Package gov.nih.mipav.model.file.rawjp2

Class ImgReaderRAW

  • All Implemented Interfaces:
    jj2000.j2k.image.BlkImgDataSrc, jj2000.j2k.image.ImgData
    public class ImgReaderRAW
extends jj2000.j2k.image.input.ImgReader
    This class implements the ImgData interface for reading 16 bit unsigned data from a binary RAW file.

    After being read the coefficients are level shifted by subtracting 2^(nominal bit range-1)

    The TransferType (see ImgData) of this class is TYPE_INT.

    NOTE: This class is not thread safe, for reasons of internal buffering.

    See Also:
    ImgData

    • Field Summary

      Fields 
      Modifier and Type Field Description
      private byte[] buf
      The line buffer.
      static int DC_OFFSET
      DC offset value used when reading image
      private ModelImage image
      image store
      private java.io.RandomAccessFile in
      Where to read the data from
      private jj2000.j2k.image.DataBlkInt intBlk
      Temporary DataBlkInt object (needed when encoder uses floating-point filters).
      private int numSlice
      Number of slices in 3D image
      private int offset
      The offset of the raw pixel data in the RAW file
      private int rb
      The number of bits that determine the nominal dynamic range

      • Fields inherited from class jj2000.j2k.image.input.ImgReader

        h, nc, w

    • Constructor Summary

      Constructors 
      Constructor Description
      ImgReaderRAW​(ModelImage image)  
      ImgReaderRAW​(java.io.File file)
      Creates a new PGM file reader from the specified file.
      ImgReaderRAW​(java.io.RandomAccessFile in)
      Creates a new PGM file reader from the specified RandomAccessFile object.
      ImgReaderRAW​(java.lang.String fname)
      Creates a new PGM file reader from the specified file name.

    • Method Summary

      All Methods Instance Methods Concrete Methods 
      Modifier and Type Method Description
      void close()
      Closes the underlying RandomAccessFile from where the image data is being read.
      private void confirmFileType()
      Checks that the RandomAccessIO begins with 'P5'
      private byte countedByteRead()
      Returns a byte read from the RandomAccessIO.
      jj2000.j2k.image.DataBlk getCompData​(jj2000.j2k.image.DataBlk blk, int c)
      Returns, in the blk argument, a block of image data containing the specifed rectangular area, in the specified component.
      int getFixedPoint​(int c)
      Returns the position of the fixed point in the specified component (i.e. the number of fractional bits), which is always 0 for this ImgReader.
      jj2000.j2k.image.DataBlk getInternCompData​(jj2000.j2k.image.DataBlk blk, int c)
      Returns, in the blk argument, the block of image data containing the specifed rectangular area, in the specified component.
      int getNomRangeBits​(int c)
      Returns the number of bits corresponding to the nominal range of the data in the specified component.
      boolean isOrigSigned​(int c)
      Returns true if the data read was originally signed in the specified component, false if not.
      private int readHeaderInt()
      Returns an int read from the header of the PGM file.
      private void skipCommentAndWhiteSpace()
      Skips any line in the header starting with '#' and any space, tab, line feed or carriage return.
      java.lang.String toString()
      Returns a string of information about the object, more than 1 line long.

      • Methods inherited from class jj2000.j2k.image.input.ImgReader

        getCompImgHeight, getCompImgWidth, getCompSubsX, getCompSubsY, getCompULX, getCompULY, getImgHeight, getImgULX, getImgULY, getImgWidth, getNomTileHeight, getNomTileWidth, getNumComps, getNumTiles, getNumTiles, getTile, getTileCompHeight, getTileCompWidth, getTileHeight, getTileIdx, getTilePartULX, getTilePartULY, getTileWidth, nextTile, setTile

      • Methods inherited from class java.lang.Object

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

    • Field Detail

      • DC_OFFSET

        public static int DC_OFFSET
        DC offset value used when reading image

      • in

        private java.io.RandomAccessFile in
        Where to read the data from

      • offset

        private int offset
        The offset of the raw pixel data in the RAW file

      • rb

        private int rb
        The number of bits that determine the nominal dynamic range

      • buf

        private byte[] buf
        The line buffer.

