ome.io.nio

Class RomioPixelBuffer

java.lang.Object

ome.io.nio.AbstractBuffer

ome.io.nio.RomioPixelBuffer

All Implemented Interfaces:

java.io.Closeable, java.lang.AutoCloseable, PixelBuffer

public class RomioPixelBuffer
extends AbstractBuffer
implements PixelBuffer

Class implementation of the PixelBuffer interface for standard "proprietary" ROMIO/OMEIS data format.

Since:

3.0

Version:

$Revision$

Author:

Chris Allan chris@glencoesoftware.com

See Also:

PixelBuffer

Field Summary

Fields

Modifier and Type	Field and Description
static int	MAXIMUM_BUFFER_SIZE Default maximum buffer size for planar data transfer. (1MB)

Constructor Summary

Constructors

Constructor and Description
RomioPixelBuffer(java.lang.String path, Pixels pixels) Creates a new instance.
RomioPixelBuffer(java.lang.String path, Pixels pixels, boolean permitModification) Creates a new instance, with manual setting of permitModification.

Method Summary

Modifier and Type	Method and Description
byte[]	calculateMessageDigest() Implemented as specified by PixelBuffer I/F.
void	checkBounds(java.lang.Integer x, java.lang.Integer y, java.lang.Integer z, java.lang.Integer c, java.lang.Integer t) Implemented as specified by PixelBuffer I/F.
void	close() Closes the buffer, cleaning up file state.
int	getByteWidth() Implemented as specified by PixelBuffer I/F.
PixelData	getCol(java.lang.Integer x, java.lang.Integer z, java.lang.Integer c, java.lang.Integer t) Implemented as specified by PixelBuffer I/F.
byte[]	getColDirect(java.lang.Integer x, java.lang.Integer z, java.lang.Integer c, java.lang.Integer t, byte[] buffer) Implemented as specified by PixelBuffer I/F.
java.lang.Integer	getColSize() Implemented as specified by PixelBuffer I/F.
PixelData	getHypercube(java.util.List<java.lang.Integer> offset, java.util.List<java.lang.Integer> size, java.util.List<java.lang.Integer> step) Implemented as specified by PixelBuffer I/F.
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) Implemented as specified by PixelBuffer I/F.
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() Implemented as specified by PixelBuffer I/F.
PixelData	getPlane(java.lang.Integer z, java.lang.Integer c, java.lang.Integer t) Implemented as specified by PixelBuffer I/F.
byte[]	getPlaneDirect(java.lang.Integer z, java.lang.Integer c, java.lang.Integer t, byte[] buffer) Implemented as specified by PixelBuffer I/F.
java.lang.Long	getPlaneOffset(java.lang.Integer z, java.lang.Integer c, java.lang.Integer t) Implemented as specified by PixelBuffer I/F.
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) Implemented as specified by ByteBuffer I/F.
byte[]	getPlaneRegionDirect(java.lang.Integer z, java.lang.Integer c, java.lang.Integer t, java.lang.Integer count, java.lang.Integer offset, byte[] buffer) Implemented as specified by PixelBuffer I/F.
java.lang.Long	getPlaneSize() Implemented as specified by PixelBuffer I/F.
PixelData	getRegion(java.lang.Integer size, java.lang.Long offset) Implemented as specified by PixelBuffer I/F.
byte[]	getRegionDirect(java.lang.Integer size, java.lang.Long offset, byte[] buffer) Implemented as specified by PixelBuffer I/F.
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.
PixelData	getRow(java.lang.Integer y, java.lang.Integer z, java.lang.Integer c, java.lang.Integer t) Implemented as specified by PixelBuffer I/F.
byte[]	getRowDirect(java.lang.Integer y, java.lang.Integer z, java.lang.Integer c, java.lang.Integer t, byte[] buffer) Implemented as specified by PixelBuffer I/F.
java.lang.Long	getRowOffset(java.lang.Integer y, java.lang.Integer z, java.lang.Integer c, java.lang.Integer t) Implemented as specified by PixelBuffer I/F.
