Class SurfaceReader

Method Details

• closeReader

  protected abstract void closeReader()

• setOutputChannel

  protected void setOutputChannel(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)

• discardTempDataSR

  protected void discardTempDataSR(boolean discardAll)

• readSurfaceData

  protected abstract void readSurfaceData(boolean isMapData) throws Exception

  Throws:

  Exception

• gotoAndReadVoxelData

  protected boolean gotoAndReadVoxelData(boolean isMapData)

• gotoData

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

  Parameters:

  n -

  nPoints -

  Throws:

  Exception

• readColorData

  protected String readColorData()

• getPlane

  public float[] getPlane(int x)

  Specified by:

  getPlane in interface VertexDataServer

• getPlaneSR

  protected float[] getPlaneSR(int x)

• 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

  Parameters:

  x -

  y -

  z -

  ptyz -

  Returns:

  value[x][y][z]

• getValue2

  protected float getValue2(int x, int y, int z, int ptyz)

• postProcessVertices

  protected void postProcessVertices()

• getSurfacePointIndexAndFraction

  public int getSurfacePointIndexAndFraction(float cutoff, boolean isCutoffAbsolute, int x, int y, int z, P3i offset, int vA, int vB, float valueA, float valueB, T3 pointA, 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 invalid input: '&'invalid input: '&' (fraction invalid input: '<' 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

  Parameters:

  cutoff -

  isCutoffAbsolute -

  x -

  y -

  z -

  offset -

  vA - [0:7]

  vB - [0:7]

  valueA -

  valueB -

  pointA -

  edgeVector - vector from A to B

  isContourType -

  fReturn -

  Returns:

  new vertex index or Integer.MAX_VALUE

• getSurfacePointAndFraction

  protected float getSurfacePointAndFraction(float cutoff, boolean isCutoffAbsolute, float valueA, float valueB, T3 pointA, V3 edgeVector, int x, int y, int z, int vA, int vB, float[] fReturn, T3 ptReturn)

• getSPF

  protected float getSPF(float cutoff, boolean isCutoffAbsolute, float valueA, float valueB, T3 pointA, V3 edgeVector, int x, int y, int z, int vA, int vB, float[] fReturn, 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(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

  Parameters:

  vertexXYZ -

  value -

  assocVertex - unique association vertex or -1

  asCopy -

  Returns:

  new vertex index

• addVC

  protected int addVC(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

  Parameters:

  iA -

  iB -

  iC -

  check -

  iContour - TODO

  isAbsolute -

  color -

  Returns:

  polygon index or -1

• getMinMaxMappedValues

  public float[] getMinMaxMappedValues(boolean haveData)

• selectPocket

  public void selectPocket(boolean doExclude)

  Parameters:

  doExclude -

• slabIsosurface

  public void slabIsosurface(Lst<Object[]> slabInfo)

• setVertexAnisotropy

  protected void setVertexAnisotropy(T3 pt)

• setVectorAnisotropy

  protected void setVectorAnisotropy(T3 v)

• setVolumetricAnisotropy

  protected void setVolumetricAnisotropy()

• setVolumetricOriginAnisotropy

  protected void setVolumetricOriginAnisotropy()

• setBBox

  protected void setBBox(T3 pt, float margin)

• getValueAtPoint

  public float getValueAtPoint(T3 pt, boolean getSource)

  Parameters:

  pt -

  getSource - TODO

  Returns:

  value

• finalizeMapping

  protected void finalizeMapping()

• getSurfaceAtomIndex

  public int getSurfaceAtomIndex()