loci.formats

Class WriterWrapper

java.lang.Object

loci.formats.WriterWrapper

All Implemented Interfaces:

java.io.Closeable, java.lang.AutoCloseable, ICompressedTileWriter, IFormatHandler, IFormatWriter, IMetadataConfigurable, IPyramidHandler

Direct Known Subclasses:

BufferedImageWriter

public abstract class WriterWrapper
extends java.lang.Object
implements IFormatWriter

Abstract superclass of writer logic that wraps other writers. All methods are simply delegated to the wrapped writer.

Field Summary

Fields

Modifier and Type	Field and Description
protected IFormatWriter	writer FormatWriter used to write the file.

Constructor Summary

Constructors

Constructor and Description
WriterWrapper() Constructs a writer wrapper around a new image writer.
WriterWrapper(IFormatWriter w) Constructs a writer wrapper around the given writer.

Method Summary

Modifier and Type	Method and Description
boolean	canDoStacks() Reports whether the writer can save multiple images to a single file.
void	changeOutputFile(java.lang.String id) Switch the output file for the current dataset.
void	close()
WriterWrapper	duplicate(java.lang.Class<? extends IFormatWriter> imageWriterClass) Performs a deep copy of the writer, including nested wrapped writers.
private WriterWrapper	duplicateRecurse(java.lang.Class<? extends IFormatWriter> imageWriterClass)
Codec	getCodec()
CodecOptions	getCodecOptions()
java.awt.image.ColorModel	getColorModel() Gets the color model.
java.lang.String	getCompression() Gets the current compression type.
java.lang.String[]	getCompressionTypes() Gets the available compression types.
java.lang.String	getFormat() Gets the name of this file format.
int	getFramesPerSecond() Gets the frames per second to use when writing.
MetadataOptions	getMetadataOptions()
MetadataRetrieve	getMetadataRetrieve() Retrieves the current metadata retrieval object for this writer.
java.lang.Class<?>	getNativeDataType() Returns the native data type of image planes for this reader, as returned by IFormatReader.openPlane(int, int, int, int, int) or IFormatWriter.savePlane(int, java.lang.Object).
int[]	getPixelTypes() Gets the supported pixel types.
int[]	getPixelTypes(java.lang.String codec) Gets the supported pixel types for the given codec.
int	getResolution() Get the current resolution level.
int	getResolutionCount() Return the number of resolutions for the current series.
java.util.List<Resolution>	getResolutions() Get a list of resolution objects for the current series.
int	getSeries() Returns the current series.
java.lang.String[]	getSuffixes() Gets the default file suffixes for this file format.
java.util.Set<MetadataLevel>	getSupportedMetadataLevels()
int	getTileSizeX() Retrieves the current tile width Defaults to 0 if not supported
int	getTileSizeY() Retrieves the current tile height Defaults to 0 if not supported
IFormatWriter	getWriter() Gets the wrapped writer.
boolean	isInterleaved() Gets whether or not the channels in an image are interleaved.
boolean	isSupportedType(int type) Checks if the given pixel type is supported.
boolean	isThisType(java.lang.String name) Checks if the given string is a valid filename for this file format.
void	saveBytes(int no, byte[] buf) Saves the given image to the current series in the current file.
void	saveBytes(int no, byte[] buf, int x, int y, int w, int h) Saves the given image tile to the current series in the current file.
void	saveBytes(int no, byte[] buf, loci.common.Region tile) Saves the given image tile to the current series in the current file.
void	saveCompressedBytes(int no, byte[] buf, int x, int y, int w, int h) Save a compressed tile to the current output file.
void	savePlane(int no, java.lang.Object plane) Saves the given image plane to the current series in the current file.
void	savePlane(int no, java.lang.Object plane, int x, int y, int w, int h) Saves the given image plane to the current series in the current file.
void	savePlane(int no, java.lang.Object plane, loci.common.Region tile) Saves the given image plane to the current series in the current file.
void	setCodecOptions(CodecOptions options) Sets the codec options.
void	setColorModel(java.awt.image.ColorModel cm) Sets the color model.
void	setCompression(java.lang.String compress) Sets the current compression type.
void	setFramesPerSecond(int rate) Sets the frames per second to use when writing.
void	setId(java.lang.String id) Sets the current file name.
void	setInterleaved(boolean interleaved) Sets whether or not the channels in an image are interleaved.
void	setMetadataOptions(MetadataOptions options)
void	setMetadataRetrieve(MetadataRetrieve r) Sets the metadata retrieval object from which to retrieve standardized metadata.
void	setResolution(int resolution) Set the resolution level.
void	setResolutions(java.util.List<Resolution> resolutions) Specify a list of resolution objects for the current series.
void	setSeries(int series) Sets the current series.
int	setTileSizeX(int tileSize) Will attempt to set the tile width to the desired value and return the actual value which will be used
int	setTileSizeY(int tileSize) Will attempt to set the tile height to the desired value and return the actual value which will be used
void	setValidBitsPerPixel(int bits) Sets the number of valid bits per pixel.
void	setWriteSequentially(boolean sequential) Sets whether or not we know that planes will be written sequentially.
IFormatWriter	unwrap() Unwraps nested wrapped writers until the core writer (i.e., not a WriterWrapper or ImageWriter) is found.
IFormatWriter	unwrap(java.lang.Class<? extends IFormatWriter> writerClass, java.lang.String id) Unwraps nested wrapped writers until the given writer class is found.
IFormatWriter	unwrap(java.lang.String id) Unwraps nested wrapped writers until the core writer (i.e., not a WriterWrapper or ImageWriter) is found.