java.lang.Integer	getRowSize() Implemented as specified by PixelBuffer I/F.
java.lang.String	getSha1()
int	getSizeC() Implemented as specified by PixelBuffer I/F.
int	getSizeT() Implemented as specified by PixelBuffer I/F.
int	getSizeX() Implemented as specified by PixelBuffer I/F.
int	getSizeY() Implemented as specified by PixelBuffer I/F.
int	getSizeZ() Implemented as specified by PixelBuffer I/F.
PixelData	getStack(java.lang.Integer c, java.lang.Integer t) Implemented as specified by PixelBuffer I/F.
byte[]	getStackDirect(java.lang.Integer c, java.lang.Integer t, byte[] buffer) Implemented as specified by PixelBuffer I/F.
java.lang.Long	getStackOffset(java.lang.Integer c, java.lang.Integer t) Implemented as specified by PixelBuffer I/F.
java.lang.Long	getStackSize() Implemented as specified by PixelBuffer I/F.
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.
PixelData	getTimepoint(java.lang.Integer t) Implemented as specified by PixelBuffer I/F.
byte[]	getTimepointDirect(java.lang.Integer t, byte[] buffer) Implemented as specified by PixelBuffer I/F.
java.lang.Long	getTimepointOffset(java.lang.Integer t) Implemented as specified by PixelBuffer I/F.
java.lang.Long	getTimepointSize() Implemented as specified by PixelBuffer I/F.
java.lang.Long	getTotalSize() Implemented as specified by PixelBuffer I/F.
boolean	isFloat() Implemented as specified by PixelBuffer I/F.
boolean	isSigned() Implemented as specified by PixelBuffer I/F.
static java.lang.Integer	safeLongToInteger(java.lang.Long v) Converts a Long value to an Integer safely.
void	setPlane(byte[] buffer, java.lang.Integer z, java.lang.Integer c, java.lang.Integer t) Implemented as specified by PixelBuffer I/F.
void	setPlane(java.nio.ByteBuffer buffer, java.lang.Integer z, java.lang.Integer c, java.lang.Integer t) Implemented as specified by PixelBuffer I/F.
void	setRegion(java.lang.Integer size, java.lang.Long offset, byte[] buffer) Implemented as specified by PixelBuffer I/F.
void	setRegion(java.lang.Integer size, java.lang.Long offset, java.nio.ByteBuffer buffer) Implemented as specified by PixelBuffer I/F.
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) Implemented as specified by PixelBuffer I/F.
void	setStack(byte[] buffer, java.lang.Integer z, java.lang.Integer c, java.lang.Integer t) Implemented as specified by PixelBuffer I/F.
void	setStack(java.nio.ByteBuffer buffer, java.lang.Integer z, java.lang.Integer c, java.lang.Integer t) Implemented as specified by PixelBuffer I/F.
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) Implemented as specified by PixelBuffer I/F.
void	setTimepoint(java.nio.ByteBuffer buffer, java.lang.Integer t) Implemented as specified by PixelBuffer I/F.

Methods inherited from class ome.io.nio.AbstractBuffer

getPath, toString

Methods inherited from class java.lang.Object

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

Methods inherited from interface ome.io.nio.PixelBuffer

getPath

Field Detail

MAXIMUM_BUFFER_SIZE

public static final int MAXIMUM_BUFFER_SIZE

Default maximum buffer size for planar data transfer. (1MB)

See Also:

Constant Field Values

Constructor Detail

RomioPixelBuffer

public RomioPixelBuffer(java.lang.String path,
                        Pixels pixels)

Creates a new instance. permitModification defaults to false.

Parameters:

path - The path to the file.

pixels - The pixels object to handle.

RomioPixelBuffer

public RomioPixelBuffer(java.lang.String path,
                        Pixels pixels,
                        boolean permitModification)

Creates a new instance, with manual setting of permitModification.

