edu.jhu.ece.iacl.jist.structures.geom.CurveCollection
The line data.
LineSearchND - Class in edu.jhu.bme.smile.commons.optimize
Uses 1D optimizers to optimize an ND function.
LineSearchND() - Constructor for class edu.jhu.bme.smile.commons.optimize.LineSearchND
Default constructor.
LineSearchND(Optimizer1DContinuous) - Constructor for class edu.jhu.bme.smile.commons.optimize.LineSearchND
Constructor to specify what 1D optimizer to use.
LineSearchND(Optimizer1DContinuous, int) - Constructor for class edu.jhu.bme.smile.commons.optimize.LineSearchND
Constructor to specify optimizer and maximum iterations
LineSearchNDDifferentiable - Class in edu.jhu.bme.smile.commons.optimize
Uses Diffentiable 1D optimizers to optimize a Differentiable ND function.
LineSearchNDDifferentiable() - Constructor for class edu.jhu.bme.smile.commons.optimize.LineSearchNDDifferentiable
Default constructor.
LineSearchNDDifferentiable(Optimizer1DContinuousDifferentiable) - Constructor for class edu.jhu.bme.smile.commons.optimize.LineSearchNDDifferentiable
Constructor to specify what 1D optimizer to use.
LineSearchNDDifferentiable(Optimizer1DContinuousDifferentiable, int) - Constructor for class edu.jhu.bme.smile.commons.optimize.LineSearchNDDifferentiable
Contructor to specify optimizer and maximum iterations
linInterp(float, float, float, float, float) - Static method in class edu.jhu.ece.iacl.algorithms.dti.tractography.FACT.FACTparameters
 
link(Vertex, Vertex) - Static method in class edu.jhu.ece.iacl.jist.structures.geom.Edge
Link.
linmin(float[], float[], int, float[], NumericalMethod, float[], int, float[]) - Method in class edu.jhu.ece.iacl.algorithms.vabra.NumericalRecipes
 
listAllJobs() - Method in class edu.jhu.ece.iacl.jist.processcontrol.DispatchController
List all jobs.
listBoxEntries - Variable in class edu.jhu.ece.iacl.jist.pipeline.view.input.InformationListBox
The list box entries.
listBoxEntries - Variable in class edu.jhu.ece.iacl.jist.pipeline.view.input.ParamFileCollectionInputView
The list box entries.
listBoxEntries - Variable in class edu.jhu.ece.iacl.jist.pipeline.view.input.ParamMultiOptionInputView
The list box entries.
listBoxEntries - Variable in class edu.jhu.ece.iacl.jist.pipeline.view.input.ParamNumberCollectionInputView
The list box entries.
listBoxEntries - Variable in class edu.jhu.ece.iacl.jist.pipeline.view.input.ParamVolumeCollectionInputView
The list box entries.
listDimension - Static variable in class edu.jhu.ece.iacl.jist.pipeline.view.input.ParamWeightedVolumesInputView
The Constant listDimension.
listDimension - Static variable in class edu.jhu.ece.iacl.jist.pipeline.view.input.ParamWeightedVolumesURIInputView
The Constant listDimension.
listeners - Variable in class edu.jhu.ece.iacl.jist.pipeline.JistPreferences
Listeners that react to changes in preferences.
listeners - Variable in class edu.jhu.ece.iacl.jist.pipeline.PipeModule
Listeners that listen for changes to this module, including input/output ports.
listeners - Variable in class edu.jhu.ece.iacl.jist.pipeline.PipePort
Listeners that are called when port is connected or disconnected.
listmodel - Variable in class edu.jhu.ece.iacl.jist.pipeline.gui.PortListBox
The listmodel.
listPane - Variable in class edu.jhu.ece.iacl.jist.pipeline.gui.PortListBox
The list pane.
listPane - Variable in class edu.jhu.ece.iacl.jist.pipeline.view.input.InformationListBox
The list pane.
listPane - Variable in class edu.jhu.ece.iacl.jist.pipeline.view.input.ParamFileCollectionInputView
The list pane.
listPane - Variable in class edu.jhu.ece.iacl.jist.pipeline.view.input.ParamMultiOptionInputView
The list pane.
listPane - Variable in class edu.jhu.ece.iacl.jist.pipeline.view.input.ParamNumberCollectionInputView
The list pane.
listPane - Variable in class edu.jhu.ece.iacl.jist.pipeline.view.input.ParamVolumeCollectionInputView
The list pane.
listSize - Variable in class edu.jhu.ece.iacl.jist.pipeline.view.input.ParamMultiOptionInputView
The list size.
LLvalue() - Method in class edu.jhu.bme.smile.commons.optimize.tensor.MLTensor
Calculates the least likelihood value
LLvalue() - Method in class edu.jhu.ece.iacl.algorithms.dti.DTEMRLTensor
Calculates the log-likelihood (LL) value
LLvalue(double[], double, double[], double[], double[]) - Static method in class edu.jhu.ece.iacl.algorithms.dti.DTEMRLTensor
 
LM() - Static method in class edu.jhu.bme.smile.commons.optimize.test.TestNDOptimizations
LM
load(PipeLayout) - Method in class edu.jhu.ece.iacl.jist.pipeline.gui.PipelineLayoutTool
Load layout into layout pane.
load(String, File, File) - Method in class edu.jhu.ece.iacl.jist.pipeline.gui.ProcessDebugInfoFrame
Load stdout and stderr from specified files.
load(PipeLayout) - Method in class edu.jhu.ece.iacl.jist.pipeline.gui.ProcessManager
Load layout.
load(File) - Method in class edu.jhu.ece.iacl.jist.pipeline.ProcessingAlgorithm
Load input parameters from file and execute algorithm.
load(File) - Method in class edu.jhu.ece.iacl.jist.pipeline.ProcessingDialog
Loads algorithm input profile from specified location into input parameters.
loadAndSaveOnValidate - Variable in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamModel
Should the parameter be validated on load.
loadContextInputParams() - Method in class edu.jhu.ece.iacl.jist.pipeline.ExecutionContext
Copy parameters for this context into pipe graph.
loadContextOutputParams() - Method in class edu.jhu.ece.iacl.jist.pipeline.ExecutionContext
Copy output parameters from this context into pipe graph.
loadData(String, String, int, int, int, double, double, double) - Method in class edu.jhu.ece.iacl.algorithms.dti.tractography.FACT.FACTapi
 
loadDefaults() - Method in class edu.jhu.ece.iacl.jist.pipeline.ProcessingDialog
Load defaults from MIPAV preferences.
loadFileSetAtlas(String) - Static method in class edu.jhu.ece.iacl.utility.AtlasList
 
loadFileSetAtlas(File) - Static method in class edu.jhu.ece.iacl.utility.AtlasList
 
loadLayoutInputParams() - Method in class edu.jhu.ece.iacl.jist.pipeline.ExecutionContext
Copy parameters from the pipe graph into this context.
loadLibraryPath() - Method in class edu.jhu.ece.iacl.jist.pipeline.PipeLibrary
Load library path from MIPAV preferences.
loadLibraryPath(boolean) - Method in class edu.jhu.ece.iacl.jist.pipeline.PipeLibrary
Load library path from MIPAV preferences.
loadPreferences() - Static method in class edu.jhu.ece.iacl.jist.pipeline.JistPreferences
Load existing modules and add them to the tree.
loadPreferences(boolean) - Static method in class edu.jhu.ece.iacl.jist.pipeline.JistPreferences
Load existing modules and add them to the tree.
loadPreferences() - Method in class edu.jhu.ece.iacl.jist.pipeline.PipeLibrary
Load existing modules and add them to the tree.
loadPreferences(boolean) - Method in class edu.jhu.ece.iacl.jist.pipeline.PipeLibrary
Load existing modules and add them to the tree.
loadResources(ParamModel, ProgressMonitor) - Method in class edu.jhu.ece.iacl.jist.pipeline.factory.ParamCollectionFactory
 
loadResources(ParamModel, ProgressMonitor) - Method in class edu.jhu.ece.iacl.jist.pipeline.factory.ParamDataLabelFactory
Load label file from file specified in foreign parameter.
loadResources(ParamModel, ProgressMonitor) - Method in class edu.jhu.ece.iacl.jist.pipeline.factory.ParamFactory
Load external resources specified in foreign parameter into this parameter.
loadResources(ParamModel, ProgressMonitor) - Method in class edu.jhu.ece.iacl.jist.pipeline.factory.ParamObjectFactory
 
loadResources(ParamModel, ProgressMonitor) - Method in class edu.jhu.ece.iacl.jist.pipeline.factory.ParamSurfaceCollectionFactory
 
loadResources(ParamModel, ProgressMonitor) - Method in class edu.jhu.ece.iacl.jist.pipeline.factory.ParamSurfaceFactory
 
loadResources(ParamModel, ProgressMonitor) - Method in class edu.jhu.ece.iacl.jist.pipeline.factory.ParamVolumeCollectionFactory
Load Model Image from file specified in foreign parameter.
loadResources(ParamModel, ProgressMonitor) - Method in class edu.jhu.ece.iacl.jist.pipeline.factory.ParamVolumeFactory
Load Model Image from file specified in foreign parameter.
loadResources(ParamModel, ProgressMonitor) - Method in class edu.jhu.ece.iacl.jist.pipeline.factory.ParamWeightedVolumeCollectionFactory
Load Model Image from file specified in foreign parameter.
loadResources(ParamModel) - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamModel
Load resources.
loadResources(ParamModel, ProgressMonitor) - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamModel
Load external resources specified in foreign parameter.
LocalNoiseEstimate - Class in edu.jhu.ece.iacl.plugins.dti
 
LocalNoiseEstimate() - Constructor for class edu.jhu.ece.iacl.plugins.dti.LocalNoiseEstimate
 
log(Matrix) - Static method in class edu.jhu.bme.smile.commons.math.MatrixMath
 
logData(boolean, int) - Method in class edu.jhu.bme.smile.commons.optimize.BrentMethod1D
Turns on logging for each iteration of the optimization.
logData(boolean, int) - Method in class edu.jhu.bme.smile.commons.optimize.DownhillSimplexND
Turns on logging for each iteration of the optimization.
logData(boolean, int) - Method in class edu.jhu.bme.smile.commons.optimize.GoldenSectionSearch1D
Turns on logging for each iteration of the optimization.
logData(boolean, int) - Method in class edu.jhu.bme.smile.commons.optimize.LevenbergMarquardt
Turns on logging for each iteration of the optimization.
logData(boolean, int) - Method in class edu.jhu.bme.smile.commons.optimize.LineSearchND
Turns on logging for each iteration of the optimization.
logData(boolean, int) - Method in class edu.jhu.bme.smile.commons.optimize.LineSearchNDDifferentiable
Turns on logging for each iteration of the optimization.
logData(boolean, int) - Method in class edu.jhu.bme.smile.commons.optimize.NewtonMethod1D
Turns on logging for each iteration of the optimization.
logError(int, String) - Static method in class edu.jhu.ece.iacl.jist.utility.JistLogger
 
logFlush() - Static method in class edu.jhu.ece.iacl.jist.utility.JistLogger
 
Logit(float[][][][], int, float, boolean) - Static method in class edu.jhu.ece.iacl.algorithms.manual_label.atlasing.LogOdds
Computes the Log-Odds of probability maps of labels.
Logit(ImageData, int, float, boolean, String, File) - Static method in class edu.jhu.ece.iacl.algorithms.manual_label.atlasing.LogOdds
Computes the Log-Odds of probability maps of labels.
logMIPAVRegistry() - Static method in class edu.jhu.ece.iacl.jist.utility.JistLogger
 
LogOdds - Class in edu.jhu.ece.iacl.algorithms.manual_label.atlasing
 
LogOdds() - Constructor for class edu.jhu.ece.iacl.algorithms.manual_label.atlasing.LogOdds
 
logOutput(int, String) - Static method in class edu.jhu.ece.iacl.jist.utility.JistLogger
 
logRicianPDF(double[], double[], double[]) - Static method in class edu.jhu.bme.smile.commons.math.StatisticsDouble
 
logScale - Variable in class edu.jhu.bme.smile.commons.math.HistogramGenerator
 
logScale - Variable in class edu.jhu.ece.iacl.jist.pipeline.view.input.ParamDoubleSliderInputView
The log scale.
logScale - Variable in class edu.jhu.ece.iacl.plugins.utilities.surface.MedicAlgorithmSurfaceHistogram
 
logScale - Variable in class edu.jhu.ece.iacl.plugins.utilities.volume.MedicAlgorithmVolumeHistogram
 
logScalingFactor - Variable in class edu.jhu.bme.smile.commons.math.HistogramGenerator
 
longdescription - Variable in class edu.jhu.ece.iacl.jist.pipeline.AlgorithmInformation
The long description.
longValue() - Method in class edu.jhu.ece.iacl.jist.structures.image.Voxel
 
LoniPipeParser - Class in edu.jhu.ece.iacl.jist.pipeline.parser
The Class LoniPipeParser.
LoniPipeParser() - Constructor for class edu.jhu.ece.iacl.jist.pipeline.parser.LoniPipeParser
Default constructor.
lookup(int, int, int, int) - Method in class edu.jhu.ece.iacl.jist.structures.data.BinaryMinFastHeap
Lookup.
lookuptoString() - Method in class edu.jhu.ece.iacl.algorithms.manual_label.simulation.ConfusionMatrix
outpus a string representation of the lookup Array
lottaEllingsen - Static variable in class edu.jhu.ece.iacl.algorithms.CommonAuthors
 
lowerBound - Variable in class edu.jhu.ece.iacl.plugins.utilities.logic.MedicAlgorithmValueGreaterThan
Input Parameters
lowerBound - Variable in class edu.jhu.ece.iacl.plugins.utilities.logic.MedicAlgorithmValueInRange
 

M

m - Variable in class edu.jhu.bme.smile.commons.math.L1LSCompressedSensing
 
M - Variable in class edu.jhu.bme.smile.commons.math.specialFunctions.SphericalHarmonics
 
mag() - Method in class edu.jhu.ece.iacl.jist.structures.matrix.VectorMatrixX
Mag.
mag() - Method in class edu.jhu.ece.iacl.jist.structures.vector.Vector2
 
mag() - Method in class edu.jhu.ece.iacl.jist.structures.vector.Vector3
 
mag() - Method in class edu.jhu.ece.iacl.jist.structures.vector.Vector4
 
mag() - Method in class edu.jhu.ece.iacl.jist.structures.vector.VectorN
 
mag() - Method in interface edu.jhu.ece.iacl.jist.structures.vector.VectorX
Mag.
magImage - Variable in class edu.jhu.cs.cisst.vent.renderer.processing.VectorField2DRenderer
The magnitude image.
magnitude() - Method in class edu.jhu.ece.iacl.jist.structures.geom.GridPt
Magnitude.
main(String[]) - Static method in class DiscoverMipavJISTPlugins
 
main(String[]) - Static method in class edu.jhmi.rad.medic.utilities.NumericsPublic
for testing purposes
main(String[]) - Static method in class edu.jhu.bme.smile.commons.math.RotationMatrix
 
main(String[]) - Static method in class edu.jhu.bme.smile.commons.math.StatisticsDouble
 
main(String[]) - Static method in class edu.jhu.bme.smile.commons.optimize.tensor.OptimizeTensor
 
main(String[]) - Static method in class edu.jhu.bme.smile.commons.optimize.test.Test1DOptimizations
 
main(String[]) - Static method in class edu.jhu.bme.smile.commons.optimize.test.TestDerivativeFunction
 
main(String[]) - Static method in class edu.jhu.bme.smile.commons.optimize.test.TestNDOptimizations
 
main(String[]) - Static method in class edu.jhu.ece.iacl.algorithms.dti.EstimateTensorLLMSE
 
main(String[]) - Static method in class edu.jhu.ece.iacl.algorithms.dti.tractography.FACT.AnalyzeDists
 
main(String[]) - Static method in class edu.jhu.ece.iacl.algorithms.dti.tractography.FACT.CompareFibers
 
main(String[]) - Static method in class edu.jhu.ece.iacl.algorithms.dti.tractography.FACT.DTIStudioReader
 
main(String[]) - Static method in class edu.jhu.ece.iacl.algorithms.dti.tractography.FACT.DtisVsIacl
 
main(String[]) - Static method in class edu.jhu.ece.iacl.algorithms.dti.tractography.FACT.FACT_INFACTcompare
 
main(String[]) - Static method in class edu.jhu.ece.iacl.algorithms.dti.tractography.FACT.FiberConverter
 
main(String[]) - Static method in class edu.jhu.ece.iacl.algorithms.dti.tractography.FACT.FiberScaler
 
main(String[]) - Static method in class edu.jhu.ece.iacl.algorithms.dti.tractography.FACT.RunFACT
FA file VEC file Parameter file
main(String[]) - Static method in class edu.jhu.ece.iacl.algorithms.dti.tractography.FACT.TestDXWriting
 
main(String[]) - Static method in class edu.jhu.ece.iacl.algorithms.dti.tractography.FACT.testFACT
 
main(String[]) - Static method in class edu.jhu.ece.iacl.algorithms.dti.tractography.FACT.triangulate
 
main(String[]) - Static method in class edu.jhu.ece.iacl.algorithms.dti.tractography.FACT.USbyte
 
main(String[]) - Static method in class edu.jhu.ece.iacl.algorithms.manual_label.simulation.ConfusionMatrix
 
main(String[]) - Static method in class edu.jhu.ece.iacl.algorithms.manual_label.staple.StaplePlugin
 
main(String[]) - Static method in class edu.jhu.ece.iacl.algorithms.manual_label.staple.StapleTester
 
main(String[]) - Static method in class edu.jhu.ece.iacl.doc.DocumentAllModules
Run me.
main(String[]) - Static method in class edu.jhu.ece.iacl.doc.DocumentAllTests
The main method.
main(String[]) - Static method in class edu.jhu.ece.iacl.jist.cli.discover
 
main(String[]) - Static method in class edu.jhu.ece.iacl.jist.cli.run
 
main(String[]) - Static method in class edu.jhu.ece.iacl.jist.cli.runLayout
 
main(String[]) - Static method in class edu.jhu.ece.iacl.jist.io.FileConverter
The main method.
main(String[]) - Static method in class edu.jhu.ece.iacl.jist.pipeline.gui.PipelineLayoutTool
The main method.
main(String[]) - Static method in class edu.jhu.ece.iacl.jist.pipeline.gui.ProcessManager
The main method.
main(String[]) - Static method in class edu.jhu.ece.iacl.jist.pipeline.PipeLayoutRunner
The main method.
main(String[]) - Static method in class edu.jhu.ece.iacl.jist.pipeline.PipeRunner
Main method to execute algorithm specified by input parameters.
main(String[]) - Static method in class edu.jhu.ece.iacl.jist.structures.image.test
The main method.
main(String[]) - Static method in class edu.jhu.ece.iacl.jist.structures.image.USbyte
The main method.
main(String[]) - Static method in class edu.jhu.ece.iacl.jist.test.JistTestHarness
The main method.
main(String[]) - Static method in class edu.jhu.ece.iacl.jist.test.MipavTestHarness
The main method.
main(String[]) - Static method in class license.JISTLicenseAbout
 
main(String[]) - Static method in class PlugInJISTPlugInSelector
The main method.
main(String[]) - Static method in class StartJIST
The main method.
main(String[]) - Static method in class StartJISTLayoutTool
The main method.
main(String[]) - Static method in class StartJISTPlugInSelector
The main method.
main(String[]) - Static method in class StartJISTProcessManager
The main method.
makeEmpty() - Method in class edu.jhu.ece.iacl.jist.structures.data.BinaryMinFastHeap
Make the priority queue logically empty.
makeEmpty() - Method in class edu.jhu.ece.iacl.jist.structures.data.BinaryMinHeap
Make the priority queue logically empty.
makeFibersInBounds(Fiber[], int, int, int) - Static method in class edu.jhu.ece.iacl.jist.structures.fiber.Fiber
Make fibers in bounds.
makeImgMatrix(Matrix, double) - Static method in class edu.jhu.bme.smile.commons.optimize.tensor.OptimizeTensor
makes the imgMatrix
makeInBounds(int, int, int) - Method in class edu.jhu.ece.iacl.jist.structures.fiber.Fiber
Make in bounds.
manager - Variable in class edu.jhu.ece.iacl.doc.DocumentAllTests
The manager.
manager - Static variable in class edu.jhu.ece.iacl.jist.pipeline.gui.ProcessManager
The manager.
manager - Variable in class edu.jhu.ece.iacl.jist.pipeline.PipeLayoutRunner
The manager.
manager - Variable in class edu.jhu.ece.iacl.jist.test.JistTestHarness
The manager.
managerPane - Variable in class edu.jhu.ece.iacl.jist.pipeline.gui.ProcessManager
The manager pane.
managerVisible - Variable in class edu.jhu.ece.iacl.jist.pipeline.gui.ProcessManager
 
mandatory - Variable in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamFileCollection
The mandatory.
mandatory - Variable in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamModel
The mandatory.
mapFile - Variable in class edu.jhu.ece.iacl.jist.pipeline.graph.PipeAlgorithmFactory
The map file.
mapFile - Variable in class edu.jhu.ece.iacl.jist.pipeline.PipeAlgorithm
file that stores this module definition.
mapped(float, float, float) - Static method in class edu.jhmi.rad.medic.utilities.NumericsPublic
returns x in [a,b] linearly mapped to [0,1]
mappingTechniquesForAligningSulci - Static variable in class edu.jhu.ece.iacl.algorithms.ReferencedPapers
 
march(double, double, double, double, double, double, int, int, int, int) - Method in class edu.jhu.cs.cisst.algorithms.segmentation.gac.DistanceField2D
March.
march(double, double, double, double, double, double, int, int, int, int, int, int) - Method in class edu.jhu.ece.iacl.algorithms.volume.DistanceField
 
marchTetrahedral(Hashtable<Long, IsoSurfaceGenerator.EdgeSplit>, LinkedList<IsoSurfaceGenerator.Triangle>, Point3i[]) - Method in class edu.jhu.cs.cisst.algorithms.geometry.surface.IsoSurfaceGenerator
March tetrahedral.
markCompleted() - Method in class edu.jhu.ece.iacl.jist.pipeline.AbstractCalculation
Mark algorithm as completed at the end of calculation It is mandatory that this method be executed at the end of the calculation.
maryamRettmann - Static variable in class edu.jhu.ece.iacl.algorithms.CommonAuthors
 
maskImage - Variable in class edu.jhu.cs.cisst.plugins.segmentation.PlugInCircleLevelSet
 
maskInterpolation(boolean[][][], float, float, float, int, int, int) - Static method in class edu.jhmi.rad.medic.libraries.ImageFunctionsPublic
interpolate a computation mask: where there is some data, the mask is set to true
MaskVolume - Interface in edu.jhu.ece.iacl.jist.structures.image
Mask Interface.
MaskVolume18 - Class in edu.jhu.ece.iacl.jist.structures.image
18-way neighbors for volume Note: the C implementations sometimes use a different ordering of these neighbors.
MaskVolume18() - Constructor for class edu.jhu.ece.iacl.jist.structures.image.MaskVolume18
 
MaskVolume26 - Class in edu.jhu.ece.iacl.jist.structures.image
26-way neighbors for volume Note: the C implementations sometimes use a different ordering of these neighbors.
MaskVolume26() - Constructor for class edu.jhu.ece.iacl.jist.structures.image.MaskVolume26
 
MaskVolume6 - Class in edu.jhu.ece.iacl.jist.structures.image
6-way neighbors for volume Note: the C implementations sometimes use a different ordering of these neighbors.
MaskVolume6() - Constructor for class edu.jhu.ece.iacl.jist.structures.image.MaskVolume6
 
mat - Variable in class edu.jhu.ece.iacl.jist.structures.matrix.Matrix3
Matrix 3d access This is not good encapsulation and will be deprectated in future iterations! Please use getters and setters when accessing matrix3d.
mat - Variable in class edu.jhu.ece.iacl.jist.structures.matrix.VectorMatrixX
Vector Matrix 3d access This is not good encapsulation and will be deprectated in future iterations! Please use getters and setters when accessing matrix3d.
matchFile(String, File, List<File>) - Method in class edu.jhu.ece.iacl.plugins.utilities.file.MedicAlgorithmChooseFileRegEx
 
matchFile(String, List<File>) - Method in class edu.jhu.ece.iacl.plugins.utilities.file.MedicAlgorithmChooseFileRegEx
 
matchFile(String, File, List<ImageData>) - Method in class edu.jhu.ece.iacl.plugins.utilities.file.MedicAlgorithmChooseVolumeRegEx
 
matchFile(String, List<ImageData>) - Method in class edu.jhu.ece.iacl.plugins.utilities.file.MedicAlgorithmChooseVolumeRegEx
 
matrix - Variable in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamMatrix
The matrix.
Matrix2 - Class in edu.jhu.ece.iacl.jist.structures.matrix
Matrix 2D implementation.
Matrix2(int, int) - Constructor for class edu.jhu.ece.iacl.jist.structures.matrix.Matrix2
Instantiates a new matrix2.
Matrix2(int, int, double) - Constructor for class edu.jhu.ece.iacl.jist.structures.matrix.Matrix2
Instantiates a new matrix2.
Matrix2(double[], int) - Constructor for class edu.jhu.ece.iacl.jist.structures.matrix.Matrix2
Instantiates a new matrix2.
Matrix2(double[][]) - Constructor for class edu.jhu.ece.iacl.jist.structures.matrix.Matrix2
Instantiates a new matrix2.
Matrix2(double[][], int, int) - Constructor for class edu.jhu.ece.iacl.jist.structures.matrix.Matrix2
Instantiates a new matrix2.
Matrix2(double[][][], int, int, int) - Constructor for class edu.jhu.ece.iacl.jist.structures.matrix.Matrix2
Instantiates a new matrix2.
Matrix2(double[][][], int) - Constructor for class edu.jhu.ece.iacl.jist.structures.matrix.Matrix2
Instantiates a new matrix2.
Matrix2Array(Matrix) - Method in class edu.jhu.ece.iacl.algorithms.dti.GradTableCorrection
 
Matrix3 - Class in edu.jhu.ece.iacl.jist.structures.matrix
Matrix 3d implementation Values are always stored as double.
Matrix3(int, int, int) - Constructor for class edu.jhu.ece.iacl.jist.structures.matrix.Matrix3
Instantiates a new matrix3.
Matrix3(int, int, int, double) - Constructor for class edu.jhu.ece.iacl.jist.structures.matrix.Matrix3
Instantiates a new matrix3.
Matrix3(ImageData) - Constructor for class edu.jhu.ece.iacl.jist.structures.matrix.Matrix3
Instantiates a new matrix3.
Matrix3(double[][][]) - Constructor for class edu.jhu.ece.iacl.jist.structures.matrix.Matrix3
Instantiates a new matrix3.
MatrixMath - Class in edu.jhu.bme.smile.commons.math
 
MatrixMath() - Constructor for class edu.jhu.bme.smile.commons.math.MatrixMath
 
matrixMultiply(double[][], double[][]) - Method in class edu.jhu.ece.iacl.algorithms.dti.DTIGradientTableCreator
 
matrixMultiply(double[][], double[][]) - Method in class edu.jhu.ece.iacl.algorithms.dti.GradTableCorrection
 
matrixMultiply(double[][], double[][]) - Static method in class edu.jhu.ece.iacl.plugins.registration.MedicAlgorithmEfficientFileCollectionRegistration
 
MatrixX - Interface in edu.jhu.ece.iacl.jist.structures.matrix
Gerneric interface for matrix types.
matSHProj - Variable in class edu.jhu.bme.smile.commons.math.specialFunctions.SphericalHarmonics
 
matSHProj() - Method in class edu.jhu.bme.smile.commons.math.specialFunctions.SphericalHarmonics
 
matSHRecon - Variable in class edu.jhu.bme.smile.commons.math.specialFunctions.SphericalHarmonics
 
max(float, float) - Static method in class edu.jhmi.rad.medic.utilities.NumericsPublic
 
max(double, double) - Static method in class edu.jhmi.rad.medic.utilities.NumericsPublic
 
max(int, int) - Static method in class edu.jhmi.rad.medic.utilities.NumericsPublic
 
max(int, int, int) - Static method in class edu.jhmi.rad.medic.utilities.NumericsPublic
 
max(float, float, float) - Static method in class edu.jhmi.rad.medic.utilities.NumericsPublic
 
max(float[]) - Static method in class edu.jhmi.rad.medic.utilities.NumericsPublic
 
max(float[], int, int) - Static method in class edu.jhmi.rad.medic.utilities.NumericsPublic
 
max - Variable in class edu.jhu.bme.smile.commons.math.HistogramGenerator
 
max(Matrix) - Static method in class edu.jhu.bme.smile.commons.math.MatrixMath
 
max(double[]) - Static method in class edu.jhu.bme.smile.commons.math.StatisticsDouble
 
max - Variable in class edu.jhu.cs.cisst.vent.renderer.processing.VolumeSliceRenderer
 
max - Variable in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamNumber
The max.
max - Variable in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamNumberCollection
The max.
max - Variable in class edu.jhu.ece.iacl.jist.pipeline.view.input.ParamDoubleSliderInputView
The max.
max - Variable in class edu.jhu.ece.iacl.plugins.utilities.surface.MedicAlgorithmSurfaceHistogram
 
max - Variable in class edu.jhu.ece.iacl.plugins.utilities.volume.MedicAlgorithmVolumeHistogram
 
MAX_DOUBLE_VALUE - Static variable in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamNumber
The Constant MAX_DOUBLE_VALUE.
MAX_FLOAT_VALUE - Static variable in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamNumber
The Constant MAX_FLOAT_VALUE.
MAX_INT_VALUE - Static variable in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamNumber
The Constant MAX_INT_VALUE.
MAX_LABELS - Static variable in class edu.jhu.ece.iacl.jist.pipeline.parameter.DataLabel
The Constant MAX_LABELS.
MAX_LENGTH - Static variable in class edu.jhu.ece.iacl.algorithms.dti.tractography.FiberTracker
 
MAX_LENGTH - Static variable in class edu.jhu.ece.iacl.algorithms.dti.tractography.WildBootFiberTracker
 
MAX_LONG_VALUE - Static variable in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamNumber
The Constant MAX_LONG_VALUE.
MAX_LS_ITER - Variable in class edu.jhu.bme.smile.commons.math.L1LSCompressedSensing
 
MAX_NT_ITER - Variable in class edu.jhu.bme.smile.commons.math.L1LSCompressedSensing
 
MAX_PATHS - Static variable in class edu.jhu.ece.iacl.jist.pipeline.graph.AvoidanceRouting
The MA x_ paths.
maxCurvatureForce - Variable in class edu.jhu.cs.cisst.algorithms.segmentation.gac.GaussianCurvatureForce2D
The max curvature force.
maxCurvatureForce - Variable in class edu.jhu.cs.cisst.algorithms.segmentation.gac.MeanCurvatureForce2D
The max curvature force.
maxDist(Fiber, Fiber, double, double, double) - Static method in class edu.jhu.ece.iacl.algorithms.dti.tractography.FiberComparator
 
maxdistance - Variable in class edu.jhu.ece.iacl.plugins.labeling.MedicAlgorithmFMLabelExtension
 
maxHistorySize - Variable in class edu.jhu.ece.iacl.jist.pipeline.JistPreferences
maximum number of files to display in history.
maximize - Variable in class edu.jhu.cs.cisst.vent.widgets.VisualizationImage
The maximize.
maximizeParam - Variable in class edu.jhu.cs.cisst.vent.widgets.VisualizationImage
The maximize param.
maximum(float[][][], int, int, int) - Static method in class edu.jhmi.rad.medic.libraries.ImageFunctionsPublic
maximum value of the image
maximum(int[][][], int, int, int) - Static method in class edu.jhmi.rad.medic.libraries.ImageFunctionsPublic
maximum value of the image
maximum(byte[][][], int, int, int) - Static method in class edu.jhmi.rad.medic.libraries.ImageFunctionsPublic
maximum value of the image
maxIncoming - Variable in class edu.jhu.ece.iacl.jist.pipeline.PipePort
Maximum number of incoming ports.
maxIterations - Variable in class edu.jhu.cs.cisst.algorithms.segmentation.gac.GradientVectorFlow2D
The max iterations.
maxIterations - Variable in class edu.jhu.cs.cisst.algorithms.segmentation.gac.VectorFieldDiffusion2D
The maximum iterations.
maxiters - Variable in class edu.jhu.ece.iacl.algorithms.manual_label.staple.STAPLE
 
maxiters - Variable in class edu.jhu.ece.iacl.algorithms.manual_label.staple.STAPLEgeneral
 
maxiters - Variable in class edu.jhu.ece.iacl.algorithms.manual_label.staple.STAPLEgeneralSingle
 
maxiters - Variable in class edu.jhu.ece.iacl.algorithms.manual_label.staple.STAPLEmulti
 
maxiters - Variable in class edu.jhu.ece.iacl.algorithms.manual_label.staple.STAPLEmulti2
 
maxiters - Variable in class edu.jhu.ece.iacl.algorithms.manual_label.staple.STAPLEsingle
 
maxiters - Variable in class edu.jhu.ece.iacl.algorithms.manual_label.staple.STAPLEsurf
 
maxLayers - Variable in class edu.jhu.cs.cisst.algorithms.segmentation.gac.GeodesicActiveContour2D
The maximum number of layers.
maxlen - Variable in class edu.jhu.ece.iacl.algorithms.dti.tractography.FiberTracker
 
maxlen - Variable in class edu.jhu.ece.iacl.algorithms.dti.tractography.WildBootFiberTracker
 
maxmag(float, float) - Static method in class edu.jhmi.rad.medic.utilities.NumericsPublic
 
maxMagnitude - Variable in class edu.jhu.cs.cisst.vent.renderer.processing.VectorField2DRenderer
The max magnitude.
maxmax - Variable in class edu.jhu.ece.iacl.algorithms.dti.tractography.Tract
 
maxOutgoing - Variable in class edu.jhu.ece.iacl.jist.pipeline.PipePort
Maximum number of outgoing ports.
maxSignedDistance(float[][]) - Static method in class edu.jhu.cs.cisst.algorithms.segmentation.gac.DistanceField2D
Max signed distance.
maxSignedDistance(float[][][]) - Static method in class edu.jhu.ece.iacl.algorithms.volume.DistanceField
 
maxSpeed - Variable in class edu.jhu.cs.cisst.algorithms.segmentation.gac.GeodesicActiveContour2D
The max speed.
maxStretch(Matrix) - Static method in class edu.jhu.ece.iacl.jist.algorithms.graphics.GeomUtil
Max stretch.
maxTractDistanceBySeed(Tract, double, double, double) - Method in class edu.jhu.ece.iacl.algorithms.dti.tractography.Tract
 
maxTractDistanceBySeed(Fiber, Tract, double, double, double) - Method in class edu.jhu.ece.iacl.algorithms.dti.tractography.Tract
 
maxTurnAngle - Variable in class edu.jhu.ece.iacl.algorithms.dti.tractography.FACT.FACTparameters
 
maxTurnAngle - Variable in class edu.jhu.ece.iacl.algorithms.dti.tractography.FiberTracker
 
maxTurnAngle - Variable in class edu.jhu.ece.iacl.algorithms.dti.tractography.WildBootFiberTracker
 
MaxUniqueLabels - Variable in class edu.jhu.ece.iacl.algorithms.manual_label.staple.STAPLEmulti
 
MaxUniqueLabels - Variable in class edu.jhu.ece.iacl.algorithms.manual_label.staple.STAPLEmulti2
 
maxY - Variable in class edu.jhu.bme.smile.commons.math.HistogramGenerator
 
MD() - Method in class edu.jhu.ece.iacl.algorithms.dti.DiffusionTensor
 
mdFontSize - Static variable in class edu.jhu.ece.iacl.jist.pipeline.JistPreferences
 
mean(double[]) - Static method in class edu.jhu.bme.smile.commons.math.StatisticsDouble
 
meanCurvature(float[][][], int, int, int) - Static method in class edu.jhmi.rad.medic.libraries.ImageFunctionsPublic
curvature estimation on a smooth distance function with no additionnal smoothing.
meanCurvature(float[][]) - Static method in class edu.jhu.cs.cisst.algorithms.util.DataOperations
Mean curvature.
MeanCurvatureForce2D - Class in edu.jhu.cs.cisst.algorithms.segmentation.gac
The Class MeanCurvatureForce2D moves the level set according to mean curvature.
MeanCurvatureForce2D() - Constructor for class edu.jhu.cs.cisst.algorithms.segmentation.gac.MeanCurvatureForce2D
 
meanDiffusivity(Matrix) - Static method in class edu.jhu.ece.iacl.jist.algorithms.graphics.GeomUtil
Mean diffusivity.
meanDistCorr(Fiber, Fiber, double, double, double) - Static method in class edu.jhu.ece.iacl.algorithms.dti.tractography.FiberComparator
 
meanDists(LabelImage) - Method in class edu.jhu.ece.iacl.algorithms.manual_label.LabelImage
 
meanDists(LabelImage, int) - Method in class edu.jhu.ece.iacl.algorithms.manual_label.LabelImage
 
meanmax - Variable in class edu.jhu.ece.iacl.algorithms.dti.tractography.Tract
 
meanmean - Variable in class edu.jhu.ece.iacl.algorithms.dti.tractography.Tract
 
meanStretch(Matrix) - Static method in class edu.jhu.ece.iacl.jist.algorithms.graphics.GeomUtil
Mean stretch.
meanValueCoordinates - Static variable in class edu.jhu.ece.iacl.algorithms.ReferencedPapers
 
measurementUnitNames - Static variable in class edu.jhu.ece.iacl.jist.structures.image.ImageHeader
The Constant measurementUnitNames.
median(double[]) - Static method in class edu.jhu.bme.smile.commons.math.StatisticsDouble
 
medianRobust(double[]) - Static method in class edu.jhu.bme.smile.commons.math.StatisticsDouble
 
MedicAlgorithmApplyFiberROI - Class in edu.jhu.ece.iacl.plugins.dti.tractography
 
MedicAlgorithmApplyFiberROI() - Constructor for class edu.jhu.ece.iacl.plugins.dti.tractography.MedicAlgorithmApplyFiberROI
 
MedicAlgorithmArithmetic - Class in edu.jhu.ece.iacl.plugins.utilities.math
 
MedicAlgorithmArithmetic() - Constructor for class edu.jhu.ece.iacl.plugins.utilities.math.MedicAlgorithmArithmetic
 
MedicAlgorithmAtlasSelection - Class in edu.jhu.ece.iacl.plugins.registration
 
MedicAlgorithmAtlasSelection() - Constructor for class edu.jhu.ece.iacl.plugins.registration.MedicAlgorithmAtlasSelection
 
MedicAlgorithmChooseFileRegEx - Class in edu.jhu.ece.iacl.plugins.utilities.file
 
MedicAlgorithmChooseFileRegEx() - Constructor for class edu.jhu.ece.iacl.plugins.utilities.file.MedicAlgorithmChooseFileRegEx
 
MedicAlgorithmChooseVolumeRegEx - Class in edu.jhu.ece.iacl.plugins.utilities.file
 
MedicAlgorithmChooseVolumeRegEx() - Constructor for class edu.jhu.ece.iacl.plugins.utilities.file.MedicAlgorithmChooseVolumeRegEx
 
MedicAlgorithmCleanSurfLabels - Class in edu.jhu.ece.iacl.plugins.labeling
 
MedicAlgorithmCleanSurfLabels() - Constructor for class edu.jhu.ece.iacl.plugins.labeling.MedicAlgorithmCleanSurfLabels
 
MedicAlgorithmCombineSurfaceComponents - Class in edu.jhu.ece.iacl.plugins.utilities.surface
 
MedicAlgorithmCombineSurfaceComponents() - Constructor for class edu.jhu.ece.iacl.plugins.utilities.surface.MedicAlgorithmCombineSurfaceComponents
 
MedicAlgorithmCombineSurfaces - Class in edu.jhu.ece.iacl.plugins.utilities.surface
 
MedicAlgorithmCombineSurfaces() - Constructor for class edu.jhu.ece.iacl.plugins.utilities.surface.MedicAlgorithmCombineSurfaces
 
MedicAlgorithmCombineVolumeComponents - Class in edu.jhu.ece.iacl.plugins.utilities.volume
 
MedicAlgorithmCombineVolumeComponents() - Constructor for class edu.jhu.ece.iacl.plugins.utilities.volume.MedicAlgorithmCombineVolumeComponents
 
MedicAlgorithmConcatArrayDoubleTextLists - Class in edu.jhu.ece.iacl.plugins.utilities.file
 
MedicAlgorithmConcatArrayDoubleTextLists() - Constructor for class edu.jhu.ece.iacl.plugins.utilities.file.MedicAlgorithmConcatArrayDoubleTextLists
 
MedicAlgorithmConstrainedFLIRT - Class in edu.jhu.ece.iacl.plugins.registration
 
MedicAlgorithmConstrainedFLIRT() - Constructor for class edu.jhu.ece.iacl.plugins.registration.MedicAlgorithmConstrainedFLIRT
 
MedicAlgorithmConstrainedFLIRT.AlgorithmConstrainedOAR3DWrapper - Class in edu.jhu.ece.iacl.plugins.registration
 
MedicAlgorithmConstrainedFLIRT.AlgorithmConstrainedOAR3DWrapper(ModelImage, ModelImage, int, int, int, float, float, float, float, float, float, int, int, int, float[][], boolean, boolean, boolean, boolean, int, int, int) - Constructor for class edu.jhu.ece.iacl.plugins.registration.MedicAlgorithmConstrainedFLIRT.AlgorithmConstrainedOAR3DWrapper
 
MedicAlgorithmConstrainedFLIRT.AlgorithmConstrainedOAR3DWrapper(ModelImage, ModelImage, ModelImage, ModelImage, int, int, int, float, float, float, float, float, float, int, int, int, float[][], boolean, boolean, boolean, boolean, int, int, int) - Constructor for class edu.jhu.ece.iacl.plugins.registration.MedicAlgorithmConstrainedFLIRT.AlgorithmConstrainedOAR3DWrapper
 
MedicAlgorithmConstrainedFLIRT.FlirtWrapper - Class in edu.jhu.ece.iacl.plugins.registration
 
MedicAlgorithmConstrainedFLIRT.FlirtWrapper() - Constructor for class edu.jhu.ece.iacl.plugins.registration.MedicAlgorithmConstrainedFLIRT.FlirtWrapper
 
MedicAlgorithmCopyEmbeddedData - Class in edu.jhu.ece.iacl.plugins.utilities.surface
 
MedicAlgorithmCopyEmbeddedData() - Constructor for class edu.jhu.ece.iacl.plugins.utilities.surface.MedicAlgorithmCopyEmbeddedData
 
MedicAlgorithmCreateSimilarityMetricVol - Class in edu.jhu.ece.iacl.plugins.registration
 
MedicAlgorithmCreateSimilarityMetricVol() - Constructor for class edu.jhu.ece.iacl.plugins.registration.MedicAlgorithmCreateSimilarityMetricVol
 
MedicAlgorithmCrop - Class in edu.jhu.ece.iacl.plugins.utilities.volume
 
MedicAlgorithmCrop() - Constructor for class edu.jhu.ece.iacl.plugins.utilities.volume.MedicAlgorithmCrop
 
MedicAlgorithmDeformFibers - Class in edu.jhu.ece.iacl.plugins.dti.tractography
 
MedicAlgorithmDeformFibers() - Constructor for class edu.jhu.ece.iacl.plugins.dti.tractography.MedicAlgorithmDeformFibers
 
MedicAlgorithmDemo - Class in edu.jhu.ece.iacl.jist.plugins.testing
 
MedicAlgorithmDemo() - Constructor for class edu.jhu.ece.iacl.jist.plugins.testing.MedicAlgorithmDemo
 
MedicAlgorithmDemo.MyAlgorithm - Class in edu.jhu.ece.iacl.jist.plugins.testing
Example algorithm
MedicAlgorithmDemo.MyAlgorithm(int) - Constructor for class edu.jhu.ece.iacl.jist.plugins.testing.MedicAlgorithmDemo.MyAlgorithm
 
MedicAlgorithmDemo.MyAlgorithm(AbstractCalculation) - Constructor for class edu.jhu.ece.iacl.jist.plugins.testing.MedicAlgorithmDemo.MyAlgorithm
Construct algorithm
MedicAlgorithmDimensions - Class in edu.jhu.ece.iacl.plugins.utilities.volume
 
MedicAlgorithmDimensions() - Constructor for class edu.jhu.ece.iacl.plugins.utilities.volume.MedicAlgorithmDimensions
 
MedicAlgorithmEfficientFileCollectionRegistration - Class in edu.jhu.ece.iacl.plugins.registration
 
MedicAlgorithmEfficientFileCollectionRegistration() - Constructor for class edu.jhu.ece.iacl.plugins.registration.MedicAlgorithmEfficientFileCollectionRegistration
 
MedicAlgorithmEfficientFileCollectionRegistration.FlirtWrapper - Class in edu.jhu.ece.iacl.plugins.registration
 
MedicAlgorithmEfficientFileCollectionRegistration.FlirtWrapper() - Constructor for class edu.jhu.ece.iacl.plugins.registration.MedicAlgorithmEfficientFileCollectionRegistration.FlirtWrapper
 
MedicAlgorithmEmbedSurface - Class in edu.jhu.ece.iacl.plugins.utilities.surface
 
MedicAlgorithmEmbedSurface() - Constructor for class edu.jhu.ece.iacl.plugins.utilities.surface.MedicAlgorithmEmbedSurface
 
MedicAlgorithmExecutableAdapter - Class in edu.jhu.ece.iacl.jist.plugins
The Class MedicAlgorithmExecutableAdapter.
MedicAlgorithmExecutableAdapter() - Constructor for class edu.jhu.ece.iacl.jist.plugins.MedicAlgorithmExecutableAdapter
Instantiates a new medic algorithm executable adapter.
MedicAlgorithmExecutableAdapter.ProcessRunner - Class in edu.jhu.ece.iacl.jist.plugins
The Class ProcessRunner.
MedicAlgorithmExecutableAdapter.ProcessRunner(String) - Constructor for class edu.jhu.ece.iacl.jist.plugins.MedicAlgorithmExecutableAdapter.ProcessRunner
Instantiates a new process runner.
MedicAlgorithmExtractAllComponents - Class in edu.jhu.ece.iacl.plugins.utilities.volume
 
MedicAlgorithmExtractAllComponents() - Constructor for class edu.jhu.ece.iacl.plugins.utilities.volume.MedicAlgorithmExtractAllComponents
 
MedicAlgorithmExtractFileCollectionComponents - Class in edu.jhu.ece.iacl.plugins.utilities.volume
 
MedicAlgorithmExtractFileCollectionComponents() - Constructor for class edu.jhu.ece.iacl.plugins.utilities.volume.MedicAlgorithmExtractFileCollectionComponents
 
MedicAlgorithmExtractSurfaceComponent - Class in edu.jhu.ece.iacl.plugins.utilities.surface
 
MedicAlgorithmExtractSurfaceComponent() - Constructor for class edu.jhu.ece.iacl.plugins.utilities.surface.MedicAlgorithmExtractSurfaceComponent
 
MedicAlgorithmExtractVolumeComponent - Class in edu.jhu.ece.iacl.plugins.utilities.volume
 
MedicAlgorithmExtractVolumeComponent() - Constructor for class edu.jhu.ece.iacl.plugins.utilities.volume.MedicAlgorithmExtractVolumeComponent
 
MedicAlgorithmFiberComparison - Class in edu.jhu.ece.iacl.plugins.dti.tractography
 
MedicAlgorithmFiberComparison() - Constructor for class edu.jhu.ece.iacl.plugins.dti.tractography.MedicAlgorithmFiberComparison
 
MedicAlgorithmFibersFromSurfaceROI - Class in edu.jhu.ece.iacl.plugins.dti.tractography
 
MedicAlgorithmFibersFromSurfaceROI() - Constructor for class edu.jhu.ece.iacl.plugins.dti.tractography.MedicAlgorithmFibersFromSurfaceROI
 
MedicAlgorithmFibersToVtk - Class in edu.jhu.ece.iacl.plugins.utilities.file
 
MedicAlgorithmFibersToVtk() - Constructor for class edu.jhu.ece.iacl.plugins.utilities.file.MedicAlgorithmFibersToVtk
 
MedicAlgorithmFiberTracker - Class in edu.jhu.ece.iacl.plugins.dti.tractography
 
MedicAlgorithmFiberTracker() - Constructor for class edu.jhu.ece.iacl.plugins.dti.tractography.MedicAlgorithmFiberTracker
 
MedicAlgorithmFiberVolumeStatistics - Class in edu.jhu.ece.iacl.plugins.dti.tractography
 
MedicAlgorithmFiberVolumeStatistics() - Constructor for class edu.jhu.ece.iacl.plugins.dti.tractography.MedicAlgorithmFiberVolumeStatistics
 
MedicAlgorithmFindEqualVolume - Class in edu.jhu.ece.iacl.plugins.utilities.volume
 
MedicAlgorithmFindEqualVolume() - Constructor for class edu.jhu.ece.iacl.plugins.utilities.volume.MedicAlgorithmFindEqualVolume
 
MedicAlgorithmFlipVectorTable - Class in edu.jhu.ece.iacl.plugins.dti
 
MedicAlgorithmFlipVectorTable() - Constructor for class edu.jhu.ece.iacl.plugins.dti.MedicAlgorithmFlipVectorTable
 
MedicAlgorithmFlipVectorVolume - Class in edu.jhu.ece.iacl.plugins.dti
 
MedicAlgorithmFlipVectorVolume() - Constructor for class edu.jhu.ece.iacl.plugins.dti.MedicAlgorithmFlipVectorVolume
 
MedicAlgorithmFLIRT - Class in edu.jhu.ece.iacl.plugins.registration
 
MedicAlgorithmFLIRT() - Constructor for class edu.jhu.ece.iacl.plugins.registration.MedicAlgorithmFLIRT
 
MedicAlgorithmFLIRT.AlgorithmRegOAR3DWrapper - Class in edu.jhu.ece.iacl.plugins.registration
 
MedicAlgorithmFLIRT.AlgorithmRegOAR3DWrapper(ModelImage, ModelImage, int, int, int, float, float, float, float, float, float, float, float, float, float, float, float, boolean, boolean, boolean, int, int, int) - Constructor for class edu.jhu.ece.iacl.plugins.registration.MedicAlgorithmFLIRT.AlgorithmRegOAR3DWrapper
 
MedicAlgorithmFLIRT.AlgorithmRegOAR3DWrapper(ModelImage, ModelImage, ModelImage, ModelImage, int, int, int, float, float, float, float, float, float, float, float, float, float, float, float, boolean, boolean, boolean, int, int, int) - Constructor for class edu.jhu.ece.iacl.plugins.registration.MedicAlgorithmFLIRT.AlgorithmRegOAR3DWrapper
 
MedicAlgorithmFLIRT.FlirtWrapper - Class in edu.jhu.ece.iacl.plugins.registration
 
MedicAlgorithmFLIRT.FlirtWrapper() - Constructor for class edu.jhu.ece.iacl.plugins.registration.MedicAlgorithmFLIRT.FlirtWrapper
 
MedicAlgorithmFLIRTCollection - Class in edu.jhu.ece.iacl.plugins.registration
 
MedicAlgorithmFLIRTCollection() - Constructor for class edu.jhu.ece.iacl.plugins.registration.MedicAlgorithmFLIRTCollection
 
MedicAlgorithmFLIRTCollection.AlgorithmRegOAR3DWrapper - Class in edu.jhu.ece.iacl.plugins.registration
 
MedicAlgorithmFLIRTCollection.AlgorithmRegOAR3DWrapper(ModelImage, ModelImage, int, int, int, float, float, float, float, float, float, float, float, float, float, float, float, boolean, boolean, boolean, int, int, int) - Constructor for class edu.jhu.ece.iacl.plugins.registration.MedicAlgorithmFLIRTCollection.AlgorithmRegOAR3DWrapper
 
MedicAlgorithmFLIRTCollection.AlgorithmRegOAR3DWrapper(ModelImage, ModelImage, ModelImage, ModelImage, int, int, int, float, float, float, float, float, float, float, float, float, float, float, float, boolean, boolean, boolean, int, int, int) - Constructor for class edu.jhu.ece.iacl.plugins.registration.MedicAlgorithmFLIRTCollection.AlgorithmRegOAR3DWrapper
 
MedicAlgorithmFLIRTCollection.FlirtWrapper - Class in edu.jhu.ece.iacl.plugins.registration
 
MedicAlgorithmFLIRTCollection.FlirtWrapper() - Constructor for class edu.jhu.ece.iacl.plugins.registration.MedicAlgorithmFLIRTCollection.FlirtWrapper
 
MedicAlgorithmFloatsToPoint - Class in edu.jhu.ece.iacl.plugins.utilities.logic
 
MedicAlgorithmFloatsToPoint() - Constructor for class edu.jhu.ece.iacl.plugins.utilities.logic.MedicAlgorithmFloatsToPoint
 
MedicAlgorithmFMLabelExtension - Class in edu.jhu.ece.iacl.plugins.labeling
 
MedicAlgorithmFMLabelExtension() - Constructor for class edu.jhu.ece.iacl.plugins.labeling.MedicAlgorithmFMLabelExtension
 
MedicAlgorithmFormatVectorImage - Class in edu.jhu.ece.iacl.plugins.dti
 
MedicAlgorithmFormatVectorImage() - Constructor for class edu.jhu.ece.iacl.plugins.dti.MedicAlgorithmFormatVectorImage
 
MedicAlgorithmIdentifySubject - Class in edu.jhu.ece.iacl.plugins.utilities.file
 
MedicAlgorithmIdentifySubject() - Constructor for class edu.jhu.ece.iacl.plugins.utilities.file.MedicAlgorithmIdentifySubject
 
MedicAlgorithmImageCalculator - Class in edu.jhu.ece.iacl.plugins.utilities.math
 
MedicAlgorithmImageCalculator() - Constructor for class edu.jhu.ece.iacl.plugins.utilities.math.MedicAlgorithmImageCalculator
 
MedicAlgorithmImageCalculatorBatch - Class in edu.jhu.ece.iacl.plugins.utilities.math
 
MedicAlgorithmImageCalculatorBatch() - Constructor for class edu.jhu.ece.iacl.plugins.utilities.math.MedicAlgorithmImageCalculatorBatch
 
MedicAlgorithmImageCalculatorModified - Class in edu.jhu.ece.iacl.plugins.utilities.math
 
MedicAlgorithmImageCalculatorModified() - Constructor for class edu.jhu.ece.iacl.plugins.utilities.math.MedicAlgorithmImageCalculatorModified
 
MedicAlgorithmImageMath - Class in edu.jhu.ece.iacl.plugins.utilities.math
 
MedicAlgorithmImageMath() - Constructor for class edu.jhu.ece.iacl.plugins.utilities.math.MedicAlgorithmImageMath
 
MedicAlgorithmIsotropicReslice - Class in edu.jhu.ece.iacl.plugins.utilities.volume
 
MedicAlgorithmIsotropicReslice() - Constructor for class edu.jhu.ece.iacl.plugins.utilities.volume.MedicAlgorithmIsotropicReslice
 
MedicAlgorithmJistLayoutAdapter - Class in edu.jhu.ece.iacl.jist.plugins
The Class MedicAlgorithmJistLayoutAdapter.
MedicAlgorithmJistLayoutAdapter() - Constructor for class edu.jhu.ece.iacl.jist.plugins.MedicAlgorithmJistLayoutAdapter
 
MedicAlgorithmKLDivergence - Class in edu.jhu.ece.iacl.plugins.utilities.math
 
MedicAlgorithmKLDivergence() - Constructor for class edu.jhu.ece.iacl.plugins.utilities.math.MedicAlgorithmKLDivergence
 
MedicAlgorithmMatchAllImages - Class in edu.jhu.ece.iacl.plugins.utilities.volume
 
MedicAlgorithmMatchAllImages() - Constructor for class edu.jhu.ece.iacl.plugins.utilities.volume.MedicAlgorithmMatchAllImages
 
MedicAlgorithmMipavAdapter - Class in edu.jhu.ece.iacl.jist.plugins
The Class MedicAlgorithmMipavAdapter.
MedicAlgorithmMipavAdapter() - Constructor for class edu.jhu.ece.iacl.jist.plugins.MedicAlgorithmMipavAdapter
 
MedicAlgorithmMipavReorient - Class in edu.jhu.ece.iacl.plugins.utilities.volume
 
MedicAlgorithmMipavReorient() - Constructor for class edu.jhu.ece.iacl.plugins.utilities.volume.MedicAlgorithmMipavReorient
 
MedicAlgorithmMipavReorient.reorientWrapper - Class in edu.jhu.ece.iacl.plugins.utilities.volume
 
MedicAlgorithmMipavReorient.reorientWrapper() - Constructor for class edu.jhu.ece.iacl.plugins.utilities.volume.MedicAlgorithmMipavReorient.reorientWrapper
 
MedicAlgorithmMultiAtlasLabeling - Class in edu.jhu.ece.iacl.plugins.labeling
 
MedicAlgorithmMultiAtlasLabeling() - Constructor for class edu.jhu.ece.iacl.plugins.labeling.MedicAlgorithmMultiAtlasLabeling
 
MedicAlgorithmMultiAtlasReg - Class in edu.jhu.ece.iacl.plugins.registration
 
MedicAlgorithmMultiAtlasReg() - Constructor for class edu.jhu.ece.iacl.plugins.registration.MedicAlgorithmMultiAtlasReg
 
MedicAlgorithmMultiAtlasSurfaceLabeling - Class in edu.jhu.ece.iacl.plugins.labeling
 
MedicAlgorithmMultiAtlasSurfaceLabeling() - Constructor for class edu.jhu.ece.iacl.plugins.labeling.MedicAlgorithmMultiAtlasSurfaceLabeling
 
MedicAlgorithmMultiAtlasSurfaceLabeling.Wrapper - Class in edu.jhu.ece.iacl.plugins.labeling
 
MedicAlgorithmMultiAtlasSurfaceLabeling.Wrapper() - Constructor for class edu.jhu.ece.iacl.plugins.labeling.MedicAlgorithmMultiAtlasSurfaceLabeling.Wrapper
 
MedicAlgorithmMultiCrop - Class in edu.jhu.ece.iacl.plugins.utilities.volume
 
MedicAlgorithmMultiCrop() - Constructor for class edu.jhu.ece.iacl.plugins.utilities.volume.MedicAlgorithmMultiCrop
Create input parameters for Cropper :cubic volume and borderSize
MedicAlgorithmMultiDeformVolume - Class in edu.jhu.ece.iacl.plugins.registration
 
MedicAlgorithmMultiDeformVolume() - Constructor for class edu.jhu.ece.iacl.plugins.registration.MedicAlgorithmMultiDeformVolume
 
MedicAlgorithmMultiDeformVolume.ExecuteWrapper - Class in edu.jhu.ece.iacl.plugins.registration
 
MedicAlgorithmMultiDeformVolume.ExecuteWrapper() - Constructor for class edu.jhu.ece.iacl.plugins.registration.MedicAlgorithmMultiDeformVolume.ExecuteWrapper
 
MedicAlgorithmMultiGradientTableCreator - Class in edu.jhu.ece.iacl.plugins.dti
 
MedicAlgorithmMultiGradientTableCreator() - Constructor for class edu.jhu.ece.iacl.plugins.dti.MedicAlgorithmMultiGradientTableCreator
 
MedicAlgorithmMultiParV3Info - Class in edu.jhu.ece.iacl.plugins.dti
 
MedicAlgorithmMultiParV3Info() - Constructor for class edu.jhu.ece.iacl.plugins.dti.MedicAlgorithmMultiParV3Info
 
MedicAlgorithmMultiParV4Info - Class in edu.jhu.ece.iacl.plugins.dti
 
MedicAlgorithmMultiParV4Info() - Constructor for class edu.jhu.ece.iacl.plugins.dti.MedicAlgorithmMultiParV4Info
 
MedicAlgorithmReshapePoints - Class in edu.jhu.ece.iacl.plugins.utilities.surface
 
MedicAlgorithmReshapePoints() - Constructor for class edu.jhu.ece.iacl.plugins.utilities.surface.MedicAlgorithmReshapePoints
 
MedicAlgorithmReshapeSurface - Class in edu.jhu.ece.iacl.plugins.utilities.surface
 
MedicAlgorithmReshapeSurface() - Constructor for class edu.jhu.ece.iacl.plugins.utilities.surface.MedicAlgorithmReshapeSurface
 
MedicAlgorithmReverseComponents - Class in edu.jhu.ece.iacl.plugins.utilities.volume
 
MedicAlgorithmReverseComponents() - Constructor for class edu.jhu.ece.iacl.plugins.utilities.volume.MedicAlgorithmReverseComponents
 
MedicAlgorithmSerializeSurfaces - Class in edu.jhu.ece.iacl.plugins.utilities.logic
 
MedicAlgorithmSerializeSurfaces() - Constructor for class edu.jhu.ece.iacl.plugins.utilities.logic.MedicAlgorithmSerializeSurfaces
 