Methods inherited from class java.lang.Object

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

Field Detail

writer

protected IFormatWriter writer

FormatWriter used to write the file.

Constructor Detail

WriterWrapper

public WriterWrapper()

Constructs a writer wrapper around a new image writer.

WriterWrapper

public WriterWrapper(IFormatWriter w)

Constructs a writer wrapper around the given writer.

Method Detail

getWriter

public IFormatWriter getWriter()

Gets the wrapped writer.

unwrap

public IFormatWriter unwrap()
                     throws FormatException,
                            java.io.IOException

Unwraps nested wrapped writers until the core writer (i.e., not a WriterWrapper or ImageWriter) is found.

Throws:

FormatException

java.io.IOException

unwrap

public IFormatWriter unwrap(java.lang.String id)
                     throws FormatException,
                            java.io.IOException

Unwraps nested wrapped writers until the core writer (i.e., not a WriterWrapper or ImageWriter) is found.

Parameters:

id - Id to use as a basis when unwrapping any nested ImageWriters. If null, the current id is used.

Throws:

FormatException

java.io.IOException

unwrap

public IFormatWriter unwrap(java.lang.Class<? extends IFormatWriter> writerClass,
                            java.lang.String id)
                     throws FormatException,
                            java.io.IOException

Unwraps nested wrapped writers until the given writer class is found.

Parameters:

writerClass - Class of the desired nested writer. If null, the core writer (i.e., deepest wrapped writer) will be returned.

id - Id to use as a basis when unwrapping any nested ImageWriters. If null, the current id is used.

Throws:

FormatException

java.io.IOException

duplicate

public WriterWrapper duplicate(java.lang.Class<? extends IFormatWriter> imageWriterClass)
                        throws FormatException

Performs a deep copy of the writer, including nested wrapped writers. Most of the writer state is preserved as well, including:

• isInterleaved()
• getColorModel()
• getFramesPerSecond()
• getCompression()

Parameters:

imageWriterClass - If non-null, any ImageWriters in the writer stack will be replaced with instances of the given class.

Throws:

FormatException - If something goes wrong during the duplication.

getSupportedMetadataLevels

public java.util.Set<MetadataLevel> getSupportedMetadataLevels()

Specified by:

getSupportedMetadataLevels in interface IMetadataConfigurable

getMetadataOptions

public MetadataOptions getMetadataOptions()

Specified by:

getMetadataOptions in interface IMetadataConfigurable

setMetadataOptions

public void setMetadataOptions(MetadataOptions options)

Specified by:

setMetadataOptions in interface IMetadataConfigurable

changeOutputFile

public void changeOutputFile(java.lang.String id)
                      throws FormatException,
                             java.io.IOException

Description copied from interface: IFormatWriter

Switch the output file for the current dataset.

Specified by:

changeOutputFile in interface IFormatWriter

Throws:

FormatException

java.io.IOException

saveBytes

public void saveBytes(int no,
                      byte[] buf)
               throws FormatException,
                      java.io.IOException

Description copied from interface: IFormatWriter

Saves the given image to the current series in the current file.