Parameters:

path - The path to the file.

pixels - The pixels object to handle.

Method Detail

safeLongToInteger

public static java.lang.Integer safeLongToInteger(java.lang.Long v)

Converts a Long value to an Integer safely.

Parameters:

v - Long value to convert.

Throws:

ApiUsageException - If the conversion would cause an overflow or an underflow.

checkBounds

public void checkBounds(java.lang.Integer x,
                        java.lang.Integer y,
                        java.lang.Integer z,
                        java.lang.Integer c,
                        java.lang.Integer t)
                 throws DimensionsOutOfBoundsException

Implemented as specified by PixelBuffer I/F.

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.

See Also:

PixelBuffer.checkBounds(Integer, Integer, Integer, Integer, Integer)

close

public void close()
           throws java.io.IOException

Closes the buffer, cleaning up file state.

Specified by:

close in interface java.io.Closeable

Specified by:

close in interface java.lang.AutoCloseable

Specified by:

close in interface PixelBuffer

Throws:

java.io.IOException - if an I/O error occurs.

getPlaneSize

public java.lang.Long getPlaneSize()

Implemented as specified by PixelBuffer I/F.

Specified by:

getPlaneSize in interface PixelBuffer

Returns:

2D image plane size in bytes (sizeX*sizeY*ByteWidth).

See Also:

PixelBuffer.getPlaneSize()

getRowSize

public java.lang.Integer getRowSize()

Implemented as specified by PixelBuffer I/F.

Specified by:

getRowSize in interface PixelBuffer

Returns:

row or scanline size in bytes (sizeX*ByteWidth)

See Also:

PixelBuffer.getRowSize()

getColSize

public java.lang.Integer getColSize()

Implemented as specified by PixelBuffer I/F.

Specified by:

getColSize in interface PixelBuffer

Returns:

column size in bytes (sizeY*ByteWidth)

See Also:

PixelBuffer.getColSize()

getStackSize

public java.lang.Long getStackSize()

Implemented as specified by PixelBuffer I/F.

Specified by:

getStackSize in interface PixelBuffer

Returns:

stack size in bytes (sizeX*sizeY*sizeZ*ByteWidth).

See Also:

PixelBuffer.getStackSize()

getTimepointSize

public java.lang.Long getTimepointSize()

Implemented as specified by PixelBuffer I/F.

Specified by:

getTimepointSize in interface PixelBuffer

Returns:

timepoint size in bytes (sizeX*sizeY*sizeZ*sizeC*ByteWidth).

See Also:

PixelBuffer.getTimepointSize()

getTotalSize

public java.lang.Long getTotalSize()

Implemented as specified by PixelBuffer I/F.

Specified by:

getTotalSize in interface PixelBuffer

Returns:

total size of the pixel size in bytes (sizeX*sizeY*sizeZ*sizeC*sizeT*ByteWidth).

See Also:

PixelBuffer.getTotalSize()

getRowOffset

public java.lang.Long getRowOffset(java.lang.Integer y,
                                   java.lang.Integer z,
                                   java.lang.Integer c,
                                   java.lang.Integer t)
                            throws DimensionsOutOfBoundsException

Implemented as specified by PixelBuffer I/F.

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 PixelBuffer.checkBounds(Integer, Integer, Integer, Integer, Integer).

See Also:

PixelBuffer.getRowOffset(Integer, Integer, Integer, Integer)

getPlaneOffset

public java.lang.Long getPlaneOffset(java.lang.Integer z,
                                     java.lang.Integer c,
                                     java.lang.Integer t)
                              throws DimensionsOutOfBoundsException

Implemented as specified by PixelBuffer I/F.

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 PixelBuffer.checkBounds(Integer, Integer, Integer, Integer, Integer).

