abstract class VolumeFileReader extends SurfaceFileReader
Modifier and Type | Field and Description |
---|---|
protected int |
ac |
protected javajs.util.P3[] |
boundingBox |
protected boolean |
canDownsample |
protected int |
downsampleFactor |
protected int[] |
downsampleRemainders |
protected boolean |
endOfData |
private int |
iPlaneRaw |
protected boolean |
isAngstroms |
private boolean |
isScaledAlready |
private int |
nData |
protected boolean |
negativeAtomCount |
protected int |
nSkipX |
protected int |
nSkipY |
protected int |
nSkipZ |
protected int |
nSurfaces |
private boolean |
preProcessPlanes |
private boolean |
readerClosed |
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, isPeriodic, 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 |
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VolumeFileReader() |
Modifier and Type | Method and Description |
---|---|
protected static boolean |
checkAtomLine(boolean isXLowToHigh,
boolean isAngstroms,
java.lang.String strAtomCount,
java.lang.String atomLine,
javajs.util.SB 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 |
getSPFv(float cutoff,
boolean isCutoffAbsolute,
float valueA,
float valueB,
javajs.util.T3 pointA,
javajs.util.V3 edgeVector,
int x,
int y,
int z,
int vA,
int vB,
float[] fReturn,
javajs.util.T3 ptReturn) |
protected float |
getSurfacePointAndFraction(float cutoff,
boolean isCutoffAbsolute,
float valueA,
float valueB,
javajs.util.T3 pointA,
javajs.util.V3 edgeVector,
int x,
int y,
int z,
int vA,
int vB,
float[] fReturn,
javajs.util.T3 ptReturn) |
float |
getValue(int x,
int y,
int z,
int ptyz)
for readers only
|
protected BS |
getVoxelBitSet(int nPoints) |
protected void |
gotoData(int n,
int nPoints) |
(package private) void |
init2(SurfaceGenerator sg,
java.io.BufferedReader br) |
(package private) void |
init2VFR(SurfaceGenerator sg,
java.io.BufferedReader br) |
(package private) void |
initializeSurfaceData() |
protected float |
nextVoxel() |
protected abstract void |
readParameters() |
protected void |
readSurfaceData(boolean isMapData) |
protected void |
readSurfaceDataVFR(boolean isMapData) |
protected boolean |
readVolumeData(boolean isMapData) |
protected boolean |
readVolumeDataVFR(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) |
protected void |
skipDataVFR(int nPoints) |
private void |
skipVoxels(int n) |
protected void |
swapXZ() |
closeReaderSFR, discardTempData, getQuotedStringNext, getTokens, init, init2SFR, newBinaryDocument, parseFloat, parseFloatArray, parseFloatArrayStr, parseFloatRange, parseFloatStr, parseInt, parseIntNext, parseIntStr, rd, setOutputChannel, setStream, skipTo
addTriangleCheck, addVC, addVertexCopy, applyColorScale, colorIsosurface, createIsosurface, discardTempDataSR, excludeMaximumSet, excludeMinimumSet, finalizeMapping, getColorPhaseIndex, getMinMaxMappedValues, getPlane2, getSPF, getSurfaceAtomIndex, getSurfacePointIndexAndFraction, getValue2, getValueAtPoint, gotoAndReadVoxelData, initializeMapping, initializeVolumetricData, initPlanes, initSR, jvxlUpdateInfo, newVoxelDataCube, postProcessVertices, readAndSetVolumeParameters, readColorData, resetIsosurface, selectPocket, setBBox, setVectorAnisotropy, setVertexAnisotropy, setVolumeDataV, setVolumetricAnisotropy, setVolumetricOriginAnisotropy, slabIsosurface, updateSurfaceData, updateTriangles
protected boolean endOfData
protected boolean negativeAtomCount
protected int ac
protected int nSurfaces
protected boolean isAngstroms
protected boolean canDownsample
protected int[] downsampleRemainders
private boolean preProcessPlanes
private int nData
private boolean readerClosed
protected int downsampleFactor
protected int nSkipX
protected int nSkipY
protected int nSkipZ
private float[][] yzPlanesRaw
private int iPlaneRaw
protected javajs.util.P3[] boundingBox
private boolean isScaledAlready
void init2(SurfaceGenerator sg, java.io.BufferedReader br)
init2
in class SurfaceFileReader
void init2VFR(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
protected boolean readVolumeDataVFR(boolean isMapData)
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
void initializeSurfaceData()
protected void readSurfaceData(boolean isMapData) throws java.lang.Exception
readSurfaceData
in class SurfaceReader
java.lang.Exception
protected void readSurfaceDataVFR(boolean isMapData) throws java.lang.Exception
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 BS 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
protected void skipDataVFR(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, javajs.util.SB bs)
isXLowToHigh
- isAngstroms
- strAtomCount
- atomLine
- bs
- protected float getSurfacePointAndFraction(float cutoff, boolean isCutoffAbsolute, float valueA, float valueB, javajs.util.T3 pointA, javajs.util.V3 edgeVector, int x, int y, int z, int vA, int vB, float[] fReturn, javajs.util.T3 ptReturn)
getSurfacePointAndFraction
in class SurfaceReader
protected float getSPFv(float cutoff, boolean isCutoffAbsolute, float valueA, float valueB, javajs.util.T3 pointA, javajs.util.V3 edgeVector, int x, int y, int z, int vA, int vB, float[] fReturn, javajs.util.T3 ptReturn)
private void scaleIsosurface(float scale)
protected void swapXZ()