Package ome.io.nio

Interface PixelBuffer

  • All Superinterfaces:
    java.lang.AutoCloseable, java.io.Closeable
    All Known Implementing Classes:
    BfPixelBuffer, BfPyramidPixelBuffer, InMemoryPlanarPixelBuffer, RomioPixelBuffer
    public interface PixelBuffer
extends java.io.Closeable
    This interface declares the I/O responsibilities of a buffer, file or otherwise, that contains a 5-dimensional Pixel array (XYZCT).
    Since:
    3.0
    See Also:
    PixelData

    • Method Summary

      All Methods Instance Methods Abstract Methods 
      Modifier and Type Method Description
      byte[] calculateMessageDigest()
      Calculates a SHA-1 message digest for the entire pixel buffer.
      void checkBounds​(java.lang.Integer x, java.lang.Integer y, java.lang.Integer z, java.lang.Integer c, java.lang.Integer t)
      Checks to ensure that no one particular axis has an offset out of bounds.
      void close()
      Closes the buffer, cleaning up file state.
      int getByteWidth()
      Returns the byte width for the pixel buffer.
      ome.util.PixelData getCol​(java.lang.Integer x, java.lang.Integer z, java.lang.Integer c, java.lang.Integer t)
      Retrieves a particular column from this pixel buffer.
      byte[] getColDirect​(java.lang.Integer x, java.lang.Integer z, java.lang.Integer c, java.lang.Integer t, byte[] buffer)
      Retrieves a particular column from this pixel buffer.
      java.lang.Integer getColSize()
      Retrieves the in memory size of a column of pixels in this pixel buffer.
      ome.util.PixelData getHypercube​(java.util.List<java.lang.Integer> offset, java.util.List<java.lang.Integer> size, java.util.List<java.lang.Integer> step)
      Retrieves a hypercube from this pixel buffer.
      byte[] getHypercubeDirect​(java.util.List<java.lang.Integer> offset, java.util.List<java.lang.Integer> size, java.util.List<java.lang.Integer> step, byte[] buffer)
      Retrieves a hypercube from the given pixels directly.
      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)
      Retrieves a the size of a hypercube from this pixel buffer.
      long getId()
      Retrieves the identifier of this pixel buffer
      java.lang.String getPath()
      Retrieves the full path to this pixel buffer on disk
      ome.util.PixelData getPlane​(java.lang.Integer z, java.lang.Integer c, java.lang.Integer t)
      Retrieves a particular 2D image plane from this pixel buffer.
      byte[] getPlaneDirect​(java.lang.Integer z, java.lang.Integer c, java.lang.Integer t, byte[] buffer)
      Retrieves a particular 2D image plane from this pixel buffer.
      java.lang.Long getPlaneOffset​(java.lang.Integer z, java.lang.Integer c, java.lang.Integer t)
      Retrieves the offset for a particular 2D image plane in this pixel buffer.
      ome.util.PixelData getPlaneRegion​(java.lang.Integer x, java.lang.Integer y, java.lang.Integer width, java.lang.Integer height, java.lang.Integer z, java.lang.Integer c, java.lang.Integer t, java.lang.Integer stride)
      Retrieves a particular region of a 2D image plane from this pixel buffer.
      byte[] getPlaneRegionDirect​(java.lang.Integer z, java.lang.Integer c, java.lang.Integer t, java.lang.Integer count, java.lang.Integer offset, byte[] buffer)
      Retrieves a region from a given plane directly.
      java.lang.Long getPlaneSize()
      Retrieves the in memory size of a 2D image plane in this pixel buffer.
      ome.util.PixelData getRegion​(java.lang.Integer size, java.lang.Long offset)
      Retrieves a region from this pixel buffer.
      byte[] getRegionDirect​(java.lang.Integer size, java.lang.Long offset, byte[] buffer)
      Retrieves a region from this pixel buffer directly.
      java.util.List<java.util.List<java.lang.Integer>> getResolutionDescriptions()
      Return a list of lists each of which has sizeX, sizeY for the resolution level matching the index of the outer index.
      int getResolutionLevel()
      Retrieves the active resolution level.
      int getResolutionLevels()
      Retrieves the number of resolution levels that the backing pixels pyramid contains.
      ome.util.PixelData getRow​(java.lang.Integer y, java.lang.Integer z, java.lang.Integer c, java.lang.Integer t)
      Retrieves a particular row or scanline from this pixel buffer.
      byte[] getRowDirect​(java.lang.Integer y, java.lang.Integer z, java.lang.Integer c, java.lang.Integer t, byte[] buffer)
      Retrieves a particular row or scanline from this pixel buffer.
      java.lang.Long getRowOffset​(java.lang.Integer y, java.lang.Integer z, java.lang.Integer c, java.lang.Integer t)
      Retrieves the offset for a particular row or scanline in this pixel buffer.
      java.lang.Integer getRowSize()
      Retrieves the in memory size of a row or scanline of pixels in this pixel buffer.
      int getSizeC()
      Retrieves the size in C of this pixel buffer
      int getSizeT()
      Retrieves the size in T of this pixel buffer
      int getSizeX()
      Retrieves the size in X of this pixel buffer
