org.jmol.jvxl.readers

Class VolumeFileReader

java.lang.Object

org.jmol.jvxl.readers.SurfaceReader

org.jmol.jvxl.readers.SurfaceFileReader

org.jmol.jvxl.readers.VolumeFileReader

All Implemented Interfaces:

VertexDataServer

Direct Known Subclasses:

ApbsReader, CastepDensityReader, CubeReader, JaguarReader, JvxlXmlReader, MapFileReader, PltFormattedReader

abstract class VolumeFileReader
extends SurfaceFileReader

Field Summary

Fields

Modifier and Type	Field and Description
protected int	atomCount
protected javax.vecmath.Point3f[]	boundingBox
protected boolean	canDownsample
protected int	downsampleFactor
private int[]	downsampleRemainders
protected boolean	endOfData
private int	iPlaneRaw
protected boolean	isAngstroms
private int	nData
protected boolean	negativeAtomCount
private int	nSkipX
private int	nSkipY
private int	nSkipZ
protected int	nSurfaces
private boolean	preProcessPlanes
(package private) boolean	readerClosed
(package private) javax.vecmath.Point4f	thePlane
private float[][]	yzPlanesRaw

Fields inherited from class org.jmol.jvxl.readers.SurfaceFileReader

binarydoc, br, line, next, os

Fields inherited from class org.jmol.jvxl.readers.SurfaceReader

allowSigma, ANGSTROMS_PER_BOHR, anisotropy, center, cJvxlEdgeNaN, colorFractionBase, colorFractionRange, contourVertexCount, dataMax, dataMean, dataMin, defaultCutoff, defaultMappedDataMax, defaultMappedDataMin, eccentricityMatrix, eccentricityMatrixInverse, eccentricityRatio, eccentricityScale, edgeFractionBase, edgeFractionRange, fractionData, hasColorData, haveSurfaceAtoms, isAnisotropic, isEccentric, isJvxl, isProgressive, isQuiet, isXLowToHigh, jvxlColorDataRead, jvxlCutoff, jvxlData, jvxlDataIs2dContour, jvxlDataIsColorDensity, jvxlDataIsColorMapped, jvxlDataIsPrecisionColor, jvxlEdgeDataRead, jvxlFileHeaderBuffer, jvxlNSurfaceInts, jvxlVoxelBitSet, marchingCubes, marchingSquares, meshData, meshDataServer, minMax, nBytes, nDataPoints, nPointsX, nPointsY, nPointsZ, params, ptTemp, qpc, sg, vertexDataOnly, volumeData, volumetricOrigin, volumetricVectors, voxelCounts, voxelData, xyzMax, xyzMin, yzCount, yzPlanes

Constructor Summary

Constructors

Constructor and Description
VolumeFileReader(SurfaceGenerator sg, java.io.BufferedReader br)

Method Summary

Methods

Modifier and Type	Method and Description
protected static boolean	checkAtomLine(boolean isXLowToHigh, boolean isAngstroms, java.lang.String strAtomCount, java.lang.String atomLine, java.lang.StringBuffer bs) checks an atom line for "ANGSTROMS", possibly overriding the data's natural units, BOHR (similar to Gaussian CUBE files).
protected void	closeReader()
private int	countData(java.lang.String str)
protected float	getNextVoxelValue()
private void	getPlane(float[] plane, boolean doRecord)
float[]	getPlane(int x)
float[]	getPlaneProcessed(int x) Retrieve raw file planes and pass them to the calculation object for processing into new data.
protected float	getSurfacePointAndFraction(float cutoff, boolean isCutoffAbsolute, float valueA, float valueB, javax.vecmath.Point3f pointA, javax.vecmath.Vector3f edgeVector, int x, int y, int z, int vA, int vB, float[] fReturn, javax.vecmath.Point3f ptReturn)
float	getValue(int x, int y, int z, int ptyz) for readers only
protected java.util.BitSet	getVoxelBitSet(int nPoints)
protected void	gotoData(int n, int nPoints)
protected void	initializeSurfaceData()
protected float	nextVoxel()
protected abstract void	readParameters()
protected void	readSurfaceData(boolean isMapData)
protected boolean	readVolumeData(boolean isMapData)
protected boolean	readVolumeParameters(boolean isMapData)
private int	readVolumetricHeader()
protected void	readVoxelVector(int voxelVectorIndex)
protected float	recordData(float value)
protected java.lang.String	skipComments(boolean allowBlankLines)
protected void	skipData(int nPoints)
private void	skipVoxels(int n)

Methods inherited from class org.jmol.jvxl.readers.SurfaceFileReader

discardTempData, getNextQuotedString, getTokens, parseFloat, parseFloat, parseFloatArray, parseFloatArray, parseInt, parseInt, parseIntNext, readLine, setOutputStream, skipTo

Methods inherited from class org.jmol.jvxl.readers.SurfaceReader

addTriangleCheck, addVertexCopy, applyColorScale, colorIsosurface, createIsosurface, excludeMaximumSet, excludeMinimumSet, finalizeMapping, getColorPhaseIndex, getMinMaxMappedValues, getSurfaceAtomIndex, getSurfacePointIndexAndFraction, getValueAtPoint, gotoAndReadVoxelData, initializeMapping, initializeVolumetricData, initPlanes, jvxlUpdateInfo, newVoxelDataCube, postProcessVertices, readAndSetVolumeParameters, readColorData, resetIsosurface, selectPocket, setBoundingBox, setVectorAnisotropy, setVertexAnisotropy, setVolumeData, setVolumetricAnisotropy, setVolumetricOriginAnisotropy, slabIsosurface, updateSurfaceData, updateTriangles