      • intBlk

        private jj2000.j2k.image.DataBlkInt intBlk
        Temporary DataBlkInt object (needed when encoder uses floating-point filters). This avoid allocating new DataBlk at each time

      • numSlice

        private int numSlice
        Number of slices in 3D image

    • Constructor Detail

      • ImgReaderRAW

        public ImgReaderRAW​(java.io.File file)
             throws java.io.IOException
        Creates a new PGM file reader from the specified file.
        Parameters:
        file - The input file.
        Throws:
        java.io.IOException - If an error occurs while opening the file.

      • ImgReaderRAW

        public ImgReaderRAW​(java.lang.String fname)
             throws java.io.IOException
        Creates a new PGM file reader from the specified file name.
        Parameters:
        fname - The input file name.
        Throws:
        java.io.IOException - If an error occurs while opening the file.

      • ImgReaderRAW

        public ImgReaderRAW​(java.io.RandomAccessFile in)
             throws java.io.EOFException,
                    java.io.IOException
        Creates a new PGM file reader from the specified RandomAccessFile object. The file header is read to acquire the image size.
        Parameters:
        in - From where to read the data
        Throws:
        java.io.EOFException - if an EOF is read
        java.io.IOException - if an error occurs when opening the file

      • ImgReaderRAW

        public ImgReaderRAW​(ModelImage image)

    • Method Detail

      • close

        public void close()
           throws java.io.IOException
        Closes the underlying RandomAccessFile from where the image data is being read. No operations are possible after a call to this method.
        Specified by:
        close in class jj2000.j2k.image.input.ImgReader
        Throws:
        java.io.IOException - If an I/O error occurs.

      • getNomRangeBits

        public int getNomRangeBits​(int c)
        Returns the number of bits corresponding to the nominal range of the data in the specified component. This is the value rb (range bits) that was specified in the constructor, which normally is 8 for non bilevel data, and 1 for bilevel data.

        If this number is b then the nominal range is between -2^(b-1) and 2^(b-1)-1, since unsigned data is level shifted to have a nominal average of 0.

        Parameters:
        c - The index of the component.
        Returns:
        The number of bits corresponding to the nominal range of the data. Fro floating-point data this value is not applicable and the return value is undefined.

      • getFixedPoint

        public int getFixedPoint​(int c)
        Returns the position of the fixed point in the specified component (i.e. the number of fractional bits), which is always 0 for this ImgReader.
        Parameters:
        c - The index of the component.
        Returns:
        The position of the fixed-point (i.e. the number of fractional bits). Always 0 for this ImgReader.

      • getInternCompData

        public final jj2000.j2k.image.DataBlk getInternCompData​(jj2000.j2k.image.DataBlk blk,
                                                        int c)
        Returns, in the blk argument, the block of image data containing the specifed rectangular area, in the specified component. The data is returned, as a reference to the internal data, if any, instead of as a copy, therefore the returned data should not be modified.

        After being read the coefficients are level shifted by subtracting 2^(nominal bit range - 1)

        The rectangular area to return is specified by the 'ulx', 'uly', 'w' and 'h' members of the 'blk' argument, relative to the current tile. These members are not modified by this method. The 'offset' and 'scanw' of the returned data can be arbitrary. See the 'DataBlk' class.

        If the data array in blk is null, then a new one is created if necessary. The implementation of this interface may choose to return the same array or a new one, depending on what is more efficient. Therefore, the data array in blk prior to the method call should not be considered to contain the returned data, a new array may have been created. Instead, get the array from blk after the method has returned.

        The returned data always has its 'progressive' attribute unset (i.e. false).

        When an I/O exception is encountered the JJ2KExceptionHandler is used. The exception is passed to its handleException method. The action that is taken depends on the action that has been registered in JJ2KExceptionHandler. See JJ2KExceptionHandler for details.