      int getSizeY()
      Retrieves the size in Y of this pixel buffer
      int getSizeZ()
      Retrieves the size in Z of this pixel buffer
      ome.util.PixelData getStack​(java.lang.Integer c, java.lang.Integer t)
      Retrieves the the entire number of optical sections for a single wavelength or channel at a particular timepoint in this pixel buffer.
      byte[] getStackDirect​(java.lang.Integer c, java.lang.Integer t, byte[] buffer)
      Retrieves the the entire number of optical sections for a single wavelength or channel at a particular timepoint in this pixel buffer.
      java.lang.Long getStackOffset​(java.lang.Integer c, java.lang.Integer t)
      Retrieves the offset for the entire number of optical sections for a single wavelength or channel at a particular timepoint in this pixel buffer.
      java.lang.Long getStackSize()
      Retrieves the in memory size of the entire number of optical sections for a single wavelength or channel at a particular timepoint in this pixel buffer.
      ome.util.PixelData getTile​(java.lang.Integer z, java.lang.Integer c, java.lang.Integer t, java.lang.Integer x, java.lang.Integer y, java.lang.Integer w, java.lang.Integer h)
      Retrieves a tile from this pixel buffer.
      byte[] getTileDirect​(java.lang.Integer z, java.lang.Integer c, java.lang.Integer t, java.lang.Integer x, java.lang.Integer y, java.lang.Integer w, java.lang.Integer h, byte[] buffer)
      Retrieves a tile from this pixel buffer.
      java.awt.Dimension getTileSize()
      Retrieves the tile size for the pixel store.
      ome.util.PixelData getTimepoint​(java.lang.Integer t)
      Retrieves the entire number of optical sections for all wavelengths or channels at a particular timepoint in this pixel buffer.
      byte[] getTimepointDirect​(java.lang.Integer t, byte[] buffer)
      Retrieves the entire number of optical sections for all wavelengths or channels at a particular timepoint in this pixel buffer.
      java.lang.Long getTimepointOffset​(java.lang.Integer t)
      Retrieves the in memory size of the entire number of optical sections for all wavelengths or channels at a particular timepoint in this pixel buffer.
      java.lang.Long getTimepointSize()
      Retrieves the in memory size of the entire number of optical sections for all wavelengths or channels at a particular timepoint in this pixel buffer.
      java.lang.Long getTotalSize()
      Retrieves the in memory size of the entire pixel buffer.
      boolean isFloat()
      Returns whether or not the pixel buffer has floating point pixels.
      boolean isSigned()
      Returns whether or not the pixel buffer has signed pixels.
      void setPlane​(byte[] buffer, java.lang.Integer z, java.lang.Integer c, java.lang.Integer t)
      Sets a particular 2D image plane in this pixel buffer.
      void setPlane​(java.nio.ByteBuffer buffer, java.lang.Integer z, java.lang.Integer c, java.lang.Integer t)
      Sets a particular 2D image plane in this pixel buffer.
      void setRegion​(java.lang.Integer size, java.lang.Long offset, byte[] buffer)
      Sets a region in this pixel buffer.
      void setRegion​(java.lang.Integer size, java.lang.Long offset, java.nio.ByteBuffer buffer)
      Sets a region in this pixel buffer.
      void setResolutionLevel​(int resolutionLevel)
      Sets the active resolution level.
      void setRow​(java.nio.ByteBuffer buffer, java.lang.Integer y, java.lang.Integer z, java.lang.Integer c, java.lang.Integer t)
      Sets a particular row or scanline in this pixel buffer.
      void setStack​(byte[] buffer, java.lang.Integer z, java.lang.Integer c, java.lang.Integer t)
      Sets the entire number of optical sections for a single wavelength or channel at a particular timepoint in this pixel buffer.
      void setStack​(java.nio.ByteBuffer buffer, java.lang.Integer z, java.lang.Integer c, java.lang.Integer t)
      Sets the entire number of optical sections for a single wavelength or channel at a particular timepoint in this pixel buffer.
      void setTile​(byte[] buffer, java.lang.Integer z, java.lang.Integer c, java.lang.Integer t, java.lang.Integer x, java.lang.Integer y, java.lang.Integer w, java.lang.Integer h)
      Sets a tile in this pixel buffer.
      void setTimepoint​(byte[] buffer, java.lang.Integer t)
      Sets the entire number of optical sections for all wavelengths or channels at a particular timepoint in this pixel buffer.
      void setTimepoint​(java.nio.ByteBuffer buffer, java.lang.Integer t)
      Sets the entire number of optical sections for all wavelengths or channels at a particular timepoint in this pixel buffer.

    • Method Detail

      • close

        void close()
    throws java.io.IOException
        Closes the buffer, cleaning up file state.
        Specified by:
        close in interface java.lang.AutoCloseable
        Specified by:
        close in interface java.io.Closeable
        Throws:
        java.io.IOException - if an I/O error occurs.

