Package WildMagic.LibImagics.Extraction

Class ExtractSurfaceCubes

java.lang.Object

WildMagic.LibImagics.Extraction.ExtractSurfaceCubes

All Implemented Interfaces:

java.io.Serializable

public class ExtractSurfaceCubes
extends java.lang.Object
implements java.io.Serializable

A level surface extractor that is based on decomposing voxels into cubes, assuming a linear interpolation on the cubes, and extracting triangular level sets for those cubes. The resulting level surface is a triangle mesh.

See Also:

Serialized Form

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
protected class	ExtractSurfaceCubes.Triangle	The triangle just stores vertex indices and is unconcerned about the actual vertex locations.
protected class	ExtractSurfaceCubes.VETable	Vertex-edge table to support mesh topology.

Field Summary

Fields

Modifier and Type	Field	Description
protected static int	EB_XMAX_YMAX	Bit mask identifier.
protected static int	EB_XMAX_YMIN	Bit mask identifier.
protected static int	EB_XMAX_ZMAX	Bit mask identifier.
protected static int	EB_XMAX_ZMIN	Bit mask identifier.
protected static int	EB_XMIN_YMAX	Bit mask identifier.
protected static int	EB_XMIN_YMIN	Bit mask identifiers.
protected static int	EB_XMIN_ZMAX	Bit mask identifier.
protected static int	EB_XMIN_ZMIN	Bit mask identifier.
protected static int	EB_YMAX_ZMAX	Bit mask identifier.
protected static int	EB_YMAX_ZMIN	Bit mask identifier.
protected static int	EB_YMIN_ZMAX	Bit mask identifier.
protected static int	EB_YMIN_ZMIN	Bit mask identifier.
protected static int	EI_XMAX_YMAX	Bit-field identifier.
protected static int	EI_XMAX_YMIN	Bit-field identifier.
protected static int	EI_XMAX_ZMAX	Bit-field identifier.
protected static int	EI_XMAX_ZMIN	Bit-field identifier.
protected static int	EI_XMIN_YMAX	Bit-field identifier.
protected static int	EI_XMIN_YMIN	Bit-field identifier.
protected static int	EI_XMIN_ZMAX	Bit-field identifier.
protected static int	EI_XMIN_ZMIN	Bit-field identifier.
protected static int	EI_YMAX_ZMAX	Bit-field identifier.
protected static int	EI_YMAX_ZMIN	Bit-field identifier.
protected static int	EI_YMIN_ZMAX	Bit-field identifier.
protected static int	EI_YMIN_ZMIN	Bit-field identifier.
protected static int	FI_XMAX	Bit-field identifier.
protected static int	FI_XMIN	Bit-field identifier.
protected static int	FI_YMAX	Bit-field identifier.
protected static int	FI_YMIN	Bit-field identifier.
protected static int	FI_ZMAX	Bit-field identifier.
protected static int	FI_ZMIN	Bit-field identifier.
protected int[]	m_aiData	Data
protected float	m_fXDelta	deltas
protected float	m_fYDelta	deltas
protected float	m_fZDelta	deltas
protected int	m_iXBound	bounds on each dimension of 3D data set and data itself.
protected int	m_iXYBound	bound
protected int	m_iYBound	bounds on each dimension of 3D data set and data itself.
protected int	m_iZBound	bounds on each dimension of 3D data set and data itself.
protected Vector3f	m_kCentroid	centroid
protected Vector3f	m_kE0	temporary variables to avoid 'new' calls.
protected Vector3f	m_kE1	temporary variable
protected Vector3f	m_kGradient	temporary variable
protected Vector3f	m_kN	temporary variable
private static long	serialVersionUID

Constructor Summary

Constructors

Constructor	Description
ExtractSurfaceCubes(int iXBound, int iYBound, int iZBound, int[] aiData)	Create a level surface extractor for a 3D image.

Method Summary

Modifier and Type	Method	Description
protected static int	addVertex(Vector3f kV, java.util.HashMap<Vector3f,java.lang.Integer> kVMap)	Called to add the specified point to the hashmap.
void	ExtractContour(float level, java.util.Vector<int[]> kTriTable, java.util.Vector<Vector3f> vertices, java.util.Vector<TriangleKey> triangles)
void	ExtractContour(float level, java.util.Vector<Vector3f> vertices, java.util.Vector<TriangleKey> triangles)
Vector3f	getGradient(Vector3f kP)	Interpolation of the gradient vector of the image.
private int	GetVertices(float level, int x, int y, int z, ExtractSurfaceCubes.VETable table)
private void	GetXMaxEdges(int x, int y, int z, int type, ExtractSurfaceCubes.VETable table)
private void	GetXMinEdges(int x, int y, int z, int type, ExtractSurfaceCubes.VETable table)
private void	GetYMaxEdges(int x, int y, int z, int type, ExtractSurfaceCubes.VETable table)
private void	GetYMinEdges(int x, int y, int z, int type, ExtractSurfaceCubes.VETable table)
private void	GetZMaxEdges(int x, int y, int z, int type, ExtractSurfaceCubes.VETable table)
private void	GetZMinEdges(int x, int y, int z, int type, ExtractSurfaceCubes.VETable table)
static void	MakeUnique(java.util.Vector<Vector3f> vertices, java.util.Vector<TriangleKey> triangles, java.util.Vector<Vector3f> newVertices, java.util.Vector<TriangleKey> newTriangles)
void	OrientTriangles(java.util.Vector<Vector3f> vertices, java.util.Vector<TriangleKey> triangles, boolean sameDir)

