Package gov.nih.mipav.view.renderer.WildMagic.Poisson.Octree

Class Octree

java.lang.Object

gov.nih.mipav.view.renderer.WildMagic.Poisson.Octree.Octree

public class Octree
extends java.lang.Object

Field Summary

Fields

Modifier and Type	Field	Description
private int	Degree
static int	DIMENSION
static float	EPSILON
FunctionData	fData
private Geometry	geo
static double	ITERATION_POWER
static double	maxMemoryUsage
static int	MEMORY_ALLOCATOR_BLOCK_SIZE
(package private) NeighborKey	neighborKey
(package private) NeighborKey2	neighborKey2
java.util.Vector<Point3D>	normals
static float	PAD_SIZE
float	postNormalSmooth
(package private) float	radius
static int	READ_SIZE
static float	ROUND_EPS
OctNode	tree
(package private) int	width

Constructor Summary

Constructors

Constructor	Description
Octree(int _Degree)

Method Summary

Modifier and Type	Method	Description
static int	AddTriangles(CoredMeshData mesh, java.util.Vector<CoredPointIndex>[] edges, java.util.Vector<Point3D> interiorPositions, int offSet)
static int	AddTriangles(CoredMeshData mesh, java.util.Vector<CoredPointIndex> edges, java.util.Vector<Point3D> interiorPositions, int offSet)
void	ClipTree()
static int	EdgeRootCount(OctNode node, int edgeIndex, int maxDepth)
void	finalize1(int refineNeighbors)
void	finalize2(int refineNeighbors)
float	getCenterValue(OctNode node)
float	getCornerValue(OctNode node, int corner)
void	getCornerValueAndNormal(OctNode node, int corner, float[] value, Point3D normal)
float	GetDivergence(int[] idx, Point3D normal)
float	GetDotProduct(int[] idx)
static int	GetEdgeLoops(java.util.Vector<Pair<java.lang.Long,java.lang.Long>> edges, java.util.Vector<java.util.Vector<Pair<java.lang.Long,java.lang.Long>>> loops)
int	GetFixedDepthLaplacian(SparseSymmetricMatrix matrix, int depth, SortedTreeNodes sNodes)
float	GetIsoValue()
float	GetLaplacian(int[] idx)
void	GetMCIsoEdges(OctNode node, java.util.HashMap<java.lang.Long,java.lang.Integer> boundaryRoots, java.util.HashMap<java.lang.Long,java.lang.Integer> interiorRoots, int sDepth, java.util.Vector<Pair<java.lang.Long,java.lang.Long>> edges)
void	GetMCIsoTriangles(float isoValue, CoredMeshData mesh, int fullDepthIso, int nonLinearFit)
int	GetMCIsoTriangles(OctNode node, CoredMeshData mesh, java.util.HashMap<java.lang.Long,java.lang.Integer> boundaryRoots, java.util.HashMap<java.lang.Long,java.lang.Integer> interiorRoots, java.util.Vector<Point3D> interiorPositions, int offSet, int sDepth)
void	GetMCIsoTriangles(java.lang.Float isoValue, int subdivideDepth, CoredMeshData mesh, int fullDepthIso, int nonLinearFit)
int	GetRestrictedFixedDepthLaplacian(SparseSymmetricMatrix matrix, int depth, int[] entries, int entryCount, OctNode rNode, float radius, SortedTreeNodes sNodes)
int	GetRoot(RootInfo ri, float isoValue, int maxDepth, Point3D position, java.util.HashMap<java.lang.Long,Pair<java.lang.Float,Point3D>> normals, Point3D normal, int nonLinearFit)
int	GetRoot(RootInfo ri, float isoValue, Point3D position, java.util.HashMap<java.lang.Long,Pair<java.lang.Float,Point3D>> normalHash, int nonLinearFit)
