edu.jhu.ece.iacl.jist.pipeline
Class ProcessingAlgorithm

java.lang.Object
  AlgorithmBase
      edu.jhu.ece.iacl.jist.pipeline.ProcessingAlgorithm

Direct Known Subclasses:

AddingNoise, AddToFileCollection, AlgorithmComputeConnectivityMatrix, AlgorithmGradientTableCorrection, AlgorithmJointROIStats, AlgorithmLogOdds, AlgorithmROIStats, AlgorithmSimulateSurfaceRater, AlgorithmSimulateVolumeRater, AlgorithmVolumeFileCollectionTo3D, CESTAsymmetry, CFARIEstimation, CFARIEstimation2, ChebyShevFitting, CombinedSlabCollectionToVolumeCollection, ComputeMeanB0, ComputeMeanDW, CreateCrossingFiber, CreateMask, CreatePlatonicSolidSurface, CreateTesselatedSurface, DefineCFARIScheme, DivideReference, DWIBallStickEstCamino, DWIBallStickEstCaminoFileCollection, DWICombineBvalTables, DWICombineGradTables, DWIDefineCaminoScheme, DWITensorColorEncodedMap, DWITensorContrasts, DWITensorEstCamino, DWITensorEstCaminoFileCollection, DWITensorEstCaminoRESTOREVariableNoiseField, DWITensorEstLikelihood, DWITensorEstLLMSE, DWIThreeTensorEstCamino, DWIThreeTensorEstCaminoFileCollection, DWITwoTensorEstCamino, DWITwoTensorEstCaminoFileCollection, EstimateMTR, EstimateMTRseries, EstimateT1FromDoubleAngle, EstimateT2FromDualEcho, ExtractBvalGradFromPAR, Fiber2Volume, FileCollectionToPins, FileCollectionToVolumeCollection, FirstPluginTest, FunkRadonTransform, GenerateTensors, GetImageDimensions, GradToSurf, ImageAlgebra, ImageArithmetic, ImageCollectionAlgebra, JistMSWASSR, LocalNoiseEstimate, MedicAlgorithmApplyFiberROI, MedicAlgorithmArithmetic, MedicAlgorithmAtlasSelection, MedicAlgorithmChooseFileRegEx, MedicAlgorithmChooseVolumeRegEx, MedicAlgorithmCleanSurfLabels, MedicAlgorithmCombineSurfaceComponents, MedicAlgorithmCombineSurfaces, MedicAlgorithmCombineVolumeComponents, MedicAlgorithmConcatArrayDoubleTextLists, MedicAlgorithmConstrainedFLIRT, MedicAlgorithmCopyEmbeddedData, MedicAlgorithmCreateSimilarityMetricVol, MedicAlgorithmCrop, MedicAlgorithmDeformFibers, MedicAlgorithmDemo, MedicAlgorithmDimensions, MedicAlgorithmEfficientFileCollectionRegistration, MedicAlgorithmEmbedSurface, MedicAlgorithmExecutableAdapter, MedicAlgorithmExtractAllComponents, MedicAlgorithmExtractFileCollectionComponents, MedicAlgorithmExtractSurfaceComponent, MedicAlgorithmExtractVolumeComponent, MedicAlgorithmFiberComparison, MedicAlgorithmFibersFromSurfaceROI, MedicAlgorithmFibersToVtk, MedicAlgorithmFiberTracker, MedicAlgorithmFiberVolumeStatistics, MedicAlgorithmFindEqualVolume, MedicAlgorithmFlipVectorTable, MedicAlgorithmFlipVectorVolume, MedicAlgorithmFLIRT, MedicAlgorithmFLIRTCollection, MedicAlgorithmFloatsToPoint, MedicAlgorithmFMLabelExtension, MedicAlgorithmFormatVectorImage, MedicAlgorithmIdentifySubject, MedicAlgorithmImageCalculator, MedicAlgorithmImageCalculatorBatch, MedicAlgorithmImageCalculatorModified, MedicAlgorithmImageMath, MedicAlgorithmIsotropicReslice, MedicAlgorithmJistLayoutAdapter, MedicAlgorithmKLDivergence, MedicAlgorithmMatchAllImages, MedicAlgorithmMipavAdapter, MedicAlgorithmMipavReorient, MedicAlgorithmMultiAtlasLabeling, MedicAlgorithmMultiAtlasReg, MedicAlgorithmMultiAtlasSurfaceLabeling, MedicAlgorithmMultiCrop, MedicAlgorithmMultiDeformVolume, MedicAlgorithmMultiGradientTableCreator, MedicAlgorithmMultiParV3Info, MedicAlgorithmMultiParV4Info, MedicAlgorithmReshapePoints, MedicAlgorithmReshapeSurface, MedicAlgorithmReverseComponents, MedicAlgorithmSerializeSurfaces, MedicAlgorithmSerializeVolumes, MedicAlgorithmSetHeaders, MedicAlgorithmSTAPLE, MedicAlgorithmSTAPLEgeneral, MedicAlgorithmSTAPLEsurface, MedicAlgorithmSubsampleFibers, MedicAlgorithmSurfaceConverter, MedicAlgorithmSurfaceHistogram, MedicAlgorithmSurfaceSplitter, MedicAlgorithmSurfaceToVolumeConverter, MedicAlgorithmTableFormat, MedicAlgorithmTensorFormatConvert, MedicAlgorithmThreshold, MedicAlgorithmTransformFibers, MedicAlgorithmTransformVolume, MedicAlgorithmUncrop, MedicAlgorithmVABRA, MedicAlgorithmValueEquals, MedicAlgorithmValueGreaterThan, MedicAlgorithmValueInRange, MedicAlgorithmValueLessThan, MedicAlgorithmVolumeConverter, MedicAlgorithmVolumeConverter2, MedicAlgorithmVolumeConverter4D, MedicAlgorithmVolumeHistogram, MedicAlgorithmVolumeListOrganizer, MedicAlgorithmVolumeSplitter, MedicAlgorithmVolumeToSurfaceLabeling, MedicAlgorithmWildBootTrac, MedicAlgorithmZip, MemoryDemo, MipavPluginParser, NameTest, NormalizeToUnitMagnitude, PlugInCircleLevelSet, PluginCombineVolumes, PlugInFuzzyMembershipThreshold2D, PlugInGeodesicActiveContour2D, PlugInGradientVectorFlow2D, PlugInIsoContourGenerator, PlugInIsoSurfaceGenerator, PlugInTestDataSelector, PlugInVisualizeActiveContour2D, PlugInVisualizeImage, PlugInVisualizeSurface, Process3DMRIImages, QBallEstimation, QBallModifiedRealProjection, QBallProjection, RandomVol, RegularizeNoiseField, ScaleImageDemo, SelectUniqueDiffusionDirections, SImageTractAnalysis, SimFramework, SurfToGrad, TesselateSurface, TractMapping, VolumeCensorRange, VolumeCollectionToCombinedSlabCollection, VolumeDirectoryNoIter