MedicAlgorithmSerializeVolumes - Class in edu.jhu.ece.iacl.plugins.utilities.logic
 
MedicAlgorithmSerializeVolumes() - Constructor for class edu.jhu.ece.iacl.plugins.utilities.logic.MedicAlgorithmSerializeVolumes
 
MedicAlgorithmSetHeaders - Class in edu.jhu.ece.iacl.plugins.utilities.volume
 
MedicAlgorithmSetHeaders() - Constructor for class edu.jhu.ece.iacl.plugins.utilities.volume.MedicAlgorithmSetHeaders
 
MedicAlgorithmSTAPLE - Class in edu.jhu.ece.iacl.plugins.labeling.staple
 
MedicAlgorithmSTAPLE() - Constructor for class edu.jhu.ece.iacl.plugins.labeling.staple.MedicAlgorithmSTAPLE
 
MedicAlgorithmSTAPLEgeneral - Class in edu.jhu.ece.iacl.plugins.labeling.staple
 
MedicAlgorithmSTAPLEgeneral() - Constructor for class edu.jhu.ece.iacl.plugins.labeling.staple.MedicAlgorithmSTAPLEgeneral
 
MedicAlgorithmSTAPLEsurface - Class in edu.jhu.ece.iacl.plugins.labeling.staple
 
MedicAlgorithmSTAPLEsurface() - Constructor for class edu.jhu.ece.iacl.plugins.labeling.staple.MedicAlgorithmSTAPLEsurface
 
MedicAlgorithmSubsampleFibers - Class in edu.jhu.ece.iacl.plugins.dti
 
MedicAlgorithmSubsampleFibers() - Constructor for class edu.jhu.ece.iacl.plugins.dti.MedicAlgorithmSubsampleFibers
 
MedicAlgorithmSubsampleFibers.StaticCurve - Class in edu.jhu.ece.iacl.plugins.dti
 
MedicAlgorithmSubsampleFibers.StaticCurve(Curve) - Constructor for class edu.jhu.ece.iacl.plugins.dti.MedicAlgorithmSubsampleFibers.StaticCurve
 
MedicAlgorithmSurfaceConverter - Class in edu.jhu.ece.iacl.plugins.utilities.file
 
MedicAlgorithmSurfaceConverter() - Constructor for class edu.jhu.ece.iacl.plugins.utilities.file.MedicAlgorithmSurfaceConverter
 
MedicAlgorithmSurfaceHistogram - Class in edu.jhu.ece.iacl.plugins.utilities.surface
 
MedicAlgorithmSurfaceHistogram() - Constructor for class edu.jhu.ece.iacl.plugins.utilities.surface.MedicAlgorithmSurfaceHistogram
 
MedicAlgorithmSurfaceSplitter - Class in edu.jhu.ece.iacl.plugins.utilities.logic
 
MedicAlgorithmSurfaceSplitter() - Constructor for class edu.jhu.ece.iacl.plugins.utilities.logic.MedicAlgorithmSurfaceSplitter
 
MedicAlgorithmSurfaceToVolumeConverter - Class in edu.jhu.ece.iacl.plugins.utilities.surface
 
MedicAlgorithmSurfaceToVolumeConverter() - Constructor for class edu.jhu.ece.iacl.plugins.utilities.surface.MedicAlgorithmSurfaceToVolumeConverter
 
MedicAlgorithmTableFormat - Class in edu.jhu.ece.iacl.plugins.dti
 
MedicAlgorithmTableFormat() - Constructor for class edu.jhu.ece.iacl.plugins.dti.MedicAlgorithmTableFormat
 
MedicAlgorithmTensorFormatConvert - Class in edu.jhu.ece.iacl.plugins.dti
 
MedicAlgorithmTensorFormatConvert() - Constructor for class edu.jhu.ece.iacl.plugins.dti.MedicAlgorithmTensorFormatConvert
 
MedicAlgorithmThreshold - Class in edu.jhu.ece.iacl.plugins.utilities.volume
 
MedicAlgorithmThreshold() - Constructor for class edu.jhu.ece.iacl.plugins.utilities.volume.MedicAlgorithmThreshold
 
MedicAlgorithmTransformFibers - Class in edu.jhu.ece.iacl.plugins.dti.tractography
 
MedicAlgorithmTransformFibers() - Constructor for class edu.jhu.ece.iacl.plugins.dti.tractography.MedicAlgorithmTransformFibers
 
MedicAlgorithmTransformVolume - Class in edu.jhu.ece.iacl.plugins.registration
 
MedicAlgorithmTransformVolume() - Constructor for class edu.jhu.ece.iacl.plugins.registration.MedicAlgorithmTransformVolume
 
MedicAlgorithmTransformVolume.ExecuteWrapper - Class in edu.jhu.ece.iacl.plugins.registration
 
MedicAlgorithmTransformVolume.ExecuteWrapper() - Constructor for class edu.jhu.ece.iacl.plugins.registration.MedicAlgorithmTransformVolume.ExecuteWrapper
 
MedicAlgorithmUncrop - Class in edu.jhu.ece.iacl.plugins.utilities.volume
 
MedicAlgorithmUncrop() - Constructor for class edu.jhu.ece.iacl.plugins.utilities.volume.MedicAlgorithmUncrop
 
MedicAlgorithmVABRA - Class in edu.jhu.ece.iacl.plugins.registration
 
MedicAlgorithmVABRA() - Constructor for class edu.jhu.ece.iacl.plugins.registration.MedicAlgorithmVABRA
 
MedicAlgorithmValueEquals - Class in edu.jhu.ece.iacl.plugins.utilities.logic
 
MedicAlgorithmValueEquals() - Constructor for class edu.jhu.ece.iacl.plugins.utilities.logic.MedicAlgorithmValueEquals
 
MedicAlgorithmValueGreaterThan - Class in edu.jhu.ece.iacl.plugins.utilities.logic
 
MedicAlgorithmValueGreaterThan() - Constructor for class edu.jhu.ece.iacl.plugins.utilities.logic.MedicAlgorithmValueGreaterThan
 
MedicAlgorithmValueInRange - Class in edu.jhu.ece.iacl.plugins.utilities.logic
 
MedicAlgorithmValueInRange() - Constructor for class edu.jhu.ece.iacl.plugins.utilities.logic.MedicAlgorithmValueInRange
 
MedicAlgorithmValueLessThan - Class in edu.jhu.ece.iacl.plugins.utilities.logic
 
MedicAlgorithmValueLessThan() - Constructor for class edu.jhu.ece.iacl.plugins.utilities.logic.MedicAlgorithmValueLessThan
 
MedicAlgorithmVolumeConverter - Class in edu.jhu.ece.iacl.plugins.utilities.file
 
MedicAlgorithmVolumeConverter() - Constructor for class edu.jhu.ece.iacl.plugins.utilities.file.MedicAlgorithmVolumeConverter
 
MedicAlgorithmVolumeConverter2 - Class in edu.jhu.ece.iacl.plugins.utilities.file
 
MedicAlgorithmVolumeConverter2() - Constructor for class edu.jhu.ece.iacl.plugins.utilities.file.MedicAlgorithmVolumeConverter2
 
MedicAlgorithmVolumeConverter4D - Class in edu.jhu.ece.iacl.plugins.utilities.file
 
MedicAlgorithmVolumeConverter4D() - Constructor for class edu.jhu.ece.iacl.plugins.utilities.file.MedicAlgorithmVolumeConverter4D
 
MedicAlgorithmVolumeHistogram - Class in edu.jhu.ece.iacl.plugins.utilities.volume
 
MedicAlgorithmVolumeHistogram() - Constructor for class edu.jhu.ece.iacl.plugins.utilities.volume.MedicAlgorithmVolumeHistogram
 
MedicAlgorithmVolumeListOrganizer - Class in edu.jhu.ece.iacl.plugins.utilities.file
 
MedicAlgorithmVolumeListOrganizer() - Constructor for class edu.jhu.ece.iacl.plugins.utilities.file.MedicAlgorithmVolumeListOrganizer
 
MedicAlgorithmVolumeSplitter - Class in edu.jhu.ece.iacl.plugins.utilities.logic
 
MedicAlgorithmVolumeSplitter() - Constructor for class edu.jhu.ece.iacl.plugins.utilities.logic.MedicAlgorithmVolumeSplitter
 
MedicAlgorithmVolumeToSurfaceLabeling - Class in edu.jhu.ece.iacl.plugins.labeling
 
MedicAlgorithmVolumeToSurfaceLabeling() - Constructor for class edu.jhu.ece.iacl.plugins.labeling.MedicAlgorithmVolumeToSurfaceLabeling
 
MedicAlgorithmWildBootTrac - Class in edu.jhu.ece.iacl.plugins.dti.tractography
 
MedicAlgorithmWildBootTrac() - Constructor for class edu.jhu.ece.iacl.plugins.dti.tractography.MedicAlgorithmWildBootTrac
 
MedicAlgorithmWildBootTrac.ExecuteWrapper - Class in edu.jhu.ece.iacl.plugins.dti.tractography
 
MedicAlgorithmWildBootTrac.ExecuteWrapper() - Constructor for class edu.jhu.ece.iacl.plugins.dti.tractography.MedicAlgorithmWildBootTrac.ExecuteWrapper
 
MedicAlgorithmZip - Class in edu.jhu.ece.iacl.plugins.utilities.file
 
MedicAlgorithmZip() - Constructor for class edu.jhu.ece.iacl.plugins.utilities.file.MedicAlgorithmZip
 
MedicUtilPublic - Class in edu.jhmi.rad.medic.utilities
A collection of utilities for I/O, GUI, interface with MIPAV, etc.
MedicUtilPublic() - Constructor for class edu.jhmi.rad.medic.utilities.MedicUtilPublic
 
MemoryDemo - Class in edu.jhu.bme.smile.demo
 
MemoryDemo() - Constructor for class edu.jhu.bme.smile.demo.MemoryDemo
 
mergeGroups(ArrayList<int[]>) - Method in class edu.jhu.ece.iacl.algorithms.manual_label.LabelImageGroup
 
mesh - Variable in class edu.jhu.cs.cisst.vent.renderer.processing.SurfaceRenderer
The mesh.
meshRegularizationAndAdaptiveSmoothing - Static variable in class edu.jhu.ece.iacl.algorithms.ReferencedPapers
 
METADATA_TAG - Static variable in class edu.jhu.ece.iacl.jist.pipeline.parser.LoniPipeParser
The Constant METADATA_TAG.
MetaImageData4D - Class in edu.jhu.ece.iacl.plugins.dti
 
MetaImageData4D(List<ImageData>) - Constructor for class edu.jhu.ece.iacl.plugins.dti.MetaImageData4D
 
method - Variable in class edu.jhu.cs.cisst.algorithms.geometry.surface.IsoSurfaceGenerator
The is-surface generation method.
methodParam - Variable in class edu.jhu.cs.cisst.plugins.utilities.surface.PlugInIsoSurfaceGenerator
 
mg(ConstBoundaryGrid, ConstNoBoundaryGrid, int, int, int, int) - Method in class edu.jhu.cs.cisst.algorithms.optimize.fmg.FMG
performs the Multigrid algorithm which is at the heart of the FMG algorithm.
mid - Variable in class edu.jhu.ece.iacl.jist.structures.geom.EmbeddedSurface.EdgeSplit
The mid.
midPoint(EmbeddedSurface.Edge) - Method in class edu.jhu.ece.iacl.jist.structures.geom.EmbeddedSurface
Mid point.
midValues(EmbeddedSurface.Edge) - Method in class edu.jhu.ece.iacl.jist.structures.geom.EmbeddedSurface
Mid values.
mimic() - Method in class edu.jhu.ece.iacl.jist.structures.image.ImageData
Create new cubic volume of the same subclass type with the same dimensions Does not copy the values in the volume.
mimic(int, int, int, int) - Method in class edu.jhu.ece.iacl.jist.structures.image.ImageData
Mimic.
mimic() - Method in class edu.jhu.ece.iacl.jist.structures.image.ImageDataByte
 
mimic(int, int, int, int) - Method in class edu.jhu.ece.iacl.jist.structures.image.ImageDataByte
 
mimic() - Method in class edu.jhu.ece.iacl.jist.structures.image.ImageDataColor
 
mimic(int, int, int, int) - Method in class edu.jhu.ece.iacl.jist.structures.image.ImageDataColor
 
mimic() - Method in class edu.jhu.ece.iacl.jist.structures.image.ImageDataDouble
 
mimic(int, int, int, int) - Method in class edu.jhu.ece.iacl.jist.structures.image.ImageDataDouble
 
mimic() - Method in class edu.jhu.ece.iacl.jist.structures.image.ImageDataFloat
 
mimic(int, int, int, int) - Method in class edu.jhu.ece.iacl.jist.structures.image.ImageDataFloat
 
mimic() - Method in class edu.jhu.ece.iacl.jist.structures.image.ImageDataInt
 
mimic(int, int, int, int) - Method in class edu.jhu.ece.iacl.jist.structures.image.ImageDataInt
 
mimic() - Method in class edu.jhu.ece.iacl.jist.structures.image.ImageDataMipav
 
mimic(int, int, int, int) - Method in class edu.jhu.ece.iacl.jist.structures.image.ImageDataMipav
 
mimic() - Method in class edu.jhu.ece.iacl.jist.structures.image.ImageDataUByte
 
mimic(int, int, int, int) - Method in class edu.jhu.ece.iacl.jist.structures.image.ImageDataUByte
 
min(float, float) - Static method in class edu.jhmi.rad.medic.utilities.NumericsPublic
 
min(double, double) - Static method in class edu.jhmi.rad.medic.utilities.NumericsPublic
 
min(int, int) - Static method in class edu.jhmi.rad.medic.utilities.NumericsPublic
 
min(long, long) - Static method in class edu.jhmi.rad.medic.utilities.NumericsPublic
 
min(float, float, float) - Static method in class edu.jhmi.rad.medic.utilities.NumericsPublic
 
min - Variable in class edu.jhu.bme.smile.commons.math.HistogramGenerator
 
min(Matrix) - Static method in class edu.jhu.bme.smile.commons.math.MatrixMath
 
min(double[]) - Static method in class edu.jhu.bme.smile.commons.math.StatisticsDouble
 
min - Variable in class edu.jhu.cs.cisst.vent.renderer.processing.VolumeSliceRenderer
 
min - Variable in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamNumber
The min.
min - Variable in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamNumberCollection
The min.
min - Variable in class edu.jhu.ece.iacl.jist.pipeline.view.input.ParamDoubleSliderInputView
The max.
min - Variable in class edu.jhu.ece.iacl.plugins.utilities.surface.MedicAlgorithmSurfaceHistogram
 
min - Variable in class edu.jhu.ece.iacl.plugins.utilities.volume.MedicAlgorithmVolumeHistogram
 
MIN_DOUBLE_VALUE - Static variable in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamNumber
The Constant MIN_DOUBLE_VALUE.
MIN_FLOAT_VALUE - Static variable in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamNumber
The Constant MIN_FLOAT_VALUE.
MIN_INT_VALUE - Static variable in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamNumber
The Constant MIN_INT_VALUE.
MIN_LONG_VALUE - Static variable in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamNumber
The Constant MIN_LONG_VALUE.
minChen - Static variable in class edu.jhu.ece.iacl.algorithms.CommonAuthors
 
mindex - Variable in class edu.jhu.ece.iacl.algorithms.manual_label.staple.STAPLEmulti2
 
minimum(float[][][], int, int, int) - Static method in class edu.jhmi.rad.medic.libraries.ImageFunctionsPublic
minimum value of the image
minimum(int[][][], int, int, int) - Static method in class edu.jhmi.rad.medic.libraries.ImageFunctionsPublic
minimum value of the image
minimum(byte[][][], int, int, int) - Static method in class edu.jhmi.rad.medic.libraries.ImageFunctionsPublic
minimum value of the image
minlabel - Variable in class edu.jhu.ece.iacl.plugins.labeling.MedicAlgorithmFMLabelExtension
 
minLen - Variable in class edu.jhu.ece.iacl.algorithms.dti.tractography.FiberTracker
 
minLen - Variable in class edu.jhu.ece.iacl.algorithms.dti.tractography.WildBootFiberTracker
 
minLength - Variable in class edu.jhu.ece.iacl.algorithms.dti.tractography.FACT.FACTparameters
 
minmag(float, float) - Static method in class edu.jhmi.rad.medic.utilities.NumericsPublic
 
MinToMax1D - Class in edu.jhu.bme.smile.commons.optimize
Finds the maximum of 1D functions by negating the function and finding the minimum.
MinToMax1D(Optimizable1DContinuous) - Constructor for class edu.jhu.bme.smile.commons.optimize.MinToMax1D
Constructor to create the negated function
MinToMax1DDifferentiable - Class in edu.jhu.bme.smile.commons.optimize
Finds the maximum of Diffentiable 1D functions by negating the function and finding the minimum.
MinToMax1DDifferentiable(Optimizable1DContinuousDifferentiable) - Constructor for class edu.jhu.bme.smile.commons.optimize.MinToMax1DDifferentiable
Constructor to create the negated function
MinToMaxND - Class in edu.jhu.bme.smile.commons.optimize
Finds the maximum of ND functions by negating the function and finding the minimum.
MinToMaxND(OptimizableNDContinuous) - Constructor for class edu.jhu.bme.smile.commons.optimize.MinToMaxND
Constructor to create the negated function
MinToMaxNDDifferentiable - Class in edu.jhu.bme.smile.commons.optimize
Finds the maximum of Differentiable ND functions by negating the function and finding the minimum.
MinToMaxNDDifferentiable(OptimizableNDContinuousDifferentiable) - Constructor for class edu.jhu.bme.smile.commons.optimize.MinToMaxNDDifferentiable
Constructor to create the negated function
minus(PT) - Method in class edu.jhu.ece.iacl.jist.structures.geom.PT
Minus.
MipavController - Class in edu.jhu.ece.iacl.jist.io
Image Manipulation Utilities that require ViewUserInterface.
MipavController() - Constructor for class edu.jhu.ece.iacl.jist.io.MipavController
 
MipavFileVOI - Class in edu.jhu.ece.iacl.jist.io
VOI reader/writer.
MipavFileVOI(String, String, ModelImage) - Constructor for class edu.jhu.ece.iacl.jist.io.MipavFileVOI
Instantiates a new mipav file voi.
MipavPluginParser - Class in edu.jhu.ece.iacl.jist.pipeline.parser
 
MipavPluginParser() - Constructor for class edu.jhu.ece.iacl.jist.pipeline.parser.MipavPluginParser
 
MipavPluginParser(ActionDiscovery) - Constructor for class edu.jhu.ece.iacl.jist.pipeline.parser.MipavPluginParser
 
MipavScriptParser - Class in edu.jhu.ece.iacl.jist.pipeline.parser
 
MipavScriptParser() - Constructor for class edu.jhu.ece.iacl.jist.pipeline.parser.MipavScriptParser
 
MipavScriptRunner - Class in edu.jhu.ece.iacl.jist.pipeline
Overload MIPAV's script runner.
MipavScriptRunner() - Constructor for class edu.jhu.ece.iacl.jist.pipeline.MipavScriptRunner
Instantiates a new mipav script runner.
MipavSurfaceReader - Class in edu.jhu.ece.iacl.jist.io
The Class MipavSurfaceReader.
MipavSurfaceReader() - Constructor for class edu.jhu.ece.iacl.jist.io.MipavSurfaceReader
 
MipavSurfaceXMLReader - Class in edu.jhu.ece.iacl.jist.io
The Class MipavSurfaceXMLReader.
MipavSurfaceXMLReader() - Constructor for class edu.jhu.ece.iacl.jist.io.MipavSurfaceXMLReader
 
MipavSurfaceXMLWriter - Class in edu.jhu.ece.iacl.jist.io
The Class MipavSurfaceXMLWriter.
MipavSurfaceXMLWriter() - Constructor for class edu.jhu.ece.iacl.jist.io.MipavSurfaceXMLWriter
 
MipavTestHarness - Class in edu.jhu.ece.iacl.jist.test
The Class MipavTestHarness.
MipavTestHarness(ProcessingApplication) - Constructor for class edu.jhu.ece.iacl.jist.test.MipavTestHarness
Instantiates a new mipav test harness.
MipavTestHarness() - Constructor for class edu.jhu.ece.iacl.jist.test.MipavTestHarness
Instantiates a new mipav test harness.
MipavTestHarness(String[]) - Constructor for class edu.jhu.ece.iacl.jist.test.MipavTestHarness
Instantiates a new mipav test harness.
MipavViewUserInterface - Class in edu.jhu.ece.iacl.jist.pipeline
Overload MIPAV's view user interface.
MipavViewUserInterface() - Constructor for class edu.jhu.ece.iacl.jist.pipeline.MipavViewUserInterface
Instantiates a new mipav view user interface.
MipavViewUserInterface(boolean) - Constructor for class edu.jhu.ece.iacl.jist.pipeline.MipavViewUserInterface
Instantiates a new mipav view user interface.
MipavVOI - Class in edu.jhu.ece.iacl.jist.structures.geom
The Class MipavVOI.
MipavVOI(String, int) - Constructor for class edu.jhu.ece.iacl.jist.structures.geom.MipavVOI
Instantiates a new mipav voi.
mixedEffectsModelEM - Static variable in class edu.jhu.ece.iacl.algorithms.ReferencedPapers
 
mixedEffectsModelLindstromBates - Static variable in class edu.jhu.ece.iacl.algorithms.ReferencedPapers
 
MLTensor - Class in edu.jhu.bme.smile.commons.optimize.tensor
This class is used to minimize the least likelihood estimator from data from diffusion weighted imaging.
MLTensor() - Constructor for class edu.jhu.bme.smile.commons.optimize.tensor.MLTensor
 
mnbrakd(double[], double[], double[], double[], double[], double[], NumericalMethod) - Method in class edu.jhu.ece.iacl.algorithms.vabra.NumericalRecipes
 
mnLen - Variable in class edu.jhu.ece.iacl.algorithms.dti.tractography.FiberTracker
 
mnLen - Variable in class edu.jhu.ece.iacl.algorithms.dti.tractography.WildBootFiberTracker
 
modality - Variable in class edu.jhu.ece.iacl.jist.structures.image.ImageHeader
The modality.
ModelImageReaderWriter - Class in edu.jhu.ece.iacl.jist.io
The Class ModelImageReaderWriter.
ModelImageReaderWriter() - Constructor for class edu.jhu.ece.iacl.jist.io.ModelImageReaderWriter
Instantiates a new model image reader writer.
MODULE_FLAVOR - Static variable in class edu.jhu.ece.iacl.jist.pipeline.tree.DraggableNode
The Constant MODULE_FLAVOR.
MODULE_GROUP_TAG - Static variable in class edu.jhu.ece.iacl.jist.pipeline.parser.LoniPipeParser
The Constant MODULE_GROUP_TAG.
MODULE_TAG - Static variable in class edu.jhu.ece.iacl.jist.pipeline.parser.LoniPipeParser
The Constant MODULE_TAG.
moduleGroup - Variable in class edu.jhu.ece.iacl.jist.pipeline.PipeAlgorithmGroup
Collection of PipeAlgorithms.
modules - Variable in class edu.jhu.ece.iacl.doc.DocumentAllTests.TestCase
 
ModuleTreePanel - Class in edu.jhu.ece.iacl.jist.pipeline.gui
Panel for selecting module components.
ModuleTreePanel() - Constructor for class edu.jhu.ece.iacl.jist.pipeline.gui.ModuleTreePanel
Default constructor.
ModuleTreePanel.DraggableTreeCellRenderer - Class in edu.jhu.ece.iacl.jist.pipeline.gui
The Class DraggableTreeCellRenderer.
ModuleTreePanel.DraggableTreeCellRenderer() - Constructor for class edu.jhu.ece.iacl.jist.pipeline.gui.ModuleTreePanel.DraggableTreeCellRenderer
Instantiates a new draggable tree cell renderer.
ModuleTreePanel.InitializeWorker - Class in edu.jhu.ece.iacl.jist.pipeline.gui
Initialize module tree.
ModuleTreePanel.InitializeWorker(Component) - Constructor for class edu.jhu.ece.iacl.jist.pipeline.gui.ModuleTreePanel.InitializeWorker
Instantiates a new initialize worker.
ModuleTreePanel.RebuildWorker - Class in edu.jhu.ece.iacl.jist.pipeline.gui
Rebuild tree.
ModuleTreePanel.RebuildWorker(Component, boolean) - Constructor for class edu.jhu.ece.iacl.jist.pipeline.gui.ModuleTreePanel.RebuildWorker
Instantiates a new rebuild worker.
monitor(double, int) - Method in class edu.jhu.cs.cisst.algorithms.segmentation.gac.GradientVectorFlow2D
 
monitor(double, Vector, int) - Method in class edu.jhu.cs.cisst.algorithms.segmentation.gac.GradientVectorFlow2D
 
monitor(double, int) - Method in class edu.jhu.cs.cisst.algorithms.segmentation.gac.VectorFieldDiffusion2D
 
monitor(double, Vector, int) - Method in class edu.jhu.cs.cisst.algorithms.segmentation.gac.VectorFieldDiffusion2D
 
monitor - Variable in class edu.jhu.ece.iacl.jist.pipeline.AbstractCalculation
monitor to track current thread.
mouseClicked(MouseEvent) - Method in class edu.jhu.ece.iacl.jist.pipeline.gui.ModuleTreePanel
 
mouseClicked(MouseEvent) - Method in class edu.jhu.ece.iacl.jist.pipeline.gui.PlugInSelector
 
mouseClicked(MouseEvent) - Method in class edu.jhu.ece.iacl.jist.pipeline.gui.ProcessManagerTable
 
mouseClicked(MouseEvent) - Method in class edu.jhu.ece.iacl.jist.pipeline.view.output.ParamSurfaceOutputView
 
mouseDragged() - Method in class edu.jhu.cs.cisst.vent.widgets.VisualizationImage
Mouse dragged.
mouseDragged() - Method in class edu.jhu.cs.cisst.vent.widgets.VisualizationTriangleMesh
 
mouseDragged(MouseEvent) - Method in class edu.jhu.ece.iacl.jist.pipeline.graph.PipeMarqueeHandler
 
mouseEntered(MouseEvent) - Method in class edu.jhu.ece.iacl.jist.pipeline.gui.ModuleTreePanel
 
mouseEntered(MouseEvent) - Method in class edu.jhu.ece.iacl.jist.pipeline.gui.PlugInSelector
 
mouseEntered(MouseEvent) - Method in class edu.jhu.ece.iacl.jist.pipeline.gui.ProcessManagerTable
 
mouseEntered(MouseEvent) - Method in class edu.jhu.ece.iacl.jist.pipeline.view.output.ParamSurfaceOutputView
 
mouseExited(MouseEvent) - Method in class edu.jhu.ece.iacl.jist.pipeline.gui.ModuleTreePanel
 
mouseExited(MouseEvent) - Method in class edu.jhu.ece.iacl.jist.pipeline.gui.PlugInSelector
 
mouseExited(MouseEvent) - Method in class edu.jhu.ece.iacl.jist.pipeline.gui.ProcessManagerTable
 
mouseExited(MouseEvent) - Method in class edu.jhu.ece.iacl.jist.pipeline.view.output.ParamSurfaceOutputView
 
mouseMoved(MouseEvent) - Method in class edu.jhu.ece.iacl.jist.pipeline.graph.PipeMarqueeHandler
 
mousePressed(MouseEvent) - Method in class edu.jhu.ece.iacl.jist.pipeline.graph.PipeMarqueeHandler
 
mousePressed(MouseEvent) - Method in class edu.jhu.ece.iacl.jist.pipeline.gui.ModuleTreePanel
 
mousePressed(MouseEvent) - Method in class edu.jhu.ece.iacl.jist.pipeline.gui.PlugInSelector
 
mousePressed(MouseEvent) - Method in class edu.jhu.ece.iacl.jist.pipeline.gui.ProcessManagerTable
 
mousePressed(MouseEvent) - Method in class edu.jhu.ece.iacl.jist.pipeline.view.output.ParamSurfaceOutputView
 
mouseReleased(MouseEvent) - Method in class edu.jhu.ece.iacl.jist.pipeline.graph.JGraphFoldingManager
Called when the mouse button is released to see if a collapse or expand request has been made.
mouseReleased(MouseEvent) - Method in class edu.jhu.ece.iacl.jist.pipeline.graph.PipeMarqueeHandler
 
mouseReleased(MouseEvent) - Method in class edu.jhu.ece.iacl.jist.pipeline.gui.ModuleTreePanel
 
mouseReleased(MouseEvent) - Method in class edu.jhu.ece.iacl.jist.pipeline.gui.PlugInSelector
 
mouseReleased(MouseEvent) - Method in class edu.jhu.ece.iacl.jist.pipeline.gui.ProcessManagerTable
 
mouseReleased(MouseEvent) - Method in class edu.jhu.ece.iacl.jist.pipeline.view.output.ParamSurfaceOutputView
 
moveAllChildrenIntoDirectory() - Method in class edu.jhu.ece.iacl.jist.pipeline.tree.PackageNode
Move all children of this package into the directory corresponding to this package if they are not already in that directory.
moveIntoDirectory(PipeAlgorithmFactory.AlgorithmNode) - Method in class edu.jhu.ece.iacl.jist.pipeline.tree.PackageNode
Move node into the directory corresponding to this package node.
moveIntoDirectory(PackageNode) - Method in class edu.jhu.ece.iacl.jist.pipeline.tree.PackageNode
Move package node into the directory corresponding to this package.
mrfICM(int) - Method in class edu.jhu.ece.iacl.algorithms.manual_label.staple.STAPLEgeneral
Attempt to solve the MRF using Iterated Conditional Modes
mrfiters - Variable in class edu.jhu.ece.iacl.algorithms.manual_label.staple.STAPLEgeneral
 
mrfMethod - Variable in class edu.jhu.ece.iacl.algorithms.manual_label.staple.STAPLEgeneral
 
mrfMethod - Variable in class edu.jhu.ece.iacl.algorithms.manual_label.staple.STAPLEmulti
 
mrfMethod - Variable in class edu.jhu.ece.iacl.algorithms.manual_label.staple.STAPLEmulti2
 
mrfRL(int) - Method in class edu.jhu.ece.iacl.algorithms.manual_label.staple.STAPLEgeneral
Attempt to solve the MRF using a Relaxation Labeling technique
Mstep() - Method in class edu.jhu.ece.iacl.algorithms.manual_label.staple.STAPLE
 
Mstep() - Method in class edu.jhu.ece.iacl.algorithms.manual_label.staple.STAPLEgeneral
 
Mstep() - Method in class edu.jhu.ece.iacl.algorithms.manual_label.staple.STAPLEgeneralSingle
 
Mstep() - Method in class edu.jhu.ece.iacl.algorithms.manual_label.staple.STAPLEmulti
 
Mstep() - Method in class edu.jhu.ece.iacl.algorithms.manual_label.staple.STAPLEmulti2
 
Mstep() - Method in class edu.jhu.ece.iacl.algorithms.manual_label.staple.STAPLEsingle
 
Mstep() - Method in class edu.jhu.ece.iacl.algorithms.manual_label.staple.STAPLEsurf
 
MstepEfficient() - Method in class edu.jhu.ece.iacl.algorithms.manual_label.staple.STAPLEmulti
 
MstepEfficient() - Method in class edu.jhu.ece.iacl.algorithms.manual_label.staple.STAPLEmulti2
 
MSWASSR - Class in edu.jhu.ece.iacl.algorithms.spectro
 
MSWASSR() - Constructor for class edu.jhu.ece.iacl.algorithms.spectro.MSWASSR
 
MSWASSR.Symscore - Class in edu.jhu.ece.iacl.algorithms.spectro
function score = symscore(X,y,c) yc=interp1(c-X,y,X,'v5cubic'); score = meannan(((y(:)-yc(:)).^2));
MSWASSR.Symscore(double[], double[]) - Constructor for class edu.jhu.ece.iacl.algorithms.spectro.MSWASSR.Symscore
 
MU - Variable in class edu.jhu.bme.smile.commons.math.L1LSCompressedSensing
 
mul(Voxel) - Method in class edu.jhu.ece.iacl.jist.structures.image.Voxel
Mul.
mul(Voxel) - Method in class edu.jhu.ece.iacl.jist.structures.image.VoxelBoolean
 
mul(Voxel) - Method in class edu.jhu.ece.iacl.jist.structures.image.VoxelColor
 
mul(Voxel) - Method in class edu.jhu.ece.iacl.jist.structures.image.VoxelDouble
 
mul(Voxel) - Method in class edu.jhu.ece.iacl.jist.structures.image.VoxelFloat
 
mul(Voxel) - Method in class edu.jhu.ece.iacl.jist.structures.image.VoxelIndexed
 
mul(Voxel) - Method in class edu.jhu.ece.iacl.jist.structures.image.VoxelInt
 
mul(Voxel) - Method in class edu.jhu.ece.iacl.jist.structures.image.VoxelMipav
 
mul(Voxel) - Method in class edu.jhu.ece.iacl.jist.structures.image.VoxelShort
 
mul(Voxel) - Method in class edu.jhu.ece.iacl.jist.structures.image.VoxelUByte
 
mul(Voxel) - Method in class edu.jhu.ece.iacl.jist.structures.image.VoxelVector
 
mul(double) - Method in class edu.jhu.ece.iacl.jist.structures.matrix.Matrix3
Mul.
mul(Matrix3) - Method in class edu.jhu.ece.iacl.jist.structures.matrix.Matrix3
Mul.
mul(double) - Method in class edu.jhu.ece.iacl.jist.structures.matrix.VectorMatrixX
Mul.
mul(VectorMatrixX) - Method in class edu.jhu.ece.iacl.jist.structures.matrix.VectorMatrixX
Mul.
mul(double) - Method in class edu.jhu.ece.iacl.jist.structures.vector.Vector2
 
mul(VectorX) - Method in class edu.jhu.ece.iacl.jist.structures.vector.Vector2
 
mul(double) - Method in class edu.jhu.ece.iacl.jist.structures.vector.Vector3
 
mul(VectorX) - Method in class edu.jhu.ece.iacl.jist.structures.vector.Vector3
 
mul(double) - Method in class edu.jhu.ece.iacl.jist.structures.vector.Vector4
 
mul(VectorX) - Method in class edu.jhu.ece.iacl.jist.structures.vector.Vector4
 
mul(double) - Method in class edu.jhu.ece.iacl.jist.structures.vector.VectorN
 
mul(VectorX) - Method in class edu.jhu.ece.iacl.jist.structures.vector.VectorN
 
mul(double) - Method in interface edu.jhu.ece.iacl.jist.structures.vector.VectorX
Mul.
mul(VectorX) - Method in interface edu.jhu.ece.iacl.jist.structures.vector.VectorX
Mul.
multiGridCycles - Variable in class edu.jhu.cs.cisst.algorithms.segmentation.gac.GradientVectorFlow2D
The multi-grid cycles.
multiGridIterations - Variable in class edu.jhu.cs.cisst.algorithms.segmentation.gac.GradientVectorFlow2D
The multi-grid iterations.
multiGridResolutions - Variable in class edu.jhu.cs.cisst.algorithms.segmentation.gac.GradientVectorFlow2D
The multi-grid resolutions.
multiGridThreads - Variable in class edu.jhu.cs.cisst.algorithms.segmentation.gac.GradientVectorFlow2D
The multigrid threads.
multiOption - Variable in class edu.jhu.ece.iacl.jist.pipeline.src.PipeSelectionSource
The multi option.
multiplyFloatImage(ImageData, ImageData) - Static method in class edu.jhu.ece.iacl.structures.image.ImageDataMath
Multiply float image.
multMatrix(Matrix, Point3f) - Static method in class edu.jhu.ece.iacl.jist.algorithms.graphics.GeomUtil
Mult matrix.
multMatrix(Matrix, double[]) - Static method in class edu.jhu.ece.iacl.jist.algorithms.graphics.GeomUtil
Mult matrix.
multMatrix(Matrix3d, double[]) - Static method in class edu.jhu.ece.iacl.jist.algorithms.graphics.GeomUtil
Mult matrix.
multMatrix(Matrix3d, Point3f) - Static method in class edu.jhu.ece.iacl.jist.algorithms.graphics.GeomUtil
Mult matrix.
multMatrix(Matrix3d, Vector3f) - Static method in class edu.jhu.ece.iacl.jist.algorithms.graphics.GeomUtil
Mult matrix.
multMatrix(Matrix3d, Point3d) - Static method in class edu.jhu.ece.iacl.jist.algorithms.graphics.GeomUtil
Mult matrix.
multMatrix3d(Matrix3d, Point3f) - Static method in class edu.jhu.ece.iacl.jist.algorithms.graphics.GeomUtil
Mult matrix3d.
multMatrix3d(Matrix3d, Point3d) - Static method in class edu.jhu.ece.iacl.jist.algorithms.graphics.GeomUtil
Mult matrix3d.
mySize(Double[]) - Method in class edu.jhu.ece.iacl.algorithms.dti.tractography.FACT.FACTapi
 

N

n - Variable in class edu.jhu.bme.smile.commons.math.L1LSCompressedSensing
 
name - Variable in class edu.jhu.cs.cisst.vent.VisualizationProcessing
The name.
name - Variable in class edu.jhu.ece.iacl.algorithms.manual_label.LabelImage
 
name - Variable in class edu.jhu.ece.iacl.algorithms.manual_label.LabelSurface
 
name - Variable in class edu.jhu.ece.iacl.jist.pipeline.AlgorithmInformation
name and label for parameter.
name - Variable in class edu.jhu.ece.iacl.jist.pipeline.graph.PipeModuleFactory
The name.
name - Variable in class edu.jhu.ece.iacl.jist.pipeline.parameter.DataLabel
The name.
name - Variable in class edu.jhu.ece.iacl.jist.pipeline.PipeModule
Unique name to identify this parameter.
name - Variable in class edu.jhu.ece.iacl.jist.pipeline.view.input.ParamVolumeInputView.VolumeListBoxItem
The name.
name - Variable in class edu.jhu.ece.iacl.jist.pipeline.view.input.ParamVolumeURIInputView.VolumeListBoxItem
The name.
name - Variable in class edu.jhu.ece.iacl.jist.structures.fiber.FiberCollection
The name.
name - Variable in class edu.jhu.ece.iacl.jist.structures.geom.CurveCollection
The name.
name - Variable in class edu.jhu.ece.iacl.jist.structures.geom.EmbeddedPointSet
The name.
name - Variable in class edu.jhu.ece.iacl.jist.structures.image.ImageData
The name.
NameTest - Class in edu.jhu.ece.iacl.pami
 
NameTest() - Constructor for class edu.jhu.ece.iacl.pami.NameTest
 
namingConvention - Variable in class edu.jhu.ece.iacl.jist.pipeline.JistPreferences
namingConvention.
nand(Voxel) - Method in class edu.jhu.ece.iacl.jist.structures.image.VoxelBoolean
Nand.
navidShiee - Static variable in class edu.jhu.ece.iacl.algorithms.CommonAuthors
 
nbhdsize - Variable in class edu.jhu.ece.iacl.algorithms.manual_label.staple.STAPLE
 
nbhdWeight - Variable in class edu.jhu.ece.iacl.algorithms.manual_label.staple.STAPLE
 
nbhdWeightIn - Variable in class edu.jhu.ece.iacl.algorithms.manual_label.staple.STAPLE
 
ncom - Variable in class edu.jhu.ece.iacl.algorithms.vabra.NumericalRecipes
 
NEAREST_NEIGHTBOR - Static variable in class edu.jhu.ece.iacl.algorithms.registration.RegistrationUtilities.InterpolationType
 
nearestNeighborInterpolation(float[][][], float, float, float, int, int, int) - Static method in class edu.jhmi.rad.medic.libraries.ImageFunctionsPublic
linear interpolation, with 0 outside the image
nearestNeighborInterpolation(byte[][][], float, float, float, int, int, int) - Static method in class edu.jhmi.rad.medic.libraries.ImageFunctionsPublic
linear interpolation, with 0 outside the image
nearestNeighborInterpolation(byte[][][], byte, float, float, float, int, int, int) - Static method in class edu.jhmi.rad.medic.libraries.ImageFunctionsPublic
linear interpolation, with given value outside the image
nearestNeighborInterpolation(byte[], byte, float, float, float, int, int, int) - Static method in class edu.jhmi.rad.medic.libraries.ImageFunctionsPublic
linear interpolation, with given value outside the image
nearestNeighborInterpolation(float[][], float, float, float, int, int, int, int) - Static method in class edu.jhmi.rad.medic.libraries.ImageFunctionsPublic
linear interpolation, with given value outside the image
nearestNeighborInterpolation(int[][][], int, float, float, float, int, int, int) - Static method in class edu.jhmi.rad.medic.libraries.ImageFunctionsPublic
linear interpolation, with given value outside the image
neg() - Method in class edu.jhu.ece.iacl.jist.structures.image.Voxel
Neg.
neg() - Method in class edu.jhu.ece.iacl.jist.structures.image.VoxelBoolean
 
neg() - Method in class edu.jhu.ece.iacl.jist.structures.image.VoxelColor
 
neg() - Method in class edu.jhu.ece.iacl.jist.structures.image.VoxelDouble
 
neg() - Method in class edu.jhu.ece.iacl.jist.structures.image.VoxelFloat
 
neg() - Method in class edu.jhu.ece.iacl.jist.structures.image.VoxelIndexed
 
neg() - Method in class edu.jhu.ece.iacl.jist.structures.image.VoxelInt
 
neg() - Method in class edu.jhu.ece.iacl.jist.structures.image.VoxelMipav
 
neg() - Method in class edu.jhu.ece.iacl.jist.structures.image.VoxelShort
 
neg() - Method in class edu.jhu.ece.iacl.jist.structures.image.VoxelUByte
 
neg() - Method in class edu.jhu.ece.iacl.jist.structures.image.VoxelVector
 
negateFloatImage(ImageData) - Static method in class edu.jhu.ece.iacl.structures.image.ImageDataMath
Negate float image.
negToPosCount - Variable in class edu.jhu.cs.cisst.algorithms.segmentation.gac.GeodesicActiveContour2D
The negative to positive transition count.
neighborEdgeFaceTable - Variable in class edu.jhu.ece.iacl.jist.structures.geom.EmbeddedSurface
The neighbor edge face table.
neighborFaceFaceTable - Variable in class edu.jhu.ece.iacl.jist.structures.geom.EmbeddedSurface
The neighbor face face table.
neighborhood() - Method in class edu.jhu.ece.iacl.jist.structures.geom.GridPt
Neighborhood.
neighborhood18C() - Method in class edu.jhu.ece.iacl.jist.structures.geom.GridPt
Neighborhood18 c.
neighborhood18C(GridPt) - Static method in class edu.jhu.ece.iacl.jist.structures.geom.GridPt
Neighborhood18 c.
neighborhood18C(int, int, int) - Static method in class edu.jhu.ece.iacl.jist.structures.geom.GridPt
Neighborhood18 c.
neighborhood26C() - Method in class edu.jhu.ece.iacl.jist.structures.geom.GridPt
Neighborhood26 c.
neighborhood26C(GridPt) - Static method in class edu.jhu.ece.iacl.jist.structures.geom.GridPt
Neighborhood26 c.
neighborhood26C(int, int, int) - Static method in class edu.jhu.ece.iacl.jist.structures.geom.GridPt
Neighborhood26 c.
neighborhood6C() - Method in class edu.jhu.ece.iacl.jist.structures.geom.GridPt
Neighborhood6 c.
neighborhood6C(GridPt) - Static method in class edu.jhu.ece.iacl.jist.structures.geom.GridPt
Neighborhood6 c.
neighborhood6C(int, int, int) - Static method in class edu.jhu.ece.iacl.jist.structures.geom.GridPt
Neighborhood6 c.
neighborsX - Static variable in class edu.jhu.cs.cisst.algorithms.segmentation.gac.GeodesicActiveContour2D
The 6-connected neighbors x.
neighborsY - Static variable in class edu.jhu.cs.cisst.algorithms.segmentation.gac.GeodesicActiveContour2D
The 6-connected neighbors y.
neighborVertexEdgeTable - Variable in class edu.jhu.ece.iacl.jist.structures.geom.EmbeddedSurface
The neighbor vertex edge table.
neighborVertexFaceTable - Variable in class edu.jhu.ece.iacl.jist.structures.geom.EmbeddedSurface
The neighbor vertex face table.
neighborVertexVertexTable - Variable in class edu.jhu.ece.iacl.jist.structures.geom.EmbeddedSurface
The neighbor vertex vertex table.
newInstance(int, int, int, int, double) - Method in interface edu.jhu.cs.cisst.algorithms.optimize.fmg.grid.ConstGrid
create a new grid with exactly the same handling of the boundary (i.e.
newInstance(int, int, int, int, double) - Method in class edu.jhu.cs.cisst.algorithms.optimize.fmg.grid.FixedBoundaryGrid
implements method from ConstGrid.
newInstance(int, int, int, int, double) - Method in class edu.jhu.cs.cisst.algorithms.optimize.fmg.grid.NoBoundaryGrid
implements method from ConstGrid.
newInstance(int, int, int, int, double) - Method in class edu.jhu.cs.cisst.algorithms.optimize.fmg.grid.PeriodicBoundaryGrid
implements method from ConstGrid.
newInstance(int, int, int, int, double) - Method in class edu.jhu.cs.cisst.algorithms.optimize.fmg.grid.RepeatBoundaryGrid
implements method from ConstGrid.
NewtonMethod() - Static method in class edu.jhu.bme.smile.commons.optimize.test.TestNDOptimizations
Line Search using Newton
NewtonMethod1D - Class in edu.jhu.bme.smile.commons.optimize
This optimizer uses Newton's Method of finding roots to find extrema.
NewtonMethod1D() - Constructor for class edu.jhu.bme.smile.commons.optimize.NewtonMethod1D
Default constructor.
NewtonMethod1D(int) - Constructor for class edu.jhu.bme.smile.commons.optimize.NewtonMethod1D
Constructor to specify optimizer and maximum iterations
NewtonMethod1D() - Static method in class edu.jhu.bme.smile.commons.optimize.test.Test1DOptimizations
Newton
nextLine(BufferedReader) - Static method in class edu.jhu.ece.iacl.utility.AtlasList
 
NMI(int[][], int[][], int[][][], int, int) - Static method in class edu.jhu.ece.iacl.algorithms.registration.RegistrationUtilities
 
NMI(int[], int[], int[][], int) - Static method in class edu.jhu.ece.iacl.algorithms.registration.RegistrationUtilities
 
NNInterpolation(ImageData, int, int, int, double, double, double) - Static method in class edu.jhu.ece.iacl.algorithms.registration.RegistrationUtilities
 
NoBoundaryGrid - Class in edu.jhu.cs.cisst.algorithms.optimize.fmg.grid
An implementation of class Grid where no boundary is allowed.
NoBoundaryGrid(int, int, int, int, double) - Constructor for class edu.jhu.cs.cisst.algorithms.optimize.fmg.grid.NoBoundaryGrid
construct from size and initial value for all elements in the interior.
nor(Voxel) - Method in class edu.jhu.ece.iacl.jist.structures.image.VoxelBoolean
Nor.
NormalGenerator - Class in edu.jhu.ece.iacl.jist.structures.geom
The Class NormalGenerator.
NormalGenerator() - Constructor for class edu.jhu.ece.iacl.jist.structures.geom.NormalGenerator
 
normalize - Variable in class edu.jhu.cs.cisst.algorithms.segmentation.gac.GradientVectorFlow2D
The normalize.
normalize(ImageData, boolean) - Static method in class edu.jhu.ece.iacl.algorithms.manual_label.atlasing.LogOdds
 
normalize(double[], double[], int) - Method in class edu.jhu.ece.iacl.algorithms.vabra.VectorVolumeVabra
 
normalize(Tuple3f) - Static method in class edu.jhu.ece.iacl.jist.algorithms.graphics.GeomUtil
Normalize.
normalize(Tuple3d) - Static method in class edu.jhu.ece.iacl.jist.algorithms.graphics.GeomUtil
Normalize.
normalize() - Method in class edu.jhu.ece.iacl.jist.structures.image.ImageDataFloat
Normalize.
normalize() - Method in class edu.jhu.ece.iacl.jist.structures.matrix.Matrix3
Normalize matrix.
normalize() - Method in class edu.jhu.ece.iacl.jist.structures.matrix.VectorMatrixX
Normalize.
normalize() - Method in class edu.jhu.ece.iacl.jist.structures.vector.Vector2
 
normalize() - Method in class edu.jhu.ece.iacl.jist.structures.vector.Vector3
 
normalize() - Method in class edu.jhu.ece.iacl.jist.structures.vector.Vector4
 
normalize() - Method in class edu.jhu.ece.iacl.jist.structures.vector.VectorN
 
normalize() - Method in interface edu.jhu.ece.iacl.jist.structures.vector.VectorX
Normalize.
normalizedAngle(Tuple3f, Tuple3f) - Static method in class edu.jhu.ece.iacl.jist.algorithms.graphics.GeomUtil
Normalized angle.
normalizedTrace() - Method in class edu.jhu.ece.iacl.algorithms.manual_label.staple.PerformanceLevel
Compute normalized trace- The sum of the traces of each rater's confusion matrix normalized by the number of labels and the number of raters
normalizeGrad(double[][]) - Static method in class edu.jhu.bme.smile.commons.optimize.tensor.OptimizeTensor
normalizes the gradient matrix
normalizeHistogram(double[][]) - Static method in class edu.jhu.bme.smile.commons.math.StatisticsDouble
 
normalizeImagesToMax() - Method in class edu.jhu.ece.iacl.algorithms.vabra.ImagePairNMI
 
normalizeJointHistogram(double[][]) - Static method in class edu.jhu.bme.smile.commons.math.StatisticsDouble
 
normalizePoint(Point3f) - Static method in class edu.jhu.bme.smile.commons.math.Point3fMath
 
normalizeSqr(Tuple3f) - Static method in class edu.jhu.ece.iacl.jist.algorithms.graphics.GeomUtil
Normalize sqr.
normalizeSqr(Tuple3d) - Static method in class edu.jhu.ece.iacl.jist.algorithms.graphics.GeomUtil
Normalize sqr.
normalizeToSphere(ModelTriangleMesh, float) - Static method in class edu.jhu.ece.iacl.algorithms.hardi.SurfaceTools
 
normalizeToUnitIntensity(ImageData) - Static method in class edu.jhu.ece.iacl.structures.image.ImageDataMath
Normalize to unit intensity.
NormalizeToUnitMagnitude - Class in edu.jhu.ece.iacl.plugins.hardi
 
NormalizeToUnitMagnitude() - Constructor for class edu.jhu.ece.iacl.plugins.hardi.NormalizeToUnitMagnitude
 
norms - Variable in class edu.jhu.cs.cisst.vent.structures.processing.PTriangleMesh
The norms.
normtrace - Variable in class edu.jhu.ece.iacl.algorithms.manual_label.staple.STAPLEgeneral
 
normtrace - Variable in class edu.jhu.ece.iacl.algorithms.manual_label.staple.STAPLEmulti
 
normtrace - Variable in class edu.jhu.ece.iacl.algorithms.manual_label.staple.STAPLEmulti2
 
notifyListeners(ExecutionContext.Update) - Method in class edu.jhu.ece.iacl.jist.pipeline.ExecutionContext
Notify listeners of change.
notifyListenersOfConnection() - Method in class edu.jhu.ece.iacl.jist.pipeline.PipePort
Notify port listeners of connections.
notifyListenersOfDisconnection(PipePort, PipeConnector) - Method in class edu.jhu.ece.iacl.jist.pipeline.PipePort
Notify port listeners of disconnections.
notifyObservers(ParamModel, ParamInputView) - Method in class edu.jhu.ece.iacl.jist.pipeline.view.input.ParamInputView
Notify all observers that this parameter has changed in this input view.
nrfunc - Variable in class edu.jhu.ece.iacl.algorithms.vabra.NumericalRecipes
 
numberOfCoefficientsInEvenOrder(int) - Static method in class edu.jhu.bme.smile.commons.math.specialFunctions.SphericalHarmonics
 
NumericalMethod - Class in edu.jhu.ece.iacl.algorithms.vabra
 
NumericalMethod(NumericalRecipes) - Constructor for class edu.jhu.ece.iacl.algorithms.vabra.NumericalMethod
 
NumericalRecipes - Class in edu.jhu.ece.iacl.algorithms.vabra
An implementation of a number of numerical recipies, as obfuscated and antiquated as they might be.
NumericalRecipes() - Constructor for class edu.jhu.ece.iacl.algorithms.vabra.NumericalRecipes
 
NumericsPublic - Class in edu.jhmi.rad.medic.utilities
This class computes various basic numerical functions.
NumericsPublic() - Constructor for class edu.jhmi.rad.medic.utilities.NumericsPublic
 
numParams - Variable in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamNumberCollection
The num params.
numPoints - Variable in class edu.jhu.ece.iacl.algorithms.dti.tractography.FiberTracker.FACTfiber
 
numPoints - Variable in class edu.jhu.ece.iacl.algorithms.dti.tractography.WildBootFiberTracker.WildBootFACTfiber
 
numvolumes - Variable in class edu.jhu.ece.iacl.algorithms.dti.GTCparams
 
Nx - Variable in class edu.jhu.ece.iacl.algorithms.dti.tractography.FACT.FACTparameters
 
Nx - Variable in class edu.jhu.ece.iacl.algorithms.dti.tractography.FiberTracker
 
Nx - Variable in class edu.jhu.ece.iacl.algorithms.dti.tractography.WildBootFiberTracker
 
Ny - Variable in class edu.jhu.ece.iacl.algorithms.dti.tractography.FACT.FACTparameters
 
Ny - Variable in class edu.jhu.ece.iacl.algorithms.dti.tractography.FiberTracker
 
Ny - Variable in class edu.jhu.ece.iacl.algorithms.dti.tractography.WildBootFiberTracker
 
Nz - Variable in class edu.jhu.ece.iacl.algorithms.dti.tractography.FACT.FACTparameters
 
Nz - Variable in class edu.jhu.ece.iacl.algorithms.dti.tractography.FiberTracker
 
Nz - Variable in class edu.jhu.ece.iacl.algorithms.dti.tractography.WildBootFiberTracker
 

O

obj - Variable in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamObject
The obj.
ObjectCollection<T> - Interface in edu.jhu.ece.iacl.jist.pipeline.parameter
A data collection is a parameter that contains a collection of parameters.
objs - Variable in class edu.jhu.ece.iacl.jist.pipeline.view.input.Refresher
The objs.
ObservableCalculation - Class in edu.jhu.ece.iacl.jist.pipeline
An empty calculation to use as the root calculation for the Calculation monitor.
ObservableCalculation(String, CalculationMonitor) - Constructor for class edu.jhu.ece.iacl.jist.pipeline.ObservableCalculation
Default constructor.
observe(AbstractCalculation) - Method in class edu.jhu.ece.iacl.jist.pipeline.CalculationMonitor
Start observing a calculation.
observer - Variable in class edu.jhu.ece.iacl.plugins.registration.MedicAlgorithmConstrainedFLIRT.AlgorithmConstrainedOAR3DWrapper
 
observer - Variable in class edu.jhu.ece.iacl.plugins.registration.MedicAlgorithmFLIRT.AlgorithmRegOAR3DWrapper
 
observer - Variable in class edu.jhu.ece.iacl.plugins.registration.MedicAlgorithmFLIRTCollection.AlgorithmRegOAR3DWrapper
 
obstacles - Variable in class edu.jhu.ece.iacl.jist.pipeline.graph.AvoidanceRouting
The obstacles.
octahedron() - Static method in class edu.jhu.ece.iacl.algorithms.hardi.SurfaceTools
 
offset - Variable in class edu.jhu.ece.iacl.algorithms.manual_label.LabelSurface
 
offset - Variable in class edu.jhu.ece.iacl.algorithms.manual_label.staple.STAPLEgeneral
 
offset - Variable in class edu.jhu.ece.iacl.algorithms.manual_label.staple.STAPLEsurf
 
offset - Variable in class edu.jhu.ece.iacl.jist.pipeline.src.PipeListSource
The offset.
okButton - Variable in class edu.jhu.ece.iacl.jist.pipeline.view.input.AlgorithmInformationDialog.AuthorDialog
The cancel button.
oldPanel - Variable in class edu.jhu.ece.iacl.jist.pipeline.gui.PlugInSelector
The old panel.
oneWayHausdorffDistance(LabelImage, int) - Method in class edu.jhu.ece.iacl.algorithms.manual_label.LabelImage
 
onlyInBounds(GridPt[], int, int, int) - Static method in class edu.jhu.ece.iacl.jist.structures.geom.GridPt
If a Grid Point is out of bounds, a null element will be put in its place.
open() - Method in class edu.jhu.ece.iacl.jist.pipeline.gui.ProcessManager
Open layout from file.
open(File) - Method in class edu.jhu.ece.iacl.jist.pipeline.gui.ProcessManager
Open specified layout file.
open(Component) - Static method in class edu.jhu.ece.iacl.jist.pipeline.PipeAlgorithm
Open file from user specified location.
open() - Static method in class edu.jhu.ece.iacl.jist.pipeline.PipeLayout
Create "Open Dialog".
open(Component) - Static method in class edu.jhu.ece.iacl.jist.pipeline.PipeLayout
Create "Open Dialog".
open(String) - Method in class edu.jhu.ece.iacl.jist.test.MipavTestHarness
Open.
openFileDialog(File) - Static method in class edu.jhu.ece.iacl.jist.io.MipavController
Create open file dialog to select either RAW or XML file types.
openLabelFile() - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamDataLabel
Open label file and load it into parameter.
openLabelFile(File) - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamDataLabel
Open the specified label file and load it into the parameter.
openLayout(File) - Method in class edu.jhu.ece.iacl.jist.pipeline.parser.LoniPipeParser
Open layout from script file.
openPipeAlgorithm() - Method in class edu.jhu.ece.iacl.jist.pipeline.parser.JistLayoutParser
 
openPipeAlgorithm() - Method in class edu.jhu.ece.iacl.jist.pipeline.parser.LoniPipeParser
Open LONI script from file.
openPipeAlgorithm() - Method in class edu.jhu.ece.iacl.jist.pipeline.parser.MipavScriptParser
Parse MIPAV script
openPipeAlgorithm() - Method in interface edu.jhu.ece.iacl.jist.pipeline.parser.ScriptParser
Opens dialog box for user to select script file and then parses the file.
opposite(int) - Method in class edu.jhu.ece.iacl.jist.structures.geom.EmbeddedSurface.Edge
Opposite.
opticalFlowAlignment - Static variable in class edu.jhu.ece.iacl.algorithms.ReferencedPapers
 
Optimizable1DContinuous - Interface in edu.jhu.bme.smile.commons.optimize
Interface for 1D functions.
Optimizable1DContinuousDifferentiable - Interface in edu.jhu.bme.smile.commons.optimize
Interface for Differentiable 1D functions.
OptimizableNDContinuous - Interface in edu.jhu.bme.smile.commons.optimize
Interface for ND functions.
OptimizableNDContinuousDifferentiable - Interface in edu.jhu.bme.smile.commons.optimize
Interface for Differentiable ND functions.
optimize(boolean) - Method in class edu.jhu.bme.smile.commons.optimize.BrentMethod1D
Optimizes the function
optimize(boolean) - Method in class edu.jhu.bme.smile.commons.optimize.DownhillSimplexND
Optimizes the function
optimize(boolean) - Method in class edu.jhu.bme.smile.commons.optimize.GoldenSectionSearch1D
Optimizes the function
optimize(boolean) - Method in class edu.jhu.bme.smile.commons.optimize.LevenbergMarquardt
Optimizes the function.
optimize(boolean) - Method in class edu.jhu.bme.smile.commons.optimize.LineSearchND
Optimizes the function
optimize(boolean) - Method in class edu.jhu.bme.smile.commons.optimize.LineSearchNDDifferentiable
Optimizes the function
optimize(boolean) - Method in class edu.jhu.bme.smile.commons.optimize.NewtonMethod1D
Optimizes the function
optimize(boolean) - Method in interface edu.jhu.bme.smile.commons.optimize.Optimizer1DContinuous
Optimizes a function.
optimize(boolean) - Method in interface edu.jhu.bme.smile.commons.optimize.Optimizer1DContinuousDifferentiable
Optimizes a funtion.
optimize(boolean) - Method in interface edu.jhu.bme.smile.commons.optimize.OptimizerNDContinuous
Optimizes a funtion.
optimize(boolean) - Method in interface edu.jhu.bme.smile.commons.optimize.OptimizerNDContinuousDifferentiable
Optimizes a funtion.
optimize6D2D(int, int) - Method in class edu.jhu.bme.smile.commons.optimize.tensor.MLTensor
Lets you specify which algorithm to use and the maximum number of iterations.
optimize6D2D() - Method in class edu.jhu.ece.iacl.algorithms.dti.DTEMRLTensor
Lets you specify which algorithm to use and the maximum number of iterations.
optimize6D2D(int) - Method in class edu.jhu.ece.iacl.algorithms.dti.DTEMRLTensor
 
optimize6D2D(int, int) - Method in class edu.jhu.ece.iacl.algorithms.dti.DTEMRLTensor
 
optimize8D(int) - Method in class edu.jhu.bme.smile.commons.optimize.tensor.MLTensor
Lets you specify which algorithm to use to optimize all 8 parameters at once.
optimize8D() - Method in class edu.jhu.ece.iacl.algorithms.dti.DTEMRLTensor
Lets you specify which algorithm to use to optimize all 8 parameters at once.
optimize8D(int) - Method in class edu.jhu.ece.iacl.algorithms.dti.DTEMRLTensor
 
Optimizer1DContinuous - Interface in edu.jhu.bme.smile.commons.optimize
Interface for 1D optimizers.
Optimizer1DContinuousDifferentiable - Interface in edu.jhu.bme.smile.commons.optimize
Interface for Differentiable 1D functions.
OptimizerNDContinuous - Interface in edu.jhu.bme.smile.commons.optimize
Interface for ND functions.
OptimizerNDContinuousDifferentiable - Interface in edu.jhu.bme.smile.commons.optimize
Interface for Differentiable ND functions.
OptimizeTensor - Class in edu.jhu.bme.smile.commons.optimize.tensor
This class is to test the different optimizers in a simple real-world case.
OptimizeTensor() - Constructor for class edu.jhu.bme.smile.commons.optimize.tensor.OptimizeTensor
 
option - Variable in class edu.jhu.ece.iacl.jist.pipeline.src.PipeSelectionListSource
The option.
option - Variable in class edu.jhu.ece.iacl.jist.pipeline.src.PipeSelectionSource
The option.
optionMap - Variable in class edu.jhu.ece.iacl.jist.pipeline.src.PipeSelectionListSource
The Map
options - Variable in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamMultiOption
The options.
options - Variable in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamOption
The options.
or(Voxel) - Method in class edu.jhu.ece.iacl.jist.structures.image.VoxelBoolean
Or.
organizeLabels() - Method in class edu.jhu.ece.iacl.algorithms.manual_label.LabelImage
 
organizeLabels() - Method in class edu.jhu.ece.iacl.algorithms.manual_label.LabelSurface
Returns a new surface with labels renamed from 1-N in the order they are found in the 'allhits' array
orientDicom - Variable in class edu.jhu.ece.iacl.plugins.utilities.volume.MedicAlgorithmMipavReorient
 
orientX - Variable in class edu.jhu.ece.iacl.plugins.utilities.volume.MedicAlgorithmMipavReorient
 
orientY - Variable in class edu.jhu.ece.iacl.plugins.utilities.volume.MedicAlgorithmMipavReorient
 
orientZ - Variable in class edu.jhu.ece.iacl.plugins.utilities.volume.MedicAlgorithmMipavReorient
 
origImageParam - Variable in class edu.jhu.cs.cisst.plugins.visualization.PlugInVisualizeActiveContour2D
 
origImageParam - Variable in class edu.jhu.cs.cisst.plugins.visualization.PlugInVisualizeImage
 
origin - Variable in class edu.jhu.ece.iacl.jist.structures.geom.EmbeddedSurface
The origin.
origin - Variable in class edu.jhu.ece.iacl.jist.structures.image.ImageHeader
The origin.
originalSubject - Variable in class edu.jhu.ece.iacl.algorithms.vabra.ImagePair
 
OriginalType - Variable in class edu.jhu.ece.iacl.algorithms.vabra.VectorVolumeVabra
 
otherThickness - Static variable in class edu.jhu.ece.iacl.algorithms.ReferencedPapers
 
outD1 - Variable in class edu.jhu.ece.iacl.pami.GenerateTensors
 
outD2 - Variable in class edu.jhu.ece.iacl.pami.GenerateTensors
 
outD3 - Variable in class edu.jhu.ece.iacl.pami.GenerateTensors
 
outerIterations - Variable in class edu.jhu.cs.cisst.algorithms.segmentation.gac.GeodesicActiveContour2D
The outer iterations.
outFrame - Variable in class edu.jhu.ece.iacl.jist.pipeline.gui.ProcessManagerTable
The out frame.
outgoingConnectors - Variable in class edu.jhu.ece.iacl.jist.pipeline.PipePort
outgoing connectors attached to this port.
outOfSync - Variable in class edu.jhu.ece.iacl.jist.pipeline.ExecutionContext
Out of sync flag.
OUTPUT_TAG - Static variable in class edu.jhu.ece.iacl.jist.pipeline.parser.LoniPipeParser
The Constant OUTPUT_TAG.
outputAliases - Variable in class edu.jhu.ece.iacl.jist.pipeline.parser.LoniPipeParser
The output aliases.
outputDir - Variable in class edu.jhu.ece.iacl.jist.dialogs.JDialogSaveAll
The output dir.
outputDirectory - Variable in class edu.jhu.ece.iacl.doc.DocumentAllTests
The output directory.
outputFileCol - Variable in class edu.jhu.ece.iacl.jist.pipeline.dest.PipeFileCollectionExternalDestination
 
outputFileCol - Variable in class edu.jhu.ece.iacl.jist.pipeline.dest.PipeFileExternalDestination
 
outputFloats - Variable in class edu.jhu.ece.iacl.jist.pipeline.dest.PipeDoubleCollectionExternalDestination
 
outputFloats - Variable in class edu.jhu.ece.iacl.jist.pipeline.dest.PipeDoubleExternalDestination
 
outputHash - Variable in class edu.jhu.ece.iacl.jist.pipeline.PipeModule
Output hash representing map from child parameter name to parameter.
outputImageParam - Variable in class edu.jhu.cs.cisst.plugins.utilities.file.PlugInTestDataSelector
 
outputIntegers - Variable in class edu.jhu.ece.iacl.jist.pipeline.dest.PipeIntegerCollectionExternalDestination
 
outputIntegers - Variable in class edu.jhu.ece.iacl.jist.pipeline.dest.PipeIntegerExternalDestination
 
outputParams - Variable in class edu.jhu.ece.iacl.jist.pipeline.ExecutionContext
The output parameters.
outputParams - Variable in class edu.jhu.ece.iacl.jist.pipeline.PipeModule
Output parameters, some of which may not be visible.
outputParams - Variable in class edu.jhu.ece.iacl.jist.pipeline.ProcessingAlgorithm
The output parameters.
outputPorts - Variable in class edu.jhu.ece.iacl.jist.pipeline.PipeModule
Input and output ports for module.
outputSurfaces - Variable in class edu.jhu.ece.iacl.jist.pipeline.dest.PipeSurfaceCollectionExternalDestination
 
outputSurfaces - Variable in class edu.jhu.ece.iacl.jist.pipeline.dest.PipeSurfaceExternalDestination
 
outputView - Variable in class edu.jhu.ece.iacl.jist.pipeline.factory.ParamFactory
Output view for parameter.
outputView - Variable in class edu.jhu.ece.iacl.jist.pipeline.ProcessingDialog
View for output parameters.
outputVolumes - Variable in class edu.jhu.ece.iacl.jist.pipeline.dest.PipeVolumeCollectionExternalDestination
 
outputVolumes - Variable in class edu.jhu.ece.iacl.jist.pipeline.dest.PipeVolumeExternalDestination
 
outsidePoints - Variable in class edu.jhu.cs.cisst.algorithms.segmentation.gac.GeodesicActiveContour2D
The outside points.
owner - Variable in class edu.jhu.ece.iacl.jist.pipeline.PipePort
Module that this port is attached to.