static int	GetRootIndex(OctNode node, int edgeIndex, int maxDepth, int sDepth, RootInfo ri)
static boolean	GetRootIndex(OctNode node, int edgeIndex, int maxDepth, RootInfo ri)
static int	GetRootIndex(java.lang.Long key, java.util.HashMap<java.lang.Long,java.lang.Integer> boundaryRoots, java.util.HashMap<java.lang.Long,java.lang.Integer> interiorRoots, CoredPointIndex index)
boolean	GetRootPair(RootInfo ri, int maxDepth, RootInfo pair)
int	HasNormals(OctNode node, float epsilon)
static int	InteriorFaceRootCount(OctNode node, int faceIndex, int maxDepth)
static boolean	IsBoundaryEdge(OctNode node, int edgeIndex, int subdivideDepth)
static boolean	IsBoundaryEdge(OctNode node, int dir, int x, int y, int subdivideDepth)
static int	IsBoundaryFace(OctNode node, int faceIndex, int subdivideDepth)
int	LaplacianMatrixIteration(int subdivideDepth)
void	NonLinearGetSampleDepthAndWeight(OctNode node, Point3D position, float samplesPerNode, float[] depth, float[] weight)
float	NonLinearGetSampleWeight(OctNode node, Point3D position)
void	NonLinearSplatOrientedPoint(Point3D position, Point3D normal, int splatDepth, float samplesPerNode, int minDepth, int maxDepth)
int	NonLinearSplatOrientedPoint(OctNode node, Point3D position, Point3D normal)
int	NonLinearUpdateWeightContribution(OctNode node, Point3D position, float weight)
static void	pause()	Pauses the display until the user hits enter.
void	PreValidate(float isoValue, int maxDepth, int subdivideDepth)
void	PreValidate(OctNode node, float isoValue, int maxDepth, int subdivideDepth)
void	printTree()
java.lang.String	readLine(java.io.InputStream in)
int	SetBoundaryMCRootPositions(int sDepth, float isoValue, java.util.HashMap<java.lang.Long,java.lang.Integer> boundaryRoots, java.util.HashMap<java.lang.Long,Pair<java.lang.Float,Point3D>> boundaryNormalHash, CoredMeshData mesh, int nonLinearFit)
void	setFunctionData(PPolynomial ReconstructionFunction, int maxDepth, int normalize, float normalSmooth)
void	SetIsoSurfaceCorners(float isoValue, int subdivideDepth, int fullDepthIso)
void	SetLaplacianWeights()
int	SetMCRootPositions(OctNode node, int sDepth, float isoValue, java.util.HashMap<java.lang.Long,java.lang.Integer> boundaryRoots, java.util.HashMap<java.lang.Long,java.lang.Integer> interiorRoots, java.util.HashMap<java.lang.Long,Pair<java.lang.Float,Point3D>> boundaryNormalHash, java.util.HashMap<java.lang.Long,Pair<java.lang.Float,Point3D>> interiorNormalHash, java.util.Vector<Point3D> interiorPositions, CoredMeshData mesh, int nonLinearFit)
void	setNodeIndices(OctNode node, int[] idx)
int	setTree(java.lang.String fileName, int maxDepth, int binary, int kernelDepth, float samplesPerNode, float scaleFactor, Point3D center, float[] scale, int resetSamples, int useConfidence)
int	SolveFixedDepthMatrix(int depth, int startingDepth, SortedTreeNodes sNodes)
int	SolveFixedDepthMatrix(int depth, SortedTreeNodes sNodes)
void	Subdivide(OctNode node, float isoValue, int maxDepth)
void	Validate(OctNode node, float isoValue, int maxDepth, int fullDepthIso)
void	Validate(OctNode node, float isoValue, int maxDepth, int fullDepthIso, int subdivideDepth)

