ome.io.nio

Interface PixelBuffer

All Superinterfaces:

AutoCloseable, Closeable

All Known Implementing Classes:

BfPixelBuffer, BfPyramidPixelBuffer, InMemoryPlanarPixelBuffer, RomioPixelBuffer

public interface PixelBuffer
extends Closeable

This interface declares the I/O responsibilities of a buffer, file or otherwise, that contains a 5-dimensional Pixel array (XYZCT).

Since:

3.0

Version:

$Revision$

Author:

Chris Allan callan@blackcat.ca

See Also:

PixelData

Method Summary

Modifier and Type	Method and Description
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.
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() Retrieves the identifier of this pixel buffer
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() Retrieves the size in C of this pixel buffer
int	getSizeT() Retrieves the size in T of this pixel buffer
int	getSizeX() Retrieves the size in X of this pixel buffer
int	getSizeY() Retrieves the size in Y of this pixel buffer
int	getSizeZ() Retrieves the size in Z of this pixel buffer
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.
boolean	isFloat() Returns whether or not the pixel buffer has floating point pixels.
boolean	isSigned() Returns whether or not the pixel buffer has signed pixels.
void	setPlane(byte[] buffer, 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.

Method Detail

close

void close()
    throws IOException

Closes the buffer, cleaning up file state.

Specified by:

close in interface AutoCloseable

Specified by:

close in interface Closeable

Throws:

IOException - if an I/O error occurs.

checkBounds

void checkBounds(Integer x,
                 Integer y,
                 Integer z,
                 Integer c,
                 Integer t)
          throws DimensionsOutOfBoundsException

Checks to ensure that no one particular axis has an offset out of bounds. null may be passed as the argument to any one of the offsets to ignore it for the purposes of bounds checking.

Parameters:

x - offset across the X-axis of the pixel buffer to check.

y - offset across the Y-axis of the pixel buffer to check.

z - offset across the Z-axis of the pixel buffer to check.

c - offset across the C-axis of the pixel buffer to check.

t - offset across the T-axis of the pixel buffer to check.

Throws:

DimensionsOutOfBoundsException - if y, z, c or t is out of bounds.

getPlaneSize

Long getPlaneSize()

Retrieves the in memory size of a 2D image plane in this pixel buffer.

Returns:

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

getRowSize

Integer getRowSize()

Retrieves the in memory size of a row or scanline of pixels in this pixel buffer.

Returns:

row or scanline size in bytes (sizeX*ByteWidth)

getColSize

Integer getColSize()

Retrieves the in memory size of a column of pixels in this pixel buffer.

Returns:

column size in bytes (sizeY*ByteWidth)

getStackSize

Long getStackSize()

Retrieves the in memory size of the entire number of optical sections for a single wavelength or channel at a particular timepoint in this pixel buffer.

Returns:

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

getTimepointSize

Long getTimepointSize()

Retrieves the in memory size of the entire number of optical sections for all wavelengths or channels at a particular timepoint in this pixel buffer.

Returns:

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

getTotalSize

Long getTotalSize()

Retrieves the in memory size of the entire pixel buffer.

Returns:

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

getHypercubeSize

Long getHypercubeSize(List<Integer> offset,
                      List<Integer> size,
                      List<Integer> step)
               throws DimensionsOutOfBoundsException

Retrieves a the size of a hypercube from this pixel buffer.

Parameters:

offset - The offset of each dimension of the pixel buffer.

size - The number of pixels to retrieve along each dimension .

step - The step size across each dimension .

Returns:

the size.

Throws:

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

DimensionsOutOfBoundsException

getRowOffset

Long getRowOffset(Integer y,
                  Integer z,
                  Integer c,
                  Integer t)
           throws DimensionsOutOfBoundsException

Retrieves the offset for a particular row or scanline in this pixel buffer.

Parameters:

y - offset across the Y-axis of the pixel buffer.

z - offset across the Z-axis of the pixel buffer.

c - offset across the C-axis of the pixel buffer.

t - offset across the T-axis of the pixel buffer.

