BfPyramidPixelBuffer (OMERO (OME Remote Objects) Server)

java.lang.Object
- ome.io.bioformats.BfPyramidPixelBuffer

All Implemented Interfaces:

Closeable, AutoCloseable, PixelBuffer
```
public class BfPyramidPixelBuffer
extends Object
implements PixelBuffer
```
PixelBuffer implementation which uses Bio-Formats to read pixels data directly from original files.

Since:

OMERO-Beta4.3

Field Summary

Fields
Modifier and Type	Field and Description
`static String`	`PYR_LOCK_EXT`
`protected OmeroPixelsPyramidReader`	`reader` Bio-Formats implementation the delegate uses to read the backing TIFF.
`protected OmeroPixelsPyramidWriter`	`writer` Bio-Formats implementation used to write to the backing TIFF.

Constructor Summary

Constructors
Modifier	Constructor and Description
	`BfPyramidPixelBuffer(Pixels pixels, String filePath, boolean write)` We may want a constructor that takes the id of an imported file or that takes a File object?
	`BfPyramidPixelBuffer(TileSizes sizes, Pixels pixels, String filePath, boolean write)` Full constructor taking a `TileSizes` implementation which defines how large the pyramid tiles will be.
`protected`	`BfPyramidPixelBuffer(TileSizes sizes, Pixels pixels, String filePath, boolean write, boolean init)`

Method Summary

Methods
Modifier and Type	Method and Description
`protected void`	`acquireLock()`
`byte[]`	`calculateMessageDigest()` Calculates a SHA-1 message digest for the entire pixel buffer.
`void`	`checkBounds(Integer x, Integer y, Integer z, Integer c, 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.
`protected void`	`closeRaf()`
`protected void`	`closeWriter()` This method should never exit without releasing the lock.
`ByteOrder`	`getByteOrder()` Returns the current pixel byte order.
`int`	`getByteWidth()` Returns the byte width for the pixel buffer.
`PixelData`	`getCol(Integer x, Integer z, Integer c, Integer t)` Retrieves a particular column from this pixel buffer.
`byte[]`	`getColDirect(Integer x, Integer z, Integer c, Integer t, byte[] buffer)` Retrieves a particular column from this pixel buffer.
`Integer`	`getColSize()` Retrieves the in memory size of a column of pixels in this pixel buffer.
`PixelData`	`getHypercube(List<Integer> offset, List<Integer> size, List<Integer> step)` Retrieves a hypercube from this pixel buffer.
`byte[]`	`getHypercubeDirect(List<Integer> offset, List<Integer> size, List<Integer> step, byte[] buffer)` Retrieves a hypercube from the given pixels directly.
`Long`	`getHypercubeSize(List<Integer> offset, List<Integer> size, List<Integer> step)` Retrieves a the size of a hypercube from this pixel buffer.
`long`	`getId()` Delegates to `Pixels.getId()`.
`String`	`getPath()` Retrieves the full path to this pixel buffer on disk
`PixelData`	`getPlane(Integer z, Integer c, Integer t)` Retrieves a particular 2D image plane from this pixel buffer.
`byte[]`	`getPlaneDirect(Integer z, Integer c, Integer t, byte[] buffer)` Retrieves a particular 2D image plane from this pixel buffer.
`Long`	`getPlaneOffset(Integer z, Integer c, Integer t)` Retrieves the offset for a particular 2D image plane in this pixel buffer.
`PixelData`	`getPlaneRegion(Integer x, Integer y, Integer width, Integer height, Integer z, Integer c, Integer t, Integer stride)` Retrieves a particular region of a 2D image plane from this pixel buffer.
`byte[]`	`getPlaneRegionDirect(Integer z, Integer c, Integer t, Integer count, Integer offset, byte[] buffer)` Retrieves a region from a given plane directly.
`Long`	`getPlaneSize()` Retrieves the in memory size of a 2D image plane in this pixel buffer.
`PixelData`	`getRegion(Integer size, Long offset)` Retrieves a region from this pixel buffer.
`byte[]`	`getRegionDirect(Integer size, Long offset, byte[] buffer)` Retrieves a region from this pixel buffer directly.
`List<List<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.
`PixelData`	`getRow(Integer y, Integer z, Integer c, Integer t)` Retrieves a particular row or scanline from this pixel buffer.
`byte[]`	`getRowDirect(Integer y, Integer z, Integer c, Integer t, byte[] buffer)` Retrieves a particular row or scanline from this pixel buffer.
`Long`	`getRowOffset(Integer y, Integer z, Integer c, Integer t)` Retrieves the offset for a particular row or scanline in this pixel buffer.
`Integer`	`getRowSize()` Retrieves the in memory size of a row or scanline of pixels in this pixel buffer.
`int`	`getSizeC()` Delegates to `Pixels.getSizeC()`.
`int`	`getSizeT()` Delegates to `Pixels.getSizeT()`.