P

PACKAGE_FLAVOR - Static variable in class edu.jhu.ece.iacl.jist.pipeline.tree.PackageNode
The Constant PACKAGE_FLAVOR.
PackageNode - Class in edu.jhu.ece.iacl.jist.pipeline.tree
A package node is a directory that contains processing nodes.
PackageNode(File) - Constructor for class edu.jhu.ece.iacl.jist.pipeline.tree.PackageNode
Default constructor.
PackageNode(File, String) - Constructor for class edu.jhu.ece.iacl.jist.pipeline.tree.PackageNode
Default constructor.
PAD_MESSAGE_LENGTH - Static variable in class edu.jhu.ece.iacl.jist.utility.JistLogger
 
padRight(String, int) - Static method in class edu.jhu.ece.iacl.jist.utility.JistLogger
 
paint(Graphics) - Method in class edu.jhu.ece.iacl.jist.pipeline.graph.PipeAlgorithmGroupView.ActivityRenderer
 
paint(Graphics) - Method in class edu.jhu.ece.iacl.jist.pipeline.graph.PipeAlgorithmView.ActivityRenderer
 
paint(Graphics) - Method in class edu.jhu.ece.iacl.jist.pipeline.graph.PipeDestinationView.ActivityRenderer
 
paint(Graphics) - Method in class edu.jhu.ece.iacl.jist.pipeline.graph.PipeEdgeView.PipeEdgeRenderer
Paint the renderer.
paint(Graphics) - Method in class edu.jhu.ece.iacl.jist.pipeline.graph.PipePortView.ActivityRenderer
 
paint(Graphics) - Method in class edu.jhu.ece.iacl.jist.pipeline.graph.PipeSourceView.ActivityRenderer
 
paintConnector(Color, Color, Graphics) - Method in class edu.jhu.ece.iacl.jist.pipeline.graph.PipeMarqueeHandler
Paint connector.
paintPort(Graphics) - Method in class edu.jhu.ece.iacl.jist.pipeline.graph.PipeMarqueeHandler
Paint port.
Parallelizable - Interface in edu.jhu.cs.cisst.algorithms.optimize.fmg.parallel
An interface to those classes that supply a method for parallel multithreaded execution.
Parallelizer - Class in edu.jhu.cs.cisst.algorithms.optimize.fmg.parallel
A class that simplifies the task of scheduling one thread per processor of a SMP machine and calling a parallel algorithm in each of these threads, so that together these threads solve a common problem in parallel.
Parallelizer() - Constructor for class edu.jhu.cs.cisst.algorithms.optimize.fmg.parallel.Parallelizer
construct using the default implementation of runParallel() and using the default number of threads.
Parallelizer(int) - Constructor for class edu.jhu.cs.cisst.algorithms.optimize.fmg.parallel.Parallelizer
construct given a certain number of threads and using the default implementation of runParallel().
Parallelizer(Parallelizable) - Constructor for class edu.jhu.cs.cisst.algorithms.optimize.fmg.parallel.Parallelizer
construct given a target object and using the default number of threads.
Parallelizer(Parallelizable, int) - Constructor for class edu.jhu.cs.cisst.algorithms.optimize.fmg.parallel.Parallelizer
construct given a target object and a certain number of threads.
ParallelRunner - Class in edu.jhu.cs.cisst.algorithms.optimize.fmg.parallel
Customized implementation of class Thread that works closely with class Parallelizer and actually calls the parallel algorithm in each thread.
ParallelRunner(Parallelizer, int) - Constructor for class edu.jhu.cs.cisst.algorithms.optimize.fmg.parallel.ParallelRunner
create a new thread working with the given Parallelizer and having the given thread number.
param - Variable in class edu.jhu.ece.iacl.jist.pipeline.factory.ParamBooleanFactory
The param.
param - Variable in class edu.jhu.ece.iacl.jist.pipeline.factory.ParamColorFactory
The param.
param - Variable in class edu.jhu.ece.iacl.jist.pipeline.factory.ParamDoubleFactory
The param.
param - Variable in class edu.jhu.ece.iacl.jist.pipeline.factory.ParamFloatFactory
The param.
param - Variable in class edu.jhu.ece.iacl.jist.pipeline.factory.ParamHiddenFactory
The param.
param - Variable in class edu.jhu.ece.iacl.jist.pipeline.factory.ParamIntegerFactory
The param.
param - Variable in class edu.jhu.ece.iacl.jist.pipeline.factory.ParamLongFactory
The param.
param - Variable in class edu.jhu.ece.iacl.jist.pipeline.factory.ParamMatrixFactory
The param.
param - Variable in class edu.jhu.ece.iacl.jist.pipeline.factory.ParamPerformanceFactory
The param.
param - Variable in class edu.jhu.ece.iacl.jist.pipeline.factory.ParamPointDoubleFactory
The param.
param - Variable in class edu.jhu.ece.iacl.jist.pipeline.factory.ParamPointFloatFactory
The param.
param - Variable in class edu.jhu.ece.iacl.jist.pipeline.factory.ParamPointIntegerFactory
The param.
param - Variable in class edu.jhu.ece.iacl.jist.pipeline.factory.ParamStringFactory
The param.
param - Variable in class edu.jhu.ece.iacl.jist.pipeline.PipeParentPort
The parameter.
param - Variable in class edu.jhu.ece.iacl.jist.pipeline.view.input.ParamInputView
The parameter.
param - Variable in class edu.jhu.ece.iacl.jist.pipeline.view.output.ParamOutputView
The param.
param_imgMatrix - Variable in class edu.jhu.ece.iacl.pami.SimFramework
 
param_Sdw - Variable in class edu.jhu.ece.iacl.pami.SimFramework
 
param_SdwNF - Variable in class edu.jhu.ece.iacl.pami.SimFramework
 
param_sigma_out - Variable in class edu.jhu.ece.iacl.pami.SimFramework
 
param_Sref_out - Variable in class edu.jhu.ece.iacl.pami.SimFramework
 
ParamArgsOrder - Class in edu.jhu.ece.iacl.jist.pipeline.parameter
Argument order for command line calls.
ParamArgsOrder() - Constructor for class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamArgsOrder
Instantiates a new param args order.
ParamArgsOrder(String, ArrayList<String>) - Constructor for class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamArgsOrder
Instantiates a new param args order.
ParamBoolean - Class in edu.jhu.ece.iacl.jist.pipeline.parameter
Boolean Parameter.
ParamBoolean() - Constructor for class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamBoolean
Default constructor.
ParamBoolean(boolean) - Constructor for class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamBoolean
Create a new boolean parameter with a default value.
ParamBoolean(String) - Constructor for class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamBoolean
Construct new boolean parameter with a default value of false.
ParamBoolean(String, boolean) - Constructor for class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamBoolean
Create a new boolean parameter with a default value.
ParamBooleanFactory - Class in edu.jhu.ece.iacl.jist.pipeline.factory
Boolean parameter factory.
ParamBooleanFactory(ParamBoolean) - Constructor for class edu.jhu.ece.iacl.jist.pipeline.factory.ParamBooleanFactory
Instantiates a new param boolean factory.
ParamBooleanInputView - Class in edu.jhu.ece.iacl.jist.pipeline.view.input
Boolean Parameter Input View creates a checkbox to enter the parameter.
ParamBooleanInputView(ParamBoolean) - Constructor for class edu.jhu.ece.iacl.jist.pipeline.view.input.ParamBooleanInputView
Construct new checkbox to represent parameter.
ParamCollection - Class in edu.jhu.ece.iacl.jist.pipeline.parameter
Parameter Collection.
ParamCollection() - Constructor for class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamCollection
Construct parameter collection.
ParamCollection(String) - Constructor for class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamCollection
Construct parameter collection.
ParamCollectionFactory - Class in edu.jhu.ece.iacl.jist.pipeline.factory
Parameter Collection Factory.
ParamCollectionFactory(ParamCollection) - Constructor for class edu.jhu.ece.iacl.jist.pipeline.factory.ParamCollectionFactory
Instantiates a new param collection factory.
ParamCollectionInputView - Class in edu.jhu.ece.iacl.jist.pipeline.view.input
Collection Parameter Input View creates a vertical list of child parameters.
ParamCollectionInputView(ParamCollection) - Constructor for class edu.jhu.ece.iacl.jist.pipeline.view.input.ParamCollectionInputView
Default constructor that uses default layout.
ParamCollectionInputView(ParamCollection, LayoutManager) - Constructor for class edu.jhu.ece.iacl.jist.pipeline.view.input.ParamCollectionInputView
Default constructor.
ParamCollectionInputView(ParamModel) - Constructor for class edu.jhu.ece.iacl.jist.pipeline.view.input.ParamCollectionInputView
Default constructor.
ParamCollectionOutputView - Class in edu.jhu.ece.iacl.jist.pipeline.view.output
Output view for a collection of parameters.
ParamCollectionOutputView(ParamCollection) - Constructor for class edu.jhu.ece.iacl.jist.pipeline.view.output.ParamCollectionOutputView
Default constructor.
ParamCollectionOutputView(ParamCollection, LayoutManager) - Constructor for class edu.jhu.ece.iacl.jist.pipeline.view.output.ParamCollectionOutputView
Build output view as tabbed pane.
ParamCollectionPaneInputView - Class in edu.jhu.ece.iacl.jist.pipeline.view.input
A collection input view that displays parameters in outlined panes instead of tabbed panes.
ParamCollectionPaneInputView(ParamCollection) - Constructor for class edu.jhu.ece.iacl.jist.pipeline.view.input.ParamCollectionPaneInputView
Default constructor with default layout.
ParamCollectionPaneInputView(ParamCollection, LayoutManager) - Constructor for class edu.jhu.ece.iacl.jist.pipeline.view.input.ParamCollectionPaneInputView
Default constructor.
ParamCollectionPipelineInputView - Class in edu.jhu.ece.iacl.jist.pipeline.view.input
Collection Parameter Input View creates a vertical list of child parameters.
ParamCollectionPipelineInputView(ParamModel, boolean) - Constructor for class edu.jhu.ece.iacl.jist.pipeline.view.input.ParamCollectionPipelineInputView
Instantiates a new parameter collection pipeline input view.
ParamCollectionWindowInputView - Class in edu.jhu.ece.iacl.jist.pipeline.view.input
Display collection of parameters in different windows.
ParamCollectionWindowInputView(ParamCollection) - Constructor for class edu.jhu.ece.iacl.jist.pipeline.view.input.ParamCollectionWindowInputView
Default constructor with default window layout.
ParamCollectionWindowInputView(ParamCollection, LayoutManager) - Constructor for class edu.jhu.ece.iacl.jist.pipeline.view.input.ParamCollectionWindowInputView
Default constructor.
ParamColor - Class in edu.jhu.ece.iacl.jist.pipeline.parameter
The Class ParamColor.
ParamColor() - Constructor for class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamColor
Default constructor.
ParamColor(Color) - Constructor for class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamColor
Instantiates a new param color.
ParamColor(String) - Constructor for class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamColor
Constructor.
ParamColor(String, Color) - Constructor for class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamColor
Instantiates a new parameter color.
ParamColorFactory - Class in edu.jhu.ece.iacl.jist.pipeline.factory
Color Parameter Factory.
ParamColorFactory(ParamColor) - Constructor for class edu.jhu.ece.iacl.jist.pipeline.factory.ParamColorFactory
Instantiates a new param color factory.
ParamColorInputView - Class in edu.jhu.ece.iacl.jist.pipeline.view.input
The Class ParamColorInputView.
ParamColorInputView(ParamColor) - Constructor for class edu.jhu.ece.iacl.jist.pipeline.view.input.ParamColorInputView
Construct text field to enter numerical value.
ParamDataLabel - Class in edu.jhu.ece.iacl.jist.pipeline.parameter
Data Label Parameter.
ParamDataLabel() - Constructor for class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamDataLabel
Default constructor.
ParamDataLabel(String) - Constructor for class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamDataLabel
Construct data labels parameter with no restrictions.
ParamDataLabel(String, VoxelType) - Constructor for class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamDataLabel
Construct data label parameter with restriction on voxel type.
ParamDataLabel(String, VoxelType, int, int, int, int) - Constructor for class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamDataLabel
Construct new data label the specified restrictions.
ParamDataLabel(VoxelType) - Constructor for class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamDataLabel
Default constructor.
ParamDataLabel(VoxelType, int, int, int, int) - Constructor for class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamDataLabel
Default constructor.
ParamDataLabelFactory - Class in edu.jhu.ece.iacl.jist.pipeline.factory
Data Label Factory.
ParamDataLabelFactory(ParamDataLabel) - Constructor for class edu.jhu.ece.iacl.jist.pipeline.factory.ParamDataLabelFactory
Instantiates a new param data label factory.
ParamDataLabelInputView - Class in edu.jhu.ece.iacl.jist.pipeline.view.input
Data Label Input View displays a combobox to select an image and a scroll pane to display the discovered data labels for that image.
ParamDataLabelInputView(ParamDataLabel) - Constructor for class edu.jhu.ece.iacl.jist.pipeline.view.input.ParamDataLabelInputView
Construct new scroll pane to display label information for image.
ParamDouble - Class in edu.jhu.ece.iacl.jist.pipeline.parameter
Double Parameter.
ParamDouble() - Constructor for class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamDouble
Construct double parameter with no restrictions on value.
ParamDouble(double, double) - Constructor for class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamDouble
Construct double parameter with restrictions on min and max value.
ParamDouble(String) - Constructor for class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamDouble
Construct double parameter with no restrictions on value.
ParamDouble(String, double) - Constructor for class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamDouble
Construct double parameter with restrictions on min and max value.
ParamDouble(String, double, double) - Constructor for class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamDouble
Construct double parameter with restrictions on min and max value.
ParamDouble(String, double, double, double) - Constructor for class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamDouble
Construct double parameter with restrictions on min and max value.
ParamDoubleFactory - Class in edu.jhu.ece.iacl.jist.pipeline.factory
Double Parameter Factory.
ParamDoubleFactory(ParamDouble) - Constructor for class edu.jhu.ece.iacl.jist.pipeline.factory.ParamDoubleFactory
Instantiates a new param double factory.
ParamDoubleSliderInputView - Class in edu.jhu.ece.iacl.jist.pipeline.view.input
The Class ParamDoubleSliderInputView.
ParamDoubleSliderInputView(ParamNumber, int, boolean) - Constructor for class edu.jhu.ece.iacl.jist.pipeline.view.input.ParamDoubleSliderInputView
Instantiates a new param double slider input view.
ParameterPanel - Class in edu.jhu.ece.iacl.jist.pipeline.gui
Panel to display input parameters.
ParameterPanel() - Constructor for class edu.jhu.ece.iacl.jist.pipeline.gui.ParameterPanel
Default constructor.
ParamExecutable - Class in edu.jhu.ece.iacl.jist.pipeline.parameter
Executable file parameter.
ParamExecutable(File) - Constructor for class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamExecutable
Default constructor.
ParamExecutable(URI) - Constructor for class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamExecutable
Default constructor.
ParamFactory - Class in edu.jhu.ece.iacl.jist.pipeline.factory
Parameter Factory is responsible for manipulating Parameter Models, which allows the factory to be substituted for a different factory if a customized factory is required.
ParamFactory() - Constructor for class edu.jhu.ece.iacl.jist.pipeline.factory.ParamFactory
 
ParamFile - Class in edu.jhu.ece.iacl.jist.pipeline.parameter
File parameter used to store a file name with a particular file extension.
ParamFile(ParamFile.DialogType) - Constructor for class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamFile
Construct parameter with specified restrictions.
ParamFile(String) - Constructor for class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamFile
Construct parameter for a mandatory file type.
ParamFile(String, ParamFile.DialogType) - Constructor for class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamFile
Construct parameter with specified restrictions.
ParamFile(String, File, ParamFile.DialogType) - Constructor for class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamFile
Construct parameter with specified restrictions.
ParamFile(String, URI, ParamFile.DialogType) - Constructor for class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamFile
Construct parameter with specified restrictions.
ParamFile(String, FileExtensionFilter) - Constructor for class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamFile
Construct parameter for a mandatory file type.
ParamFile.DialogType - Enum in edu.jhu.ece.iacl.jist.pipeline.parameter
The Enum DialogType.
ParamFileCollection - Class in edu.jhu.ece.iacl.jist.pipeline.parameter
File collection stores a collection of files.
ParamFileCollection() - Constructor for class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamFileCollection
Default constructor.
ParamFileCollection(String) - Constructor for class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamFileCollection
Default constructor.
ParamFileCollection(String, FileExtensionFilter) - Constructor for class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamFileCollection
Constructor.
ParamFileCollection(String, FileReaderWriter) - Constructor for class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamFileCollection
Constructor.
ParamFileCollectionFactory - Class in edu.jhu.ece.iacl.jist.pipeline.factory
File Collection Parameter Factory.
ParamFileCollectionFactory() - Constructor for class edu.jhu.ece.iacl.jist.pipeline.factory.ParamFileCollectionFactory
Instantiates a new param file collection factory.
ParamFileCollectionFactory(ParamFileCollection) - Constructor for class edu.jhu.ece.iacl.jist.pipeline.factory.ParamFileCollectionFactory
Instantiates a new param file collection factory.
ParamFileCollectionInputView - Class in edu.jhu.ece.iacl.jist.pipeline.view.input
Input view to select multiple files.
ParamFileCollectionInputView(ParamFileCollection) - Constructor for class edu.jhu.ece.iacl.jist.pipeline.view.input.ParamFileCollectionInputView
Default constructor.
ParamFileCollectionOutputView - Class in edu.jhu.ece.iacl.jist.pipeline.view.output
Output view for a collection of file parameters.
ParamFileCollectionOutputView(ParamFileCollection) - Constructor for class edu.jhu.ece.iacl.jist.pipeline.view.output.ParamFileCollectionOutputView
Default constructor.
ParamFileFactory - Class in edu.jhu.ece.iacl.jist.pipeline.factory
File Parameter Factory.
ParamFileFactory() - Constructor for class edu.jhu.ece.iacl.jist.pipeline.factory.ParamFileFactory
Instantiates a new param file factory.
ParamFileFactory(ParamFile) - Constructor for class edu.jhu.ece.iacl.jist.pipeline.factory.ParamFileFactory
Construct factory for specified parameter.
ParamFileInputView - Class in edu.jhu.ece.iacl.jist.pipeline.view.input
File Parameter Input View creates a text field to enter a file and a browse button to select a file.
ParamFileInputView(ParamFile) - Constructor for class edu.jhu.ece.iacl.jist.pipeline.view.input.ParamFileInputView
Construct text field to enter file name and browse button to select file.
ParamFloat - Class in edu.jhu.ece.iacl.jist.pipeline.parameter
Float Parameter.
ParamFloat() - Constructor for class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamFloat
Construct float parameter with no restrictions on value.
ParamFloat(float, float) - Constructor for class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamFloat
Construct float parameter with restrictions on min and max value.
ParamFloat(String) - Constructor for class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamFloat
Construct float parameter with no restrictions on value.
ParamFloat(String, float) - Constructor for class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamFloat
Construct float parameter with restrictions on min and max value.
ParamFloat(String, float, float) - Constructor for class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamFloat
Construct float parameter with restrictions on min and max value.
ParamFloat(String, float, float, float) - Constructor for class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamFloat
Construct float parameter with restrictions on min and max value.
ParamFloatFactory - Class in edu.jhu.ece.iacl.jist.pipeline.factory
Float Parameter Factory.
ParamFloatFactory(ParamFloat) - Constructor for class edu.jhu.ece.iacl.jist.pipeline.factory.ParamFloatFactory
Instantiates a new param float factory.
ParamHeader - Class in edu.jhu.ece.iacl.jist.pipeline.parameter
Header identifies plug-in.
ParamHeader() - Constructor for class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamHeader
Default constructor.
ParamHeader(String, Class) - Constructor for class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamHeader
Instantiates a new param header.
ParamHeaderFactory - Class in edu.jhu.ece.iacl.jist.pipeline.factory
 
ParamHeaderFactory(ParamHidden) - Constructor for class edu.jhu.ece.iacl.jist.pipeline.factory.ParamHeaderFactory
 
ParamHidden<T> - Class in edu.jhu.ece.iacl.jist.pipeline.parameter
Hidden parameter.
ParamHidden() - Constructor for class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamHidden
Default constructor.
ParamHiddenFactory - Class in edu.jhu.ece.iacl.jist.pipeline.factory
Hidden Parameter Factory.
ParamHiddenFactory(ParamHidden) - Constructor for class edu.jhu.ece.iacl.jist.pipeline.factory.ParamHiddenFactory
Instantiates a new param hidden factory.
ParamHiddenInputView - Class in edu.jhu.ece.iacl.jist.pipeline.view.input
A hidden input field.
ParamHiddenInputView(ParamModel) - Constructor for class edu.jhu.ece.iacl.jist.pipeline.view.input.ParamHiddenInputView
Default constructor.
paramInfoRegex - Static variable in class edu.jhu.ece.iacl.jist.pipeline.ProcessingDialog
Regular expression to find parameter information in a string *.
ParamInformation - Class in edu.jhu.ece.iacl.jist.pipeline.parameter
Stores information about algorithm.
ParamInformation() - Constructor for class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamInformation
Default constructor.
ParamInformation(AlgorithmInformation) - Constructor for class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamInformation
Constructor.
ParamInformation(String) - Constructor for class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamInformation
Constructor.
ParamInformation(String, AlgorithmInformation) - Constructor for class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamInformation
Constructor.
ParamInformationFactory - Class in edu.jhu.ece.iacl.jist.pipeline.factory
Algorithm Information Parameter Factory.
ParamInformationFactory() - Constructor for class edu.jhu.ece.iacl.jist.pipeline.factory.ParamInformationFactory
Instantiates a new param information factory.
ParamInformationFactory(ParamInformation) - Constructor for class edu.jhu.ece.iacl.jist.pipeline.factory.ParamInformationFactory
Construct factory for specified parameter.
ParamInformationInputView - Class in edu.jhu.ece.iacl.jist.pipeline.view.input
File Parameter Input View creates a text field to enter a file and a browse button to select a file.
ParamInformationInputView(ParamInformation) - Constructor for class edu.jhu.ece.iacl.jist.pipeline.view.input.ParamInformationInputView
Construct textfield to enter file name and browse button to select file.
ParamInputView - Class in edu.jhu.ece.iacl.jist.pipeline.view.input
Generic input view to enter a parameter value.
ParamInputView(ParamModel) - Constructor for class edu.jhu.ece.iacl.jist.pipeline.view.input.ParamInputView
Instantiates a new parameter input view.
ParamInteger - Class in edu.jhu.ece.iacl.jist.pipeline.parameter
Integer Parameter.
ParamInteger() - Constructor for class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamInteger
Construct integer parameter with no restrictions on value.
ParamInteger(int, int) - Constructor for class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamInteger
Construct integer parameter with restrictions on min and max value.
ParamInteger(int, int, int) - Constructor for class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamInteger
Construct integer parameter with restrictions on min and max value.
ParamInteger(String) - Constructor for class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamInteger
Construct integer parameter with no restrictions on value.
ParamInteger(String, int) - Constructor for class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamInteger
Construct integer parameter.
ParamInteger(String, int, int) - Constructor for class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamInteger
Construct integer parameter with restrictions on min and max value.
ParamInteger(String, int, int, int) - Constructor for class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamInteger
Construct integer parameter with restrictions on min and max value.
ParamIntegerFactory - Class in edu.jhu.ece.iacl.jist.pipeline.factory
Integer Parameter Factory.
ParamIntegerFactory(ParamInteger) - Constructor for class edu.jhu.ece.iacl.jist.pipeline.factory.ParamIntegerFactory
Instantiates a new param integer factory.
ParamIntegerSliderInputView - Class in edu.jhu.ece.iacl.jist.pipeline.view.input
The Class ParamIntegerSliderInputView.
ParamIntegerSliderInputView(ParamNumber, int) - Constructor for class edu.jhu.ece.iacl.jist.pipeline.view.input.ParamIntegerSliderInputView
Instantiates a new param integer slider input view.
paramListDelimiter - Static variable in class edu.jhu.ece.iacl.jist.pipeline.ProcessingDialog
Delimeter used for parameters *.
ParamLong - Class in edu.jhu.ece.iacl.jist.pipeline.parameter
Long Parameter.
ParamLong() - Constructor for class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamLong
Construct long parameter with no restrictions on value.
ParamLong(long, long) - Constructor for class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamLong
Construct long parameter with restrictions on min and max value.
ParamLong(long, long, long) - Constructor for class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamLong
Construct long parameter with restrictions on min and max value.
ParamLong(String) - Constructor for class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamLong
Construct long parameter with no restrictions on value.
ParamLong(String, long) - Constructor for class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamLong
Construct long parameter.
ParamLong(String, long, long) - Constructor for class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamLong
Construct long parameter with restrictions on min and max value.
ParamLong(String, long, long, long) - Constructor for class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamLong
Construct long parameter with restrictions on min and max value.
ParamLongFactory - Class in edu.jhu.ece.iacl.jist.pipeline.factory
Long Parameter Factory.
ParamLongFactory(ParamLong) - Constructor for class edu.jhu.ece.iacl.jist.pipeline.factory.ParamLongFactory
Instantiates a new param long factory.
ParamMatrix - Class in edu.jhu.ece.iacl.jist.pipeline.parameter
Number Parameter storage.
ParamMatrix() - Constructor for class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamMatrix
Instantiates a new param matrix.
ParamMatrix(Matrix) - Constructor for class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamMatrix
Instantiates a new param matrix.
ParamMatrix(String, Matrix) - Constructor for class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamMatrix
Instantiates a new param matrix.
ParamMatrix(String, int, int) - Constructor for class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamMatrix
Instantiates a new param matrix.
ParamMatrix(int, int) - Constructor for class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamMatrix
Instantiates a new param matrix.
ParamMatrixFactory - Class in edu.jhu.ece.iacl.jist.pipeline.factory
Double Parameter Factory.
ParamMatrixFactory(ParamMatrix) - Constructor for class edu.jhu.ece.iacl.jist.pipeline.factory.ParamMatrixFactory
Instantiates a new param matrix factory.
ParamMatrixInputView - Class in edu.jhu.ece.iacl.jist.pipeline.view.input
Input View creates a text field to enter a numerical value.
ParamMatrixInputView(ParamMatrix) - Constructor for class edu.jhu.ece.iacl.jist.pipeline.view.input.ParamMatrixInputView
Construct text field to enter numerical value.
ParamMipavDialog - Class in edu.jhu.ece.iacl.jist.pipeline.parameter
Parameter for storing reference to mipav dialog.
ParamMipavDialog(Class) - Constructor for class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamMipavDialog
Constructor.
ParamMipavDialog(String) - Constructor for class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamMipavDialog
Constructor.
ParamMipavDialog(String, Class) - Constructor for class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamMipavDialog
Constructor.
ParamMipavDialogFactory - Class in edu.jhu.ece.iacl.jist.pipeline.factory
Mipav Dialog Parameter Factory.
ParamMipavDialogFactory() - Constructor for class edu.jhu.ece.iacl.jist.pipeline.factory.ParamMipavDialogFactory
Instantiates a new param mipav dialog factory.
ParamMipavDialogFactory(ParamMipavDialog) - Constructor for class edu.jhu.ece.iacl.jist.pipeline.factory.ParamMipavDialogFactory
Construct factory for specified parameter.
ParamMipavDialogInputView - Class in edu.jhu.ece.iacl.jist.pipeline.view.input
Displays a mipav dialog to input information.
ParamMipavDialogInputView(ParamMipavDialog) - Constructor for class edu.jhu.ece.iacl.jist.pipeline.view.input.ParamMipavDialogInputView
Default constructor.
ParamModel<T> - Class in edu.jhu.ece.iacl.jist.pipeline.parameter
Generic Parameter with a bridge to interface with methods in the parameter getFactory().
ParamModel() - Constructor for class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamModel
Default constructor.
ParamMultiOption - Class in edu.jhu.ece.iacl.jist.pipeline.parameter
An parameter that allows the user to select more than one option.
ParamMultiOption(ArrayList<String>) - Constructor for class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamMultiOption
Construct a list of possible options.
ParamMultiOption(String) - Constructor for class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamMultiOption
Constructor.
ParamMultiOption(String, ArrayList<String>) - Constructor for class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamMultiOption
Construct a list of possible options.
ParamMultiOption(String, String[]) - Constructor for class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamMultiOption
Construct a list of possible options.
ParamMultiOption(String[]) - Constructor for class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamMultiOption
Construct a list of possible options.
ParamMultiOptionFactory - Class in edu.jhu.ece.iacl.jist.pipeline.factory
Multi-Option Parameter Factory.
ParamMultiOptionFactory(ParamMultiOption) - Constructor for class edu.jhu.ece.iacl.jist.pipeline.factory.ParamMultiOptionFactory
Instantiates a new param multi option factory.
ParamMultiOptionInputView - Class in edu.jhu.ece.iacl.jist.pipeline.view.input
Input view to select multiple options.
ParamMultiOptionInputView(ParamMultiOption) - Constructor for class edu.jhu.ece.iacl.jist.pipeline.view.input.ParamMultiOptionInputView
Default constructor.
ParamNumber - Class in edu.jhu.ece.iacl.jist.pipeline.parameter
Number Parameter storage.
ParamNumber() - Constructor for class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamNumber
 
ParamNumberCollection - Class in edu.jhu.ece.iacl.jist.pipeline.parameter
Number collection stores a collection of numbers.
ParamNumberCollection() - Constructor for class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamNumberCollection
Construct double parameter with no restrictions on value.
ParamNumberCollection(Number, Number) - Constructor for class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamNumberCollection
Construct double parameter with restrictions on min and max value.
ParamNumberCollection(String) - Constructor for class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamNumberCollection
Construct double parameter with no restrictions on value.
ParamNumberCollection(String, Number, Number) - Constructor for class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamNumberCollection
Construct double parameter with restrictions on min and max value.
ParamNumberCollectionFactory - Class in edu.jhu.ece.iacl.jist.pipeline.factory
Number Collection Parameter Factory.
ParamNumberCollectionFactory() - Constructor for class edu.jhu.ece.iacl.jist.pipeline.factory.ParamNumberCollectionFactory
Instantiates a new param number collection factory.
ParamNumberCollectionFactory(ParamNumberCollection) - Constructor for class edu.jhu.ece.iacl.jist.pipeline.factory.ParamNumberCollectionFactory
Instantiates a new param number collection factory.
ParamNumberCollectionInputView - Class in edu.jhu.ece.iacl.jist.pipeline.view.input
Input view to select multiple numbers.
ParamNumberCollectionInputView(ParamNumberCollection) - Constructor for class edu.jhu.ece.iacl.jist.pipeline.view.input.ParamNumberCollectionInputView
Default constructor.
ParamNumberCollectionOutputView - Class in edu.jhu.ece.iacl.jist.pipeline.view.output
Output view for a collection of number parameters.
ParamNumberCollectionOutputView(ParamNumberCollection) - Constructor for class edu.jhu.ece.iacl.jist.pipeline.view.output.ParamNumberCollectionOutputView
Default constructor.
ParamNumberSliderInputView - Class in edu.jhu.ece.iacl.jist.pipeline.view.input
Input view to select a number via a slider.
ParamNumberSliderInputView(ParamNumber) - Constructor for class edu.jhu.ece.iacl.jist.pipeline.view.input.ParamNumberSliderInputView
Default constructor.
ParamNumberSpinnerInputView - Class in edu.jhu.ece.iacl.jist.pipeline.view.input
Input View creates a spinner box to enter an integer value between the minimum and maximum value for the parameter.
ParamNumberSpinnerInputView(ParamDouble, double) - Constructor for class edu.jhu.ece.iacl.jist.pipeline.view.input.ParamNumberSpinnerInputView
Construct spinner to select a double value.
ParamNumberSpinnerInputView(ParamInteger) - Constructor for class edu.jhu.ece.iacl.jist.pipeline.view.input.ParamNumberSpinnerInputView
Construct spinner to select an integer value.
ParamNumberSpinnerInputView(ParamLong) - Constructor for class edu.jhu.ece.iacl.jist.pipeline.view.input.ParamNumberSpinnerInputView
Construct spinner to select an long value.
ParamNumberTextInputView - Class in edu.jhu.ece.iacl.jist.pipeline.view.input
Input View creates a text field to enter a numerical value.
ParamNumberTextInputView(ParamNumber) - Constructor for class edu.jhu.ece.iacl.jist.pipeline.view.input.ParamNumberTextInputView
Construct text field to enter numerical value.
ParamObject<T> - Class in edu.jhu.ece.iacl.jist.pipeline.parameter
Parameter for generic object which uses specified reader/writer.
ParamObject(ParamFile.DialogType) - Constructor for class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamObject
Constructor.
ParamObject(String) - Constructor for class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamObject
Constructor.
ParamObject(String, ParamFile.DialogType) - Constructor for class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamObject
Constructor.
ParamObject(String, FileReaderWriter<T>) - Constructor for class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamObject
Constructor.
ParamObjectFactory - Class in edu.jhu.ece.iacl.jist.pipeline.factory
Object Parameter Factory.
ParamObjectFactory(ParamObject) - Constructor for class edu.jhu.ece.iacl.jist.pipeline.factory.ParamObjectFactory
Construct factory for specified parameter.
ParamOption - Class in edu.jhu.ece.iacl.jist.pipeline.parameter
Option Parameter to select between different text options.
ParamOption(List<String>) - Constructor for class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamOption
Construct a list of possible options.
ParamOption(String, List<String>) - Constructor for class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamOption
Construct a list of possible options.
ParamOption(String, String[]) - Constructor for class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamOption
Construct a list of possible options.
ParamOption(String[]) - Constructor for class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamOption
Construct a list of possible options.
ParamOptionCollectionInputView - Class in edu.jhu.ece.iacl.jist.pipeline.view.input
Input View to select multiple options from list.
ParamOptionCollectionInputView(ParamOption, ParamCollection) - Constructor for class edu.jhu.ece.iacl.jist.pipeline.view.input.ParamOptionCollectionInputView
Construct combobox with options from ParamOption.
ParamOptionFactory - Class in edu.jhu.ece.iacl.jist.pipeline.factory
Option Parameter Factory.
ParamOptionFactory(ParamOption) - Constructor for class edu.jhu.ece.iacl.jist.pipeline.factory.ParamOptionFactory
Instantiates a new param option factory.
ParamOptionInputView - Class in edu.jhu.ece.iacl.jist.pipeline.view.input
Input view to select a particular text option from a combobox.
ParamOptionInputView(ParamOption) - Constructor for class edu.jhu.ece.iacl.jist.pipeline.view.input.ParamOptionInputView
Construct combobox with options from ParamOption.
ParamOutputView - Class in edu.jhu.ece.iacl.jist.pipeline.view.output
Generic Output View to display an output value.
ParamOutputView() - Constructor for class edu.jhu.ece.iacl.jist.pipeline.view.output.ParamOutputView
Constructor does nothing.
ParamOutputView(ParamModel) - Constructor for class edu.jhu.ece.iacl.jist.pipeline.view.output.ParamOutputView
Construct output view as string representation of parameter.
ParamPerformance - Class in edu.jhu.ece.iacl.jist.pipeline.parameter
Parameter to store algorithm performance information.
ParamPerformance(String) - Constructor for class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamPerformance
Constructor.
ParamPerformanceFactory - Class in edu.jhu.ece.iacl.jist.pipeline.factory
Performance parameter factory.
ParamPerformanceFactory(ParamPerformance) - Constructor for class edu.jhu.ece.iacl.jist.pipeline.factory.ParamPerformanceFactory
Instantiates a new param performance factory.
ParamPoint - Interface in edu.jhu.ece.iacl.jist.pipeline.parameter
Parameter that stores a 3d point.
ParamPointDouble - Class in edu.jhu.ece.iacl.jist.pipeline.parameter
3D Point parameter for double floating point.
ParamPointDouble() - Constructor for class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamPointDouble
Default constructor.
ParamPointDouble(Point3d) - Constructor for class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamPointDouble
Constructor.
ParamPointDouble(String, Point3d) - Constructor for class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamPointDouble
Constructor.
ParamPointDoubleFactory - Class in edu.jhu.ece.iacl.jist.pipeline.factory
Point Double Parameter Factory.
ParamPointDoubleFactory(ParamPointDouble) - Constructor for class edu.jhu.ece.iacl.jist.pipeline.factory.ParamPointDoubleFactory
Instantiates a new param point double factory.
ParamPointDoubleTextInputView - Class in edu.jhu.ece.iacl.jist.pipeline.view.input
Input View creates a text field to enter a point value.
ParamPointDoubleTextInputView(ParamPointDouble) - Constructor for class edu.jhu.ece.iacl.jist.pipeline.view.input.ParamPointDoubleTextInputView
Construct text field to enter numerical value.
ParamPointFloat - Class in edu.jhu.ece.iacl.jist.pipeline.parameter
3D Point parameter for floating point.
ParamPointFloat() - Constructor for class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamPointFloat
Default constructor.
ParamPointFloat(Point3f) - Constructor for class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamPointFloat
Constructor.
ParamPointFloat(String, Point3f) - Constructor for class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamPointFloat
Constructor.
ParamPointFloatFactory - Class in edu.jhu.ece.iacl.jist.pipeline.factory
Point Float Parameter Factory.
ParamPointFloatFactory(ParamPointFloat) - Constructor for class edu.jhu.ece.iacl.jist.pipeline.factory.ParamPointFloatFactory
Instantiates a new param point float factory.
ParamPointFloatTextInputView - Class in edu.jhu.ece.iacl.jist.pipeline.view.input
Input View creates a text field to enter a point value.
ParamPointFloatTextInputView(ParamPointFloat) - Constructor for class edu.jhu.ece.iacl.jist.pipeline.view.input.ParamPointFloatTextInputView
Construct text field to enter numerical value.
ParamPointInteger - Class in edu.jhu.ece.iacl.jist.pipeline.parameter
The Class ParamPointInteger.
ParamPointInteger() - Constructor for class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamPointInteger
Default constructor.
ParamPointInteger(Point3i) - Constructor for class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamPointInteger
Constructor.
ParamPointInteger(String, Point3i) - Constructor for class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamPointInteger
Constructor.
ParamPointIntegerFactory - Class in edu.jhu.ece.iacl.jist.pipeline.factory
Point Integer Parameter Factory.
ParamPointIntegerFactory(ParamPointInteger) - Constructor for class edu.jhu.ece.iacl.jist.pipeline.factory.ParamPointIntegerFactory
Instantiates a new param point integer factory.
ParamPointSpinnerInputView - Class in edu.jhu.ece.iacl.jist.pipeline.view.input
Input View creates a text field to enter a point value.
ParamPointSpinnerInputView(ParamPointInteger) - Constructor for class edu.jhu.ece.iacl.jist.pipeline.view.input.ParamPointSpinnerInputView
Construct text field to enter numerical value.
params - Variable in class edu.jhu.ece.iacl.jist.pipeline.PipeLayout
Layout preferences.
ParamString - Class in edu.jhu.ece.iacl.jist.pipeline.parameter
String parameter.
ParamString() - Constructor for class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamString
Constructor.
ParamString(String) - Constructor for class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamString
Constructor.
ParamString(String, String) - Constructor for class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamString
Constructor.
ParamStringFactory - Class in edu.jhu.ece.iacl.jist.pipeline.factory
String Parameter Factory.
ParamStringFactory(ParamString) - Constructor for class edu.jhu.ece.iacl.jist.pipeline.factory.ParamStringFactory
Instantiates a new param string factory.
paramSummaryFile - Variable in class edu.jhu.ece.iacl.jist.pipeline.dest.PipeParamCopyDestination
The param summary file.
paramSummaryFile - Variable in class edu.jhu.ece.iacl.jist.pipeline.dest.PipeParamSummaryDestination
The param summary file.
ParamSurface - Class in edu.jhu.ece.iacl.jist.pipeline.parameter
Surface parameter file.
ParamSurface(ParamFile.DialogType) - Constructor for class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamSurface
Constructor.
ParamSurface(String) - Constructor for class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamSurface
Construct parameter for a mandatory file type.
ParamSurface(String, ParamFile.DialogType) - Constructor for class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamSurface
Construct parameter with specified restrictions.
ParamSurfaceCollection - Class in edu.jhu.ece.iacl.jist.pipeline.parameter
Surface collection stores a collection of files.
ParamSurfaceCollection() - Constructor for class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamSurfaceCollection
Default constructor.
ParamSurfaceCollection(String) - Constructor for class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamSurfaceCollection
Constructor.
ParamSurfaceCollectionFactory - Class in edu.jhu.ece.iacl.jist.pipeline.factory
Surface Collection Parameter Factory.
ParamSurfaceCollectionFactory(ParamSurfaceCollection) - Constructor for class edu.jhu.ece.iacl.jist.pipeline.factory.ParamSurfaceCollectionFactory
Instantiates a new param surface collection factory.
ParamSurfaceFactory - Class in edu.jhu.ece.iacl.jist.pipeline.factory
Surface Parameter Factory.
ParamSurfaceFactory(ParamSurface) - Constructor for class edu.jhu.ece.iacl.jist.pipeline.factory.ParamSurfaceFactory
Instantiates a new param surface factory.
ParamSurfaceLocation - Class in edu.jhu.ece.iacl.jist.pipeline.parameter
 
ParamSurfaceLocation() - Constructor for class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamSurfaceLocation
Default constructor.
ParamSurfaceLocation(String) - Constructor for class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamSurfaceLocation
 
ParamSurfaceLocationCollection - Class in edu.jhu.ece.iacl.jist.pipeline.parameter
 
ParamSurfaceLocationCollection() - Constructor for class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamSurfaceLocationCollection
 
ParamSurfaceLocationCollection(String) - Constructor for class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamSurfaceLocationCollection
 
ParamSurfaceOutputView - Class in edu.jhu.ece.iacl.jist.pipeline.view.output
Simple 3D viewer for surfaces.
ParamSurfaceOutputView() - Constructor for class edu.jhu.ece.iacl.jist.pipeline.view.output.ParamSurfaceOutputView
Default constructor.
ParamSurfaceOutputView(GeometryArray, String) - Constructor for class edu.jhu.ece.iacl.jist.pipeline.view.output.ParamSurfaceOutputView
Default constructor.
ParamSurfaceOutputView(ParamSurface) - Constructor for class edu.jhu.ece.iacl.jist.pipeline.view.output.ParamSurfaceOutputView
Default constructor.
ParamSwitch - Class in edu.jhu.ece.iacl.jist.pipeline.parameter
Command line switch parameter.
ParamSwitch() - Constructor for class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamSwitch
Default constructor.
ParamSwitch(String, String) - Constructor for class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamSwitch
Constructor.
ParamSwitch(String, String, boolean) - Constructor for class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamSwitch
Constructor.
ParamTextInputView - Class in edu.jhu.ece.iacl.jist.pipeline.view.input
Input View creates a text field to enter a numerical value.
ParamTextInputView(ParamString) - Constructor for class edu.jhu.ece.iacl.jist.pipeline.view.input.ParamTextInputView
Construct text field to enter numerical value.
ParamURIInputView - Class in edu.jhu.ece.iacl.jist.pipeline.view.input
File Parameter Input View creates a text field to enter a file and a browse button to select a file.
ParamURIInputView(ParamFile) - Constructor for class edu.jhu.ece.iacl.jist.pipeline.view.input.ParamURIInputView
Construct text field to enter file name and browse button to select file.
ParamViewObserver - Interface in edu.jhu.ece.iacl.jist.pipeline.view.input
Observer to observe parameter changes.
ParamVolume - Class in edu.jhu.ece.iacl.jist.pipeline.parameter
Parameter volume specifies a CubicVolume with restrictions for the dimensions and data type.
ParamVolume() - Constructor for class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamVolume
Default constructor.
ParamVolume(String) - Constructor for class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamVolume
Constructor.
ParamVolume(String, VoxelType) - Constructor for class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamVolume
Constructor.
ParamVolume(String, VoxelType, int, int, int, int) - Constructor for class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamVolume
Construct volume parameter with a restriction on the dimensions and data type.
ParamVolume(VoxelType) - Constructor for class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamVolume
Construct volume parameter with a restriction on the data type.
ParamVolume(VoxelType, int, int, int, int) - Constructor for class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamVolume
Construct volume parameter with a restriction on the dimensions and data type.
ParamVolumeCollection - Class in edu.jhu.ece.iacl.jist.pipeline.parameter
Volume collection stores a collection of files.
ParamVolumeCollection() - Constructor for class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamVolumeCollection
Default constructor.
ParamVolumeCollection(String) - Constructor for class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamVolumeCollection
Constructor.
ParamVolumeCollection(String, VoxelType) - Constructor for class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamVolumeCollection
Construct volume collection with specified restrictions.
ParamVolumeCollection(String, VoxelType, int, int, int, int) - Constructor for class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamVolumeCollection
Construct volume collection parameter with a restriction on the dimensions and data type.
ParamVolumeCollection(VoxelType) - Constructor for class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamVolumeCollection
Constructor.
ParamVolumeCollection(VoxelType, int, int, int, int) - Constructor for class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamVolumeCollection
Construct volume collection parameter with a restriction on the dimensions and data type.
ParamVolumeCollectionFactory - Class in edu.jhu.ece.iacl.jist.pipeline.factory
Volume collection parameter factory.
ParamVolumeCollectionFactory() - Constructor for class edu.jhu.ece.iacl.jist.pipeline.factory.ParamVolumeCollectionFactory
Instantiates a new param volume collection factory.
ParamVolumeCollectionFactory(ParamVolumeCollection) - Constructor for class edu.jhu.ece.iacl.jist.pipeline.factory.ParamVolumeCollectionFactory
Instantiates a new param volume collection factory.
ParamVolumeCollectionInputView - Class in edu.jhu.ece.iacl.jist.pipeline.view.input
Input view to select multiple images.
ParamVolumeCollectionInputView(ParamVolumeCollection) - Constructor for class edu.jhu.ece.iacl.jist.pipeline.view.input.ParamVolumeCollectionInputView
Default constructor.
ParamVolumeCollectionOutputView - Class in edu.jhu.ece.iacl.jist.pipeline.view.output
Output view for a collection of volumes.
ParamVolumeCollectionOutputView(ParamVolumeCollection) - Constructor for class edu.jhu.ece.iacl.jist.pipeline.view.output.ParamVolumeCollectionOutputView
Default constructor for volumetric view.
ParamVolumeFactory - Class in edu.jhu.ece.iacl.jist.pipeline.factory
Volume Parameter Factory.
ParamVolumeFactory() - Constructor for class edu.jhu.ece.iacl.jist.pipeline.factory.ParamVolumeFactory
Instantiates a new param volume factory.
ParamVolumeFactory(ParamVolume) - Constructor for class edu.jhu.ece.iacl.jist.pipeline.factory.ParamVolumeFactory
Instantiates a new param volume factory.
ParamVolumeInputView - Class in edu.jhu.ece.iacl.jist.pipeline.view.input
Volume Parameter Input View allows the user to select a currently opened image from a combobox.
ParamVolumeInputView(ParamVolume) - Constructor for class edu.jhu.ece.iacl.jist.pipeline.view.input.ParamVolumeInputView
Construct combox to select a currently opened image.
ParamVolumeInputView.VolumeListBoxItem - Class in edu.jhu.ece.iacl.jist.pipeline.view.input
List box item that displays the image name.
ParamVolumeInputView.VolumeListBoxItem() - Constructor for class edu.jhu.ece.iacl.jist.pipeline.view.input.ParamVolumeInputView.VolumeListBoxItem
 
ParamVolumeOutputView - Class in edu.jhu.ece.iacl.jist.pipeline.view.output
Output view for a volume parameter.
ParamVolumeOutputView(ParamVolume) - Constructor for class edu.jhu.ece.iacl.jist.pipeline.view.output.ParamVolumeOutputView
Default constructor.
ParamVolumeURICollectionInputView - Class in edu.jhu.ece.iacl.jist.pipeline.view.input
Input view to select multiple images.
ParamVolumeURICollectionInputView(ParamVolumeCollection) - Constructor for class edu.jhu.ece.iacl.jist.pipeline.view.input.ParamVolumeURICollectionInputView
Default constructor.
ParamVolumeURIInputView - Class in edu.jhu.ece.iacl.jist.pipeline.view.input
Volume Parameter Input View allows the user to select a currently opened image from a combobox.
ParamVolumeURIInputView(ParamVolume) - Constructor for class edu.jhu.ece.iacl.jist.pipeline.view.input.ParamVolumeURIInputView
Construct combox to select a currently opened image.
ParamVolumeURIInputView.VolumeListBoxItem - Class in edu.jhu.ece.iacl.jist.pipeline.view.input
 
ParamVolumeURIInputView.VolumeListBoxItem() - Constructor for class edu.jhu.ece.iacl.jist.pipeline.view.input.ParamVolumeURIInputView.VolumeListBoxItem
 
ParamWeightedVolume<T> - Class in edu.jhu.ece.iacl.jist.pipeline.parameter
Weighted volume to store a volume and a weight associated with the volume.
ParamWeightedVolume(ParamModel<T>) - Constructor for class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamWeightedVolume
Inherits constructor from ParamVolume.
ParamWeightedVolume(String, ParamModel<T>, VoxelType, int, int, int, int) - Constructor for class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamWeightedVolume
Inherits constructor from ParamVolume.
ParamWeightedVolume(VoxelType, ParamModel<T>) - Constructor for class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamWeightedVolume
Inherits constructor from ParamVolume.
ParamWeightedVolume(VoxelType, ParamModel<T>, int, int, int, int) - Constructor for class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamWeightedVolume
Inherits constructor from ParamVolume.
ParamWeightedVolumeCollection<T> - Class in edu.jhu.ece.iacl.jist.pipeline.parameter
Weighted volumes stores a collection of cubic volumes and weights associated with each volume.
ParamWeightedVolumeCollection() - Constructor for class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamWeightedVolumeCollection
Construct a new weighted volume collection with no restrictions.
ParamWeightedVolumeCollection(String, ParamModel<T>) - Constructor for class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamWeightedVolumeCollection
Construct a new weighted volume collection with specified restrictions.
ParamWeightedVolumeCollection(String, ParamModel<T>, VoxelType) - Constructor for class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamWeightedVolumeCollection
Construct a new weighted volume collection with specified restrictions.
ParamWeightedVolumeCollection(String, ParamModel<T>, VoxelType, int, int, int, int) - Constructor for class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamWeightedVolumeCollection
Construct a new weighted volume collection with specified restrictions.
ParamWeightedVolumeCollection(VoxelType, ParamModel<T>) - Constructor for class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamWeightedVolumeCollection
Construct a new weighted volume collection with specified restrictions.
ParamWeightedVolumeCollection(VoxelType, ParamModel<T>, int, int, int, int) - Constructor for class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamWeightedVolumeCollection
Construct a new weighted volume collection with specified restrictions.
ParamWeightedVolumeCollectionFactory - Class in edu.jhu.ece.iacl.jist.pipeline.factory
Weighted Volume Parameter Factory.
ParamWeightedVolumeCollectionFactory(ParamWeightedVolumeCollection) - Constructor for class edu.jhu.ece.iacl.jist.pipeline.factory.ParamWeightedVolumeCollectionFactory
Instantiates a new param weighted volumes factory.
ParamWeightedVolumesInputView - Class in edu.jhu.ece.iacl.jist.pipeline.view.input
Input view to specify a collection of volumes with a specific weight.
ParamWeightedVolumesInputView(ParamVolumeCollection) - Constructor for class edu.jhu.ece.iacl.jist.pipeline.view.input.ParamWeightedVolumesInputView
Construct multiple image selection scroll pane with weight inputs.
ParamWeightedVolumesURIInputView - Class in edu.jhu.ece.iacl.jist.pipeline.view.input
Input view to specify a collection of volumes with a specific weight.
ParamWeightedVolumesURIInputView(ParamVolumeCollection) - Constructor for class edu.jhu.ece.iacl.jist.pipeline.view.input.ParamWeightedVolumesURIInputView
Construct multiple image selection scroll pane with weight inputs.
parent - Variable in class edu.jhu.ece.iacl.jist.pipeline.PipeAlgorithm
parent graph cell if this algorithm is in a group.
parent - Variable in class edu.jhu.ece.iacl.jist.pipeline.PipeLibrary.InitializeTask
The parent.
parent - Variable in class edu.jhu.ece.iacl.jist.pipeline.PipeLibrary.RebuildTask
The parent.
parentFrame - Variable in class edu.jhu.ece.iacl.jist.pipeline.ProcessingDialog
parent MIPAV frame.
parentPort - Variable in class edu.jhu.ece.iacl.jist.pipeline.PipeSource
Port for parent source.
parfile - Variable in class edu.jhu.ece.iacl.algorithms.dti.GTCparams
 
parse(String[]) - Method in class edu.jhu.ece.iacl.jist.cli.JistCLI
 
parseConnections(Element, PipeAlgorithmGroup) - Method in class edu.jhu.ece.iacl.jist.pipeline.parser.LoniPipeParser
Parse connections.
parseConnections(Element, PipeLayout) - Method in class edu.jhu.ece.iacl.jist.pipeline.parser.LoniPipeParser
Parse connections.
parseCVSRevision(String) - Static method in class edu.jhu.ece.iacl.plugins.JistPluginUtil
 
parseDataSources(Elements) - Method in class edu.jhu.ece.iacl.jist.pipeline.parser.LoniPipeParser
Parse data sources and connect them to modules.
parseDoubleFile() - Method in class edu.jhu.bme.smile.commons.textfiles.TextFileReader
 
parseFloatFile() - Method in class edu.jhu.bme.smile.commons.textfiles.TextFileReader
 
parseIntFile() - Method in class edu.jhu.bme.smile.commons.textfiles.TextFileReader
 
parseLayout(File) - Method in class edu.jhu.ece.iacl.jist.pipeline.parser.LoniPipeParser
Parse layout.
parseModule(Element) - Method in class edu.jhu.ece.iacl.jist.pipeline.parser.LoniPipeParser
Parse element.
parseModuleGroup(Element) - Method in class edu.jhu.ece.iacl.jist.pipeline.parser.LoniPipeParser
parse algorithm group.
parseParam(Element, ParamCollection, Hashtable<Integer, String>) - Method in class edu.jhu.ece.iacl.jist.pipeline.parser.LoniPipeParser
Parse particular parameter.
parsePipeAlgorithm(File) - Method in class edu.jhu.ece.iacl.jist.pipeline.parser.JistLayoutParser
 
parsePipeAlgorithm(File) - Method in class edu.jhu.ece.iacl.jist.pipeline.parser.LoniPipeParser
Parse LONI script from file.
parsePipeAlgorithm(ActionDiscovery) - Static method in class edu.jhu.ece.iacl.jist.pipeline.parser.MipavPluginParser
Parse MIPAV Plugin Class
parsePipeAlgorithm(File) - Method in class edu.jhu.ece.iacl.jist.pipeline.parser.MipavScriptParser
Parse MIPAV script
parsePipeAlgorithm(File) - Method in interface edu.jhu.ece.iacl.jist.pipeline.parser.ScriptParser
Parses specified file.
parseRevisionNumber(String) - Static method in class edu.jhu.ece.iacl.algorithms.VersionUtil
 
parseTableFile(String) - Static method in class edu.jhu.ece.iacl.algorithms.dti.DTIGradientTableCreator
 
parseVector(String) - Method in class edu.jhu.ece.iacl.jist.io.StringArrayToStringXML
Parses the vector.
parseVector(String) - Method in class edu.jhu.ece.iacl.jist.io.StringArrayXMLReaderWriter
Parses the vector.
partition(IntRange1D, int, int) - Static method in class edu.jhu.cs.cisst.algorithms.optimize.fmg.parallel.Parallelizer
partition a 1-dimensional range of (consecutive!) numbers (usually values for a loop variable) into a given number of portions and return one of these portions as a range.
ParV3Info - Class in edu.jhu.ece.iacl.algorithms.dti
The ParV3Info class parses par version 3 files for information relevant to CATNAP.
ParV3Info(String) - Constructor for class edu.jhu.ece.iacl.algorithms.dti.ParV3Info
 