Specified by:

saveBytes in interface IFormatWriter

Parameters:

no - the plane index within the series.

buf - the byte array that represents the image.

Throws:

FormatException - if one of the parameters is invalid.

java.io.IOException - if there was a problem writing to the file.

saveBytes

public void saveBytes(int no,
                      byte[] buf,
                      int x,
                      int y,
                      int w,
                      int h)
               throws FormatException,
                      java.io.IOException

Description copied from interface: IFormatWriter

Saves the given image tile to the current series in the current file.

Specified by:

saveBytes in interface IFormatWriter

Parameters:

no - the plane index within the series.

buf - the byte array that represents the image tile.

x - the X coordinate of the upper-left corner of the image tile.

y - the Y coordinate of the upper-left corner of the image tile.

w - the width (in pixels) of the image tile.

h - the height (in pixels) of the image tile.

Throws:

FormatException - if one of the parameters is invalid.

java.io.IOException - if there was a problem writing to the file.

saveBytes

public void saveBytes(int no,
                      byte[] buf,
                      loci.common.Region tile)
               throws FormatException,
                      java.io.IOException

Description copied from interface: IFormatWriter

Saves the given image tile to the current series in the current file.

Specified by:

saveBytes in interface IFormatWriter

Parameters:

no - the plane index within the series.

buf - the byte array that represents the image tile.

tile - the Region representing the image tile to be read.

Throws:

FormatException - if one of the parameters is invalid.

java.io.IOException - if there was a problem writing to the file.

savePlane

public void savePlane(int no,
                      java.lang.Object plane)
               throws FormatException,
                      java.io.IOException

Description copied from interface: IFormatWriter

Saves the given image plane to the current series in the current file.

Specified by:

savePlane in interface IFormatWriter

Parameters:

no - the plane index within the series.

plane - the image plane.

Throws:

FormatException - if one of the parameters is invalid.

java.io.IOException - if there was a problem writing to the file.

savePlane

public void savePlane(int no,
                      java.lang.Object plane,
                      int x,
                      int y,
                      int w,
                      int h)
               throws FormatException,
                      java.io.IOException

Description copied from interface: IFormatWriter

Saves the given image plane to the current series in the current file.

Specified by:

savePlane in interface IFormatWriter

Parameters:

no - the plane index within the series.

plane - the image plane.

x - the X coordinate of the upper-left corner of the image tile.

y - the Y coordinate of the upper-left corner of the image tile.

w - the width (in pixels) of the image tile.

h - the height (in pixels) of the image tile.

Throws:

FormatException - if one of the parameters is invalid.

java.io.IOException - if there was a problem writing to the file.

savePlane

public void savePlane(int no,
                      java.lang.Object plane,
                      loci.common.Region tile)
               throws FormatException,
                      java.io.IOException

Description copied from interface: IFormatWriter

Saves the given image plane to the current series in the current file.

Specified by:

savePlane in interface IFormatWriter

Parameters:

no - the plane index within the series.

plane - the image plane.

tile - the Region representing the image tile to be read.

Throws:

FormatException - if one of the parameters is invalid.

java.io.IOException - if there was a problem writing to the file.

setSeries

public void setSeries(int series)
               throws FormatException

Description copied from interface: IFormatWriter

Sets the current series.

Specified by:

setSeries in interface IFormatWriter

Parameters:

series - the series index, starting from 0.

Throws:

FormatException - if the specified series is invalid.

getSeries

public int getSeries()

Description copied from interface: IFormatWriter

Returns the current series.

Specified by:

getSeries in interface IFormatWriter

setInterleaved

public void setInterleaved(boolean interleaved)

Description copied from interface: IFormatWriter

Sets whether or not the channels in an image are interleaved.

Specified by:

setInterleaved in interface IFormatWriter

isInterleaved

public boolean isInterleaved()

Description copied from interface: IFormatWriter

Gets whether or not the channels in an image are interleaved.

Specified by:

isInterleaved in interface IFormatWriter

setValidBitsPerPixel

public void setValidBitsPerPixel(int bits)

Description copied from interface: IFormatWriter

Sets the number of valid bits per pixel.

Specified by:

setValidBitsPerPixel in interface IFormatWriter

canDoStacks

public boolean canDoStacks()

Description copied from interface: IFormatWriter

Reports whether the writer can save multiple images to a single file.