Methods inherited from class java.lang.Object

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

Field Detail

serialVersionUID

private static final long serialVersionUID

See Also:

Constant Field Values

EI_XMIN_YMIN

protected static final int EI_XMIN_YMIN

Bit-field identifier.

See Also:

Constant Field Values

EI_XMIN_YMAX

protected static final int EI_XMIN_YMAX

Bit-field identifier.

See Also:

Constant Field Values

EI_XMAX_YMIN

protected static final int EI_XMAX_YMIN

Bit-field identifier.

See Also:

Constant Field Values

EI_XMAX_YMAX

protected static final int EI_XMAX_YMAX

Bit-field identifier.

See Also:

Constant Field Values

EI_XMIN_ZMIN

protected static final int EI_XMIN_ZMIN

Bit-field identifier.

See Also:

Constant Field Values

EI_XMIN_ZMAX

protected static final int EI_XMIN_ZMAX

Bit-field identifier.

See Also:

Constant Field Values

EI_XMAX_ZMIN

protected static final int EI_XMAX_ZMIN

Bit-field identifier.

See Also:

Constant Field Values

EI_XMAX_ZMAX

protected static final int EI_XMAX_ZMAX

Bit-field identifier.

See Also:

Constant Field Values

EI_YMIN_ZMIN

protected static final int EI_YMIN_ZMIN

Bit-field identifier.

See Also:

Constant Field Values

EI_YMIN_ZMAX

protected static final int EI_YMIN_ZMAX

Bit-field identifier.

See Also:

Constant Field Values

EI_YMAX_ZMIN

protected static final int EI_YMAX_ZMIN

Bit-field identifier.

See Also:

Constant Field Values

EI_YMAX_ZMAX

protected static final int EI_YMAX_ZMAX

Bit-field identifier.

See Also:

Constant Field Values

FI_XMIN

protected static final int FI_XMIN

Bit-field identifier.

See Also:

Constant Field Values

FI_XMAX

protected static final int FI_XMAX

Bit-field identifier.

See Also:

Constant Field Values

FI_YMIN

protected static final int FI_YMIN

Bit-field identifier.

See Also:

Constant Field Values

FI_YMAX

protected static final int FI_YMAX

Bit-field identifier.

See Also:

Constant Field Values

FI_ZMIN

protected static final int FI_ZMIN

Bit-field identifier.

See Also:

Constant Field Values

FI_ZMAX

protected static final int FI_ZMAX

Bit-field identifier.

See Also:

Constant Field Values

EB_XMIN_YMIN

protected static final int EB_XMIN_YMIN

Bit mask identifiers.

See Also:

Constant Field Values

EB_XMIN_YMAX

protected static final int EB_XMIN_YMAX

Bit mask identifier.

See Also:

Constant Field Values

EB_XMAX_YMIN

protected static final int EB_XMAX_YMIN

Bit mask identifier.

See Also:

Constant Field Values

EB_XMAX_YMAX

protected static final int EB_XMAX_YMAX

Bit mask identifier.

See Also:

Constant Field Values

EB_XMIN_ZMIN

protected static final int EB_XMIN_ZMIN

Bit mask identifier.

See Also:

Constant Field Values

EB_XMIN_ZMAX

protected static final int EB_XMIN_ZMAX

Bit mask identifier.

See Also:

Constant Field Values

EB_XMAX_ZMIN

protected static final int EB_XMAX_ZMIN

Bit mask identifier.

See Also:

Constant Field Values

EB_XMAX_ZMAX

protected static final int EB_XMAX_ZMAX

Bit mask identifier.

See Also:

Constant Field Values

EB_YMIN_ZMIN

protected static final int EB_YMIN_ZMIN

Bit mask identifier.

See Also:

Constant Field Values

EB_YMIN_ZMAX

protected static final int EB_YMIN_ZMAX

Bit mask identifier.

See Also:

Constant Field Values

EB_YMAX_ZMIN

protected static final int EB_YMAX_ZMIN

Bit mask identifier.

