IsoSurfaceGenerator

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edu.jhu.cs.cisst.algorithms.geometry.surface
Class IsoSurfaceGenerator

java.lang.Object
  edu.jhu.ece.iacl.jist.pipeline.AbstractCalculation
      edu.jhu.cs.cisst.algorithms.geometry.surface.IsoSurfaceGenerator

public class IsoSurfaceGenerator
extends AbstractCalculation
extends AbstractCalculation

The IsoSurface Generator generates an iso-surface using either the marching-cubes or marching-tetrahedral algorithm. The patent for marching-cubes has expired as of 2005 and is now available for use in the public domain. This implementation is a reimplementation of a C++ version with enhancements that preserve mesh connectivity.

Author:: Cory Bloyd

Nested Class Summary
`protected class`	`IsoSurfaceGenerator.EdgeSplit` The Class EdgeSplit is a container to describe a level set crossing point.
`static class`	`IsoSurfaceGenerator.Method` The Iso-surface generation method
`protected class`	`IsoSurfaceGenerator.Triangle` The Class Triangle stores vertex ids.
`static class`	`IsoSurfaceGenerator.Winding` The winding order for triangle vertices.

Field Summary
`protected static float[][]`	`a2fEdgeDirection` a2fEdgeDirection lists the direction vector (vertex1-vertex0) for each edge in the cube.
`protected static int[][]`	`a2fVertexOffset` Lists the positions, relative to vertex 0, of each of the 8 vertices of a cube.
`protected static int[][]`	`a2iEdgeConnection` Lists the index of the endpoint vertices for each of the 12 edges of the cube.
`protected static int[][]`	`a2iTetrahedronEdgeConnection` Lists the index of the endpoint vertices for each of the 6 edges of the tetrahedron.
`protected static int[][]`	`a2iTetrahedronsInACube` Lists the index of verticies from a cube that made up each of the six tetrahedrons within the cube.
`protected static int[][]`	`a2iTetrahedronTriangles` For each of the possible vertex states listed in aiTetrahedronEdgeFlags there is a specific triangulation of the edge intersection points.
`protected static int[][]`	`a2iTriangleConnectionTable` For each of the possible vertex states listed in aiCubeEdgeFlags there is a specific triangulation of the edge intersection points.
`protected static int[]`	`aiCubeEdgeFlags` 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.
`protected static int[]`	`aiTetrahedronEdgeFlags` 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.
`protected int`	`cols` The slices.
`protected float`	`isoLevel` The target iso-level.
`protected IsoSurfaceGenerator.Method`	`method` The is-surface generation method.
`protected float`	`resX` The resolution in X.
`protected float`	`resY` The resolution in Y.
`protected float`	`resZ` The resolution in Z.
`protected int`	`rows` The slices.
`protected int`	`slices` The slices.
`protected boolean`	`useResolutions` The use image resolutions flag.
`protected int`	`vertCount` The vertex count.
`protected float[][][]`	`volMat` The volume matrix
`protected IsoSurfaceGenerator.Winding`	`winding` The winding order.

Fields inherited from class edu.jhu.ece.iacl.jist.pipeline.AbstractCalculation
`monitor`

Constructor Summary
`IsoSurfaceGenerator()` Instantiates a new iso surface generator.
`IsoSurfaceGenerator(AbstractCalculation parent)` Instantiates a new iso surface generator.