      • checkBounds

        void checkBounds​(java.lang.Integer x,
                 java.lang.Integer y,
                 java.lang.Integer z,
                 java.lang.Integer c,
                 java.lang.Integer t)
          throws DimensionsOutOfBoundsException
        Checks to ensure that no one particular axis has an offset out of bounds. null may be passed as the argument to any one of the offsets to ignore it for the purposes of bounds checking.
        Parameters:
        x - offset across the X-axis of the pixel buffer to check.
        y - offset across the Y-axis of the pixel buffer to check.
        z - offset across the Z-axis of the pixel buffer to check.
        c - offset across the C-axis of the pixel buffer to check.
        t - offset across the T-axis of the pixel buffer to check.
        Throws:
        DimensionsOutOfBoundsException - if y, z, c or t is out of bounds.

      • getPlaneSize

        java.lang.Long getPlaneSize()
        Retrieves the in memory size of a 2D image plane in this pixel buffer.
        Returns:
        2D image plane size in bytes (sizeX*sizeY*ByteWidth).

      • getRowSize

        java.lang.Integer getRowSize()
        Retrieves the in memory size of a row or scanline of pixels in this pixel buffer.
        Returns:
        row or scanline size in bytes (sizeX*ByteWidth)

      • getColSize

        java.lang.Integer getColSize()
        Retrieves the in memory size of a column of pixels in this pixel buffer.
        Returns:
        column size in bytes (sizeY*ByteWidth)

      • getStackSize

        java.lang.Long getStackSize()
        Retrieves the in memory size of the entire number of optical sections for a single wavelength or channel at a particular timepoint in this pixel buffer.
        Returns:
        stack size in bytes (sizeX*sizeY*sizeZ*ByteWidth).

      • getTimepointSize

        java.lang.Long getTimepointSize()
        Retrieves the in memory size of the entire number of optical sections for all wavelengths or channels at a particular timepoint in this pixel buffer.
        Returns:
        timepoint size in bytes (sizeX*sizeY*sizeZ*sizeC*ByteWidth).

      • getTotalSize

        java.lang.Long getTotalSize()
        Retrieves the in memory size of the entire pixel buffer.
        Returns:
        total size of the pixel size in bytes (sizeX*sizeY*sizeZ*sizeC*sizeT*ByteWidth).

      • getHypercubeSize

        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)
                         throws DimensionsOutOfBoundsException
        Retrieves a the size of a hypercube from this pixel buffer.
        Parameters:
        offset - The offset of each dimension of the pixel buffer.
        size - The number of pixels to retrieve along each dimension .
        step - The step size across each dimension .
        Returns:
        the size.
        Throws:
        java.io.IOException - if there is a problem reading from the pixel buffer.
        DimensionsOutOfBoundsException

      • getRowOffset

        java.lang.Long getRowOffset​(java.lang.Integer y,
                            java.lang.Integer z,
                            java.lang.Integer c,
                            java.lang.Integer t)
                     throws DimensionsOutOfBoundsException
        Retrieves the offset for a particular row or scanline in this pixel buffer.
        Parameters:
        y - offset across the Y-axis of the pixel buffer.
        z - offset across the Z-axis of the pixel buffer.
        c - offset across the C-axis of the pixel buffer.
        t - offset across the T-axis of the pixel buffer.
        Returns:
        offset of the row or scaline.
        Throws:
        DimensionsOutOfBoundsException - if offsets are out of bounds after checking with checkBounds(Integer, Integer, Integer, Integer, Integer).

      • getHypercube

        ome.util.PixelData getHypercube​(java.util.List<java.lang.Integer> offset,
                                java.util.List<java.lang.Integer> size,
                                java.util.List<java.lang.Integer> step)
                         throws java.io.IOException,
                                DimensionsOutOfBoundsException
        Retrieves a hypercube from this pixel buffer.
        Parameters:
        offset - The offset of each dimension of the pixel buffer.
        size - The number of pixels to retrieve along each dimension .
        step - The step size across each dimension .
        Returns:
        buffer containing the data.
        Throws:
        java.io.IOException - if there is a problem reading from the pixel buffer.
        DimensionsOutOfBoundsException

      • getHypercubeDirect

        byte[] getHypercubeDirect​(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
        Retrieves a hypercube from the given pixels directly.
        Parameters:
        offset - The offset of each dimension of the pixel buffer.
        size - The number of pixels to retrieve along each dimension .
        step - The step size across each dimension .
        buffer - pre-allocated buffer, count in size.
        Returns:
        buffer containing the data.
        Throws:
        java.io.IOException - if there is a problem reading from the pixel buffer.
        DimensionsOutOfBoundsException