`int`	`getSizeX()` Delegates to `Pixels.getSizeX()`.
`int`	`getSizeY()` Delegates to `Pixels.getSizeY()`.
`int`	`getSizeZ()` Delegates to `Pixels.getSizeZ()`.
`PixelData`	`getStack(Integer c, 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(Integer c, 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.
`Long`	`getStackOffset(Integer c, 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.
`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.
`PixelData`	`getTile(Integer z, Integer c, Integer t, Integer x, Integer y, Integer w, Integer h)` Retrieves a tile from this pixel buffer.
`byte[]`	`getTileDirect(Integer z, Integer c, Integer t, Integer x, Integer y, Integer w, Integer h, byte[] buffer)` Retrieves a tile from this pixel buffer.
`Dimension`	`getTileSize()` Retrieves the tile size for the pixel store.
`PixelData`	`getTimepoint(Integer t)` Retrieves the entire number of optical sections for all wavelengths or channels at a particular timepoint in this pixel buffer.
`byte[]`	`getTimepointDirect(Integer t, byte[] buffer)` Retrieves the entire number of optical sections for all wavelengths or channels at a particular timepoint in this pixel buffer.
`Long`	`getTimepointOffset(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.
`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.
`Long`	`getTotalSize()` Retrieves the in memory size of the entire pixel buffer.
`protected void`	`init(String filePath, boolean write)`
`protected void`	`initializeReader()` If the pyramid file exists (which the constructor guarantees) then we assume that even if a lock file is present, that it's no longer valid.
`protected void`	`initializeWriter(String output, String compression, boolean bigTiff, int tileWidth, int tileLength)` Initializes the writer.
`boolean`	`isFloat()` Returns whether or not the pixel buffer has floating point pixels.
`protected boolean`	`isLockedByOthers()`
`boolean`	`isSigned()` Returns whether or not the pixel buffer has signed pixels.
`boolean`	`isWrite()` Whether or not this instance is in writing-mode.
`void`	`setByteOrder(ByteOrder byteOrder)` Sets the pixel byte order.
`void`	`setPlane(byte[] buffer, Integer z, Integer c, Integer t)` Sets a particular 2D image plane in this pixel buffer.
`void`	`setPlane(ByteBuffer buffer, Integer z, Integer c, Integer t)` Sets a particular 2D image plane in this pixel buffer.
`void`	`setRegion(Integer size, Long offset, byte[] buffer)` Sets a region in this pixel buffer.
`void`	`setRegion(Integer size, Long offset, ByteBuffer buffer)` Sets a region in this pixel buffer.
`void`	`setResolutionLevel(int resolutionLevel)` Sets the active resolution level.
`void`	`setRow(ByteBuffer buffer, Integer y, Integer z, Integer c, Integer t)` Sets a particular row or scanline in this pixel buffer.
`void`	`setStack(byte[] buffer, Integer z, Integer c, 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(ByteBuffer buffer, Integer z, Integer c, 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, Integer z, Integer c, Integer t, Integer x, Integer y, Integer w, Integer h)` Sets a tile in this pixel buffer.
`void`	`setTimepoint(byte[] buffer, Integer t)` Sets the entire number of optical sections for all wavelengths or channels at a particular timepoint in this pixel buffer.
`void`	`setTimepoint(ByteBuffer buffer, Integer t)` Sets the entire number of optical sections for all wavelengths or channels at a particular timepoint in this pixel buffer.

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

- Field Detail
  - writer
```
protected OmeroPixelsPyramidWriter writer
```
    Bio-Formats implementation used to write to the backing TIFF.
  - reader
```
protected OmeroPixelsPyramidReader reader
```
    Bio-Formats implementation the delegate uses to read the backing TIFF.
  - PYR_LOCK_EXT
```
public static final String PYR_LOCK_EXT
```
    See Also:
    Constant Field Values
- Constructor Detail
  - BfPyramidPixelBuffer
```
public BfPyramidPixelBuffer(Pixels pixels,
                    String filePath,
                    boolean write)
                     throws 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. Upon construction, the pixel buffer is available for reading or writing. However, on the first read, writing will be subsequently disabled.
    
    Throws:
    
    IOException
    
    loci.formats.FormatException
    See Also:
    ticket:5083
  - BfPyramidPixelBuffer
```
public BfPyramidPixelBuffer(TileSizes sizes,
                    Pixels pixels,
                    String filePath,
                    boolean write)
                     throws IOException,
                            loci.formats.FormatException
```
    Full constructor taking a TileSizes implementation which defines how large the pyramid tiles will be.