Returns:

offset of the row or scaline.

Throws:

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

getPlaneOffset

Long getPlaneOffset(Integer z,
                    Integer c,
                    Integer t)
             throws DimensionsOutOfBoundsException

Retrieves the offset for a particular 2D image plane in this pixel buffer.

Parameters:

z - offset across the Z-axis of the pixel buffer.

c - offset across the C-axis of the pixel buffer.

t - offset across the T-axis of the pixel buffer.

Returns:

offset of the 2D image plane.

Throws:

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

getStackOffset

Long getStackOffset(Integer c,
                    Integer t)
             throws DimensionsOutOfBoundsException

Retrieves the offset for the entire number of optical sections for a single wavelength or channel at a particular timepoint in this pixel buffer.

Parameters:

c - offset across the C-axis of the pixel buffer.

t - offset across the T-axis of the pixel buffer.

Returns:

offset of the stack.

Throws:

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

getTimepointOffset

Long getTimepointOffset(Integer t)
                 throws DimensionsOutOfBoundsException

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.

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(Integer, Integer, Integer, Integer, Integer).

getHypercube

PixelData getHypercube(List<Integer> offset,
                       List<Integer> size,
                       List<Integer> step)
                throws IOException,
                       DimensionsOutOfBoundsException

Retrieves a hypercube from this pixel buffer.

Parameters:

offset - The offset of each dimension of the pixel buffer.

size - The number of pixels to retrieve along each dimension .

step - The step size across each dimension .

Returns:

buffer containing the data.

Throws:

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

DimensionsOutOfBoundsException

getHypercubeDirect

byte[] getHypercubeDirect(List<Integer> offset,
                          List<Integer> size,
                          List<Integer> step,
                          byte[] buffer)
                   throws IOException,
                          DimensionsOutOfBoundsException

Retrieves a hypercube from the given pixels directly.

Parameters:

offset - The offset of each dimension of the pixel buffer.

size - The number of pixels to retrieve along each dimension .

step - The step size across each dimension .

buffer - pre-allocated buffer, count in size.

Returns:

buffer containing the data.

Throws:

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

DimensionsOutOfBoundsException

getPlaneRegionDirect

byte[] getPlaneRegionDirect(Integer z,
                            Integer c,
                            Integer t,
                            Integer count,
                            Integer offset,
                            byte[] buffer)
                     throws IOException,
                            DimensionsOutOfBoundsException

Retrieves a region from a given plane directly.

Parameters:

z - offset across the Z-axis of the pixel buffer.

c - offset across the C-axis of the pixel buffer.

t - offset across the T-axis of the pixel buffer.

count - the number of pixels to retrieve.

offset - the offset at which to retrieve count pixels.

buffer - pre-allocated buffer, count in size.

Returns:

buffer containing the data which comprises the region of the given 2D image plane. It is guaranteed that this buffer will have been byte swapped.

Throws:

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

DimensionsOutOfBoundsException

See Also:

getRegionDirect(Integer, Long, byte[])

getTile

PixelData getTile(Integer z,
                  Integer c,
                  Integer t,
                  Integer x,
                  Integer y,
                  Integer w,
                  Integer h)
           throws IOException

Retrieves a tile from this pixel buffer.

Parameters:

z - offset across the Z-axis of the pixel buffer.

c - offset across the C-axis of the pixel buffer.

t - offset across the T-axis of the pixel buffer.

x - Top left corner of the tile, X offset.

y - Top left corner of the tile, Y offset.

w - Width of the tile.

h - Height of the tile.

Returns:

buffer containing the data which comprises the region of the given 2D image plane. It is guaranteed that this buffer will have been byte swapped.

Throws:

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

See Also:

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

getTileDirect

byte[] getTileDirect(Integer z,
                     Integer c,
                     Integer t,
                     Integer x,
                     Integer y,
                     Integer w,
                     Integer h,
                     byte[] buffer)
              throws IOException

Retrieves a tile from this pixel buffer.