Methods inherited from class java.lang.Object

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

Field Detail

DIMENSION

public static int DIMENSION

neighborKey

NeighborKey neighborKey

neighborKey2

NeighborKey2 neighborKey2

radius

float radius

width

int width

maxMemoryUsage

public static double maxMemoryUsage

normals

public java.util.Vector<Point3D> normals

postNormalSmooth

public float postNormalSmooth

tree

public OctNode tree

fData

public FunctionData fData

ITERATION_POWER

public static double ITERATION_POWER

MEMORY_ALLOCATOR_BLOCK_SIZE

public static int MEMORY_ALLOCATOR_BLOCK_SIZE

READ_SIZE

public static int READ_SIZE

PAD_SIZE

public static float PAD_SIZE

EPSILON

public static float EPSILON

ROUND_EPS

public static float ROUND_EPS

geo

private Geometry geo

Degree

private int Degree

Constructor Detail

Octree

public Octree(int _Degree)

Method Detail

setNodeIndices

public void setNodeIndices(OctNode node,
                           int[] idx)

NonLinearSplatOrientedPoint

public int NonLinearSplatOrientedPoint(OctNode node,
                                       Point3D position,
                                       Point3D normal)

NonLinearSplatOrientedPoint

public void NonLinearSplatOrientedPoint(Point3D position,
                                        Point3D normal,
                                        int splatDepth,
                                        float samplesPerNode,
                                        int minDepth,
                                        int maxDepth)

NonLinearGetSampleDepthAndWeight

public void NonLinearGetSampleDepthAndWeight(OctNode node,
                                             Point3D position,
                                             float samplesPerNode,
                                             float[] depth,
                                             float[] weight)

NonLinearGetSampleWeight

public float NonLinearGetSampleWeight(OctNode node,
                                      Point3D position)

NonLinearUpdateWeightContribution

public int NonLinearUpdateWeightContribution(OctNode node,
                                             Point3D position,
                                             float weight)

pause

public static void pause()

Pauses the display until the user hits enter.

readLine

public java.lang.String readLine(java.io.InputStream in)
                          throws java.io.IOException

Throws:

java.io.IOException

setTree

public int setTree(java.lang.String fileName,
                   int maxDepth,
                   int binary,
                   int kernelDepth,
                   float samplesPerNode,
                   float scaleFactor,
                   Point3D center,
                   float[] scale,
                   int resetSamples,
                   int useConfidence)

setFunctionData

public void setFunctionData(PPolynomial ReconstructionFunction,
                            int maxDepth,
                            int normalize,
                            float normalSmooth)

finalize1

public void finalize1(int refineNeighbors)

finalize2

public void finalize2(int refineNeighbors)

GetDivergence

public final float GetDivergence(int[] idx,
                                 Point3D normal)

GetLaplacian

public final float GetLaplacian(int[] idx)

GetDotProduct

public final float GetDotProduct(int[] idx)

GetFixedDepthLaplacian

public int GetFixedDepthLaplacian(SparseSymmetricMatrix matrix,
                                  int depth,
                                  SortedTreeNodes sNodes)

GetRestrictedFixedDepthLaplacian

public int GetRestrictedFixedDepthLaplacian(SparseSymmetricMatrix matrix,
                                            int depth,
                                            int[] entries,
                                            int entryCount,
                                            OctNode rNode,
                                            float radius,
                                            SortedTreeNodes sNodes)

LaplacianMatrixIteration

public int LaplacianMatrixIteration(int subdivideDepth)

SolveFixedDepthMatrix

public int SolveFixedDepthMatrix(int depth,
                                 SortedTreeNodes sNodes)

SolveFixedDepthMatrix

public int SolveFixedDepthMatrix(int depth,
                                 int startingDepth,
                                 SortedTreeNodes sNodes)

HasNormals

public int HasNormals(OctNode node,
                      float epsilon)

printTree

public void printTree()

ClipTree

public void ClipTree()

SetLaplacianWeights

public void SetLaplacianWeights()

GetMCIsoTriangles

public void GetMCIsoTriangles(float isoValue,
                              CoredMeshData mesh,
                              int fullDepthIso,
                              int nonLinearFit)

GetMCIsoTriangles

public void GetMCIsoTriangles(java.lang.Float isoValue,
                              int subdivideDepth,
                              CoredMeshData mesh,
                              int fullDepthIso,
                              int nonLinearFit)

getCenterValue

public float getCenterValue(OctNode node)

getCornerValue

public float getCornerValue(OctNode node,
                            int corner)

getCornerValueAndNormal

public void getCornerValueAndNormal(OctNode node,
                                    int corner,
                                    float[] value,
                                    Point3D normal)

GetIsoValue

public float GetIsoValue()

SetIsoSurfaceCorners

public void SetIsoSurfaceCorners(float isoValue,
                                 int subdivideDepth,
                                 int fullDepthIso)

Subdivide

public void Subdivide(OctNode node,
                      float isoValue,
                      int maxDepth)

InteriorFaceRootCount

public static int InteriorFaceRootCount(OctNode node,
                                        int faceIndex,
                                        int maxDepth)

EdgeRootCount

public static int EdgeRootCount(OctNode node,
                                int edgeIndex,
                                int maxDepth)

IsBoundaryFace

public static int IsBoundaryFace(OctNode node,
                                 int faceIndex,
                                 int subdivideDepth)

IsBoundaryEdge

public static boolean IsBoundaryEdge(OctNode node,
                                     int edgeIndex,
                                     int subdivideDepth)