    
    Parameters:
    sizes -
    pixels -
    filePath -
    write -
    
    Throws:
    
    IOException
    
    loci.formats.FormatException
  - BfPyramidPixelBuffer
```
protected BfPyramidPixelBuffer(TileSizes sizes,
                    Pixels pixels,
                    String filePath,
                    boolean write,
                    boolean init)
                        throws IOException,
                               loci.formats.FormatException
```
    Throws:
    
    IOException
    
    loci.formats.FormatException
- Method Detail
  - init
```
protected void init(String filePath,
        boolean write)
             throws IOException,
                    loci.formats.FormatException
```
    Throws:
    
    IOException
    
    loci.formats.FormatException
  - initializeReader
```
protected void initializeReader()
                         throws IOException,
                                loci.formats.FormatException
```
    If the pyramid file exists (which the constructor guarantees) then we assume that even if a lock file is present, that it's no longer valid.
    
    Throws:
    
    IOException
    
    loci.formats.FormatException
  - initializeWriter
```
protected void initializeWriter(String output,
                    String compression,
                    boolean bigTiff,
                    int tileWidth,
                    int tileLength)
                         throws loci.formats.FormatException
```
    Initializes the writer. Since the reader location is not present until this instance is closed, other ByPyramidPixelBuffer instances may try to also call this method in which case acquireLock() will throw a LockTimeout.
    
    Parameters:
    output - The file where to write the compressed data.
    compression - The compression to use.
    bigTiff - Pass true to set the bigTiff flag, false otherwise.
    
    Throws:
    
    Exception - Thrown if an error occurred.
    
    loci.formats.FormatException
  - acquireLock
```
protected void acquireLock()
```
  - closeRaf
```
protected void closeRaf()
```
  - isLockedByOthers
```
protected boolean isLockedByOthers()
```
  - closeWriter
```
protected void closeWriter()
                    throws IOException
```
    This method should never exit without releasing the lock.
    
    Throws:
    
    IOException
  - isWrite
```
public boolean isWrite()
```
    Whether or not this instance is in writing-mode. Any of the calls to reader methods called while this method returns true will close the writer, saving it to disk and preventing any further write methods.
  - setTile
```
public void setTile(byte[] buffer,
           Integer z,
           Integer c,
           Integer t,
           Integer x,
           Integer y,
           Integer w,
           Integer h)
             throws IOException,
                    BufferOverflowException
```
    Description copied from interface: PixelBuffer
    
    Sets a tile in this pixel buffer.
    
    Specified by:
    
    setTile in interface PixelBuffer
    
    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:
    
    IOException - if there is a problem writing to the pixel buffer.
    
    BufferOverflowException - if an attempt is made to write off the end of the file.
  - getByteOrder
```
public ByteOrder getByteOrder()
```
    Returns the current pixel byte order.
    
    Returns:
    See above.
  - setByteOrder
```
public void setByteOrder(ByteOrder byteOrder)
```
    Sets the pixel byte order.
    
    Parameters:
    byteOrder - The pixel byte order to set.
  - calculateMessageDigest
```
public byte[] calculateMessageDigest()
                              throws IOException
```
    Description copied from interface: PixelBuffer
    
    Calculates a SHA-1 message digest for the entire pixel buffer.
    
    Specified by:
    
    calculateMessageDigest in interface PixelBuffer
    
    Returns:
    byte array containing the message digest.
    
    Throws:
    
    IOException - if there is a problem reading from the pixel buffer.
  - checkBounds
```
public void checkBounds(Integer x,
               Integer y,
               Integer z,
               Integer c,
               Integer t)
                 throws DimensionsOutOfBoundsException
```
    Description copied from interface: PixelBuffer
    
    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.
    
    Specified by:
    
    checkBounds in interface PixelBuffer
    
    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.
  - close
```
public void close()
           throws IOException
```
    Description copied from interface: PixelBuffer
    
    Closes the buffer, cleaning up file state.
    
    Specified by:
    
    close in interface Closeable
    
    Specified by:
    
    close in interface AutoCloseable
    
    Specified by:
    
    close in interface PixelBuffer
    
    Throws:
    
    IOException - if an I/O error occurs.
  - getByteWidth
```
public int getByteWidth()
```
    Description copied from interface: PixelBuffer
    
    Returns the byte width for the pixel buffer.
    
    Specified by:
    
    getByteWidth in interface PixelBuffer
    
    Returns:
    See above.
  - getCol
```
public PixelData getCol(Integer x,
               Integer z,
               Integer c,
               Integer t)
                 throws IOException,
                        DimensionsOutOfBoundsException
```
    Description copied from interface: PixelBuffer
    
    Retrieves a particular column from this pixel buffer.
    
    Specified by:
    
    getCol in interface PixelBuffer
    
    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:
    
    IOException - if there is a problem reading from the pixel buffer.
    
    DimensionsOutOfBoundsException - if offsets are out of bounds after checking with checkBounds().
    See Also:
    getColDirect()
  - getColDirect
```
public byte[] getColDirect(Integer x,
                  Integer z,
                  Integer c,
                  Integer t,
                  byte[] buffer)
                    throws IOException,
                           DimensionsOutOfBoundsException
```
    Description copied from interface: PixelBuffer
    
    Retrieves a particular column from this pixel buffer.