ParV4Info - Class in edu.jhu.ece.iacl.algorithms.dti
The ParV3Info class parses par version 4 files for information relevant to CATNAP.
ParV4Info(String) - Constructor for class edu.jhu.ece.iacl.algorithms.dti.ParV4Info
 
parversion - Variable in class edu.jhu.ece.iacl.algorithms.dti.GTCparams
 
passedDir - Variable in class edu.jhu.ece.iacl.doc.DocumentAllTests
The passed dir.
passedDir - Variable in class edu.jhu.ece.iacl.jist.test.JistTestHarness
The passed dir.
passedFiles - Variable in class edu.jhu.ece.iacl.doc.DocumentAllTests
The passed files.
passedFiles - Variable in class edu.jhu.ece.iacl.jist.pipeline.PipeLayoutRunner
The passed files.
passedFiles - Variable in class edu.jhu.ece.iacl.jist.test.JistTestHarness
The passed files.
paste - Variable in class edu.jhu.ece.iacl.jist.pipeline.gui.PipeInternalFrame
The expand.
pasteItem - Variable in class edu.jhu.ece.iacl.jist.pipeline.gui.PipelineLayoutTool
The paste item.
patient_orientation - Variable in class edu.jhu.ece.iacl.algorithms.dti.GTCparams
 
patient_position - Variable in class edu.jhu.ece.iacl.algorithms.dti.GTCparams
 
pause - Variable in class edu.jhu.ece.iacl.jist.pipeline.gui.ProcessInfoPanel
The restart.
pause() - Method in class edu.jhu.ece.iacl.jist.pipeline.PipeScheduler
Pausing the scheduler will prevent new execution contexts from starting or completing.
pauseAll() - Method in class edu.jhu.ece.iacl.jist.pipeline.view.input.Refresher
Pause all refreshing.
pauseCount - Variable in class edu.jhu.ece.iacl.jist.pipeline.PipeScheduler
The pause count.
pcom - Variable in class edu.jhu.ece.iacl.algorithms.vabra.NumericalRecipes
 
PCurveCollection - Class in edu.jhu.cs.cisst.vent.structures.processing
The Class PCurveCollection wraps a curve collection for rendering.
PCurveCollection(CurveCollection, boolean) - Constructor for class edu.jhu.cs.cisst.vent.structures.processing.PCurveCollection
Instantiates a new p curve collection.
PDE - Interface in edu.jhu.cs.cisst.algorithms.optimize.fmg.pde
The interface to a linear elliptic partial differential equation (PDE) as needed by the Full Multigrid (FMG) algorithm and relaxation algorithms used by the FMG algorithm.
peek() - Method in class edu.jhu.ece.iacl.jist.structures.data.BinaryMinFastHeap
Find the smallest item in the priority queue.
peek() - Method in class edu.jhu.ece.iacl.jist.structures.data.BinaryMinHeap
Find the smallest item in the priority queue.
percolateUp(int) - Method in class edu.jhu.ece.iacl.jist.structures.data.BinaryMinFastHeap
Percolate up.
percolateUp(int) - Method in class edu.jhu.ece.iacl.jist.structures.data.BinaryMinHeap
Percolate up.
performance - Variable in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamPerformance
The performance.
performance - Variable in class edu.jhu.ece.iacl.jist.pipeline.ProcessingAlgorithm
Algorithm performance information.
PerformanceLevel - Class in edu.jhu.ece.iacl.algorithms.manual_label.staple
 
PerformanceLevel() - Constructor for class edu.jhu.ece.iacl.algorithms.manual_label.staple.PerformanceLevel
 
PerformanceLevel(int, int) - Constructor for class edu.jhu.ece.iacl.algorithms.manual_label.staple.PerformanceLevel
 
PerformanceLevel(int, int, boolean) - Constructor for class edu.jhu.ece.iacl.algorithms.manual_label.staple.PerformanceLevel
 
PerformanceSummary - Class in edu.jhu.ece.iacl.jist.pipeline
Summary of start and stop times for different tasks within an algorithm.
PerformanceSummary() - Constructor for class edu.jhu.ece.iacl.jist.pipeline.PerformanceSummary
Default constructor.
PerformanceSummary.TimeAndMemoryStamp - Class in edu.jhu.ece.iacl.jist.pipeline
The Class TimeAndMemoryStamp.
PerformanceSummary.TimeAndMemoryStamp() - Constructor for class edu.jhu.ece.iacl.jist.pipeline.PerformanceSummary.TimeAndMemoryStamp
Default constructor.
PerformanceSummary.TimeAndMemoryStamp(String, long, long, long, long) - Constructor for class edu.jhu.ece.iacl.jist.pipeline.PerformanceSummary.TimeAndMemoryStamp
Default constructor.
PeriodicBoundaryGrid - Class in edu.jhu.cs.cisst.algorithms.optimize.fmg.grid
An implementation of BoundaryGrid where the boundary elements are periodic images of interior grid elements.
PeriodicBoundaryGrid(int, int, int, int, double) - Constructor for class edu.jhu.cs.cisst.algorithms.optimize.fmg.grid.PeriodicBoundaryGrid
construct from size and initial value for all elements in the interior.
pev() - Method in class edu.jhu.ece.iacl.algorithms.dti.DiffusionTensor
 
PI - Static variable in class edu.jhmi.rad.medic.utilities.NumericsPublic
mathematical constants
pi2 - Static variable in class edu.jhu.ece.iacl.algorithms.dti.tractography.FiberTracker
 
pi2 - Static variable in class edu.jhu.ece.iacl.algorithms.dti.tractography.WildBootFiberTracker
 
pickedFunc - Static variable in class edu.jhu.bme.smile.commons.optimize.test.Test1DOptimizations
 
pickedFunc - Static variable in class edu.jhu.bme.smile.commons.optimize.test.TestNDOptimizations
 
pierreLouisBazin - Static variable in class edu.jhu.ece.iacl.algorithms.CommonAuthors
 
pipe - Variable in class edu.jhu.ece.iacl.jist.pipeline.graph.PipeModuleCell
The pipe.
pipe - Variable in class edu.jhu.ece.iacl.jist.pipeline.gui.PortToggleButton
The pipe.
PipeAlgorithm - Class in edu.jhu.ece.iacl.jist.pipeline
A pipe module for processing algorithms.
PipeAlgorithm() - Constructor for class edu.jhu.ece.iacl.jist.pipeline.PipeAlgorithm
Default constructor.
PipeAlgorithm(ProcessingAlgorithm) - Constructor for class edu.jhu.ece.iacl.jist.pipeline.PipeAlgorithm
The Constructor.
pipeAlgorithm - Variable in class edu.jhu.ece.iacl.jist.pipeline.ProcessingGroupDialog
The pipe algorithm.
PipeAlgorithmFactory - Class in edu.jhu.ece.iacl.jist.pipeline.graph
Creates algorithm modules from a module definition.
PipeAlgorithmFactory(File) - Constructor for class edu.jhu.ece.iacl.jist.pipeline.graph.PipeAlgorithmFactory
Constructor.
PipeAlgorithmFactory(String, Class) - Constructor for class edu.jhu.ece.iacl.jist.pipeline.graph.PipeAlgorithmFactory
Constructor.
PipeAlgorithmFactory.AlgorithmCell - Class in edu.jhu.ece.iacl.jist.pipeline.graph
Get module cell that represents algorithm.
PipeAlgorithmFactory.AlgorithmCell(String, PipeModule) - Constructor for class edu.jhu.ece.iacl.jist.pipeline.graph.PipeAlgorithmFactory.AlgorithmCell
Constructor.
PipeAlgorithmFactory.AlgorithmGroupCell - Class in edu.jhu.ece.iacl.jist.pipeline.graph
Get module cell that represents algorithm group.
PipeAlgorithmFactory.AlgorithmGroupCell(String, PipeModule) - Constructor for class edu.jhu.ece.iacl.jist.pipeline.graph.PipeAlgorithmFactory.AlgorithmGroupCell
Constructor.
PipeAlgorithmFactory.AlgorithmGroupNode - Class in edu.jhu.ece.iacl.jist.pipeline.graph
Tree node to represent algorithm.
PipeAlgorithmFactory.AlgorithmGroupNode(PipeModuleFactory) - Constructor for class edu.jhu.ece.iacl.jist.pipeline.graph.PipeAlgorithmFactory.AlgorithmGroupNode
Instantiates a new algorithm group node.
PipeAlgorithmFactory.AlgorithmNode - Class in edu.jhu.ece.iacl.jist.pipeline.graph
Tree node to represent algorithm.
PipeAlgorithmFactory.AlgorithmNode(PipeModuleFactory) - Constructor for class edu.jhu.ece.iacl.jist.pipeline.graph.PipeAlgorithmFactory.AlgorithmNode
Instantiates a new algorithm node.
PipeAlgorithmGroup - Class in edu.jhu.ece.iacl.jist.pipeline
Algorithm group is an aggregation of PipeAlgorithms.
PipeAlgorithmGroup() - Constructor for class edu.jhu.ece.iacl.jist.pipeline.PipeAlgorithmGroup
Default constructor.
PipeAlgorithmGroupView - Class in edu.jhu.ece.iacl.jist.pipeline.graph
Algorithm group cell view.
PipeAlgorithmGroupView() - Constructor for class edu.jhu.ece.iacl.jist.pipeline.graph.PipeAlgorithmGroupView
Default constructor.
PipeAlgorithmGroupView.ActivityRenderer - Class in edu.jhu.ece.iacl.jist.pipeline.graph
The Class ActivityRenderer.
PipeAlgorithmGroupView.ActivityRenderer() - Constructor for class edu.jhu.ece.iacl.jist.pipeline.graph.PipeAlgorithmGroupView.ActivityRenderer
 
PipeAlgorithmView - Class in edu.jhu.ece.iacl.jist.pipeline.graph
Cell view renderer for algorithm.
PipeAlgorithmView() - Constructor for class edu.jhu.ece.iacl.jist.pipeline.graph.PipeAlgorithmView
Instantiates a new pipe algorithm view.
PipeAlgorithmView.ActivityRenderer - Class in edu.jhu.ece.iacl.jist.pipeline.graph
The Class ActivityRenderer.
PipeAlgorithmView.ActivityRenderer() - Constructor for class edu.jhu.ece.iacl.jist.pipeline.graph.PipeAlgorithmView.ActivityRenderer
 
PipeAssertionTestDestination - Class in edu.jhu.ece.iacl.jist.pipeline.dest
 
PipeAssertionTestDestination() - Constructor for class edu.jhu.ece.iacl.jist.pipeline.dest.PipeAssertionTestDestination
 
PipeCellViewFactory - Class in edu.jhu.ece.iacl.jist.pipeline.graph
Factory to create graph cells for different module types.
PipeCellViewFactory(PipeJGraph) - Constructor for class edu.jhu.ece.iacl.jist.pipeline.graph.PipeCellViewFactory
Instantiates a new pipe cell view factory.
PipeChildPort - Class in edu.jhu.ece.iacl.jist.pipeline
Port that allows a Pipe Source to be a child of another Pipe Source.
PipeChildPort() - Constructor for class edu.jhu.ece.iacl.jist.pipeline.PipeChildPort
Port is always initialized as an input port.
PipeConnector - Class in edu.jhu.ece.iacl.jist.pipeline
A Pipe Connector provides a connection between an input and output port.
PipeConnector() - Constructor for class edu.jhu.ece.iacl.jist.pipeline.PipeConnector
Default constructor.
PipeConnector(PipePort, PipePort) - Constructor for class edu.jhu.ece.iacl.jist.pipeline.PipeConnector
Default constructor.
PipeConnector(PipePort, PipePort, PipeModuleEdge) - Constructor for class edu.jhu.ece.iacl.jist.pipeline.PipeConnector
Create connection between a source and destination.
PipeDestination - Class in edu.jhu.ece.iacl.jist.pipeline
Pipe Module for processing destinations.
PipeDestination() - Constructor for class edu.jhu.ece.iacl.jist.pipeline.PipeDestination
Instantiates a new pipe destination.
PipeDestinationFactory - Class in edu.jhu.ece.iacl.jist.pipeline.graph
Factory to create destination cell modules.
PipeDestinationFactory(String, Class) - Constructor for class edu.jhu.ece.iacl.jist.pipeline.graph.PipeDestinationFactory
Instantiates a new pipe destination factory.
PipeDestinationFactory.DestinationCell - Class in edu.jhu.ece.iacl.jist.pipeline.graph
Graph cell to represent destination.
PipeDestinationFactory.DestinationCell(String, PipeModule) - Constructor for class edu.jhu.ece.iacl.jist.pipeline.graph.PipeDestinationFactory.DestinationCell
Instantiates a new destination cell.
PipeDestinationFactory.DestinationNode - Class in edu.jhu.ece.iacl.jist.pipeline.graph
Tree node to destination.
PipeDestinationFactory.DestinationNode(PipeModuleFactory) - Constructor for class edu.jhu.ece.iacl.jist.pipeline.graph.PipeDestinationFactory.DestinationNode
Instantiates a new destination node.
PipeDestinationView - Class in edu.jhu.ece.iacl.jist.pipeline.graph
Cell view to render destination.
PipeDestinationView() - Constructor for class edu.jhu.ece.iacl.jist.pipeline.graph.PipeDestinationView
Instantiates a new pipe destination view.
PipeDestinationView(Object) - Constructor for class edu.jhu.ece.iacl.jist.pipeline.graph.PipeDestinationView
Instantiates a new pipe destination view.
PipeDestinationView.ActivityRenderer - Class in edu.jhu.ece.iacl.jist.pipeline.graph
The Class ActivityRenderer.
PipeDestinationView.ActivityRenderer() - Constructor for class edu.jhu.ece.iacl.jist.pipeline.graph.PipeDestinationView.ActivityRenderer
 
PipeDoubleCollectionExternalDestination - Class in edu.jhu.ece.iacl.jist.pipeline.dest
Destination to collect a summary of parameter values for all experiments.
PipeDoubleCollectionExternalDestination() - Constructor for class edu.jhu.ece.iacl.jist.pipeline.dest.PipeDoubleCollectionExternalDestination
 
PipeDoubleCollectionExternalSource - Class in edu.jhu.ece.iacl.jist.pipeline.src
 
PipeDoubleCollectionExternalSource() - Constructor for class edu.jhu.ece.iacl.jist.pipeline.src.PipeDoubleCollectionExternalSource
 
PipeDoubleCollectionListSource - Class in edu.jhu.ece.iacl.jist.pipeline.src
Iterate through list of floats.
PipeDoubleCollectionListSource() - Constructor for class edu.jhu.ece.iacl.jist.pipeline.src.PipeDoubleCollectionListSource
Default constructor.
PipeDoubleExternalDestination - Class in edu.jhu.ece.iacl.jist.pipeline.dest
Destination to collect a summary of parameter values for all experiments.
PipeDoubleExternalDestination() - Constructor for class edu.jhu.ece.iacl.jist.pipeline.dest.PipeDoubleExternalDestination
 
PipeDoubleExternalSource - Class in edu.jhu.ece.iacl.jist.pipeline.src
 
PipeDoubleExternalSource() - Constructor for class edu.jhu.ece.iacl.jist.pipeline.src.PipeDoubleExternalSource
 
PipeDoubleListSource - Class in edu.jhu.ece.iacl.jist.pipeline.src
Iterate through list of double values.
PipeDoubleListSource() - Constructor for class edu.jhu.ece.iacl.jist.pipeline.src.PipeDoubleListSource
Double list source.
PipeDoubleSweepSource - Class in edu.jhu.ece.iacl.jist.pipeline.src
Sweep through range of double values.
PipeDoubleSweepSource() - Constructor for class edu.jhu.ece.iacl.jist.pipeline.src.PipeDoubleSweepSource
Default constructor.
PipeEdgeEditor - Class in edu.jhu.ece.iacl.jist.pipeline.graph
Editor for index spinner box.
PipeEdgeEditor() - Constructor for class edu.jhu.ece.iacl.jist.pipeline.graph.PipeEdgeEditor
Instantiates a new pipe edge editor.
PipeEdgeEditor.DefaultSpinner - Class in edu.jhu.ece.iacl.jist.pipeline.graph
The Class DefaultSpinner.
PipeEdgeEditor.DefaultSpinner(Border) - Constructor for class edu.jhu.ece.iacl.jist.pipeline.graph.PipeEdgeEditor.DefaultSpinner
Constructs a DefaultTreeCellEditor$DefaultTextField object.
PipeEdgeRealEditor - Class in edu.jhu.ece.iacl.jist.pipeline.graph
The Class PipeEdgeRealEditor.
PipeEdgeRealEditor(JSpinner) - Constructor for class edu.jhu.ece.iacl.jist.pipeline.graph.PipeEdgeRealEditor
Constructs a DefaultCellEditor that uses a text field.
PipeEdgeRealEditor.EditorDelegate - Class in edu.jhu.ece.iacl.jist.pipeline.graph
The protected EditorDelegate class.
PipeEdgeRealEditor.EditorDelegate() - Constructor for class edu.jhu.ece.iacl.jist.pipeline.graph.PipeEdgeRealEditor.EditorDelegate
 
PipeEdgeView - Class in edu.jhu.ece.iacl.jist.pipeline.graph
Cell view to render edge.
PipeEdgeView(Object) - Constructor for class edu.jhu.ece.iacl.jist.pipeline.graph.PipeEdgeView
Instantiates a new pipe edge view.
PipeEdgeView.PipeEdgeRenderer - Class in edu.jhu.ece.iacl.jist.pipeline.graph
The Class PipeEdgeRenderer.
PipeEdgeView.PipeEdgeRenderer() - Constructor for class edu.jhu.ece.iacl.jist.pipeline.graph.PipeEdgeView.PipeEdgeRenderer
Instantiates a new pipe edge renderer.
PipeExternalDestination - Class in edu.jhu.ece.iacl.jist.pipeline.dest
Destination to collect a summary of parameter values for all experiments.
PipeExternalDestination() - Constructor for class edu.jhu.ece.iacl.jist.pipeline.dest.PipeExternalDestination
 
PipeExternalSource - Class in edu.jhu.ece.iacl.jist.pipeline.src
Sweep through range of integers.
PipeExternalSource() - Constructor for class edu.jhu.ece.iacl.jist.pipeline.src.PipeExternalSource
Instantiates a new pipe integer sweep source.
PipeFileCollectionExternalDestination - Class in edu.jhu.ece.iacl.jist.pipeline.dest
Destination to collect a summary of parameter values for all experiments.
PipeFileCollectionExternalDestination() - Constructor for class edu.jhu.ece.iacl.jist.pipeline.dest.PipeFileCollectionExternalDestination
 
PipeFileCollectionExternalSource - Class in edu.jhu.ece.iacl.jist.pipeline.src
 
PipeFileCollectionExternalSource() - Constructor for class edu.jhu.ece.iacl.jist.pipeline.src.PipeFileCollectionExternalSource
 
PipeFileCollectionListSource - Class in edu.jhu.ece.iacl.jist.pipeline.src
 
PipeFileCollectionListSource() - Constructor for class edu.jhu.ece.iacl.jist.pipeline.src.PipeFileCollectionListSource
Default constructor.
PipeFileCollectionSource - Class in edu.jhu.ece.iacl.jist.pipeline.src
Iterate through list of files.
PipeFileCollectionSource() - Constructor for class edu.jhu.ece.iacl.jist.pipeline.src.PipeFileCollectionSource
Default constructor.
PipeFileDirectorySource - Class in edu.jhu.ece.iacl.jist.pipeline.src
Iterate through all files in specified directory.
PipeFileDirectorySource() - Constructor for class edu.jhu.ece.iacl.jist.pipeline.src.PipeFileDirectorySource
Default constructor.
PipeFileExternalDestination - Class in edu.jhu.ece.iacl.jist.pipeline.dest
Destination to collect a summary of parameter values for all experiments.
PipeFileExternalDestination() - Constructor for class edu.jhu.ece.iacl.jist.pipeline.dest.PipeFileExternalDestination
 
PipeFileExternalSource - Class in edu.jhu.ece.iacl.jist.pipeline.src
 
PipeFileExternalSource() - Constructor for class edu.jhu.ece.iacl.jist.pipeline.src.PipeFileExternalSource
 
PipeFileListSource - Class in edu.jhu.ece.iacl.jist.pipeline.src
Iterate through list of files.
PipeFileListSource() - Constructor for class edu.jhu.ece.iacl.jist.pipeline.src.PipeFileListSource
Default constructor.
PipeGraphModel - Class in edu.jhu.ece.iacl.jist.pipeline.graph
Graph model that has been modified to clone cell modules correctly.
PipeGraphModel() - Constructor for class edu.jhu.ece.iacl.jist.pipeline.graph.PipeGraphModel
 
PipeGraphUI - Class in edu.jhu.ece.iacl.jist.pipeline.graph
The Class PipeGraphUI.
PipeGraphUI() - Constructor for class edu.jhu.ece.iacl.jist.pipeline.graph.PipeGraphUI
Instantiates a new pipe graph ui.
PipeIntegerCollectionExternalDestination - Class in edu.jhu.ece.iacl.jist.pipeline.dest
Destination to collect a summary of parameter values for all experiments.
PipeIntegerCollectionExternalDestination() - Constructor for class edu.jhu.ece.iacl.jist.pipeline.dest.PipeIntegerCollectionExternalDestination
 
PipeIntegerCollectionExternalSource - Class in edu.jhu.ece.iacl.jist.pipeline.src
 
PipeIntegerCollectionExternalSource() - Constructor for class edu.jhu.ece.iacl.jist.pipeline.src.PipeIntegerCollectionExternalSource
 
PipeIntegerCollectionListSource - Class in edu.jhu.ece.iacl.jist.pipeline.src
Iterate through list of integers.
PipeIntegerCollectionListSource() - Constructor for class edu.jhu.ece.iacl.jist.pipeline.src.PipeIntegerCollectionListSource
Default constructor.
PipeIntegerExternalDestination - Class in edu.jhu.ece.iacl.jist.pipeline.dest
Destination to collect a summary of parameter values for all experiments.
PipeIntegerExternalDestination() - Constructor for class edu.jhu.ece.iacl.jist.pipeline.dest.PipeIntegerExternalDestination
 
PipeIntegerExternalSource - Class in edu.jhu.ece.iacl.jist.pipeline.src
 
PipeIntegerExternalSource() - Constructor for class edu.jhu.ece.iacl.jist.pipeline.src.PipeIntegerExternalSource
 
PipeIntegerListSource - Class in edu.jhu.ece.iacl.jist.pipeline.src
Iterate through list of integers.
PipeIntegerListSource() - Constructor for class edu.jhu.ece.iacl.jist.pipeline.src.PipeIntegerListSource
Default constructor.
PipeIntegerSweepSource - Class in edu.jhu.ece.iacl.jist.pipeline.src
Sweep through range of integers.
PipeIntegerSweepSource() - Constructor for class edu.jhu.ece.iacl.jist.pipeline.src.PipeIntegerSweepSource
Instantiates a new pipe integer sweep source.
PipeInternalFrame - Class in edu.jhu.ece.iacl.jist.pipeline.gui
Internal frame to display graph of pipeline.
PipeInternalFrame(String) - Constructor for class edu.jhu.ece.iacl.jist.pipeline.gui.PipeInternalFrame
Default constructor.
PipeInternalFrame.EventRedirector - Class in edu.jhu.ece.iacl.jist.pipeline.gui
The Class EventRedirector.
PipeInternalFrame.EventRedirector(Action) - Constructor for class edu.jhu.ece.iacl.jist.pipeline.gui.PipeInternalFrame.EventRedirector
Instantiates a new event redirector.
PipeJGraph - Class in edu.jhu.ece.iacl.jist.pipeline.graph
MAPS customized graph.
PipeJGraph(PipeInternalFrame) - Constructor for class edu.jhu.ece.iacl.jist.pipeline.graph.PipeJGraph
References the folding manager.
PipeLayout - Class in edu.jhu.ece.iacl.jist.pipeline
Pipe Layout stores all information necessary to construct the pipe graph and layout preferences.
PipeLayout() - Constructor for class edu.jhu.ece.iacl.jist.pipeline.PipeLayout
Instantiates a new pipe layout.
PipeLayout(PipeAlgorithm) - Constructor for class edu.jhu.ece.iacl.jist.pipeline.PipeLayout
Instantiates a new pipe layout.
PipeLayout(PipeInternalFrame) - Constructor for class edu.jhu.ece.iacl.jist.pipeline.PipeLayout
The Constructor.
PipeLayout.RunParameters - Class in edu.jhu.ece.iacl.jist.pipeline
The Class RunParameters.
PipeLayout.RunParameters() - Constructor for class edu.jhu.ece.iacl.jist.pipeline.PipeLayout.RunParameters
 
PipeLayoutRunner - Class in edu.jhu.ece.iacl.jist.pipeline
The Class PipeLayoutRunner.
PipeLayoutRunner() - Constructor for class edu.jhu.ece.iacl.jist.pipeline.PipeLayoutRunner
Instantiates a new pipe layout runner.
PipeLibrary - Class in edu.jhu.ece.iacl.jist.pipeline
Interface to open, edit, and save module definitions.
PipeLibrary() - Constructor for class edu.jhu.ece.iacl.jist.pipeline.PipeLibrary
Default constructor.
PipeLibrary.CompareFactories - Class in edu.jhu.ece.iacl.jist.pipeline
The Class CompareFactories.
PipeLibrary.CompareFactories() - Constructor for class edu.jhu.ece.iacl.jist.pipeline.PipeLibrary.CompareFactories
 
PipeLibrary.CompareFiles - Class in edu.jhu.ece.iacl.jist.pipeline
The Class CompareFiles.
PipeLibrary.CompareFiles() - Constructor for class edu.jhu.ece.iacl.jist.pipeline.PipeLibrary.CompareFiles
 
PipeLibrary.InitializeTask - Class in edu.jhu.ece.iacl.jist.pipeline
Worker to find and initialize module definitions in library directory.
PipeLibrary.InitializeTask(Component) - Constructor for class edu.jhu.ece.iacl.jist.pipeline.PipeLibrary.InitializeTask
Instantiates a new initialize task.
PipeLibrary.RebuildTask - Class in edu.jhu.ece.iacl.jist.pipeline
Worker to rebuild library from module definitions in the library directory.
PipeLibrary.RebuildTask(Component, boolean) - Constructor for class edu.jhu.ece.iacl.jist.pipeline.PipeLibrary.RebuildTask
Instantiates a new rebuild task.
PIPELINE_TAG - Static variable in class edu.jhu.ece.iacl.jist.pipeline.parser.LoniPipeParser
The Constant PIPELINE_TAG.
PipelineLayoutTool - Class in edu.jhu.ece.iacl.jist.pipeline.gui
Main class for creating pipelines.
PipelineLayoutTool() - Constructor for class edu.jhu.ece.iacl.jist.pipeline.gui.PipelineLayoutTool
Default constructor.
PipelineLayoutTool.InitializeLayout - Class in edu.jhu.ece.iacl.jist.pipeline.gui
The Class InitializeLayout.
PipelineLayoutTool.InitializeLayout(PipeLayout) - Constructor for class edu.jhu.ece.iacl.jist.pipeline.gui.PipelineLayoutTool.InitializeLayout
Instantiates a new initialize layout.
PipeListCollectionSource - Class in edu.jhu.ece.iacl.jist.pipeline.src
Iterate through list of parameters.
PipeListCollectionSource() - Constructor for class edu.jhu.ece.iacl.jist.pipeline.src.PipeListCollectionSource
Default constructor.
PipeListSource - Class in edu.jhu.ece.iacl.jist.pipeline.src
Iterate through list of parameters.
PipeListSource() - Constructor for class edu.jhu.ece.iacl.jist.pipeline.src.PipeListSource
Default constructor.
PipeLogic - Class in edu.jhu.ece.iacl.jist.pipeline
Module for performing logical operations on parameters that do not require algorithms (i.e.
PipeLogic() - Constructor for class edu.jhu.ece.iacl.jist.pipeline.PipeLogic
 
PipeMarqueeHandler - Class in edu.jhu.ece.iacl.jist.pipeline.graph
The Class PipeMarqueeHandler.
PipeMarqueeHandler(PipeJGraph) - Constructor for class edu.jhu.ece.iacl.jist.pipeline.graph.PipeMarqueeHandler
Instantiates a new pipe marquee handler.
PipeModule - Class in edu.jhu.ece.iacl.jist.pipeline
A Pipe Module is the generic class for graph objects.
PipeModule() - Constructor for class edu.jhu.ece.iacl.jist.pipeline.PipeModule
Default constructor.
PipeModule.PipeListener - Interface in edu.jhu.ece.iacl.jist.pipeline
Listener class to monitor for updates to pipe modules.
PipeModuleCell - Class in edu.jhu.ece.iacl.jist.pipeline.graph
Module cell to display on graph.
PipeModuleCell(String, PipeModule) - Constructor for class edu.jhu.ece.iacl.jist.pipeline.graph.PipeModuleCell
Constructor.
PipeModuleEdge - Class in edu.jhu.ece.iacl.jist.pipeline.graph
Edge cell to display on graph.
PipeModuleEdge() - Constructor for class edu.jhu.ece.iacl.jist.pipeline.graph.PipeModuleEdge
Instantiates a new pipe module edge.
PipeModuleEdge(PipeConnector) - Constructor for class edu.jhu.ece.iacl.jist.pipeline.graph.PipeModuleEdge
Instantiates a new pipe module edge.
PipeModuleFactory - Class in edu.jhu.ece.iacl.jist.pipeline.graph
Factory to create new graph cell modules, tree nodes, and pipes.
PipeModuleFactory() - Constructor for class edu.jhu.ece.iacl.jist.pipeline.graph.PipeModuleFactory
Instantiates a new pipe module factory.
PipeModuleFactory(String, Class) - Constructor for class edu.jhu.ece.iacl.jist.pipeline.graph.PipeModuleFactory
Instantiates a new pipe module factory.
PipeModulePort - Class in edu.jhu.ece.iacl.jist.pipeline.graph
Graph module port.
PipeModulePort(double, double, PipePort) - Constructor for class edu.jhu.ece.iacl.jist.pipeline.graph.PipeModulePort
Instantiates a new pipe module port.
PipeParamCopyDestination - Class in edu.jhu.ece.iacl.jist.pipeline.dest
Destination for copying output files to specified directory location.
PipeParamCopyDestination() - Constructor for class edu.jhu.ece.iacl.jist.pipeline.dest.PipeParamCopyDestination
 
PipeParamSummaryDestination - Class in edu.jhu.ece.iacl.jist.pipeline.dest
Destination to collect a summary of parameter values for all experiments.
PipeParamSummaryDestination() - Constructor for class edu.jhu.ece.iacl.jist.pipeline.dest.PipeParamSummaryDestination
 
PipeParentPort - Class in edu.jhu.ece.iacl.jist.pipeline
Port that allows a Pipe Source to be a parent of another Pipe Source.
PipeParentPort() - Constructor for class edu.jhu.ece.iacl.jist.pipeline.PipeParentPort
Parent ports are always initialized as output ports.
PipePointDoubleSweepSource - Class in edu.jhu.ece.iacl.jist.pipeline.src
Sweep through range of double values.
PipePointDoubleSweepSource() - Constructor for class edu.jhu.ece.iacl.jist.pipeline.src.PipePointDoubleSweepSource
Default constructor.
PipePointListSource - Class in edu.jhu.ece.iacl.jist.pipeline.src
Iterate through list of points.
PipePointListSource() - Constructor for class edu.jhu.ece.iacl.jist.pipeline.src.PipePointListSource
Default constructor.
PipePort<T> - Class in edu.jhu.ece.iacl.jist.pipeline
The Class PipePort.
PipePort() - Constructor for class edu.jhu.ece.iacl.jist.pipeline.PipePort
Default constructor.
PipePort(PipeModule, PipePort.type) - Constructor for class edu.jhu.ece.iacl.jist.pipeline.PipePort
Default constructor.
PipePort.PortListener - Interface in edu.jhu.ece.iacl.jist.pipeline
Listener class to monitor for changes to a port.
PipePort.type - Enum in edu.jhu.ece.iacl.jist.pipeline
Differentiate between input and output ports.
PipePortView - Class in edu.jhu.ece.iacl.jist.pipeline.graph
Cell view for port.
PipePortView() - Constructor for class edu.jhu.ece.iacl.jist.pipeline.graph.PipePortView
Default constructor.
PipePortView(Object) - Constructor for class edu.jhu.ece.iacl.jist.pipeline.graph.PipePortView
Constructor.
PipePortView.ActivityRenderer - Class in edu.jhu.ece.iacl.jist.pipeline.graph
The Class ActivityRenderer.
PipePortView.ActivityRenderer() - Constructor for class edu.jhu.ece.iacl.jist.pipeline.graph.PipePortView.ActivityRenderer
Instantiates a new activity renderer.
pipeRenderer - Variable in class edu.jhu.ece.iacl.jist.pipeline.graph.PipeEdgeView
The pipe renderer.
PipeRunner - Class in edu.jhu.ece.iacl.jist.pipeline
Pipe Runner is responsible for executing a particular pipe algorithm given an input parameter file.
PipeRunner() - Constructor for class edu.jhu.ece.iacl.jist.pipeline.PipeRunner
 
pipes - Variable in class edu.jhu.ece.iacl.jist.pipeline.PipeLayout
List of all modules for this layout.
PipeScheduler - Class in edu.jhu.ece.iacl.jist.pipeline
Pipe scheduler creates and schedules the execution of execution contexts.
PipeScheduler(PipeLayout, ProcessManager) - Constructor for class edu.jhu.ece.iacl.jist.pipeline.PipeScheduler
Constructor.
PipeScheduler.CleanAllDialog - Class in edu.jhu.ece.iacl.jist.pipeline
The Class CleanAllDialog.
PipeScheduler.CleanAllDialog() - Constructor for class edu.jhu.ece.iacl.jist.pipeline.PipeScheduler.CleanAllDialog
Instantiates a new clean all dialog.
PipeScheduler.CleanAllDialog(boolean) - Constructor for class edu.jhu.ece.iacl.jist.pipeline.PipeScheduler.CleanAllDialog
 
PipeScheduler.CleanAllDialog.DeleteDirectoriesWorker - Class in edu.jhu.ece.iacl.jist.pipeline
The Class DeleteDirectoriesWorker.
PipeScheduler.CleanAllDialog.DeleteDirectoriesWorker() - Constructor for class edu.jhu.ece.iacl.jist.pipeline.PipeScheduler.CleanAllDialog.DeleteDirectoriesWorker
Instantiates a new destination processor.
PipeScheduler.DestinationProcessor - Class in edu.jhu.ece.iacl.jist.pipeline
The Class DestinationProcessor.
PipeScheduler.DestinationProcessor() - Constructor for class edu.jhu.ece.iacl.jist.pipeline.PipeScheduler.DestinationProcessor
Instantiates a new destination processor.
PipeSelectionExternalSource - Class in edu.jhu.ece.iacl.jist.pipeline.src
Source to select multiple options.
PipeSelectionExternalSource() - Constructor for class edu.jhu.ece.iacl.jist.pipeline.src.PipeSelectionExternalSource
Instantiates a new pipe selection source.
PipeSelectionListSource - Class in edu.jhu.ece.iacl.jist.pipeline.src
A parameter that allows the user to input a number of options from a text file
PipeSelectionListSource() - Constructor for class edu.jhu.ece.iacl.jist.pipeline.src.PipeSelectionListSource
Instantiates a new pipe selection List source.
PipeSelectionSource - Class in edu.jhu.ece.iacl.jist.pipeline.src
Source to select multiple options.
PipeSelectionSource() - Constructor for class edu.jhu.ece.iacl.jist.pipeline.src.PipeSelectionSource
Instantiates a new pipe selection source.
PipeSource - Class in edu.jhu.ece.iacl.jist.pipeline
Module for generating parameters used as input to algorithm modules.
PipeSource() - Constructor for class edu.jhu.ece.iacl.jist.pipeline.PipeSource
Constructor for source creates all associated input and output parameters.
PipeSourceFactory - Class in edu.jhu.ece.iacl.jist.pipeline.graph
Factory for creating source modules.
PipeSourceFactory(String, Class) - Constructor for class edu.jhu.ece.iacl.jist.pipeline.graph.PipeSourceFactory
Instantiates a new pipe source factory.
PipeSourceFactory.SourceCell - Class in edu.jhu.ece.iacl.jist.pipeline.graph
Source graph cell.
PipeSourceFactory.SourceCell(String, PipeModule) - Constructor for class edu.jhu.ece.iacl.jist.pipeline.graph.PipeSourceFactory.SourceCell
Instantiates a new source cell.
PipeSourceFactory.SourceNode - Class in edu.jhu.ece.iacl.jist.pipeline.graph
Source tree node.
PipeSourceFactory.SourceNode(PipeModuleFactory) - Constructor for class edu.jhu.ece.iacl.jist.pipeline.graph.PipeSourceFactory.SourceNode
Instantiates a new source node.
PipeSourceView - Class in edu.jhu.ece.iacl.jist.pipeline.graph
Cell view renderer for sources.
PipeSourceView() - Constructor for class edu.jhu.ece.iacl.jist.pipeline.graph.PipeSourceView
Instantiates a new pipe source view.
PipeSourceView(Object) - Constructor for class edu.jhu.ece.iacl.jist.pipeline.graph.PipeSourceView
Instantiates a new pipe source view.
PipeSourceView.ActivityRenderer - Class in edu.jhu.ece.iacl.jist.pipeline.graph
The Class ActivityRenderer.
PipeSourceView.ActivityRenderer() - Constructor for class edu.jhu.ece.iacl.jist.pipeline.graph.PipeSourceView.ActivityRenderer
 
PipeStringListSource - Class in edu.jhu.ece.iacl.jist.pipeline.src
Iterate through list of double values.
PipeStringListSource() - Constructor for class edu.jhu.ece.iacl.jist.pipeline.src.PipeStringListSource
Default constructor.
PipeSurfaceCollectionExternalDestination - Class in edu.jhu.ece.iacl.jist.pipeline.dest
Destination to collect a summary of parameter values for all experiments.
PipeSurfaceCollectionExternalDestination() - Constructor for class edu.jhu.ece.iacl.jist.pipeline.dest.PipeSurfaceCollectionExternalDestination
 
PipeSurfaceCollectionExternalSource - Class in edu.jhu.ece.iacl.jist.pipeline.src
 
PipeSurfaceCollectionExternalSource() - Constructor for class edu.jhu.ece.iacl.jist.pipeline.src.PipeSurfaceCollectionExternalSource
 
PipeSurfaceCollectionListSource - Class in edu.jhu.ece.iacl.jist.pipeline.src
 
PipeSurfaceCollectionListSource() - Constructor for class edu.jhu.ece.iacl.jist.pipeline.src.PipeSurfaceCollectionListSource
Default constructor.
PipeSurfaceCollectionSource - Class in edu.jhu.ece.iacl.jist.pipeline.src
Iterate through a list of surfaces.
PipeSurfaceCollectionSource() - Constructor for class edu.jhu.ece.iacl.jist.pipeline.src.PipeSurfaceCollectionSource
Default constructor.
PipeSurfaceDirectorySurface - Class in edu.jhu.ece.iacl.jist.pipeline.src
Iterate through all surfaces in a directory.
PipeSurfaceDirectorySurface() - Constructor for class edu.jhu.ece.iacl.jist.pipeline.src.PipeSurfaceDirectorySurface
Instantiates a new pipe surface directory surface.
PipeSurfaceExternalDestination - Class in edu.jhu.ece.iacl.jist.pipeline.dest
Destination to collect a summary of parameter values for all experiments.
PipeSurfaceExternalDestination() - Constructor for class edu.jhu.ece.iacl.jist.pipeline.dest.PipeSurfaceExternalDestination
 
PipeSurfaceExternalSource - Class in edu.jhu.ece.iacl.jist.pipeline.src
 
PipeSurfaceExternalSource() - Constructor for class edu.jhu.ece.iacl.jist.pipeline.src.PipeSurfaceExternalSource
 
PipeSurfaceListSource - Class in edu.jhu.ece.iacl.jist.pipeline.src
Iterate through all surfaces in file.
PipeSurfaceListSource() - Constructor for class edu.jhu.ece.iacl.jist.pipeline.src.PipeSurfaceListSource
Default constructor.
PipeToggleSource - Class in edu.jhu.ece.iacl.jist.pipeline.src
Toggle between true/false.
PipeToggleSource() - Constructor for class edu.jhu.ece.iacl.jist.pipeline.src.PipeToggleSource
Default constructor.
PipeVolumeCollectionExternalDestination - Class in edu.jhu.ece.iacl.jist.pipeline.dest
Destination to collect a summary of parameter values for all experiments.
PipeVolumeCollectionExternalDestination() - Constructor for class edu.jhu.ece.iacl.jist.pipeline.dest.PipeVolumeCollectionExternalDestination
 
PipeVolumeCollectionExternalSource - Class in edu.jhu.ece.iacl.jist.pipeline.src
 
PipeVolumeCollectionExternalSource() - Constructor for class edu.jhu.ece.iacl.jist.pipeline.src.PipeVolumeCollectionExternalSource
 
PipeVolumeCollectionListSource - Class in edu.jhu.ece.iacl.jist.pipeline.src
 
PipeVolumeCollectionListSource() - Constructor for class edu.jhu.ece.iacl.jist.pipeline.src.PipeVolumeCollectionListSource
Default constructor.
PipeVolumeCollectionSource - Class in edu.jhu.ece.iacl.jist.pipeline.src
Iterate through list of volumes.
PipeVolumeCollectionSource() - Constructor for class edu.jhu.ece.iacl.jist.pipeline.src.PipeVolumeCollectionSource
Default constructor.
PipeVolumeDirectoryCollectionSource - Class in edu.jhu.ece.iacl.jist.pipeline.src
Iterate through all volumes in directory.
PipeVolumeDirectoryCollectionSource() - Constructor for class edu.jhu.ece.iacl.jist.pipeline.src.PipeVolumeDirectoryCollectionSource
Instantiates a new pipe volume directory surface.
PipeVolumeDirectorySource - Class in edu.jhu.ece.iacl.jist.pipeline.src
Iterate through all volumes in directory.
PipeVolumeDirectorySource() - Constructor for class edu.jhu.ece.iacl.jist.pipeline.src.PipeVolumeDirectorySource
Instantiates a new pipe volume directory surface.
PipeVolumeExternalDestination - Class in edu.jhu.ece.iacl.jist.pipeline.dest
Destination to collect a summary of parameter values for all experiments.
PipeVolumeExternalDestination() - Constructor for class edu.jhu.ece.iacl.jist.pipeline.dest.PipeVolumeExternalDestination
 
PipeVolumeExternalSource - Class in edu.jhu.ece.iacl.jist.pipeline.src
 
PipeVolumeExternalSource() - Constructor for class edu.jhu.ece.iacl.jist.pipeline.src.PipeVolumeExternalSource
 
PipeVolumeListSource - Class in edu.jhu.ece.iacl.jist.pipeline.src
Iterate through all volumes in file.
PipeVolumeListSource() - Constructor for class edu.jhu.ece.iacl.jist.pipeline.src.PipeVolumeListSource
Default constructor.
pkg - Variable in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamCollection
The Category
pl - Variable in class edu.jhu.ece.iacl.algorithms.manual_label.staple.PerformanceLevel
 
pl - Variable in class edu.jhu.ece.iacl.algorithms.manual_label.staple.STAPLE
 
pl - Variable in class edu.jhu.ece.iacl.algorithms.manual_label.staple.STAPLEgeneral
 
pl - Variable in class edu.jhu.ece.iacl.algorithms.manual_label.staple.STAPLEgeneralSingle
 
pl - Variable in class edu.jhu.ece.iacl.algorithms.manual_label.staple.STAPLEmulti
 
pl - Variable in class edu.jhu.ece.iacl.algorithms.manual_label.staple.STAPLEmulti2
 
pl - Variable in class edu.jhu.ece.iacl.algorithms.manual_label.staple.STAPLEsingle
 
pl - Variable in class edu.jhu.ece.iacl.algorithms.manual_label.staple.STAPLEsurf
 
pl2 - Variable in class edu.jhu.ece.iacl.algorithms.manual_label.staple.STAPLEmulti2
 
PlaceHolder - Interface in edu.jhu.cs.cisst.test.data
 
PlaceHolder - Interface in edu.jhu.cs.cisst.vent.resources
 
PlaceHolder - Class in edu.jhu.ece.iacl.jist.pipeline.gui.resources
The Class PlaceHolder.
PlaceHolder() - Constructor for class edu.jhu.ece.iacl.jist.pipeline.gui.resources.PlaceHolder
 
play - Variable in class edu.jhu.ece.iacl.jist.pipeline.gui.ProcessInfoPanel
The restart.
PlugInCircleLevelSet - Class in edu.jhu.cs.cisst.plugins.segmentation
 
PlugInCircleLevelSet() - Constructor for class edu.jhu.cs.cisst.plugins.segmentation.PlugInCircleLevelSet
 
PluginCombineVolumes - Class in edu.vanderbilt.masi.plugins.utilities.volume
 
PluginCombineVolumes() - Constructor for class edu.vanderbilt.masi.plugins.utilities.volume.PluginCombineVolumes
 
PlugInFuzzyMembershipThreshold2D - Class in edu.jhu.cs.cisst.plugins.classification
 
PlugInFuzzyMembershipThreshold2D() - Constructor for class edu.jhu.cs.cisst.plugins.classification.PlugInFuzzyMembershipThreshold2D
 
PlugInGeodesicActiveContour2D - Class in edu.jhu.cs.cisst.plugins.segmentation
 
PlugInGeodesicActiveContour2D() - Constructor for class edu.jhu.cs.cisst.plugins.segmentation.PlugInGeodesicActiveContour2D
 
PlugInGradientVectorFlow2D - Class in edu.jhu.cs.cisst.plugins.segmentation
The Class PlugInGradientVectorFlow2D extends a gradient field using vector field diffusion.
PlugInGradientVectorFlow2D() - Constructor for class edu.jhu.cs.cisst.plugins.segmentation.PlugInGradientVectorFlow2D
 
PlugInIsoContourGenerator - Class in edu.jhu.cs.cisst.plugins.utilities.surface
The Iso-Contour Generator creates an iso-contour using the marching-squares algorithm.
PlugInIsoContourGenerator() - Constructor for class edu.jhu.cs.cisst.plugins.utilities.surface.PlugInIsoContourGenerator
 
PlugInIsoSurfaceGenerator - Class in edu.jhu.cs.cisst.plugins.utilities.surface
The PlugInIsoSurfaceGenerator generates an iso-surface using either the marching-cubes or marching-tetrahedral algorithm.
PlugInIsoSurfaceGenerator() - Constructor for class edu.jhu.cs.cisst.plugins.utilities.surface.PlugInIsoSurfaceGenerator
 
PlugInJISTLayoutTool - Class in <Unnamed>
The Class PlugInJISTLayoutTool.
PlugInJISTLayoutTool() - Constructor for class PlugInJISTLayoutTool
Instantiates a new plug in jist layout tool.
PlugInJISTPlugInSelector - Class in <Unnamed>
The Class PlugInJISTPlugInSelector.
PlugInJISTPlugInSelector() - Constructor for class PlugInJISTPlugInSelector
 
PlugInJISTProcessManager - Class in <Unnamed>
The Class PlugInJISTProcessManager.
PlugInJISTProcessManager() - Constructor for class PlugInJISTProcessManager
Instantiates a new plug in jist process manager.
PlugInSelector - Class in edu.jhu.ece.iacl.jist.pipeline.gui
Plug-In to select any plug-in in the MAPS library.
PlugInSelector(Frame) - Constructor for class edu.jhu.ece.iacl.jist.pipeline.gui.PlugInSelector
Constructor.
PlugInSelector.InitializeWorker - Class in edu.jhu.ece.iacl.jist.pipeline.gui
Initalize plug-in library.
PlugInSelector.InitializeWorker(Component, JScrollPane) - Constructor for class edu.jhu.ece.iacl.jist.pipeline.gui.PlugInSelector.InitializeWorker
Instantiates a new initialize worker.
PlugInSelector.RebuildWorker - Class in edu.jhu.ece.iacl.jist.pipeline.gui
Rebuild library.
PlugInSelector.RebuildWorker(Component, boolean) - Constructor for class edu.jhu.ece.iacl.jist.pipeline.gui.PlugInSelector.RebuildWorker
Instantiates a new rebuild worker.
PlugInTestDataSelector - Class in edu.jhu.cs.cisst.plugins.utilities.file
 
PlugInTestDataSelector() - Constructor for class edu.jhu.cs.cisst.plugins.utilities.file.PlugInTestDataSelector
 
PlugInVisualizeActiveContour2D - Class in edu.jhu.cs.cisst.plugins.visualization
 
PlugInVisualizeActiveContour2D() - Constructor for class edu.jhu.cs.cisst.plugins.visualization.PlugInVisualizeActiveContour2D
 
PlugInVisualizeImage - Class in edu.jhu.cs.cisst.plugins.visualization
 
PlugInVisualizeImage() - Constructor for class edu.jhu.cs.cisst.plugins.visualization.PlugInVisualizeImage
 
PlugInVisualizeSurface - Class in edu.jhu.cs.cisst.plugins.visualization
 
PlugInVisualizeSurface() - Constructor for class edu.jhu.cs.cisst.plugins.visualization.PlugInVisualizeSurface
 
plus(PT) - Method in class edu.jhu.ece.iacl.jist.structures.geom.PT
Plus.
PLUS_EPSILON - Static variable in class edu.jhu.bme.smile.commons.optimize.tensor.MLTensor
 
PLUS_EPSILON - Static variable in class edu.jhu.ece.iacl.algorithms.dti.DTEMRLTensor
 
Point3 - Class in edu.jhu.ece.iacl.jist.structures.geom
The Class Point3.
Point3() - Constructor for class edu.jhu.ece.iacl.jist.structures.geom.Point3
Instantiates a new point3.
Point3(double, double, double) - Constructor for class edu.jhu.ece.iacl.jist.structures.geom.Point3
Instantiates a new point3.
Point3(float, float, float) - Constructor for class edu.jhu.ece.iacl.jist.structures.geom.Point3
Instantiates a new point3.
Point3(double[]) - Constructor for class edu.jhu.ece.iacl.jist.structures.geom.Point3
Instantiates a new point3.
Point3fMath - Class in edu.jhu.bme.smile.commons.math
 
Point3fMath() - Constructor for class edu.jhu.bme.smile.commons.math.Point3fMath
 
pointData - Variable in class edu.jhu.ece.iacl.jist.structures.geom.EmbeddedPointSet
The point data.
pointDistributionModel - Static variable in class edu.jhu.ece.iacl.algorithms.ReferencedPapers
 
pointParam - Variable in class edu.jhu.ece.iacl.jist.pipeline.src.PipePointListSource
The point param.
points - Variable in class edu.jhu.cs.cisst.vent.structures.processing.PTriangleMesh
The points.
points - Variable in class edu.jhu.ece.iacl.jist.structures.geom.EmbeddedPointSet
The points.
PointSetVtkReaderWriter - Class in edu.jhu.ece.iacl.jist.io
The Class PointSetVtkReaderWriter.
PointSetVtkReaderWriter() - Constructor for class edu.jhu.ece.iacl.jist.io.PointSetVtkReaderWriter
Instantiates a new point set vtk reader writer.
pointTrackingLevelSets - Static variable in class edu.jhu.ece.iacl.algorithms.ReferencedPapers
 
Polygon - Class in edu.jhu.ece.iacl.jist.structures.geom
Created by IntelliJ IDEA.
Polygon(double[][], double[][]) - Constructor for class edu.jhu.ece.iacl.jist.structures.geom.Polygon
Instantiates a new polygon.
Polyhedron - Class in edu.jhu.ece.iacl.jist.structures.geom
Created by IntelliJ IDEA.
Polyhedron(Vector) - Constructor for class edu.jhu.ece.iacl.jist.structures.geom.Polyhedron
Instantiates a new polyhedron.
Polyhedron(double[][], double[][]) - Constructor for class edu.jhu.ece.iacl.jist.structures.geom.Polyhedron
Instantiates a new polyhedron.
PolySpline - Class in edu.jhu.ece.iacl.jist.structures.geom
The Class PolySpline.
PolySpline(int) - Constructor for class edu.jhu.ece.iacl.jist.structures.geom.PolySpline
Instantiates a new poly spline.
populateGUI() - Method in class edu.jhu.ece.iacl.jist.pipeline.view.input.AlgorithmInformationDialog
Populate GUI with values from algorithm information.
populateInfo() - Method in class edu.jhu.ece.iacl.jist.pipeline.view.input.AlgorithmInformationDialog
Populate algorithm information with values from GUI.
popupMenu - Variable in class edu.jhu.ece.iacl.jist.pipeline.gui.ProcessManagerTable
The popup menu.
port - Variable in class edu.jhu.ece.iacl.jist.pipeline.graph.PipeMarqueeHandler
The port.
port - Variable in class edu.jhu.ece.iacl.jist.pipeline.gui.PortComboBox
The port.
port - Variable in class edu.jhu.ece.iacl.jist.pipeline.gui.PortListBox
The port.
port - Variable in class edu.jhu.ece.iacl.jist.pipeline.gui.PortToggleButton
The port.
PORT_CLASS_KEY - Static variable in class edu.jhu.ece.iacl.jist.pipeline.graph.PipeCellViewFactory
The Constant PORT_CLASS_KEY.
portCheck - Variable in class edu.jhu.ece.iacl.jist.pipeline.graph.PipeJGraph
The port check.
PortChildView - Class in edu.jhu.ece.iacl.jist.pipeline.graph
Cell view render for child ports.
PortChildView() - Constructor for class edu.jhu.ece.iacl.jist.pipeline.graph.PortChildView
Instantiates a new port child view.
PortChildView(Object) - Constructor for class edu.jhu.ece.iacl.jist.pipeline.graph.PortChildView
Instantiates a new port child view.
PortChildView.ActivityRenderer - Class in edu.jhu.ece.iacl.jist.pipeline.graph
The Class ActivityRenderer.
PortChildView.ActivityRenderer() - Constructor for class edu.jhu.ece.iacl.jist.pipeline.graph.PortChildView.ActivityRenderer
Instantiates a new activity renderer.
PortComboBox - Class in edu.jhu.ece.iacl.jist.pipeline.gui
Combo box to select single incoming port.
PortComboBox(PipePort, Vector<PipePort>) - Constructor for class edu.jhu.ece.iacl.jist.pipeline.gui.PortComboBox
Constructor.
PortInputView - Class in edu.jhu.ece.iacl.jist.pipeline.graph
Cell view renderer for input ports.
PortInputView() - Constructor for class edu.jhu.ece.iacl.jist.pipeline.graph.PortInputView
Instantiates a new port input view.
PortInputView(Object) - Constructor for class edu.jhu.ece.iacl.jist.pipeline.graph.PortInputView
Instantiates a new port input view.
PortInputView.ActivityRenderer - Class in edu.jhu.ece.iacl.jist.pipeline.graph
The Class ActivityRenderer.
PortInputView.ActivityRenderer() - Constructor for class edu.jhu.ece.iacl.jist.pipeline.graph.PortInputView.ActivityRenderer
Instantiates a new activity renderer.
PortListBox - Class in edu.jhu.ece.iacl.jist.pipeline.gui
Allow user to select more than one incoming port.
PortListBox(PipePort, Vector<PipePort>) - Constructor for class edu.jhu.ece.iacl.jist.pipeline.gui.PortListBox
Constructor.
PortOutputView - Class in edu.jhu.ece.iacl.jist.pipeline.graph
Cell view renderer for output ports.
PortOutputView() - Constructor for class edu.jhu.ece.iacl.jist.pipeline.graph.PortOutputView
Instantiates a new port output view.
PortOutputView(Object) - Constructor for class edu.jhu.ece.iacl.jist.pipeline.graph.PortOutputView
Instantiates a new port output view.
PortOutputView.ActivityRenderer - Class in edu.jhu.ece.iacl.jist.pipeline.graph
The Class ActivityRenderer.
PortOutputView.ActivityRenderer() - Constructor for class edu.jhu.ece.iacl.jist.pipeline.graph.PortOutputView.ActivityRenderer
Instantiates a new activity renderer.
PortParentView - Class in edu.jhu.ece.iacl.jist.pipeline.graph
Cell view renderer for parent ports.
PortParentView() - Constructor for class edu.jhu.ece.iacl.jist.pipeline.graph.PortParentView
Instantiates a new port parent view.
PortParentView(Object) - Constructor for class edu.jhu.ece.iacl.jist.pipeline.graph.PortParentView
Instantiates a new port parent view.
PortParentView.ActivityRenderer - Class in edu.jhu.ece.iacl.jist.pipeline.graph
The Class ActivityRenderer.
PortParentView.ActivityRenderer() - Constructor for class edu.jhu.ece.iacl.jist.pipeline.graph.PortParentView.ActivityRenderer
Instantiates a new activity renderer.
ports - Variable in class edu.jhu.ece.iacl.jist.pipeline.gui.PortListBox
The ports.
portSize - Static variable in class edu.jhu.ece.iacl.jist.pipeline.graph.PipePortView
The Constant portSize.
PortToggleButton - Class in edu.jhu.ece.iacl.jist.pipeline.gui
Toggle button to select whether to use a connection or not use a connection.
PortToggleButton(PipePort) - Constructor for class edu.jhu.ece.iacl.jist.pipeline.gui.PortToggleButton
Constructor.
portType - Variable in class edu.jhu.ece.iacl.jist.pipeline.PipePort
indicates whether this is an input or output port.
post(boolean, String) - Static method in class edu.jhu.cs.cisst.algorithms.optimize.fmg.util.Contract
check if postcondition is met and throw exception if not.
PostconditionNotMetException - Exception in edu.jhu.cs.cisst.algorithms.optimize.fmg.util
Exception class that is thrown if a postcondition of a method is not met.
PostconditionNotMetException() - Constructor for exception edu.jhu.cs.cisst.algorithms.optimize.fmg.util.PostconditionNotMetException
construct with no particular message.
PostconditionNotMetException(String) - Constructor for exception edu.jhu.cs.cisst.algorithms.optimize.fmg.util.PostconditionNotMetException
construct with the given message.
posToNegCount - Variable in class edu.jhu.cs.cisst.algorithms.segmentation.gac.GeodesicActiveContour2D
The positive to negative transition count.
pow(float, float) - Static method in class edu.jhmi.rad.medic.utilities.NumericsPublic
 
practicalSphericalEmbedding - Static variable in class edu.jhu.ece.iacl.algorithms.ReferencedPapers
 
pre - Variable in class edu.jhu.bme.smile.commons.math.L1LSCompressedSensing
 
pre(boolean, String) - Static method in class edu.jhu.cs.cisst.algorithms.optimize.fmg.util.Contract
check if precondition is met and throw exception if not.
PreconditionNotMetException - Exception in edu.jhu.cs.cisst.algorithms.optimize.fmg.util
Exception class that is thrown if a precondition of a method is not met.
PreconditionNotMetException() - Constructor for exception edu.jhu.cs.cisst.algorithms.optimize.fmg.util.PreconditionNotMetException
construct with no particular message.
PreconditionNotMetException(String) - Constructor for exception edu.jhu.cs.cisst.algorithms.optimize.fmg.util.PreconditionNotMetException
construct with the given message.
preferredextension - Variable in class edu.jhu.ece.iacl.jist.pipeline.JistPreferences
Preferred output extension for CubicVolumeReaderWriter.
preferredSize - Variable in class edu.jhu.ece.iacl.jist.pipeline.graph.PipeModuleCell
The preferred size.
prepareForNextLevel() - Method in class edu.jhu.ece.iacl.algorithms.vabra.ImagePairNMI
 
prepareForNextLevelParent() - Method in class edu.jhu.ece.iacl.algorithms.vabra.ImagePairNMI
 
pressureForce - Variable in class edu.jhu.cs.cisst.algorithms.segmentation.gac.PressureForce2D
The pressure force.
PressureForce2D - Class in edu.jhu.cs.cisst.algorithms.segmentation.gac
The Class PressureForce2D moves the level set outwards in regions of positive pressure and inwards in regions of negative pressure.
PressureForce2D() - Constructor for class edu.jhu.cs.cisst.algorithms.segmentation.gac.PressureForce2D
 