IsBoundaryEdge

public static boolean IsBoundaryEdge(OctNode node,
                                     int dir,
                                     int x,
                                     int y,
                                     int subdivideDepth)

PreValidate

public void PreValidate(OctNode node,
                        float isoValue,
                        int maxDepth,
                        int subdivideDepth)

PreValidate

public void PreValidate(float isoValue,
                        int maxDepth,
                        int subdivideDepth)

Validate

public void Validate(OctNode node,
                     float isoValue,
                     int maxDepth,
                     int fullDepthIso)

Validate

public void Validate(OctNode node,
                     float isoValue,
                     int maxDepth,
                     int fullDepthIso,
                     int subdivideDepth)

GetRoot

public int GetRoot(RootInfo ri,
                   float isoValue,
                   Point3D position,
                   java.util.HashMap<java.lang.Long,Pair<java.lang.Float,Point3D>> normalHash,
                   int nonLinearFit)

GetRoot

public int GetRoot(RootInfo ri,
                   float isoValue,
                   int maxDepth,
                   Point3D position,
                   java.util.HashMap<java.lang.Long,Pair<java.lang.Float,Point3D>> normals,
                   Point3D normal,
                   int nonLinearFit)

GetRootIndex

public static int GetRootIndex(OctNode node,
                               int edgeIndex,
                               int maxDepth,
                               int sDepth,
                               RootInfo ri)

GetRootIndex

public static boolean GetRootIndex(OctNode node,
                                   int edgeIndex,
                                   int maxDepth,
                                   RootInfo ri)

GetRootPair

public boolean GetRootPair(RootInfo ri,
                           int maxDepth,
                           RootInfo pair)

GetRootIndex

public static int GetRootIndex(java.lang.Long key,
                               java.util.HashMap<java.lang.Long,java.lang.Integer> boundaryRoots,
                               java.util.HashMap<java.lang.Long,java.lang.Integer> interiorRoots,
                               CoredPointIndex index)

SetMCRootPositions

public int SetMCRootPositions(OctNode node,
                              int sDepth,
                              float isoValue,
                              java.util.HashMap<java.lang.Long,java.lang.Integer> boundaryRoots,
                              java.util.HashMap<java.lang.Long,java.lang.Integer> interiorRoots,
                              java.util.HashMap<java.lang.Long,Pair<java.lang.Float,Point3D>> boundaryNormalHash,
                              java.util.HashMap<java.lang.Long,Pair<java.lang.Float,Point3D>> interiorNormalHash,
                              java.util.Vector<Point3D> interiorPositions,
                              CoredMeshData mesh,
                              int nonLinearFit)

SetBoundaryMCRootPositions

public int SetBoundaryMCRootPositions(int sDepth,
                                      float isoValue,
                                      java.util.HashMap<java.lang.Long,java.lang.Integer> boundaryRoots,
                                      java.util.HashMap<java.lang.Long,Pair<java.lang.Float,Point3D>> boundaryNormalHash,
                                      CoredMeshData mesh,
                                      int nonLinearFit)

GetMCIsoEdges

public void GetMCIsoEdges(OctNode node,
                          java.util.HashMap<java.lang.Long,java.lang.Integer> boundaryRoots,
                          java.util.HashMap<java.lang.Long,java.lang.Integer> interiorRoots,
                          int sDepth,
                          java.util.Vector<Pair<java.lang.Long,java.lang.Long>> edges)

GetMCIsoTriangles

public int GetMCIsoTriangles(OctNode node,
                             CoredMeshData mesh,
                             java.util.HashMap<java.lang.Long,java.lang.Integer> boundaryRoots,
                             java.util.HashMap<java.lang.Long,java.lang.Integer> interiorRoots,
                             java.util.Vector<Point3D> interiorPositions,
                             int offSet,
                             int sDepth)

GetEdgeLoops

public static int GetEdgeLoops(java.util.Vector<Pair<java.lang.Long,java.lang.Long>> edges,
                               java.util.Vector<java.util.Vector<Pair<java.lang.Long,java.lang.Long>>> loops)

AddTriangles

public static int AddTriangles(CoredMeshData mesh,
                               java.util.Vector<CoredPointIndex>[] edges,
                               java.util.Vector<Point3D> interiorPositions,
                               int offSet)

AddTriangles

public static int AddTriangles(CoredMeshData mesh,
                               java.util.Vector<CoredPointIndex> edges,
                               java.util.Vector<Point3D> interiorPositions,
                               int offSet)