class VolumeDataReader extends SurfaceReader
Modifier and Type | Field and Description |
---|---|
protected boolean |
allowMapData |
protected int |
dataType |
protected int |
maxGrid |
protected javajs.util.P3 |
point |
protected boolean |
precalculateVoxelData |
protected float |
ptsPerAngstrom |
protected boolean |
useOriginStepsPoints |
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 |
---|
VolumeDataReader() |
Modifier and Type | Method and Description |
---|---|
protected void |
closeReader() |
protected void |
generateCube() |
(package private) void |
init(SurfaceGenerator sg)
implemented in SurfaceFileReader and
|
protected void |
initVDR(SurfaceGenerator sg) |
protected void |
readSurfaceData(boolean isMapData) |
protected void |
readSurfaceDataVDR(boolean isMapData) |
protected boolean |
readVolumeData(boolean isMapData) |
protected boolean |
readVolumeParameters(boolean isMapData) |
protected void |
readVoxelDataIndividually(boolean isMapData) |
(package private) void |
setup(boolean isMapData) |
protected void |
setVolumeData() |
protected boolean |
setVolumeDataParams() |
protected int |
setVoxelRange(int index,
float min,
float max,
float ptsPerAngstrom,
int gridMax,
float minPointsPerAngstrom) |
protected void |
showGridInfo() |
addTriangleCheck, addVC, addVertexCopy, applyColorScale, colorIsosurface, createIsosurface, discardTempData, discardTempDataSR, excludeMaximumSet, excludeMinimumSet, finalizeMapping, getColorPhaseIndex, getMinMaxMappedValues, getPlane, getPlane2, getSPF, getSurfaceAtomIndex, getSurfacePointAndFraction, getSurfacePointIndexAndFraction, getValue, getValue2, getValueAtPoint, gotoAndReadVoxelData, gotoData, initializeMapping, initializeVolumetricData, initPlanes, initSR, jvxlUpdateInfo, newVoxelDataCube, postProcessVertices, readAndSetVolumeParameters, readColorData, resetIsosurface, selectPocket, setBBox, setOutputChannel, setVectorAnisotropy, setVertexAnisotropy, setVolumeDataV, setVolumetricAnisotropy, setVolumetricOriginAnisotropy, slabIsosurface, updateSurfaceData, updateTriangles
protected int dataType
protected boolean precalculateVoxelData
protected boolean allowMapData
protected javajs.util.P3 point
protected float ptsPerAngstrom
protected int maxGrid
protected boolean useOriginStepsPoints
void init(SurfaceGenerator sg)
SurfaceReader
init
in class SurfaceReader
protected void initVDR(SurfaceGenerator sg)
void setup(boolean isMapData)
isMapData
- protected boolean readVolumeParameters(boolean isMapData)
readVolumeParameters
in class SurfaceReader
protected boolean readVolumeData(boolean isMapData)
readVolumeData
in class SurfaceReader
protected void readVoxelDataIndividually(boolean isMapData) throws java.lang.Exception
java.lang.Exception
protected void setVolumeData()
protected boolean setVolumeDataParams()
protected void showGridInfo()
protected int setVoxelRange(int index, float min, float max, float ptsPerAngstrom, int gridMax, float minPointsPerAngstrom)
index
- min
- max
- ptsPerAngstrom
- gridMax
- minPointsPerAngstrom
- -- added, but not necessaryprotected void readSurfaceData(boolean isMapData) throws java.lang.Exception
readSurfaceData
in class SurfaceReader
java.lang.Exception
protected void readSurfaceDataVDR(boolean isMapData) throws java.lang.Exception
java.lang.Exception
protected void generateCube()
protected void closeReader()
closeReader
in class SurfaceReader