abstract class VolumeFileReader extends SurfaceFileReader
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 boolean |
isScaledAlready |
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 |
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 and Description |
---|
VolumeFileReader(SurfaceGenerator sg,
java.io.BufferedReader br) |
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) |
private void |
scaleIsosurface(float scale) |
protected java.lang.String |
skipComments(boolean allowBlankLines) |
protected void |
skipData(int nPoints) |
private void |
skipVoxels(int n) |
discardTempData, getNextQuotedString, getTokens, parseFloat, parseFloat, parseFloatArray, parseFloatArray, parseInt, parseInt, parseIntNext, readLine, setOutputStream, skipTo
addTriangleCheck, addVertexCopy, applyColorScale, colorIsosurface, createIsosurface, excludeMaximumSet, excludeMinimumSet, finalizeMapping, getColorPhaseIndex, getMinMaxMappedValues, getSpanningVectors, getSurfaceAtomIndex, getSurfacePointIndexAndFraction, getValueAtPoint, gotoAndReadVoxelData, initializeMapping, initializeVolumetricData, initPlanes, jvxlUpdateInfo, newVoxelDataCube, postProcessVertices, readAndSetVolumeParameters, readColorData, resetIsosurface, selectPocket, setBoundingBox, setVectorAnisotropy, setVertexAnisotropy, setVolumeData, setVolumetricAnisotropy, setVolumetricOriginAnisotropy, slabIsosurface, updateSurfaceData, updateTriangles
protected boolean endOfData
protected boolean negativeAtomCount
protected int atomCount
protected int nSurfaces
protected boolean isAngstroms
protected boolean canDownsample
private int[] downsampleRemainders
private boolean preProcessPlanes
private int nData
boolean readerClosed
javax.vecmath.Point4f thePlane
protected int downsampleFactor
private int nSkipX
private int nSkipY
private int nSkipZ
private float[][] yzPlanesRaw
private int iPlaneRaw
protected javax.vecmath.Point3f[] boundingBox
private boolean isScaledAlready
VolumeFileReader(SurfaceGenerator sg, java.io.BufferedReader br)
protected float recordData(float value)
protected void closeReader()
closeReader
in class SurfaceFileReader
protected boolean readVolumeParameters(boolean isMapData)
readVolumeParameters
in class SurfaceReader
protected boolean readVolumeData(boolean isMapData)
readVolumeData
in class SurfaceReader
private int readVolumetricHeader()
protected abstract void readParameters() throws java.lang.Exception
java.lang.Exception
protected java.lang.String skipComments(boolean allowBlankLines) throws java.lang.Exception
java.lang.Exception
protected void readVoxelVector(int voxelVectorIndex) throws java.lang.Exception
java.lang.Exception
protected void initializeSurfaceData()
protected void readSurfaceData(boolean isMapData) throws java.lang.Exception
readSurfaceData
in class SurfaceReader
java.lang.Exception
public float[] getPlane(int x)
getPlane
in interface VertexDataServer
getPlane
in class SurfaceReader
public float[] getPlaneProcessed(int x)
x
- private void getPlane(float[] plane, boolean doRecord)
public float getValue(int x, int y, int z, int ptyz)
VertexDataServer
getValue
in interface VertexDataServer
getValue
in class SurfaceReader
private void skipVoxels(int n) throws java.lang.Exception
java.lang.Exception
protected java.util.BitSet getVoxelBitSet(int nPoints) throws java.lang.Exception
nPoints
- java.lang.Exception
protected float getNextVoxelValue() throws java.lang.Exception
java.lang.Exception
protected float nextVoxel() throws java.lang.Exception
java.lang.Exception
protected void gotoData(int n, int nPoints) throws java.lang.Exception
gotoData
in class SurfaceReader
java.lang.Exception
protected void skipData(int nPoints) throws java.lang.Exception
java.lang.Exception
private int countData(java.lang.String str)
protected static boolean checkAtomLine(boolean isXLowToHigh, boolean isAngstroms, java.lang.String strAtomCount, java.lang.String atomLine, java.lang.StringBuffer bs)
isXLowToHigh
- isAngstroms
- strAtomCount
- atomLine
- bs
- 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)
getSurfacePointAndFraction
in class SurfaceReader
x
- TODOy
- TODOz
- TODOprivate void scaleIsosurface(float scale)