public abstract class ProcessingAlgorithm
extends AlgorithmBase

Processing Algorithm for MAPS. This class should be extended for each particular algorithm implementation. Methods createInputParameters(), createOutputParameters() and execute() should be overridden for each algorithm. createInputParameters() and createOutputParameters() are executed in the default constructor for ProcessingAlgorithm. execute() is executed after the user presses "OK" and all the input parameters validate.

Author:

Blake Lucas

Field Summary

protected AlgorithmInformation	algorithmInformation Algorithm information associated with all algorithms.
protected ParamCollection	inputParams The input parameters.
static float	JIST_VERSION The Constant MAPS version.
protected ParamCollection	outputParams The output parameters.
protected ParamPerformance	performance Algorithm performance information.
protected boolean	runningInSeparateProcess Run in separate process.

Constructor Summary

ProcessingAlgorithm()
Constructor creates input and output parameters and assigns the title of this algorithm to be the label for the input parameters.

Method Summary

protected abstract void	createInputParameters(ParamCollection inputParams) Create input parameters.
protected abstract void	createOutputParameters(ParamCollection outputParams) Create output parameters.
protected abstract void	execute(CalculationMonitor monitor) Execute your algorithm.
java.io.File	getAboutFile() Location of file that describes the algorithm.
AlgorithmInformation	getAlgorithmInformation() Get algorithm information for this algorithm.
java.lang.String	getAlgorithmLabel() Get algorithm label from input parameters.
java.lang.String	getAlgorithmName() Get algorithm name from input parameters.
java.lang.String[]	getDefaultJVMArgs() Default JVM Arguments --- currently only the Sun VM is supported
ParamCollection	getInput() Get input parameters.
java.io.File	getMapFile() Get module definition file.
ParamCollection	getOutput() Get output parameters.
java.io.File	getOutputDirectory() Get output directory.
java.awt.Dimension	getPreferredSize() Get preferred size for algorithm The default is null.
long	getTimeStamp() Get cpu timestamp for this thread in msec.
java.io.File	getUsageFile() Location of file that describes how to use the algorithm.
void	init(java.io.File pipeFile) Initialize parameters and algorithm.
void	init(PipeAlgorithm pipe) Initialize parameters and algorithm.
boolean	isRunningInSeparateProcess() Checks if is running in separate process.
boolean	load(java.io.File f) Load input parameters from file and execute algorithm.
void	runAlgorithm() Run algorithm with new calculation monitor.
boolean	runAlgorithm(CalculationMonitor monitor) Run algorithm with calculation monitor.
void	saveResources(boolean overrideSubdirectories)
void	setInput(ParamCollection inputParams) Set input parameters.
void	setMapFile(java.io.File mapFile) Set module definition file.
void	setOutput(ParamCollection outputParams) Set output parameters.
void	setOutputDirectory(java.io.File outputDir) Set output directory.
void	setOutputMetaFile(java.io.File file)
void	setPreferredSize(java.awt.Dimension d) Get preferred size for algorithm The default is null.
void	setRunningInSeparateProcess(boolean runningInSeperateProcess) Sets the running in separate process.
void	writeSummaryFile()

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

JIST_VERSION

public static final float JIST_VERSION

The Constant MAPS version.