See Also:

PixelBuffer.getPlaneOffset(Integer, Integer, Integer)

getStackOffset

public java.lang.Long getStackOffset(java.lang.Integer c,
                                     java.lang.Integer t)
                              throws DimensionsOutOfBoundsException

Implemented as specified by PixelBuffer I/F.

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 PixelBuffer.checkBounds(Integer, Integer, Integer, Integer, Integer).

See Also:

PixelBuffer.getStackOffset(Integer, Integer)

getTimepointOffset

public java.lang.Long getTimepointOffset(java.lang.Integer t)
                                  throws DimensionsOutOfBoundsException

Implemented as specified by PixelBuffer I/F.

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 PixelBuffer.checkBounds(Integer, Integer, Integer, Integer, Integer).

See Also:

PixelBuffer.getTimepointOffset(Integer)

getRegion

public PixelData getRegion(java.lang.Integer size,
                           java.lang.Long offset)
                    throws java.io.IOException

Implemented as specified by PixelBuffer I/F.

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:

java.io.IOException - if there is a problem reading from the pixel buffer.

See Also:

PixelBuffer.getRegion(Integer, Long)

getRegionDirect

public byte[] getRegionDirect(java.lang.Integer size,
                              java.lang.Long offset,
                              byte[] buffer)
                       throws java.io.IOException

Implemented as specified by PixelBuffer I/F.

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:

java.io.IOException - if there is a problem reading from the pixel buffer.

See Also:

PixelBuffer.getRegionDirect(Integer, Long, byte[])

getRow

public PixelData getRow(java.lang.Integer y,
                        java.lang.Integer z,
                        java.lang.Integer c,
                        java.lang.Integer t)
                 throws java.io.IOException,
                        DimensionsOutOfBoundsException

Implemented as specified by PixelBuffer I/F.

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:

java.io.IOException - if there is a problem reading from the pixel buffer.

DimensionsOutOfBoundsException - if offsets are out of bounds after checking with PixelBuffer.checkBounds(Integer, Integer, Integer, Integer, Integer).

See Also:

PixelBuffer.getRow(Integer, Integer, Integer, Integer)

getCol

public PixelData getCol(java.lang.Integer x,
                        java.lang.Integer z,
                        java.lang.Integer c,
                        java.lang.Integer t)
                 throws java.io.IOException,
                        DimensionsOutOfBoundsException

Implemented as specified by PixelBuffer I/F.

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:

java.io.IOException - if there is a problem reading from the pixel buffer.

DimensionsOutOfBoundsException - if offsets are out of bounds after checking with PixelBuffer.checkBounds(Integer, Integer, Integer, Integer, Integer).

See Also:

PixelBuffer.getCol(Integer, Integer, Integer, Integer)

getRowDirect

public 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

Implemented as specified by PixelBuffer I/F.

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:

java.io.IOException - if there is a problem reading from the pixel buffer.

DimensionsOutOfBoundsException - if offsets are out of bounds after checking with PixelBuffer.checkBounds(Integer, Integer, Integer, Integer, Integer).

See Also:

PixelBuffer.getRowDirect(Integer, Integer, Integer, Integer, byte[])

getColDirect

public 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

Implemented as specified by PixelBuffer I/F.

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:

java.io.IOException - if there is a problem reading from the pixel buffer.

DimensionsOutOfBoundsException - if offsets are out of bounds after checking with PixelBuffer.checkBounds(Integer, Integer, Integer, Integer, Integer).

See Also:

PixelBuffer.getColDirect(Integer, Integer, Integer, Integer, byte[])

getHypercube

public 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

Implemented as specified by PixelBuffer I/F.

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:

java.io.IOException - if there is a problem reading from the pixel buffer.

DimensionsOutOfBoundsException

See Also:

PixelBuffer.getHypercube(List, List, List)

getHypercubeDirect

public 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

Implemented as specified by PixelBuffer I/F.

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:

java.io.IOException - if there is a problem reading from the pixel buffer.