PressureForce2D(float[][]) - Constructor for class edu.jhu.cs.cisst.algorithms.segmentation.gac.PressureForce2D
Instantiates a new pressure force.
pressureForceParam - Variable in class edu.jhu.cs.cisst.plugins.visualization.PlugInVisualizeActiveContour2D
 
print() - Method in class edu.jhu.ece.iacl.algorithms.dti.tractography.Tract
 
printArray(int[]) - Static method in class edu.jhu.ece.iacl.algorithms.dti.tractography.FACT.ArrayPrinter
 
printArray(float[]) - Static method in class edu.jhu.ece.iacl.algorithms.dti.tractography.FACT.ArrayPrinter
 
printArray(Object[]) - Static method in class edu.jhu.ece.iacl.algorithms.dti.tractography.FACT.ArrayPrinter
 
printArray(double[]) - Static method in class edu.jhu.ece.iacl.algorithms.dti.tractography.FACT.ArrayPrinter
 
printArrray(int[][]) - Static method in class edu.jhu.ece.iacl.algorithms.dti.tractography.FACT.ArrayPrinter
 
printArrray(float[][]) - Static method in class edu.jhu.ece.iacl.algorithms.dti.tractography.FACT.ArrayPrinter
 
printArrray(Object[][]) - Static method in class edu.jhu.ece.iacl.algorithms.dti.tractography.FACT.ArrayPrinter
 
printArrray(int[][][]) - Static method in class edu.jhu.ece.iacl.algorithms.dti.tractography.FACT.ArrayPrinter
 
printConfusion() - Method in class edu.jhu.ece.iacl.algorithms.manual_label.simulation.ConfusionMatrix
Prints the confusion Matrix
printFiberArray(Fiber[]) - Static method in class edu.jhu.ece.iacl.algorithms.dti.tractography.FACT.ArrayPrinter
 
printInfo() - Method in class edu.jhu.ece.iacl.algorithms.dti.ParV3Info
 
printLookup() - Method in class edu.jhu.ece.iacl.algorithms.manual_label.simulation.ConfusionMatrix
Prints the lookup Array
printNonZeroString(int) - Method in class edu.jhu.ece.iacl.jist.structures.matrix.Matrix3
Debugging routine for printing non-zero matrix elements.
printParams() - Method in class edu.jhu.ece.iacl.algorithms.dti.GTCparams
 
printPerformanceLevels() - Method in class edu.jhu.ece.iacl.algorithms.manual_label.staple.STAPLE
 
printPerformanceLevels() - Method in class edu.jhu.ece.iacl.algorithms.manual_label.staple.STAPLEgeneral
 
printPerformanceLevels() - Method in class edu.jhu.ece.iacl.algorithms.manual_label.staple.STAPLEgeneralSingle
 
printPerformanceLevels() - Method in class edu.jhu.ece.iacl.algorithms.manual_label.staple.STAPLEmulti
 
printPerformanceLevels() - Method in class edu.jhu.ece.iacl.algorithms.manual_label.staple.STAPLEmulti2
 
printPerformanceLevels() - Method in class edu.jhu.ece.iacl.algorithms.manual_label.staple.STAPLEsingle
 
printPerformanceLevels() - Method in class edu.jhu.ece.iacl.algorithms.manual_label.staple.STAPLEsurf
 
printPerformanceLevels2() - Method in class edu.jhu.ece.iacl.algorithms.manual_label.staple.STAPLE
 
printPerformanceLevels2() - Method in class edu.jhu.ece.iacl.algorithms.manual_label.staple.STAPLEgeneralSingle
 
printPerformanceLevels2() - Method in class edu.jhu.ece.iacl.algorithms.manual_label.staple.STAPLEsingle
 
printResults(String, String, long, double, double, double) - Static method in class edu.jhu.bme.smile.commons.optimize.test.Test1DOptimizations
Prints the results.
printResults(String, String, long, double[], double[], double) - Static method in class edu.jhu.bme.smile.commons.optimize.test.TestNDOptimizations
Prints the results.
prior - Variable in class edu.jhu.ece.iacl.algorithms.manual_label.staple.STAPLE
 
prior - Variable in class edu.jhu.ece.iacl.algorithms.manual_label.staple.STAPLEgeneralSingle
 
prior - Variable in class edu.jhu.ece.iacl.algorithms.manual_label.staple.STAPLEsingle
 
priorArray - Variable in class edu.jhu.ece.iacl.algorithms.manual_label.staple.STAPLEmulti2
 
priority - Variable in class edu.jhu.ece.iacl.jist.pipeline.ExecutionContext
The execution priority.
priors - Variable in class edu.jhu.ece.iacl.algorithms.manual_label.staple.STAPLEgeneral
 
priors - Variable in class edu.jhu.ece.iacl.algorithms.manual_label.staple.STAPLEmulti
 
priors - Variable in class edu.jhu.ece.iacl.algorithms.manual_label.staple.STAPLEmulti2
 
priors - Variable in class edu.jhu.ece.iacl.algorithms.manual_label.staple.STAPLEsurf
 
probability - Variable in class edu.jhu.bme.smile.commons.math.HistogramGenerator
 
probability - Variable in class edu.jhu.ece.iacl.plugins.utilities.volume.MedicAlgorithmVolumeHistogram
 
probeDefaultValue() - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamArgsOrder
 
probeDefaultValue() - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamBoolean
 
probeDefaultValue() - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamCollection
 
probeDefaultValue() - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamColor
 
probeDefaultValue() - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamFile
 
probeDefaultValue() - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamFileCollection
 
probeDefaultValue() - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamHeader
 
probeDefaultValue() - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamInformation
 
probeDefaultValue() - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamMatrix
 
probeDefaultValue() - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamMipavDialog
 
probeDefaultValue() - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamModel
 
probeDefaultValue() - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamMultiOption
 
probeDefaultValue() - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamNumber
 
probeDefaultValue() - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamNumberCollection
 
probeDefaultValue() - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamOption
 
probeDefaultValue() - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamPerformance
 
probeDefaultValue() - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamPointDouble
 
probeDefaultValue() - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamPointFloat
 
probeDefaultValue() - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamPointInteger
 
probeDefaultValue() - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamString
 
probeDefaultValue() - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamSwitch
 
proc - Variable in class edu.jhu.ece.iacl.jist.pipeline.ExecutionContext
Running process.
process - Variable in class edu.jhu.ece.iacl.jist.pipeline.ExecutionContext
Running process.
Process3DMRIImages - Class in edu.jhu.ece.iacl.plugins.hardi
 
Process3DMRIImages() - Constructor for class edu.jhu.ece.iacl.plugins.hardi.Process3DMRIImages
 
ProcessControlAction - Enum in edu.jhu.ece.iacl.jist.processcontrol
The Enum ProcessControlAction.
ProcessController - Interface in edu.jhu.ece.iacl.jist.processcontrol
The Interface ProcessController.
ProcessControllerDRMAA - Class in edu.jhu.ece.iacl.jist.processcontrol
The Class ProcessControllerDRMAA.
ProcessControllerDRMAA() - Constructor for class edu.jhu.ece.iacl.jist.processcontrol.ProcessControllerDRMAA
Instantiates a new process controller drmaa.
ProcessControllerNative - Class in edu.jhu.ece.iacl.jist.processcontrol
The Class ProcessControllerNative.
ProcessControllerNative(List<String>) - Constructor for class edu.jhu.ece.iacl.jist.processcontrol.ProcessControllerNative
Instantiates a new process controller native.
ProcessDebugInfoFrame - Class in edu.jhu.ece.iacl.jist.pipeline.gui
Display debug information for stdout and stderr.
ProcessDebugInfoFrame() - Constructor for class edu.jhu.ece.iacl.jist.pipeline.gui.ProcessDebugInfoFrame
Default constructor.
ProcessDebugInfoFrame.FileReaderWorker - Class in edu.jhu.ece.iacl.jist.pipeline.gui
Worker to load stdout/stderr in a safe threaded way.
ProcessDebugInfoFrame.FileReaderWorker(Component, JTextArea, File) - Constructor for class edu.jhu.ece.iacl.jist.pipeline.gui.ProcessDebugInfoFrame.FileReaderWorker
Instantiates a new file reader worker.
ProcessDebugInfoFrame.FileText - Class in edu.jhu.ece.iacl.jist.pipeline.gui
Split plane to display stdout and stderr.
ProcessDebugInfoFrame.FileText(File, File) - Constructor for class edu.jhu.ece.iacl.jist.pipeline.gui.ProcessDebugInfoFrame.FileText
Instantiates a new file text.
processDestinations() - Method in class edu.jhu.ece.iacl.jist.pipeline.gui.ProcessManager
 
processDestinations(ProgressMonitor) - Method in class edu.jhu.ece.iacl.jist.pipeline.PipeScheduler.DestinationProcessor
Process destinations.
processDestinations() - Method in class edu.jhu.ece.iacl.jist.pipeline.PipeScheduler
Process all destinations for this scheduler.
ProcessInfoPanel - Class in edu.jhu.ece.iacl.jist.pipeline.gui
Display process information.
ProcessInfoPanel(ProcessManagerTable, ProcessNode.Hierarchy) - Constructor for class edu.jhu.ece.iacl.jist.pipeline.gui.ProcessInfoPanel
Instantiates a new process info panel.
ProcessingAlgorithm - Class in edu.jhu.ece.iacl.jist.pipeline
Processing Algorithm for MAPS.
ProcessingAlgorithm() - Constructor for class edu.jhu.ece.iacl.jist.pipeline.ProcessingAlgorithm
Constructor creates input and output parameters and assigns the title of this algorithm to be the label for the input parameters.
ProcessingApplication - Class in edu.jhu.ece.iacl.jist.pipeline
Processing Application for MAPS.
ProcessingApplication() - Constructor for class edu.jhu.ece.iacl.jist.pipeline.ProcessingApplication
Default constructor.
ProcessingApplication(ProcessingAlgorithm) - Constructor for class edu.jhu.ece.iacl.jist.pipeline.ProcessingApplication
Specify the processing algorithm to be executed by this module.
ProcessingDialog - Class in edu.jhu.ece.iacl.jist.pipeline
Processing Dialog is a generic class that replaces all MIPAV plug-in dialogs The dialogs are auto-generated based on the input and output parameters.
ProcessingDialog() - Constructor for class edu.jhu.ece.iacl.jist.pipeline.ProcessingDialog
Empty constructor needed for dynamic instantiation.
ProcessingDialog(ProcessingAlgorithm) - Constructor for class edu.jhu.ece.iacl.jist.pipeline.ProcessingDialog
Constructor creates input and output parameters from algorithm and uses the algorithm name as title.
ProcessingGroupDialog - Class in edu.jhu.ece.iacl.jist.pipeline
Processing Dialog is a generic class that replaces all MIPAV plug-in dialogs The dialogs are auto-generated based on the input and output parameters.
ProcessingGroupDialog() - Constructor for class edu.jhu.ece.iacl.jist.pipeline.ProcessingGroupDialog
Empty constructor needed for dynamic instantiation.
ProcessingGroupDialog(PipeAlgorithmGroup) - Constructor for class edu.jhu.ece.iacl.jist.pipeline.ProcessingGroupDialog
Constructor creates input and output parameters from algorithm and uses the algorithm name as title.
ProcessManager - Class in edu.jhu.ece.iacl.jist.pipeline.gui
Process manager GUI to manage the execution of experiments.
ProcessManager() - Constructor for class edu.jhu.ece.iacl.jist.pipeline.gui.ProcessManager
Default constructor.
ProcessManager.LoadLayout - Class in edu.jhu.ece.iacl.jist.pipeline.gui
Worker to load layout.
ProcessManager.LoadLayout() - Constructor for class edu.jhu.ece.iacl.jist.pipeline.gui.ProcessManager.LoadLayout
 
ProcessManagerTable - Class in edu.jhu.ece.iacl.jist.pipeline.gui
Manager table that displays information about execution contexts.
ProcessManagerTable() - Constructor for class edu.jhu.ece.iacl.jist.pipeline.gui.ProcessManagerTable
Default constructor.
ProcessManagerTable.ClassRenderer - Class in edu.jhu.ece.iacl.jist.pipeline.gui
Renderer for class name.
ProcessManagerTable.ClassRenderer() - Constructor for class edu.jhu.ece.iacl.jist.pipeline.gui.ProcessManagerTable.ClassRenderer
Instantiates a new class renderer.
ProcessManagerTable.MemoryStampWrapper - Class in edu.jhu.ece.iacl.jist.pipeline.gui
 
ProcessManagerTable.MemoryStampWrapper(int, int, String) - Constructor for class edu.jhu.ece.iacl.jist.pipeline.gui.ProcessManagerTable.MemoryStampWrapper
 
ProcessManagerTable.ProcessTableModel - Class in edu.jhu.ece.iacl.jist.pipeline.gui
The Class ProcessTableModel.
ProcessManagerTable.ProcessTableModel() - Constructor for class edu.jhu.ece.iacl.jist.pipeline.gui.ProcessManagerTable.ProcessTableModel
Instantiates a new process table model.
ProcessManagerTable.ProgressRenderer - Class in edu.jhu.ece.iacl.jist.pipeline.gui
Render for progress.
ProcessManagerTable.ProgressRenderer() - Constructor for class edu.jhu.ece.iacl.jist.pipeline.gui.ProcessManagerTable.ProgressRenderer
 
ProcessManagerTable.StatusRenderer - Class in edu.jhu.ece.iacl.jist.pipeline.gui
Renderer to execution status.
ProcessManagerTable.StatusRenderer() - Constructor for class edu.jhu.ece.iacl.jist.pipeline.gui.ProcessManagerTable.StatusRenderer
Instantiates a new status renderer.
ProcessManagerTable.StringRenderer - Class in edu.jhu.ece.iacl.jist.pipeline.gui
Renderer for text.
ProcessManagerTable.StringRenderer() - Constructor for class edu.jhu.ece.iacl.jist.pipeline.gui.ProcessManagerTable.StringRenderer
Instantiates a new string renderer.
ProcessManagerTable.TimeStampWrapper - Class in edu.jhu.ece.iacl.jist.pipeline.gui
 
ProcessManagerTable.TimeStampWrapper(long, long, String) - Constructor for class edu.jhu.ece.iacl.jist.pipeline.gui.ProcessManagerTable.TimeStampWrapper
 
ProcessNode - Class in edu.jhu.ece.iacl.jist.pipeline.tree
Node to display in tree.
ProcessNode() - Constructor for class edu.jhu.ece.iacl.jist.pipeline.tree.ProcessNode
Instantiates a new process node.
ProcessNode(ExecutionContext, ProcessNode.Hierarchy) - Constructor for class edu.jhu.ece.iacl.jist.pipeline.tree.ProcessNode
Render process node as HTML.
ProcessNode.Hierarchy - Enum in edu.jhu.ece.iacl.jist.pipeline.tree
The Enum Hierarchy.
processSquare(int, int, Hashtable<Long, IsoContourGenerator.EdgeSplit>, LinkedList<IsoContourGenerator.Edge>) - Method in class edu.jhu.cs.cisst.algorithms.geometry.surface.IsoContourGenerator
Process square.
ProcessStatus - Enum in edu.jhu.ece.iacl.jist.processcontrol
The Enum ProcessStatus.
procTable - Variable in class edu.jhu.ece.iacl.jist.pipeline.gui.ProcessManagerTable
The proc table.
produceSyntheticRatersDX(int, float[], float[]) - Static method in class edu.jhu.ece.iacl.algorithms.manual_label.staple.StapleTester
 
produceSyntheticRatersVol(int[], float[], float[]) - Static method in class edu.jhu.ece.iacl.algorithms.manual_label.staple.StapleTester
 
product(double[]) - Static method in class edu.jhu.bme.smile.commons.math.StatisticsDouble
 
progressiveMesh - Static variable in class edu.jhu.ece.iacl.algorithms.ReferencedPapers
 
ProjectNDto1DOptimizable - Class in edu.jhu.bme.smile.commons.optimize
Projects an ND function to 1D so that LineSearchND can optimize in one dimension at a time.
ProjectNDto1DOptimizable(OptimizableNDContinuous) - Constructor for class edu.jhu.bme.smile.commons.optimize.ProjectNDto1DOptimizable
Constructor to create the projected function
ProjectNDto1DOptimizableDifferentiable - Class in edu.jhu.bme.smile.commons.optimize
Projects a Differentiable ND function to 1D so that LineSearchNDDifferentiable can optimize in one dimension at a time.
ProjectNDto1DOptimizableDifferentiable(OptimizableNDContinuousDifferentiable) - Constructor for class edu.jhu.bme.smile.commons.optimize.ProjectNDto1DOptimizableDifferentiable
Constructor to create the projected differentiable function.
projectRealSphericalHarmonics(float[][][][], float[][][][], float[][], int) - Static method in class edu.jhu.ece.iacl.algorithms.hardi.QBall
 
projectSphericalHarmonics(float[][][][], float[][][][], float[][][][], float[][][][], float[][], int) - Static method in class edu.jhu.ece.iacl.algorithms.hardi.QBall
 
projectTensor(float, float[], SchemeV1) - Static method in class edu.jhu.ece.iacl.algorithms.dti.DiffusionTensor
 
projectToSurface(Point3d) - Method in class edu.jhu.ece.iacl.jist.structures.geom.CollisionDetection
Project to surface.
promote() - Method in class edu.jhu.ece.iacl.jist.pipeline.ExecutionContext
Increase context queue priority.
promote - Variable in class edu.jhu.ece.iacl.jist.pipeline.gui.ProcessManagerTable
The debug.
promote(Vector<ExecutionContext>) - Method in class edu.jhu.ece.iacl.jist.pipeline.PipeScheduler
Promote position of processes in queue.
promptForParameterValue(Parameter) - Static method in class DiscoverMipavJISTPlugins
 
propertyChange(PropertyChangeEvent) - Method in class edu.jhu.ece.iacl.jist.pipeline.gui.PipeInternalFrame
Refresh parameter view if frame has been selected.
prototype - Variable in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamWeightedVolumeCollection
Prototype class for weights
pseudoInverse(Matrix) - Static method in class edu.jhu.bme.smile.commons.math.FieldRegularize
 
PT - Class in edu.jhu.ece.iacl.jist.structures.geom
Created by IntelliJ IDEA.
PT() - Constructor for class edu.jhu.ece.iacl.jist.structures.geom.PT
Instantiates a new pT.
PT(float, float, float) - Constructor for class edu.jhu.ece.iacl.jist.structures.geom.PT
Instantiates a new pT.
PT(double, double, double) - Constructor for class edu.jhu.ece.iacl.jist.structures.geom.PT
Instantiates a new pT.
PTriangleMesh - Class in edu.jhu.cs.cisst.vent.structures.processing
The Class PTriangleMesh.
PTriangleMesh(Point3f[], Vector3f[], int[]) - Constructor for class edu.jhu.cs.cisst.vent.structures.processing.PTriangleMesh
Instantiates a new p triangle mesh.
pts - Variable in class edu.jhu.ece.iacl.jist.structures.geom.TriangleSigned
The pts.
pull(ProgressMonitor) - Method in class edu.jhu.ece.iacl.jist.pipeline.PipeDestination
Pull value from layout my forwarding values along connectors and iterate.
push() - Method in class edu.jhu.ece.iacl.jist.pipeline.ExecutionContext
Push output parameters to input parameters.
push() - Method in class edu.jhu.ece.iacl.jist.pipeline.PipeModule
Forward information from output ports to all child input ports.
px - Variable in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamPointDouble
The px.
px - Variable in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamPointFloat
The px.
px - Variable in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamPointInteger
The px.
py - Variable in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamPointDouble
The py.
py - Variable in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamPointFloat
The py.
py - Variable in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamPointInteger
The py.
pz - Variable in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamPointDouble
The pz.
pz - Variable in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamPointFloat
The pz.
pz - Variable in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamPointInteger
The pz.

Q

QBall - Class in edu.jhu.ece.iacl.algorithms.hardi
 
QBall() - Constructor for class edu.jhu.ece.iacl.algorithms.hardi.QBall
 
QBallEstimation - Class in edu.jhu.ece.iacl.plugins.hardi
 
QBallEstimation() - Constructor for class edu.jhu.ece.iacl.plugins.hardi.QBallEstimation
 
QBallModifiedRealProjection - Class in edu.jhu.ece.iacl.plugins.hardi
 
QBallModifiedRealProjection() - Constructor for class edu.jhu.ece.iacl.plugins.hardi.QBallModifiedRealProjection
 
QBallProjection - Class in edu.jhu.ece.iacl.plugins.hardi
 
QBallProjection() - Constructor for class edu.jhu.ece.iacl.plugins.hardi.QBallProjection
 
QKSort2(float[]) - Static method in class edu.jhu.ece.iacl.algorithms.registration.RegistrationUtilities
 
Qn(double[]) - Static method in class edu.jhu.bme.smile.commons.math.StatisticsDouble
 
QnRobust(double[]) - Static method in class edu.jhu.bme.smile.commons.math.StatisticsDouble
 
quickHull - Static variable in class edu.jhu.ece.iacl.algorithms.ReferencedPapers
 
quickHull3D(Point3f[]) - Static method in class edu.jhu.ece.iacl.algorithms.hardi.SurfaceTools
 
quiet - Static variable in class edu.jhmi.rad.medic.utilities.MedicUtilPublic
The quiet.
quiet - Static variable in class edu.jhu.ece.iacl.jist.io.MipavController
The quiet.
quit() - Method in class edu.jhu.ece.iacl.jist.pipeline.gui.ProcessManager
 
quit(boolean) - Method in class edu.jhu.ece.iacl.jist.pipeline.gui.ProcessManager
Quit process manager.

R

r - Variable in class edu.jhu.ece.iacl.algorithms.dti.tractography.FACT.RGB
 
r - Variable in class edu.jhu.ece.iacl.jist.structures.image.RGB
The b.
RA() - Method in class edu.jhu.ece.iacl.algorithms.dti.DiffusionTensor
 
radialBasisFunction - Static variable in class edu.jhu.ece.iacl.algorithms.ReferencedPapers
 
radius - Variable in class edu.jhu.cs.cisst.plugins.segmentation.PlugInCircleLevelSet
 
randomGaussian() - Static method in class edu.jhmi.rad.medic.utilities.NumericsPublic
Gaussian random numbers (from the Box-Muller method, as in NRC) mean 0, variance 1
randomT3(double) - Static method in class edu.jhmi.rad.medic.utilities.NumericsPublic
Student T 3rd order random numbers mean 0, variance given note: the formula should be the inverse of the probability integral (wrong here!)
RandomVol - Class in edu.jhu.bme.smile.demo
 
RandomVol() - Constructor for class edu.jhu.bme.smile.demo.RandomVol
 
randTensor() - Static method in class edu.jhu.bme.smile.commons.optimize.tensor.OptimizeTensor
Creates a random tensor.
randTensor() - Method in class edu.jhu.ece.iacl.pami.GenerateTensors
 
raters - Variable in class edu.jhu.ece.iacl.algorithms.manual_label.staple.STAPLEmulti
 
raters - Variable in class edu.jhu.ece.iacl.algorithms.manual_label.staple.STAPLEmulti2
 
RawReader - Class in edu.jhu.ece.iacl.algorithms.manual_label.staple
 
RawReader() - Constructor for class edu.jhu.ece.iacl.algorithms.manual_label.staple.RawReader
 
RawWriter - Class in edu.jhu.ece.iacl.algorithms.manual_label.staple
 
RawWriter() - Constructor for class edu.jhu.ece.iacl.algorithms.manual_label.staple.RawWriter
 
RBF(float) - Static method in class edu.jhu.ece.iacl.algorithms.registration.RegistrationUtilities
 
RBF3D(int, int, int, int, int, int, float) - Static method in class edu.jhu.ece.iacl.algorithms.registration.RegistrationUtilities
 
read(String) - Method in class edu.jhu.ece.iacl.algorithms.dti.tractography.FACT.DTIStudioReader
 
read(LEFileReader) - Static method in class edu.jhu.ece.iacl.algorithms.dti.tractography.FACT.RGB
 
read(File) - Method in class edu.jhu.ece.iacl.jist.io.FileReaderWriter
The public method for reading files.
read(File) - Method in class edu.jhu.ece.iacl.jist.pipeline.factory.ParamFactory
Read parameter from XML file.
read(String, boolean) - Method in class edu.jhu.ece.iacl.jist.pipeline.factory.ParamFactory
Read parameter from String.
read(File) - Static method in class edu.jhu.ece.iacl.jist.pipeline.JistPreferences
Read preferences from file.
read(File) - Static method in class edu.jhu.ece.iacl.jist.pipeline.parameter.DataLabelCollection
Read labels from XML file.
read(File) - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamModel
Read parameter information from file.
read(String, boolean) - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamModel
Read parameter information from string.
read(File) - Static method in class edu.jhu.ece.iacl.jist.pipeline.PipeAlgorithm
Read algorithm from file.
read(File) - Static method in class edu.jhu.ece.iacl.jist.pipeline.PipeLayout
Read layout from file.
read(LEFileReader) - Method in class edu.jhu.ece.iacl.jist.structures.fiber.DTIStudioHDR
Read.
read(LEFileReader, int) - Method in class edu.jhu.ece.iacl.jist.structures.fiber.Fiber
Read.
read(LEFileReader) - Static method in class edu.jhu.ece.iacl.jist.structures.fiber.XYZ
Read.
read(LEFileReader) - Static method in class edu.jhu.ece.iacl.jist.structures.image.RGB
Read.
readBinImage() - Method in class edu.jhu.ece.iacl.algorithms.dti.tractography.FACT.ROIReader
 
readByte() - Method in class edu.jhu.ece.iacl.jist.io.LEFileReader
Read byte.
readByteImg(String, int[]) - Static method in class edu.jhu.ece.iacl.algorithms.manual_label.staple.RawReader
 
readCC(String) - Method in class edu.jhu.ece.iacl.algorithms.dti.tractography.FACT.DTIStudioReader
 
readColorVolume(String) - Method in class edu.jhu.ece.iacl.algorithms.dti.tractography.FACT.DTIStudioReader
 
readColorVolumeSoft(String) - Method in class edu.jhu.ece.iacl.algorithms.dti.tractography.FACT.DTIStudioReader
 
readData(String) - Method in class edu.jhu.ece.iacl.algorithms.dti.tractography.FACT.DXFiberData
 
readDXFibers(String) - Static method in class edu.jhu.ece.iacl.algorithms.dti.tractography.FACT.DxFiberReaderWriter
 
readerWriter - Static variable in class edu.jhu.ece.iacl.jist.io.ArrayDoubleDxReaderWriter
The Constant readerWriter.
readerWriter - Static variable in class edu.jhu.ece.iacl.jist.io.ArrayDoubleListTxtReaderWriter
The Constant readerWriter.
readerWriter - Static variable in class edu.jhu.ece.iacl.jist.io.ArrayDoubleMtxReaderWriter
The Constant readerWriter.
readerWriter - Static variable in class edu.jhu.ece.iacl.jist.io.ArrayDoubleReaderWriter
The Constant readerWriter.
readerWriter - Static variable in class edu.jhu.ece.iacl.jist.io.ArrayDoubleTxtReaderWriter
The Constant readerWriter.
readerWriter - Static variable in class edu.jhu.ece.iacl.jist.io.ArrayIntegerDxReaderWriter
The Constant readerWriter.
readerWriter - Static variable in class edu.jhu.ece.iacl.jist.io.ArrayIntegerReaderWriter
The Constant readerWriter.
readerWriter - Static variable in class edu.jhu.ece.iacl.jist.io.ArrayIntegerTxtReaderWriter
The Constant readerWriter.
readerWriter - Static variable in class edu.jhu.ece.iacl.jist.io.ArrayObjectTxtReaderWriter
The Constant readerWriter.
readerWriter - Static variable in class edu.jhu.ece.iacl.jist.io.CurveVtkReaderWriter
The Constant readerWriter.
readerWriter - Static variable in class edu.jhu.ece.iacl.jist.io.FiberCollectionReaderWriter
The Constant readerWriter.
readerWriter - Static variable in class edu.jhu.ece.iacl.jist.io.ImageDataReaderWriter
The Constant readerWriter.
readerWriter - Static variable in class edu.jhu.ece.iacl.jist.io.ModelImageReaderWriter
The Constant readerWriter.
readerWriter - Static variable in class edu.jhu.ece.iacl.jist.io.PointSetVtkReaderWriter
The Constant readerWriter.
readerWriter - Static variable in class edu.jhu.ece.iacl.jist.io.RibbonVtkReaderWriter
The Constant readerWriter.
readerWriter - Static variable in class edu.jhu.ece.iacl.jist.io.StringReaderWriter
The Constant readerWriter.
readerWriter - Static variable in class edu.jhu.ece.iacl.jist.io.SurfaceBrainSuiteReaderWriter
The Constant readerWriter.
readerWriter - Static variable in class edu.jhu.ece.iacl.jist.io.SurfaceDxReaderWriter
The Constant readerWriter.
readerWriter - Static variable in class edu.jhu.ece.iacl.jist.io.SurfaceFreeSurferReaderWriter
The Constant readerWriter.
readerWriter - Static variable in class edu.jhu.ece.iacl.jist.io.SurfaceMipavReaderWriter
The Constant readerWriter.
readerWriter - Static variable in class edu.jhu.ece.iacl.jist.io.SurfaceReaderWriter
The Constant readerWriter.
readerWriter - Static variable in class edu.jhu.ece.iacl.jist.io.SurfaceVrmlReaderWriter
The Constant readerWriter.
readerWriter - Static variable in class edu.jhu.ece.iacl.jist.io.SurfaceVtkReaderWriter
The Constant readerWriter.
readerWriter - Static variable in class edu.jhu.ece.iacl.jist.io.VertexDoubleDxReaderWriter
The Constant readerWriter.
readerWriter - Static variable in class edu.jhu.ece.iacl.jist.io.VertexFloatDxReaderWriter
The Constant readerWriter.
readerWriter - Static variable in class edu.jhu.ece.iacl.jist.io.VolumeVtkReaderWriter
The Constant readerWriter.
readerWriter - Static variable in class edu.jhu.ece.iacl.jist.io.ZipFileReaderWriter
The Constant readerWriter.
readerWriter - Variable in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamFileCollection
The reader writer.
readerWriter - Variable in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamObject
The reader writer.
readFloat() - Method in class edu.jhu.ece.iacl.jist.io.LEFileReader
Read float.
readFloatImgB(String, int[]) - Static method in class edu.jhu.ece.iacl.algorithms.manual_label.staple.RawReader
 
readFloatImgF(String, int[]) - Static method in class edu.jhu.ece.iacl.algorithms.manual_label.staple.RawReader
 
readFloatVecImg(String, int[]) - Static method in class edu.jhu.ece.iacl.algorithms.manual_label.staple.RawReader
 
readFloatVecImg(String, int, int, int) - Static method in class edu.jhu.ece.iacl.jist.io.DTISVecReader
Read float vec img.
readFloatVecImgB(String, int[]) - Static method in class edu.jhu.ece.iacl.algorithms.manual_label.staple.RawReader
 
readFloatVecImgMIPAV(String, int[]) - Static method in class edu.jhu.ece.iacl.algorithms.manual_label.staple.RawReader
 
readFloatVecImgMIPAVCorrect(String, int[]) - Static method in class edu.jhu.ece.iacl.algorithms.manual_label.staple.RawReader
 
readGraphics() - Method in class edu.jhu.ece.iacl.algorithms.dti.tractography.FACT.ROIReader
 
readImgs(String[], int[]) - Static method in class edu.jhu.ece.iacl.algorithms.manual_label.staple.StapleReader
 
readInt() - Method in class edu.jhu.ece.iacl.jist.io.LEFileReader
Read int.
readIntImg(String, int[]) - Static method in class edu.jhu.ece.iacl.algorithms.manual_label.staple.RawReader
 
readIntImg2d(String, int[]) - Static method in class edu.jhu.ece.iacl.algorithms.manual_label.staple.RawReader
 
readLEInt(InputStream) - Method in class edu.jhu.ece.iacl.algorithms.dti.tractography.FACT.FACTapi
 
readObject(File) - Method in class edu.jhu.ece.iacl.jist.io.ArrayDoubleDxReaderWriter
 
readObject(File) - Method in class edu.jhu.ece.iacl.jist.io.ArrayDoubleListTxtReaderWriter
 
readObject(File) - Method in class edu.jhu.ece.iacl.jist.io.ArrayDoubleMtxReaderWriter
 
readObject(File) - Method in class edu.jhu.ece.iacl.jist.io.ArrayDoubleReaderWriter
 
readObject(File) - Method in class edu.jhu.ece.iacl.jist.io.ArrayDoubleTxtReaderWriter
 
readObject(File) - Method in class edu.jhu.ece.iacl.jist.io.ArrayIntegerDxReaderWriter
 
readObject(File) - Method in class edu.jhu.ece.iacl.jist.io.ArrayIntegerReaderWriter
 
readObject(File) - Method in class edu.jhu.ece.iacl.jist.io.ArrayIntegerTxtReaderWriter
 
readObject(File) - Method in class edu.jhu.ece.iacl.jist.io.ArrayObjectTxtReaderWriter
 
readObject(File) - Method in class edu.jhu.ece.iacl.jist.io.CurveVtkReaderWriter
 
readObject(File) - Method in class edu.jhu.ece.iacl.jist.io.FiberCollectionReaderWriter
 
readObject(File) - Method in class edu.jhu.ece.iacl.jist.io.FileReaderWriter
Read object.
readObject(File) - Method in class edu.jhu.ece.iacl.jist.io.ImageDataReaderWriter
 
readObject(File) - Method in class edu.jhu.ece.iacl.jist.io.JistLayoutReaderWriter
 
readObject(File) - Method in class edu.jhu.ece.iacl.jist.io.ModelImageReaderWriter
 
readObject(File) - Method in class edu.jhu.ece.iacl.jist.io.PointSetVtkReaderWriter
 
readObject(File) - Method in class edu.jhu.ece.iacl.jist.io.RibbonVtkReaderWriter
 
readObject(File) - Method in class edu.jhu.ece.iacl.jist.io.ScriptReader
 
readObject(File) - Method in class edu.jhu.ece.iacl.jist.io.StringReaderWriter
 
readObject(File) - Method in class edu.jhu.ece.iacl.jist.io.SurfaceBrainSuiteReaderWriter
 
readObject(File) - Method in class edu.jhu.ece.iacl.jist.io.SurfaceDxReaderWriter
 
readObject(File) - Method in class edu.jhu.ece.iacl.jist.io.SurfaceFreeSurferReaderWriter
 
readObject(File) - Method in class edu.jhu.ece.iacl.jist.io.SurfaceMipavReaderWriter
 
readObject(File) - Method in class edu.jhu.ece.iacl.jist.io.SurfaceReaderWriter
 
readObject(File) - Method in class edu.jhu.ece.iacl.jist.io.SurfaceVrmlReaderWriter
 
readObject(File) - Method in class edu.jhu.ece.iacl.jist.io.SurfaceVtkReaderWriter
 
readObject(File) - Method in class edu.jhu.ece.iacl.jist.io.VertexDoubleDxReaderWriter
 
readObject(File) - Method in class edu.jhu.ece.iacl.jist.io.VertexFloatDxReaderWriter
 
readObject(File) - Method in class edu.jhu.ece.iacl.jist.io.VOIReaderWriter
 
readObject(File) - Method in class edu.jhu.ece.iacl.jist.io.VolumeVtkReaderWriter
 
readObject(File) - Method in class edu.jhu.ece.iacl.jist.io.ZipFileReaderWriter
 
readParameters(String) - Method in class edu.jhu.ece.iacl.algorithms.dti.tractography.FACT.FACTparameters
 
readParamFile(String) - Method in class edu.jhu.ece.iacl.algorithms.dti.tractography.FACT.FACTapi
 
readShort() - Method in class edu.jhu.ece.iacl.jist.io.LEFileReader
Read short.
readString(LEFileReader, int) - Method in class edu.jhu.ece.iacl.jist.structures.fiber.DTIStudioHDR
Read string.
readStrings(String) - Method in class edu.jhu.ece.iacl.jist.io.StringArrayToStringXML
Read strings.
readStrings(String) - Method in class edu.jhu.ece.iacl.jist.io.StringArrayXMLReaderWriter
Read strings.
readSurface(File) - Static method in class edu.jhu.ece.iacl.jist.io.MipavSurfaceReader
Read surface.
readSurfaceFile(File) - Static method in class edu.jhu.ece.iacl.jist.io.DxSurfaceReader
Read surface file.
readSurfaceFile(File) - Static method in class edu.jhu.ece.iacl.jist.io.FreeSurferAsciiReader
Read surface file.
readSurfaceFile(File) - Static method in class edu.jhu.ece.iacl.jist.io.FreeSurferReader
Read surface file.
readSurfaceFile(File) - Static method in class edu.jhu.ece.iacl.jist.io.MipavSurfaceXMLReader
Read surface file.
readTable(File) - Method in class edu.jhu.ece.iacl.algorithms.dti.GradientTable
Reads a Gradient table from a text file.
readUSByteImgB(String, int[]) - Static method in class edu.jhu.ece.iacl.algorithms.manual_label.staple.RawReader
 
readUSByteImgF(String, int[]) - Static method in class edu.jhu.ece.iacl.algorithms.manual_label.staple.RawReader
 
readXML(File) - Method in class edu.jhu.ece.iacl.algorithms.vabra.VabraConfiguration
 
rebuild() - Method in class edu.jhu.ece.iacl.jist.pipeline.gui.ModuleTreePanel
Rebuild module tree.
rebuild(boolean) - Method in class edu.jhu.ece.iacl.jist.pipeline.gui.ModuleTreePanel
Rebuild module tree.
rebuild() - Method in class edu.jhu.ece.iacl.jist.pipeline.gui.PlugInSelector
Rebuild library.
rebuildItem - Variable in class edu.jhu.ece.iacl.jist.pipeline.gui.PlugInSelector
The set dir item.
recipe - Variable in class edu.jhu.ece.iacl.algorithms.vabra.NumericalMethod
 
record(PerformanceSummary) - Method in class edu.jhu.ece.iacl.jist.pipeline.PerformanceSummary
Add child performance summary to this summary.
record(String, long, long, long, long) - Method in class edu.jhu.ece.iacl.jist.pipeline.PerformanceSummary
Record completion of task.
recordLM(int[][]) - Method in class edu.jhu.bme.smile.commons.math.specialFunctions.SphericalHarmonics
 
recoverUnsafeFilename(String) - Static method in class edu.jhu.ece.iacl.jist.utility.FileUtil
Recover unsafe filename.
RedBlackGaussSeidel - Class in edu.jhu.cs.cisst.algorithms.optimize.fmg.smoother
An implementation of the Red-Black Gauss-Seidel method of relaxing (thereby smoothing) the solution of a linear elliptic PDE.
RedBlackGaussSeidel(PDE) - Constructor for class edu.jhu.cs.cisst.algorithms.optimize.fmg.smoother.RedBlackGaussSeidel
construct from PDE.
redirect(File, File) - Static method in class edu.jhu.ece.iacl.jist.utility.FileUtil
Redirect stdout and stderr to files.
redo - Variable in class edu.jhu.ece.iacl.jist.pipeline.gui.PipeInternalFrame
The expand.
redo() - Method in class edu.jhu.ece.iacl.jist.pipeline.gui.PipeInternalFrame
Redo the last Change to the Model or the View.
redoItem - Variable in class edu.jhu.ece.iacl.jist.pipeline.gui.PipelineLayoutTool
The paste item.
ReferencedPapers - Class in edu.jhu.ece.iacl.algorithms
 
ReferencedPapers() - Constructor for class edu.jhu.ece.iacl.algorithms.ReferencedPapers
 
refImageParam - Variable in class edu.jhu.cs.cisst.plugins.segmentation.PlugInCircleLevelSet
 
refresh() - Method in class edu.jhu.cs.cisst.vent.widgets.VisualizationImage
Refresh.
refresh() - Method in class edu.jhu.cs.cisst.vent.widgets.VisualizationTriangleMesh
 
refresh() - Method in class edu.jhu.ece.iacl.jist.pipeline.graph.PipeJGraph
Refresh.
refresh() - Method in class edu.jhu.ece.iacl.jist.pipeline.gui.ProcessDebugInfoFrame.FileText
Refresh.
refresh() - Method in class edu.jhu.ece.iacl.jist.pipeline.gui.ProcessDebugInfoFrame
Refresh file display.
refresh() - Method in class edu.jhu.ece.iacl.jist.pipeline.view.input.ParamMultiOptionInputView
Refresh view by rebuilding list box.
refresh() - Method in class edu.jhu.ece.iacl.jist.pipeline.view.input.ParamVolumeCollectionInputView
Refresh view by rebuilding list box.
refresh() - Method in class edu.jhu.ece.iacl.jist.pipeline.view.input.ParamVolumeInputView
Refresh volume selection input by rebuilding combobox.
refresh() - Method in class edu.jhu.ece.iacl.jist.pipeline.view.input.ParamVolumeURICollectionInputView
Refresh view by rebuilding list box.
refresh() - Method in class edu.jhu.ece.iacl.jist.pipeline.view.input.ParamVolumeURIInputView
Refresh volume selection input by rebuilding combobox.
refresh() - Method in interface edu.jhu.ece.iacl.jist.pipeline.view.input.Refreshable
Refresh object.
Refreshable - Interface in edu.jhu.ece.iacl.jist.pipeline.view.input
Refreshable defines a class that is periodicaly refreshed to reflect external changes to the system.
refreshAll() - Method in class edu.jhu.ece.iacl.jist.pipeline.view.input.Refresher
 
refreshCurrentContext() - Method in class edu.jhu.ece.iacl.jist.pipeline.gui.ProcessInfoPanel
Refresh current context.
refresher - Variable in class edu.jhu.cs.cisst.vent.widgets.VisualizationImage
The refresher.
refresher - Variable in class edu.jhu.cs.cisst.vent.widgets.VisualizationTriangleMesh
The refresher.
Refresher - Class in edu.jhu.ece.iacl.jist.pipeline.view.input
The Class Refresher.
Refresher() - Constructor for class edu.jhu.ece.iacl.jist.pipeline.view.input.Refresher
Constructs new refresher for refreshable view.
refresher - Static variable in class edu.jhu.ece.iacl.jist.pipeline.view.input.Refresher
The refresher.
refreshLock - Variable in class edu.jhu.cs.cisst.vent.widgets.VisualizationImage
The refresh lock.
refreshQueues() - Method in class edu.jhu.ece.iacl.jist.pipeline.PipeScheduler
Refresh queues based on current status of context.
refreshQueuesLock - Variable in class edu.jhu.ece.iacl.jist.pipeline.PipeScheduler
Semaphore for locking queue.
refreshView() - Method in class edu.jhu.ece.iacl.jist.pipeline.gui.ParameterPanel
Refresh view of input parameters.
regFLIRTB0(List<ImageData>, int, int) - Method in class edu.jhu.ece.iacl.algorithms.dti.DWICoReg
 
regFLIRTStruct(int) - Method in class edu.jhu.ece.iacl.algorithms.dti.DWICoReg
 
registerImages() - Method in class edu.jhu.ece.iacl.algorithms.vabra.VabraSolver
 
RegistrationUtilities - Class in edu.jhu.ece.iacl.algorithms.registration
 
RegistrationUtilities() - Constructor for class edu.jhu.ece.iacl.algorithms.registration.RegistrationUtilities
 
RegistrationUtilities.IndexedFloat - Class in edu.jhu.ece.iacl.algorithms.registration
 
RegistrationUtilities.IndexedFloat(float, int) - Constructor for class edu.jhu.ece.iacl.algorithms.registration.RegistrationUtilities.IndexedFloat
 
RegistrationUtilities.InterpolationType - Class in edu.jhu.ece.iacl.algorithms.registration
 
RegistrationUtilities.InterpolationType() - Constructor for class edu.jhu.ece.iacl.algorithms.registration.RegistrationUtilities.InterpolationType
 
regRADAR(int[]) - Method in class edu.jhu.ece.iacl.algorithms.dti.DWICoReg
 
regStrucToB0(int) - Method in class edu.jhu.ece.iacl.algorithms.dti.DWICoReg
 
regStrucToB0_rdr(int) - Method in class edu.jhu.ece.iacl.algorithms.dti.DWICoReg
 
regularize2DChebyshev(int, int, float[][]) - Static method in class edu.jhu.bme.smile.commons.math.FieldRegularize
 
regularize2DChebyshevWLS(int, int, float[][], float[][]) - Static method in class edu.jhu.bme.smile.commons.math.FieldRegularize
 
regularize2DChebyshevWLS(int, int, float[][], float[][], Matrix) - Static method in class edu.jhu.bme.smile.commons.math.FieldRegularize
 
RegularizeNoiseField - Class in edu.jhu.ece.iacl.plugins.dti
 
RegularizeNoiseField() - Constructor for class edu.jhu.ece.iacl.plugins.dti.RegularizeNoiseField
 
relationToCircumsphere(Point3f, Point3f, Point3f, Point3f, Point3f) - Static method in class edu.jhu.ece.iacl.jist.algorithms.graphics.GeomUtil
Relation to circumsphere.
relationToPlane(Point3f, Point3f, Point3f, Point3f) - Static method in class edu.jhu.ece.iacl.jist.algorithms.graphics.GeomUtil
Relation to plane.
relativePath - Static variable in class edu.jhu.ece.iacl.jist.io.MipavController
The relative path.
release - Variable in class edu.jhu.ece.iacl.algorithms.dti.GTCparams
 
release() - Method in class edu.jhu.ece.iacl.jist.pipeline.PipeDestination
 
remove - Variable in class edu.jhu.ece.iacl.jist.pipeline.gui.PipeInternalFrame
The expand.
remove(ParamModel) - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamCollection
Add parameter to children.
remove(PipeAlgorithm) - Method in class edu.jhu.ece.iacl.jist.pipeline.PipeAlgorithmGroup
Remove algorithm from collection.
remove(PipeModule) - Method in class edu.jhu.ece.iacl.jist.pipeline.PipeLayout
Remove module from layout.
remove - Variable in class edu.jhu.ece.iacl.jist.pipeline.PipeLibrary.RebuildTask
The remove.
remove(Refreshable) - Method in class edu.jhu.ece.iacl.jist.pipeline.view.input.Refresher
Remove refreshable object.
remove() - Method in class edu.jhu.ece.iacl.jist.structures.data.BinaryMinFastHeap
Remove the smallest item from the priority queue.
remove() - Method in class edu.jhu.ece.iacl.jist.structures.data.BinaryMinHeap
Remove the smallest item from the priority queue.
removeAll() - Method in class edu.jhu.ece.iacl.jist.pipeline.view.input.Refresher
Remove all refreshable objects.
removeAllChildren() - Method in class edu.jhu.ece.iacl.jist.pipeline.PipeAlgorithmGroup
Remove all algorithms from collection.
removeAllContextListeners() - Method in class edu.jhu.ece.iacl.jist.pipeline.ExecutionContext
Remove all context listeners.
removeAllListeners() - Method in class edu.jhu.ece.iacl.jist.pipeline.PipeModule
Remove all listeners for this module.
removeAllListeners() - Method in class edu.jhu.ece.iacl.jist.pipeline.PipePort
Remove all listeners.
removeAtomicModules(ProgressMonitor) - Method in class edu.jhu.ece.iacl.jist.pipeline.PipeLibrary
Remove non-group modules that can be rebuilt from existing script/pipe files or from the source tree.
removeItem - Variable in class edu.jhu.ece.iacl.jist.pipeline.gui.PipelineLayoutTool
The paste item.
removeListener(ExecutionContext.ContextListener) - Method in class edu.jhu.ece.iacl.jist.pipeline.ExecutionContext
Remove context listener.
removeListener(JistPreferences.PreferenceListener) - Method in class edu.jhu.ece.iacl.jist.pipeline.JistPreferences
Remove listener.
removeListener(PipeModule.PipeListener) - Method in class edu.jhu.ece.iacl.jist.pipeline.PipeModule
Remove listener for this module.
removeListener(PipePort.PortListener) - Method in class edu.jhu.ece.iacl.jist.pipeline.PipePort
Remove listener.
removeObserver(ParamViewObserver) - Method in class edu.jhu.ece.iacl.jist.pipeline.view.input.ParamInputView
Remove observer from list of observers
removeScheduler() - Method in class edu.jhu.ece.iacl.jist.pipeline.gui.ProcessManagerTable
Remove scheduler and clear rows.
rename(String) - Method in class edu.jhu.ece.iacl.jist.pipeline.graph.PipeAlgorithmFactory
Rename module and save the change to the module definition file.
render() - Method in class edu.jhu.ece.iacl.jist.pipeline.view.output.ParamSurfaceOutputView
Render mesh.
renderer - Static variable in class edu.jhu.ece.iacl.jist.pipeline.graph.PipeAlgorithmGroupView
The renderer.
renderer - Static variable in class edu.jhu.ece.iacl.jist.pipeline.graph.PipeAlgorithmView
The renderer.
renderer - Static variable in class edu.jhu.ece.iacl.jist.pipeline.graph.PipeDestinationView
The renderer.
renderer - Static variable in class edu.jhu.ece.iacl.jist.pipeline.graph.PipeSourceView
The renderer.
renderer - Variable in class edu.jhu.ece.iacl.jist.pipeline.graph.PortChildView
The renderer.
renderer - Variable in class edu.jhu.ece.iacl.jist.pipeline.graph.PortInputView
The renderer.
renderer - Variable in class edu.jhu.ece.iacl.jist.pipeline.graph.PortOutputView
The renderer.
renderer - Variable in class edu.jhu.ece.iacl.jist.pipeline.graph.PortParentView
The renderer.
RendererProcessing - Class in edu.jhu.cs.cisst.vent.renderer.processing
The Class RendererProcessing.
RendererProcessing() - Constructor for class edu.jhu.cs.cisst.vent.renderer.processing.RendererProcessing
 
RendererProcessing2D - Class in edu.jhu.cs.cisst.vent.renderer.processing
The Class RendererProcessing2D.
RendererProcessing2D() - Constructor for class edu.jhu.cs.cisst.vent.renderer.processing.RendererProcessing2D
 
RendererProcessing3D - Class in edu.jhu.cs.cisst.vent.renderer.processing
JIST Extensions for Computer-Integrated Surgery Center for Computer-Integrated Surgical Systems and Technology & Johns Hopkins Applied Physics Laboratory & The Johns Hopkins University This library is free software; you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation; either version 2.1 of the License, or (at your option) any later version.
RendererProcessing3D() - Constructor for class edu.jhu.cs.cisst.vent.renderer.processing.RendererProcessing3D
 
renderers - Variable in class edu.jhu.cs.cisst.vent.VisualizationProcessing2D
The renderers.
renderers - Variable in class edu.jhu.cs.cisst.vent.VisualizationProcessing3D
The renderers.
repairDegenerateMappings(float, float) - Method in class edu.jhu.ece.iacl.jist.structures.geom.EmbeddedSurface
Repair degenerate mappings.
repairDegenerateTriangles(float, float) - Method in class edu.jhu.ece.iacl.jist.structures.geom.EmbeddedSurface
Repair degenerate triangles.
RepeatBoundaryGrid - Class in edu.jhu.cs.cisst.algorithms.optimize.fmg.grid
Uses a repeating value boundary condition, which is equivalent to having Neumann boundary conditions with the derivative at the boundary being zero.
RepeatBoundaryGrid(int, int, int, int, double, double) - Constructor for class edu.jhu.cs.cisst.algorithms.optimize.fmg.grid.RepeatBoundaryGrid
construct from size, initial value for all elements in the interior and initial value for all elements at the boundary.
replacePath(File, File) - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamCollection
 
replacePath(File, File) - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamFile
 
replacePath(File, File) - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamFileCollection
 
replacePath(File, File) - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamModel
Replace path in all file type objects with this path.
replacePath(PipeLayout, File, File) - Static method in class edu.jhu.ece.iacl.jist.pipeline.PipeLayout
Replace path.
reportiIntersect(Polygon) - Method in class edu.jhu.ece.iacl.jist.structures.fiber.Fiber
Reporti intersect.
reportIntersect(PT, PT) - Method in class edu.jhu.ece.iacl.jist.structures.geom.Polygon
Report intersect.
requestScreenShot - Variable in class edu.jhu.cs.cisst.vent.VisualizationProcessing
The request screen shot.
requestTreeUpdate - Variable in class edu.jhu.ece.iacl.jist.pipeline.PipeScheduler
Flag indicating a request to update input/output information about the experiments.
requestUpdate - Variable in class edu.jhu.cs.cisst.vent.widgets.VisualizationImage
The request update.
requestUpdate - Variable in class edu.jhu.cs.cisst.vent.widgets.VisualizationTriangleMesh
The request update.
resample(ImageData, IsotropicResample.InterpolationMethod) - Static method in class edu.jhu.ece.iacl.algorithms.volume.IsotropicResample
 
resample(ImageDataMipav, IsotropicResample.InterpolationMethod) - Static method in class edu.jhu.ece.iacl.algorithms.volume.IsotropicResample
 
resample(Fiber, int, double, double, double) - Method in class edu.jhu.ece.iacl.plugins.dti.tractography.SImageTractAnalysis
 
resample(Fiber, int, double, double, double) - Method in class edu.jhu.ece.iacl.plugins.dti.tractography.TractMapping
 
rescale(double) - Method in class edu.jhu.cs.cisst.algorithms.segmentation.gac.PressureForce2D
Rescale the pressure field so that the min and max are normalized to one and zero pressure is at the specified offset.
reset() - Method in class edu.jhu.ece.iacl.algorithms.manual_label.simulation.SurfaceRater
clean up everything related to the rater data to prepare to create a new rater
reset() - Method in class edu.jhu.ece.iacl.algorithms.manual_label.simulation.VolumeRater
clean up everything related to the rater data to prepare to create a new rater
reset() - Method in class edu.jhu.ece.iacl.jist.pipeline.AbstractCalculation
Reset the completed units for this calculation and all child calculations.
reset() - Method in class edu.jhu.ece.iacl.jist.pipeline.dest.PipeAssertionTestDestination
 
reset() - Method in class edu.jhu.ece.iacl.jist.pipeline.dest.PipeDoubleCollectionExternalDestination
 
reset() - Method in class edu.jhu.ece.iacl.jist.pipeline.dest.PipeDoubleExternalDestination
 
reset() - Method in class edu.jhu.ece.iacl.jist.pipeline.dest.PipeExternalDestination
 
reset() - Method in class edu.jhu.ece.iacl.jist.pipeline.dest.PipeFileCollectionExternalDestination
 
reset() - Method in class edu.jhu.ece.iacl.jist.pipeline.dest.PipeFileExternalDestination
 
reset() - Method in class edu.jhu.ece.iacl.jist.pipeline.dest.PipeIntegerCollectionExternalDestination
 
reset() - Method in class edu.jhu.ece.iacl.jist.pipeline.dest.PipeIntegerExternalDestination
 
reset() - Method in class edu.jhu.ece.iacl.jist.pipeline.dest.PipeParamCopyDestination
Reset data objects to be saved.
reset() - Method in class edu.jhu.ece.iacl.jist.pipeline.dest.PipeParamSummaryDestination
 
reset() - Method in class edu.jhu.ece.iacl.jist.pipeline.dest.PipeSurfaceCollectionExternalDestination
 
reset() - Method in class edu.jhu.ece.iacl.jist.pipeline.dest.PipeSurfaceExternalDestination
 
reset() - Method in class edu.jhu.ece.iacl.jist.pipeline.dest.PipeVolumeCollectionExternalDestination
 
reset() - Method in class edu.jhu.ece.iacl.jist.pipeline.dest.PipeVolumeExternalDestination
 
reset() - Method in class edu.jhu.ece.iacl.jist.pipeline.ExecutionContext
Reset status for context.
reset() - Method in class edu.jhu.ece.iacl.jist.pipeline.PipeDestination
Reset destination after iterating through all values.
reset() - Method in class edu.jhu.ece.iacl.jist.pipeline.PipeSource
Reset this source and all child sources.
reset() - Method in class edu.jhu.ece.iacl.jist.pipeline.src.PipeDoubleSweepSource
Reset iterator.
reset() - Method in class edu.jhu.ece.iacl.jist.pipeline.src.PipeExternalSource
 
reset() - Method in class edu.jhu.ece.iacl.jist.pipeline.src.PipeFileCollectionSource
Reset iterator.
reset() - Method in class edu.jhu.ece.iacl.jist.pipeline.src.PipeFileDirectorySource
Reset iterator.
reset() - Method in class edu.jhu.ece.iacl.jist.pipeline.src.PipeIntegerSweepSource
 
reset() - Method in class edu.jhu.ece.iacl.jist.pipeline.src.PipeListCollectionSource
Reset iterator.
reset() - Method in class edu.jhu.ece.iacl.jist.pipeline.src.PipeListSource
Reset iterator.
reset() - Method in class edu.jhu.ece.iacl.jist.pipeline.src.PipePointDoubleSweepSource
Reset iterator.
reset() - Method in class edu.jhu.ece.iacl.jist.pipeline.src.PipeSelectionListSource
Reset iterator.
reset() - Method in class edu.jhu.ece.iacl.jist.pipeline.src.PipeSelectionSource
Reset iterator.
reset() - Method in class edu.jhu.ece.iacl.jist.pipeline.src.PipeToggleSource
Reset iterator.
reset() - Method in class edu.jhu.ece.iacl.jist.pipeline.src.PipeVolumeDirectoryCollectionSource
 
reset() - Method in class edu.jhu.ece.iacl.jist.pipeline.view.output.ParamSurfaceOutputView
Reset 3d universe.
reset() - Method in class edu.jhu.ece.iacl.plugins.utilities.file.VolumeDirectoryNoIter
 
resetScale() - Method in class edu.jhu.cs.cisst.vent.widgets.VisualizationTriangleMesh
Reset scale.
resetStatus() - Method in class edu.jhu.ece.iacl.jist.pipeline.ExecutionContext
Reset status for this contexts and its dependents.
resetVariables() - Static method in class edu.jhu.bme.smile.commons.optimize.test.Test1DOptimizations
Resets all variables.
resetVariables() - Static method in class edu.jhu.bme.smile.commons.optimize.test.TestNDOptimizations
Resets the variables.
resizeData(int) - Method in class edu.jhu.ece.iacl.jist.structures.geom.EmbeddedSurface
Resize data.
resolution - Variable in class edu.jhu.ece.iacl.plugins.utilities.volume.MedicAlgorithmMipavReorient
 
resolutions - Variable in class edu.jhu.cs.cisst.algorithms.optimize.fmg.DefaultSolverResolutionLevels2D
The resolutions.
resolutions - Variable in class edu.jhu.cs.cisst.algorithms.optimize.fmg.DefaultSolverResolutionLevels3D
The resolutions.
resolutions - Variable in class edu.jhu.ece.iacl.jist.structures.fiber.FiberCollection
The resolutions.
resourceData - Variable in class edu.jhu.ece.iacl.jist.pipeline.factory.ParamDataLabelFactory
The resource data.
resourceVolume - Variable in class edu.jhu.ece.iacl.jist.pipeline.factory.ParamDataLabelFactory
The resource volume.
restart() - Method in class edu.jhu.ece.iacl.jist.pipeline.ExecutionContext
Restart algorithm by stopping, cleaning, and then starting the algorithm.
restart - Variable in class edu.jhu.ece.iacl.jist.pipeline.gui.ProcessInfoPanel
The restart.
restart - Variable in class edu.jhu.ece.iacl.jist.pipeline.gui.ProcessManagerTable
The debug.
restart(Vector<ExecutionContext>) - Method in class edu.jhu.ece.iacl.jist.pipeline.PipeScheduler
Restart specified contexts.
restoreDRMAASession(File) - Method in class edu.jhu.ece.iacl.jist.processcontrol.DispatchController
Restore drmaa session.
restoreRedirect() - Static method in class edu.jhu.ece.iacl.jist.utility.FileUtil
 
restrict(ConstGrid, SolverResolutionLevels) - Method in interface edu.jhu.cs.cisst.algorithms.optimize.fmg.restrictor.Restrictor
restricts a function sampled on a specific grid to the next coarser grid.
restrict(ConstGrid, SolverResolutionLevels) - Method in class edu.jhu.cs.cisst.algorithms.optimize.fmg.restrictor.RestrictorByStencil
implements method from Restrictor.
restrict(float[][], Stencil, int, int) - Static method in class edu.jhu.cs.cisst.algorithms.util.DataOperations
Restrict.
restrict(float[][][], Stencil, int, int, int) - Static method in class edu.jhu.cs.cisst.algorithms.util.DataOperations
Restrict.
RestrictByStencilParallelizer - Class in edu.jhu.cs.cisst.algorithms.optimize.fmg.restrictor
A helper class of class RestrictorByStencil that helps parallelizing method RestrictorByStencil.restrict().
RestrictByStencilParallelizer(RestrictorByStencil, Grid, ConstGrid) - Constructor for class edu.jhu.cs.cisst.algorithms.optimize.fmg.restrictor.RestrictByStencilParallelizer
construct.
Restrictor - Interface in edu.jhu.cs.cisst.algorithms.optimize.fmg.restrictor
This interface defines the restrict() method which produces a coarse grid from the next finer grid by restriction.
RestrictorByStencil - Class in edu.jhu.cs.cisst.algorithms.optimize.fmg.restrictor
The Class RestrictorByStencil.
RestrictorByStencil(Stencil) - Constructor for class edu.jhu.cs.cisst.algorithms.optimize.fmg.restrictor.RestrictorByStencil
construct from restriction stencil.
restrictProper(Grid, ConstGrid, int, int) - Method in class edu.jhu.cs.cisst.algorithms.optimize.fmg.restrictor.RestrictorByStencil
Restrict proper.
result - Variable in class edu.jhu.ece.iacl.plugins.utilities.volume.MedicAlgorithmMipavReorient
 
resultCode - Variable in class edu.jhu.ece.iacl.jist.structures.geom.IntersectResult
The result code.
resultVolParam - Variable in class edu.jhu.ece.iacl.pami.DivideReference
 
resultVolParam - Variable in class edu.jhu.ece.iacl.pami.NameTest
 
resultVolParam - Variable in class edu.jhu.ece.iacl.plugins.segmentation.CreateMask
 
resume() - Method in class edu.jhu.ece.iacl.jist.pipeline.PipeScheduler
Resume the scheduler.
resumeAll() - Method in class edu.jhu.ece.iacl.jist.pipeline.view.input.Refresher
Resume all refreshing.
resX - Variable in class edu.jhu.cs.cisst.algorithms.geometry.surface.IsoContourGenerator
The res y.
resX - Variable in class edu.jhu.cs.cisst.algorithms.geometry.surface.IsoSurfaceGenerator
The resolution in X.
resX - Variable in class edu.jhu.ece.iacl.algorithms.dti.tractography.FACT.FACTparameters
 
resX - Variable in class edu.jhu.ece.iacl.algorithms.dti.tractography.FiberTracker.FACTfiber
 
resX - Variable in class edu.jhu.ece.iacl.algorithms.dti.tractography.WildBootFiberTracker.WildBootFACTfiber
 
resX - Variable in class edu.jhu.ece.iacl.algorithms.manual_label.LabelImage
 
resY - Variable in class edu.jhu.cs.cisst.algorithms.geometry.surface.IsoContourGenerator
The res y.
resY - Variable in class edu.jhu.cs.cisst.algorithms.geometry.surface.IsoSurfaceGenerator
The resolution in Y.
resY - Variable in class edu.jhu.ece.iacl.algorithms.dti.tractography.FACT.FACTparameters
 
resY - Variable in class edu.jhu.ece.iacl.algorithms.dti.tractography.FiberTracker.FACTfiber
 
resY - Variable in class edu.jhu.ece.iacl.algorithms.dti.tractography.WildBootFiberTracker.WildBootFACTfiber
 
resY - Variable in class edu.jhu.ece.iacl.algorithms.manual_label.LabelImage
 
resZ - Variable in class edu.jhu.cs.cisst.algorithms.geometry.surface.IsoSurfaceGenerator
The resolution in Z.
resZ - Variable in class edu.jhu.ece.iacl.algorithms.dti.tractography.FACT.FACTparameters
 
resZ - Variable in class edu.jhu.ece.iacl.algorithms.dti.tractography.FiberTracker.FACTfiber
 
resZ - Variable in class edu.jhu.ece.iacl.algorithms.dti.tractography.WildBootFiberTracker.WildBootFACTfiber
 
resZ - Variable in class edu.jhu.ece.iacl.algorithms.manual_label.LabelImage
 
ReverseComparator<T extends java.lang.Comparable<? super T>> - Class in edu.jhu.ece.iacl.jist.structures.data
Reverse comparator used for Binary Max Heap.
ReverseComparator() - Constructor for class edu.jhu.ece.iacl.jist.structures.data.ReverseComparator
 
revnum - Static variable in class edu.jhu.ece.iacl.algorithms.manual_label.LabelImage
 
revnum - Static variable in class edu.jhu.ece.iacl.algorithms.manual_label.LabelSurface
 
