org.jmol.jvxl.readers

Class VoxelReader

public abstract class VoxelReader extends Object implements VertexDataServer

Field Summary
static floatANGSTROMS_PER_BOHR
floatassocCutoff
protected charcJvxlEdgeNaN
protected ColorEncodercolorEncoder
protected intcolorFractionBase
protected intcolorFractionRange
static String[]colorPhases
protected intcontourVertexCount
static intdefaultColorFractionBase
static intdefaultColorFractionRange
static floatdefaultCutoff
static intdefaultEdgeFractionBase
static intdefaultEdgeFractionRange
static floatdefaultMappedDataMax
static floatdefaultMappedDataMin
intedgeCount
protected intedgeFractionBase
protected intedgeFractionRange
protected StringBufferfractionData
float[]fReturn
protected booleanisApbsDx
protected booleanisJvxl
protected booleanisProgressive
protected booleanisXLowToHigh
protected StringjvxlColorDataRead
protected floatjvxlCutoff
protected JvxlDatajvxlData
protected booleanjvxlDataIs2dContour
protected booleanjvxlDataIsColorMapped
protected booleanjvxlDataIsPrecisionColor
protected StringjvxlEdgeDataRead
protected StringBufferjvxlFileHeaderBuffer
protected intjvxlNSurfaceInts
MarchingCubesmarchingCubes
protected MarchingSquaresmarchingSquares
protected MeshDatameshData
protected MeshDataServermeshDataServer
protected intnBytes
protected intnDataPoints
protected intnPointsX
protected intnPointsY
protected intnPointsZ
protected Parametersparams
protected Point3fptTemp
protected SurfaceGeneratorsg
protected VolumeDatavolumeData
protected Point3fvolumetricOrigin
protected Vector3f[]volumetricVectors
protected int[]voxelCounts
protected float[][][]voxelData
Constructor Summary
VoxelReader(SurfaceGenerator sg)
Method Summary
voidaddTriangleCheck(int iA, int iB, int iC, int check, boolean isAbsolute)
intaddVertexCopy(Point3f vertexXYZ, float value, int assocVertex)
voidapplyColorScale()
voidcolorData()
voidcolorIsosurface()
booleancreateIsosurface(boolean justForPlane)
voiddiscardTempData(boolean discardAll)
voidexcludeMaximumSet()
voidexcludeMinimumSet()
voidgenerateSurfaceData()
voidgetCalcPoint(Point3f pt)
protected shortgetColorIndexFromPalette(float value)
static intgetColorPhaseIndex(String color)
floatgetMaxMappedValue()
floatgetMinMappedValue()
floatgetPhase(Point3f pt)
intgetSurfacePointIndex(float cutoff, boolean isCutoffAbsolute, int x, int y, int z, Point3i offset, int vA, int vB, float valueA, float valueB, Point3f pointA, Vector3f edgeVector, boolean isContourType)
protected voidgotoAndReadVoxelData(boolean isMapData)
protected voidgotoData(int n, int nPoints)
protected voidinitializeVolumetricData()
protected static booleanisInside(float voxelValue, float max, boolean isAbsolute)
voidjvxlUpdateInfo()
protected StringreadColorData()
protected floatreadSurfacePoint(float cutoff, boolean isCutoffAbsolute, float valueA, float valueB, Point3f pointA, Vector3f edgeVector, float[] fReturn, Point3f ptReturn)
abstract voidreadVolumeData(boolean isMapData)
abstract voidreadVolumeParameters()
protected abstract voidreadVoxelData(boolean isMapData)
voidresetIsosurface()
voidselectPocket(boolean doExclude)
voidsetVolumeData(VolumeData v)
voidupdateSurfaceData()
voidupdateTriangles()

