org.jmol.jvxl.data

Class VolumeData

java.lang.Object

org.jmol.jvxl.data.VolumeData

All Implemented Interfaces:

VolumeDataInterface

public class VolumeData
extends java.lang.Object
implements VolumeDataInterface

Field Summary

Fields

Modifier and Type	Field and Description
boolean	doIterate
private javax.vecmath.Vector3f	edgeVector
private javax.vecmath.Matrix3f	inverseMatrix
boolean	isPeriodic
private boolean	isSquared
javax.vecmath.Point4f	mappingPlane
(package private) float	mappingPlaneNormalMag
float	maxGrid
private float	maxVectorLength
float	minGrid
private float	minToPlaneDistance
int	nPoints
float[]	origin
private javax.vecmath.Point3f	ptTemp
private javax.vecmath.Point3f	ptXyzTemp
SurfaceReader	sr
private javax.vecmath.Point4f	thePlane
private float	thePlaneNormalMag
javax.vecmath.Vector3f[]	unitVolumetricVectors
private javax.vecmath.Matrix3f	volumetricMatrix
javax.vecmath.Point3f	volumetricOrigin
float[]	volumetricVectorLengths
javax.vecmath.Vector3f[]	volumetricVectors
int[]	voxelCounts
private float[][][]	voxelData
private java.util.Map<java.lang.Integer,java.lang.Float>	voxelMap
float	voxelVolume
java.lang.String	xmlData
private int	yzCount

Constructor Summary

Constructors

Constructor and Description
VolumeData()

Method Summary

Methods

Modifier and Type	Method and Description
float	calculateFractionalPoint(float cutoff, javax.vecmath.Point3f pointA, javax.vecmath.Point3f pointB, float valueA, float valueB, javax.vecmath.Point3f pt)
float	calcVoxelPlaneDistance(int x, int y, int z)
void	capData(javax.vecmath.Point4f plane, float cutoff)
float	distancePointToPlane(javax.vecmath.Point3f pt)
float	distanceToMappingPlane(javax.vecmath.Point3f pt)
void	filterData(boolean isSquared, float invertCutoff)
static float	getFractional2DValue(float fx, float fy, float x11, float x12, float x21, float x22)
float[]	getOriginFloat()
void	getPoint(int ipt, javax.vecmath.Point3f pt)
int	getPointIndex(int x, int y, int z)
float	getToPlaneParameter()
float[]	getVolumetricVectorLengths()
int[]	getVoxelCounts()
float[][][]	getVoxelData()
float	getVoxelData(int pt)
float	getVoxelValue(int x, int y, int z)
int	getYzCount()
boolean	hasPlane()
private static int	indexDown(float value, int iMax)
boolean	isNearPlane(int x, int y, int z, float toPlaneParameter)
float	lookupInterpolatedVoxelValue(javax.vecmath.Point3f point)
(package private) void	offsetCenter(javax.vecmath.Point3f center)
void	setDataDistanceToPlane(javax.vecmath.Point4f plane)
void	setMappingPlane(javax.vecmath.Point4f plane)
private boolean	setMatrix()
void	setPlaneParameters(javax.vecmath.Point4f plane)
boolean	setUnitVectors()
void	setVolumetricOrigin(float x, float y, float z)
void	setVolumetricVector(int i, float x, float y, float z)
java.lang.String	setVolumetricXml()
int	setVoxelCounts(int nPointsX, int nPointsY, int nPointsZ)
void	setVoxelData(float[][][] voxelData)
void	setVoxelData(int pt, float value)
void	setVoxelMap()
void	setVoxelMapValue(int x, int y, int z, float v) for sparse data mapping, as for a plane
void	transform(javax.vecmath.Vector3f v1, javax.vecmath.Vector3f v2)
void	voxelPtToXYZ(int x, int y, int z, javax.vecmath.Point3f pt)
void	xyzToVoxelPt(float x, float y, float z, javax.vecmath.Point3i pt3i)

Methods inherited from class java.lang.Object

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

Field Detail

sr

public SurfaceReader sr

doIterate

public boolean doIterate

volumetricOrigin

public final javax.vecmath.Point3f volumetricOrigin

origin

public final float[] origin

volumetricVectors

public final javax.vecmath.Vector3f[] volumetricVectors

voxelCounts

public final int[] voxelCounts

nPoints

public int nPoints

voxelData

private float[][][] voxelData

voxelMap

private java.util.Map<java.lang.Integer,java.lang.Float> voxelMap

volumetricVectorLengths

public final float[] volumetricVectorLengths

maxVectorLength

private float maxVectorLength

minToPlaneDistance

private float minToPlaneDistance

yzCount

private int yzCount

unitVolumetricVectors

public final javax.vecmath.Vector3f[] unitVolumetricVectors

volumetricMatrix

private final javax.vecmath.Matrix3f volumetricMatrix

inverseMatrix

private final javax.vecmath.Matrix3f inverseMatrix

thePlane

private javax.vecmath.Point4f thePlane

thePlaneNormalMag

private float thePlaneNormalMag

ptXyzTemp

private final javax.vecmath.Point3f ptXyzTemp

xmlData

public java.lang.String xmlData

mappingPlane

public javax.vecmath.Point4f mappingPlane

mappingPlaneNormalMag

float mappingPlaneNormalMag

minGrid

public float minGrid

maxGrid

public float maxGrid

voxelVolume

public float voxelVolume

isPeriodic

public boolean isPeriodic

isSquared

private boolean isSquared

edgeVector

private final javax.vecmath.Vector3f edgeVector

ptTemp

private javax.vecmath.Point3f ptTemp

Constructor Detail

VolumeData

public VolumeData()