DimensionsOutOfBoundsException

See Also:

PixelBuffer.getHypercubeDirect(List, List, List, byte[])

getPlaneRegionDirect

public 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

Implemented as specified by PixelBuffer I/F.

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:

java.io.IOException - if there is a problem reading from the pixel buffer.

DimensionsOutOfBoundsException

See Also:

PixelBuffer.getPlaneRegionDirect(Integer, Integer, Integer, Integer, Integer, byte[])

getPlane

public PixelData getPlane(java.lang.Integer z,
                          java.lang.Integer c,
                          java.lang.Integer t)
                   throws java.io.IOException,
                          DimensionsOutOfBoundsException

Implemented as specified by PixelBuffer I/F.

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:

java.io.IOException - if there is a problem reading from the pixel buffer.

DimensionsOutOfBoundsException - if offsets are out of bounds after checking with PixelBuffer.checkBounds(Integer, Integer, Integer, Integer, Integer).

See Also:

PixelBuffer.getPlane(Integer, Integer, Integer)

getPlaneRegion

public 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

Implemented as specified by ByteBuffer I/F.

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:

java.io.IOException - if there is a problem reading from the pixel buffer.

DimensionsOutOfBoundsException - if offsets are out of bounds after checking with PixelBuffer.checkBounds(Integer, Integer, Integer, Integer, Integer).

See Also:

PixelBuffer.getPlaneRegion(Integer, Integer, Integer, Integer, Integer, Integer, Integer, Integer)

getPlaneDirect

public byte[] getPlaneDirect(java.lang.Integer z,
                             java.lang.Integer c,
                             java.lang.Integer t,
                             byte[] buffer)
                      throws java.io.IOException,
                             DimensionsOutOfBoundsException

Implemented as specified by PixelBuffer I/F.

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:

java.io.IOException - if there is a problem reading from the pixel buffer.

DimensionsOutOfBoundsException - if offsets are out of bounds after checking with PixelBuffer.checkBounds(Integer, Integer, Integer, Integer, Integer).

See Also:

PixelBuffer.getPlaneDirect(Integer, Integer, Integer, byte[])

getStack

public PixelData getStack(java.lang.Integer c,
                          java.lang.Integer t)
                   throws java.io.IOException,
                          DimensionsOutOfBoundsException

Implemented as specified by PixelBuffer I/F.

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:

java.io.IOException - if there is a problem reading from the pixel buffer.

DimensionsOutOfBoundsException - if offsets are out of bounds after checking with PixelBuffer.checkBounds(Integer, Integer, Integer, Integer, Integer).

See Also:

PixelBuffer.getStack(Integer, Integer)

getStackDirect

public byte[] getStackDirect(java.lang.Integer c,
                             java.lang.Integer t,
                             byte[] buffer)
                      throws java.io.IOException,
                             DimensionsOutOfBoundsException

Implemented as specified by PixelBuffer I/F.

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:

java.io.IOException - if there is a problem reading from the pixel buffer.

DimensionsOutOfBoundsException - if offsets are out of bounds after checking with PixelBuffer.checkBounds(Integer, Integer, Integer, Integer, Integer).

See Also:

PixelBuffer.getStackDirect(Integer, Integer, byte[])

getTimepoint

public PixelData getTimepoint(java.lang.Integer t)
                       throws java.io.IOException,
                              DimensionsOutOfBoundsException

Implemented as specified by PixelBuffer I/F.

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:

java.io.IOException - if there is a problem reading from the pixel buffer.

DimensionsOutOfBoundsException - if offsets are out of bounds after checking with PixelBuffer.checkBounds(Integer, Integer, Integer, Integer, Integer).

See Also:

PixelBuffer.getTimepoint(Integer)

getTimepointDirect

public byte[] getTimepointDirect(java.lang.Integer t,
                                 byte[] buffer)
                          throws java.io.IOException,
                                 DimensionsOutOfBoundsException

Implemented as specified by PixelBuffer I/F.

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:

java.io.IOException - if there is a problem reading from the pixel buffer.

