ome.io.bioformats

Class BfPixelBuffer

java.lang.Object

ome.io.bioformats.BfPixelBuffer

All Implemented Interfaces:

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

public class BfPixelBuffer
extends java.lang.Object
implements PixelBuffer, java.io.Serializable

PixelBuffer implementation which uses Bio-Formats to read pixels data directly from original files.

Since:

Beta4.1

See Also:

Serialized Form

Field Summary

Fields

Modifier and Type	Field and Description
protected IFormatReader	bfReader
protected java.lang.String	filePath
protected java.util.concurrent.atomic.AtomicReference<BfPixelsWrapper>	reader

Constructor Summary

Constructors

Constructor and Description
BfPixelBuffer(java.lang.String filePath, IFormatReader bfReader) We may want a constructor that takes the id of an imported file or that takes a File object?

Method Summary

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

Methods inherited from class java.lang.Object

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

Field Detail

filePath

protected final java.lang.String filePath

bfReader

protected final IFormatReader bfReader

reader

protected final java.util.concurrent.atomic.AtomicReference<BfPixelsWrapper> reader

Constructor Detail

BfPixelBuffer

public BfPixelBuffer(java.lang.String filePath,
                     IFormatReader bfReader)
              throws java.io.IOException,
                     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.

Throws:

java.io.IOException

FormatException

Method Detail

reader

protected BfPixelsWrapper reader()

Do not call this method when looking to close the reader. Instead, call `reader.get()` directly.

isLittleEndian

public boolean isLittleEndian()

Delegates to IFormatReader.isLittleEndian().

Returns:

See above.

setSeries

public void setSeries(int series)

Sets the current series in the underlying Bio-Formats reader.

Parameters:

series - The series to set.

getSeries

public int getSeries()

Retrieves the current series of the underlying Bio-Formats reader.

Returns:

The series.

calculateMessageDigest

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

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

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

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 java.io.IOException

Description copied from interface: PixelBuffer

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.

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(java.lang.Integer x,
                        java.lang.Integer z,
                        java.lang.Integer c,
                        java.lang.Integer t)
                 throws java.io.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:

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[])

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

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:

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)

getColSize

public java.lang.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)

getId

public long getId()

Description copied from interface: PixelBuffer

Retrieves the identifier of this pixel buffer

Specified by:

getId in interface PixelBuffer

getPath

public java.lang.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(java.lang.Integer z,
                          java.lang.Integer c,
                          java.lang.Integer t)
                   throws java.io.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:

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).

getPlaneDirect

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

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).

getPlaneOffset

public java.lang.Long getPlaneOffset(java.lang.Integer z,
                                     java.lang.Integer c,
                                     java.lang.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 PixelBuffer.checkBounds(Integer, Integer, Integer, Integer, Integer).

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

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:

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

DimensionsOutOfBoundsException

See Also:

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

getPlaneSize

public java.lang.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(java.lang.Integer size,
                           java.lang.Long offset)
                    throws java.io.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:

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

See Also:

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

getRegionDirect

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

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

See Also:

PixelBuffer.getRegion(Integer, Long)

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

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:

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[])

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

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:

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)

getRowOffset

public java.lang.Long getRowOffset(java.lang.Integer y,
                                   java.lang.Integer z,
                                   java.lang.Integer c,
                                   java.lang.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 PixelBuffer.checkBounds(Integer, Integer, Integer, Integer, Integer).

getRowSize

public java.lang.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

Retrieves the size in C of this pixel buffer

Specified by:

getSizeC in interface PixelBuffer

getSizeT

public int getSizeT()

Description copied from interface: PixelBuffer

Retrieves the size in T of this pixel buffer

Specified by:

getSizeT in interface PixelBuffer

getSizeX

public int getSizeX()

Description copied from interface: PixelBuffer

Retrieves the size in X of this pixel buffer

Specified by:

getSizeX in interface PixelBuffer

getSizeY

public int getSizeY()

Description copied from interface: PixelBuffer

Retrieves the size in Y of this pixel buffer

Specified by:

getSizeY in interface PixelBuffer

getSizeZ

public int getSizeZ()

Description copied from interface: PixelBuffer

Retrieves the size in Z of this pixel buffer

Specified by:

getSizeZ in interface PixelBuffer

getStack

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

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).

getStackDirect

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

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).

getStackOffset

public java.lang.Long getStackOffset(java.lang.Integer c,
                                     java.lang.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 PixelBuffer.checkBounds(Integer, Integer, Integer, Integer, Integer).

getStackSize

public java.lang.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).

getTimepoint

public PixelData getTimepoint(java.lang.Integer t)
                       throws java.io.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:

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).

getTimepointDirect

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

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).

getTimepointOffset

public java.lang.Long getTimepointOffset(java.lang.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 PixelBuffer.checkBounds(Integer, Integer, Integer, Integer, Integer).

getTimepointSize

public java.lang.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 java.lang.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:

true if the pixel buffer as floating point, false otherwise

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

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).

java.nio.BufferOverflowException - if buffer.length > PixelBuffer.getPlaneSize().

setPlane

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

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).

java.nio.BufferOverflowException - if buffer.length > PixelBuffer.getPlaneSize().

setRegion

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

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

java.nio.BufferOverflowException - if buffer.length > size.

setRegion

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

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

java.nio.BufferOverflowException - if buffer.length > size.

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,
                   java.nio.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:

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).

java.nio.BufferOverflowException - if buffer.length > PixelBuffer.getRowSize().

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,
                     java.nio.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:

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).

java.nio.BufferOverflowException - if buffer.length > PixelBuffer.getStackSize().

setStack

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

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).

java.nio.BufferOverflowException - if buffer.length > PixelBuffer.getStackSize()().

setTimepoint

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

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).

java.nio.BufferOverflowException - if buffer.length > PixelBuffer.getTimepointSize().

setTimepoint

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

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).

java.nio.BufferOverflowException - if buffer.length > PixelBuffer.getTimepointSize().

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

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

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:

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

DimensionsOutOfBoundsException

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

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:

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

DimensionsOutOfBoundsException

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

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:

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).

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

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.

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.

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

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. The level should be non-negative and less than PixelBuffer.getResolutionLevels(). Resolution level 0 is the smallest resolution and resolution level getResolutionLevels() - 1 is the largest resolution. This is the inverse of how Bio-Formats indexes resolutions.