Parameters:

z - offset across the Z-axis of the pixel buffer.

c - offset across the C-axis of the pixel buffer.

t - offset across the T-axis of the pixel buffer.

x - Top left corner of the tile, X offset.

y - Top left corner of the tile, Y offset.

w - Width of the tile.

h - Height of the tile.

buffer - Pre-allocated buffer of the tile's size.

Returns:

buffer containing the data which comprises this region. It is guaranteed that this buffer will have been byte swapped. The buffer is essentially directly from disk.

Throws:

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

See Also:

getTile(Integer, Integer, Integer, Integer, Integer, Integer, Integer)

getRegion

PixelData getRegion(Integer size,
                    Long offset)
             throws IOException

Retrieves a region from this pixel buffer.

Parameters:

size - byte width of the region to retrieve.

offset - offset within the pixel buffer.

Returns:

buffer containing the data. It is guaranteed that this buffer will have its order set correctly but not that the backing buffer will have been byte swapped. The buffer is essentially directly from disk.

Throws:

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

See Also:

getRegionDirect(Integer, Long, byte[])

getRegionDirect

byte[] getRegionDirect(Integer size,
                       Long offset,
                       byte[] buffer)
                throws IOException

Retrieves a region from this pixel buffer directly.

Parameters:

size - byte width of the region to retrieve.

offset - offset within the pixel buffer.

buffer - pre-allocated buffer of the row's size.

Returns:

buffer containing the data which comprises this region. It is guaranteed that this buffer will have been byte swapped. The buffer is essentially directly from disk.

Throws:

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

See Also:

getRegion(Integer, Long)

getRow

PixelData getRow(Integer y,
                 Integer z,
                 Integer c,
                 Integer t)
          throws IOException,
                 DimensionsOutOfBoundsException

Retrieves a particular row or scanline from this pixel buffer.

Parameters:

y - offset across the Y-axis of the pixel buffer.

z - offset across the Z-axis of the pixel buffer.

c - offset across the C-axis of the pixel buffer.

t - offset across the T-axis of the pixel buffer.

Returns:

buffer containing the data which comprises this row or scanline. It is guaranteed that this buffer will have its order set correctly but not that the backing buffer will have been byte swapped.

Throws:

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

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

See Also:

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

getCol

PixelData getCol(Integer x,
                 Integer z,
                 Integer c,
                 Integer t)
          throws IOException,
                 DimensionsOutOfBoundsException

Retrieves a particular column from this pixel buffer.

Parameters:

x - offset across the X-axis of the pixel buffer.

z - offset across the Z-axis of the pixel buffer.

c - offset across the C-axis of the pixel buffer.

t - offset across the T-axis of the pixel buffer.

Returns:

buffer containing the data which comprises this column. It is guaranteed that this buffer will have its order set correctly but not that the backing buffer will have been byte swapped.

Throws:

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

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

See Also:

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

getRowDirect

byte[] getRowDirect(Integer y,
                    Integer z,
                    Integer c,
                    Integer t,
                    byte[] buffer)
             throws IOException,
                    DimensionsOutOfBoundsException

Retrieves a particular row or scanline from this pixel buffer.

Parameters:

y - offset across the Y-axis of the pixel buffer.

z - offset across the Z-axis of the pixel buffer.

c - offset across the C-axis of the pixel buffer.

t - offset across the T-axis of the pixel buffer.

buffer - pre-allocated buffer of the row's size.

Returns:

buffer containing the data which comprises this row or scanline. It is guaranteed that this buffer will have been byte swapped.

Throws:

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

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

See Also:

getRow(Integer, Integer, Integer, Integer)

getColDirect

byte[] getColDirect(Integer x,
                    Integer z,
                    Integer c,
                    Integer t,
                    byte[] buffer)
             throws IOException,
                    DimensionsOutOfBoundsException

Retrieves a particular column from this pixel buffer.

