Package org.jmol.jvxl.readers
Class SurfaceReader
java.lang.Object
org.jmol.jvxl.readers.SurfaceReader
- All Implemented Interfaces:
VertexDataServer
- Direct Known Subclasses:
SurfaceFileReader
,VolumeDataReader
-
Field Summary
FieldsModifier and TypeFieldDescriptionprotected boolean
(package private) static final float
protected float[]
private float
protected javajs.util.P3
protected char
protected int
protected int
private static final String[]
protected int
protected float
protected float
protected float
(package private) static final float
(package private) static final float
(package private) static final float
protected javajs.util.M3
protected javajs.util.M3
protected float
protected float
private int
private String
protected int
protected int
protected javajs.util.SB
(package private) boolean
private boolean
protected boolean
protected boolean
protected boolean
protected boolean
protected boolean
protected boolean
protected boolean
protected boolean
protected String
protected float
protected float[]
protected JvxlData
protected boolean
protected boolean
protected boolean
protected boolean
protected String
protected javajs.util.SB
protected int
protected javajs.util.BS
protected MarchingCubes
protected MarchingSquares
protected MeshData
protected MeshDataServer
protected float[]
protected long
protected int
protected int
protected int
protected int
protected Parameters
protected final javajs.util.P3
protected QuantumPlaneCalculation
protected SurfaceGenerator
(package private) boolean
(package private) VolumeData
protected javajs.util.P3
protected javajs.util.V3[]
protected int[]
protected float[][][]
protected javajs.util.P3
protected javajs.util.P3
protected int
protected float[][]
-
Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionint
addTriangleCheck
(int iA, int iB, int iC, int check, int iContour, boolean isAbsolute, int color) addTriangleCheck adds a triangle along with a 3-bit check indicating which edges to draw in mesh mode: 1 (iA-iB) + 2 (iB-iC) + 4 (iC-iA)protected int
addVC
(javajs.util.T3 vertexXYZ, float value, int assocVertex, boolean asCopy) int
addVertexCopy
(javajs.util.T3 vertexXYZ, float value, int assocVertex, boolean asCopy) addVertexCopy is used by the Marching Squares algorithm to uniquely identify a new vertex when an edge is crossed in the 2D plane.(package private) void
protected abstract void
private void
(package private) void
(package private) boolean
createIsosurface
(boolean justForPlane) (package private) void
discardTempData
(boolean discardAll) protected void
discardTempDataSR
(boolean discardAll) (package private) void
(package private) void
protected void
private void
(package private) static int
getColorPhaseIndex
(String color) float[]
getMinMaxMappedValues
(boolean haveData) private float
getPhase
(javajs.util.T3 pt) float[]
getPlane
(int x) protected float[]
getPlaneSR
(int x) protected float
getSPF
(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) int
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) int
getSurfacePointIndexAndFraction
(float cutoff, boolean isCutoffAbsolute, int x, int y, int z, javajs.util.P3i offset, int vA, int vB, float valueA, float valueB, javajs.util.T3 pointA, javajs.util.V3 edgeVector, boolean isContourType, float[] fReturn) getSurfacePointIndex is used by the Marching Cubes algorithm and must return a unique integer identifier for a vertex created by the Marching Cube algorithm when it finds an edge.float
getValue
(int x, int y, int z, int ptyz) for readers onlyprotected float
getValue2
(int x, int y, int z, int ptyz) float
getValueAtPoint
(javajs.util.T3 pt, boolean getSource) protected boolean
gotoAndReadVoxelData
(boolean isMapData) protected void
gotoData
(int n, int nPoints) (package private) abstract void
init
(SurfaceGenerator sg) implemented in SurfaceFileReader and(package private) void
(package private) void
(package private) void
(package private) void
(package private) void
protected void
protected void
(package private) boolean
readAndSetVolumeParameters
(boolean isMapData) protected String
protected abstract void
readSurfaceData
(boolean isMapData) protected abstract boolean
readVolumeData
(boolean isMapData) protected abstract boolean
readVolumeParameters
(boolean isMapData) (package private) void
void
selectPocket
(boolean doExclude) protected void
setBBox
(javajs.util.T3 pt, float margin) private void
protected void
setOutputChannel
(javajs.util.OC out) protected void