    
    Specified by:
    
    getColDirect in interface PixelBuffer
    
    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:
    
    IOException - if there is a problem reading from the pixel buffer.
    
    DimensionsOutOfBoundsException - if offsets are out of bounds after checking with checkBounds().
    See Also:
    getCol()
  - getColSize
```
public Integer getColSize()
```
    Description copied from interface: PixelBuffer
    
    Retrieves the in memory size of a column of pixels in this pixel buffer.
    
    Specified by:
    
    getColSize in interface PixelBuffer
    
    Returns:
    column size in bytes (sizeY*ByteWidth)
  - getHypercube
```
public PixelData getHypercube(List<Integer> offset,
                     List<Integer> size,
                     List<Integer> step)
                       throws IOException,
                              DimensionsOutOfBoundsException
```
    Description copied from interface: PixelBuffer
    
    Retrieves a hypercube from this pixel buffer.
    
    Specified by:
    
    getHypercube in interface PixelBuffer
    
    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:
    
    IOException - if there is a problem reading from the pixel buffer.
    
    DimensionsOutOfBoundsException
  - getHypercubeDirect
```
public byte[] getHypercubeDirect(List<Integer> offset,
                        List<Integer> size,
                        List<Integer> step,
                        byte[] buffer)
                          throws IOException,
                                 DimensionsOutOfBoundsException
```
    Description copied from interface: PixelBuffer
    
    Retrieves a hypercube from the given pixels directly.
    
    Specified by:
    
    getHypercubeDirect in interface PixelBuffer
    
    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:
    
    IOException - if there is a problem reading from the pixel buffer.
    
    DimensionsOutOfBoundsException
  - getHypercubeSize
```
public Long getHypercubeSize(List<Integer> offset,
                    List<Integer> size,
                    List<Integer> step)
                      throws DimensionsOutOfBoundsException
```
    Description copied from interface: PixelBuffer
    
    Retrieves a the size of a hypercube from this pixel buffer.
    
    Specified by:
    
    getHypercubeSize in interface PixelBuffer
    
    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:
    
    DimensionsOutOfBoundsException
  - getId
```
public long getId()
```
    Description copied from interface: PixelBuffer
    
    Delegates to Pixels.getId().
    
    Specified by:
    
    getId in interface PixelBuffer
  - getPath
```
public String getPath()
```
    Description copied from interface: PixelBuffer
    
    Retrieves the full path to this pixel buffer on disk
    
    Specified by:
    
    getPath in interface PixelBuffer
    
    Returns:
    fully qualified path.
  - getPlane
```
public PixelData getPlane(Integer z,
                 Integer c,
                 Integer t)
                   throws IOException,
                          DimensionsOutOfBoundsException
```
    Description copied from interface: PixelBuffer
    
    Retrieves a particular 2D image plane from this pixel buffer.
    
    Specified by:
    
    getPlane in interface PixelBuffer
    
    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:
    
    IOException - if there is a problem reading from the pixel buffer.
    
    DimensionsOutOfBoundsException - if offsets are out of bounds after checking with checkBounds().
  - getPlaneDirect
```
public byte[] getPlaneDirect(Integer z,
                    Integer c,
                    Integer t,
                    byte[] buffer)
                      throws IOException,
                             DimensionsOutOfBoundsException
```
    Description copied from interface: PixelBuffer
    
    Retrieves a particular 2D image plane from this pixel buffer.
    
    Specified by:
    
    getPlaneDirect in interface PixelBuffer
    
    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:
    
    IOException - if there is a problem reading from the pixel buffer.
    
    DimensionsOutOfBoundsException - if offsets are out of bounds after checking with checkBounds().
  - getPlaneOffset
```
public Long getPlaneOffset(Integer z,
                  Integer c,
                  Integer t)
                    throws DimensionsOutOfBoundsException
```
    Description copied from interface: PixelBuffer
    
    Retrieves the offset for a particular 2D image plane in this pixel buffer.
    
    Specified by:
    
    getPlaneOffset in interface PixelBuffer
    
    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:
    offset of the 2D image plane.
    
    Throws:
    
    DimensionsOutOfBoundsException - if offsets are out of bounds after checking with checkBounds().
  - getPlaneRegion
```
public PixelData getPlaneRegion(Integer x,
                       Integer y,
                       Integer width,
                       Integer height,
                       Integer z,
                       Integer c,
                       Integer t,
                       Integer stride)
                         throws IOException,
                                DimensionsOutOfBoundsException
```
    Description copied from interface: PixelBuffer
    
    Retrieves a particular region of a 2D image plane from this pixel buffer.
    
    Specified by:
    
    getPlaneRegion in interface PixelBuffer
    
    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:
    
    IOException - if there is a problem reading from the pixel buffer.
    
    DimensionsOutOfBoundsException - if offsets are out of bounds after checking with checkBounds().