Parameters:

x - offset across the X-axis of the pixel buffer.

z - offset across the Z-axis of the pixel buffer.

c - offset across the C-axis of the pixel buffer.

t - offset across the T-axis of the pixel buffer.

buffer - pre-allocated buffer of the row's size.

Returns:

buffer containing the data which comprises this column. It is guaranteed that this buffer will have been byte swapped.

Throws:

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

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

See Also:

getCol(Integer, Integer, Integer, Integer)

getPlane

PixelData getPlane(Integer z,
                   Integer c,
                   Integer t)
            throws IOException,
                   DimensionsOutOfBoundsException

Retrieves a particular 2D image plane from this pixel buffer.

Parameters:

z - offset across the Z-axis of the pixel buffer.

c - offset across the C-axis of the pixel buffer.

t - offset across the T-axis of the pixel buffer.

Returns:

buffer containing the data which comprises this 2D image plane. It is guaranteed that this buffer will have its order set correctly but not that the backing buffer will have been byte swapped.

Throws:

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

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

getPlaneRegion

PixelData getPlaneRegion(Integer x,
                         Integer y,
                         Integer width,
                         Integer height,
                         Integer z,
                         Integer c,
                         Integer t,
                         Integer stride)
                  throws IOException,
                         DimensionsOutOfBoundsException

Retrieves a particular region of a 2D image plane from this pixel buffer.

Parameters:

x - offset across the X-axis of the pixel buffer.

y - offset across the Y-axis of the pixel buffer.

width - The number of pixels to retrieve along the X-axis.

height - The number of pixels to retrieve along the Y-axis.

z - offset across the Z-axis of the pixel buffer.

c - offset across the C-axis of the pixel buffer.

t - offset across the T-axis of the pixel buffer.

stride - The step size.

Returns:

buffer containing the data which comprises this 2D image plane. It is guaranteed that this buffer will have its order set correctly but not that the backing buffer will have been byte swapped.

Throws:

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

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

getPlaneDirect

byte[] getPlaneDirect(Integer z,
                      Integer c,
                      Integer t,
                      byte[] buffer)
               throws IOException,
                      DimensionsOutOfBoundsException

Retrieves a particular 2D image plane from this pixel buffer.

Parameters:

z - offset across the Z-axis of the pixel buffer.

c - offset across the C-axis of the pixel buffer.

t - offset across the T-axis of the pixel buffer.

buffer - pre-allocated buffer of the plane's size.

Returns:

buffer containing the data which comprises this 2D image plane. It is guaranteed that this buffer will have been byte swapped.

Throws:

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

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

getStack

PixelData getStack(Integer c,
                   Integer t)
            throws IOException,
                   DimensionsOutOfBoundsException

Retrieves the the entire number of optical sections for a single wavelength or channel at a particular timepoint in this pixel buffer.

Parameters:

c - offset across the C-axis of the pixel buffer.

t - offset across the T-axis of the pixel buffer.

Returns:

buffer containing the data which comprises this stack. It is guaranteed that this buffer will have its order set correctly but not that the backing buffer will have been byte swapped.

Throws:

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

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

getStackDirect

byte[] getStackDirect(Integer c,
                      Integer t,
                      byte[] buffer)
               throws IOException,
                      DimensionsOutOfBoundsException

Retrieves the the entire number of optical sections for a single wavelength or channel at a particular timepoint in this pixel buffer.

Parameters:

c - offset across the C-axis of the pixel buffer.

t - offset across the T-axis of the pixel buffer.

buffer - pre-allocated buffer of the stack's size.

Returns:

buffer containing the data which comprises this stack. It is guaranteed that this buffer will have been byte swapped.

Throws:

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

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

getTimepoint

PixelData getTimepoint(Integer t)
                throws IOException,
                       DimensionsOutOfBoundsException

Retrieves the entire number of optical sections for all wavelengths or channels at a particular timepoint in this pixel buffer.

Parameters:

t - offset across the T-axis of the pixel buffer.