setVectorAnisotropy
(javajs.util.T3 v) protected void
setVertexAnisotropy
(javajs.util.T3 pt) protected void
protected void
protected void
void
slabIsosurface
(javajs.util.Lst<Object[]> slabInfo) (package private) void
(package private) void
-
Field Details
-
sg
-
meshDataServer
-
params
-
meshData
-
jvxlData
-
volumeData
VolumeData volumeData -
edgeData
-
haveSurfaceAtoms
protected boolean haveSurfaceAtoms -
allowSigma
protected boolean allowSigma -
isProgressive
protected boolean isProgressive -
isXLowToHigh
protected boolean isXLowToHigh -
assocCutoff
private float assocCutoff -
isQuiet
protected boolean isQuiet -
isPeriodic
protected boolean isPeriodic -
vertexDataOnly
boolean vertexDataOnly -
hasColorData
boolean hasColorData -
dataMin
protected float dataMin -
dataMax
protected float dataMax -
dataMean
protected float dataMean -
xyzMin
protected javajs.util.P3 xyzMin -
xyzMax
protected javajs.util.P3 xyzMax -
center
protected javajs.util.P3 center -
anisotropy
protected float[] anisotropy -
isAnisotropic
protected boolean isAnisotropic -
eccentricityMatrix
protected javajs.util.M3 eccentricityMatrix -
eccentricityMatrixInverse
protected javajs.util.M3 eccentricityMatrixInverse -
isEccentric
protected boolean isEccentric -
eccentricityScale
protected float eccentricityScale -
eccentricityRatio
protected float eccentricityRatio -
ANGSTROMS_PER_BOHR
static final float ANGSTROMS_PER_BOHR- See Also:
-
defaultMappedDataMin
static final float defaultMappedDataMin- See Also:
-
defaultMappedDataMax
static final float defaultMappedDataMax- See Also:
-
defaultCutoff
static final float defaultCutoff- See Also:
-
edgeCount
private int edgeCount -
volumetricOrigin
protected javajs.util.P3 volumetricOrigin -
volumetricVectors
protected javajs.util.V3[] volumetricVectors -
voxelCounts
protected int[] voxelCounts -
voxelData
protected float[][][] voxelData -
nBytes
protected long nBytes -
nDataPoints
protected int nDataPoints -
nPointsX
protected int nPointsX -
nPointsY
protected int nPointsY -
nPointsZ
protected int nPointsZ -
isJvxl
protected boolean isJvxl -
edgeFractionBase
protected int edgeFractionBase -
edgeFractionRange
protected int edgeFractionRange -
colorFractionBase
protected int colorFractionBase -
colorFractionRange
protected int colorFractionRange -
jvxlFileHeaderBuffer
protected javajs.util.SB jvxlFileHeaderBuffer -
fractionData
protected javajs.util.SB fractionData -
jvxlEdgeDataRead
-
jvxlColorDataRead
-
jvxlVoxelBitSet
protected javajs.util.BS jvxlVoxelBitSet -
jvxlDataIsColorMapped
protected boolean jvxlDataIsColorMapped -
jvxlDataIsPrecisionColor
protected boolean jvxlDataIsPrecisionColor -
jvxlDataIs2dContour
protected boolean jvxlDataIs2dContour -
jvxlDataIsColorDensity
protected boolean jvxlDataIsColorDensity -
jvxlCutoff
protected float jvxlCutoff -
jvxlCutoffRange
protected float[] jvxlCutoffRange -
jvxlNSurfaceInts
protected int jvxlNSurfaceInts -
cJvxlEdgeNaN
protected char cJvxlEdgeNaN -
contourVertexCount
protected int contourVertexCount -
marchingSquares
-
marchingCubes
-
yzPlanes
protected float[][] yzPlanes -
yzCount
protected int yzCount -
qpc
-
ptTemp
protected final javajs.util.P3 ptTemp -
colorPhases
-
minMax
protected float[] minMax -
haveSetAnisotropy
private boolean haveSetAnisotropy
-
-
Constructor Details
-
SurfaceReader
SurfaceReader()
-
-
Method Details
-
init
implemented in SurfaceFileReader and- Parameters:
sg
-
-
initSR
-
closeReader
protected abstract void closeReader() -
setOutputChannel
protected void setOutputChannel(javajs.util.OC out) - Parameters:
out
-
-
newVoxelDataCube
protected void newVoxelDataCube() -
setVolumeDataV
-
readVolumeParameters
protected abstract boolean readVolumeParameters(boolean isMapData) -
readVolumeData
protected abstract boolean readVolumeData(boolean isMapData) -
jvxlUpdateInfo
void jvxlUpdateInfo() -
readAndSetVolumeParameters
boolean readAndSetVolumeParameters(boolean isMapData) -
createIsosurface
boolean createIsosurface(boolean justForPlane) -
resetIsosurface
void resetIsosurface() -
discardTempData
void discardTempData(boolean discardAll) -
discardTempDataSR
protected void discardTempDataSR(boolean discardAll) -
initializeVolumetricData
void initializeVolumetricData() -
readSurfaceData
- Throws:
Exception
-
gotoAndReadVoxelData
protected boolean gotoAndReadVoxelData(boolean isMapData) -
gotoData
- Parameters:
n
-nPoints
-- Throws:
Exception
-
readColorData
-
getPlane