  - getPlaneRegionDirect
```
public byte[] getPlaneRegionDirect(Integer z,
                          Integer c,
                          Integer t,
                          Integer count,
                          Integer offset,
                          byte[] buffer)
                            throws IOException,
                                   DimensionsOutOfBoundsException
```
    Description copied from interface: PixelBuffer
    
    Retrieves a region from a given plane directly.
    
    Specified by:
    
    getPlaneRegionDirect in interface PixelBuffer
    
    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:
    
    IOException - if there is a problem reading from the pixel buffer.
    
    DimensionsOutOfBoundsException
    See Also:
    getRegionDirect()
  - getPlaneSize
```
public Long getPlaneSize()
```
    Description copied from interface: PixelBuffer
    
    Retrieves the in memory size of a 2D image plane in this pixel buffer.
    
    Specified by:
    
    getPlaneSize in interface PixelBuffer
    
    Returns:
    2D image plane size in bytes (sizeX*sizeY*ByteWidth).
  - getRegion
```
public PixelData getRegion(Integer size,
                  Long offset)
                    throws IOException
```
    Description copied from interface: PixelBuffer
    
    Retrieves a region from this pixel buffer.
    
    Specified by:
    
    getRegion in interface PixelBuffer
    
    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:
    
    IOException - if there is a problem reading from the pixel buffer.
    See Also:
    getRegionDirect()
  - getRegionDirect
```
public byte[] getRegionDirect(Integer size,
                     Long offset,
                     byte[] buffer)
                       throws IOException
```
    Description copied from interface: PixelBuffer
    
    Retrieves a region from this pixel buffer directly.
    
    Specified by:
    
    getRegionDirect in interface PixelBuffer
    
    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:
    
    IOException - if there is a problem reading from the pixel buffer.
    See Also:
    getRegion()
  - getRow
```
public PixelData getRow(Integer y,
               Integer z,
               Integer c,
               Integer t)
                 throws IOException,
                        DimensionsOutOfBoundsException
```
    Description copied from interface: PixelBuffer
    
    Retrieves a particular row or scanline from this pixel buffer.
    
    Specified by:
    
    getRow in interface PixelBuffer
    
    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:
    
    IOException - if there is a problem reading from the pixel buffer.
    
    DimensionsOutOfBoundsException - if offsets are out of bounds after checking with checkBounds().
    See Also:
    getRowDirect()
  - getRowDirect
```
public byte[] getRowDirect(Integer y,
                  Integer z,
                  Integer c,
                  Integer t,
                  byte[] buffer)
                    throws IOException,
                           DimensionsOutOfBoundsException
```
    Description copied from interface: PixelBuffer
    
    Retrieves a particular row or scanline from this pixel buffer.
    
    Specified by:
    
    getRowDirect in interface PixelBuffer
    
    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:
    
    IOException - if there is a problem reading from the pixel buffer.
    
    DimensionsOutOfBoundsException - if offsets are out of bounds after checking with checkBounds().
    See Also:
    getRow()
  - getRowOffset
```
public Long getRowOffset(Integer y,
                Integer z,
                Integer c,
                Integer t)
                  throws DimensionsOutOfBoundsException
```
    Description copied from interface: PixelBuffer
    
    Retrieves the offset for a particular row or scanline in this pixel buffer.
    
    Specified by:
    
    getRowOffset in interface PixelBuffer
    
    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().
  - getRowSize
```
public Integer getRowSize()
```
    Description copied from interface: PixelBuffer
    
    Retrieves the in memory size of a row or scanline of pixels in this pixel buffer.
    
    Specified by:
    
    getRowSize in interface PixelBuffer
    
    Returns:
    row or scanline size in bytes (sizeX*ByteWidth)
  - getSizeC
```
public int getSizeC()
```
    Description copied from interface: PixelBuffer
    
    Delegates to Pixels.getSizeC().
    
    Specified by:
    
    getSizeC in interface PixelBuffer
  - getSizeT
```
public int getSizeT()
```
    Description copied from interface: PixelBuffer
    
    Delegates to Pixels.getSizeT().
    
    Specified by:
    
    getSizeT in interface PixelBuffer
  - getSizeX
```
public int getSizeX()
```
    Description copied from interface: PixelBuffer
    
    Delegates to Pixels.getSizeX().
    
    Specified by:
    
    getSizeX in interface PixelBuffer
  - getSizeY
```
public int getSizeY()
```
    Description copied from interface: PixelBuffer
    
    Delegates to Pixels.getSizeY().
    
    Specified by:
    
    getSizeY in interface PixelBuffer
  - getSizeZ
```
public int getSizeZ()
```
    Description copied from interface: PixelBuffer
    
    Delegates to Pixels.getSizeZ().
    
    Specified by:
    
    getSizeZ in interface PixelBuffer
  - getStack
```
public PixelData getStack(Integer c,
                 Integer t)
                   throws IOException,
                          DimensionsOutOfBoundsException
```
    Description copied from interface: PixelBuffer
    
    Retrieves the the entire number of optical sections for a single wavelength or channel at a particular timepoint in this pixel buffer.