Method Detail

getVoxelData

public float[][][] getVoxelData()

Specified by:

getVoxelData in interface VolumeDataInterface

setVoxelData

public void setVoxelData(float[][][] voxelData)

Specified by:

setVoxelData in interface VolumeDataInterface

hasPlane

public boolean hasPlane()

setMappingPlane

public void setMappingPlane(javax.vecmath.Point4f plane)

distanceToMappingPlane

public float distanceToMappingPlane(javax.vecmath.Point3f pt)

setVolumetricOrigin

public void setVolumetricOrigin(float x,
                       float y,
                       float z)

Specified by:

setVolumetricOrigin in interface VolumeDataInterface

getOriginFloat

public float[] getOriginFloat()

Specified by:

getOriginFloat in interface VolumeDataInterface

getYzCount

public int getYzCount()

getVolumetricVectorLengths

public float[] getVolumetricVectorLengths()

Specified by:

getVolumetricVectorLengths in interface VolumeDataInterface

setVolumetricVector

public void setVolumetricVector(int i,
                       float x,
                       float y,
                       float z)

Specified by:

setVolumetricVector in interface VolumeDataInterface

getVoxelCounts

public int[] getVoxelCounts()

Specified by:

getVoxelCounts in interface VolumeDataInterface

setVoxelCounts

public int setVoxelCounts(int nPointsX,
                 int nPointsY,
                 int nPointsZ)

Specified by:

setVoxelCounts in interface VolumeDataInterface

getVoxelData

public float getVoxelData(int pt)

getPointIndex

public int getPointIndex(int x,
                int y,
                int z)

getPoint

public void getPoint(int ipt,
            javax.vecmath.Point3f pt)

setVoxelData

public void setVoxelData(int pt,
                float value)

setVoxelMap

public void setVoxelMap()

setMatrix

private boolean setMatrix()

transform

public void transform(javax.vecmath.Vector3f v1,
             javax.vecmath.Vector3f v2)

Specified by:

transform in interface VolumeDataInterface

setPlaneParameters

public void setPlaneParameters(javax.vecmath.Point4f plane)

Specified by:

setPlaneParameters in interface VolumeDataInterface

calcVoxelPlaneDistance

public float calcVoxelPlaneDistance(int x,
                           int y,
                           int z)

Specified by:

calcVoxelPlaneDistance in interface VolumeDataInterface

getToPlaneParameter

public float getToPlaneParameter()

isNearPlane

public boolean isNearPlane(int x,
                  int y,
                  int z,
                  float toPlaneParameter)

distancePointToPlane

public float distancePointToPlane(javax.vecmath.Point3f pt)

Specified by:

distancePointToPlane in interface VolumeDataInterface

voxelPtToXYZ

public void voxelPtToXYZ(int x,
                int y,
                int z,
                javax.vecmath.Point3f pt)

Specified by:

voxelPtToXYZ in interface VolumeDataInterface

setUnitVectors

public boolean setUnitVectors()

xyzToVoxelPt

public void xyzToVoxelPt(float x,
                float y,
                float z,
                javax.vecmath.Point3i pt3i)

Specified by:

xyzToVoxelPt in interface VolumeDataInterface

lookupInterpolatedVoxelValue

public float lookupInterpolatedVoxelValue(javax.vecmath.Point3f point)

Specified by:

lookupInterpolatedVoxelValue in interface VolumeDataInterface

getVoxelValue

public float getVoxelValue(int x,
                  int y,
                  int z)

getFractional2DValue

public static float getFractional2DValue(float fx,
                         float fy,
                         float x11,
                         float x12,
                         float x21,
                         float x22)

indexDown

private static int indexDown(float value,
            int iMax)

offsetCenter

void offsetCenter(javax.vecmath.Point3f center)

setDataDistanceToPlane

public void setDataDistanceToPlane(javax.vecmath.Point4f plane)

Specified by:

setDataDistanceToPlane in interface VolumeDataInterface

filterData

public void filterData(boolean isSquared,
              float invertCutoff)

Specified by:

filterData in interface VolumeDataInterface

capData

public void capData(javax.vecmath.Point4f plane,
           float cutoff)

Specified by:

capData in interface VolumeDataInterface

setVolumetricXml

public java.lang.String setVolumetricXml()

setVoxelMapValue

public void setVoxelMapValue(int x,
                    int y,
                    int z,
                    float v)

for sparse data mapping, as for a plane

Parameters:

x -

y -

z -

v -

calculateFractionalPoint

public float calculateFractionalPoint(float cutoff,
                             javax.vecmath.Point3f pointA,
                             javax.vecmath.Point3f pointB,
                             float valueA,
                             float valueB,
                             javax.vecmath.Point3f pt)