public float[] getPlane(int x) - Specified by:
getPlane
in interfaceVertexDataServer
-
getPlaneSR
protected float[] getPlaneSR(int x) -
initPlanes
void initPlanes() -
getValue
public float getValue(int x, int y, int z, int ptyz) Description copied from interface:VertexDataServer
for readers only- Specified by:
getValue
in interfaceVertexDataServer
- Returns:
- value[x][y][z]
-
getValue2
protected float getValue2(int x, int y, int z, int ptyz) -
generateSurfaceData
private void generateSurfaceData() -
postProcessVertices
protected void postProcessVertices() -
getSurfacePointIndexAndFraction
public int getSurfacePointIndexAndFraction(float cutoff, boolean isCutoffAbsolute, int x, int y, int z, javajs.util.P3i offset, int vA, int vB, float valueA, float valueB, javajs.util.T3 pointA, javajs.util.V3 edgeVector, boolean isContourType, float[] fReturn) Description copied from interface:VertexDataServer
getSurfacePointIndex is used by the Marching Cubes algorithm and must return a unique integer identifier for a vertex created by the Marching Cube algorithm when it finds an edge. If a vertex is discarded, then Integer.MAX_VALUE should be returned. the 3D coordinate of the point can be calculated using surfacePoint.scaleAdd(fraction, edgeVector, pointA); where fraction is generally calculated as: fraction = (cutoff - valueA) / (valueB - valueA); if (isCutoffAbsolute && (fraction < 0 || fraction > 1)) fraction = (-cutoff - valueA) / (valueB - valueA); This method is also used by MarchingCubes to deliver the appropriate oblique planar coordinate to MarchingSquares for later contouring.- Specified by:
getSurfacePointIndexAndFraction
in interfaceVertexDataServer
vA
- [0:7]vB
- [0:7]edgeVector
- vector from A to B- Returns:
- new vertex index or Integer.MAX_VALUE
-
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) -
getSPF
protected float getSPF(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) - Parameters:
cutoff
-isCutoffAbsolute
-valueA
-valueB
-pointA
-edgeVector
-x
- TODOy
- TODOz
- TODOvA
-vB
-fReturn
-ptReturn
-- Returns:
- fractional distance from A to B
-
addVertexCopy
public int addVertexCopy(javajs.util.T3 vertexXYZ, float value, int assocVertex, boolean asCopy) Description copied from interface:VertexDataServer
addVertexCopy is used by the Marching Squares algorithm to uniquely identify a new vertex when an edge is crossed in the 2D plane. The implementing method should COPY the Point3f using Point3f.set(). The data consumer can use the association key to group this vertex with others near the same gridpoint.- Specified by:
addVertexCopy
in interfaceVertexDataServer
assocVertex
- unique association vertex or -1- Returns:
- new vertex index
-
addVC
protected int addVC(javajs.util.T3 vertexXYZ, float value, int assocVertex, boolean asCopy) -
addTriangleCheck
public int addTriangleCheck(int iA, int iB, int iC, int check, int iContour, boolean isAbsolute, int color) Description copied from interface:VertexDataServer
addTriangleCheck adds a triangle along with a 3-bit check indicating which edges to draw in mesh mode: 1 (iA-iB) + 2 (iB-iC) + 4 (iC-iA)- Specified by:
addTriangleCheck
in interfaceVertexDataServer
iContour
- TODO- Returns:
- polygon index or -1
-
colorIsosurface
void colorIsosurface() -
applyColorScale
void applyColorScale() -
colorData
private void colorData() -
getColorPhaseIndex
-
getPhase
private float getPhase(javajs.util.T3 pt) -
getMinMaxMappedValues
public float[] getMinMaxMappedValues(boolean haveData) -
updateTriangles
void updateTriangles() -
updateSurfaceData
void updateSurfaceData() -
selectPocket
public void selectPocket(boolean doExclude) - Parameters:
doExclude
-
-
excludeMinimumSet
void excludeMinimumSet() -
excludeMaximumSet
void excludeMaximumSet() -
slabIsosurface
-
setVertexAnisotropy
protected void setVertexAnisotropy(javajs.util.T3 pt) -
setVectorAnisotropy
protected void setVectorAnisotropy(javajs.util.T3 v) -
setVolumetricAnisotropy
protected void setVolumetricAnisotropy() -
setVolumetricOriginAnisotropy
protected void setVolumetricOriginAnisotropy() -
setBBoxAll
private void setBBoxAll() -
setBBox
protected void setBBox(javajs.util.T3 pt, float margin) -
getValueAtPoint
public float getValueAtPoint(javajs.util.T3 pt, boolean getSource) - Parameters:
pt
-getSource
- TODO- Returns:
- value
-
initializeMapping
void initializeMapping() -
finalizeMapping
protected void finalizeMapping() -
getSurfaceAtomIndex
public int getSurfaceAtomIndex()
-