    
    Specified by:
    
    getStack in interface PixelBuffer
    
    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:
    
    IOException - if there is a problem reading from the pixel buffer.
    
    DimensionsOutOfBoundsException - if offsets are out of bounds after checking with checkBounds().
  - getStackDirect
```
public byte[] getStackDirect(Integer c,
                    Integer t,
                    byte[] buffer)
                      throws IOException,
                             DimensionsOutOfBoundsException
```
    Description copied from interface: PixelBuffer
    
    Retrieves the the entire number of optical sections for a single wavelength or channel at a particular timepoint in this pixel buffer.
    
    Specified by:
    
    getStackDirect in interface PixelBuffer
    
    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:
    
    IOException - if there is a problem reading from the pixel buffer.
    
    DimensionsOutOfBoundsException - if offsets are out of bounds after checking with checkBounds().
  - getStackOffset
```
public Long getStackOffset(Integer c,
                  Integer t)
                    throws DimensionsOutOfBoundsException
```
    Description copied from interface: PixelBuffer
    
    Retrieves the offset for the entire number of optical sections for a single wavelength or channel at a particular timepoint in this pixel buffer.
    
    Specified by:
    
    getStackOffset in interface PixelBuffer
    
    Parameters:
    c - offset across the C-axis of the pixel buffer.
    t - offset across the T-axis of the pixel buffer.
    
    Returns:
    offset of the stack.
    
    Throws:
    
    DimensionsOutOfBoundsException - if offsets are out of bounds after checking with checkBounds().
  - getStackSize
```
public Long getStackSize()
```
    Description copied from interface: PixelBuffer
    
    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.
    
    Specified by:
    
    getStackSize in interface PixelBuffer
    
    Returns:
    stack size in bytes (sizeX*sizeY*sizeZ*ByteWidth).
  - getTile
```
public PixelData getTile(Integer z,
                Integer c,
                Integer t,
                Integer x,
                Integer y,
                Integer w,
                Integer h)
                  throws IOException
```
    Description copied from interface: PixelBuffer
    
    Retrieves a tile from this pixel buffer.
    
    Specified by:
    
    getTile in interface PixelBuffer
    
    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:
    
    IOException - if there is a problem reading from the pixel buffer.
    See Also:
    getTileDirect()
  - getTileDirect
```
public byte[] getTileDirect(Integer z,
                   Integer c,
                   Integer t,
                   Integer x,
                   Integer y,
                   Integer w,
                   Integer h,
                   byte[] buffer)
                     throws IOException
```
    Description copied from interface: PixelBuffer
    
    Retrieves a tile from this pixel buffer.
    
    Specified by:
    
    getTileDirect in interface PixelBuffer
    
    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:
    
    IOException - if there is a problem reading from the pixel buffer.
    See Also:
    getTile()
  - getTimepoint
```
public PixelData getTimepoint(Integer t)
                       throws IOException,
                              DimensionsOutOfBoundsException
```
    Description copied from interface: PixelBuffer
    
    Retrieves the entire number of optical sections for all wavelengths or channels at a particular timepoint in this pixel buffer.
    
    Specified by:
    
    getTimepoint in interface PixelBuffer
    
    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:
    
    IOException - if there is a problem reading from the pixel buffer.
    
    DimensionsOutOfBoundsException - if offsets are out of bounds after checking with checkBounds().
  - getTimepointDirect
```
public byte[] getTimepointDirect(Integer t,
                        byte[] buffer)
                          throws IOException,
                                 DimensionsOutOfBoundsException
```
    Description copied from interface: PixelBuffer
    
    Retrieves the entire number of optical sections for all wavelengths or channels at a particular timepoint in this pixel buffer.
    
    Specified by:
    
    getTimepointDirect in interface PixelBuffer
    
    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:
    
    IOException - if there is a problem reading from the pixel buffer.
    
    DimensionsOutOfBoundsException - if offsets are out of bounds after checking with checkBounds().
  - getTimepointOffset
```
public Long getTimepointOffset(Integer t)
                        throws DimensionsOutOfBoundsException
```
    Description copied from interface: PixelBuffer
    
    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.
    
    Specified by:
    
    getTimepointOffset in interface PixelBuffer
    
    Parameters:
    t - offset across the T-axis of the pixel buffer.
    
    Returns:
    offset of the timepoint.
    
    Throws:
    
    DimensionsOutOfBoundsException - if offsets are out of bounds after checking with checkBounds().
  - getTimepointSize
```
public Long getTimepointSize()
```
    Description copied from interface: PixelBuffer
    
    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.
    
    Specified by:
    
    getTimepointSize in interface PixelBuffer
    
    Returns:
    timepoint size in bytes (sizeX*sizeY*sizeZ*sizeC*ByteWidth).
  - getTotalSize
```
public Long getTotalSize()
```
    Description copied from interface: PixelBuffer
    
    Retrieves the in memory size of the entire pixel buffer.