RGB - Class in edu.jhu.ece.iacl.algorithms.dti.tractography.FACT
Created by IntelliJ IDEA.
RGB(byte, byte, byte) - Constructor for class edu.jhu.ece.iacl.algorithms.dti.tractography.FACT.RGB
 
RGB - Class in edu.jhu.ece.iacl.jist.structures.image
Created by IntelliJ IDEA.
RGB(byte, byte, byte) - Constructor for class edu.jhu.ece.iacl.jist.structures.image.RGB
Instantiates a new rGB.
RibbonVtkReaderWriter - Class in edu.jhu.ece.iacl.jist.io
The Class RibbonVtkReaderWriter.
RibbonVtkReaderWriter() - Constructor for class edu.jhu.ece.iacl.jist.io.RibbonVtkReaderWriter
Instantiates a new ribbon vtk reader writer.
robustLogRicianPDF(double[], double[], double[], double[]) - Static method in class edu.jhu.bme.smile.commons.math.StatisticsDouble
 
robustMaximum(float[][][], float, int, int, int, int) - Static method in class edu.jhmi.rad.medic.libraries.ImageFunctionsPublic
Robust maximum estimation
robustMaximum(ImageData, float, int, int, int, int) - Static method in class edu.jhmi.rad.medic.libraries.ImageFunctionsPublic
Robust maximum estimation
robustMaximum(float[][], float, int) - Method in class edu.jhu.bme.smile.commons.math.HistogramGenerator
 
robustMaximum(double[][], double, int) - Method in class edu.jhu.bme.smile.commons.math.HistogramGenerator
 
robustMinimum(float[][][], float, int, int, int, int) - Static method in class edu.jhmi.rad.medic.libraries.ImageFunctionsPublic
Robust maximum estimation
robustMinimum(ImageData, float, int, int, int, int) - Static method in class edu.jhmi.rad.medic.libraries.ImageFunctionsPublic
Robust maximum estimation
robustMinimum(float[][], float, int) - Method in class edu.jhu.bme.smile.commons.math.HistogramGenerator
 
robustMinimum(double[][], double, int) - Method in class edu.jhu.bme.smile.commons.math.HistogramGenerator
 
robustMinMax - Variable in class edu.jhu.bme.smile.commons.math.HistogramGenerator
 
robustMinMax - Variable in class edu.jhu.ece.iacl.plugins.utilities.surface.MedicAlgorithmSurfaceHistogram
 
robustMinMax - Variable in class edu.jhu.ece.iacl.plugins.utilities.volume.MedicAlgorithmVolumeHistogram
 
robustParameterizationBrainSurface - Static variable in class edu.jhu.ece.iacl.algorithms.ReferencedPapers
 
robustSphericalParameterization - Static variable in class edu.jhu.ece.iacl.algorithms.ReferencedPapers
 
ROI - Class in edu.jhu.ece.iacl.algorithms.manual_label
 
ROI() - Constructor for class edu.jhu.ece.iacl.algorithms.manual_label.ROI
 
ROI(ImageData) - Constructor for class edu.jhu.ece.iacl.algorithms.manual_label.ROI
 
ROI(ImageData, ImageData) - Constructor for class edu.jhu.ece.iacl.algorithms.manual_label.ROI
 
ROIReader - Class in edu.jhu.ece.iacl.algorithms.dti.tractography.FACT
 
ROIReader(String, int) - Constructor for class edu.jhu.ece.iacl.algorithms.dti.tractography.FACT.ROIReader
 
rootfactorialratio(int, int) - Static method in class edu.jhu.bme.smile.commons.math.specialFunctions.SFunc
 
rotateInverseMatrix(Point3f) - Static method in class edu.jhu.ece.iacl.jist.algorithms.graphics.GeomUtil
Rotate inverse matrix.
rotateInverseMatrix(double, double) - Static method in class edu.jhu.ece.iacl.jist.algorithms.graphics.GeomUtil
Rotate inverse matrix.
rotateInverseMatrix3d(Point3f) - Static method in class edu.jhu.ece.iacl.jist.algorithms.graphics.GeomUtil
Rotate inverse matrix3d.
rotateInverseMatrix3d(double, double) - Static method in class edu.jhu.ece.iacl.jist.algorithms.graphics.GeomUtil
Rotate inverse matrix3d.
rotateMatrix(double, double) - Static method in class edu.jhu.ece.iacl.jist.algorithms.graphics.GeomUtil
Rotate matrix.
rotateMatrix3d(double, double) - Static method in class edu.jhu.ece.iacl.jist.algorithms.graphics.GeomUtil
Rotate matrix3d.
rotateMatrix3f(double, double) - Static method in class edu.jhu.ece.iacl.jist.algorithms.graphics.GeomUtil
Rotate matrix3f.
rotateVertices(float, float) - Method in class edu.jhu.ece.iacl.jist.structures.geom.EmbeddedSurface
Rotate vertices.
RotationMatrix - Class in edu.jhu.bme.smile.commons.math
This class handles 3x3 rotation matrices with inverse Rodrigues parametrization.
RotationMatrix() - Constructor for class edu.jhu.bme.smile.commons.math.RotationMatrix
 
rotRate - Variable in class edu.jhu.cs.cisst.vent.widgets.VisualizationImage
The rotation rate in radians.
rotRate - Variable in class edu.jhu.cs.cisst.vent.widgets.VisualizationTriangleMesh
The rotation rate in radians.
rotx - Variable in class edu.jhu.cs.cisst.vent.widgets.VisualizationTriangleMesh
The rotation in x.
rotxParam - Variable in class edu.jhu.cs.cisst.vent.widgets.VisualizationTriangleMesh
The scale param.
roty - Variable in class edu.jhu.cs.cisst.vent.widgets.VisualizationTriangleMesh
The rotation in y.
rotyParam - Variable in class edu.jhu.cs.cisst.vent.widgets.VisualizationTriangleMesh
The scale param.
rotz - Variable in class edu.jhu.cs.cisst.vent.widgets.VisualizationImage
The scale.
rotz - Variable in class edu.jhu.cs.cisst.vent.widgets.VisualizationTriangleMesh
The rotation in z.
rotzParam - Variable in class edu.jhu.cs.cisst.vent.widgets.VisualizationImage
The scale param.
rotzParam - Variable in class edu.jhu.cs.cisst.vent.widgets.VisualizationTriangleMesh
The scale param.
round(float) - Static method in class edu.jhmi.rad.medic.utilities.NumericsPublic
rounding function (faster than regular Java)
round(double) - Static method in class edu.jhmi.rad.medic.utilities.NumericsPublic
 
round(Voxel, int) - Static method in class edu.jhu.ece.iacl.jist.structures.image.Voxel
Round.
round(Vector3, int) - Static method in class edu.jhu.ece.iacl.jist.structures.vector.Vector3
Round.
roundInBounds(int, int, int) - Method in class edu.jhu.ece.iacl.jist.structures.geom.GridPt
Round in bounds.
route(GraphLayoutCache, EdgeView) - Method in class edu.jhu.ece.iacl.jist.pipeline.graph.AvoidanceRouting
 
routeEdge(GraphLayoutCache, EdgeView) - Method in class edu.jhu.ece.iacl.jist.pipeline.graph.AvoidanceRouting
Route edge.
rows - Variable in class edu.jhmi.rad.medic.utilities.CropParameters
The rows.
rows - Variable in class edu.jhu.cs.cisst.algorithms.geometry.surface.IsoContourGenerator
The cols.
rows - Variable in class edu.jhu.cs.cisst.algorithms.geometry.surface.IsoSurfaceGenerator
The slices.
rows - Variable in class edu.jhu.cs.cisst.algorithms.segmentation.gac.ActiveContourForce2D
The columns.
rows - Variable in class edu.jhu.cs.cisst.algorithms.segmentation.gac.GeodesicActiveContour2D
The rows.
rows - Variable in class edu.jhu.cs.cisst.algorithms.segmentation.gac.GradientVectorFlow2D
The rows.
rows - Variable in class edu.jhu.cs.cisst.plugins.segmentation.PlugInCircleLevelSet
 
rows - Variable in class edu.jhu.cs.cisst.vent.renderer.processing.ImageRenderer
The cols.
rows - Variable in class edu.jhu.cs.cisst.vent.renderer.processing.VectorField2DRenderer
The cols.
rows - Variable in class edu.jhu.cs.cisst.vent.renderer.processing.VolumeSliceRenderer
The slices.
rows - Variable in class edu.jhu.cs.cisst.vent.widgets.VisualizationImage
The columns.
rows - Variable in class edu.jhu.ece.iacl.algorithms.manual_label.staple.STAPLEmulti
 
rows - Variable in class edu.jhu.ece.iacl.algorithms.manual_label.staple.STAPLEmulti2
 
rows - Variable in class edu.jhu.ece.iacl.jist.pipeline.gui.ProcessManagerTable.ProcessTableModel
The rows.
rows - Variable in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamMatrix
The rows.
rows - Variable in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamVolume
The rows.
rows - Variable in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamVolumeCollection
The rows.
rows - Variable in class edu.jhu.ece.iacl.jist.structures.image.ImageData
The rows.
rows - Variable in class edu.jhu.ece.iacl.plugins.utilities.math.MedicAlgorithmKLDivergence
 
rows - Variable in class edu.jhu.ece.iacl.plugins.utilities.surface.MedicAlgorithmSurfaceHistogram
 
rows - Variable in class edu.jhu.ece.iacl.plugins.utilities.volume.MedicAlgorithmVolumeHistogram
 
run() - Method in class edu.jhu.cs.cisst.algorithms.optimize.fmg.FMGThread
re-routes to FMG.fmgProper()
run() - Method in class edu.jhu.cs.cisst.algorithms.optimize.fmg.parallel.ParallelRunner
the Threads main method.
run() - Method in class edu.jhu.ece.iacl.algorithms.dti.DTIGradientTableCreator
 
run() - Method in class edu.jhu.ece.iacl.algorithms.dti.DWICoReg
 
run - Class in edu.jhu.ece.iacl.jist.cli
 
run() - Constructor for class edu.jhu.ece.iacl.jist.cli.run
 
run() - Method in class edu.jhu.ece.iacl.jist.pipeline.CalculationMonitor
Periodically poll the algorithm to determine its current progress.
run() - Method in class edu.jhu.ece.iacl.jist.pipeline.ExecutionContext.ProcessStatusParser
 
run() - Method in class edu.jhu.ece.iacl.jist.pipeline.ExecutionContext
Thread method for running the algorithm.
run(File) - Method in class edu.jhu.ece.iacl.jist.pipeline.gui.ProcessManager
 
run(PipeLayout, boolean) - Method in class edu.jhu.ece.iacl.jist.pipeline.gui.ProcessManager
 
run() - Method in class edu.jhu.ece.iacl.jist.pipeline.gui.ProcessManager
Main process manager thread.
run - Variable in class edu.jhu.ece.iacl.jist.pipeline.gui.ProcessManagerTable
The debug.
run(File, boolean) - Static method in class edu.jhu.ece.iacl.jist.pipeline.PipeRunner
Run.
run() - Method in class edu.jhu.ece.iacl.jist.pipeline.PipeScheduler
Schedule and run all experiments.
run(Vector<ExecutionContext>) - Method in class edu.jhu.ece.iacl.jist.pipeline.PipeScheduler
Enqueue and run processes.
run() - Method in class edu.jhu.ece.iacl.jist.pipeline.ProcessingApplication
This method is inherited from MIPAV and should not be overridden.
run() - Method in class edu.jhu.ece.iacl.jist.pipeline.view.input.Refresher
Periodically refresh view.
run(List<String>, File) - Method in class edu.jhu.ece.iacl.jist.plugins.MedicAlgorithmExecutableAdapter.ProcessRunner
Run.
run() - Method in class edu.jhu.ece.iacl.plugins.hardi.CFARIEstimation2.CFARIWrapper
 
run() - Method in class PlugInJISTLayoutTool
This method is inherited from MIPAV and should not be overridden.
run() - Method in class PlugInJISTProcessManager
This method is inherited from MIPAV and should not be overridden.
runAlgorithm() - Method in class edu.jhu.ece.iacl.jist.pipeline.ProcessingAlgorithm
Run algorithm with new calculation monitor.
runAlgorithm(CalculationMonitor) - Method in class edu.jhu.ece.iacl.jist.pipeline.ProcessingAlgorithm
Run algorithm with calculation monitor.
runAlgorithm() - Method in class edu.jhu.ece.iacl.plugins.registration.MedicAlgorithmConstrainedFLIRT.AlgorithmConstrainedOAR3DWrapper
 
runAlgorithm() - Method in class edu.jhu.ece.iacl.plugins.registration.MedicAlgorithmFLIRT.AlgorithmRegOAR3DWrapper
 
runAlgorithm() - Method in class edu.jhu.ece.iacl.plugins.registration.MedicAlgorithmFLIRTCollection.AlgorithmRegOAR3DWrapper
 
runAllComparisons(List<ImageData>, int) - Static method in class edu.jhu.ece.iacl.algorithms.manual_label.LabelImage
 
runAllComparisons(List<EmbeddedSurface>, int) - Static method in class edu.jhu.ece.iacl.algorithms.manual_label.LabelSurface
 
runAndWait() - Method in class edu.jhu.cs.cisst.vent.VisualizationApplication
Run and wait.
runAndWait(PipeLayout, boolean) - Method in class edu.jhu.ece.iacl.jist.pipeline.gui.ProcessManager
 
runCenterOfMasses(List<ImageData>, int) - Static method in class edu.jhu.ece.iacl.algorithms.manual_label.LabelImage
 
runCFARI() - Method in class edu.jhu.ece.iacl.plugins.hardi.CFARIEstimation2.CFARIWrapper
 
runCMDistance(List<ImageData>, int, int) - Static method in class edu.jhu.ece.iacl.algorithms.manual_label.LabelImage
 
runCmdLine(String, Vector, Vector) - Method in class edu.jhu.ece.iacl.jist.pipeline.MipavViewUserInterface
Run command line from script file.
runFACT() - Static method in class edu.jhu.ece.iacl.algorithms.dti.tractography.FACT.FACT_INFACTcompare
 
RunFACT - Class in edu.jhu.ece.iacl.algorithms.dti.tractography.FACT
 
RunFACT() - Constructor for class edu.jhu.ece.iacl.algorithms.dti.tractography.FACT.RunFACT
 
runHausdorfDistance(List<LabelImage>, int) - Static method in class edu.jhu.ece.iacl.algorithms.manual_label.LabelImage
 
runInProcess() - Method in class edu.jhu.ece.iacl.jist.pipeline.ProcessingApplication
 
runLayout - Class in edu.jhu.ece.iacl.jist.cli
 
runLayout() - Constructor for class edu.jhu.ece.iacl.jist.cli.runLayout
 
runMeanDistance(List<ImageData>, int, int) - Static method in class edu.jhu.ece.iacl.algorithms.manual_label.LabelImage
 
running - Variable in class edu.jhu.ece.iacl.jist.pipeline.ExecutionContext.ProcessStatusParser
The running.
runningFlag - Variable in class edu.jhu.ece.iacl.jist.pipeline.ExecutionContext
Flag indicating the thread is running.
runningFlag - Variable in class edu.jhu.ece.iacl.jist.pipeline.PipeScheduler
Flag indicates the scheduler is running.
runningInSeparateProcess - Variable in class edu.jhu.ece.iacl.jist.pipeline.ProcessingAlgorithm
Run in separate process.
runningQueue - Variable in class edu.jhu.ece.iacl.jist.pipeline.PipeScheduler
Queue to store contexts that are currently running.
runParallel(int, int) - Method in class edu.jhu.cs.cisst.algorithms.optimize.fmg.CalcResidualParallelizer
re-route.
runParallel(int, int) - Method in interface edu.jhu.cs.cisst.algorithms.optimize.fmg.parallel.Parallelizable
the method that will be run by several threads in parallel.
runParallel(int, int) - Method in class edu.jhu.cs.cisst.algorithms.optimize.fmg.parallel.Parallelizer
the default implementation of the parallel algorithm, which does nothing.
runParallel(int, int) - Method in class edu.jhu.cs.cisst.algorithms.optimize.fmg.restrictor.RestrictByStencilParallelizer
re-route.
runParallel(int, int) - Method in class edu.jhu.cs.cisst.algorithms.optimize.fmg.smoother.DampedJacobiSmoothParallelizer
re-route.
runParallel(int, int) - Method in class edu.jhu.cs.cisst.algorithms.optimize.fmg.solver.SolveThroughSmootherParallelizer
re-route.
runScript(String) - Static method in class edu.jhu.ece.iacl.jist.pipeline.MipavScriptRunner
Parses and runs the commands contained within a given script file.
runScript(String, Vector, Vector) - Method in class edu.jhu.ece.iacl.jist.pipeline.MipavScriptRunner
Execute a script, using a set of images.
RunSTAPLE - Class in edu.jhu.ece.iacl.algorithms.manual_label.staple
 
RunSTAPLE() - Constructor for class edu.jhu.ece.iacl.algorithms.manual_label.staple.RunSTAPLE
 
runTest(File, File, boolean) - Method in class edu.jhu.ece.iacl.doc.DocumentAllTests
Run test.
runTest(File) - Method in class edu.jhu.ece.iacl.jist.test.JistTestHarness
Run test.
runTests(boolean, boolean) - Method in class edu.jhu.ece.iacl.doc.DocumentAllTests
Run tests.
runTests() - Method in class edu.jhu.ece.iacl.jist.test.JistTestHarness
Run tests.
runVolumes(List<ImageData>, int) - Static method in class edu.jhu.ece.iacl.algorithms.manual_label.LabelImage
 

S

s - Variable in class edu.jhu.cs.cisst.algorithms.optimize.fmg.interpolator.InterpolatorByStencil
The stencil.
s - Variable in class edu.jhu.cs.cisst.algorithms.optimize.fmg.restrictor.RestrictorByStencil
The stencil.
safeInverse() - Method in class edu.jhu.bme.smile.commons.math.specialFunctions.ComplexMatrix
 
sameDims(LabelImage) - Method in class edu.jhu.ece.iacl.algorithms.manual_label.LabelImage
 
sameDims(LabelSurface) - Method in class edu.jhu.ece.iacl.algorithms.manual_label.LabelSurface
 
sampleMatrix(int, int, int, int) - Method in class edu.jhu.cs.cisst.algorithms.optimize.fmg.pde.CachingPDE
a caching frontend to calculating a representation of the matrix A of the PDE for a specific grid size.
sampleRate - Variable in class edu.jhu.cs.cisst.vent.renderer.processing.VectorField2DRenderer
The sample rate.
sampleRateParam - Variable in class edu.jhu.cs.cisst.vent.renderer.processing.VectorField2DRenderer
The sample rate param.
sampleRHS(int, int, int, int) - Method in class edu.jhu.cs.cisst.algorithms.optimize.fmg.pde.CachingPDE
implements method from PDE.
sampleRHS(int, int, int, int) - Method in interface edu.jhu.cs.cisst.algorithms.optimize.fmg.pde.PDE
sample the right hand side f on a cubic grid of the given size.
save(boolean) - Method in class edu.jhu.ece.iacl.jist.pipeline.PipeLayout
Open "Save" dialog.
saveAll(File) - Method in class edu.jhu.ece.iacl.jist.pipeline.ProcessingDialog
Save all input and output parameters and their external resources.
saveAs() - Method in class edu.jhu.ece.iacl.jist.pipeline.PipeAlgorithm
Save algorithm in specified user location.
saveAs() - Method in class edu.jhu.ece.iacl.jist.pipeline.PipeAlgorithmGroup
Save group to user selected file.
saveAs() - Method in class edu.jhu.ece.iacl.jist.pipeline.PipeLayout
Open "Save As" dialog.
saveAs(boolean) - Method in class edu.jhu.ece.iacl.jist.pipeline.PipeLayout
Open "Save As" dialog.
saveDefaults() - Method in class edu.jhu.ece.iacl.jist.pipeline.ProcessingDialog
Saves input dialog settings to XML file.
saveDRMAASession(File) - Method in class edu.jhu.ece.iacl.jist.processcontrol.DispatchController
Save drmaa session.
saveInput(File) - Method in class edu.jhu.ece.iacl.jist.pipeline.ProcessingDialog
Save all input parameters to specified file.
saveInputBeforeRun() - Method in class edu.jhu.ece.iacl.jist.pipeline.ProcessingDialog
Save all input params after run so that inputs can be checked for current consistency 2009.06.21 DO NOT SAVE INPUTs after run
saveInputContext() - Method in class edu.jhu.ece.iacl.jist.pipeline.ExecutionContext
Save input parameters to file.
saveInputParams(File) - Method in class edu.jhu.ece.iacl.jist.pipeline.PipeAlgorithm
Write input parameters to file.
saveOutputParams(File) - Method in class edu.jhu.ece.iacl.jist.pipeline.PipeAlgorithm
Write output parameters to file.
savePreferences() - Static method in class edu.jhu.ece.iacl.jist.pipeline.JistPreferences
Save preferences along library path as getDefaultPreferencesFileName().
saveResources(File, boolean) - Method in class edu.jhu.ece.iacl.jist.pipeline.factory.ParamCollectionFactory
 
saveResources(File, boolean) - Method in class edu.jhu.ece.iacl.jist.pipeline.factory.ParamDataLabelFactory
Save both the Model Image and label file to specified directory The label file is saved with extension .label
saveResources(File, boolean) - Method in class edu.jhu.ece.iacl.jist.pipeline.factory.ParamFactory
Save external resources to specified directory.
saveResources(File, boolean) - Method in class edu.jhu.ece.iacl.jist.pipeline.factory.ParamObjectFactory
Save Resource to specified directory.
saveResources(File, boolean) - Method in class edu.jhu.ece.iacl.jist.pipeline.factory.ParamSurfaceCollectionFactory
Save Surfaces to specified directory.
saveResources(File, boolean) - Method in class edu.jhu.ece.iacl.jist.pipeline.factory.ParamSurfaceFactory
Save Model Mesh to specified directory.
saveResources(File, boolean) - Method in class edu.jhu.ece.iacl.jist.pipeline.factory.ParamVolumeCollectionFactory
Save Surfaces to specified directory.
saveResources(File, boolean) - Method in class edu.jhu.ece.iacl.jist.pipeline.factory.ParamVolumeFactory
Save Model Image to specified directory.
saveResources(File, boolean) - Method in class edu.jhu.ece.iacl.jist.pipeline.factory.ParamWeightedVolumeCollectionFactory
Save Model Image to specified directory.
saveResources(File, boolean) - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamModel
Save external resources associated with the parameter to the specified directory.
saveResources(boolean) - Method in class edu.jhu.ece.iacl.jist.pipeline.ProcessingAlgorithm
 
scalar(Matrix) - Static method in class edu.jhu.bme.smile.commons.math.MatrixMath
 
scale - Variable in class edu.jhu.cs.cisst.vent.widgets.VisualizationImage
The scale.
scale - Variable in class edu.jhu.ece.iacl.jist.pipeline.view.output.ParamSurfaceOutputView
The scale.
scale(double) - Method in class edu.jhu.ece.iacl.jist.structures.fiber.XYZ
Scale.
scale(float, float, float) - Method in class edu.jhu.ece.iacl.jist.structures.fiber.XYZ
Scale.
scale(double, double, double) - Method in class edu.jhu.ece.iacl.jist.structures.fiber.XYZ
Scale.
scale - Variable in class edu.jhu.ece.iacl.jist.structures.geom.CollisionDetection
The scale.
scale - Variable in class edu.jhu.ece.iacl.jist.structures.geom.EmbeddedSurface
The scale.
scaleData(float) - Method in class edu.jhu.ece.iacl.jist.structures.geom.EmbeddedSurface
Scale data.
scaleFloatValue(ImageData, float) - Static method in class edu.jhu.ece.iacl.structures.image.ImageDataMath
Scale float value.
scaleForVisualization(float, float, float) - Method in class edu.jhu.ece.iacl.jist.structures.fiber.Fiber
Scale for visualization.
scaleForVisualization(Fiber[], float, float, float) - Static method in class edu.jhu.ece.iacl.jist.structures.fiber.Fiber
Scale for visualization.
ScaleImageDemo - Class in edu.jhu.bme.smile.demo
 
ScaleImageDemo() - Constructor for class edu.jhu.bme.smile.demo.ScaleImageDemo
 
scaleObject - Variable in class edu.jhu.cs.cisst.vent.widgets.VisualizationTriangleMesh
The scale object.
scaleParam - Variable in class edu.jhu.cs.cisst.vent.widgets.VisualizationImage
The scale param.
scaleParam - Variable in class edu.jhu.cs.cisst.vent.widgets.VisualizationTriangleMesh
The scale param.
scaleRate - Variable in class edu.jhu.cs.cisst.vent.widgets.VisualizationImage
The scale rate.
scaleRate - Variable in class edu.jhu.cs.cisst.vent.widgets.VisualizationTriangleMesh
The scale rate.
scaleVertices(float) - Method in class edu.jhu.ece.iacl.jist.structures.geom.EmbeddedSurface
Scale vertices.
scaleVertices(float[]) - Method in class edu.jhu.ece.iacl.jist.structures.geom.EmbeddedSurface
Scale vertices.
scanner - Variable in class edu.jhu.ece.iacl.algorithms.dti.GTCparams
 
scenarioId - Variable in class edu.jhu.ece.iacl.jist.pipeline.ExecutionContext
Identifying scenario number.
scenarioRoot - Variable in class edu.jhu.ece.iacl.jist.pipeline.ExecutionContext
Root directory for scenario.
sceneParams - Variable in class edu.jhu.cs.cisst.vent.widgets.VisualizationImage
The scene params.
sceneParams - Variable in class edu.jhu.cs.cisst.vent.widgets.VisualizationTriangleMesh
The scene params.
schedule - Variable in class edu.jhu.ece.iacl.jist.pipeline.PipeScheduler
List storing all contexts.
scheduler - Variable in class edu.jhu.ece.iacl.jist.pipeline.PipeLayout
scheduler used to schedule execution of this layout.
screenshot - Variable in class edu.jhu.cs.cisst.vent.VisualizationProcessing
The screenshot.
ScriptParser - Interface in edu.jhu.ece.iacl.jist.pipeline.parser
Interface for parsing third party script files.
ScriptReader - Class in edu.jhu.ece.iacl.jist.io
The Class ScriptReader.
ScriptReader() - Constructor for class edu.jhu.ece.iacl.jist.io.ScriptReader
Instantiates a new script reader.
scrollPane - Variable in class edu.jhu.ece.iacl.jist.pipeline.gui.PortListBox
The scroll pane.
scrollPane - Variable in class edu.jhu.ece.iacl.jist.pipeline.view.input.InformationListBox
The scroll pane.
scrollPane - Variable in class edu.jhu.ece.iacl.jist.pipeline.view.input.ParamFileCollectionInputView
The scroll pane.
scrollPane - Variable in class edu.jhu.ece.iacl.jist.pipeline.view.input.ParamMultiOptionInputView
The scroll pane.
scrollPane - Variable in class edu.jhu.ece.iacl.jist.pipeline.view.input.ParamNumberCollectionInputView
The scroll pane.
scrollPane - Variable in class edu.jhu.ece.iacl.jist.pipeline.view.input.ParamVolumeCollectionInputView
The scroll pane.
searchDepth - Variable in class edu.jhu.ece.iacl.jist.pipeline.src.PipeFileDirectorySource
The search depth.
searchDepth - Variable in class edu.jhu.ece.iacl.jist.pipeline.src.PipeVolumeDirectoryCollectionSource
The search depth.
searchDepth - Variable in class edu.jhu.ece.iacl.plugins.utilities.file.VolumeDirectoryNoIter
The search depth.
searched - Variable in class edu.jhu.ece.iacl.algorithms.manual_label.LabelImage
 
seek(int) - Method in class edu.jhu.ece.iacl.jist.io.LEFileReader
Seek.
seek(int) - Method in class edu.jhu.ece.iacl.jist.io.LEFileWriter
Seek.
Segment - Class in edu.jhu.ece.iacl.jist.structures.geom
The Class Segment.
Segment(Vertex, Vertex) - Constructor for class edu.jhu.ece.iacl.jist.structures.geom.Segment
Instantiates a new segment.
segmentTractFromData(Vector<Fiber>, double[][], double, int) - Static method in class edu.jhu.ece.iacl.algorithms.dti.tractography.FiberStatistics
 
segmentTractFromMemberships(Vector<Fiber>, ImageData, double, int, double) - Static method in class edu.jhu.ece.iacl.algorithms.dti.tractography.FiberStatistics
 
select(PipeModule) - Method in class edu.jhu.ece.iacl.jist.pipeline.gui.ParameterPanel
Focus panel on module properties.
select() - Method in class edu.jhu.ece.iacl.jist.pipeline.gui.PipeInternalFrame
Select this frame.
selectedFactory - Variable in class edu.jhu.ece.iacl.jist.pipeline.gui.PlugInSelector
The selected factory.
SelectedNode - Variable in class edu.jhu.ece.iacl.jist.pipeline.tree.DraggableJTree
The Selected node.
selectedParams - Variable in class edu.jhu.ece.iacl.jist.pipeline.PipeDestination
Parameter to store collection of other parameters.
SelectedTreePath - Variable in class edu.jhu.ece.iacl.jist.pipeline.tree.DraggableJTree
The Selected tree path.
selection - Variable in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamMultiOption
The selection.
selection - Variable in class edu.jhu.ece.iacl.jist.pipeline.src.PipeFileCollectionSource
The selection.
selection - Variable in class edu.jhu.ece.iacl.jist.pipeline.src.PipeSelectionExternalSource
The selection.
selection - Variable in class edu.jhu.ece.iacl.jist.pipeline.src.PipeSelectionSource
The selection.
selectSaveDirectory() - Method in class edu.jhu.ece.iacl.jist.pipeline.ProcessingDialog
Open dialog to specify output directory for parameters.
selectSaveFile() - Method in class edu.jhu.ece.iacl.jist.pipeline.PipeAlgorithm
Select location to save algorithm.
SelectUniqueDiffusionDirections - Class in edu.jhu.ece.iacl.plugins.hardi
 
SelectUniqueDiffusionDirections() - Constructor for class edu.jhu.ece.iacl.plugins.hardi.SelectUniqueDiffusionDirections
 
selectUniqueDirectionsAndReflections(EmbeddedSurface, double) - Static method in class edu.jhu.ece.iacl.algorithms.hardi.SurfaceTools
 
separableConvolution(float[][][], int, int, int, float[][], int, int, int) - Static method in class edu.jhmi.rad.medic.libraries.ImageFunctionsPublic
convolution with a separable kernel (the kernel is 3x{kx,ky,kz})
separableGaussianKernel(float, float, float) - Static method in class edu.jhmi.rad.medic.libraries.ImageFunctionsPublic
Gaussian kernel for separable convolution
separateLabels() - Method in class edu.jhu.ece.iacl.algorithms.manual_label.LabelImage
 
separateLabels() - Method in class edu.jhu.ece.iacl.algorithms.manual_label.LabelSurface
 
serialVersionUID - Static variable in class edu.jhu.ece.iacl.jist.pipeline.ProcessingDialog
The Constant serialVersionUID.
set(int, int, int, double) - Method in interface edu.jhu.cs.cisst.algorithms.optimize.fmg.grid.ConstGrid
Set the value for a grid node.
set(int, int, int, double) - Method in class edu.jhu.cs.cisst.algorithms.optimize.fmg.grid.Grid
set the element at the specified position, which must be in the interior of the grid.
set(int, int, int, float) - Method in class edu.jhu.ece.iacl.algorithms.manual_label.staple.PerformanceLevel
 
set(int, int, int, double) - Method in class edu.jhu.ece.iacl.algorithms.manual_label.staple.PerformanceLevel
 
set(int, T) - Method in interface edu.jhu.ece.iacl.jist.pipeline.parameter.ObjectCollection
Set item value in list
set(int, Object) - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamCollection
 
set(int, File) - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamFileCollection
 
set(int, Object) - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamFileCollection
 
set(int, Number) - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamNumberCollection
 
set(int, Object) - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamNumberCollection
Set value
set(int, int, boolean) - Method in class edu.jhu.ece.iacl.jist.structures.image.ImageData
Debugging routine for printing non-zero entries in matrix.
set(int, int, byte) - Method in class edu.jhu.ece.iacl.jist.structures.image.ImageData
Sets the.
set(int, int, Color) - Method in class edu.jhu.ece.iacl.jist.structures.image.ImageData
Sets the.
set(int, int, double) - Method in class edu.jhu.ece.iacl.jist.structures.image.ImageData
Sets the.
set(int, int, float) - Method in class edu.jhu.ece.iacl.jist.structures.image.ImageData
Sets the.
set(int, int, int) - Method in class edu.jhu.ece.iacl.jist.structures.image.ImageData
Sets the.
set(int, int, int, boolean) - Method in class edu.jhu.ece.iacl.jist.structures.image.ImageData
Sets the.
set(int, int, int, byte) - Method in class edu.jhu.ece.iacl.jist.structures.image.ImageData
Sets the.
set(int, int, int, Color) - Method in class edu.jhu.ece.iacl.jist.structures.image.ImageData
Sets the.
set(int, int, int, double) - Method in class edu.jhu.ece.iacl.jist.structures.image.ImageData
Sets the.
set(int, int, int, float) - Method in class edu.jhu.ece.iacl.jist.structures.image.ImageData
Sets the.
set(int, int, int, int) - Method in class edu.jhu.ece.iacl.jist.structures.image.ImageData
Sets the.
set(int, int, int, short) - Method in class edu.jhu.ece.iacl.jist.structures.image.ImageData
Sets the.
set(int, int, short) - Method in class edu.jhu.ece.iacl.jist.structures.image.ImageData
Sets the.
set(int, int, int, int, boolean) - Method in class edu.jhu.ece.iacl.jist.structures.image.ImageData
Sets the.
set(int, int, int, int, short) - Method in class edu.jhu.ece.iacl.jist.structures.image.ImageData
Sets the.
set(int, int, int, int, int) - Method in class edu.jhu.ece.iacl.jist.structures.image.ImageData
Sets the.
set(int, int, int, int, double) - Method in class edu.jhu.ece.iacl.jist.structures.image.ImageData
Sets the.
set(int, int, int, int, float) - Method in class edu.jhu.ece.iacl.jist.structures.image.ImageData
Sets the.
set(int, int, int, int, Color) - Method in class edu.jhu.ece.iacl.jist.structures.image.ImageData
Sets the.
set(int, int, int, int, Number) - Method in class edu.jhu.ece.iacl.jist.structures.image.ImageData
Sets the.
set(int, int, int, Number) - Method in class edu.jhu.ece.iacl.jist.structures.image.ImageData
Sets the.
set(int, int, Number) - Method in class edu.jhu.ece.iacl.jist.structures.image.ImageData
Sets the.
set(Voxel) - Method in class edu.jhu.ece.iacl.jist.structures.image.ImageData
Sets the.
set(int, int, int, int, boolean) - Method in class edu.jhu.ece.iacl.jist.structures.image.ImageDataByte
 
set(int, int, int, int, byte) - Method in class edu.jhu.ece.iacl.jist.structures.image.ImageDataByte
Sets the.
set(int, int, int, int, float) - Method in class edu.jhu.ece.iacl.jist.structures.image.ImageDataByte
 
set(int, int, int, int, Number) - Method in class edu.jhu.ece.iacl.jist.structures.image.ImageDataByte
 
set(int, int, int, int, int) - Method in class edu.jhu.ece.iacl.jist.structures.image.ImageDataByte
 
set(int, int, int, int, Color) - Method in class edu.jhu.ece.iacl.jist.structures.image.ImageDataByte
 
set(int, int, int, int, double) - Method in class edu.jhu.ece.iacl.jist.structures.image.ImageDataByte
 
set(int, int, int, int, short) - Method in class edu.jhu.ece.iacl.jist.structures.image.ImageDataByte
 
set(Voxel) - Method in class edu.jhu.ece.iacl.jist.structures.image.ImageDataByte
 
set(int, int, int, int, boolean) - Method in class edu.jhu.ece.iacl.jist.structures.image.ImageDataColor
 
set(int, int, int, int, byte) - Method in class edu.jhu.ece.iacl.jist.structures.image.ImageDataColor
Sets the.
set(int, int, int, int, Color) - Method in class edu.jhu.ece.iacl.jist.structures.image.ImageDataColor
 
set(int, int, int, int, short) - Method in class edu.jhu.ece.iacl.jist.structures.image.ImageDataColor
 
set(Voxel) - Method in class edu.jhu.ece.iacl.jist.structures.image.ImageDataColor
 
set(int, int, int, int, int) - Method in class edu.jhu.ece.iacl.jist.structures.image.ImageDataColor
 
set(int, int, int, int, double) - Method in class edu.jhu.ece.iacl.jist.structures.image.ImageDataColor
 
set(int, int, int, int, float) - Method in class edu.jhu.ece.iacl.jist.structures.image.ImageDataColor
 
set(int, int, int, int, Number) - Method in class edu.jhu.ece.iacl.jist.structures.image.ImageDataColor
 
set(int, int, int, int, boolean) - Method in class edu.jhu.ece.iacl.jist.structures.image.ImageDataDouble
 
set(int, int, int, int, byte) - Method in class edu.jhu.ece.iacl.jist.structures.image.ImageDataDouble
Sets the.
set(int, int, int, int, float) - Method in class edu.jhu.ece.iacl.jist.structures.image.ImageDataDouble
 
set(int, int, int, int, Number) - Method in class edu.jhu.ece.iacl.jist.structures.image.ImageDataDouble
 
set(int, int, int, int, int) - Method in class edu.jhu.ece.iacl.jist.structures.image.ImageDataDouble
 
set(int, int, int, int, Color) - Method in class edu.jhu.ece.iacl.jist.structures.image.ImageDataDouble
 
set(int, int, int, int, double) - Method in class edu.jhu.ece.iacl.jist.structures.image.ImageDataDouble
 
set(int, int, int, int, short) - Method in class edu.jhu.ece.iacl.jist.structures.image.ImageDataDouble
 
set(Voxel) - Method in class edu.jhu.ece.iacl.jist.structures.image.ImageDataDouble
 
set(int, int, int, int, boolean) - Method in class edu.jhu.ece.iacl.jist.structures.image.ImageDataFloat
 
set(int, int, int, int, byte) - Method in class edu.jhu.ece.iacl.jist.structures.image.ImageDataFloat
Sets the.
set(int, int, int, int, float) - Method in class edu.jhu.ece.iacl.jist.structures.image.ImageDataFloat
 
set(int, int, int, int, int) - Method in class edu.jhu.ece.iacl.jist.structures.image.ImageDataFloat
 
set(int, int, int, int, Color) - Method in class edu.jhu.ece.iacl.jist.structures.image.ImageDataFloat
 
set(int, int, int, int, double) - Method in class edu.jhu.ece.iacl.jist.structures.image.ImageDataFloat
 
set(int, int, int, int, Number) - Method in class edu.jhu.ece.iacl.jist.structures.image.ImageDataFloat
 
set(int, int, int, int, short) - Method in class edu.jhu.ece.iacl.jist.structures.image.ImageDataFloat
 
set(Voxel) - Method in class edu.jhu.ece.iacl.jist.structures.image.ImageDataFloat
 
set(int, int, int, int, boolean) - Method in class edu.jhu.ece.iacl.jist.structures.image.ImageDataInt
 
set(int, int, int, int, byte) - Method in class edu.jhu.ece.iacl.jist.structures.image.ImageDataInt
Sets the.
set(int, int, int, int, float) - Method in class edu.jhu.ece.iacl.jist.structures.image.ImageDataInt
 
set(int, int, int, int, Number) - Method in class edu.jhu.ece.iacl.jist.structures.image.ImageDataInt
 
set(int, int, int, int, int) - Method in class edu.jhu.ece.iacl.jist.structures.image.ImageDataInt
 
set(int, int, int, int, Color) - Method in class edu.jhu.ece.iacl.jist.structures.image.ImageDataInt
 
set(int, int, int, int, double) - Method in class edu.jhu.ece.iacl.jist.structures.image.ImageDataInt
 
set(int, int, int, int, short) - Method in class edu.jhu.ece.iacl.jist.structures.image.ImageDataInt
 
set(Voxel) - Method in class edu.jhu.ece.iacl.jist.structures.image.ImageDataInt
 
set(int, int, int, int, boolean) - Method in class edu.jhu.ece.iacl.jist.structures.image.ImageDataMipav
 
set(int, int, int, int, byte) - Method in class edu.jhu.ece.iacl.jist.structures.image.ImageDataMipav
Sets the.
set(int, int, Color) - Method in class edu.jhu.ece.iacl.jist.structures.image.ImageDataMipav
 
set(int, int, int, int, double) - Method in class edu.jhu.ece.iacl.jist.structures.image.ImageDataMipav
 
set(int, int, int, int, float) - Method in class edu.jhu.ece.iacl.jist.structures.image.ImageDataMipav
 
set(int, int, int, int, int) - Method in class edu.jhu.ece.iacl.jist.structures.image.ImageDataMipav
 
set(int, int, int, int, Color) - Method in class edu.jhu.ece.iacl.jist.structures.image.ImageDataMipav
 
set(int, int, int, int, short) - Method in class edu.jhu.ece.iacl.jist.structures.image.ImageDataMipav
Set vector Component.
set(Voxel) - Method in class edu.jhu.ece.iacl.jist.structures.image.ImageDataMipav
 
set(int, int, int, int, Number) - Method in class edu.jhu.ece.iacl.jist.structures.image.ImageDataMipav
 
set(int, int, int, int, boolean) - Method in class edu.jhu.ece.iacl.jist.structures.image.ImageDataNumber
 
set(int, int, int, int, byte) - Method in class edu.jhu.ece.iacl.jist.structures.image.ImageDataNumber
Sets the.
set(int, int, int, int, float) - Method in class edu.jhu.ece.iacl.jist.structures.image.ImageDataNumber
 
set(int, int, int, int, int) - Method in class edu.jhu.ece.iacl.jist.structures.image.ImageDataNumber
 
set(int, int, int, int, Color) - Method in class edu.jhu.ece.iacl.jist.structures.image.ImageDataNumber
 
set(int, int, int, int, double) - Method in class edu.jhu.ece.iacl.jist.structures.image.ImageDataNumber
 
set(int, int, int, int, Number) - Method in class edu.jhu.ece.iacl.jist.structures.image.ImageDataNumber
Sets the.
set(int, int, int, int, short) - Method in class edu.jhu.ece.iacl.jist.structures.image.ImageDataNumber
 
set(Voxel) - Method in class edu.jhu.ece.iacl.jist.structures.image.ImageDataNumber
 
set(int, int, int, int, boolean) - Method in class edu.jhu.ece.iacl.jist.structures.image.ImageDataUByte
 
set(int, int, int, int, byte) - Method in class edu.jhu.ece.iacl.jist.structures.image.ImageDataUByte
Sets the.
set(int, int, int, int, float) - Method in class edu.jhu.ece.iacl.jist.structures.image.ImageDataUByte
 
set(int, int, int, int, int) - Method in class edu.jhu.ece.iacl.jist.structures.image.ImageDataUByte
 
set(int, int, int, int, Color) - Method in class edu.jhu.ece.iacl.jist.structures.image.ImageDataUByte
 
set(int, int, int, int, double) - Method in class edu.jhu.ece.iacl.jist.structures.image.ImageDataUByte
 
set(int, int, int, int, short) - Method in class edu.jhu.ece.iacl.jist.structures.image.ImageDataUByte
 
set(Voxel) - Method in class edu.jhu.ece.iacl.jist.structures.image.ImageDataUByte
 
set(int, int, int, int, Number) - Method in class edu.jhu.ece.iacl.jist.structures.image.ImageDataUByte
 
set(VectorX) - Method in class edu.jhu.ece.iacl.jist.structures.image.Voxel
Sets the.
set(Voxel) - Method in class edu.jhu.ece.iacl.jist.structures.image.Voxel
Sets the.
set(boolean) - Method in class edu.jhu.ece.iacl.jist.structures.image.Voxel
Sets the.
set(short) - Method in class edu.jhu.ece.iacl.jist.structures.image.Voxel
Sets the.
set(byte) - Method in class edu.jhu.ece.iacl.jist.structures.image.Voxel
Sets the.
set(float) - Method in class edu.jhu.ece.iacl.jist.structures.image.Voxel
Sets the.
set(int) - Method in class edu.jhu.ece.iacl.jist.structures.image.Voxel
Sets the.
set(Color) - Method in class edu.jhu.ece.iacl.jist.structures.image.Voxel
Sets the.
set(double) - Method in class edu.jhu.ece.iacl.jist.structures.image.Voxel
Sets the.
set(Voxel) - Method in class edu.jhu.ece.iacl.jist.structures.image.VoxelBoolean
 
set(boolean) - Method in class edu.jhu.ece.iacl.jist.structures.image.VoxelBoolean
 
set(short) - Method in class edu.jhu.ece.iacl.jist.structures.image.VoxelBoolean
 
set(Color) - Method in class edu.jhu.ece.iacl.jist.structures.image.VoxelBoolean
 
set(double) - Method in class edu.jhu.ece.iacl.jist.structures.image.VoxelBoolean
 
set(int) - Method in class edu.jhu.ece.iacl.jist.structures.image.VoxelBoolean
 
set(Voxel) - Method in class edu.jhu.ece.iacl.jist.structures.image.VoxelColor
 
set(boolean) - Method in class edu.jhu.ece.iacl.jist.structures.image.VoxelColor
 
set(short) - Method in class edu.jhu.ece.iacl.jist.structures.image.VoxelColor
 
set(Color) - Method in class edu.jhu.ece.iacl.jist.structures.image.VoxelColor
 
set(double) - Method in class edu.jhu.ece.iacl.jist.structures.image.VoxelColor
 
set(int) - Method in class edu.jhu.ece.iacl.jist.structures.image.VoxelColor
 
set(Voxel) - Method in class edu.jhu.ece.iacl.jist.structures.image.VoxelDouble
 
set(boolean) - Method in class edu.jhu.ece.iacl.jist.structures.image.VoxelDouble
 
set(short) - Method in class edu.jhu.ece.iacl.jist.structures.image.VoxelDouble
 
set(Color) - Method in class edu.jhu.ece.iacl.jist.structures.image.VoxelDouble
 
set(double) - Method in class edu.jhu.ece.iacl.jist.structures.image.VoxelDouble
 
set(int) - Method in class edu.jhu.ece.iacl.jist.structures.image.VoxelDouble
 
set(float) - Method in class edu.jhu.ece.iacl.jist.structures.image.VoxelFloat
 
set(Voxel) - Method in class edu.jhu.ece.iacl.jist.structures.image.VoxelFloat
 
set(boolean) - Method in class edu.jhu.ece.iacl.jist.structures.image.VoxelFloat
 
set(short) - Method in class edu.jhu.ece.iacl.jist.structures.image.VoxelFloat
 
set(Color) - Method in class edu.jhu.ece.iacl.jist.structures.image.VoxelFloat
 
set(double) - Method in class edu.jhu.ece.iacl.jist.structures.image.VoxelFloat
 
set(int) - Method in class edu.jhu.ece.iacl.jist.structures.image.VoxelFloat
 
set(Voxel) - Method in class edu.jhu.ece.iacl.jist.structures.image.VoxelIndexed
 
set(boolean) - Method in class edu.jhu.ece.iacl.jist.structures.image.VoxelIndexed
 
set(short) - Method in class edu.jhu.ece.iacl.jist.structures.image.VoxelIndexed
 
set(int) - Method in class edu.jhu.ece.iacl.jist.structures.image.VoxelIndexed
 
set(Color) - Method in class edu.jhu.ece.iacl.jist.structures.image.VoxelIndexed
 
set(double) - Method in class edu.jhu.ece.iacl.jist.structures.image.VoxelIndexed
 
set(Voxel) - Method in class edu.jhu.ece.iacl.jist.structures.image.VoxelInt
 
set(boolean) - Method in class edu.jhu.ece.iacl.jist.structures.image.VoxelInt
 
set(short) - Method in class edu.jhu.ece.iacl.jist.structures.image.VoxelInt
 
set(int) - Method in class edu.jhu.ece.iacl.jist.structures.image.VoxelInt
 
set(Color) - Method in class edu.jhu.ece.iacl.jist.structures.image.VoxelInt
 
set(double) - Method in class edu.jhu.ece.iacl.jist.structures.image.VoxelInt
 
set(Voxel) - Method in class edu.jhu.ece.iacl.jist.structures.image.VoxelMipav
 
set(boolean) - Method in class edu.jhu.ece.iacl.jist.structures.image.VoxelMipav
 
set(short) - Method in class edu.jhu.ece.iacl.jist.structures.image.VoxelMipav
 
set(int) - Method in class edu.jhu.ece.iacl.jist.structures.image.VoxelMipav
 
set(Color) - Method in class edu.jhu.ece.iacl.jist.structures.image.VoxelMipav
 
set(double) - Method in class edu.jhu.ece.iacl.jist.structures.image.VoxelMipav
 
set(Voxel) - Method in class edu.jhu.ece.iacl.jist.structures.image.VoxelShort
 
set(boolean) - Method in class edu.jhu.ece.iacl.jist.structures.image.VoxelShort
 
set(short) - Method in class edu.jhu.ece.iacl.jist.structures.image.VoxelShort
 
set(int) - Method in class edu.jhu.ece.iacl.jist.structures.image.VoxelShort
 
set(Color) - Method in class edu.jhu.ece.iacl.jist.structures.image.VoxelShort
 
set(double) - Method in class edu.jhu.ece.iacl.jist.structures.image.VoxelShort
 
set(Voxel) - Method in class edu.jhu.ece.iacl.jist.structures.image.VoxelUByte
 
set(byte) - Method in class edu.jhu.ece.iacl.jist.structures.image.VoxelUByte
 
set(boolean) - Method in class edu.jhu.ece.iacl.jist.structures.image.VoxelUByte
 
set(short) - Method in class edu.jhu.ece.iacl.jist.structures.image.VoxelUByte
 
set(int) - Method in class edu.jhu.ece.iacl.jist.structures.image.VoxelUByte
 
set(Color) - Method in class edu.jhu.ece.iacl.jist.structures.image.VoxelUByte
 
set(double) - Method in class edu.jhu.ece.iacl.jist.structures.image.VoxelUByte
 
set(Voxel) - Method in class edu.jhu.ece.iacl.jist.structures.image.VoxelVector
 
set(boolean) - Method in class edu.jhu.ece.iacl.jist.structures.image.VoxelVector
 
set(short) - Method in class edu.jhu.ece.iacl.jist.structures.image.VoxelVector
 
set(int) - Method in class edu.jhu.ece.iacl.jist.structures.image.VoxelVector
 
set(Color) - Method in class edu.jhu.ece.iacl.jist.structures.image.VoxelVector
 
set(double) - Method in class edu.jhu.ece.iacl.jist.structures.image.VoxelVector
 
set(int, int, int, double) - Method in class edu.jhu.ece.iacl.jist.structures.matrix.Matrix3
Sets the.
set(int, int, int, VectorX) - Method in class edu.jhu.ece.iacl.jist.structures.matrix.VectorMatrixX
Sets the.
set(int, int, int, int, Number) - Method in class edu.jhu.ece.iacl.jist.structures.matrix.VectorMatrixX
Sets the.
set(Vector2) - Method in class edu.jhu.ece.iacl.jist.structures.vector.Vector2
Sets the.
set(Number, int) - Method in class edu.jhu.ece.iacl.jist.structures.vector.Vector2
 
set(Vector3) - Method in class edu.jhu.ece.iacl.jist.structures.vector.Vector3
Sets the.
set(Number, int) - Method in class edu.jhu.ece.iacl.jist.structures.vector.Vector3
 
set(Vector4) - Method in class edu.jhu.ece.iacl.jist.structures.vector.Vector4
Sets the.
set(Number, int) - Method in class edu.jhu.ece.iacl.jist.structures.vector.Vector4
 
set(Number, int) - Method in class edu.jhu.ece.iacl.jist.structures.vector.VectorN
 
set(Number, int) - Method in interface edu.jhu.ece.iacl.jist.structures.vector.VectorX
Sets the.
setActualTime(long) - Method in class edu.jhu.ece.iacl.jist.pipeline.ExecutionContext
Set elapsed actual time in milliseconds.
setAdjacencies(int[]) - Method in class edu.jhu.ece.iacl.jist.structures.geom.EmbeddedPointSet
Sets the adjacencies.
setAffiliation(String) - Method in class edu.jhu.ece.iacl.jist.pipeline.AlgorithmInformation
Sets the affiliation.
setAlgorithm(PipeAlgorithm) - Method in class edu.jhu.ece.iacl.jist.pipeline.ExecutionContext
Set algorithm.
setAlgorithm(ProcessingAlgorithm) - Method in class edu.jhu.ece.iacl.jist.pipeline.PipeAlgorithm
Automatically creates all the input and output ports using the input and output parameters in the Processing Algorithm.
setAlgorithmClass(Class) - Method in class edu.jhu.ece.iacl.jist.pipeline.AlgorithmInformation
Sets the algorithm class.
setAllocatedMemory(int) - Method in class edu.jhu.ece.iacl.jist.pipeline.ExecutionContext
Set amount of allocated memory.
setAlltoRobustHist() - Method in class edu.jhu.ece.iacl.algorithms.vabra.ImagePairNMI
 
setArrowColor(Color) - Method in class edu.jhu.cs.cisst.vent.renderer.processing.VectorField2DRenderer
Sets the arrow color.
setArrowHeadHeight(float) - Method in class edu.jhu.cs.cisst.vent.renderer.processing.VectorField2DRenderer
Sets the arrow head height.
setArrowHeadWidth(float) - Method in class edu.jhu.cs.cisst.vent.renderer.processing.VectorField2DRenderer
Sets the arrow head width.
setAuthor(String) - Method in class edu.jhu.ece.iacl.jist.pipeline.AlgorithmInformation.AlgorithmAuthor
Sets the author.
setAuthors(LinkedList<AlgorithmInformation.AlgorithmAuthor>) - Method in class edu.jhu.ece.iacl.jist.pipeline.AlgorithmInformation
Sets the authors.
setAutoMinMax(boolean) - Method in class edu.jhu.bme.smile.commons.math.HistogramGenerator
 
setAxesVisible(boolean) - Method in class edu.jhu.cs.cisst.vent.widgets.VisualizationTriangleMesh
Sets the axes visible.
setAxisColor(Color3f) - Method in class edu.jhu.ece.iacl.jist.pipeline.view.output.ParamSurfaceOutputView
Set axis color.
setAxisOrientation(ImageHeader.AxisOrientation[]) - Method in class edu.jhu.ece.iacl.jist.structures.image.ImageHeader
Sets the axis orientation.
setB0(double) - Method in class edu.jhu.ece.iacl.algorithms.dti.DTEMRLTensor
 
setBasisSet(Vector<CFARIBasisFunction>) - Method in class edu.jhu.ece.iacl.algorithms.hardi.CFARIBasisSet
 
setBeta(float) - Method in class edu.jhu.ece.iacl.algorithms.manual_label.staple.STAPLEgeneral
 
setBeta(float) - Method in class edu.jhu.ece.iacl.algorithms.manual_label.staple.STAPLEmulti
 
setBeta(float) - Method in class edu.jhu.ece.iacl.algorithms.manual_label.staple.STAPLEmulti2
 
setBins(int) - Method in class edu.jhu.bme.smile.commons.math.HistogramGenerator
 
setBoundaries(ArrayList<Point2i>) - Method in class edu.jhu.ece.iacl.algorithms.manual_label.simulation.VolumeRater
 