      • getPlaneRegionDirect

        byte[] getPlaneRegionDirect​(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
        Retrieves a region from a given plane directly.
        Parameters:
        z - offset across the Z-axis of the pixel buffer.
        c - offset across the C-axis of the pixel buffer.
        t - offset across the T-axis of the pixel buffer.
        count - the number of pixels to retrieve.
        offset - the offset at which to retrieve count pixels.
        buffer - pre-allocated buffer, count in size.
        Returns:
        buffer containing the data which comprises the region of the given 2D image plane. It is guaranteed that this buffer will have been byte swapped.
        Throws:
        java.io.IOException - if there is a problem reading from the pixel buffer.
        DimensionsOutOfBoundsException
        See Also:
        getRegionDirect(Integer, Long, byte[])

      • getTile

        ome.util.PixelData getTile​(java.lang.Integer z,
                           java.lang.Integer c,
                           java.lang.Integer t,
                           java.lang.Integer x,
                           java.lang.Integer y,
                           java.lang.Integer w,
                           java.lang.Integer h)
                    throws java.io.IOException
        Retrieves a tile from this pixel buffer.
        Parameters:
        z - offset across the Z-axis of the pixel buffer.
        c - offset across the C-axis of the pixel buffer.
        t - offset across the T-axis of the pixel buffer.
        x - Top left corner of the tile, X offset.
        y - Top left corner of the tile, Y offset.
        w - Width of the tile.
        h - Height of the tile.
        Returns:
        buffer containing the data which comprises the region of the given 2D image plane. It is guaranteed that this buffer will have been byte swapped.
        Throws:
        java.io.IOException - if there is a problem reading from the pixel buffer.
        See Also:
        getTileDirect(Integer, Integer, Integer, Integer, Integer, Integer, Integer, byte[])

      • getTileDirect

        byte[] getTileDirect​(java.lang.Integer z,
                     java.lang.Integer c,
                     java.lang.Integer t,
                     java.lang.Integer x,
                     java.lang.Integer y,
                     java.lang.Integer w,
                     java.lang.Integer h,
                     byte[] buffer)
              throws java.io.IOException
        Retrieves a tile from this pixel buffer.
        Parameters:
        z - offset across the Z-axis of the pixel buffer.
        c - offset across the C-axis of the pixel buffer.
        t - offset across the T-axis of the pixel buffer.
        x - Top left corner of the tile, X offset.
        y - Top left corner of the tile, Y offset.
        w - Width of the tile.
        h - Height of the tile.
        buffer - Pre-allocated buffer of the tile's size.
        Returns:
        buffer containing the data which comprises this region. It is guaranteed that this buffer will have been byte swapped. The buffer is essentially directly from disk.
        Throws:
        java.io.IOException - if there is a problem reading from the pixel buffer.
        See Also:
        getTile(Integer, Integer, Integer, Integer, Integer, Integer, Integer)

      • getRegion

        ome.util.PixelData getRegion​(java.lang.Integer size,
                             java.lang.Long offset)
                      throws java.io.IOException
        Retrieves a region from this pixel buffer.
        Parameters:
        size - byte width of the region to retrieve.
        offset - offset within the pixel buffer.
        Returns:
        buffer containing the data. It is guaranteed that this buffer will have its order set correctly but not that the backing buffer will have been byte swapped. The buffer is essentially directly from disk.
        Throws:
        java.io.IOException - if there is a problem reading from the pixel buffer.
        See Also:
        getRegionDirect(Integer, Long, byte[])

      • getRegionDirect

        byte[] getRegionDirect​(java.lang.Integer size,
                       java.lang.Long offset,
                       byte[] buffer)
                throws java.io.IOException
        Retrieves a region from this pixel buffer directly.
        Parameters:
        size - byte width of the region to retrieve.
        offset - offset within the pixel buffer.
        buffer - pre-allocated buffer of the row's size.
        Returns:
        buffer containing the data which comprises this region. It is guaranteed that this buffer will have been byte swapped. The buffer is essentially directly from disk.
        Throws:
        java.io.IOException - if there is a problem reading from the pixel buffer.
        See Also:
        getRegion(Integer, Long)

      • getRow

        ome.util.PixelData getRow​(java.lang.Integer y,
                          java.lang.Integer z,
                          java.lang.Integer c,
                          java.lang.Integer t)
                   throws java.io.IOException,
                          DimensionsOutOfBoundsException
        Retrieves a particular row or scanline from this pixel buffer.
        Parameters:
        y - offset across the Y-axis of the pixel buffer.
        z - offset across the Z-axis of the pixel buffer.
        c - offset across the C-axis of the pixel buffer.
        t - offset across the T-axis of the pixel buffer.
        Returns:
        buffer containing the data which comprises this row or scanline. It is guaranteed that this buffer will have its order set correctly but not that the backing buffer will have been byte swapped.
        Throws:
        java.io.IOException - if there is a problem reading from the pixel buffer.
        DimensionsOutOfBoundsException - if offsets are out of bounds after checking with checkBounds(Integer, Integer, Integer, Integer, Integer).
        See Also:
        getRowDirect(Integer, Integer, Integer, Integer, byte[])