See Also:

Constant Field Values

EB_YMAX_ZMAX

protected static final int EB_YMAX_ZMAX

Bit mask identifier.

See Also:

Constant Field Values

m_aiData

protected int[] m_aiData

Data

m_fXDelta

protected float m_fXDelta

deltas

m_fYDelta

protected float m_fYDelta

deltas

m_fZDelta

protected float m_fZDelta

deltas

m_iXBound

protected int m_iXBound

bounds on each dimension of 3D data set and data itself.

m_iYBound

protected int m_iYBound

bounds on each dimension of 3D data set and data itself.

m_iZBound

protected int m_iZBound

bounds on each dimension of 3D data set and data itself.

m_iXYBound

protected int m_iXYBound

bound

m_kCentroid

protected Vector3f m_kCentroid

centroid

m_kE0

protected Vector3f m_kE0

temporary variables to avoid 'new' calls.

m_kE1

protected Vector3f m_kE1

temporary variable

m_kGradient

protected Vector3f m_kGradient

temporary variable

m_kN

protected Vector3f m_kN

temporary variable

Constructor Detail

ExtractSurfaceCubes

public ExtractSurfaceCubes(int iXBound,
                           int iYBound,
                           int iZBound,
                           int[] aiData)

Create a level surface extractor for a 3D image. The delta input values are important when the voxels are not cubic. For example, a typical MRI might have z-slice spacing about 5 times that of the x and y spacing. In this case, dx = 1, dy = 1, and dz = 5. The idea is that 1 is a 'voxel unit' and the z-slices are spaced by 5 voxel units.

Parameters:

iXBound - the number of columns in the 3D image

iYBound - the number of rows in the 3D image

iZBound - the number of slices in the 3D image

aiData - The image data stored in order of slice indices, each slice stored in row-major order. That is, slice z=0 is stored first, slice z=1 is stored next, and so on. In slice z=0, the y=0 row is stored first, the y=1 row is stored next, and so on.

Method Detail

addVertex

protected static int addVertex(Vector3f kV,
                               java.util.HashMap<Vector3f,java.lang.Integer> kVMap)

Called to add the specified point to the hashmap. If the specified point already exists in the hashmap, then it is not added. If it is added, the Integer value of the hashmap is set to the order of insertion index. The Integer value of this point in the hashmap, if added or if already found in the hashmap, is returned.

Parameters:

kV - Vector3f sample space coordinates of the point

kVMap - HashMap hashmap with Vector3f key and Integer value for adding the point if not already present

Returns:

insertion order index for the specified point

ExtractContour

public void ExtractContour(float level,
                           java.util.Vector<int[]> kTriTable,
                           java.util.Vector<Vector3f> vertices,
                           java.util.Vector<TriangleKey> triangles)

ExtractContour

public void ExtractContour(float level,
                           java.util.Vector<Vector3f> vertices,
                           java.util.Vector<TriangleKey> triangles)

getGradient

public Vector3f getGradient(Vector3f kP)

Interpolation of the gradient vector of the image. The voxel containing the input point is determined. A weighted combination of the gradient values at the vertices is used for the interpolated value. This vector is used to determine consistent normals for the triangles in the mesh representing the level surface.

Parameters:

kP - the sample space coordinates of the point to be interpolated

Returns:

the gradient at the input point

MakeUnique

public static void MakeUnique(java.util.Vector<Vector3f> vertices,
                              java.util.Vector<TriangleKey> triangles,
                              java.util.Vector<Vector3f> newVertices,
                              java.util.Vector<TriangleKey> newTriangles)

OrientTriangles

public void OrientTriangles(java.util.Vector<Vector3f> vertices,
                            java.util.Vector<TriangleKey> triangles,
                            boolean sameDir)

GetVertices

private int GetVertices(float level,
                        int x,
                        int y,
                        int z,
                        ExtractSurfaceCubes.VETable table)

GetXMaxEdges

private void GetXMaxEdges(int x,
                          int y,
                          int z,
                          int type,
                          ExtractSurfaceCubes.VETable table)

GetXMinEdges

private void GetXMinEdges(int x,
                          int y,
                          int z,
                          int type,
                          ExtractSurfaceCubes.VETable table)

GetYMaxEdges

private void GetYMaxEdges(int x,
                          int y,
                          int z,
                          int type,
                          ExtractSurfaceCubes.VETable table)

GetYMinEdges

private void GetYMinEdges(int x,
                          int y,
                          int z,
                          int type,
                          ExtractSurfaceCubes.VETable table)

GetZMaxEdges

private void GetZMaxEdges(int x,
                          int y,
                          int z,
                          int type,
                          ExtractSurfaceCubes.VETable table)

GetZMinEdges

private void GetZMinEdges(int x,
                          int y,
                          int z,
                          int type,
                          ExtractSurfaceCubes.VETable table)