        Parameters:
        blk - Its coordinates and dimensions specify the area to return. Some fields in this object are modified to return the data.
        c - The index of the component from which to get the data. Only 0 is valid.
        Returns:
        The requested DataBlk
        See Also:
        getCompData(jj2000.j2k.image.DataBlk, int), JJ2KExceptionHandler

      • getCompData

        public jj2000.j2k.image.DataBlk getCompData​(jj2000.j2k.image.DataBlk blk,
                                            int c)
        Returns, in the blk argument, a block of image data containing the specifed rectangular area, in the specified component. The data is returned, as a copy of the internal data, therefore the returned data can be modified "in place".

        After being read the coefficients are level shifted by subtracting 2^(nominal bit range - 1)

        The rectangular area to return is specified by the 'ulx', 'uly', 'w' and 'h' members of the 'blk' argument, relative to the current tile. These members are not modified by this method. The 'offset' of the returned data is 0, and the 'scanw' is the same as the block's width. See the 'DataBlk' class.

        If the data array in 'blk' is 'null', then a new one is created. If the data array is not 'null' then it is reused, and it must be large enough to contain the block's data. Otherwise an 'ArrayStoreException' or an 'IndexOutOfBoundsException' is thrown by the Java system.

        The returned data has its 'progressive' attribute unset (i.e. false).

        This method just calls 'getInternCompData(blk, n)'.

        When an I/O exception is encountered the JJ2KExceptionHandler is used. The exception is passed to its handleException method. The action that is taken depends on the action that has been registered in JJ2KExceptionHandler. See JJ2KExceptionHandler for details.

        Parameters:
        blk - Its coordinates and dimensions specify the area to return. If it contains a non-null data array, then it must have the correct dimensions. If it contains a null data array a new one is created. The fields in this object are modified to return the data.
        c - The index of the component from which to get the data. Only 0 is valid.
        Returns:
        The requested DataBlk
        See Also:
        getInternCompData(jj2000.j2k.image.DataBlk, int), JJ2KExceptionHandler

      • countedByteRead

        private byte countedByteRead()
                      throws java.io.IOException,
                             java.io.EOFException
        Returns a byte read from the RandomAccessIO. The number of read byted are counted to keep track of the offset of the pixel data in the PGM file
        Returns:
        One byte read from the header of the PGM file.
        Throws:
        java.io.IOException - If an I/O error occurs.
        java.io.EOFException - If an EOF is read

      • confirmFileType

        private void confirmFileType()
                      throws java.io.IOException,
                             java.io.EOFException
        Checks that the RandomAccessIO begins with 'P5'
        Throws:
        java.io.IOException - If an I/O error occurs.
        java.io.EOFException - If an EOF is read

      • skipCommentAndWhiteSpace

        private void skipCommentAndWhiteSpace()
                               throws java.io.IOException,
                                      java.io.EOFException
        Skips any line in the header starting with '#' and any space, tab, line feed or carriage return.
        Throws:
        java.io.IOException - If an I/O error occurs.
        java.io.EOFException - if an EOF is read

      • readHeaderInt

        private int readHeaderInt()
                   throws java.io.IOException,
                          java.io.EOFException
        Returns an int read from the header of the PGM file.
        Returns:
        One int read from the header of the PGM file.
        Throws:
        java.io.IOException - If an I/O error occurs.
        java.io.EOFException - If an EOF is read

      • isOrigSigned

        public boolean isOrigSigned​(int c)
        Returns true if the data read was originally signed in the specified component, false if not. This method returns always false since PGM data is always unsigned.
        Specified by:
        isOrigSigned in class jj2000.j2k.image.input.ImgReader
        Parameters:
        c - The index of the component, from 0 to N-1.
        Returns:
        always false, since PGM data is always unsigned.

      • toString

        public java.lang.String toString()
        Returns a string of information about the object, more than 1 line long. The information string includes information from the underlying RandomAccessIO (its toString() method is called in turn).
        Overrides:
        toString in class java.lang.Object
        Returns:
        A string of information about the object.