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, CubeReader, DelPhiBinaryReader, JaguarReader, JvxlXmlReader, MapFileReader, PeriodicVolumeFileReader, PltFormattedReader, UhbdReader, XsfReader
```
abstract class VolumeFileReader
extends SurfaceFileReader
```

Field Summary

Fields
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`
`private boolean`	`readerClosed`
`private float[][]`	`yzPlanesRaw`

Fields inherited from class org.jmol.jvxl.readers.SurfaceFileReader
binarydoc, br, line, next, out

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, 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 Summary

Constructors
Constructor and Description

VolumeFileReader()

Constructors
Constructor and Description
`VolumeFileReader()`

Method Summary

All Methods Static Methods Instance Methods Abstract Methods Concrete Methods
Modifier and Type	Method and Description
`protected static boolean`	`checkAtomLine(boolean isXLowToHigh, boolean isAngstroms, String strAtomCount, 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(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 BS`	`getVoxelBitSet(int nPoints)`
`protected void`	`gotoData(int n, int nPoints)`
`(package private) void`	`init2(SurfaceGenerator sg, BufferedReader br)`
`(package private) void`	`init2VFR(SurfaceGenerator sg, 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 String`	`skipComments(boolean allowBlankLines)`
`protected void`	`skipData(int nPoints)`
`protected void`	`skipDataVFR(int nPoints)`
`private void`	`skipVoxels(int n)`
`protected void`	`swapXZ()`

Methods inherited from class org.jmol.jvxl.readers.SurfaceFileReader
closeReaderSFR, discardTempData, getQuotedStringNext, getTokens, init, init2SFR, newBinaryDocument, parseFloat, parseFloatArray, parseFloatArrayStr, parseFloatRange, parseFloatStr, parseInt, parseIntNext, parseIntStr, rd, setOutputChannel, setStream, skipTo

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
```

ac
```
protected int ac
```

nSurfaces
```
protected int nSurfaces
```

isAngstroms
```
protected boolean isAngstroms
```

canDownsample
```
protected boolean canDownsample
```

downsampleRemainders
```
protected int[] downsampleRemainders
```

getNCIPlanes
```
private boolean getNCIPlanes
```

nData
```
protected int nData
```

readerClosed
```
private boolean readerClosed
```

downsampleFactor
```
protected int downsampleFactor
```

nSkipX
```
protected int nSkipX
```

nSkipY
```
protected int nSkipY
```

nSkipZ
```
protected int nSkipZ
```

yzPlanesRaw
```
private float[][] yzPlanesRaw
```

iPlaneNCI
```
private int iPlaneNCI
```

boundingBox
```
protected javajs.util.P3[] boundingBox
```

isScaledAlready
```
private boolean isScaledAlready
```

Constructor Detail
- VolumeFileReader
```
VolumeFileReader()
```

Method Detail

init2

void init2(SurfaceGenerator sg,
           BufferedReader br)

Overrides:: init2 in class SurfaceFileReader

init2VFR

void init2VFR(SurfaceGenerator sg,
              BufferedReader br)

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

readVolumeDataVFR

protected boolean readVolumeDataVFR(boolean isMapData)

readVolumetricHeader
```
private int readVolumetricHeader()
```

readParameters

protected abstract void readParameters()
                                throws Exception

Throws:: Exception

skipComments

protected String skipComments(boolean allowBlankLines)
                       throws Exception

Throws:: Exception

readVoxelVector

protected void readVoxelVector(int voxelVectorIndex)
                        throws Exception

Throws:: Exception

initializeSurfaceData
```
void initializeSurfaceData()
```

readSurfaceData

protected void readSurfaceData(boolean isMapData)
                        throws Exception

Specified by:: readSurfaceData in class SurfaceReader
Throws:: Exception

readSurfaceDataVFR

protected void readSurfaceDataVFR(boolean isMapData)
                           throws Exception

Throws:: Exception

getPlane
```
public float[] getPlane(int x)
```
Specified by:

getPlane in interface VertexDataServer

Overrides:

getPlane in class SurfaceReader

getPlaneNCI
```
public float[] getPlaneNCI(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)

getPlaneVFR

private void getPlaneVFR(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 Exception

Throws:: Exception

getVoxelBitSet

protected BS getVoxelBitSet(int nPoints)
                     throws Exception

Parameters:: nPoints -
Returns:: JVXL bitset
Throws:: Exception

getNextVoxelValue

protected float getNextVoxelValue()
                           throws Exception

Throws:: Exception

nextVoxel

protected float nextVoxel()
                   throws Exception

Throws:: Exception

gotoData

protected void gotoData(int n,
                        int nPoints)
                 throws Exception

Overrides:: gotoData in class SurfaceReader
Throws:: Exception

skipData

protected void skipData(int nPoints)
                 throws Exception

Throws:: Exception

skipDataVFR

protected void skipDataVFR(int nPoints)
                    throws Exception

Throws:: Exception

countData
```
private int countData(String str)
```

checkAtomLine

protected static boolean checkAtomLine(boolean isXLowToHigh,
                                       boolean isAngstroms,
                                       String strAtomCount,
                                       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).

Parameters:: isXLowToHigh -; isAngstroms -; strAtomCount -; atomLine -; bs -
Returns:: isAngstroms

getSurfacePointAndFraction

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)

Overrides:: getSurfacePointAndFraction in class SurfaceReader

getSPFv

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)

scaleIsosurface

private void scaleIsosurface(float scale)

swapXZ
```
protected void swapXZ()
```

Class VolumeFileReader

Field Summary

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

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

Constructor Summary

Method Summary

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

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

Methods inherited from class java.lang.Object

Field Detail

endOfData

negativeAtomCount

ac

nSurfaces

isAngstroms

canDownsample

downsampleRemainders

getNCIPlanes

nData

readerClosed

downsampleFactor

nSkipX

nSkipY

nSkipZ

yzPlanesRaw

iPlaneNCI

boundingBox

isScaledAlready

Constructor Detail

VolumeFileReader

Method Detail

init2

init2VFR

recordData

closeReader

readVolumeParameters

readVolumeData

readVolumeDataVFR

readVolumetricHeader

readParameters

skipComments

readVoxelVector

initializeSurfaceData

readSurfaceData

readSurfaceDataVFR

getPlane

getPlaneNCI

getPlaneVFR

getValue

skipVoxels

getVoxelBitSet

getNextVoxelValue

nextVoxel

gotoData

skipData

skipDataVFR

countData

checkAtomLine

getSurfacePointAndFraction

getSPFv

scaleIsosurface

swapXZ