loci.formats

Interface IFormatWriter

All Superinterfaces:

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

All Known Implementing Classes:

APNGWriter, AVIWriter, BufferedImageWriter, CellH5Writer, DicomWriter, EPSWriter, FormatWriter, ICSWriter, ImageIOWriter, ImageWriter, JavaWriter, JPEG2000Writer, JPEGWriter, OMETiffWriter, OMEXMLWriter, PyramidOMETiffWriter, QTWriter, TiffWriter, V3DrawWriter, WriterWrapper

public interface IFormatWriter
extends IFormatHandler, IPyramidHandler, ICompressedTileWriter

Interface for all biological file format writers.

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.
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.
int	getFramesPerSecond() Gets the frames per second to use when writing.
MetadataRetrieve	getMetadataRetrieve() Retrieves the current metadata retrieval object for this writer.
int[]	getPixelTypes() Gets the supported pixel types.
int[]	getPixelTypes(java.lang.String codec) Gets the supported pixel types for the given codec.
java.util.List<Resolution>	getResolutions() Get a list of resolution objects for the current series.
int	getSeries() Returns the current series.
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
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.
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	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	setInterleaved(boolean interleaved) Sets whether or not the channels in an image are interleaved.
void	setMetadataRetrieve(MetadataRetrieve r) Sets the metadata retrieval object from which to retrieve standardized metadata.
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.

Methods inherited from interface loci.formats.IFormatHandler

getFormat, getNativeDataType, getSuffixes, isThisType, setId

Methods inherited from interface java.io.Closeable

close

Methods inherited from interface loci.formats.IMetadataConfigurable

getMetadataOptions, getSupportedMetadataLevels, setMetadataOptions

Methods inherited from interface loci.formats.IPyramidHandler

getResolution, getResolutionCount, setResolution

Methods inherited from interface loci.formats.ICompressedTileWriter

getCodec, getCodecOptions, saveCompressedBytes

Method Detail

saveBytes

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

void setSeries(int series)
        throws FormatException

Sets the current series.

Parameters:

series - the series index, starting from 0.

Throws:

FormatException - if the specified series is invalid.

getSeries

int getSeries()

Returns the current series.

setInterleaved

void setInterleaved(boolean interleaved)

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

setValidBitsPerPixel

void setValidBitsPerPixel(int bits)

Sets the number of valid bits per pixel.

isInterleaved

boolean isInterleaved()

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

canDoStacks

boolean canDoStacks()

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

setMetadataRetrieve

void setMetadataRetrieve(MetadataRetrieve r)

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

getMetadataRetrieve

MetadataRetrieve getMetadataRetrieve()

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

Returns:

A metadata retrieval object.

setColorModel

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

Sets the color model.

getColorModel

java.awt.image.ColorModel getColorModel()

Gets the color model.

setFramesPerSecond

void setFramesPerSecond(int rate)

Sets the frames per second to use when writing.

getFramesPerSecond

int getFramesPerSecond()

Gets the frames per second to use when writing.

getCompressionTypes

java.lang.String[] getCompressionTypes()

Gets the available compression types.

getPixelTypes

int[] getPixelTypes()

Gets the supported pixel types.

getPixelTypes

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

Gets the supported pixel types for the given codec.

isSupportedType

boolean isSupportedType(int type)

Checks if the given pixel type is supported.

setCompression

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

Sets the current compression type.

Throws:

FormatException

setCodecOptions

void setCodecOptions(CodecOptions options)

Sets the codec options.

Parameters:

options - The options to set.

getCompression

java.lang.String getCompression()

Gets the current compression type.

changeOutputFile

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

Switch the output file for the current dataset.

Throws:

FormatException

java.io.IOException

setWriteSequentially

void setWriteSequentially(boolean sequential)

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.

getTileSizeX

int getTileSizeX()
          throws FormatException

Retrieves the current tile width Defaults to 0 if not supported

Returns:

The current tile width being used

Throws:

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

setTileSizeX

int setTileSizeX(int tileSize)
          throws FormatException

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

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

int getTileSizeY()
          throws FormatException

Retrieves the current tile height Defaults to 0 if not supported

Returns:

The current tile height being used

Throws:

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

setTileSizeY

int setTileSizeY(int tileSize)
          throws FormatException

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

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

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

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.

getResolutions

java.util.List<Resolution> getResolutions()

Get a list of resolution objects for the current series.