Specified by:

canDoStacks in interface IFormatWriter

setMetadataRetrieve

public void setMetadataRetrieve(MetadataRetrieve r)

Description copied from interface: IFormatWriter

Sets the metadata retrieval object from which to retrieve standardized metadata.

Specified by:

setMetadataRetrieve in interface IFormatWriter

getMetadataRetrieve

public MetadataRetrieve getMetadataRetrieve()

Description copied from interface: IFormatWriter

Retrieves the current metadata retrieval object for this writer. You can be assured that this method will never return a null metadata retrieval object.

Specified by:

getMetadataRetrieve in interface IFormatWriter

Returns:

A metadata retrieval object.

setColorModel

public void setColorModel(java.awt.image.ColorModel cm)

Description copied from interface: IFormatWriter

Sets the color model.

Specified by:

setColorModel in interface IFormatWriter

getColorModel

public java.awt.image.ColorModel getColorModel()

Description copied from interface: IFormatWriter

Gets the color model.

Specified by:

getColorModel in interface IFormatWriter

setFramesPerSecond

public void setFramesPerSecond(int rate)

Description copied from interface: IFormatWriter

Sets the frames per second to use when writing.

Specified by:

setFramesPerSecond in interface IFormatWriter

getFramesPerSecond

public int getFramesPerSecond()

Description copied from interface: IFormatWriter

Gets the frames per second to use when writing.

Specified by:

getFramesPerSecond in interface IFormatWriter

getCompressionTypes

public java.lang.String[] getCompressionTypes()

Description copied from interface: IFormatWriter

Gets the available compression types.

Specified by:

getCompressionTypes in interface IFormatWriter

getPixelTypes

public int[] getPixelTypes()

Description copied from interface: IFormatWriter

Gets the supported pixel types.

Specified by:

getPixelTypes in interface IFormatWriter

getPixelTypes

public int[] getPixelTypes(java.lang.String codec)

Description copied from interface: IFormatWriter

Gets the supported pixel types for the given codec.

Specified by:

getPixelTypes in interface IFormatWriter

isSupportedType

public boolean isSupportedType(int type)

Description copied from interface: IFormatWriter

Checks if the given pixel type is supported.

Specified by:

isSupportedType in interface IFormatWriter

setCompression

public void setCompression(java.lang.String compress)
                    throws FormatException

Description copied from interface: IFormatWriter

Sets the current compression type.

Specified by:

setCompression in interface IFormatWriter

Throws:

FormatException

setCodecOptions

public void setCodecOptions(CodecOptions options)

Description copied from interface: IFormatWriter

Sets the codec options.

Specified by:

setCodecOptions in interface IFormatWriter

Parameters:

options - The options to set.

getCompression

public java.lang.String getCompression()

Description copied from interface: IFormatWriter

Gets the current compression type.

Specified by:

getCompression in interface IFormatWriter

setWriteSequentially

public void setWriteSequentially(boolean sequential)

Description copied from interface: IFormatWriter

Sets whether or not we know that planes will be written sequentially. If planes are written sequentially and this flag is set, then performance will be slightly improved.

Specified by:

setWriteSequentially in interface IFormatWriter

getTileSizeX

public int getTileSizeX()
                 throws FormatException

Description copied from interface: IFormatWriter

Retrieves the current tile width Defaults to 0 if not supported

Specified by:

getTileSizeX in interface IFormatWriter

Returns:

The current tile width being used

Throws:

FormatException - Image metadata including Pixels Size X must be set prior to calling getTileSizeX()

setTileSizeX

public int setTileSizeX(int tileSize)
                 throws FormatException

Description copied from interface: IFormatWriter

Will attempt to set the tile width to the desired value and return the actual value which will be used

Specified by:

setTileSizeX in interface IFormatWriter

Parameters:

tileSize - The tile width you wish to use. Setting to 0 will disable tiling

Returns:

The tile width which will actually be used, this may differ from the value requested. If the requested value is not supported the writer will return and use the closest appropriate value.

Throws:

FormatException - Tile size must be greater than or equal to 0 and less than the image width

getTileSizeY

public int getTileSizeY()
                 throws FormatException

Description copied from interface: IFormatWriter

Retrieves the current tile height Defaults to 0 if not supported

Specified by:

getTileSizeY in interface IFormatWriter

Returns:

The current tile height being used

Throws:

FormatException - Image metadata including Pixels Size Y must be set prior to calling getTileSizeY()

setTileSizeY

public int setTileSizeY(int tileSize)
                 throws FormatException

Description copied from interface: IFormatWriter

Will attempt to set the tile height to the desired value and return the actual value which will be used

Specified by:

setTileSizeY in interface IFormatWriter

Parameters:

tileSize - The tile height you wish to use. Setting to 0 will disable tiling

Returns:

The tile height which will actually be used, this may differ from the value requested. If the requested value is not supported the writer will return and use the closest appropriate value.