    
    Specified by:
    
    getTotalSize in interface PixelBuffer
    
    Returns:
    total size of the pixel size in bytes (sizeX*sizeY*sizeZ*sizeC*sizeT*ByteWidth).
  - isFloat
```
public boolean isFloat()
```
    Description copied from interface: PixelBuffer
    
    Returns whether or not the pixel buffer has floating point pixels.
    
    Specified by:
    
    isFloat in interface PixelBuffer
    
    Returns:
  - isSigned
```
public boolean isSigned()
```
    Description copied from interface: PixelBuffer
    
    Returns whether or not the pixel buffer has signed pixels.
    
    Specified by:
    
    isSigned in interface PixelBuffer
    
    Returns:
    See above.
  - setPlane
```
public void setPlane(ByteBuffer buffer,
            Integer z,
            Integer c,
            Integer t)
              throws IOException,
                     DimensionsOutOfBoundsException,
                     BufferOverflowException
```
    Description copied from interface: PixelBuffer
    
    Sets a particular 2D image plane in this pixel buffer.
    
    Specified by:
    
    setPlane in interface PixelBuffer
    
    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:
    
    IOException - if there is a problem writing to the pixel buffer.
    
    DimensionsOutOfBoundsException - if offsets are out of bounds after checking with checkBounds().
    
    BufferOverflowException - if buffer.length > PixelBuffer.getPlaneSize().
  - setPlane
```
public void setPlane(byte[] buffer,
            Integer z,
            Integer c,
            Integer t)
              throws IOException,
                     DimensionsOutOfBoundsException,
                     BufferOverflowException
```
    Description copied from interface: PixelBuffer
    
    Sets a particular 2D image plane in this pixel buffer.
    
    Specified by:
    
    setPlane in interface PixelBuffer
    
    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:
    
    IOException - if there is a problem writing to the pixel buffer.
    
    DimensionsOutOfBoundsException - if offsets are out of bounds after checking with checkBounds().
    
    BufferOverflowException - if buffer.length > PixelBuffer.getPlaneSize().
  - setRegion
```
public void setRegion(Integer size,
             Long offset,
             byte[] buffer)
               throws IOException,
                      BufferOverflowException
```
    Description copied from interface: PixelBuffer
    
    Sets a region in this pixel buffer.
    
    Specified by:
    
    setRegion in interface PixelBuffer
    
    Parameters:
    size - byte width of the region to set.
    offset - offset within the pixel buffer.
    buffer - a byte array of the data.
    
    Throws:
    
    IOException - if there is a problem writing to the pixel buffer.
    
    BufferOverflowException - if buffer.length > size.
  - setRegion
```
public void setRegion(Integer size,
             Long offset,
             ByteBuffer buffer)
               throws IOException,
                      BufferOverflowException
```
    Description copied from interface: PixelBuffer
    
    Sets a region in this pixel buffer.
    
    Specified by:
    
    setRegion in interface PixelBuffer
    
    Parameters:
    size - byte width of the region to set.
    offset - offset within the pixel buffer.
    buffer - a byte buffer of the data.
    
    Throws:
    
    IOException - if there is a problem writing to the pixel buffer.
    
    BufferOverflowException - if buffer.length > size.
  - setRow
```
public void setRow(ByteBuffer buffer,
          Integer y,
          Integer z,
          Integer c,
          Integer t)
            throws IOException,
                   DimensionsOutOfBoundsException,
                   BufferOverflowException
```
    Description copied from interface: PixelBuffer
    
    Sets a particular row or scanline in this pixel buffer.
    
    Specified by:
    
    setRow in interface PixelBuffer
    
    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:
    
    IOException - if there is a problem reading from the pixel buffer.
    
    DimensionsOutOfBoundsException - if offsets are out of bounds after checking with checkBounds().
    
    BufferOverflowException - if buffer.length > PixelBuffer.getRowSize().
  - setStack
```
public void setStack(ByteBuffer buffer,
            Integer z,
            Integer c,
            Integer t)
              throws IOException,
                     DimensionsOutOfBoundsException,
                     BufferOverflowException
```
    Description copied from interface: PixelBuffer
    
    Sets the entire number of optical sections for a single wavelength or channel at a particular timepoint in this pixel buffer.
    
    Specified by:
    
    setStack in interface PixelBuffer
    
    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:
    
    IOException - if there is a problem writing to the pixel buffer.
    
    DimensionsOutOfBoundsException - if offsets are out of bounds after checking with checkBounds().
    
    BufferOverflowException - if buffer.length > PixelBuffer.getStackSize().
  - setStack
```
public void setStack(byte[] buffer,
            Integer z,
            Integer c,
            Integer t)
              throws IOException,
                     DimensionsOutOfBoundsException,
                     BufferOverflowException
```
    Description copied from interface: PixelBuffer
    
    Sets the entire number of optical sections for a single wavelength or channel at a particular timepoint in this pixel buffer.
    
    Specified by:
    
    setStack in interface PixelBuffer
    
    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:
    
    IOException - if there is a problem writing to the pixel buffer.