      • getCol

        ome.util.PixelData getCol​(java.lang.Integer x,
                          java.lang.Integer z,
                          java.lang.Integer c,
                          java.lang.Integer t)
                   throws java.io.IOException,
                          DimensionsOutOfBoundsException
        Retrieves a particular column from this pixel buffer.
        Parameters:
        x - offset across the X-axis of the pixel buffer.
        z - offset across the Z-axis of the pixel buffer.
        c - offset across the C-axis of the pixel buffer.
        t - offset across the T-axis of the pixel buffer.
        Returns:
        buffer containing the data which comprises this column. It is guaranteed that this buffer will have its order set correctly but not that the backing buffer will have been byte swapped.
        Throws:
        java.io.IOException - if there is a problem reading from the pixel buffer.
        DimensionsOutOfBoundsException - if offsets are out of bounds after checking with checkBounds(Integer, Integer, Integer, Integer, Integer).
        See Also:
        getColDirect(Integer, Integer, Integer, Integer, byte[])

      • getRowDirect

        byte[] getRowDirect​(java.lang.Integer y,
                    java.lang.Integer z,
                    java.lang.Integer c,
                    java.lang.Integer t,
                    byte[] buffer)
             throws java.io.IOException,
                    DimensionsOutOfBoundsException
        Retrieves a particular row or scanline from this pixel buffer.
        Parameters:
        y - offset across the Y-axis of the pixel buffer.
        z - offset across the Z-axis of the pixel buffer.
        c - offset across the C-axis of the pixel buffer.
        t - offset across the T-axis of the pixel buffer.
        buffer - pre-allocated buffer of the row's size.
        Returns:
        buffer containing the data which comprises this row or scanline. It is guaranteed that this buffer will have been byte swapped.
        Throws:
        java.io.IOException - if there is a problem reading from the pixel buffer.
        DimensionsOutOfBoundsException - if offsets are out of bounds after checking with checkBounds(Integer, Integer, Integer, Integer, Integer).
        See Also:
        getRow(Integer, Integer, Integer, Integer)

      • getColDirect

        byte[] getColDirect​(java.lang.Integer x,
                    java.lang.Integer z,
                    java.lang.Integer c,
                    java.lang.Integer t,
                    byte[] buffer)
             throws java.io.IOException,
                    DimensionsOutOfBoundsException
        Retrieves a particular column from this pixel buffer.
        Parameters:
        x - offset across the X-axis of the pixel buffer.
        z - offset across the Z-axis of the pixel buffer.
        c - offset across the C-axis of the pixel buffer.
        t - offset across the T-axis of the pixel buffer.
        buffer - pre-allocated buffer of the row's size.
        Returns:
        buffer containing the data which comprises this column. It is guaranteed that this buffer will have been byte swapped.
        Throws:
        java.io.IOException - if there is a problem reading from the pixel buffer.
        DimensionsOutOfBoundsException - if offsets are out of bounds after checking with checkBounds(Integer, Integer, Integer, Integer, Integer).
        See Also:
        getCol(Integer, Integer, Integer, Integer)

      • getPlane

        ome.util.PixelData getPlane​(java.lang.Integer z,
                            java.lang.Integer c,
                            java.lang.Integer t)
                     throws java.io.IOException,
                            DimensionsOutOfBoundsException
        Retrieves a particular 2D image plane from this pixel buffer.
        Parameters:
        z - offset across the Z-axis of the pixel buffer.
        c - offset across the C-axis of the pixel buffer.
        t - offset across the T-axis of the pixel buffer.
        Returns:
        buffer containing the data which comprises this 2D image plane. It is guaranteed that this buffer will have its order set correctly but not that the backing buffer will have been byte swapped.
        Throws:
        java.io.IOException - if there is a problem reading from the pixel buffer.
        DimensionsOutOfBoundsException - if offsets are out of bounds after checking with checkBounds(Integer, Integer, Integer, Integer, Integer).

      • getPlaneRegion

        ome.util.PixelData getPlaneRegion​(java.lang.Integer x,
                                  java.lang.Integer y,
                                  java.lang.Integer width,
                                  java.lang.Integer height,
                                  java.lang.Integer z,
                                  java.lang.Integer c,
                                  java.lang.Integer t,
                                  java.lang.Integer stride)
                           throws java.io.IOException,
                                  DimensionsOutOfBoundsException
        Retrieves a particular region of a 2D image plane from this pixel buffer.
        Parameters:
        x - offset across the X-axis of the pixel buffer.
        y - offset across the Y-axis of the pixel buffer.
        width - The number of pixels to retrieve along the X-axis.
        height - The number of pixels to retrieve along the Y-axis.
        z - offset across the Z-axis of the pixel buffer.
        c - offset across the C-axis of the pixel buffer.
        t - offset across the T-axis of the pixel buffer.
        stride - The step size.
        Returns:
        buffer containing the data which comprises this 2D image plane. It is guaranteed that this buffer will have its order set correctly but not that the backing buffer will have been byte swapped.
        Throws:
        java.io.IOException - if there is a problem reading from the pixel buffer.
        DimensionsOutOfBoundsException - if offsets are out of bounds after checking with checkBounds(Integer, Integer, Integer, Integer, Integer).

