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 boolean |
getNCIPlanes |
private int |
iPlaneNCI |
protected boolean |
isAngstroms |
private boolean |
isScaledAlready |
protected int |
nData |
protected boolean |
negativeAtomCount |
protected int |
nSkipX |
protected int |
nSkipY |
protected int |
nSkipZ |
protected int |
nSurfaces |
protected 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 |
|---|
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() |
float[] |
getPlane(int x) |
float[] |
getPlaneNCI(int x)
Retrieve raw file planes and pass them to the calculation object for
processing into new data.
|
private void |
getPlaneVFR(float[] plane,
boolean doRecord) |
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 javajs.util.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, skipToaddTriangleCheck, addVC, addVertexCopy, applyColorScale, colorIsosurface, createIsosurface, discardTempDataSR, excludeMaximumSet, excludeMinimumSet, finalizeMapping, getColorPhaseIndex, getMinMaxMappedValues, getPlaneSR, 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, updateTrianglesprotected boolean endOfData
protected boolean negativeAtomCount
protected int ac
protected int nSurfaces
protected boolean isAngstroms
protected boolean canDownsample
protected int[] downsampleRemainders
private boolean getNCIPlanes
protected int nData
protected boolean readerClosed
protected int downsampleFactor
protected int nSkipX
protected int nSkipY
protected int nSkipZ
private float[][] yzPlanesRaw
private int iPlaneNCI
protected javajs.util.P3[] boundingBox
private boolean isScaledAlready
void init2(SurfaceGenerator sg, java.io.BufferedReader br)
init2 in class SurfaceFileReadervoid init2VFR(SurfaceGenerator sg, java.io.BufferedReader br)
protected float recordData(float value)
protected void closeReader()
closeReader in class SurfaceFileReaderprotected boolean readVolumeParameters(boolean isMapData)
readVolumeParameters in class SurfaceReaderprotected boolean readVolumeData(boolean isMapData)
readVolumeData in class SurfaceReaderprotected boolean readVolumeDataVFR(boolean isMapData)
private int readVolumetricHeader()
protected abstract void readParameters()
throws java.lang.Exception
java.lang.Exceptionprotected java.lang.String skipComments(boolean allowBlankLines)
throws java.lang.Exception
java.lang.Exceptionprotected void readVoxelVector(int voxelVectorIndex)
throws java.lang.Exception
java.lang.Exceptionvoid initializeSurfaceData()
protected void readSurfaceData(boolean isMapData)
throws java.lang.Exception
readSurfaceData in class SurfaceReaderjava.lang.Exceptionprotected void readSurfaceDataVFR(boolean isMapData)
throws java.lang.Exception
java.lang.Exceptionpublic float[] getPlane(int x)
getPlane in interface VertexDataServergetPlane in class SurfaceReaderpublic float[] getPlaneNCI(int x)
x - private void getPlaneVFR(float[] plane,
boolean doRecord)
public float getValue(int x,
int y,
int z,
int ptyz)
VertexDataServergetValue in interface VertexDataServergetValue in class SurfaceReaderprivate void skipVoxels(int n)
throws java.lang.Exception
java.lang.Exceptionprotected javajs.util.BS getVoxelBitSet(int nPoints)
throws java.lang.Exception
nPoints - java.lang.Exceptionprotected float getNextVoxelValue()
throws java.lang.Exception
java.lang.Exceptionprotected float nextVoxel()
throws java.lang.Exception
java.lang.Exceptionprotected void gotoData(int n,
int nPoints)
throws java.lang.Exception
gotoData in class SurfaceReaderjava.lang.Exceptionprotected void skipData(int nPoints)
throws java.lang.Exception
java.lang.Exceptionprotected void skipDataVFR(int nPoints)
throws java.lang.Exception
java.lang.Exceptionprivate 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 SurfaceReaderprotected 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()