setBoundingBox(BoundingBox) - Method in class edu.jhu.cs.cisst.vent.renderer.processing.RendererProcessing3D
Sets the bounding box.
setBounds(double, double, double, double) - Method in class edu.jhu.cs.cisst.vent.renderer.processing.RendererProcessing2D
Sets the bounds.
setBounds(Rectangle2D) - Method in class edu.jhu.ece.iacl.jist.pipeline.graph.PipeModuleCell
Set the size of this module.
setBounds(Rectangle2D) - Method in class edu.jhu.ece.iacl.jist.pipeline.PipeModule
Set dimensions for graph cell.
setBounds(double[]) - Method in class edu.jhu.ece.iacl.jist.structures.geom.CollisionDetection
Sets the bounds.
setBrightness(float) - Method in class edu.jhu.cs.cisst.vent.renderer.processing.ImageRenderer
Sets the brightness.
setBrightness(float) - Method in class edu.jhu.cs.cisst.vent.renderer.processing.VectorField2DRenderer
Sets the brightness.
setBrightness(float) - Method in class edu.jhu.cs.cisst.vent.renderer.processing.VolumeSliceRenderer
Sets the brightness.
setCategory(String) - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamCollection
 
setCellData(double[][]) - Method in class edu.jhu.ece.iacl.jist.structures.geom.EmbeddedPointSet
Sets the cell data.
setCellData(double[][]) - Method in class edu.jhu.ece.iacl.jist.structures.geom.EmbeddedSurface
 
setChainIndex(int) - Method in interface edu.jhu.ece.iacl.jist.structures.data.Indexable
Sets the chain index.
setChainIndex(int) - Method in class edu.jhu.ece.iacl.jist.structures.geom.EdgeIndexed
 
setChainIndex(int) - Method in class edu.jhu.ece.iacl.jist.structures.geom.VertexIndexed
 
setChainIndex(int) - Method in class edu.jhu.ece.iacl.jist.structures.image.VoxelIndexed
 
setChainIndex(int) - Method in class edu.jhu.ece.iacl.jist.structures.image.VoxelMipav
 
setChecker(CompatibilityChecker) - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamCollection
Set compatibility checker.
setChildrenCells(Vector<PipeAlgorithmFactory.AlgorithmCell>) - Method in class edu.jhu.ece.iacl.jist.pipeline.graph.PipeAlgorithmFactory.AlgorithmGroupCell
Set children cells.
setCitations(LinkedList<AlgorithmInformation.Citation>) - Method in class edu.jhu.ece.iacl.jist.pipeline.AlgorithmInformation
Sets the citations.
setClickCountToStart(int) - Method in class edu.jhu.ece.iacl.jist.pipeline.graph.PipeEdgeRealEditor
Specifies the number of clicks needed to start editing.
setCliTag(String) - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamModel
 
setCloseOnlyOnExit(boolean) - Method in class edu.jhu.ece.iacl.jist.pipeline.gui.PipelineLayoutTool
 
setCloseOnlyOnExit(boolean) - Method in class edu.jhu.ece.iacl.jist.pipeline.gui.ProcessManager
 
setCoarsestLevelResolution(double) - Method in class edu.jhu.cs.cisst.algorithms.segmentation.gac.GradientVectorFlow2D
Sets the coarsest level resolution.
setCollection(int, ObjectCollection<T>) - Method in interface edu.jhu.ece.iacl.jist.pipeline.parameter.ObjectCollection
Set item value in list to the first element of the colleciton.
setCollection(int, ObjectCollection) - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamCollection
 
setCollection(int, ObjectCollection) - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamFileCollection
 
setCollection(int, ObjectCollection) - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamNumberCollection
 
setColor(int, Color) - Method in class edu.jhu.ece.iacl.jist.structures.geom.EmbeddedSurface
Sets the color.
setCols(int) - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamMatrix
Sets the cols.
setCompletedAssertions(int) - Method in class edu.jhu.ece.iacl.doc.DocumentAllTests.TestCase
 
setCompletedUnits(double) - Method in class edu.jhu.ece.iacl.jist.pipeline.AbstractCalculation
Set the percent completed [0,1] Requires that the total number of units is non-zero, (i.e.
setCompletedUnits(int) - Method in class edu.jhu.ece.iacl.jist.pipeline.AbstractCalculation
Set the number of units completed.
setComplex(int, int, double, double) - Method in class edu.jhu.bme.smile.commons.math.specialFunctions.ComplexMatrix
 
setComponent(int) - Method in class edu.jhu.cs.cisst.vent.renderer.processing.VolumeIsoContourRenderer
 
setComponent(int) - Method in class edu.jhu.cs.cisst.vent.renderer.processing.VolumeSliceRenderer
Sets the component.
setCompressionType(ImageHeader.Compression) - Method in class edu.jhu.ece.iacl.jist.structures.image.ImageHeader
Sets the compression type.
setConnectable(boolean) - Method in class edu.jhu.ece.iacl.jist.pipeline.PipePort
Set whether this port is connectible.
setConnectivity(byte) - Method in class edu.jhu.ece.iacl.algorithms.manual_label.simulation.VolumeRater
 
setConnectivity(GridPt.Connectivity) - Method in class edu.jhu.ece.iacl.algorithms.manual_label.simulation.VolumeRater
 
setConnectivity(GridPt.Connectivity) - Method in class edu.jhu.ece.iacl.algorithms.manual_label.staple.STAPLEmulti
 
setConnectivity(GridPt.Connectivity) - Method in class edu.jhu.ece.iacl.algorithms.manual_label.staple.STAPLEmulti2
 
setConnectivity(GridPt.Connectivity) - Method in class edu.jhu.ece.iacl.jist.structures.geom.GridPt
Sets the connectivity.
setConnector(PipeConnector) - Method in class edu.jhu.ece.iacl.jist.pipeline.graph.PipeModuleEdge
Set connector associated with edge.
setContextId(String) - Method in class edu.jhu.ece.iacl.jist.pipeline.ExecutionContext
Set context id.
setContourColor(Color) - Method in class edu.jhu.cs.cisst.vent.renderer.processing.VolumeIsoContourRenderer
Sets the contour color.
setContourVisible(boolean) - Method in class edu.jhu.cs.cisst.vent.renderer.processing.VolumeIsoContourRenderer
Sets the contour visible.
setContrast(float) - Method in class edu.jhu.cs.cisst.vent.renderer.processing.ImageRenderer
Sets the contrast.
setContrast(float) - Method in class edu.jhu.cs.cisst.vent.renderer.processing.VectorField2DRenderer
Sets the contrast.
setContrast(float) - Method in class edu.jhu.cs.cisst.vent.renderer.processing.VolumeSliceRenderer
Sets the contrast.
setCopy(Action) - Method in class edu.jhu.ece.iacl.jist.pipeline.gui.PipeInternalFrame
Sets the copy.
setCpuTime(long) - Method in class edu.jhu.ece.iacl.jist.pipeline.ExecutionContext
Set elapsed cpu time in milliseconds.
setCreationDate(Date) - Method in class edu.jhu.ece.iacl.jist.pipeline.AlgorithmInformation
Sets the creation date.
setCurrentContext(ExecutionContext) - Method in class edu.jhu.ece.iacl.jist.pipeline.PipeModule
Set current context used to execute this module.
setCurrentDimension(int) - Method in class edu.jhu.bme.smile.commons.optimize.ProjectNDto1DOptimizable
Sets the current dimension.
setCurrentLayout(PipeLayout) - Method in class edu.jhu.ece.iacl.jist.pipeline.PipeDestination
Sets the current layout.
setCurrentLocation(double) - Method in class edu.jhu.bme.smile.commons.optimize.ProjectNDto1DOptimizable
Sets the location of the current dimension
setCut(Action) - Method in class edu.jhu.ece.iacl.jist.pipeline.gui.PipeInternalFrame
Sets the cut.
setD(double[]) - Method in class edu.jhu.ece.iacl.algorithms.dti.DTEMRLTensor
 
setD(float[]) - Method in class edu.jhu.ece.iacl.algorithms.dti.DTEMRLTensor
 
setData(ArrayList<double[][]>) - Method in class edu.jhu.ece.iacl.algorithms.manual_label.staple.STAPLEgeneral
 
setData(float) - Method in class edu.jhu.ece.iacl.jist.structures.geom.GridPt
Sets the data.
setDebugLevel(int) - Method in class edu.jhu.ece.iacl.jist.pipeline.JistPreferences
 
setDefaultMaxProcesses(int) - Method in class edu.jhu.ece.iacl.jist.pipeline.JistPreferences
Set default maximum number of processes.
setDefaultMemory(int) - Method in class edu.jhu.ece.iacl.jist.pipeline.JistPreferences
Set default maximum heap size.
setDefaultNumberOfThreads(int) - Static method in class edu.jhu.cs.cisst.algorithms.optimize.fmg.parallel.Parallelizer
set the default number of threads for all objects of this type.
setDefaultParameters() - Method in class edu.jhu.ece.iacl.algorithms.dti.tractography.FACT.FACTparameters
 
setDefaultWorkingDirectory(File) - Static method in class edu.jhu.ece.iacl.jist.io.MipavController
Sets the default working directory.
setDescription(String) - Method in class edu.jhu.ece.iacl.jist.pipeline.AlgorithmInformation
Sets the description.
setDescription(String) - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamModel
 
setDestination(PipePort) - Method in class edu.jhu.ece.iacl.jist.pipeline.PipeConnector
Set destination port.
setDFactor(double) - Method in class edu.jhu.bme.smile.commons.optimize.tensor.MLTensor
Sets the scaling factor for D.
setDFactor(double) - Method in class edu.jhu.ece.iacl.algorithms.dti.DTEMRLTensor
Sets the scaling factor for D.
setDiceThreshold(double) - Method in class edu.jhu.cs.cisst.algorithms.segmentation.gac.GeodesicActiveContour2D
Sets the dice threshold.
setDiffusionWeight(double) - Method in class edu.jhu.cs.cisst.algorithms.segmentation.gac.GradientVectorFlow2D
Sets the diffusion weight.
setDimensions(Point3i) - Method in class edu.jhu.ece.iacl.jist.structures.fiber.FiberCollection
Sets the dimensions.
setDimResolutions(float[]) - Method in class edu.jhu.ece.iacl.jist.structures.image.ImageHeader
Sets the dim resolutions.
setDir(String) - Method in class edu.jhu.ece.iacl.algorithms.manual_label.staple.STAPLE
 
setDir(String) - Method in class edu.jhu.ece.iacl.algorithms.manual_label.staple.STAPLEgeneral
 
setDir(String) - Method in class edu.jhu.ece.iacl.algorithms.manual_label.staple.STAPLEgeneralSingle
 
setDir(String) - Method in class edu.jhu.ece.iacl.algorithms.manual_label.staple.STAPLEmulti
 
setDir(String) - Method in class edu.jhu.ece.iacl.algorithms.manual_label.staple.STAPLEmulti2
 
setDir(String) - Method in class edu.jhu.ece.iacl.algorithms.manual_label.staple.STAPLEsingle
 
setDir(String) - Method in class edu.jhu.ece.iacl.algorithms.manual_label.staple.STAPLEsurf
 
setDirectory(File) - Method in class edu.jhu.ece.iacl.jist.pipeline.tree.PackageNode
Set associated directory.
setDirItem - Variable in class edu.jhu.ece.iacl.jist.pipeline.gui.PlugInSelector
The set dir item.
setDirty(boolean) - Method in class edu.jhu.ece.iacl.jist.pipeline.PipeLayout
Indicate that the layout has changed since last save.
setDomain(double[], double[]) - Method in class edu.jhu.bme.smile.commons.optimize.tensor.MLTensor
Sets the domain minimum and maximum values.
setDomain(double[], double[]) - Method in class edu.jhu.ece.iacl.algorithms.dti.DTEMRLTensor
Sets the domain minimum and maximum values.
setDownSampleResolutions(ArrayList<Integer>) - Method in class edu.jhu.ece.iacl.algorithms.vabra.VabraConfiguration
 
setDWScheme(Scheme) - Method in class edu.jhu.ece.iacl.algorithms.hardi.CFARIBasisSet
 
setEditable(boolean) - Method in class edu.jhu.ece.iacl.jist.pipeline.AlgorithmInformation
Set whether information can be edited.
setEditable(boolean) - Method in class edu.jhu.ece.iacl.jist.pipeline.graph.PipeModuleEdge
Set whether connector will have spinner and be editable.
setEditable(boolean) - Method in class edu.jhu.ece.iacl.jist.pipeline.tree.PackageNode
Set editable.
setEmail(String) - Method in class edu.jhu.ece.iacl.jist.pipeline.AlgorithmInformation.AlgorithmAuthor
Sets the email.
setEnabled(boolean) - Method in class edu.jhu.ece.iacl.jist.pipeline.gui.ModuleTreePanel
Indicate that the module tree can be edited.
setEnabled(boolean) - Method in class edu.jhu.ece.iacl.jist.pipeline.gui.ParameterPanel
Enable parameter panel.
setEnabled(boolean) - Method in class edu.jhu.ece.iacl.jist.pipeline.gui.PipeInternalFrame
Set whether pipeline is editable.
setEndianess(ImageHeader.Endianess) - Method in class edu.jhu.ece.iacl.jist.structures.image.ImageHeader
Sets the endianess.
setEps(double) - Method in class edu.jhu.ece.iacl.algorithms.manual_label.staple.STAPLEgeneral
 
setEps(double) - Method in class edu.jhu.ece.iacl.algorithms.manual_label.staple.STAPLEmulti
 
setEps(double) - Method in class edu.jhu.ece.iacl.algorithms.manual_label.staple.STAPLEmulti2
 
setEps(double) - Method in class edu.jhu.ece.iacl.algorithms.manual_label.staple.STAPLEsingle
 
setEps(double) - Method in class edu.jhu.ece.iacl.algorithms.manual_label.staple.STAPLEsurf
 
setExitOnClose(boolean) - Method in class edu.jhu.ece.iacl.jist.pipeline.gui.ProcessManager
Set true if process manager should exit when closed.
setExtensionFilter(FileExtensionFilter) - Method in class edu.jhu.ece.iacl.jist.io.FileReaderWriter
Sets the extension filter.
setExtensionFilter(FileExtensionFilter) - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamFile
Sets the extension filter.
setExtensionFilter(FileExtensionFilter) - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamFileCollection
Set extension filter.
setExtensions(Vector<String>) - Method in class edu.jhu.ece.iacl.jist.io.FileExtensionFilter
Sets the extensions.
setFactory(ParamFactory) - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamModel
Use a different factory for manipulating this parameter model.
setFibers(Vector<Fiber>) - Method in class edu.jhu.ece.iacl.algorithms.dti.tractography.FiberStatistics
 
setFibers(FiberCollection) - Method in class edu.jhu.ece.iacl.algorithms.dti.tractography.FiberStatistics
 
setFile(File) - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.DataLabelCollection
Set location of XML file.
setFileLocation(File) - Method in class edu.jhu.ece.iacl.jist.pipeline.PipeLayout
Set file location for this layout.
setFileName(String) - Method in class edu.jhu.ece.iacl.jist.io.FileReaderWriter
Sets the file name.
setFileName(String) - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamObject
Set filename to store object.
setFlag(String) - Method in class edu.jhu.ece.iacl.algorithms.dti.GTCparams
 
setFrame(PipeInternalFrame) - Method in class edu.jhu.ece.iacl.jist.pipeline.PipeLayout
Set frame used to render this layout.
setGamma(double, double) - Method in class edu.jhu.bme.smile.commons.optimize.LevenbergMarquardt
Sets the initial and maximum lambda values.
setGamma(double) - Method in class edu.jhu.bme.smile.commons.optimize.NewtonMethod1D
Sets gamma, the coefficient to multiply the step by.
setgrad_choice(String) - Method in class edu.jhu.ece.iacl.algorithms.dti.GTCparams
 
setGraph(PipeJGraph) - Method in class edu.jhu.ece.iacl.jist.pipeline.graph.PipePortView
Set graph that contains this port.
setGraphEdge(PipeModuleEdge) - Method in class edu.jhu.ece.iacl.jist.pipeline.PipeConnector
Set graph edge used to render this connector.
setGraphPort(PipeModulePort) - Method in class edu.jhu.ece.iacl.jist.pipeline.PipePort
Set port to display on graph.
setGridPoints(GridPoint2D[][]) - Method in class edu.jhu.cs.cisst.algorithms.segmentation.gac.ActiveContourForce2D
Sets the grid points.
setGUIFromParams() - Method in class edu.jhu.ece.iacl.jist.dialogs.JDialogSaveAll
 
setGUIFromParams() - Method in class edu.jhu.ece.iacl.jist.pipeline.ProcessingDialog
Set up the dialog GUI based on the parameters before running the algorithm as part of a script.
setHeader(ImageHeader) - Method in class edu.jhu.ece.iacl.jist.structures.image.ImageData
Sets the header.
setHeader(ImageHeader) - Method in class edu.jhu.ece.iacl.jist.structures.image.ImageDataMipav
 
setHidden(boolean) - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamModel
Set hidden status.
setId(int) - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.DataLabel
Set id.
setIgnoreRefresh(boolean) - Method in class edu.jhu.ece.iacl.jist.pipeline.gui.ParameterPanel
Set true if panel should ignore refreshes.
setImageOrientation(ImageHeader.ImageOrientation) - Method in class edu.jhu.ece.iacl.jist.structures.image.ImageHeader
Sets the image orientation.
setImages(PImage[]) - Method in class edu.jhu.cs.cisst.vent.renderer.processing.VolumeSliceRenderer
Sets the images.
setImages(int[][][][]) - Method in class edu.jhu.ece.iacl.algorithms.manual_label.staple.STAPLE
 
setImages(List<double[][]>) - Method in class edu.jhu.ece.iacl.algorithms.manual_label.staple.STAPLEgeneralSingle
 
setImages(int[][][][]) - Method in class edu.jhu.ece.iacl.algorithms.manual_label.staple.STAPLEmulti
 
setImages(int[][][][]) - Method in class edu.jhu.ece.iacl.algorithms.manual_label.staple.STAPLEmulti2
 
setImages(int[][][][]) - Method in class edu.jhu.ece.iacl.algorithms.manual_label.staple.STAPLEsingle
 
setImageVariableTable(ImageVariableTable) - Static method in class edu.jhu.ece.iacl.jist.io.MipavController
Sets the image variable table.
setimg(ImageData) - Method in class edu.jhu.ece.iacl.algorithms.manual_label.LabelImage
 
setimg(EmbeddedSurface) - Method in class edu.jhu.ece.iacl.algorithms.manual_label.LabelSurface
 
setIndex(int) - Method in class edu.jhu.bme.smile.commons.math.HistogramGenerator
 
setIndex(int) - Method in interface edu.jhu.ece.iacl.jist.structures.data.Indexable
Set index into heap.
setIndex(int) - Method in class edu.jhu.ece.iacl.jist.structures.geom.EdgeIndexed
 
setIndex(int) - Method in class edu.jhu.ece.iacl.jist.structures.geom.VertexIndexed
 
setIndex(int) - Method in class edu.jhu.ece.iacl.jist.structures.image.VoxelIndexed
 
setIndex(int) - Method in class edu.jhu.ece.iacl.jist.structures.image.VoxelMipav
 
setIndexes(int[]) - Method in class edu.jhu.ece.iacl.jist.structures.geom.EmbeddedPointSet
Sets the indexes.
setInit(String) - Method in class edu.jhu.ece.iacl.algorithms.manual_label.staple.STAPLEgeneral
 
setInit(String) - Method in class edu.jhu.ece.iacl.algorithms.manual_label.staple.STAPLEmulti
 
setInit(String) - Method in class edu.jhu.ece.iacl.algorithms.manual_label.staple.STAPLEmulti2
 
setInit(String) - Method in class edu.jhu.ece.iacl.algorithms.manual_label.staple.STAPLEsurf
 
setInnerIterations(int) - Method in class edu.jhu.cs.cisst.algorithms.segmentation.gac.GeodesicActiveContour2D
Sets the inner iterations.
setInnerPoint(int, Point3f) - Method in class edu.jhu.ece.iacl.jist.structures.geom.EmbeddedSurface
Sets the inner point.
setInput(ParamCollection) - Method in class edu.jhu.ece.iacl.jist.pipeline.ProcessingAlgorithm
Set input parameters.
setInputDir(File) - Method in class edu.jhu.ece.iacl.jist.pipeline.PipeLayout
Set root input directory.
setInputDir(URI) - Method in class edu.jhu.ece.iacl.jist.pipeline.PipeLayout
Set root input directory.
setInputDirectory(URI) - Method in class edu.jhu.ece.iacl.jist.pipeline.PipeLayout.RunParameters
Sets the input directory.
setInputDirectory(File) - Method in class edu.jhu.ece.iacl.jist.pipeline.PipeLayout.RunParameters
Sets the input directory.
setInputView(ParamInputView) - Method in class edu.jhu.ece.iacl.jist.pipeline.factory.ParamFactory
Set the input view used to enter the parameter value.
setInputView(ParamInputView) - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamModel
Set the input view used to specify the parameter value.
setIntensity(float) - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.DataLabel
Set intensity.
setIsoLevel(float) - Method in class edu.jhu.cs.cisst.vent.renderer.processing.VolumeIsoContourRenderer
Sets the iso level.
setItem(Object) - Method in class edu.jhu.ece.iacl.jist.pipeline.gui.ConnectionEditor
Set selected item.
setJre(String) - Method in class edu.jhu.ece.iacl.jist.pipeline.JistPreferences
Set JRE executable.
setLabel(String) - Method in class edu.jhu.ece.iacl.jist.pipeline.AbstractCalculation
Set label to display in progress bar for this calculation.
setLabel(String) - Method in class edu.jhu.ece.iacl.jist.pipeline.AlgorithmInformation
Sets the label.
setLabel(String) - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamModel
Set the label to be displayed in the input and output views.
setLabel(String) - Method in class edu.jhu.ece.iacl.jist.pipeline.PipeChildPort
Unimplemented.
setLabel(String) - Method in class edu.jhu.ece.iacl.jist.pipeline.PipeModule
Set display label for this module.
setLabel(String) - Method in class edu.jhu.ece.iacl.jist.pipeline.PipeParentPort
Unimplemented.
setLabel(String) - Method in class edu.jhu.ece.iacl.jist.pipeline.PipePort
Set label to display next to port.
setLabelFile(File) - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamDataLabel
Set the label file location for this parameter.
setLastDirectory(File) - Method in class edu.jhu.ece.iacl.jist.pipeline.JistPreferences
Set last directory entered.
setLayout(PipeLayout) - Method in class edu.jhu.ece.iacl.jist.pipeline.ExecutionContext
Set layout owner.
setLayoutConstraints(Object) - Method in class edu.jhu.ece.iacl.jist.pipeline.view.input.ParamInputView
Set layout constraints.
setLayoutConstraints(Object) - Method in class edu.jhu.ece.iacl.jist.pipeline.view.output.ParamOutputView
Set layout constraints.
setLength(double) - Method in class edu.jhu.ece.iacl.jist.structures.geom.PolySpline
Sets the length.
setLevel(int) - Method in interface edu.jhu.cs.cisst.algorithms.optimize.fmg.grid.ConstGrid
Set the resolution level.
setLevel(int) - Method in class edu.jhu.cs.cisst.algorithms.optimize.fmg.grid.Grid
 
setLevels(ArrayList<Integer>) - Method in class edu.jhu.ece.iacl.algorithms.vabra.VabraConfiguration
 
setLgFontSize(int) - Method in class edu.jhu.ece.iacl.jist.pipeline.JistPreferences
 
setLibraryPath(File) - Method in class edu.jhu.ece.iacl.jist.pipeline.PipeLibrary
Set library directory.
setLikelihoodThreshold(double) - Method in class edu.jhu.ece.iacl.algorithms.dti.DTEMRLTensor
 
setLineData(double[][]) - Method in class edu.jhu.ece.iacl.jist.structures.geom.CurveCollection
Sets the line data.
setList(List<T>) - Method in class edu.jhu.ece.iacl.jist.pipeline.view.input.InformationListBox
Set list box entries from existing list.
setLoadAndSaveOnValidate(boolean) - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamModel
Allow memory saving operations by reducing the level of validation performed.
setLocation(int, int) - Method in class edu.jhu.ece.iacl.jist.pipeline.graph.PipeAlgorithmFactory.AlgorithmGroupCell
Set location of group cell.
setLocation(int, int) - Method in class edu.jhu.ece.iacl.jist.pipeline.graph.PipeModuleCell
Set the location of the module.
setLogScale(boolean) - Method in class edu.jhu.bme.smile.commons.math.HistogramGenerator
 
setLogScalingFactor(double) - Method in class edu.jhu.bme.smile.commons.math.HistogramGenerator
 
setLongDescription(String) - Method in class edu.jhu.ece.iacl.jist.pipeline.AlgorithmInformation
Sets the long description.
setMandatory(boolean) - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamFileCollection
Set the mandatory field.
setMandatory(boolean) - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamModel
Set the mandatory field.
setMandatory(boolean) - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamNumberCollection
Set the mandatory field.
setMapFile(File) - Method in class edu.jhu.ece.iacl.jist.pipeline.graph.PipeAlgorithmFactory
Set module definition file.
setMapFile(File) - Method in class edu.jhu.ece.iacl.jist.pipeline.PipeAlgorithm
Set file that stores this algorithm.
setMapFile(File) - Method in class edu.jhu.ece.iacl.jist.pipeline.ProcessingAlgorithm
Set module definition file.
setMarkerPoint(double, int) - Method in class edu.jhu.ece.iacl.jist.structures.fiber.Fiber
Sets the marker point.
setMatrix(float[][]) - Method in class edu.jhu.bme.smile.commons.math.RotationMatrix
 
setMatrix(double[][]) - Method in class edu.jhu.bme.smile.commons.math.RotationMatrix
 
setMax(double) - Method in class edu.jhu.bme.smile.commons.math.HistogramGenerator
 
setMax(Number) - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamNumberCollection
Sets the max.
setMaxCurvatureForce(double) - Method in class edu.jhu.cs.cisst.algorithms.segmentation.gac.GaussianCurvatureForce2D
Sets the max curvature force.
setMaxCurvatureForce(double) - Method in class edu.jhu.cs.cisst.algorithms.segmentation.gac.MeanCurvatureForce2D
Sets the max curvature force.
setMaxHeap(int) - Method in class edu.jhu.ece.iacl.jist.pipeline.PipeLayout.RunParameters
Sets the max heap.
setMaxHeap(int) - Method in class edu.jhu.ece.iacl.jist.pipeline.PipeLayout
Set maximum allowable heap.
setMaxIncoming(int) - Method in class edu.jhu.ece.iacl.jist.pipeline.PipePort
Set maximum number of input ports.
setMaxIterations(int) - Method in class edu.jhu.cs.cisst.algorithms.segmentation.gac.GradientVectorFlow2D
Sets the max iterations.
setmaxIters(int) - Method in class edu.jhu.ece.iacl.algorithms.manual_label.staple.STAPLE
 
setmaxIters(int) - Method in class edu.jhu.ece.iacl.algorithms.manual_label.staple.STAPLEgeneral
 
setmaxIters(int) - Method in class edu.jhu.ece.iacl.algorithms.manual_label.staple.STAPLEgeneralSingle
 
setmaxIters(int) - Method in class edu.jhu.ece.iacl.algorithms.manual_label.staple.STAPLEmulti
 
setmaxIters(int) - Method in class edu.jhu.ece.iacl.algorithms.manual_label.staple.STAPLEmulti2
 
setmaxIters(int) - Method in class edu.jhu.ece.iacl.algorithms.manual_label.staple.STAPLEsingle
 
setmaxIters(int) - Method in class edu.jhu.ece.iacl.algorithms.manual_label.staple.STAPLEsurf
 
setMaxLayers(int) - Method in class edu.jhu.cs.cisst.algorithms.segmentation.gac.GeodesicActiveContour2D
Sets the maximum number of layers.
setMaxOutgoing(int) - Method in class edu.jhu.ece.iacl.jist.pipeline.PipePort
Set maximum number of outgoing ports.
setMaxProcs(int) - Method in class edu.jhu.ece.iacl.jist.pipeline.PipeLayout.RunParameters
Sets the max processes.
setMaxProcs(int) - Method in class edu.jhu.ece.iacl.jist.pipeline.PipeLayout
Set maximum allowable simultaneous processes.
setMdFontSize(int) - Method in class edu.jhu.ece.iacl.jist.pipeline.JistPreferences
 
setMenuItemsEnabled(boolean) - Method in class edu.jhu.ece.iacl.jist.pipeline.gui.PipelineLayoutTool
Enable/Disable all layout specific menu items.
setMesh(GeometryArray) - Method in class edu.jhu.ece.iacl.jist.pipeline.view.output.ParamSurfaceOutputView
set mesh to render.
setMeshColor(Color3f) - Method in class edu.jhu.ece.iacl.jist.pipeline.view.output.ParamSurfaceOutputView
set mesh color.
setMethod(int) - Method in class edu.jhu.bme.smile.commons.optimize.tensor.MLTensor
Sets the method used to calculate the derivatives.
setMethod(IsoSurfaceGenerator.Method) - Method in class edu.jhu.cs.cisst.algorithms.geometry.surface.IsoSurfaceGenerator
Sets the iso-surface generation method.
setMethod(int) - Method in class edu.jhu.ece.iacl.algorithms.dti.DTEMRLTensor
Sets the method used to calculate the derivatives.
setMin(double) - Method in class edu.jhu.bme.smile.commons.math.HistogramGenerator
 
setMin(Number) - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamNumberCollection
Sets the min.
setModality(ImageHeader.ImageModality) - Method in class edu.jhu.ece.iacl.jist.structures.image.ImageHeader
Sets the modality.
setModelImageCompression(ModelImage, int) - Static method in class edu.jhu.ece.iacl.jist.utility.FileUtil
Sets the model image compression.
setModuleCell(PipeModuleCell) - Method in class edu.jhu.ece.iacl.jist.pipeline.PipeModule
Set graph cell representing this module.
setMonitor(CalculationMonitor) - Method in class edu.jhu.ece.iacl.jist.pipeline.AbstractCalculation
Set monitor that observes this calculation.
setMultiGridCycles(int) - Method in class edu.jhu.cs.cisst.algorithms.segmentation.gac.GradientVectorFlow2D
Sets the multigrid cycles.
setMultiGridIterations(int) - Method in class edu.jhu.cs.cisst.algorithms.segmentation.gac.GradientVectorFlow2D
Sets the multi grid iterations.
setMultiGridResolutions(int) - Method in class edu.jhu.cs.cisst.algorithms.segmentation.gac.GradientVectorFlow2D
Sets the multi grid resolutions.
setMultiGridSmoothIterations(int) - Method in class edu.jhu.cs.cisst.algorithms.segmentation.gac.GradientVectorFlow2D
Sets the multi grid smooth iterations.
setMultiGridThreads(int) - Method in class edu.jhu.cs.cisst.algorithms.segmentation.gac.GradientVectorFlow2D
Sets the multi grid threads.
setName(String) - Method in interface edu.jhu.cs.cisst.vent.Visualization
Sets the name.
setName(String) - Method in class edu.jhu.cs.cisst.vent.VisualizationProcessing
Sets the name.
setName(String) - Method in class edu.jhu.ece.iacl.algorithms.manual_label.simulation.SurfaceRater
 
setName(String) - Method in class edu.jhu.ece.iacl.algorithms.manual_label.simulation.VolumeRater
 
setName(String) - Method in class edu.jhu.ece.iacl.jist.pipeline.AlgorithmInformation
Sets the name.
setName(String) - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.DataLabel
Set name.
setName(String) - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamModel
Set the name of the parameter, which will appear as the label if the label is not specified.
setName(String) - Method in class edu.jhu.ece.iacl.jist.pipeline.PipeChildPort
Unimplemented.
setName(String) - Method in class edu.jhu.ece.iacl.jist.pipeline.PipeModule
Set unique name that identifies this parameter.
setName(String) - Method in class edu.jhu.ece.iacl.jist.pipeline.PipeParentPort
Unimplemented.
setName(String) - Method in class edu.jhu.ece.iacl.jist.pipeline.PipePort
Set name to identify port.
setName(String) - Method in class edu.jhu.ece.iacl.jist.structures.fiber.FiberCollection
Sets the name.
setName(String) - Method in class edu.jhu.ece.iacl.jist.structures.geom.CurveCollection
Sets the name.
setName(String) - Method in class edu.jhu.ece.iacl.jist.structures.geom.EmbeddedPointSet
Sets the name.
setName(String) - Method in class edu.jhu.ece.iacl.jist.structures.image.ImageData
Volume name used my MIPAV images when saving.
setName(String) - Method in class edu.jhu.ece.iacl.jist.structures.image.ImageDataByte
 
setName(String) - Method in class edu.jhu.ece.iacl.jist.structures.image.ImageDataColor
 
setName(String) - Method in class edu.jhu.ece.iacl.jist.structures.image.ImageDataDouble
 
setName(String) - Method in class edu.jhu.ece.iacl.jist.structures.image.ImageDataInt
 
setName(String) - Method in class edu.jhu.ece.iacl.jist.structures.image.ImageDataMipav
 
setName(String) - Method in class edu.jhu.ece.iacl.jist.structures.image.ImageDataNumber
 
setName(String) - Method in class edu.jhu.ece.iacl.jist.structures.image.ImageDataUByte
 
setNamingConvention(JistPreferences.NamingConvention) - Method in class edu.jhu.ece.iacl.jist.pipeline.JistPreferences
Sets the naming convention.
setNamingConvention(JistPreferences.NamingConvention) - Method in class edu.jhu.ece.iacl.jist.pipeline.PipeLayout
Set naming convention for output directory.
setNDWb0(int[]) - Method in class edu.jhu.ece.iacl.algorithms.dti.DWICoReg
 
setNeighborTable(int[][]) - Method in class edu.jhu.ece.iacl.algorithms.manual_label.simulation.SurfaceRater
 
setNoiseLevelPrior(double, double) - Method in class edu.jhu.ece.iacl.algorithms.dti.DTEMRLTensor
 
setNoiseLevelPriorOff() - Method in class edu.jhu.ece.iacl.algorithms.dti.DTEMRLTensor
 
setNormalize(boolean) - Method in class edu.jhu.cs.cisst.algorithms.segmentation.gac.GradientVectorFlow2D
Sets the normalize.
setNumberFormat(NumberFormat) - Method in class edu.jhu.ece.iacl.jist.io.ArrayDoubleDxReaderWriter
 
setNumberFormat(NumberFormat) - Method in class edu.jhu.ece.iacl.jist.io.ArrayDoubleReaderWriter
Sets the number format.
setObject(T) - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamObject
Set object.
setObject(EmbeddedSurface) - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamSurface
Set surface.
setObject(ImageData) - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamVolume
Set volume.
setObservableCalculation(AbstractCalculation) - Method in class edu.jhu.ece.iacl.jist.pipeline.CalculationMonitor
Set root calculation for this monitor.
setObserver(AbstractCalculation) - Method in class edu.jhu.ece.iacl.plugins.registration.MedicAlgorithmConstrainedFLIRT.AlgorithmConstrainedOAR3DWrapper
 
setObserver(AbstractCalculation) - Method in class edu.jhu.ece.iacl.plugins.registration.MedicAlgorithmFLIRT.AlgorithmRegOAR3DWrapper
 
setObserver(AbstractCalculation) - Method in class edu.jhu.ece.iacl.plugins.registration.MedicAlgorithmFLIRTCollection.AlgorithmRegOAR3DWrapper
 
setOffset(int) - Method in class edu.jhu.ece.iacl.algorithms.manual_label.LabelSurface
 
setoffset(int) - Method in class edu.jhu.ece.iacl.algorithms.manual_label.simulation.SurfaceRater
 
setOffset(int) - Method in class edu.jhu.ece.iacl.algorithms.manual_label.staple.STAPLEsurf
 
setOptions(ArrayList<String>) - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamMultiOption
Sets the options.
setOptions(List<String>) - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamOption
Set list of options.
setOrigin(Point3f) - Method in class edu.jhu.ece.iacl.jist.structures.geom.EmbeddedSurface
Sets the origin.
setOrigin(float[]) - Method in class edu.jhu.ece.iacl.jist.structures.image.ImageHeader
Sets the origin.
setOriginalImage(ImageData) - Method in class edu.jhu.cs.cisst.vent.widgets.VisualizationActiveContour2D
Sets the original image.
setOuterIterations(int) - Method in class edu.jhu.cs.cisst.algorithms.segmentation.gac.GeodesicActiveContour2D
Sets the outer iterations.
setOuterPoint(int, Point3f) - Method in class edu.jhu.ece.iacl.jist.structures.geom.EmbeddedSurface
Sets the outer point.
setOutput(ParamCollection) - Method in class edu.jhu.ece.iacl.jist.pipeline.ProcessingAlgorithm
Set output parameters.
setOutputDir(File) - Method in class edu.jhu.ece.iacl.jist.pipeline.PipeLayout
Set root output directory.
setOutputDir(URI) - Method in class edu.jhu.ece.iacl.jist.pipeline.PipeLayout
Set root output directory.
setOutputDirectory(File) - Method in class edu.jhu.ece.iacl.jist.pipeline.PipeLayout.RunParameters
Sets the input directory.
setOutputDirectory(URI) - Method in class edu.jhu.ece.iacl.jist.pipeline.PipeLayout.RunParameters
Sets the output directory.
setOutputDirectory(File) - Method in class edu.jhu.ece.iacl.jist.pipeline.ProcessingAlgorithm
Set output directory.
setOutputDirectory(File) - Method in class edu.jhu.ece.iacl.jist.pipeline.ProcessingDialog
Set directory to store output results.
setOutputMetaFile(File) - Method in class edu.jhu.ece.iacl.jist.pipeline.ProcessingAlgorithm
 
setOutputView(ParamOutputView) - Method in class edu.jhu.ece.iacl.jist.pipeline.factory.ParamFactory
Set the output view used to display the parameter value.
setOutputView(ParamOutputView) - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamModel
Set the output view used to display the parameter value.
setOverrideRunOutOfProcess(boolean) - Method in class edu.jhu.ece.iacl.jist.pipeline.PipeScheduler
 
setOwner(PipeModule) - Method in class edu.jhu.ece.iacl.jist.pipeline.PipePort
Set module that owns this port.
setPackage(String) - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamCollection
 
setParameter(ParamModel) - Method in class edu.jhu.ece.iacl.jist.pipeline.PipeParentPort
Set output parameter that is associated with this parent port.
setParameters(double, double, double) - Method in class edu.jhu.bme.smile.commons.math.RotationMatrix
 
setParameters(double[]) - Method in class edu.jhu.bme.smile.commons.math.RotationMatrix
 
setParameters(double[], int) - Method in class edu.jhu.bme.smile.commons.math.RotationMatrix
 
setParameters(float, float, float) - Method in class edu.jhu.ece.iacl.algorithms.dti.tractography.FACT.FACTapi
 
setParentFrame(ViewJFrameBase) - Method in class edu.jhu.ece.iacl.jist.pipeline.ProcessingDialog
Set parent MIPAV frame.
setParentGroup(PipeAlgorithmGroup) - Method in class edu.jhu.ece.iacl.jist.pipeline.PipeAlgorithm
Set parent module.
setPaste(Action) - Method in class edu.jhu.ece.iacl.jist.pipeline.gui.PipeInternalFrame
Sets the paste.
setPipelineLayout(PipeLayout, ProgressMonitor) - Method in class edu.jhu.ece.iacl.jist.pipeline.graph.PipeJGraph
Sets the pipeline layout.
setPipelineLayout(PipeLayout, ProgressMonitor) - Method in class edu.jhu.ece.iacl.jist.pipeline.gui.LayoutPanel
Set the layout for the current active frame.
setPipelineLayout(PipeLayout, ProgressMonitor) - Method in class edu.jhu.ece.iacl.jist.pipeline.gui.PipeInternalFrame
Set layout for graph.
setPointData(double[][]) - Method in class edu.jhu.ece.iacl.jist.structures.geom.EmbeddedPointSet
Sets the point data.
setPoints(Point3f[]) - Method in class edu.jhu.ece.iacl.jist.structures.geom.EmbeddedPointSet
Sets the points.
setPollInterval(long) - Static method in class edu.jhu.ece.iacl.jist.pipeline.CalculationMonitor
Set interval at which the algorithm is polled.
setPortClass(Map, String) - Static method in class edu.jhu.ece.iacl.jist.pipeline.graph.PipeCellViewFactory
Sets the port class.
setPortToCheck(PipePort) - Method in class edu.jhu.ece.iacl.jist.pipeline.graph.PipeJGraph
Set port to check for compatibility.
setPortType(PipePort.type) - Method in class edu.jhu.ece.iacl.jist.pipeline.PipePort
Set port type as either input or output.
setPosition(int, int, int) - Method in class edu.jhu.ece.iacl.jist.structures.geom.EdgeIndexed
Sets the position.
setPosition(int) - Method in class edu.jhu.ece.iacl.jist.structures.geom.VertexIndexed
Sets the position.
setPreferences(JistPreferences) - Static method in class edu.jhu.ece.iacl.jist.pipeline.JistPreferences
Set singleton reference to preferences.
setPreferredExtension(int) - Method in class edu.jhu.ece.iacl.jist.io.FileExtensionFilter
Sets the preferred extension.
setPreferredExtension(String) - Method in class edu.jhu.ece.iacl.jist.io.FileExtensionFilter
Sets the preferred extension.
setPreferredExtension(String) - Method in class edu.jhu.ece.iacl.jist.pipeline.JistPreferences
Set the preferred extension (for CubicVolumeReaderWriter).
setPreferredSize(Dimension) - Method in class edu.jhu.ece.iacl.jist.pipeline.ProcessingAlgorithm
Get preferred size for algorithm The default is null.
setPressureForce(ImageDataFloat) - Method in class edu.jhu.cs.cisst.vent.widgets.VisualizationActiveContour2D
Sets the pressure force.
setPriority(int) - Method in class edu.jhu.ece.iacl.jist.pipeline.ExecutionContext
Set execution priority.
setProbability(boolean) - Method in class edu.jhu.bme.smile.commons.math.HistogramGenerator
 
setProcess(Process) - Method in class edu.jhu.ece.iacl.jist.pipeline.ExecutionContext
Set running process.
setPrototype(ParamModel<T>) - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamWeightedVolumeCollection
 
setQuiet(boolean) - Static method in class edu.jhmi.rad.medic.utilities.MedicUtilPublic
Sets the quiet.
setQuiet(boolean) - Static method in class edu.jhu.ece.iacl.jist.io.MipavController
Sets the quiet.
setRand(Random) - Method in class edu.jhu.ece.iacl.algorithms.manual_label.simulation.VolumeRater
 
setReaderWriter(FileReaderWriter) - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamFileCollection
Set extension filter.
setReaderWriter(FileReaderWriter<T>) - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamObject
Set reader writer.
setRefPosition(int, int, int) - Method in interface edu.jhu.ece.iacl.jist.structures.data.Indexable
Set position in volume.
setRefPosition(int, int, int) - Method in class edu.jhu.ece.iacl.jist.structures.geom.EdgeIndexed
 
setRefPosition(int, int, int) - Method in class edu.jhu.ece.iacl.jist.structures.geom.VertexIndexed
 
setRefPosition(int, int, int) - Method in class edu.jhu.ece.iacl.jist.structures.image.VoxelIndexed
 
setRefPosition(int, int, int) - Method in class edu.jhu.ece.iacl.jist.structures.image.VoxelMipav
 
setRefreshInterval(long) - Method in class edu.jhu.ece.iacl.jist.pipeline.view.input.Refresher
Set refresh interval.
setRegMeth(String) - Method in class edu.jhu.ece.iacl.algorithms.dti.DWICoReg
 
setRelativePath(File, File) - Static method in class edu.jhu.ece.iacl.jist.io.MipavController
Sets the relative path.
setRelativePath(File) - Static method in class edu.jhu.ece.iacl.jist.io.MipavController
Sets the relative path.
setRemove(Action) - Method in class edu.jhu.ece.iacl.jist.pipeline.gui.PipeInternalFrame
Sets the remove.
setRes(double, double, double) - Method in class edu.jhu.ece.iacl.algorithms.dti.tractography.FiberStatistics
 
setRes(float, float, float) - Method in class edu.jhu.ece.iacl.algorithms.dti.tractography.FiberTracker.FACTfiber
 
setRes(float, float, float) - Method in class edu.jhu.ece.iacl.algorithms.dti.tractography.WildBootFiberTracker.WildBootFACTfiber
 
setRes(float, float, float) - Method in class edu.jhu.ece.iacl.algorithms.manual_label.LabelImage
 
setResolution(float) - Method in class edu.jhu.ece.iacl.algorithms.vabra.ImagePair
 
setResolution(float) - Method in class edu.jhu.ece.iacl.algorithms.vabra.ImagePairNMI
 
setResolutionParent(float) - Method in class edu.jhu.ece.iacl.algorithms.vabra.ImagePairNMI
 
setResolutions(Point3f) - Method in class edu.jhu.ece.iacl.jist.structures.fiber.FiberCollection
Sets the resolutions.
setResolutionSwitches(ArrayList<Integer>) - Method in class edu.jhu.ece.iacl.algorithms.vabra.VabraConfiguration
 
setRobustMinMax(boolean) - Method in class edu.jhu.bme.smile.commons.math.HistogramGenerator
 
setRows(int) - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamMatrix
Sets the rows.
setRunningInSeparateProcess(boolean) - Method in class edu.jhu.ece.iacl.jist.pipeline.ProcessingAlgorithm
Sets the running in separate process.
setRunParams(PipeLayout.RunParameters) - Method in class edu.jhu.ece.iacl.jist.pipeline.PipeLayout
Set runtime parameters.
setSafeMinMax(ModelImage) - Static method in class edu.jhu.ece.iacl.jist.utility.ImageUtil
Sets the safe min max.
setSampleRate(int) - Method in class edu.jhu.cs.cisst.vent.renderer.processing.VectorField2DRenderer
Sets the sample rate.
setScale(float, float, float) - Method in class edu.jhu.ece.iacl.algorithms.vabra.ImagePair
 
setScale(float, float, float) - Method in class edu.jhu.ece.iacl.algorithms.vabra.ImagePairRBF
 
setScale(Vector3f) - Method in class edu.jhu.ece.iacl.jist.structures.geom.EmbeddedSurface
Sets the scale.
setScanner(String) - Method in class edu.jhu.ece.iacl.algorithms.dti.GTCparams
 
setScenarioId(int) - Method in class edu.jhu.ece.iacl.jist.pipeline.ExecutionContext
Set scenario id.
setScheduler(PipeScheduler) - Method in class edu.jhu.ece.iacl.jist.pipeline.gui.ProcessManagerTable
Set scheduler that will force updates to the manager table.
setScheduler(PipeScheduler) - Method in class edu.jhu.ece.iacl.jist.pipeline.PipeLayout
Set scheduler.
setSeed(long) - Method in class edu.jhu.ece.iacl.algorithms.manual_label.simulation.SurfaceRater
 
setSeed(long) - Method in class edu.jhu.ece.iacl.algorithms.manual_label.simulation.VolumeRater
 
setSegment(boolean) - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.DataLabel
Set segment flag.
setSelected(List<ImageData>) - Method in class edu.jhu.ece.iacl.jist.pipeline.view.input.ParamVolumeCollectionInputView
Select the specified images in the combo box.
setSelected(ImageData) - Method in class edu.jhu.ece.iacl.jist.pipeline.view.input.ParamVolumeInputView
Set the selected ModelImage in the combobox.
setSelected(ImageData) - Method in class edu.jhu.ece.iacl.jist.pipeline.view.input.ParamVolumeURIInputView
Set the selected ModelImage in the combobox.
setSelectedFactory(PipeAlgorithmFactory) - Method in class edu.jhu.ece.iacl.jist.pipeline.gui.PlugInSelector
Set selected module factory and close dialog.
setSelectedPort(PipePort) - Method in class edu.jhu.ece.iacl.jist.pipeline.gui.PortComboBox
Set selected port.
setSelection(ArrayList<Integer>) - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamMultiOption
Set the selected option.
setSensingMatrix(Matrix) - Method in class edu.jhu.ece.iacl.algorithms.hardi.CFARIBasisSet
 
setShortLabel(String) - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamModel
Set the shortLabel to be used as a command line switch.
setShowManager(boolean) - Method in class edu.jhu.ece.iacl.jist.pipeline.gui.ProcessManager
 
setSigma(double) - Method in class edu.jhu.ece.iacl.algorithms.dti.DTEMRLTensor
 
setSigma(float) - Method in class edu.jhu.ece.iacl.algorithms.manual_label.staple.STAPLEgeneral
 
setSigmaFactor(double) - Method in class edu.jhu.bme.smile.commons.optimize.tensor.MLTensor
Sets the scaling factor for sigma.
setSigmaFactor(double) - Method in class edu.jhu.ece.iacl.algorithms.dti.DTEMRLTensor
Sets the scaling factor for sigma.
setSlice(int) - Method in class edu.jhu.cs.cisst.vent.renderer.processing.VolumeSliceRenderer
Sets the slice.
setSliceThickness(float) - Method in class edu.jhu.ece.iacl.jist.structures.image.ImageHeader
Sets the slice thickness.
setSmFontSize(int) - Method in class edu.jhu.ece.iacl.jist.pipeline.JistPreferences
 
setSource(PipePort) - Method in class edu.jhu.ece.iacl.jist.pipeline.PipeConnector
Set source port.
setSourceIndex(int) - Method in class edu.jhu.ece.iacl.jist.pipeline.PipeConnector
Set the index into the source if the source is a variable collection of different parameters.
setStandardDeviation(double) - Method in class edu.jhu.cs.cisst.algorithms.segmentation.gac.GradientVectorFlow2D
Sets the standard deviation.
setStartTime(long) - Method in class edu.jhu.ece.iacl.doc.DocumentAllTests.TestCase
 
setStatus(DocumentAllTests.TestCase.Status) - Method in class edu.jhu.ece.iacl.doc.DocumentAllTests.TestCase
 
setStatus(DevelopmentStatus) - Method in class edu.jhu.ece.iacl.jist.pipeline.AlgorithmInformation
Sets the status.
setStatus(ExecutionContext.Status) - Method in class edu.jhu.ece.iacl.jist.pipeline.ExecutionContext
Set status for context.
setStepSize(double) - Method in class edu.jhu.bme.smile.commons.optimize.tensor.MLTensor
Sets the step size used in calculating derivatives.
setStepSize(double) - Method in class edu.jhu.ece.iacl.algorithms.dti.DTEMRLTensor
Sets the step size used in calculating derivatives.
setStopTime(long) - Method in class edu.jhu.ece.iacl.doc.DocumentAllTests.TestCase
 
setStrokeWeight(float) - Method in class edu.jhu.cs.cisst.vent.renderer.processing.VolumeIsoContourRenderer
Sets the stroke weight.
setSurface(EmbeddedSurface) - Method in class edu.jhu.ece.iacl.algorithms.manual_label.staple.STAPLEgeneral
 
setSurfaces(List<EmbeddedSurface>) - Method in class edu.jhu.ece.iacl.algorithms.manual_label.staple.STAPLEsurf
 
setSwitchSpaced(boolean) - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamSwitch
Indicates whether there should be a space after the switch.
setTestVolume(ImageData) - Method in class edu.jhu.ece.iacl.algorithms.manual_label.ROI
 
setText(String) - Method in class edu.jhu.ece.iacl.jist.pipeline.AlgorithmInformation.Citation
Sets the text.
setTextureCoordinates(double[][]) - Method in class edu.jhu.ece.iacl.jist.structures.geom.EmbeddedSurface
Sets the texture coordinates.
setThickness(int, double) - Method in class edu.jhu.ece.iacl.jist.structures.geom.EmbeddedSurface
Sets the thickness.
setTitle(String) - Method in class edu.jhu.ece.iacl.jist.pipeline.gui.PipeInternalFrame
 
setToback(Action) - Method in class edu.jhu.ece.iacl.jist.pipeline.gui.PipeInternalFrame
Sets the toback.
setTofront(Action) - Method in class edu.jhu.ece.iacl.jist.pipeline.gui.PipeInternalFrame
Sets the tofront.
setTolerance(double) - Method in class edu.jhu.bme.smile.commons.optimize.LineSearchND
Sets the tolerance.
setTolerance(double) - Method in class edu.jhu.bme.smile.commons.optimize.LineSearchNDDifferentiable
Sets the tolerance.
setTolerance(double) - Method in class edu.jhu.bme.smile.commons.optimize.tensor.MLTensor
Sets the tolerance.
setTolerance(double) - Method in class edu.jhu.ece.iacl.algorithms.dti.DTEMRLTensor
Sets the tolerance.
setTotalAssertions(int) - Method in class edu.jhu.ece.iacl.doc.DocumentAllTests.TestCase
 
setTotalUnits(long) - Method in class edu.jhu.ece.iacl.jist.pipeline.AbstractCalculation
Set total computational units for this calculation.
setTransparency(float) - Method in class edu.jhu.cs.cisst.vent.renderer.processing.ImageRenderer
Sets the transparency.
setTransparency(float) - Method in class edu.jhu.cs.cisst.vent.renderer.processing.VectorField2DRenderer
Sets the transparency.
setTransparency(float) - Method in class edu.jhu.cs.cisst.vent.renderer.processing.VolumeSliceRenderer
Sets the transparency.
setType(int) - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.DataLabel
Set object type.
setUnitsOfMeasure(ImageHeader.MeasurementUnit[]) - Method in class edu.jhu.ece.iacl.jist.structures.image.ImageHeader
Sets the units of measure.
setup() - Method in class edu.jhu.cs.cisst.vent.renderer.processing.ImageRenderer
 
setup() - Method in class edu.jhu.cs.cisst.vent.renderer.processing.RendererProcessing
Setup.
setup() - Method in class edu.jhu.cs.cisst.vent.renderer.processing.SurfaceRenderer
 
setup() - Method in class edu.jhu.cs.cisst.vent.renderer.processing.VectorField2DRenderer
Setup.
setup() - Method in class edu.jhu.cs.cisst.vent.renderer.processing.VolumeSliceRenderer
Setup.
setup() - Method in class edu.jhu.cs.cisst.vent.VisualizationProcessing2D
Setup.
setup() - Method in class edu.jhu.cs.cisst.vent.VisualizationProcessing3D
Setup.
setup() - Method in class edu.jhu.cs.cisst.vent.widgets.VisualizationImage
Setup.
setup() - Method in class edu.jhu.cs.cisst.vent.widgets.VisualizationTriangleMesh
 
Setup(List<String>) - Method in interface edu.jhu.ece.iacl.jist.processcontrol.ProcessController
Setup.
Setup(List<String>) - Method in class edu.jhu.ece.iacl.jist.processcontrol.ProcessControllerDRMAA
 
