Package ome.io.bioformats

Class BfPixelsWrapper

  • public class BfPixelsWrapper
extends java.lang.Object
    Since:
    Beta4.3

    • Constructor Summary

      Constructors 
      Constructor Description
      BfPixelsWrapper​(java.lang.String path, loci.formats.IFormatReader reader)
      We may want a constructor that takes the id of an imported file or that takes a File object? There should ultimately be some sort of check here that the file is in a/the repository.

    • Method Summary

      All Methods Instance Methods Concrete Methods 
      Modifier and Type Method Description
      void checkBounds​(java.lang.Integer x, java.lang.Integer y, java.lang.Integer z, java.lang.Integer c, java.lang.Integer t)  
      void close()  
      int getByteWidth()  
      byte[] getCol​(java.lang.Integer x, java.lang.Integer z, java.lang.Integer c, java.lang.Integer t, byte[] buffer)  
      java.lang.Integer getColSize()  
      byte[] getHypercube​(java.util.List<java.lang.Integer> offset, java.util.List<java.lang.Integer> size, java.util.List<java.lang.Integer> step, byte[] buffer)  
      java.lang.Long getHypercubeSize​(java.util.List<java.lang.Integer> offset, java.util.List<java.lang.Integer> size, java.util.List<java.lang.Integer> step)  
      long getId()  
      byte[] getMessageDigest()  
      java.lang.String getPath()  
      java.lang.String getPixelsType()
      cgb - created from the methods below? Retrieves how many bytes per pixel the current plane or section has.
      byte[] getPlane​(java.lang.Integer z, java.lang.Integer c, java.lang.Integer t, byte[] buffer)  
      java.lang.Long getPlaneOffset​(java.lang.Integer z, java.lang.Integer c, java.lang.Integer t)  
      byte[] getPlaneRegion​(java.lang.Integer z, java.lang.Integer c, java.lang.Integer t, java.lang.Integer count, java.lang.Integer offset, byte[] buffer)  
      java.lang.Long getPlaneSize()  
      byte[] getRegion​(java.lang.Integer size, java.lang.Long offset, byte[] buffer)  
      byte[] getRow​(java.lang.Integer y, java.lang.Integer z, java.lang.Integer c, java.lang.Integer t, byte[] buffer)  
      java.lang.Long getRowOffset​(java.lang.Integer y, java.lang.Integer z, java.lang.Integer c, java.lang.Integer t)  
      java.lang.Integer getRowSize()  
      int getSizeC()  
      int getSizeT()  
      int getSizeX()  
      int getSizeY()  
      int getSizeZ()  
      byte[] getStack​(java.lang.Integer c, java.lang.Integer t, byte[] buffer)  
      java.lang.Long getStackOffset​(java.lang.Integer c, java.lang.Integer t)  
      java.lang.Long getStackSize()  
      byte[] getTile​(int z, int c, int t, int x, int y, int w, int h, byte[] buffer)  
      byte[] getTimepoint​(java.lang.Integer t, byte[] buffer)  
      java.lang.Long getTimepointOffset​(java.lang.Integer t)  
      java.lang.Long getTimepointSize()  
      java.lang.Long getTotalSize()  
      boolean isFloat()  
      boolean isLittleEndian()  
      boolean isSigned()  
      byte[] swapIfRequired​(byte[] bytes)
      cgb - stolen from ImportLibrary - slightly modified Examines a byte array to see if it needs to be byte swapped and modifies the byte array directly.

      • Methods inherited from class java.lang.Object

        clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

    • Constructor Detail

      • BfPixelsWrapper

        public BfPixelsWrapper​(java.lang.String path,
                       loci.formats.IFormatReader reader)
                throws java.io.IOException,
                       loci.formats.FormatException
        We may want a constructor that takes the id of an imported file or that takes a File object? There should ultimately be some sort of check here that the file is in a/the repository.
        Throws:
        java.io.IOException
        loci.formats.FormatException

    • Method Detail

      • getMessageDigest

        public byte[] getMessageDigest()
                        throws java.io.IOException
        Throws:
        java.io.IOException

      • close

        public void close()
           throws java.io.IOException
        Throws:
        java.io.IOException

      • getId

        public long getId()

      • getPath

        public java.lang.String getPath()

      • getSizeC

        public int getSizeC()

      • getSizeT

        public int getSizeT()

      • getSizeX

        public int getSizeX()

      • getSizeY

        public int getSizeY()

      • getSizeZ

        public int getSizeZ()

      • getByteWidth

        public int getByteWidth()

      • getRowSize

        public java.lang.Integer getRowSize()

      • getColSize

        public java.lang.Integer getColSize()

      • getPlaneSize

        public java.lang.Long getPlaneSize()

      • getStackSize

        public java.lang.Long getStackSize()

      • getTimepointSize

        public java.lang.Long getTimepointSize()

      • getTotalSize

        public java.lang.Long getTotalSize()

      • getPlaneRegion

        public byte[] getPlaneRegion​(java.lang.Integer z,
                             java.lang.Integer c,
                             java.lang.Integer t,
                             java.lang.Integer count,
                             java.lang.Integer offset,
                             byte[] buffer)
                      throws java.io.IOException,
                             DimensionsOutOfBoundsException
        Throws:
        java.io.IOException
        DimensionsOutOfBoundsException

      • getRegion

        public byte[] getRegion​(java.lang.Integer size,
                        java.lang.Long offset,
                        byte[] buffer)
                 throws java.io.IOException
        Throws:
        java.io.IOException

      • getHypercube

        public byte[] getHypercube​(java.util.List<java.lang.Integer> offset,
                           java.util.List<java.lang.Integer> size,
                           java.util.List<java.lang.Integer> step,
                           byte[] buffer)
                    throws java.io.IOException,
                           DimensionsOutOfBoundsException
        Throws:
        java.io.IOException
        DimensionsOutOfBoundsException

      • getTile

        public byte[] getTile​(int z,
                      int c,
                      int t,
                      int x,
                      int y,
                      int w,
                      int h,
                      byte[] buffer)
               throws loci.formats.FormatException,
                      java.io.IOException
        Throws:
        loci.formats.FormatException
        java.io.IOException

      • getPixelsType

        public java.lang.String getPixelsType()
        cgb - created from the methods below? Retrieves how many bytes per pixel the current plane or section has.
        Returns:
        the number of bytes per pixel.

      • isFloat

        public boolean isFloat()

      • isSigned

        public boolean isSigned()

      • isLittleEndian

        public boolean isLittleEndian()

      • swapIfRequired

        public byte[] swapIfRequired​(byte[] bytes)
                      throws loci.formats.FormatException,
                             java.io.IOException
        cgb - stolen from ImportLibrary - slightly modified Examines a byte array to see if it needs to be byte swapped and modifies the byte array directly.
        Parameters:
        bytes - The byte array to check and modify if required.
        Returns:
        the byteArray either swapped or not for convenience.
        Throws:
        java.io.IOException - if there is an error read from the file.
        loci.formats.FormatException - if there is an error during metadata parsing.