Field Detail

ANGSTROMS_PER_BOHR

static final float ANGSTROMS_PER_BOHR

assocCutoff

private float assocCutoff

cJvxlEdgeNaN

protected char cJvxlEdgeNaN

colorEncoder

protected ColorEncoder colorEncoder

colorFractionBase

protected int colorFractionBase

colorFractionRange

protected int colorFractionRange

colorPhases

private static final String[] colorPhases

contourVertexCount

protected int contourVertexCount

defaultColorFractionBase

static final int defaultColorFractionBase

defaultColorFractionRange

static final int defaultColorFractionRange

defaultCutoff

static final float defaultCutoff

defaultEdgeFractionBase

static final int defaultEdgeFractionBase

defaultEdgeFractionRange

static final int defaultEdgeFractionRange

defaultMappedDataMax

static final float defaultMappedDataMax

defaultMappedDataMin

static final float defaultMappedDataMin

edgeCount

private int edgeCount

edgeFractionBase

protected int edgeFractionBase

edgeFractionRange

protected int edgeFractionRange

fractionData

protected StringBuffer fractionData

fReturn

final float[] fReturn

isApbsDx

protected boolean isApbsDx

isJvxl

protected boolean isJvxl

isProgressive

protected boolean isProgressive

isXLowToHigh

protected boolean isXLowToHigh

jvxlColorDataRead

protected String jvxlColorDataRead

jvxlCutoff

protected float jvxlCutoff

jvxlData

protected JvxlData jvxlData

jvxlDataIs2dContour

protected boolean jvxlDataIs2dContour

jvxlDataIsColorMapped

protected boolean jvxlDataIsColorMapped

jvxlDataIsPrecisionColor

protected boolean jvxlDataIsPrecisionColor

jvxlEdgeDataRead

protected String jvxlEdgeDataRead

jvxlFileHeaderBuffer

protected StringBuffer jvxlFileHeaderBuffer

jvxlNSurfaceInts

protected int jvxlNSurfaceInts

marchingCubes

private MarchingCubes marchingCubes

marchingSquares

protected MarchingSquares marchingSquares

meshData

protected MeshData meshData

meshDataServer

protected MeshDataServer meshDataServer

nBytes

protected int nBytes

nDataPoints

protected int nDataPoints

nPointsX

protected int nPointsX

nPointsY

protected int nPointsY

nPointsZ

protected int nPointsZ

params

protected Parameters params

ptTemp

protected final Point3f ptTemp

sg

protected SurfaceGenerator sg

volumeData

protected VolumeData volumeData

volumetricOrigin

protected Point3f volumetricOrigin

volumetricVectors

protected Vector3f[] volumetricVectors

voxelCounts

protected int[] voxelCounts

voxelData

protected float[][][] voxelData

Constructor Detail

VoxelReader

VoxelReader(SurfaceGenerator sg)

Method Detail

addTriangleCheck

public void addTriangleCheck(int iA, int iB, int iC, int check, boolean isAbsolute)

addVertexCopy

public int addVertexCopy(Point3f vertexXYZ, float value, int assocVertex)

applyColorScale

void applyColorScale()

colorData

private void colorData()

colorIsosurface

void colorIsosurface()

createIsosurface

boolean createIsosurface(boolean justForPlane)

discardTempData

void discardTempData(boolean discardAll)

excludeMaximumSet

void excludeMaximumSet()

excludeMinimumSet

void excludeMinimumSet()

generateSurfaceData

private void generateSurfaceData()

getCalcPoint

public void getCalcPoint(Point3f pt)

getColorIndexFromPalette

protected short getColorIndexFromPalette(float value)

getColorPhaseIndex

static int getColorPhaseIndex(String color)

getMaxMappedValue

float getMaxMappedValue()

getMinMappedValue

float getMinMappedValue()

getPhase

private float getPhase(Point3f pt)

getSurfacePointIndex

public int getSurfacePointIndex(float cutoff, boolean isCutoffAbsolute, int x, int y, int z, Point3i offset, int vA, int vB, float valueA, float valueB, Point3f pointA, Vector3f edgeVector, boolean isContourType)

gotoAndReadVoxelData

protected void gotoAndReadVoxelData(boolean isMapData)

gotoData

protected void gotoData(int n, int nPoints)

initializeVolumetricData

protected void initializeVolumetricData()

isInside

protected static boolean isInside(float voxelValue, float max, boolean isAbsolute)

jvxlUpdateInfo

void jvxlUpdateInfo()

readColorData

protected String readColorData()

readSurfacePoint

protected float readSurfacePoint(float cutoff, boolean isCutoffAbsolute, float valueA, float valueB, Point3f pointA, Vector3f edgeVector, float[] fReturn, Point3f ptReturn)

readVolumeData

abstract void readVolumeData(boolean isMapData)

readVolumeParameters

abstract void readVolumeParameters()

readVoxelData

protected abstract void readVoxelData(boolean isMapData)

resetIsosurface

void resetIsosurface()

selectPocket

public void selectPocket(boolean doExclude)

setVolumeData

void setVolumeData(VolumeData v)

updateSurfaceData

void updateSurfaceData()

updateTriangles

void updateTriangles()