Setup(List<String>) - Method in class edu.jhu.ece.iacl.jist.processcontrol.ProcessControllerNative
 
setup3DCubicLagrangianInterpolation() - Static method in class edu.jhmi.rad.medic.libraries.ImageFunctionsPublic
Setup 3D cubic Lagrangian
setUseConnector(boolean) - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamWeightedVolumeCollection
 
setUseConnector(boolean) - Method in class edu.jhu.ece.iacl.jist.pipeline.PipePort
Indicate that this port should use a connector instead of a default value.
setUseDirectTensorRepresentation(boolean) - Method in class edu.jhu.ece.iacl.algorithms.dti.DTEMRLTensor
 
setUsedMemory(int) - Method in class edu.jhu.ece.iacl.jist.pipeline.ExecutionContext
Set used memory.
setUseGridEngine(boolean) - Method in class edu.jhu.ece.iacl.jist.pipeline.JistPreferences
Sets the use grid engine.
setUseGridEngine(boolean) - Method in class edu.jhu.ece.iacl.jist.pipeline.PipeLayout.RunParameters
Sets the use grid engine.
setUseGridEngine(boolean) - Method in class edu.jhu.ece.iacl.jist.pipeline.PipeLayout
Sets the use grid engine.
setUseResolutions(boolean) - Method in class edu.jhu.cs.cisst.algorithms.geometry.surface.IsoContourGenerator
Sets the use resolutions.
setUseResolutions(boolean) - Method in class edu.jhu.cs.cisst.algorithms.geometry.surface.IsoSurfaceGenerator
Sets the use image resolutions flag.
setUserObject(Object) - Method in class edu.jhu.ece.iacl.jist.pipeline.graph.PipeAlgorithmFactory.AlgorithmNode
 
setUserObject(Object) - Method in class edu.jhu.ece.iacl.jist.pipeline.tree.PackageNode
Set the user object for this package node, which should be the directory name.
setUseWorker(boolean) - Method in class edu.jhu.ece.iacl.jist.pipeline.gui.ProcessManager
 
setUseWorker(boolean) - Method in class edu.jhu.ece.iacl.jist.pipeline.PipeScheduler
Sets the use worker.
setUUID(String) - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamHeader
 
setVal(int, int, int, int) - Method in class edu.jhu.ece.iacl.algorithms.manual_label.LabelImage
 
setVal(int, GridPt) - Method in class edu.jhu.ece.iacl.algorithms.manual_label.LabelImage
 
setVal(int, int) - Method in class edu.jhu.ece.iacl.algorithms.manual_label.LabelSurface
 
setValue(Object) - Method in class edu.jhu.ece.iacl.jist.pipeline.graph.PipeEdgeRealEditor.EditorDelegate
Sets the value of this cell.
setValue(ArrayList<String>) - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamArgsOrder
 
setValue(Boolean) - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamBoolean
The parameter value must be a boolean.
setValue(Vector<ParamModel>) - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamCollection
 
setValue(Color) - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamColor
Set color value.
setValue(ImageData) - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamDataLabel
Set volume.
setValue(DataLabelCollection) - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamDataLabel
The set value method accepts all value types inherited from ParamVolume plus DataLabelCollection.
setValue(File) - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamDataLabel
Set file location.
setValue(String) - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamDataLabel
Set file location.
setValue(String) - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamDouble
Set value from string.
setValue(Number) - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamDouble
 
setValue(File) - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamFile
Set the file location for this parameter.
setValue(URI) - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamFile
Set the uri location for this parameter.
setValue(String) - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamFile
Set file location.
setValue(List) - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamFileCollection
Set the file collection.
setValue(String) - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamFloat
Set value from string.
setValue(Number) - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamFloat
 
setValue(Class) - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamHeader
Set class.
setValue(String) - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamHeader
Set class by canonical name.
setValue(AlgorithmInformation) - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamInformation
Set algorithm information.
setValue(String) - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamInteger
Set value from string.
setValue(Number) - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamInteger
 
setValue(String) - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamLong
Set value from string.
setValue(Matrix) - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamMatrix
Set the parameter.
setValue(int, int, double) - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamMatrix
Sets the value.
setValue(Class) - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamMipavDialog
Set mipav dialog class.
setValue(T) - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamModel
Set the parameter value.
setValue(List<String>) - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamMultiOption
Set list of selected options.
setValue(Number) - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamNumber
Set the parameter.
setValue(String) - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamNumber
Set the parameter.
setValue(List) - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamNumberCollection
Set the file collection.
setValue(File) - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamObject
Set file to store object.
setValue(String) - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamObject
Set filename as string.
setValue(Integer) - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamOption
Set the selected option.
setValue(String) - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamOption
 
setValue(PerformanceSummary) - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamPerformance
Set algorithm performance.
setValue(Point3d) - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamPointDouble
Set double point value.
setValue(Point3f) - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamPointDouble
Set float point value.
setValue(Point3i) - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamPointDouble
Set integer point value.
setValue(Point3d) - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamPointFloat
Set double point value.
setValue(Point3f) - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamPointFloat
Set float point value.
setValue(Point3i) - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamPointFloat
Set integer point value.
setValue(Point3d) - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamPointInteger
Set double point value.
setValue(Point3f) - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamPointInteger
Set float point value.
setValue(Point3i) - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamPointInteger
Set integer point value.
setValue(String) - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamString
Set string.
setValue(EmbeddedSurface) - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamSurface
Set surface.
setValue(List) - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamSurfaceCollection
Set the volume collection.
setValue(String) - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamSwitch
Set switch string.
setValue(ImageData) - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamVolume
Set the value for the parameter.
setValue(File) - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamVolume
Set volume filename.
setValue(URI) - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamVolume
Set volume filename.
setValue(Object) - Method in class edu.jhu.ece.iacl.jist.pipeline.PipeChildPort
Unimplemented.
setValue(Object) - Method in class edu.jhu.ece.iacl.jist.pipeline.PipeParentPort
Unimplemented.
setValue(T) - Method in class edu.jhu.ece.iacl.jist.pipeline.PipePort
Set value for this parameter.
setValue(Object[]) - Method in class edu.jhu.ece.iacl.jist.pipeline.src.PipeDoubleCollectionListSource
Set value.
setValue(Object) - Method in class edu.jhu.ece.iacl.jist.pipeline.src.PipeDoubleListSource
Set value.
setValue(Object) - Method in class edu.jhu.ece.iacl.jist.pipeline.src.PipeFileCollectionListSource
 
setValue(Object) - Method in class edu.jhu.ece.iacl.jist.pipeline.src.PipeFileListSource
Set file value.
setValue(Object[]) - Method in class edu.jhu.ece.iacl.jist.pipeline.src.PipeIntegerCollectionListSource
Set value.
setValue(Object) - Method in class edu.jhu.ece.iacl.jist.pipeline.src.PipeIntegerListSource
Set value.
setValue(Object[]) - Method in class edu.jhu.ece.iacl.jist.pipeline.src.PipeListCollectionSource
Set list value.
setValue(Object) - Method in class edu.jhu.ece.iacl.jist.pipeline.src.PipeListSource
Set list value.
setValue(Object) - Method in class edu.jhu.ece.iacl.jist.pipeline.src.PipePointListSource
Set value.
setValue(Object) - Method in class edu.jhu.ece.iacl.jist.pipeline.src.PipeSelectionListSource
 
setValue(Object) - Method in class edu.jhu.ece.iacl.jist.pipeline.src.PipeStringListSource
 
setValue(Object) - Method in class edu.jhu.ece.iacl.jist.pipeline.src.PipeSurfaceCollectionListSource
 
setValue(Object) - Method in class edu.jhu.ece.iacl.jist.pipeline.src.PipeSurfaceListSource
Set value.
setValue(Object) - Method in class edu.jhu.ece.iacl.jist.pipeline.src.PipeVolumeCollectionListSource
 
setValue(Object) - Method in class edu.jhu.ece.iacl.jist.pipeline.src.PipeVolumeListSource
Set value.
setValue(Comparable) - Method in interface edu.jhu.ece.iacl.jist.structures.data.Indexable
Sets the value.
setValue(double) - Method in class edu.jhu.ece.iacl.jist.structures.geom.EdgeIndexed
Sets the value.
setValue(Comparable) - Method in class edu.jhu.ece.iacl.jist.structures.geom.EdgeIndexed
 
setValue(double) - Method in class edu.jhu.ece.iacl.jist.structures.geom.EmbeddedCurvePath
Sets the value.
setValue(double) - Method in class edu.jhu.ece.iacl.jist.structures.geom.PolySpline
Sets the value.
setValue(double) - Method in class edu.jhu.ece.iacl.jist.structures.geom.VertexIndexed
Sets the value.
setValue(Comparable) - Method in class edu.jhu.ece.iacl.jist.structures.geom.VertexIndexed
 
setValue(Comparable) - Method in class edu.jhu.ece.iacl.jist.structures.image.VoxelIndexed
 
setValue(Comparable) - Method in class edu.jhu.ece.iacl.jist.structures.image.VoxelMipav
 
setVectorFieldForce(ImageDataFloat) - Method in class edu.jhu.cs.cisst.vent.widgets.VisualizationActiveContour2D
Sets the vector field force.
setVerbose(boolean) - Method in class edu.jhu.bme.smile.commons.math.L1LSCompressedSensing
 
setVersion(String) - Method in class edu.jhu.ece.iacl.jist.pipeline.AlgorithmInformation
Sets the version.
setVersion(float) - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamHeader
Set MAPS version number.
setVertex(int, Tuple3f) - Method in class edu.jhu.ece.iacl.jist.structures.geom.EmbeddedSurface
Sets the vertex.
setVertexData(double[][]) - Method in class edu.jhu.ece.iacl.jist.structures.geom.EmbeddedSurface
 
setVertexData(int, double) - Method in class edu.jhu.ece.iacl.jist.structures.geom.EmbeddedSurface
 
setVertexData(int, double[]) - Method in class edu.jhu.ece.iacl.jist.structures.geom.EmbeddedSurface
 
setVertexData(int, int, double) - Method in class edu.jhu.ece.iacl.jist.structures.geom.EmbeddedSurface
 
setViewClass(Map, String) - Static method in class edu.jhu.ece.iacl.jist.pipeline.graph.PipeCellViewFactory
Sets the view class.
setVisible(boolean) - Method in class edu.jhu.cs.cisst.vent.renderer.processing.ImageRenderer
Sets the visible.
setVisible(boolean) - Method in class edu.jhu.cs.cisst.vent.renderer.processing.SurfaceRenderer
Sets the visible.
setVisible(boolean) - Method in class edu.jhu.cs.cisst.vent.renderer.processing.VectorField2DRenderer
Sets the visible.
setVisible(boolean) - Method in class edu.jhu.cs.cisst.vent.renderer.processing.VolumeSliceRenderer
Sets the visible.
setVisible(boolean) - Method in class edu.jhu.ece.iacl.jist.pipeline.view.input.ParamCollectionInputView
Set visibility of this view and its children.
setVisible(boolean) - Method in class edu.jhu.ece.iacl.jist.pipeline.view.input.ParamCollectionPipelineInputView
Set visibility for panel.
setVisible(boolean) - Method in class edu.jhu.ece.iacl.jist.pipeline.view.input.ParamCollectionWindowInputView
Set visibility for windows.
setVolume(ModelImage) - Method in class edu.jhu.ece.iacl.jist.structures.geom.MipavVOI
Sets the volume.
setW(Number) - Method in class edu.jhu.ece.iacl.jist.structures.vector.Vector2
 
setW(Number) - Method in class edu.jhu.ece.iacl.jist.structures.vector.Vector3
 
setW(Number) - Method in class edu.jhu.ece.iacl.jist.structures.vector.Vector4
 
setW(Number) - Method in class edu.jhu.ece.iacl.jist.structures.vector.VectorN
 
setW(Number) - Method in interface edu.jhu.ece.iacl.jist.structures.vector.VectorX
Sets the w.
setWebsite(String) - Method in class edu.jhu.ece.iacl.jist.pipeline.AlgorithmInformation.AlgorithmAuthor
Sets the website.
setWebsite(String) - Method in class edu.jhu.ece.iacl.jist.pipeline.AlgorithmInformation
Sets the website.
setWeight(double) - Method in class edu.jhu.cs.cisst.algorithms.segmentation.gac.ActiveContourForce2D
Sets the weight.
setWeight(T) - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamWeightedVolume
Set weight.
setWeight(int, T) - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamWeightedVolumeCollection
Set the volume weight for the specified volume index.
setWinding(IsoContourGenerator.Winding) - Method in class edu.jhu.cs.cisst.algorithms.geometry.surface.IsoContourGenerator
Sets the winding.
setWinding(IsoSurfaceGenerator.Winding) - Method in class edu.jhu.cs.cisst.algorithms.geometry.surface.IsoSurfaceGenerator
Sets the winding order.
setX(Number) - Method in class edu.jhu.ece.iacl.jist.structures.vector.Vector2
 
setX(Number) - Method in class edu.jhu.ece.iacl.jist.structures.vector.Vector3
 
setX(Number) - Method in class edu.jhu.ece.iacl.jist.structures.vector.Vector4
 
setX(Number) - Method in class edu.jhu.ece.iacl.jist.structures.vector.VectorN
 
setX(Number) - Method in interface edu.jhu.ece.iacl.jist.structures.vector.VectorX
Sets the x.
setXMLValue(String) - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamArgsOrder
 
setXMLValue(String) - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamBoolean
 
setXMLValue(String) - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamCollection
 
setXMLValue(String) - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamColor
 
setXMLValue(String) - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamDouble
 
setXMLValue(String) - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamFile
 
setXMLValue(String) - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamFileCollection
 
setXMLValue(String) - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamFloat
 
setXMLValue(String) - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamHeader
 
setXMLValue(String) - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamInformation
 
setXMLValue(String) - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamInteger
 
setXMLValue(String) - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamLong
 
setXMLValue(String) - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamMatrix
 
setXMLValue(String) - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamMipavDialog
 
setXMLValue(String) - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamModel
 
setXMLValue(String) - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamMultiOption
 
setXMLValue(String) - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamNumberCollection
 
setXMLValue(String) - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamOption
 
setXMLValue(String) - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamPerformance
 
setXMLValue(String) - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamPointDouble
 
setXMLValue(String) - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamPointFloat
 
setXMLValue(String) - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamPointInteger
 
setXMLValue(String) - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamString
 
setXMLValue(String) - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamSwitch
 
setXMLValue(String) - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamWeightedVolume
 
setXMLValue(String) - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamWeightedVolumeCollection
 
setY(Number) - Method in class edu.jhu.ece.iacl.jist.structures.vector.Vector2
 
setY(Number) - Method in class edu.jhu.ece.iacl.jist.structures.vector.Vector3
 
setY(Number) - Method in class edu.jhu.ece.iacl.jist.structures.vector.Vector4
 
setY(Number) - Method in class edu.jhu.ece.iacl.jist.structures.vector.VectorN
 
setY(Number) - Method in interface edu.jhu.ece.iacl.jist.structures.vector.VectorX
Sets the y.
setZ(Number) - Method in class edu.jhu.ece.iacl.jist.structures.vector.Vector2
 
setZ(Number) - Method in class edu.jhu.ece.iacl.jist.structures.vector.Vector3
 
setZ(Number) - Method in class edu.jhu.ece.iacl.jist.structures.vector.Vector4
 
setZ(Number) - Method in class edu.jhu.ece.iacl.jist.structures.vector.VectorN
 
setZ(Number) - Method in interface edu.jhu.ece.iacl.jist.structures.vector.VectorX
Sets the z.
SEVERE - Static variable in class edu.jhu.ece.iacl.jist.utility.JistLogger
 
SFunc - Class in edu.jhu.bme.smile.commons.math.specialFunctions
 
SFunc() - Constructor for class edu.jhu.bme.smile.commons.math.specialFunctions.SFunc
 
SHFT(float[], float[], float[], float[]) - Method in class edu.jhu.ece.iacl.algorithms.vabra.NumericalRecipes
 
SHFT(double[], double[], double[], double[]) - Method in class edu.jhu.ece.iacl.algorithms.vabra.NumericalRecipes
 
shortLabel - Variable in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamModel
The shortLabel --- "command line flag"
shortValue() - Method in class edu.jhu.ece.iacl.jist.structures.image.Voxel
 
shouldSelectCell(EventObject) - Method in class edu.jhu.ece.iacl.jist.pipeline.graph.PipeEdgeRealEditor.EditorDelegate
Returns true to indicate that the editing cell may be selected.
shouldSelectCell(EventObject) - Method in class edu.jhu.ece.iacl.jist.pipeline.graph.PipeEdgeRealEditor
Forwards the message from the CellEditor to the delegate.
showAxes - Variable in class edu.jhu.cs.cisst.vent.widgets.VisualizationTriangleMesh
The show axes.
showAxesParam - Variable in class edu.jhu.cs.cisst.vent.widgets.VisualizationTriangleMesh
The show axes param.
showContourParam - Variable in class edu.jhu.cs.cisst.vent.renderer.processing.VolumeIsoContourRenderer
The show contour parameter.
showDialog(Component, JistPreferences) - Static method in class edu.jhu.ece.iacl.jist.pipeline.gui.GlobalPreferencePanel
Show dialog.
showDialog(Component, PipeLayout) - Static method in class edu.jhu.ece.iacl.jist.pipeline.gui.LayoutPreferencePanel
Show dialog.
showDialog() - Static method in class license.JISTLicenseAbout
Create the GUI and show it.
showHelp() - Method in class edu.jhu.ece.iacl.jist.cli.JistCLI
 
showSliceNumber - Variable in class edu.jhu.cs.cisst.vent.renderer.processing.VolumeSliceRenderer
The show slice number.
showSliceNumberParam - Variable in class edu.jhu.cs.cisst.vent.renderer.processing.VolumeSliceRenderer
The show slice number param.
showToggle - Variable in class edu.jhu.ece.iacl.jist.pipeline.view.input.ParamCollectionPipelineInputView
show toggle button.
shrinkWrapRemeshing - Static variable in class edu.jhu.ece.iacl.algorithms.ReferencedPapers
 
sigma - Variable in class edu.jhu.ece.iacl.algorithms.manual_label.staple.STAPLEgeneral
 
sign(float) - Static method in class edu.jhmi.rad.medic.utilities.NumericsPublic
 
sign(double) - Static method in class edu.jhmi.rad.medic.utilities.NumericsPublic
 
SIGN(float, float) - Method in class edu.jhu.ece.iacl.algorithms.vabra.NumericalRecipes
 
SIGN(double, double) - Method in class edu.jhu.ece.iacl.algorithms.vabra.NumericalRecipes
 
signed2unsigned(byte) - Method in class edu.jhu.ece.iacl.algorithms.dti.tractography.FACT.USbyte
 
signed2unsigned(byte) - Method in class edu.jhu.ece.iacl.jist.structures.image.USbyte
Signed2unsigned.
SImageTractAnalysis - Class in edu.jhu.ece.iacl.plugins.dti.tractography
 
SImageTractAnalysis() - Constructor for class edu.jhu.ece.iacl.plugins.dti.tractography.SImageTractAnalysis
 
SimFramework - Class in edu.jhu.ece.iacl.pami
 
SimFramework() - Constructor for class edu.jhu.ece.iacl.pami.SimFramework
 
simplifyPath(Vector<Point2D>, int) - Method in class edu.jhu.ece.iacl.jist.pipeline.graph.AvoidanceRouting
The avoidance path may have lots of unnecessary bends in it.
size() - Method in class edu.jhu.cs.cisst.algorithms.optimize.fmg.util.IntRange1D
return the number of integer values lying in the range.
size() - Method in interface edu.jhu.ece.iacl.jist.pipeline.parameter.ObjectCollection
Returns size of collection.
size() - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamCollection
Get size of collection.
size() - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamFileCollection
 
size() - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamNumberCollection
 
size() - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamSurfaceCollection
 
size() - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamVolumeCollection
Get size of volume collection.
size() - Method in class edu.jhu.ece.iacl.jist.pipeline.PipeAlgorithmGroup
Returns size of collection.
size() - Method in class edu.jhu.ece.iacl.jist.structures.data.BinaryMinFastHeap
Returns size.
size() - Method in class edu.jhu.ece.iacl.jist.structures.data.BinaryMinHeap
Returns size.
size() - Method in class edu.jhu.ece.iacl.jist.structures.vector.Vector2
 
size() - Method in class edu.jhu.ece.iacl.jist.structures.vector.Vector3
 
size() - Method in class edu.jhu.ece.iacl.jist.structures.vector.Vector4
 
size() - Method in class edu.jhu.ece.iacl.jist.structures.vector.VectorN
 
size() - Method in interface edu.jhu.ece.iacl.jist.structures.vector.VectorX
Size.
slerp(Tuple3f, Tuple3f, double) - Static method in class edu.jhu.ece.iacl.jist.algorithms.graphics.GeomUtil
Slerp.
slerp(Tuple2d, Tuple2d, double) - Static method in class edu.jhu.ece.iacl.jist.algorithms.graphics.GeomUtil
Slerp.
slice - Variable in class edu.jhu.cs.cisst.algorithms.geometry.surface.IsoContourGenerator
The slice.
slice - Variable in class edu.jhu.cs.cisst.vent.renderer.processing.VolumeSliceRenderer
The slice.
slice_ori - Variable in class edu.jhu.ece.iacl.jist.structures.fiber.DTIStudioHDR
The slice_ori.
slice_orient - Variable in class edu.jhu.ece.iacl.algorithms.dti.GTCparams
 
slice_seq - Variable in class edu.jhu.ece.iacl.jist.structures.fiber.DTIStudioHDR
The slice_seq.
sliceAng - Variable in class edu.jhu.ece.iacl.algorithms.dti.GTCparams
 
sliceParam - Variable in class edu.jhu.cs.cisst.vent.renderer.processing.VolumeSliceRenderer
The slice param.
slicerXMLaddParam(ParamModel, boolean) - Method in class edu.jhu.ece.iacl.jist.cli.JistCLI
 
slicerXMLaddParamCollection(ParamCollection, boolean) - Method in class edu.jhu.ece.iacl.jist.cli.JistCLI
 
slicerXMLparseCollection(ParamCollection, boolean) - Method in class edu.jhu.ece.iacl.jist.cli.JistCLI
 
slices - Variable in class edu.jhmi.rad.medic.utilities.CropParameters
The slices.
slices - Variable in class edu.jhu.cs.cisst.algorithms.geometry.surface.IsoSurfaceGenerator
The slices.
slices - Variable in class edu.jhu.cs.cisst.vent.renderer.processing.VolumeSliceRenderer
The slices.
slices - Variable in class edu.jhu.ece.iacl.algorithms.manual_label.staple.STAPLEmulti
 
slices - Variable in class edu.jhu.ece.iacl.algorithms.manual_label.staple.STAPLEmulti2
 
slices - Variable in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamVolume
The slices.
slices - Variable in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamVolumeCollection
The slices.
slices - Variable in class edu.jhu.ece.iacl.jist.structures.image.ImageData
The slices.
sliceThickness - Variable in class edu.jhu.ece.iacl.jist.structures.image.ImageHeader
The slice thickness.
smFontSize - Static variable in class edu.jhu.ece.iacl.jist.pipeline.JistPreferences
 
smooth(ConstBoundaryGrid, ConstNoBoundaryGrid) - Method in class edu.jhu.cs.cisst.algorithms.optimize.fmg.smoother.DampedJacobi
implements method from Smoother.
smooth(ConstBoundaryGrid, ConstNoBoundaryGrid) - Method in class edu.jhu.cs.cisst.algorithms.optimize.fmg.smoother.RedBlackGaussSeidel
implements method from Smoother.
smooth(ConstBoundaryGrid, ConstNoBoundaryGrid) - Method in interface edu.jhu.cs.cisst.algorithms.optimize.fmg.smoother.Smoother
smooth an approximate solution to a linear elliptic PDE on a regular cubic grid in 3D.
Smoother - Interface in edu.jhu.cs.cisst.algorithms.optimize.fmg.smoother
This interface defines the smooth() method which is used for smoothing the approximate solution of a linear elliptic partial differential equation (PDE) on a regular cubic grid in 3D before and/or after going to the next coarser grid in the Multigrid (MG) algorithm.
smoothIterations - Variable in class edu.jhu.cs.cisst.algorithms.segmentation.gac.GradientVectorFlow2D
The smooth iterations.
snehashisRoy - Static variable in class edu.jhu.ece.iacl.algorithms.CommonAuthors
 
softThresholdArcTan(float[][], double) - Static method in class edu.jhu.cs.cisst.algorithms.util.DataOperations
Soft threshold arc tan.
softThresholdSigmoid(float[][], double) - Static method in class edu.jhu.cs.cisst.algorithms.util.DataOperations
Soft threshold sigmoid.
softThresholdSin(float[][], double) - Static method in class edu.jhu.cs.cisst.algorithms.util.DataOperations
Soft threshold sin.
solve(float[][]) - Method in class edu.jhu.bme.smile.commons.math.HistogramGenerator
 
solve(double[][]) - Method in class edu.jhu.bme.smile.commons.math.HistogramGenerator
 
solve(ImageData) - Method in class edu.jhu.bme.smile.commons.math.HistogramGenerator
 
solve(double[], double) - Method in class edu.jhu.bme.smile.commons.math.L1LSCompressedSensing
 
solve(double[], double, double) - Method in class edu.jhu.bme.smile.commons.math.L1LSCompressedSensing
 
solve(double[], double, double, double) - Method in class edu.jhu.bme.smile.commons.math.L1LSCompressedSensing
 
solve(double[], double, double, double, boolean) - Method in class edu.jhu.bme.smile.commons.math.L1LSCompressedSensing
 
solve(Matrix, double) - Method in class edu.jhu.bme.smile.commons.math.L1LSCompressedSensing
 
solve(Matrix, double, double, double, boolean) - Method in class edu.jhu.bme.smile.commons.math.L1LSCompressedSensing
 
solve(Matrix, double, double, double, boolean) - Method in class edu.jhu.bme.smile.commons.math.L1LSCompressedSensingNonNeg
 
solve(Matrix, double, double, double, boolean) - Method in class edu.jhu.bme.smile.commons.math.L1LSCompressedSensingUnconstrained
 
solve(ImageDataFloat, float) - Method in class edu.jhu.cs.cisst.algorithms.geometry.surface.IsoContourGenerator
Solve for iso-contour.
solve(ImageDataFloat, float, int, int) - Method in class edu.jhu.cs.cisst.algorithms.geometry.surface.IsoContourGenerator
Solve for iso-contour.
solve(ImageDataFloat, float) - Method in class edu.jhu.cs.cisst.algorithms.geometry.surface.IsoSurfaceGenerator
Solve for iso-surface
solve(int, int, int, int) - Method in class edu.jhu.cs.cisst.algorithms.optimize.fmg.FMG
the body fo the FMG Algorithm that executes in its own thread.
solve(ConstBoundaryGrid, ConstNoBoundaryGrid) - Method in interface edu.jhu.cs.cisst.algorithms.optimize.fmg.pde.PDE
Solve PDE directly at coarsest grid level.
solve(ConstBoundaryGrid, ConstNoBoundaryGrid) - Method in class edu.jhu.cs.cisst.algorithms.optimize.fmg.solver.ArithmeticSolver
Solves pde at coarsest grid level.
solve(ConstBoundaryGrid, ConstNoBoundaryGrid) - Method in interface edu.jhu.cs.cisst.algorithms.optimize.fmg.solver.Solver
exactly solve a linear elliptic PDE on a regular cubic grid in 3D given an approximation to the solution and the right hand side (source term) of the PDE If Ax = f defines the PDE, this method solves for the true solution x given an approximation u of x and the right hand side f.
solve(ConstBoundaryGrid, ConstNoBoundaryGrid) - Method in class edu.jhu.cs.cisst.algorithms.optimize.fmg.solver.SolverThroughSmoother
implements method from Solver.
solve(ImageDataFloat, double) - Method in class edu.jhu.cs.cisst.algorithms.segmentation.gac.DistanceField2D
Solve.
solve(ImageDataFloat) - Method in class edu.jhu.cs.cisst.algorithms.segmentation.gac.GeodesicActiveContour2D
Solve.
solve(ImageDataFloat, GradientVectorFlow2D.Method) - Method in class edu.jhu.cs.cisst.algorithms.segmentation.gac.GradientVectorFlow2D
Solve using either multigrid or a sparse matrix method.
solve(ConstBoundaryGrid, ConstNoBoundaryGrid) - Method in class edu.jhu.cs.cisst.algorithms.segmentation.gac.VectorFieldDiffusion2D
 
solve() - Method in class edu.jhu.ece.iacl.algorithms.dti.tractography.FiberTracker
 
solve(Point3i) - Method in class edu.jhu.ece.iacl.algorithms.dti.tractography.FiberTracker
 
solve() - Method in class edu.jhu.ece.iacl.algorithms.dti.tractography.WildBootFiberTracker
 
solve(ImageData, int, float) - Method in class edu.jhu.ece.iacl.algorithms.manual_label.FastMarchingLabelExtension
 
solve(List<ImageData>, List<Number>, List<ImageData>, List<Number>, File) - Method in class edu.jhu.ece.iacl.algorithms.vabra.VabraAlgorithm
 
solve(List<ImageData>, List<Number>, List<ImageData>, List<Number>, File, float, float, int, int[]) - Method in class edu.jhu.ece.iacl.algorithms.vabra.VabraAlgorithm
 
solve(ImageDataFloat, double) - Method in class edu.jhu.ece.iacl.algorithms.volume.DistanceField
 
SOLVED - Static variable in class edu.jhu.ece.iacl.algorithms.manual_label.FastMarchingLabelExtension
 
solveLinear(ImageDataFloat, GradientVectorFlow2D.Method) - Method in class edu.jhu.cs.cisst.algorithms.segmentation.gac.GradientVectorFlow2D
Solve using a sparse matrix method.
solveMultiGrid(ImageDataFloat) - Method in class edu.jhu.cs.cisst.algorithms.segmentation.gac.GradientVectorFlow2D
Solve using multi-grid.
solveParallel(int, int, int, int) - Method in class edu.jhu.cs.cisst.algorithms.optimize.fmg.FMG
starts the FMG Algorithm with the given parameters in a separate thread and returns immediately.
solveProper(ConstBoundaryGrid, ConstBoundaryGrid, int, int) - Method in class edu.jhu.cs.cisst.algorithms.optimize.fmg.solver.SolverThroughSmoother
implements the parallel part of solve().
Solver - Interface in edu.jhu.cs.cisst.algorithms.optimize.fmg.solver
The interface to objects that exactly solve a linear elliptic partial differential equation (PDE) on a regular cubic grid in 3D.
SolverResolutionLevels - Interface in edu.jhu.cs.cisst.algorithms.optimize.fmg
The Interface SolverResolutionLevels.
SolverThroughSmoother - Class in edu.jhu.cs.cisst.algorithms.optimize.fmg.solver
Solve a PDE by iteratively applying a smoothing (i.e.
SolverThroughSmoother(Smoother, double) - Constructor for class edu.jhu.cs.cisst.algorithms.optimize.fmg.solver.SolverThroughSmoother
construct from smoother and allowed error.
SolveThroughSmootherParallelizer - Class in edu.jhu.cs.cisst.algorithms.optimize.fmg.solver
A helper class of class SolverThroughSmoother that helps parallelizing method SolverThroughSmoother.solve().
SolveThroughSmootherParallelizer(SolverThroughSmoother, ConstBoundaryGrid, ConstBoundaryGrid) - Constructor for class edu.jhu.cs.cisst.algorithms.optimize.fmg.solver.SolveThroughSmootherParallelizer
construct.
solveVerbose(ImageDataFloat) - Method in class edu.jhu.cs.cisst.algorithms.segmentation.gac.GeodesicActiveContour2D
Solve and generate verbose output.
sort_image - Variable in class edu.jhu.ece.iacl.algorithms.dti.GTCparams
 
source - Variable in class edu.jhu.ece.iacl.plugins.utilities.volume.MedicAlgorithmMipavReorient
 
spectre - Static variable in class edu.jhu.ece.iacl.algorithms.ReferencedPapers
 
sphereToStereo(Tuple3f) - Static method in class edu.jhu.ece.iacl.jist.algorithms.graphics.GeomUtil
Sphere to stereo.
sphericalAngle(Vector3d, Vector3d, Vector3d) - Static method in class edu.jhu.ece.iacl.jist.algorithms.graphics.GeomUtil
Spherical angle.
sphericalAngle(Vector3f, Vector3f, Vector3f) - Static method in class edu.jhu.ece.iacl.jist.algorithms.graphics.GeomUtil
Spherical angle.
SphericalHarmonicRepresentation - Class in edu.jhu.bme.smile.commons.math.specialFunctions
 
SphericalHarmonicRepresentation(SphericalHarmonics, ComplexMatrix) - Constructor for class edu.jhu.bme.smile.commons.math.specialFunctions.SphericalHarmonicRepresentation
 
SphericalHarmonics - Class in edu.jhu.bme.smile.commons.math.specialFunctions
 
SphericalHarmonics() - Constructor for class edu.jhu.bme.smile.commons.math.specialFunctions.SphericalHarmonics
 
sphericalParameterizationAndRemeshing - Static variable in class edu.jhu.ece.iacl.algorithms.ReferencedPapers
 
Spline - Class in edu.jhu.bme.smile.commons.math
 
Spline(double[], double[]) - Constructor for class edu.jhu.bme.smile.commons.math.Spline
 
spline_value(double) - Method in class edu.jhu.bme.smile.commons.math.Spline
 
sqrdistance(XYZ) - Method in class edu.jhu.ece.iacl.jist.structures.geom.GridPt
Sqrdistance.
sqrdistance(double, double, double, double, double, double) - Static method in class edu.jhu.ece.iacl.jist.structures.geom.GridPt
Sqrdistance.
square(double) - Static method in class edu.jhu.bme.smile.commons.math.StatisticsDouble
 
src - Variable in class edu.jhu.ece.iacl.jist.pipeline.PipeConnector
source port.
srcIndex - Variable in class edu.jhu.ece.iacl.jist.pipeline.PipeConnector
index into source if port can accept multiple connections.
srcRoots - Variable in class edu.jhu.ece.iacl.jist.pipeline.PipeScheduler
List of all source roots.
stampUUID() - Method in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamHeader
 
STAPLE - Class in edu.jhu.ece.iacl.algorithms.manual_label.staple
 
STAPLE() - Constructor for class edu.jhu.ece.iacl.algorithms.manual_label.staple.STAPLE
 
STAPLE(int[][][][]) - Constructor for class edu.jhu.ece.iacl.algorithms.manual_label.staple.STAPLE
 
STAPLE(String[], int[]) - Constructor for class edu.jhu.ece.iacl.algorithms.manual_label.staple.STAPLE
 
STAPLE(List<ImageData>) - Constructor for class edu.jhu.ece.iacl.algorithms.manual_label.staple.STAPLE
 
STAPLEgeneral - Class in edu.jhu.ece.iacl.algorithms.manual_label.staple
 
STAPLEgeneral() - Constructor for class edu.jhu.ece.iacl.algorithms.manual_label.staple.STAPLEgeneral
 
STAPLEgeneral(ArrayList<double[][]>) - Constructor for class edu.jhu.ece.iacl.algorithms.manual_label.staple.STAPLEgeneral
 
STAPLEgeneral(ArrayList<double[][]>, int) - Constructor for class edu.jhu.ece.iacl.algorithms.manual_label.staple.STAPLEgeneral
 
STAPLEgeneralSingle - Class in edu.jhu.ece.iacl.algorithms.manual_label.staple
 
STAPLEgeneralSingle() - Constructor for class edu.jhu.ece.iacl.algorithms.manual_label.staple.STAPLEgeneralSingle
 
STAPLEgeneralSingle(List<double[][]>) - Constructor for class edu.jhu.ece.iacl.algorithms.manual_label.staple.STAPLEgeneralSingle
 
STAPLEmulti - Class in edu.jhu.ece.iacl.algorithms.manual_label.staple
 
STAPLEmulti() - Constructor for class edu.jhu.ece.iacl.algorithms.manual_label.staple.STAPLEmulti
 
STAPLEmulti(int[][][][]) - Constructor for class edu.jhu.ece.iacl.algorithms.manual_label.staple.STAPLEmulti
 
STAPLEmulti(float[][][][]) - Constructor for class edu.jhu.ece.iacl.algorithms.manual_label.staple.STAPLEmulti
 
STAPLEmulti(List<ImageData>) - Constructor for class edu.jhu.ece.iacl.algorithms.manual_label.staple.STAPLEmulti
 
STAPLEmulti2 - Class in edu.jhu.ece.iacl.algorithms.manual_label.staple
 
STAPLEmulti2() - Constructor for class edu.jhu.ece.iacl.algorithms.manual_label.staple.STAPLEmulti2
 
STAPLEmulti2(int[][][][]) - Constructor for class edu.jhu.ece.iacl.algorithms.manual_label.staple.STAPLEmulti2
 
STAPLEmulti2(float[][][][]) - Constructor for class edu.jhu.ece.iacl.algorithms.manual_label.staple.STAPLEmulti2
 
StaplePlugin - Class in edu.jhu.ece.iacl.algorithms.manual_label.staple
 
StaplePlugin() - Constructor for class edu.jhu.ece.iacl.algorithms.manual_label.staple.StaplePlugin
 
StapleReader - Class in edu.jhu.ece.iacl.algorithms.manual_label.staple
 
StapleReader() - Constructor for class edu.jhu.ece.iacl.algorithms.manual_label.staple.StapleReader
 
STAPLEsingle - Class in edu.jhu.ece.iacl.algorithms.manual_label.staple
 
STAPLEsingle() - Constructor for class edu.jhu.ece.iacl.algorithms.manual_label.staple.STAPLEsingle
 
STAPLEsingle(int[][][][]) - Constructor for class edu.jhu.ece.iacl.algorithms.manual_label.staple.STAPLEsingle
 
STAPLEsingle(String[], int[]) - Constructor for class edu.jhu.ece.iacl.algorithms.manual_label.staple.STAPLEsingle
 
STAPLEsingle(List<ImageData>) - Constructor for class edu.jhu.ece.iacl.algorithms.manual_label.staple.STAPLEsingle
 
STAPLEsurf - Class in edu.jhu.ece.iacl.algorithms.manual_label.staple
 
STAPLEsurf() - Constructor for class edu.jhu.ece.iacl.algorithms.manual_label.staple.STAPLEsurf
 
STAPLEsurf(List<EmbeddedSurface>) - Constructor for class edu.jhu.ece.iacl.algorithms.manual_label.staple.STAPLEsurf
 
STAPLEsurf(List<EmbeddedSurface>, int) - Constructor for class edu.jhu.ece.iacl.algorithms.manual_label.staple.STAPLEsurf
 
StapleTester - Class in edu.jhu.ece.iacl.algorithms.manual_label.staple
 
StapleTester() - Constructor for class edu.jhu.ece.iacl.algorithms.manual_label.staple.StapleTester
 
start() - Method in class edu.jhu.cs.cisst.algorithms.optimize.fmg.parallel.Parallelizer
start the Parallelizer by creating the requested number of threads, calling the runParallel() method of the target object (of type Parallelizable) in each thread and waiting for all threads to finish before returning.
start() - Method in class edu.jhu.ece.iacl.jist.pipeline.CalculationMonitor
Start calculation monitor.
start() - Method in class edu.jhu.ece.iacl.jist.pipeline.ExecutionContext
Start running the algorithm.
start - Variable in class edu.jhu.ece.iacl.jist.pipeline.graph.PipeMarqueeHandler
The current.
start - Variable in class edu.jhu.ece.iacl.jist.pipeline.PerformanceSummary.TimeAndMemoryStamp
The cpu start time.
start() - Method in class edu.jhu.ece.iacl.jist.pipeline.PipeScheduler
Start scheduler thread.
start() - Method in class edu.jhu.ece.iacl.jist.pipeline.ProcessingDialog
Start dialog with input parameters from algorithm.
start - Variable in class edu.jhu.ece.iacl.jist.pipeline.src.PipeDoubleSweepSource
The start.
start - Variable in class edu.jhu.ece.iacl.jist.pipeline.src.PipeIntegerSweepSource
The start.
start - Variable in class edu.jhu.ece.iacl.jist.pipeline.src.PipePointDoubleSweepSource
The start.
start - Variable in class edu.jhu.ece.iacl.jist.pipeline.src.PipeToggleSource
The start.
start() - Method in class edu.jhu.ece.iacl.jist.pipeline.view.input.Refresher
Start refresher.
startCellEditing(EventObject) - Method in class edu.jhu.ece.iacl.jist.pipeline.graph.PipeEdgeRealEditor.EditorDelegate
Returns true to indicate that editing has begun.
startElement(String, String, String, Attributes) - Method in class edu.jhu.ece.iacl.algorithms.vabra.VabraConfiguration
 
startEntry - Variable in class edu.jhu.ece.iacl.jist.pipeline.src.PipeListCollectionSource
The start entry.
startEntry - Variable in class edu.jhu.ece.iacl.jist.pipeline.src.PipeListSource
The start entry.
startFA - Variable in class edu.jhu.ece.iacl.algorithms.dti.tractography.FACT.FACTparameters
 
startFA - Variable in class edu.jhu.ece.iacl.algorithms.dti.tractography.FiberTracker
 
startFA - Variable in class edu.jhu.ece.iacl.algorithms.dti.tractography.WildBootFiberTracker
 
StartJIST - Class in <Unnamed>
The Class StartJIST.
StartJIST() - Constructor for class StartJIST
 
StartJISTLayoutTool - Class in <Unnamed>
The Class StartJISTLayoutTool.
StartJISTLayoutTool() - Constructor for class StartJISTLayoutTool
 
StartJISTPlugInSelector - Class in <Unnamed>
 
StartJISTPlugInSelector() - Constructor for class StartJISTPlugInSelector
 
StartJISTProcessManager - Class in <Unnamed>
The Class StartJISTProcessManager.
StartJISTProcessManager() - Constructor for class StartJISTProcessManager
 
startParam - Variable in class edu.jhu.ece.iacl.jist.pipeline.src.PipeDoubleSweepSource
The val param.
startParam - Variable in class edu.jhu.ece.iacl.jist.pipeline.src.PipeIntegerSweepSource
The val param.
startParam - Variable in class edu.jhu.ece.iacl.jist.pipeline.src.PipePointDoubleSweepSource
The val param.
startTime - Variable in class edu.jhu.ece.iacl.doc.DocumentAllTests.TestCase
 
stateChanged(ChangeEvent) - Method in class edu.jhu.ece.iacl.jist.pipeline.graph.PipeEdgeRealEditor.EditorDelegate
 
stateChanged(ChangeEvent) - Method in class edu.jhu.ece.iacl.jist.pipeline.gui.ConnectionEditor
Index selection has changed.
stateChanged(ChangeEvent) - Method in class edu.jhu.ece.iacl.jist.pipeline.gui.ConnectorRenderer
 
stateChanged(ChangeEvent) - Method in class edu.jhu.ece.iacl.jist.pipeline.gui.ParameterPanel
Remember last panel selection.
stateChanged(ChangeEvent) - Method in class edu.jhu.ece.iacl.jist.pipeline.view.input.ParamBooleanInputView
Update parameter with checkbox value.
stateChanged(ChangeEvent) - Method in class edu.jhu.ece.iacl.jist.pipeline.view.input.ParamCollectionInputView
The selected tab pane has changed so notify observers.
stateChanged(ChangeEvent) - Method in class edu.jhu.ece.iacl.jist.pipeline.view.input.ParamCollectionPipelineInputView
The selected tab pane has changed so notify observers.
stateChanged(ChangeEvent) - Method in class edu.jhu.ece.iacl.jist.pipeline.view.input.ParamColorInputView
State changed.
stateChanged(ChangeEvent) - Method in class edu.jhu.ece.iacl.jist.pipeline.view.input.ParamDoubleSliderInputView
The slider value has changed.
stateChanged(ChangeEvent) - Method in class edu.jhu.ece.iacl.jist.pipeline.view.input.ParamNumberSliderInputView
The slider value has changed.
stateChanged(ChangeEvent) - Method in class edu.jhu.ece.iacl.jist.pipeline.view.input.ParamNumberSpinnerInputView
The spinner value has changed.
stateChanged(ChangeEvent) - Method in class edu.jhu.ece.iacl.jist.pipeline.view.input.ParamPointSpinnerInputView
 
StatisticsDouble - Class in edu.jhu.bme.smile.commons.math
 
StatisticsDouble() - Constructor for class edu.jhu.bme.smile.commons.math.StatisticsDouble
 
status - Variable in class edu.jhu.ece.iacl.doc.DocumentAllTests.TestCase
 
statusBar - Variable in class edu.jhu.ece.iacl.jist.pipeline.ExecutionContext
progress bar to monitor execution status.
statusConverged - Variable in class edu.jhu.bme.smile.commons.math.L1LSCompressedSensing
 
statusMessage() - Method in class edu.jhu.bme.smile.commons.optimize.BrentMethod1D
Gets the status message from the optimizing process
statusMessage() - Method in class edu.jhu.bme.smile.commons.optimize.DownhillSimplexND
Gets the status message from the optimizing process
statusMessage() - Method in class edu.jhu.bme.smile.commons.optimize.GoldenSectionSearch1D
Gets the status message from the optimizing process
statusMessage() - Method in class edu.jhu.bme.smile.commons.optimize.LevenbergMarquardt
Gets the status message.
statusMessage() - Method in class edu.jhu.bme.smile.commons.optimize.LineSearchND
Gets the status message from the optimizing process
statusMessage() - Method in class edu.jhu.bme.smile.commons.optimize.LineSearchNDDifferentiable
Gets the status message from the optimizing process
statusMessage() - Method in class edu.jhu.bme.smile.commons.optimize.NewtonMethod1D
Gets the status message from the optimizing process
statusMessage() - Method in interface edu.jhu.bme.smile.commons.optimize.Optimizer1DContinuous
Gets any status message.
statusMessage() - Method in interface edu.jhu.bme.smile.commons.optimize.Optimizer1DContinuousDifferentiable
Gets any status message.
statusMessage() - Method in interface edu.jhu.bme.smile.commons.optimize.OptimizerNDContinuous
Gets any status message.
statusMessage() - Method in interface edu.jhu.bme.smile.commons.optimize.OptimizerNDContinuousDifferentiable
Gets any status message.
std(double[]) - Static method in class edu.jhu.bme.smile.commons.math.StatisticsDouble
 
stdDeviation - Variable in class edu.jhu.cs.cisst.algorithms.segmentation.gac.GradientVectorFlow2D
The std.
Stencil - Interface in edu.jhu.cs.cisst.algorithms.optimize.fmg
A Stencil contains 27 doubles and can be used to represent the relationship between a grid element and its 26 nearest neighbours in 3D.
StencilImpl - Class in edu.jhu.cs.cisst.algorithms.optimize.fmg
A concrete implementation of interface Stencil.
StencilImpl(double[][][]) - Constructor for class edu.jhu.cs.cisst.algorithms.optimize.fmg.StencilImpl
construct from the 27 double values in an array.
StencilImpl(double, double, double, double, double, double, double, double, double, double, double, double, double, double, double, double, double, double, double, double, double, double, double, double, double, double, double) - Constructor for class edu.jhu.cs.cisst.algorithms.optimize.fmg.StencilImpl
construct from the 27 double values.
Step() - Method in class edu.jhu.ece.iacl.algorithms.manual_label.staple.STAPLEmulti2
 
stepSize - Static variable in class edu.jhu.ece.iacl.algorithms.dti.tractography.FiberTracker
 
stepSize - Static variable in class edu.jhu.ece.iacl.algorithms.dti.tractography.WildBootFiberTracker
 
stereoToSphere(Tuple2d) - Static method in class edu.jhu.ece.iacl.jist.algorithms.graphics.GeomUtil
Stereo to sphere.
stop() - Method in class edu.jhu.ece.iacl.jist.pipeline.CalculationMonitor
Stop progress monitoring.
stop() - Method in class edu.jhu.ece.iacl.jist.pipeline.ExecutionContext
Force algorithm to stop running.
stop - Variable in class edu.jhu.ece.iacl.jist.pipeline.gui.ProcessInfoPanel
The restart.
stop - Variable in class edu.jhu.ece.iacl.jist.pipeline.gui.ProcessManagerTable
The debug.
stop - Variable in class edu.jhu.ece.iacl.jist.pipeline.PerformanceSummary.TimeAndMemoryStamp
The cpu stop time.
stop() - Method in class edu.jhu.ece.iacl.jist.pipeline.PipeScheduler
Stop scheduler thread.
stop(Vector<ExecutionContext>) - Method in class edu.jhu.ece.iacl.jist.pipeline.PipeScheduler
Stop running specified contexts.
stop() - Method in class edu.jhu.ece.iacl.jist.pipeline.view.input.Refresher
Force refresher to stop prematurely.
stopAll() - Method in class edu.jhu.ece.iacl.jist.pipeline.view.input.Refresher
Stop refresher.
stopCellEditing() - Method in class edu.jhu.ece.iacl.jist.pipeline.graph.PipeEdgeRealEditor.EditorDelegate
Stops editing and returns true to indicate that editing has stopped.
stopCellEditing() - Method in class edu.jhu.ece.iacl.jist.pipeline.graph.PipeEdgeRealEditor
Forwards the message from the CellEditor to the delegate.
stopFA - Variable in class edu.jhu.ece.iacl.algorithms.dti.tractography.FACT.FACTparameters
 
stopFA - Variable in class edu.jhu.ece.iacl.algorithms.dti.tractography.FiberTracker
 
stopFA - Variable in class edu.jhu.ece.iacl.algorithms.dti.tractography.WildBootFiberTracker
 
stopParsing() - Method in class edu.jhu.ece.iacl.jist.pipeline.ExecutionContext.ProcessStatusParser
Stop parsing.
stopped - Variable in class edu.jhu.ece.iacl.jist.pipeline.PipeScheduler
Flag indicating a request to stop the running process.
stopTime - Variable in class edu.jhu.ece.iacl.doc.DocumentAllTests.TestCase
 
storeParamsFromGUI() - Method in class edu.jhu.ece.iacl.jist.dialogs.JDialogSaveAll
 
storeParamsFromGUI() - Method in class edu.jhu.ece.iacl.jist.pipeline.ProcessingDialog
Store the parameters from the dialog to record the execution of this algorithm.
STRAIGHT_INJECTION - Static variable in class edu.jhu.cs.cisst.algorithms.optimize.fmg.restrictor.RestrictorByStencil
the stencil that characterises straight injection where elements of those elements of the fine grid that are also present in the coarse grid are simply copied from the fine grid to the coarse grid.
streams - Static variable in class edu.jhu.ece.iacl.jist.pipeline.gui.ProcessManager
The streams.
string - Variable in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamString
The string.
StringArrayToStringXML - Class in edu.jhu.ece.iacl.jist.io
The Class StringArrayToStringXML.
StringArrayToStringXML() - Constructor for class edu.jhu.ece.iacl.jist.io.StringArrayToStringXML
Instantiates a new string array to string xml.
StringArrayXMLReaderWriter - Class in edu.jhu.ece.iacl.jist.io
The Class StringArrayXMLReaderWriter.
StringArrayXMLReaderWriter() - Constructor for class edu.jhu.ece.iacl.jist.io.StringArrayXMLReaderWriter
Instantiates a new string array xml reader writer.
stringParam - Variable in class edu.jhu.ece.iacl.jist.pipeline.src.PipeStringListSource
The string param.
StringReaderWriter - Class in edu.jhu.ece.iacl.jist.io
The Class StringReaderWriter.
StringReaderWriter() - Constructor for class edu.jhu.ece.iacl.jist.io.StringReaderWriter
Instantiates a new string reader writer.
StringReaderWriter(FileExtensionFilter) - Constructor for class edu.jhu.ece.iacl.jist.io.StringReaderWriter
Instantiates a new string reader writer.
strokeWeight - Variable in class edu.jhu.cs.cisst.vent.renderer.processing.VolumeIsoContourRenderer
The stroke weight.
strokeWeightParam - Variable in class edu.jhu.cs.cisst.vent.renderer.processing.VolumeIsoContourRenderer
The stroke weight param.
sub(Voxel) - Method in class edu.jhu.ece.iacl.jist.structures.image.Voxel
Sub.
sub(Voxel) - Method in class edu.jhu.ece.iacl.jist.structures.image.VoxelBoolean
 
sub(Voxel) - Method in class edu.jhu.ece.iacl.jist.structures.image.VoxelColor
 
sub(Voxel) - Method in class edu.jhu.ece.iacl.jist.structures.image.VoxelDouble
 
sub(Voxel) - Method in class edu.jhu.ece.iacl.jist.structures.image.VoxelFloat
 
sub(Voxel) - Method in class edu.jhu.ece.iacl.jist.structures.image.VoxelIndexed
 
sub(Voxel) - Method in class edu.jhu.ece.iacl.jist.structures.image.VoxelInt
 
sub(Voxel) - Method in class edu.jhu.ece.iacl.jist.structures.image.VoxelMipav
 
sub(Voxel) - Method in class edu.jhu.ece.iacl.jist.structures.image.VoxelShort
 
sub(Voxel) - Method in class edu.jhu.ece.iacl.jist.structures.image.VoxelUByte
 
sub(Voxel) - Method in class edu.jhu.ece.iacl.jist.structures.image.VoxelVector
 
sub(double) - Method in class edu.jhu.ece.iacl.jist.structures.matrix.Matrix3
Sub.
sub(Matrix3) - Method in class edu.jhu.ece.iacl.jist.structures.matrix.Matrix3
Sub.
sub(double) - Method in class edu.jhu.ece.iacl.jist.structures.matrix.VectorMatrixX
Sub.
sub(VectorMatrixX) - Method in class edu.jhu.ece.iacl.jist.structures.matrix.VectorMatrixX
Sub.
sub(double) - Method in class edu.jhu.ece.iacl.jist.structures.vector.Vector2
 
sub(VectorX) - Method in class edu.jhu.ece.iacl.jist.structures.vector.Vector2
 
sub(double) - Method in class edu.jhu.ece.iacl.jist.structures.vector.Vector3
 
sub(VectorX) - Method in class edu.jhu.ece.iacl.jist.structures.vector.Vector3
 
sub(double) - Method in class edu.jhu.ece.iacl.jist.structures.vector.Vector4
 
sub(VectorX) - Method in class edu.jhu.ece.iacl.jist.structures.vector.Vector4
 
sub(double) - Method in class edu.jhu.ece.iacl.jist.structures.vector.VectorN
 
sub(VectorX) - Method in class edu.jhu.ece.iacl.jist.structures.vector.VectorN
 
sub(double) - Method in interface edu.jhu.ece.iacl.jist.structures.vector.VectorX
Sub.
sub(VectorX) - Method in interface edu.jhu.ece.iacl.jist.structures.vector.VectorX
Sub.
subject - Variable in class edu.jhu.ece.iacl.algorithms.vabra.ImagePair
 
subjectVols - Variable in class edu.jhu.ece.iacl.algorithms.vabra.ImagePair
 
subjectWeights - Variable in class edu.jhu.ece.iacl.algorithms.vabra.ImagePair
 
subjectXMLFile - Variable in class edu.jhu.ece.iacl.algorithms.vabra.ImagePair
 
submit() - Method in interface edu.jhu.ece.iacl.jist.processcontrol.ProcessController
Submit.
submit() - Method in class edu.jhu.ece.iacl.jist.processcontrol.ProcessControllerDRMAA
 
submit() - Method in class edu.jhu.ece.iacl.jist.processcontrol.ProcessControllerNative
 
subsample(float[][][], int, int, int, int) - Static method in class edu.jhmi.rad.medic.libraries.ImageFunctionsPublic
scale down by a factor
subsample(float[], int, int, int, int) - Static method in class edu.jhmi.rad.medic.libraries.ImageFunctionsPublic
scale down by a factor
subsample(float[][][][], int, int, int, int, int) - Static method in class edu.jhmi.rad.medic.libraries.ImageFunctionsPublic
scale down a vector image by a factor
subsample(float[][], int, int, int, int, int) - Static method in class edu.jhmi.rad.medic.libraries.ImageFunctionsPublic
scale down a vector image by a factor
sum(Matrix) - Static method in class edu.jhu.bme.smile.commons.math.MatrixMath
 
sum(double[]) - Static method in class edu.jhu.bme.smile.commons.math.StatisticsDouble
 
supplied_grad_file - Variable in class edu.jhu.ece.iacl.algorithms.dti.GTCparams
 
supportedFileExtensions - Static variable in class edu.jhu.ece.iacl.jist.io.ModelImageReaderWriter
The supported file extensions.
surf - Variable in class edu.jhu.cs.cisst.vent.renderer.processing.SurfaceRenderer
The surf.
surf - Variable in class edu.jhu.ece.iacl.algorithms.manual_label.LabelSurface
 
surf - Variable in class edu.jhu.ece.iacl.plugins.utilities.surface.MedicAlgorithmSurfaceHistogram
 
surf2sphere - Static variable in class edu.jhu.ece.iacl.algorithms.ReferencedPapers
 
Surface - Class in edu.jhu.ece.iacl.jist.structures.geom
The Class Surface.
Surface(int) - Constructor for class edu.jhu.ece.iacl.jist.structures.geom.Surface
Instantiates a new surface.
SurfaceBrainSuiteReaderWriter - Class in edu.jhu.ece.iacl.jist.io
The Class SurfaceBrainSuiteReaderWriter.
SurfaceBrainSuiteReaderWriter() - Constructor for class edu.jhu.ece.iacl.jist.io.SurfaceBrainSuiteReaderWriter
Instantiates a new surface brain suite reader writer.
SurfaceDxReaderWriter - Class in edu.jhu.ece.iacl.jist.io
The Class SurfaceDxReaderWriter.
SurfaceDxReaderWriter() - Constructor for class edu.jhu.ece.iacl.jist.io.SurfaceDxReaderWriter
Instantiates a new surface dx reader writer.
SurfaceFreeSurferReaderWriter - Class in edu.jhu.ece.iacl.jist.io
The Class SurfaceFreeSurferReaderWriter.
SurfaceFreeSurferReaderWriter() - Constructor for class edu.jhu.ece.iacl.jist.io.SurfaceFreeSurferReaderWriter
Instantiates a new surface free surfer reader writer.
surfaceInflation - Static variable in class edu.jhu.ece.iacl.algorithms.ReferencedPapers
 
SurfaceMipavReaderWriter - Class in edu.jhu.ece.iacl.jist.io
The Class SurfaceMipavReaderWriter.
SurfaceMipavReaderWriter() - Constructor for class edu.jhu.ece.iacl.jist.io.SurfaceMipavReaderWriter
Instantiates a new surface mipav reader writer.
surfaceParam - Variable in class edu.jhu.cs.cisst.plugins.utilities.surface.PlugInIsoSurfaceGenerator
 
surfaceParameterizationSurvey - Static variable in class edu.jhu.ece.iacl.algorithms.ReferencedPapers
 
SurfaceRater - Class in edu.jhu.ece.iacl.algorithms.manual_label.simulation
Simulates a random surface rater characterized by their 1) Probability of error 2) Probability of boundary error (vs global error) 3) Confusion Matrix (for global error) 4) Probability that boundary errors will occur on particular boundaries 5) Probability that the boundary will "shrink" or "grow".
SurfaceRater(EmbeddedSurface) - Constructor for class edu.jhu.ece.iacl.algorithms.manual_label.simulation.SurfaceRater
 
SurfaceRater(EmbeddedSurface, float, int[], float[][], int) - Constructor for class edu.jhu.ece.iacl.algorithms.manual_label.simulation.SurfaceRater
 
SurfaceRater(EmbeddedSurface, float[], float, int) - Constructor for class edu.jhu.ece.iacl.algorithms.manual_label.simulation.SurfaceRater
 
SurfaceRater(EmbeddedSurface, float[][], float[], float, int) - Constructor for class edu.jhu.ece.iacl.algorithms.manual_label.simulation.SurfaceRater
 
SurfaceRater(EmbeddedSurface, float, ArrayList<Point2i>, float[], float[], int) - Constructor for class edu.jhu.ece.iacl.algorithms.manual_label.simulation.SurfaceRater
 
SurfaceRater(EmbeddedSurface, float, float[][], ArrayList<Point2i>, float[], float[], int) - Constructor for class edu.jhu.ece.iacl.algorithms.manual_label.simulation.SurfaceRater
 
SurfaceReaderWriter - Class in edu.jhu.ece.iacl.jist.io
The Class SurfaceReaderWriter.
SurfaceReaderWriter() - Constructor for class edu.jhu.ece.iacl.jist.io.SurfaceReaderWriter
Instantiates a new surface reader writer.
SurfaceReaderWriter(FileExtensionFilter) - Constructor for class edu.jhu.ece.iacl.jist.io.SurfaceReaderWriter
Instantiates a new surface reader writer.
SurfaceRenderer - Class in edu.jhu.cs.cisst.vent.renderer.processing
The Class SurfaceRenderer.
SurfaceRenderer(VisualizationProcessing3D, EmbeddedSurface) - Constructor for class edu.jhu.cs.cisst.vent.renderer.processing.SurfaceRenderer
Instantiates a new surface renderer.
SurfaceTools - Class in edu.jhu.ece.iacl.algorithms.hardi
 
SurfaceTools() - Constructor for class edu.jhu.ece.iacl.algorithms.hardi.SurfaceTools
 
surfaceTopologyCorrection - Static variable in class edu.jhu.ece.iacl.algorithms.ReferencedPapers
 
SurfaceVrmlReaderWriter - Class in edu.jhu.ece.iacl.jist.io
The Class SurfaceVrmlReaderWriter.
SurfaceVrmlReaderWriter() - Constructor for class edu.jhu.ece.iacl.jist.io.SurfaceVrmlReaderWriter
Instantiates a new surface vrml reader writer.
SurfaceVtkReaderWriter - Class in edu.jhu.ece.iacl.jist.io
The Class SurfaceVtkReaderWriter.
SurfaceVtkReaderWriter() - Constructor for class edu.jhu.ece.iacl.jist.io.SurfaceVtkReaderWriter
Instantiates a new surface vtk reader writer.
surfcolParam - Variable in class edu.jhu.ece.iacl.jist.pipeline.src.PipeSurfaceCollectionListSource
The volume collection param.
surfInflate - Static variable in class edu.jhu.ece.iacl.algorithms.ReferencedPapers
 
surfParam - Variable in class edu.jhu.cs.cisst.plugins.visualization.PlugInVisualizeSurface
 
surfParam - Variable in class edu.jhu.ece.iacl.jist.pipeline.src.PipeSurfaceListSource
The surf param.
SurfToGrad - Class in edu.jhu.ece.iacl.plugins.hardi
 
SurfToGrad() - Constructor for class edu.jhu.ece.iacl.plugins.hardi.SurfToGrad
 
svdNorm(Matrix) - Static method in class edu.jhu.bme.smile.commons.math.MatrixMath
 
switchSpaced - Variable in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamSwitch
The switch spaced.
switchString - Variable in class edu.jhu.ece.iacl.jist.pipeline.parameter.ParamSwitch
The switch string.
sx - Variable in class edu.jhu.cs.cisst.algorithms.optimize.fmg.grid.Grid
 
sy - Variable in class edu.jhu.cs.cisst.algorithms.optimize.fmg.grid.Grid
 
synchronizedPush() - Method in class edu.jhu.ece.iacl.jist.pipeline.ExecutionContext
Push data from output parameters into child contexts.
sz - Variable in class edu.jhu.cs.cisst.algorithms.optimize.fmg.grid.Grid
 

T

t - Variable in class edu.jhu.ece.iacl.algorithms.manual_label.staple.STAPLEmulti2
 
t1 - Variable in class edu.jhu.ece.iacl.jist.structures.tensor.Tensor2
The t2.
t1 - Variable in class edu.jhu.ece.iacl.jist.structures.tensor.Tensor3
The t3.
t2 - Variable in class edu.jhu.ece.iacl.jist.structures.tensor.Tensor2
The t2.
t2 - Variable in class edu.jhu.ece.iacl.jist.structures.tensor.Tensor3
The t3.
t3 - Variable in class edu.jhu.ece.iacl.jist.structures.tensor.Tensor3
The t3.
table - Variable in class edu.jhu.ece.iacl.jist.pipeline.gui.ProcessManagerTable
The table.
tableChanged(TableModelEvent) - Method in class edu.jhu.ece.iacl.jist.pipeline.gui.ProcessManagerTable
 
tableChoice() - Method in class edu.jhu.ece.iacl.algorithms.dti.DTIGradientTableCreator
 
tableToString(double[][]) - Static method in class edu.jhu.ece.iacl.algorithms.dti.DTIGradientTableCreator
 
tableToStringLong(double[][]) - Static method in class edu.jhu.ece.iacl.algorithms.dti.DTIGradientTableCreator
 
tabPane - Variable in class edu.jhu.ece.iacl.jist.pipeline.view.input.ParamCollectionPipelineInputView
The tab pane.
tagWithXML(String, String, boolean) - Method in class edu.jhu.ece.iacl.jist.cli.JistCLI
 
talley() - Method in class edu.jhu.ece.iacl.jist.structures.matrix.VectorMatrixX
Debugging routine for printing non-zero vector matrix elements.
tanAngle(Tuple3f, Tuple3f, Tuple3f) - Static method in class edu.jhu.ece.iacl.jist.algorithms.graphics.GeomUtil
Tan angle.
target - Variable in class edu.jhu.ece.iacl.algorithms.vabra.ImagePair
 
targetVols - Variable in class edu.jhu.ece.iacl.algorithms.vabra.ImagePair
 
targetWeights - Variable in class edu.jhu.ece.iacl.algorithms.vabra.ImagePair
 
targetXMLFile - Variable in class edu.jhu.ece.iacl.algorithms.vabra.ImagePair
 
taskName - Variable in class edu.jhu.ece.iacl.jist.pipeline.PerformanceSummary.TimeAndMemoryStamp
The task name.
tb - Variable in class edu.jhu.ece.iacl.jist.pipeline.PerformanceSummary
Thread to get cpu time.
te - Variable in class edu.jhu.ece.iacl.algorithms.manual_label.staple.STAPLEmulti2
 
template - Variable in class edu.jhu.ece.iacl.plugins.utilities.volume.MedicAlgorithmMipavReorient
 
Tensor2 - Class in edu.jhu.ece.iacl.jist.structures.tensor
Tensor with 2 vectors.
Tensor2() - Constructor for class edu.jhu.ece.iacl.jist.structures.tensor.Tensor2
 
Tensor3 - Class in edu.jhu.ece.iacl.jist.structures.tensor
Tensor with 3 vectors.
Tensor3() - Constructor for class edu.jhu.ece.iacl.jist.structures.tensor.Tensor3
 
TensorX<E extends java.lang.Number> - Interface in edu.jhu.ece.iacl.jist.structures.tensor
Interface for all Tensor implementations.
tesselate(ModelTriangleMesh, int) - Static method in class edu.jhu.ece.iacl.algorithms.hardi.SurfaceTools
 
TesselateSurface - Class in edu.jhu.ece.iacl.plugins.hardi
 
TesselateSurface() - Constructor for class edu.jhu.ece.iacl.plugins.hardi.TesselateSurface
 
tesselateTriangle(Vector<Point3f>, Vector<Integer>, int, int) - Static method in class edu.jhu.ece.iacl.algorithms.hardi.SurfaceTools
 
test() - Static method in class edu.jhu.ece.iacl.algorithms.dti.EstimateTensorLLMSE
 
test(int) - Static method in class edu.jhu.ece.iacl.algorithms.dti.EstimateTensorLLMSE
 
test - Class in edu.jhu.ece.iacl.jist.structures.image
The Class test.
test() - Constructor for class edu.jhu.ece.iacl.jist.structures.image.test
 
Test1DOptimizations - Class in edu.jhu.bme.smile.c