DimensionsOutOfBoundsException - if offsets are out of bounds after checking with PixelBuffer.checkBounds(Integer, Integer, Integer, Integer, Integer).

See Also:

PixelBuffer.getTimepointDirect(Integer, byte[])

setRegion

public void setRegion(java.lang.Integer size,
                      java.lang.Long offset,
                      byte[] buffer)
               throws java.io.IOException

Implemented as specified by PixelBuffer I/F.

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:

java.io.IOException - if there is a problem writing to the pixel buffer.

See Also:

PixelBuffer.setRegion(Integer, Long, byte[])

setRegion

public void setRegion(java.lang.Integer size,
                      java.lang.Long offset,
                      java.nio.ByteBuffer buffer)
               throws java.io.IOException

Implemented as specified by PixelBuffer I/F.

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:

java.io.IOException - if there is a problem writing to the pixel buffer.

See Also:

PixelBuffer.setRegion(Integer, Long, ByteBuffer)

setRow

public 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

Implemented as specified by PixelBuffer I/F.

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:

java.io.IOException - if there is a problem reading from the pixel buffer.

DimensionsOutOfBoundsException - if offsets are out of bounds after checking with PixelBuffer.checkBounds(Integer, Integer, Integer, Integer, Integer).

See Also:

PixelBuffer.setRow(ByteBuffer, Integer, Integer, Integer, Integer)

setPlane

public void setPlane(java.nio.ByteBuffer buffer,
                     java.lang.Integer z,
                     java.lang.Integer c,
                     java.lang.Integer t)
              throws java.io.IOException,
                     DimensionsOutOfBoundsException

Implemented as specified by PixelBuffer I/F.

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:

java.io.IOException - if there is a problem writing to the pixel buffer.

DimensionsOutOfBoundsException - if offsets are out of bounds after checking with PixelBuffer.checkBounds(Integer, Integer, Integer, Integer, Integer).

See Also:

PixelBuffer.setPlane(ByteBuffer, Integer, Integer, Integer)

setPlane

public void setPlane(byte[] buffer,
                     java.lang.Integer z,
                     java.lang.Integer c,
                     java.lang.Integer t)
              throws java.io.IOException,
                     DimensionsOutOfBoundsException

Implemented as specified by PixelBuffer I/F.

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:

java.io.IOException - if there is a problem writing to the pixel buffer.

DimensionsOutOfBoundsException - if offsets are out of bounds after checking with PixelBuffer.checkBounds(Integer, Integer, Integer, Integer, Integer).

See Also:

PixelBuffer.setPlane(byte[], Integer, Integer, Integer)

setStack

public void setStack(java.nio.ByteBuffer buffer,
                     java.lang.Integer z,
                     java.lang.Integer c,
                     java.lang.Integer t)
              throws java.io.IOException,
                     DimensionsOutOfBoundsException

Implemented as specified by PixelBuffer I/F.

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:

java.io.IOException - if there is a problem writing to the pixel buffer.

DimensionsOutOfBoundsException - if offsets are out of bounds after checking with PixelBuffer.checkBounds(Integer, Integer, Integer, Integer, Integer).

See Also:

PixelBuffer.setStack(ByteBuffer, Integer, Integer, Integer)

setStack

public void setStack(byte[] buffer,
                     java.lang.Integer z,
                     java.lang.Integer c,
                     java.lang.Integer t)
              throws java.io.IOException,
                     DimensionsOutOfBoundsException

Implemented as specified by PixelBuffer I/F.

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:

java.io.IOException - if there is a problem writing to the pixel buffer.

DimensionsOutOfBoundsException - if offsets are out of bounds after checking with PixelBuffer.checkBounds(Integer, Integer, Integer, Integer, Integer).

See Also:

PixelBuffer.setStack(byte[], Integer, Integer, Integer)

setTimepoint

public void setTimepoint(java.nio.ByteBuffer buffer,
                         java.lang.Integer t)
                  throws java.io.IOException,
                         DimensionsOutOfBoundsException

Implemented as specified by PixelBuffer I/F.