      • getPlaneDirect

        byte[] getPlaneDirect​(java.lang.Integer z,
                      java.lang.Integer c,
                      java.lang.Integer t,
                      byte[] buffer)
               throws java.io.IOException,
                      DimensionsOutOfBoundsException
        Retrieves a particular 2D image plane from this pixel buffer.
        Parameters:
        z - offset across the Z-axis of the pixel buffer.
        c - offset across the C-axis of the pixel buffer.
        t - offset across the T-axis of the pixel buffer.
        buffer - pre-allocated buffer of the plane's size.
        Returns:
        buffer containing the data which comprises this 2D image plane. It is guaranteed that this buffer will have been byte swapped.
        Throws:
        java.io.IOException - if there is a problem reading from the pixel buffer.
        DimensionsOutOfBoundsException - if offsets are out of bounds after checking with checkBounds(Integer, Integer, Integer, Integer, Integer).

      • getStack

        ome.util.PixelData getStack​(java.lang.Integer c,
                            java.lang.Integer t)
                     throws java.io.IOException,
                            DimensionsOutOfBoundsException
        Retrieves the the entire number of optical sections for a single wavelength or channel at a particular timepoint in this pixel buffer.
        Parameters:
        c - offset across the C-axis of the pixel buffer.
        t - offset across the T-axis of the pixel buffer.
        Returns:
        buffer containing the data which comprises this stack. It is guaranteed that this buffer will have its order set correctly but not that the backing buffer will have been byte swapped.
        Throws:
        java.io.IOException - if there is a problem reading from the pixel buffer.
        DimensionsOutOfBoundsException - if offsets are out of bounds after checking with checkBounds(Integer, Integer, Integer, Integer, Integer).

      • getStackDirect

        byte[] getStackDirect​(java.lang.Integer c,
                      java.lang.Integer t,
                      byte[] buffer)
               throws java.io.IOException,
                      DimensionsOutOfBoundsException
        Retrieves the the entire number of optical sections for a single wavelength or channel at a particular timepoint in this pixel buffer.
        Parameters:
        c - offset across the C-axis of the pixel buffer.
        t - offset across the T-axis of the pixel buffer.
        buffer - pre-allocated buffer of the stack's size.
        Returns:
        buffer containing the data which comprises this stack. It is guaranteed that this buffer will have been byte swapped.
        Throws:
        java.io.IOException - if there is a problem reading from the pixel buffer.
        DimensionsOutOfBoundsException - if offsets are out of bounds after checking with checkBounds(Integer, Integer, Integer, Integer, Integer).

      • getTimepoint

        ome.util.PixelData getTimepoint​(java.lang.Integer t)
                         throws java.io.IOException,
                                DimensionsOutOfBoundsException
        Retrieves the entire number of optical sections for all wavelengths or channels at a particular timepoint in this pixel buffer.
        Parameters:
        t - offset across the T-axis of the pixel buffer.
        Returns:
        buffer containing the data which comprises this timepoint. It is guaranteed that this buffer will have its order set correctly but not that the backing buffer will have been byte swapped.
        Throws:
        java.io.IOException - if there is a problem reading from the pixel buffer.
        DimensionsOutOfBoundsException - if offsets are out of bounds after checking with checkBounds(Integer, Integer, Integer, Integer, Integer).

      • getTimepointDirect

        byte[] getTimepointDirect​(java.lang.Integer t,
                          byte[] buffer)
                   throws java.io.IOException,
                          DimensionsOutOfBoundsException
        Retrieves the entire number of optical sections for all wavelengths or channels at a particular timepoint in this pixel buffer.
        Parameters:
        t - offset across the T-axis of the pixel buffer.
        buffer - pre-allocated buffer of the timepoint's size.
        Returns:
        buffer containing the data which comprises this timepoint. It is guaranteed that this buffer will have been byte swapped.
        Throws:
        java.io.IOException - if there is a problem reading from the pixel buffer.
        DimensionsOutOfBoundsException - if offsets are out of bounds after checking with checkBounds(Integer, Integer, Integer, Integer, Integer).

      • setTile

        void setTile​(byte[] buffer,
             java.lang.Integer z,
             java.lang.Integer c,
             java.lang.Integer t,
             java.lang.Integer x,
             java.lang.Integer y,
             java.lang.Integer w,
             java.lang.Integer h)
      throws java.io.IOException,
             java.nio.BufferOverflowException
        Sets a tile in this pixel buffer.
        Parameters:
        buffer - A byte array of the data.
        z - offset across the Z-axis of the pixel buffer.
        c - offset across the C-axis of the pixel buffer.
        t - offset across the T-axis of the pixel buffer.
        x - Top left corner of the tile, X offset.
        y - Top left corner of the tile, Y offset.
        w - Width of the tile.
        h - Height of the tile.
        Throws:
        java.io.IOException - if there is a problem writing to the pixel buffer.
        java.nio.BufferOverflowException - if an attempt is made to write off the end of the file.