Method Summary
`protected int`	`clampColumn(int c)` Clamp column index.
`protected int`	`clampRow(int r)` Clamp row.
`protected int`	`clampSlice(int s)` Clamp slice.
`protected float`	`fGetOffset(Point3i v1, Point3i v2)` Interpolate position along edge.
`static java.lang.String`	`getVersion()`
`protected void`	`marchTetrahedral(java.util.Hashtable<java.lang.Long,IsoSurfaceGenerator.EdgeSplit> splits, java.util.LinkedList<IsoSurfaceGenerator.Triangle> triangles, Point3i[] pasTetrahedronPosition)` March tetrahedral.
`void`	`setMethod(IsoSurfaceGenerator.Method method)` Sets the iso-surface generation method.
`void`	`setUseResolutions(boolean value)` Sets the use image resolutions flag.
`void`	`setWinding(IsoSurfaceGenerator.Winding winding)` Sets the winding order.
`EmbeddedSurface`	`solve(ImageDataFloat vol, float isoLevel)` Solve for iso-surface
`protected void`	`triangulateUsingMarchingCubes(java.util.Hashtable<java.lang.Long,IsoSurfaceGenerator.EdgeSplit> splits, java.util.LinkedList<IsoSurfaceGenerator.Triangle> triangles, int x, int y, int z)` Triangulate using marching cubes.
`protected void`	`triangulateUsingMarchingTetrahedrals(java.util.Hashtable<java.lang.Long,IsoSurfaceGenerator.EdgeSplit> splits, java.util.LinkedList<IsoSurfaceGenerator.Triangle> triangles, int x, int y, int z)` Triangulate using marching tetrahedrals.

Methods inherited from class edu.jhu.ece.iacl.jist.pipeline.AbstractCalculation
`add, addTotalUnits, decrementCompletedUnits, decrementCompletedUnits, getCompletedUnits, getCurrentLabel, getCurrentProgress, getLabel, getPerformance, getProgress, getTotalUnits, incrementCompletedUnits, incrementCompletedUnits, isCompleted, markCompleted, reset, setCompletedUnits, setCompletedUnits, setLabel, setMonitor, setTotalUnits`

Methods inherited from class java.lang.Object
`clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait`

Field Detail

method

protected IsoSurfaceGenerator.Method method

The is-surface generation method.

winding

protected IsoSurfaceGenerator.Winding winding

The winding order.

isoLevel

protected float isoLevel

The target iso-level.

vertCount

protected int vertCount

The vertex count.

volMat

protected float[][][] volMat

The volume matrix

rows

protected int rows

The slices.

cols

protected int cols

The slices.

slices

protected int slices

The slices.

resX

protected float resX

The resolution in X.

resY

protected float resY

The resolution in Y.

resZ

protected float resZ

The resolution in Z.

useResolutions

protected boolean useResolutions

The use image resolutions flag.

a2fVertexOffset

protected static final int[][] a2fVertexOffset

Lists the positions, relative to vertex 0, of each of the 8 vertices of a cube.

a2iEdgeConnection

protected static final int[][] a2iEdgeConnection

Lists the index of the endpoint vertices for each of the 12 edges of the cube.

a2fEdgeDirection

protected static final float[][] a2fEdgeDirection

a2fEdgeDirection lists the direction vector (vertex1-vertex0) for each edge in the cube.

a2iTetrahedronEdgeConnection

protected static final int[][] a2iTetrahedronEdgeConnection

Lists the index of the endpoint vertices for each of the 6 edges of the tetrahedron.

a2iTetrahedronsInACube

protected static final int[][] a2iTetrahedronsInACube

Lists the index of verticies from a cube that made up each of the six tetrahedrons within the cube.

aiCubeEdgeFlags

protected static final int[] aiCubeEdgeFlags

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. For each entry in the table, if edge #n is intersected, then bit #n is set to 1

a2iTriangleConnectionTable

protected static final int[][] a2iTriangleConnectionTable

For each of the possible vertex states listed in aiCubeEdgeFlags there is a specific triangulation of the edge intersection points. a2iTriangleConnectionTable lists all of them in the form of 0-5 edge triples with the list terminated by the invalid value -1. For example: a2iTriangleConnectionTable[3] list the 2 triangles formed when corner[0] and corner[1] are inside of the surface, but the rest of the cube is not. I found this table in an example program someone wrote long ago. It was probably generated by hand

aiTetrahedronEdgeFlags

protected static final int[] aiTetrahedronEdgeFlags

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. For each entry in the table, if edge #n is intersected, then bit #n is set to 1

a2iTetrahedronTriangles

protected static final int[][] a2iTetrahedronTriangles

For each of the possible vertex states listed in aiTetrahedronEdgeFlags there is a specific triangulation of the edge intersection points. a2iTetrahedronTriangles lists all of them in the form of 0-2 edge triples with the list terminated by the invalid value -1.

Constructor Detail