Field Detail

• sg

  protected SurfaceGenerator sg

• meshDataServer

  protected MeshDataServer meshDataServer

• params

  protected Parameters params

• meshData

  protected MeshData meshData

• jvxlData

  protected JvxlData jvxlData

• volumeData

  VolumeData volumeData

• edgeData

  private java.lang.String 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:

  Constant Field Values

• defaultMappedDataMin

  static final float defaultMappedDataMin

  See Also:

  Constant Field Values

• defaultMappedDataMax

  static final float defaultMappedDataMax

  See Also:

  Constant Field Values

• defaultCutoff

  static final float defaultCutoff

  See Also:

  Constant Field Values

• 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

  protected java.lang.String jvxlEdgeDataRead

• jvxlColorDataRead

  protected java.lang.String jvxlColorDataRead

• jvxlVoxelBitSet

  protected BS jvxlVoxelBitSet

• jvxlDataIsColorMapped

  protected boolean jvxlDataIsColorMapped

• jvxlDataIsPrecisionColor

  protected boolean jvxlDataIsPrecisionColor

• jvxlDataIs2dContour

  protected boolean jvxlDataIs2dContour

• jvxlDataIsColorDensity

  protected boolean jvxlDataIsColorDensity

• jvxlCutoff

  protected float jvxlCutoff

• jvxlNSurfaceInts

  protected int jvxlNSurfaceInts

• cJvxlEdgeNaN

  protected char cJvxlEdgeNaN

• contourVertexCount

  protected int contourVertexCount

• marchingSquares

  protected MarchingSquares marchingSquares

• marchingCubes

  protected MarchingCubes marchingCubes

• yzPlanes

  protected float[][] yzPlanes

• yzCount

  protected int yzCount

• qpc

  protected QuantumPlaneCalculation qpc

• ptTemp

  protected final javajs.util.P3 ptTemp

• colorPhases

  private static final java.lang.String[] colorPhases

• minMax

  protected float[] minMax

• haveSetAnisotropy

  private boolean haveSetAnisotropy

Constructor Detail

• SurfaceReader

  SurfaceReader()

Method Detail

• init

  abstract void init​(SurfaceGenerator sg)

  implemented in SurfaceFileReader and

  Parameters:

  sg -

• initSR

  void initSR​(SurfaceGenerator sg)

• closeReader

  protected abstract void closeReader()

• setOutputChannel

  protected void setOutputChannel​(javajs.util.OC out)

  Parameters:

  out -

• newVoxelDataCube

  protected void newVoxelDataCube()

• setVolumeDataV

  protected void setVolumeDataV​(VolumeData v)

• 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

  protected abstract void readSurfaceData​(boolean isMapData)
                                   throws java.lang.Exception

  Throws:

  java.lang.Exception

• gotoAndReadVoxelData

  protected boolean gotoAndReadVoxelData​(boolean isMapData)

• gotoData

  protected void gotoData​(int n,
                          int nPoints)
                   throws java.lang.Exception

  Parameters:

  n -

  nPoints -

  Throws:

  java.lang.Exception

• readColorData

  protected java.lang.String readColorData()

• getPlane

  public float[] getPlane​(int x)

  Specified by:

  getPlane in interface VertexDataServer

• 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 interface VertexDataServer

  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 interface VertexDataServer

  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 - TODO

  y - TODO

  z - TODO

  vA -

  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 interface VertexDataServer

  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 interface VertexDataServer

  iContour - TODO

  Returns:

  polygon index or -1

• colorIsosurface

  void colorIsosurface()

• applyColorScale

  void applyColorScale()

• colorData

  private void colorData()

• getColorPhaseIndex

  static int getColorPhaseIndex​(java.lang.String color)

• 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

  public void slabIsosurface​(javajs.util.Lst<java.lang.Object[]> slabInfo)

• 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()