      • setRegion

        void setRegion​(java.lang.Integer size,
               java.lang.Long offset,
               byte[] buffer)
        throws java.io.IOException,
               java.nio.BufferOverflowException
        Sets a region in this pixel buffer.
        Parameters:
        size - byte width of the region to set.
        offset - offset within the pixel buffer.
        buffer - a byte array of the data.
        Throws:
        java.io.IOException - if there is a problem writing to the pixel buffer.
        java.nio.BufferOverflowException - if buffer.length > size.

      • setRegion

        void setRegion​(java.lang.Integer size,
               java.lang.Long offset,
               java.nio.ByteBuffer buffer)
        throws java.io.IOException,
               java.nio.BufferOverflowException
        Sets a region in this pixel buffer.
        Parameters:
        size - byte width of the region to set.
        offset - offset within the pixel buffer.
        buffer - a byte buffer of the data.
        Throws:
        java.io.IOException - if there is a problem writing to the pixel buffer.
        java.nio.BufferOverflowException - if buffer.length > size.

      • setRow

        void setRow​(java.nio.ByteBuffer buffer,
            java.lang.Integer y,
            java.lang.Integer z,
            java.lang.Integer c,
            java.lang.Integer t)
     throws java.io.IOException,
            DimensionsOutOfBoundsException,
            java.nio.BufferOverflowException
        Sets a particular row or scanline in this pixel buffer.
        Parameters:
        buffer - a byte buffer of the data comprising this row or scanline.
        y - offset across the Y-axis of the pixel buffer.
        z - offset across the Z-axis of the pixel buffer.
        c - offset across the C-axis of the pixel buffer.
        t - offset across the T-axis of the pixel buffer.
        Throws:
        java.io.IOException - if there is a problem reading from the pixel buffer.
        DimensionsOutOfBoundsException - if offsets are out of bounds after checking with checkBounds(Integer, Integer, Integer, Integer, Integer).
        java.nio.BufferOverflowException - if buffer.length > {@link #getRowSize()}.

      • setPlane

        void setPlane​(java.nio.ByteBuffer buffer,
              java.lang.Integer z,
              java.lang.Integer c,
              java.lang.Integer t)
       throws java.io.IOException,
              DimensionsOutOfBoundsException,
              java.nio.BufferOverflowException
        Sets a particular 2D image plane in this pixel buffer.
        Parameters:
        buffer - a byte array of the data comprising this 2D image plane.
        z - offset across the Z-axis of the pixel buffer.
        c - offset across the C-axis of the pixel buffer.
        t - offset across the T-axis of the pixel buffer.
        Throws:
        java.io.IOException - if there is a problem writing to the pixel buffer.
        DimensionsOutOfBoundsException - if offsets are out of bounds after checking with checkBounds(Integer, Integer, Integer, Integer, Integer).
        java.nio.BufferOverflowException - if buffer.length > {@link #getPlaneSize()}.

      • setPlane

        void setPlane​(byte[] buffer,
              java.lang.Integer z,
              java.lang.Integer c,
              java.lang.Integer t)
       throws java.io.IOException,
              DimensionsOutOfBoundsException,
              java.nio.BufferOverflowException
        Sets a particular 2D image plane in this pixel buffer.
        Parameters:
        buffer - a byte buffer of the data comprising this 2D image plane.
        z - offset across the Z-axis of the pixel buffer.
        c - offset across the C-axis of the pixel buffer.
        t - offset across the T-axis of the pixel buffer.
        Throws:
        java.io.IOException - if there is a problem writing to the pixel buffer.
        DimensionsOutOfBoundsException - if offsets are out of bounds after checking with checkBounds(Integer, Integer, Integer, Integer, Integer).
        java.nio.BufferOverflowException - if buffer.length > {@link #getPlaneSize()}.

      • setStack

        void setStack​(java.nio.ByteBuffer buffer,
              java.lang.Integer z,
              java.lang.Integer c,
              java.lang.Integer t)
       throws java.io.IOException,
              DimensionsOutOfBoundsException,
              java.nio.BufferOverflowException
        Sets the entire number of optical sections for a single wavelength or channel at a particular timepoint in this pixel buffer.
        Parameters:
        buffer - a byte buffer of the data comprising this stack.
        c - offset across the C-axis of the pixel buffer.
        t - offset across the T-axis of the pixel buffer.
        Throws:
        java.io.IOException - if there is a problem writing to the pixel buffer.
        DimensionsOutOfBoundsException - if offsets are out of bounds after checking with checkBounds(Integer, Integer, Integer, Integer, Integer).
        java.nio.BufferOverflowException - if buffer.length > {@link #getStackSize()}.