Throws:

FormatException - Tile size must be greater than or equal to 0 and less than the image height

setResolutions

public void setResolutions(java.util.List<Resolution> resolutions)

Description copied from interface: IFormatWriter

Specify a list of resolution objects for the current series. If resolutions are specified using this method, then any resolution data supplied via the MetadataRetrieve will be ignored.

Specified by:

setResolutions in interface IFormatWriter

getResolutions

public java.util.List<Resolution> getResolutions()

Description copied from interface: IFormatWriter

Get a list of resolution objects for the current series.

Specified by:

getResolutions in interface IFormatWriter

saveCompressedBytes

public void saveCompressedBytes(int no,
                                byte[] buf,
                                int x,
                                int y,
                                int w,
                                int h)
                         throws FormatException,
                                java.io.IOException

Description copied from interface: ICompressedTileWriter

Save a compressed tile to the current output file. The compression type of the tile should match the compression type set in the writer.

Specified by:

saveCompressedBytes in interface ICompressedTileWriter

Parameters:

no - plane index

buf - compressed tile bytes

x - pixel X coordinate of the upper-left corner of the tile

y - pixel Y coordinate of the upper-left corner of the tile

w - width in pixels of the compressed tile

h - height in pixels of the compressed tile

Throws:

FormatException

java.io.IOException

getCodec

public Codec getCodec()

Specified by:

getCodec in interface ICompressedTileWriter

Returns:

the codec that can be used to compress tiles

getCodecOptions

public CodecOptions getCodecOptions()

Specified by:

getCodecOptions in interface ICompressedTileWriter

Returns:

the codec options that can be used to compress tiles

isThisType

public boolean isThisType(java.lang.String name)

Description copied from interface: IFormatHandler

Checks if the given string is a valid filename for this file format.

Specified by:

isThisType in interface IFormatHandler

getFormat

public java.lang.String getFormat()

Description copied from interface: IFormatHandler

Gets the name of this file format.

Specified by:

getFormat in interface IFormatHandler

getSuffixes

public java.lang.String[] getSuffixes()

Description copied from interface: IFormatHandler

Gets the default file suffixes for this file format.

Specified by:

getSuffixes in interface IFormatHandler

getNativeDataType

public java.lang.Class<?> getNativeDataType()

Description copied from interface: IFormatHandler

Returns the native data type of image planes for this reader, as returned by IFormatReader.openPlane(int, int, int, int, int) or IFormatWriter.savePlane(int, java.lang.Object). For most readers this type will be a byte array; however, some readers call external APIs that work with other types such as BufferedImage.

Specified by:

getNativeDataType in interface IFormatHandler

setId

public void setId(java.lang.String id)
           throws FormatException,
                  java.io.IOException

Description copied from interface: IFormatHandler

Sets the current file name.

Specified by:

setId in interface IFormatHandler

Throws:

FormatException

java.io.IOException

close

public void close()
           throws java.io.IOException

Specified by:

close in interface java.io.Closeable

Specified by:

close in interface java.lang.AutoCloseable

Throws:

java.io.IOException

getResolutionCount

public int getResolutionCount()

Description copied from interface: IPyramidHandler

Return the number of resolutions for the current series. Resolutions are stored in descending order, so the largest resolution is first and the smallest resolution is last.

Specified by:

getResolutionCount in interface IPyramidHandler

getResolution

public int getResolution()

Description copied from interface: IPyramidHandler

Get the current resolution level.

Specified by:

getResolution in interface IPyramidHandler

See Also:

IPyramidHandler.getResolutionCount()

setResolution

public void setResolution(int resolution)

Description copied from interface: IPyramidHandler

Set the resolution level.

Specified by:

setResolution in interface IPyramidHandler

See Also:

IPyramidHandler.getResolutionCount()

duplicateRecurse

private WriterWrapper duplicateRecurse(java.lang.Class<? extends IFormatWriter> imageWriterClass)
                                throws FormatException

Throws:

FormatException