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 javajs.util.V3	edgeVector
private javajs.util.M3	inverseMatrix
boolean	isPeriodic
private boolean	isSquared
javajs.util.P4	mappingPlane
(package private) float	mappingPlaneNormalMag
float	maxGrid
private float	maxVectorLength
float	minGrid
private float	minToPlaneDistance
int	nPoints
float[]	origin
private javajs.util.P3	ptTemp
private javajs.util.P3	ptXyzTemp
javajs.util.V3[]	spanningVectors
SurfaceReader	sr
private javajs.util.P4	thePlane
private float	thePlaneNormalMag
javajs.util.V3[]	unitVolumetricVectors
private javajs.util.M3	volumetricMatrix
javajs.util.P3	volumetricOrigin
float[]	volumetricVectorLengths
javajs.util.V3[]	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

Modifier and Type	Method and Description
float	calculateFractionalPoint(float cutoff, javajs.util.P3 pointA, javajs.util.P3 pointB, float valueA, float valueB, javajs.util.P3 pt)
float	calcVoxelPlaneDistance(int x, int y, int z)
void	capData(javajs.util.P4 plane, float cutoff)
float	distancePointToPlane(javajs.util.T3 pt)
float	distanceToMappingPlane(javajs.util.T3 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, javajs.util.P3 pt)
int	getPointIndex(int x, int y, int z)
float	getToPlaneParameter()
float[]	getVolumetricVectorLengths()
int[]	getVoxelCounts()
float[][][]	getVoxelData()
float	getVoxelDataAt(int pt)
float	getVoxelValue(int x, int y, int z)
int	getYzCount()
boolean	hasPlane()
private int	indexLower(float x, int xMax) periodic grids should have val[0] == val[xMax] voxelCount: 1....2....3....4....5 xMax/index: 0....1....2....3....4....
private int	indexUpper(float x, int xLower, int xMax)
boolean	isNearPlane(int x, int y, int z, float toPlaneParameter)
float	lookupInterpolatedVoxelValue(javajs.util.T3 point, boolean getSource)
private float	mantissa(float f)
(package private) void	offsetCenter(javajs.util.P3 center)
void	setDataDistanceToPlane(javajs.util.P4 plane)
void	setMappingPlane(javajs.util.P4 plane)
private boolean	setMatrix()
void	setPlaneParameters(javajs.util.P4 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(int pt, float value)
void	setVoxelDataAsArray(float[][][] voxelData)
void	setVoxelMap()
void	setVoxelMapValue(int x, int y, int z, float v) for sparse data mapping, as for a plane
void	transform(javajs.util.V3 v1, javajs.util.V3 v2)
void	voxelPtToXYZ(int x, int y, int z, javajs.util.T3 pt)
void	xyzToVoxelPt(float x, float y, float z, javajs.util.T3i 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 javajs.util.P3 volumetricOrigin

origin

public final float[] origin

volumetricVectors

public final javajs.util.V3[] 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 javajs.util.V3[] unitVolumetricVectors

volumetricMatrix

private final javajs.util.M3 volumetricMatrix

inverseMatrix

private final javajs.util.M3 inverseMatrix

thePlane

private javajs.util.P4 thePlane

thePlaneNormalMag

private float thePlaneNormalMag

ptXyzTemp

private final javajs.util.P3 ptXyzTemp

xmlData

public java.lang.String xmlData

mappingPlane

public javajs.util.P4 mappingPlane

mappingPlaneNormalMag

float mappingPlaneNormalMag

minGrid

public float minGrid

maxGrid

public float maxGrid

voxelVolume

public float voxelVolume

spanningVectors

public javajs.util.V3[] spanningVectors

isPeriodic

public boolean isPeriodic

isSquared

private boolean isSquared

edgeVector

private final javajs.util.V3 edgeVector

ptTemp

private javajs.util.P3 ptTemp

Constructor Detail

VolumeData

public VolumeData()

Method Detail

getVoxelData

public float[][][] getVoxelData()

Specified by:

getVoxelData in interface VolumeDataInterface

setVoxelDataAsArray

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

Specified by:

setVoxelDataAsArray in interface VolumeDataInterface

hasPlane

public boolean hasPlane()

setMappingPlane

public void setMappingPlane(javajs.util.P4 plane)

distanceToMappingPlane

public float distanceToMappingPlane(javajs.util.T3 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

getVoxelDataAt

public float getVoxelDataAt(int pt)

getPointIndex

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

getPoint

public void getPoint(int ipt,
                     javajs.util.P3 pt)

setVoxelData

public void setVoxelData(int pt,
                         float value)

setVoxelMap

public void setVoxelMap()

setMatrix

private boolean setMatrix()

transform

public void transform(javajs.util.V3 v1,
                      javajs.util.V3 v2)

Specified by:

transform in interface VolumeDataInterface

setPlaneParameters

public void setPlaneParameters(javajs.util.P4 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(javajs.util.T3 pt)

Specified by:

distancePointToPlane in interface VolumeDataInterface

voxelPtToXYZ

public void voxelPtToXYZ(int x,
                         int y,
                         int z,
                         javajs.util.T3 pt)

Specified by:

voxelPtToXYZ in interface VolumeDataInterface

setUnitVectors

public boolean setUnitVectors()

xyzToVoxelPt

public void xyzToVoxelPt(float x,
                         float y,
                         float z,
                         javajs.util.T3i pt3i)

Specified by:

xyzToVoxelPt in interface VolumeDataInterface

lookupInterpolatedVoxelValue

public float lookupInterpolatedVoxelValue(javajs.util.T3 point,
                                          boolean getSource)

Specified by:

lookupInterpolatedVoxelValue in interface VolumeDataInterface

mantissa

private float mantissa(float f)

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)

indexLower

private int indexLower(float x,
                       int xMax)

periodic grids should have val[0] == val[xMax] voxelCount: 1....2....3....4....5 xMax/index: 0....1....2....3....4.... nonper. ^ ---> [0,0] ^ --> [4, 4] periodic ^ ---> [3,4] ^ --> [0, 1]

Parameters:

x -

xMax -

Returns:

lower index in range

indexUpper

private int indexUpper(float x,
                       int xLower,
                       int xMax)

offsetCenter

void offsetCenter(javajs.util.P3 center)

setDataDistanceToPlane

public void setDataDistanceToPlane(javajs.util.P4 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(javajs.util.P4 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,
                                      javajs.util.P3 pointA,
                                      javajs.util.P3 pointB,
                                      float valueA,
                                      float valueB,
                                      javajs.util.P3 pt)