Returns:

buffer containing the data which comprises this timepoint. It is guaranteed that this buffer will have its order set correctly but not that the backing buffer will have been byte swapped.

Throws:

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

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

getTimepointDirect

byte[] getTimepointDirect(Integer t,
                          byte[] buffer)
                   throws IOException,
                          DimensionsOutOfBoundsException

Retrieves the entire number of optical sections for all wavelengths or channels at a particular timepoint in this pixel buffer.

Parameters:

t - offset across the T-axis of the pixel buffer.

buffer - pre-allocated buffer of the timepoint's size.

Returns:

buffer containing the data which comprises this timepoint. It is guaranteed that this buffer will have been byte swapped.

Throws:

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

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

setTile

void setTile(byte[] buffer,
             Integer z,
             Integer c,
             Integer t,
             Integer x,
             Integer y,
             Integer w,
             Integer h)
      throws IOException,
             BufferOverflowException

Sets a tile in this pixel buffer.

Parameters:

buffer - A byte array of the data.

z - offset across the Z-axis of the pixel buffer.

c - offset across the C-axis of the pixel buffer.

t - offset across the T-axis of the pixel buffer.

x - Top left corner of the tile, X offset.

y - Top left corner of the tile, Y offset.

w - Width of the tile.

h - Height of the tile.

Throws:

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.

setRegion

void setRegion(Integer size,
               Long offset,
               byte[] buffer)
        throws IOException,
               BufferOverflowException

Sets a region in this pixel buffer.

Parameters:

size - byte width of the region to set.

offset - offset within the pixel buffer.

buffer - a byte array of the data.

Throws:

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

BufferOverflowException - if buffer.length > size.

setRegion

void setRegion(Integer size,
               Long offset,
               ByteBuffer buffer)
        throws IOException,
               BufferOverflowException

Sets a region in this pixel buffer.

Parameters:

size - byte width of the region to set.

offset - offset within the pixel buffer.

buffer - a byte buffer of the data.

Throws:

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

BufferOverflowException - if buffer.length > size.

setRow

void setRow(ByteBuffer buffer,
            Integer y,
            Integer z,
            Integer c,
            Integer t)
     throws IOException,
            DimensionsOutOfBoundsException,
            BufferOverflowException

Sets a particular row or scanline in this pixel buffer.

Parameters:

buffer - a byte buffer of the data comprising this row or scanline.

y - offset across the Y-axis of the pixel buffer.

z - offset across the Z-axis of the pixel buffer.

c - offset across the C-axis of the pixel buffer.

t - offset across the T-axis of the pixel buffer.

Throws:

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

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

BufferOverflowException - if buffer.length > getRowSize().

setPlane

void setPlane(ByteBuffer buffer,
              Integer z,
              Integer c,
              Integer t)
       throws IOException,
              DimensionsOutOfBoundsException,
              BufferOverflowException

Sets a particular 2D image plane in this pixel buffer.

Parameters:

buffer - a byte array of the data comprising this 2D image plane.

z - offset across the Z-axis of the pixel buffer.

c - offset across the C-axis of the pixel buffer.

t - offset across the T-axis of the pixel buffer.

Throws:

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

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

BufferOverflowException - if buffer.length > getPlaneSize().

setPlane

void setPlane(byte[] buffer,
              Integer z,
              Integer c,
              Integer t)
       throws IOException,
              DimensionsOutOfBoundsException,
              BufferOverflowException

Sets a particular 2D image plane in this pixel buffer.

Parameters:

buffer - a byte buffer of the data comprising this 2D image plane.

z - offset across the Z-axis of the pixel buffer.

c - offset across the C-axis of the pixel buffer.

t - offset across the T-axis of the pixel buffer.

Throws:

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

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

BufferOverflowException - if buffer.length > getPlaneSize().

setStack

void setStack(ByteBuffer buffer,
              Integer z,
              Integer c,
              Integer t)
       throws IOException,
              DimensionsOutOfBoundsException,
              BufferOverflowException

Sets the entire number of optical sections for a single wavelength or channel at a particular timepoint in this pixel buffer.

