Class VolumeFileReader

    • 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

        protected 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

      • recordData

        protected float recordData​(float value)
      • readVolumeDataVFR

        protected boolean readVolumeDataVFR​(boolean isMapData)
      • readVolumetricHeader

        private int readVolumetricHeader()
      • readParameters

        protected abstract void readParameters()
                                        throws Exception
        Throws:
        Exception
      • readVoxelVector

        protected void readVoxelVector​(int voxelVectorIndex)
                                throws Exception
        Throws:
        Exception
      • initializeSurfaceData

        void initializeSurfaceData()
      • readSurfaceDataVFR

        protected void readSurfaceDataVFR​(boolean isMapData)
                                   throws Exception
        Throws:
        Exception
      • 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)
      • getVoxelBitSet

        protected javajs.util.BS getVoxelBitSet​(int nPoints)
                                         throws Exception
        Parameters:
        nPoints -
        Returns:
        JVXL bitset
        Throws:
        Exception
      • getNextVoxelValue

        protected float getNextVoxelValue()
                                   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()