Methods inherited from class java.lang.Object

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

Field Detail

endOfData

protected boolean endOfData

negativeAtomCount

protected boolean negativeAtomCount

atomCount

protected int atomCount

nSurfaces

protected int nSurfaces

isAngstroms

protected boolean isAngstroms

canDownsample

protected boolean canDownsample

downsampleRemainders

private int[] downsampleRemainders

preProcessPlanes

private boolean preProcessPlanes

nData

private int nData

readerClosed

boolean readerClosed

thePlane

javax.vecmath.Point4f thePlane

downsampleFactor

protected int downsampleFactor

nSkipX

private int nSkipX

nSkipY

private int nSkipY

nSkipZ

private int nSkipZ

yzPlanesRaw

private float[][] yzPlanesRaw

iPlaneRaw

private int iPlaneRaw

boundingBox

protected javax.vecmath.Point3f[] boundingBox

Constructor Detail

VolumeFileReader

VolumeFileReader(SurfaceGenerator sg,
                java.io.BufferedReader br)

Method Detail

recordData

protected float recordData(float value)

closeReader

protected void closeReader()

Overrides:

closeReader in class SurfaceFileReader

readVolumeParameters

protected boolean readVolumeParameters(boolean isMapData)

Specified by:

readVolumeParameters in class SurfaceReader

readVolumeData

protected boolean readVolumeData(boolean isMapData)

Specified by:

readVolumeData in class SurfaceReader

readVolumetricHeader

private int readVolumetricHeader()

readParameters

protected abstract void readParameters()
                                throws java.lang.Exception

Throws:

java.lang.Exception

skipComments

protected java.lang.String skipComments(boolean allowBlankLines)
                                 throws java.lang.Exception

Throws:

java.lang.Exception

readVoxelVector

protected void readVoxelVector(int voxelVectorIndex)
                        throws java.lang.Exception

Throws:

java.lang.Exception

initializeSurfaceData

protected void initializeSurfaceData()

readSurfaceData

protected void readSurfaceData(boolean isMapData)
                        throws java.lang.Exception

Specified by:

readSurfaceData in class SurfaceReader

Throws:

java.lang.Exception

getPlane

public float[] getPlane(int x)

Specified by:

getPlane in interface VertexDataServer

Overrides:

getPlane in class SurfaceReader

getPlaneProcessed

public float[] getPlaneProcessed(int x)

Retrieve raw file planes and pass them to the calculation object for processing into new data. Bob Hanson hansonr@stolaf.edu 6/7/2011

Parameters:

x -

Returns:

plane (for testing)

getPlane

private void getPlane(float[] plane,
            boolean doRecord)

getValue

public float getValue(int x,
             int y,
             int z,
             int ptyz)

Description copied from interface: VertexDataServer

for readers only

Specified by:

getValue in interface VertexDataServer

Overrides:

getValue in class SurfaceReader

Returns:

value[x][y][z]

skipVoxels

private void skipVoxels(int n)
                 throws java.lang.Exception

Throws:

java.lang.Exception

getVoxelBitSet

protected java.util.BitSet getVoxelBitSet(int nPoints)
                                   throws java.lang.Exception

Parameters:

nPoints -

Returns:

JVXL bitset

Throws:

java.lang.Exception

getNextVoxelValue

protected float getNextVoxelValue()
                           throws java.lang.Exception

Throws:

java.lang.Exception

nextVoxel

protected float nextVoxel()
                   throws java.lang.Exception

Throws:

java.lang.Exception

gotoData

protected void gotoData(int n,
            int nPoints)
                 throws java.lang.Exception

Overrides:

gotoData in class SurfaceReader

Throws:

java.lang.Exception

skipData

protected void skipData(int nPoints)
                 throws java.lang.Exception

Throws:

java.lang.Exception

countData

private int countData(java.lang.String str)

checkAtomLine

protected static boolean checkAtomLine(boolean isXLowToHigh,
                    boolean isAngstroms,
                    java.lang.String strAtomCount,
                    java.lang.String atomLine,
                    java.lang.StringBuffer bs)

checks an atom line for "ANGSTROMS", possibly overriding the data's natural units, BOHR (similar to Gaussian CUBE files).

Parameters:

isXLowToHigh -

isAngstroms -

strAtomCount -

atomLine -

bs -

Returns:

isAngstroms

getSurfacePointAndFraction

protected float getSurfacePointAndFraction(float cutoff,
                               boolean isCutoffAbsolute,
                               float valueA,
                               float valueB,
                               javax.vecmath.Point3f pointA,
                               javax.vecmath.Vector3f edgeVector,
                               int x,
                               int y,
                               int z,
                               int vA,
                               int vB,
                               float[] fReturn,
                               javax.vecmath.Point3f ptReturn)

Overrides:

getSurfacePointAndFraction in class SurfaceReader

x - TODO

y - TODO

z - TODO

Returns:

fractional distance from A to B