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:

java.io.IOException - if there is a problem writing to the pixel buffer.

DimensionsOutOfBoundsException - if offsets are out of bounds after checking with PixelBuffer.checkBounds(Integer, Integer, Integer, Integer, Integer).

See Also:

PixelBuffer.setTimepoint(ByteBuffer, Integer)

setTimepoint

public void setTimepoint(byte[] buffer,
                         java.lang.Integer t)
                  throws java.io.IOException,
                         DimensionsOutOfBoundsException

Implemented as specified by PixelBuffer I/F.

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:

java.io.IOException - if there is a problem writing to the pixel buffer.

DimensionsOutOfBoundsException - if offsets are out of bounds after checking with PixelBuffer.checkBounds(Integer, Integer, Integer, Integer, Integer).

See Also:

PixelBuffer.setTimepoint(ByteBuffer, Integer)

calculateMessageDigest

public byte[] calculateMessageDigest()
                              throws java.io.IOException

Implemented as specified by PixelBuffer I/F.

Specified by:

calculateMessageDigest in interface PixelBuffer

Returns:

byte array containing the message digest.

Throws:

java.io.IOException - if there is a problem reading from the pixel buffer.

See Also:

PixelBuffer.calculateMessageDigest()

getByteWidth

public int getByteWidth()

Implemented as specified by PixelBuffer I/F.

Specified by:

getByteWidth in interface PixelBuffer

Returns:

See above.

See Also:

PixelBuffer.getByteWidth()

isSigned

public boolean isSigned()

Implemented as specified by PixelBuffer I/F.

Specified by:

isSigned in interface PixelBuffer

Returns:

See above.

See Also:

PixelBuffer.isSigned()

isFloat

public boolean isFloat()

Implemented as specified by PixelBuffer I/F.

Specified by:

isFloat in interface PixelBuffer

Returns:

true if the pixel buffer as floating point, false otherwise

See Also:

PixelBuffer.isFloat()

getSizeC

public int getSizeC()

Implemented as specified by PixelBuffer I/F.

Specified by:

getSizeC in interface PixelBuffer

See Also:

PixelBuffer.getSizeC()

getSizeT

public int getSizeT()

Implemented as specified by PixelBuffer I/F.

Specified by:

getSizeT in interface PixelBuffer

See Also:

PixelBuffer.getSizeT()

getSizeX

public int getSizeX()

Implemented as specified by PixelBuffer I/F.

Specified by:

getSizeX in interface PixelBuffer

See Also:

PixelBuffer.getSizeX()

getSizeY

public int getSizeY()

Implemented as specified by PixelBuffer I/F.

Specified by:

getSizeY in interface PixelBuffer

See Also:

PixelBuffer.getSizeY()

getSizeZ

public int getSizeZ()

Implemented as specified by PixelBuffer I/F.

Specified by:

getSizeZ in interface PixelBuffer

See Also:

PixelBuffer.getSizeZ()

getId

public long getId()

Implemented as specified by PixelBuffer I/F.

Specified by:

getId in interface PixelBuffer

See Also:

PixelBuffer.getId()

getSha1

public java.lang.String getSha1()

getTile

public 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

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:

java.io.IOException - if there is a problem reading from the pixel buffer.

See Also:

PixelBuffer.getTileDirect(Integer, Integer, Integer, Integer, Integer, Integer, Integer, byte[])

getTileDirect

public 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

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:

java.io.IOException - if there is a problem reading from the pixel buffer.

See Also:

PixelBuffer.getTile(Integer, Integer, Integer, Integer, Integer, Integer, Integer)

setTile

public 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

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:

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.

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 java.util.List<java.util.List<java.lang.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:

a list of lists containing sizeX, sizeY for each resolution level

getTileSize

public java.awt.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.

getHypercubeSize

public 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

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