    
    DimensionsOutOfBoundsException - if offsets are out of bounds after checking with checkBounds().
    
    BufferOverflowException - if buffer.length > PixelBuffer.getStackSize()().
  - setTimepoint
```
public void setTimepoint(ByteBuffer buffer,
                Integer t)
                  throws IOException,
                         DimensionsOutOfBoundsException,
                         BufferOverflowException
```
    Description copied from interface: PixelBuffer
    
    Sets the entire number of optical sections for all wavelengths or channels at a particular timepoint in this pixel buffer.
    
    Specified by:
    
    setTimepoint in interface PixelBuffer
    
    Parameters:
    buffer - a byte buffer of the data comprising this timepoint.
    t - offset across the T-axis of the pixel buffer.
    
    Throws:
    
    IOException - if there is a problem writing to the pixel buffer.
    
    DimensionsOutOfBoundsException - if offsets are out of bounds after checking with checkBounds().
    
    BufferOverflowException - if buffer.length > PixelBuffer.getTimepointSize().
  - setTimepoint
```
public void setTimepoint(byte[] buffer,
                Integer t)
                  throws IOException,
                         DimensionsOutOfBoundsException,
                         BufferOverflowException
```
    Description copied from interface: PixelBuffer
    
    Sets the entire number of optical sections for all wavelengths or channels at a particular timepoint in this pixel buffer.
    
    Specified by:
    
    setTimepoint in interface PixelBuffer
    
    Parameters:
    buffer - a byte array of the data comprising this timepoint.
    t - offset across the T-axis of the pixel buffer.
    
    Throws:
    
    IOException - if there is a problem writing to the pixel buffer.
    
    DimensionsOutOfBoundsException - if offsets are out of bounds after checking with checkBounds().
    
    BufferOverflowException - if buffer.length > PixelBuffer.getTimepointSize().
  - getResolutionLevel
```
public int getResolutionLevel()
```
    Description copied from interface: PixelBuffer
    
    Retrieves the active resolution level.
    
    Specified by:
    
    getResolutionLevel in interface PixelBuffer
    
    Returns:
    The active resolution level.
  - getResolutionLevels
```
public int getResolutionLevels()
```
    Description copied from interface: PixelBuffer
    
    Retrieves the number of resolution levels that the backing pixels pyramid contains.
    
    Specified by:
    
    getResolutionLevels in interface PixelBuffer
    
    Returns:
    The number of resolution levels. This value does not necessarily indicate either the presence or absence of a pixels pyramid.
  - getResolutionDescriptions
```
public List<List<Integer>> getResolutionDescriptions()
```
    Description copied from interface: PixelBuffer
    
    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]]
    
    Specified by:
    
    getResolutionDescriptions in interface PixelBuffer
    
    Returns:
  - getTileSize
```
public Dimension getTileSize()
```
    Description copied from interface: PixelBuffer
    
    Retrieves the tile size for the pixel store.
    
    Specified by:
    
    getTileSize in interface PixelBuffer
    
    Returns:
    The dimension of the tile or null if the pixel buffer is not tiled.
  - setResolutionLevel
```
public void setResolutionLevel(int resolutionLevel)
```
    Description copied from interface: PixelBuffer
    
    Sets the active resolution level.
    
    Specified by:
    
    setResolutionLevel in interface PixelBuffer
    
    Parameters:
    resolutionLevel - The resolution level to be used by the pixel buffer.

Class BfPyramidPixelBuffer

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

writer

reader

PYR_LOCK_EXT

Constructor Detail

BfPyramidPixelBuffer

BfPyramidPixelBuffer

BfPyramidPixelBuffer

Method Detail

init

initializeReader

initializeWriter

acquireLock

closeRaf

isLockedByOthers

closeWriter

isWrite

setTile

getByteOrder

setByteOrder

calculateMessageDigest

checkBounds

close

getByteWidth

getCol

getColDirect

getColSize

getHypercube

getHypercubeDirect

getHypercubeSize

getId

getPath

getPlane

getPlaneDirect

getPlaneOffset

getPlaneRegion

getPlaneRegionDirect

getPlaneSize

getRegion

getRegionDirect

getRow

getRowDirect

getRowOffset

getRowSize

getSizeC

getSizeT

getSizeX

getSizeY

getSizeZ

getStack

getStackDirect

getStackOffset

getStackSize

getTile

getTileDirect

getTimepoint

getTimepointDirect

getTimepointOffset

getTimepointSize

getTotalSize

isFloat

isSigned

setPlane

setPlane

setRegion

setRegion

setRow

setStack

setStack

setTimepoint

setTimepoint

getResolutionLevel

getResolutionLevels

getResolutionDescriptions

getTileSize