Parameters:

buffer - a byte buffer of the data comprising this stack.

c - offset across the C-axis of the pixel buffer.

t - offset across the T-axis of the pixel buffer.

Throws:

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

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

BufferOverflowException - if buffer.length > getStackSize().

setStack

void setStack(byte[] buffer,
              Integer z,
              Integer c,
              Integer t)
       throws IOException,
              DimensionsOutOfBoundsException,
              BufferOverflowException

Sets the entire number of optical sections for a single wavelength or channel at a particular timepoint in this pixel buffer.

Parameters:

buffer - a byte array of the data comprising this stack.

z - offset across the Z-axis of the pixel buffer.

c - offset across the C-axis of the pixel buffer.

t - offset across the T-axis of the pixel buffer.

Throws:

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

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

BufferOverflowException - if buffer.length > getStackSize()().

setTimepoint

void setTimepoint(ByteBuffer buffer,
                  Integer t)
           throws IOException,
                  DimensionsOutOfBoundsException,
                  BufferOverflowException

Sets the entire number of optical sections for all wavelengths or channels at a particular timepoint in this pixel buffer.

Parameters:

buffer - a byte buffer of the data comprising this timepoint.

t - offset across the T-axis of the pixel buffer.

Throws:

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

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

BufferOverflowException - if buffer.length > getTimepointSize().

setTimepoint

void setTimepoint(byte[] buffer,
                  Integer t)
           throws IOException,
                  DimensionsOutOfBoundsException,
                  BufferOverflowException

Sets the entire number of optical sections for all wavelengths or channels at a particular timepoint in this pixel buffer.

Parameters:

buffer - a byte array of the data comprising this timepoint.

t - offset across the T-axis of the pixel buffer.

Throws:

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

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

BufferOverflowException - if buffer.length > getTimepointSize().

calculateMessageDigest

byte[] calculateMessageDigest()
                       throws IOException

Calculates a SHA-1 message digest for the entire pixel buffer.

Returns:

byte array containing the message digest.

Throws:

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

getByteWidth

int getByteWidth()

Returns the byte width for the pixel buffer.

Returns:

See above.

isSigned

boolean isSigned()

Returns whether or not the pixel buffer has signed pixels.

Returns:

See above.

isFloat

boolean isFloat()

Returns whether or not the pixel buffer has floating point pixels.

Returns:

true if the pixel buffer as floating point, false otherwise

getPath

String getPath()

Retrieves the full path to this pixel buffer on disk

Returns:

fully qualified path.

getId

long getId()

Retrieves the identifier of this pixel buffer

getSizeX

int getSizeX()

Retrieves the size in X of this pixel buffer

getSizeY

int getSizeY()

Retrieves the size in Y of this pixel buffer

getSizeZ

int getSizeZ()

Retrieves the size in Z of this pixel buffer

getSizeC

int getSizeC()

Retrieves the size in C of this pixel buffer

getSizeT

int getSizeT()

Retrieves the size in T of this pixel buffer

getResolutionLevels

int getResolutionLevels()

Retrieves the number of resolution levels that the backing pixels pyramid contains.

Returns:

The number of resolution levels. This value does not necessarily indicate either the presence or absence of a pixels pyramid.

getResolutionLevel

int getResolutionLevel()

Retrieves the active resolution level.

Returns:

The active resolution level.

setResolutionLevel

void setResolutionLevel(int resolutionLevel)

Sets the active resolution level.

Parameters:

resolutionLevel - The resolution level to be used by the pixel buffer.

getTileSize

Dimension getTileSize()

Retrieves the tile size for the pixel store.

Returns:

The dimension of the tile or null if the pixel buffer is not tiled.

getResolutionDescriptions

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. For example, if an image has 2 resolution levels of size 2048x1024 and 1024x512 then this returns: [[2048,1024],[1024,512]]

Returns:

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