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,
             java.io.BufferedReader br)

  Overrides:

  init2 in class SurfaceFileReader

• init2VFR

  void init2VFR​(SurfaceGenerator sg,
                java.io.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 java.lang.Exception

  Throws:

  java.lang.Exception

• skipComments

  protected java.lang.String skipComments​(boolean allowBlankLines)
                                   throws java.lang.Exception

  Throws:

  java.lang.Exception

• readVoxelVector

  protected void readVoxelVector​(int voxelVectorIndex)
                          throws java.lang.Exception

  Throws:

  java.lang.Exception

• initializeSurfaceData

  void initializeSurfaceData()

• readSurfaceData

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

  Specified by:

  readSurfaceData in class SurfaceReader

  Throws:

  java.lang.Exception

• readSurfaceDataVFR

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

  Throws:

  java.lang.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 java.lang.Exception

  Throws:

  java.lang.Exception

• getVoxelBitSet

  protected BS getVoxelBitSet​(int nPoints)
                       throws java.lang.Exception

  Parameters:

  nPoints -

  Returns:

  JVXL bitset

  Throws:

  java.lang.Exception

• getNextVoxelValue

  protected float getNextVoxelValue()
                             throws java.lang.Exception

  Throws:

  java.lang.Exception

• nextVoxel

  protected float nextVoxel()
                     throws java.lang.Exception

  Throws:

  java.lang.Exception

• gotoData

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

  Overrides:

  gotoData in class SurfaceReader

  Throws:

  java.lang.Exception

• skipData

  protected void skipData​(int nPoints)
                   throws java.lang.Exception

  Throws:

  java.lang.Exception

• skipDataVFR

  protected void skipDataVFR​(int nPoints)
                      throws java.lang.Exception

  Throws:

  java.lang.Exception

• countData

  private int countData​(java.lang.String str)

• checkAtomLine

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