See Also:

Constant Field Values

inputParams

protected ParamCollection inputParams

The input parameters.

outputParams

protected ParamCollection outputParams

The output parameters.

performance

protected ParamPerformance performance

Algorithm performance information.

algorithmInformation

protected AlgorithmInformation algorithmInformation

Algorithm information associated with all algorithms.

runningInSeparateProcess

protected boolean runningInSeparateProcess

Run in separate process.

Constructor Detail

ProcessingAlgorithm

public ProcessingAlgorithm()

Constructor creates input and output parameters and assigns the title of this algorithm to be the label for the input parameters.

Method Detail

getDefaultJVMArgs

public java.lang.String[] getDefaultJVMArgs()

Default JVM Arguments --- currently only the Sun VM is supported

createInputParameters

protected abstract void createInputParameters(ParamCollection inputParams)

Create input parameters.

Parameters:

inputParams - the input parameters

createOutputParameters

protected abstract void createOutputParameters(ParamCollection outputParams)

Create output parameters.

Parameters:

outputParams - the output parameters

execute

protected abstract void execute(CalculationMonitor monitor)
                         throws AlgorithmRuntimeException

Execute your algorithm.

Parameters:

monitor - progress monitor

Throws:

AlgorithmRuntimeException - the algorithm runtime exception

getAboutFile

public java.io.File getAboutFile()

Location of file that describes the algorithm.

Returns:

the about file

getAlgorithmInformation

public AlgorithmInformation getAlgorithmInformation()

Get algorithm information for this algorithm.

Returns:

algorithm information

getAlgorithmLabel

public java.lang.String getAlgorithmLabel()

Get algorithm label from input parameters.

Returns:

algorithm label

getAlgorithmName

public java.lang.String getAlgorithmName()

Get algorithm name from input parameters.

Returns:

algorithm name

getInput

public ParamCollection getInput()

Get input parameters.

Returns:

input parameters

getMapFile

public java.io.File getMapFile()

Get module definition file.

Returns:

module file

getOutput

public ParamCollection getOutput()

Get output parameters.

Returns:

output parameters

getOutputDirectory

public java.io.File getOutputDirectory()

Get output directory.

Returns:

output directory

getPreferredSize

public java.awt.Dimension getPreferredSize()

Get preferred size for algorithm The default is null.

Returns:

preferred dimension

getTimeStamp

public long getTimeStamp()

Get cpu timestamp for this thread in msec.

Returns:

the time stamp

getUsageFile

public java.io.File getUsageFile()

Location of file that describes how to use the algorithm.

Returns:

the usage file

init

public void init(java.io.File pipeFile)

Initialize parameters and algorithm.

Parameters:

pipeFile - the pipe file

init

public void init(PipeAlgorithm pipe)

Initialize parameters and algorithm.

Parameters:

pipe - the pipe

load

public boolean load(java.io.File f)

Load input parameters from file and execute algorithm.

Parameters:

f - input parameter file

Returns:

true if algorithm executed

runAlgorithm

public void runAlgorithm()

Run algorithm with new calculation monitor.

runAlgorithm

public boolean runAlgorithm(CalculationMonitor monitor)

Run algorithm with calculation monitor.

Parameters:

monitor - calculation monitor

Returns:

true if algorithm successful

setInput

public void setInput(ParamCollection inputParams)

Set input parameters.

Parameters:

inputParams - input parameters

setMapFile

public void setMapFile(java.io.File mapFile)

Set module definition file.

Parameters:

mapFile - module file

setOutput

public void setOutput(ParamCollection outputParams)

Set output parameters.

Parameters:

outputParams - output parameters

setOutputDirectory

public void setOutputDirectory(java.io.File outputDir)

Set output directory.

Parameters:

outputDir - output directory

setPreferredSize

public void setPreferredSize(java.awt.Dimension d)

Get preferred size for algorithm The default is null.

Parameters:

d - the dimension

isRunningInSeparateProcess

public boolean isRunningInSeparateProcess()

Checks if is running in separate process.

Returns:

the runninInSeperateProcess

setRunningInSeparateProcess

public void setRunningInSeparateProcess(boolean runningInSeperateProcess)

Sets the running in separate process.

Parameters:

runningInSeperateProcess - the runInSeperateProcess to set

setOutputMetaFile

public void setOutputMetaFile(java.io.File file)

saveResources

public void saveResources(boolean overrideSubdirectories)

writeSummaryFile

public void writeSummaryFile()
                      throws java.io.IOException

Throws:

java.io.IOException