      • setStack

        void setStack​(byte[] buffer,
              java.lang.Integer z,
              java.lang.Integer c,
              java.lang.Integer t)
       throws java.io.IOException,
              DimensionsOutOfBoundsException,
              java.nio.BufferOverflowException
        Sets the entire number of optical sections for a single wavelength or channel at a particular timepoint in this pixel buffer.
        Parameters:
        buffer - a byte array of the data comprising this stack.
        z - offset across the Z-axis of the pixel buffer.
        c - offset across the C-axis of the pixel buffer.
        t - offset across the T-axis of the pixel buffer.
        Throws:
        java.io.IOException - if there is a problem writing to the pixel buffer.
        DimensionsOutOfBoundsException - if offsets are out of bounds after checking with checkBounds(Integer, Integer, Integer, Integer, Integer).
        java.nio.BufferOverflowException - if buffer.length > {@link #getStackSize()}.

      • setTimepoint

        void setTimepoint​(java.nio.ByteBuffer buffer,
                  java.lang.Integer t)
           throws java.io.IOException,
                  DimensionsOutOfBoundsException,
                  java.nio.BufferOverflowException
        Sets the entire number of optical sections for all wavelengths or channels at a particular timepoint in this pixel buffer.
        Parameters:
        buffer - a byte buffer of the data comprising this timepoint.
        t - offset across the T-axis of the pixel buffer.
        Throws:
        java.io.IOException - if there is a problem writing to the pixel buffer.
        DimensionsOutOfBoundsException - if offsets are out of bounds after checking with checkBounds(Integer, Integer, Integer, Integer, Integer).
        java.nio.BufferOverflowException - if buffer.length > {@link #getTimepointSize()}.

      • setTimepoint

        void setTimepoint​(byte[] buffer,
                  java.lang.Integer t)
           throws java.io.IOException,
                  DimensionsOutOfBoundsException,
                  java.nio.BufferOverflowException
        Sets the entire number of optical sections for all wavelengths or channels at a particular timepoint in this pixel buffer.
        Parameters:
        buffer - a byte array of the data comprising this timepoint.
        t - offset across the T-axis of the pixel buffer.
        Throws:
        java.io.IOException - if there is a problem writing to the pixel buffer.
        DimensionsOutOfBoundsException - if offsets are out of bounds after checking with checkBounds(Integer, Integer, Integer, Integer, Integer).
        java.nio.BufferOverflowException - if buffer.length > {@link #getTimepointSize()}.

      • calculateMessageDigest

        byte[] calculateMessageDigest()
                       throws java.io.IOException
        Calculates a SHA-1 message digest for the entire pixel buffer.
        Returns:
        byte array containing the message digest.
        Throws:
        java.io.IOException - if there is a problem reading from the pixel buffer.

      • getByteWidth

        int getByteWidth()
        Returns the byte width for the pixel buffer.
        Returns:
        See above.

      • isSigned

        boolean isSigned()
        Returns whether or not the pixel buffer has signed pixels.
        Returns:
        See above.

      • isFloat

        boolean isFloat()
        Returns whether or not the pixel buffer has floating point pixels.
        Returns:
        true if the pixel buffer as floating point, false otherwise

      • getPath

        java.lang.String getPath()
        Retrieves the full path to this pixel buffer on disk
        Returns:
        fully qualified path.

      • getId

        long getId()
        Retrieves the identifier of this pixel buffer

      • getSizeX

        int getSizeX()
        Retrieves the size in X of this pixel buffer

      • getSizeY

        int getSizeY()
        Retrieves the size in Y of this pixel buffer

      • getSizeZ

        int getSizeZ()
        Retrieves the size in Z of this pixel buffer

      • getSizeC

        int getSizeC()
        Retrieves the size in C of this pixel buffer

      • getSizeT

        int getSizeT()
        Retrieves the size in T of this pixel buffer

      • getResolutionLevels

        int getResolutionLevels()
        Retrieves the number of resolution levels that the backing pixels pyramid contains.
        Returns:
        The number of resolution levels. This value does not necessarily indicate either the presence or absence of a pixels pyramid.

      • getResolutionLevel

        int getResolutionLevel()
        Retrieves the active resolution level.
        Returns:
        The active resolution level. The level will be non-negative and less than getResolutionLevels(). Resolution level 0 is the smallest resolution and resolution level getResolutionLevels() - 1 is the largest resolution. This is the inverse of how Bio-Formats indexes resolutions.

      • setResolutionLevel

        void setResolutionLevel​(int resolutionLevel)
        Sets the active resolution level.
        Parameters:
        resolutionLevel - The resolution level to be used by the pixel buffer. The level should be non-negative and less than getResolutionLevels(). Resolution level 0 is the smallest resolution and resolution level getResolutionLevels() - 1 is the largest resolution. This is the inverse of how Bio-Formats indexes resolutions.

      • getTileSize

        java.awt.Dimension getTileSize()
        Retrieves the tile size for the pixel store.
        Returns:
        The dimension of the tile or null if the pixel buffer is not tiled.

      • getResolutionDescriptions

        java.util.List<java.util.List<java.lang.Integer>> getResolutionDescriptions()
        Return a list of lists each of which has sizeX, sizeY for the resolution level matching the index of the outer index. For example, if an image has 2 resolution levels of size 2048x1024 and 1024x512 then this returns: [[2048,1024],[1024,512]]
        Returns:
        a list of lists containing sizeX, sizeY for each resolution level