io.scif.formats

Class TIFFFormat.Writer<M extends TIFFFormat.Metadata>

java.lang.Object

org.scijava.AbstractContextual

org.scijava.plugin.AbstractRichPlugin

io.scif.AbstractSCIFIOPlugin

io.scif.AbstractHasFormat

io.scif.AbstractHasSource

io.scif.AbstractWriter<M>

io.scif.formats.TIFFFormat.Writer<M>

All Implemented Interfaces:

HasFormat, HasSource, SCIFIOPlugin, TypedWriter<M>, Writer, Comparable<org.scijava.Prioritized>, org.scijava.Contextual, org.scijava.Identifiable, org.scijava.Locatable, org.scijava.log.Logged, org.scijava.plugin.HasPluginInfo, org.scijava.plugin.RichPlugin, org.scijava.plugin.SciJavaPlugin, org.scijava.Prioritized, org.scijava.Versioned

Enclosing class:

TIFFFormat

public static class TIFFFormat.Writer<M extends TIFFFormat.Metadata>
extends AbstractWriter<M>

TiffWriter is the file format writer for TIFF files.

NB: BigTIFF writing can be controlled via the setBigTiff(boolean) method, or by passing a SCIFIOConfig with a key of BIG_TIFF_KEY paired to the desired value. If not explicitly turned on or off, BigTIFF will be written if the output dataset is larger than 2GB in size.

Field Summary

Fields

Modifier and Type	Field and Description
static String	BIG_TIFF_KEY
static String	COMPRESSION_J2K
static String	COMPRESSION_J2K_LOSSY
static String	COMPRESSION_JPEG
static String	COMPRESSION_LZW
static String	COMPRESSION_UNCOMPRESSED
static String	COMPRESSION_ZLIB

Constructor Summary

Constructors

Constructor and Description
Writer()

Method Summary

Modifier and Type	Method and Description
boolean	canDoStacks()
void	close() Closes the image source(s) associated with this component and resets the component to its default state.
int[]	getPixelTypes(String codec) Gets the supported pixel types for the given codec.
protected void	initialize(int imageIndex, long planeIndex, net.imglib2.Interval bounds) Ensures this writer is prepared to write the given plane of the given image.
boolean	isBigTiff()
protected String[]	makeCompressionTypes()
void	savePlane(int imageIndex, long planeIndex, Plane plane, IFD ifd, net.imglib2.Interval bounds) Saves the given image to the specified series in the current file.
void	setBigTiff(boolean bigTiff) Sets whether or not BigTIFF files should be written.
void	setDest(org.scijava.io.handle.DataHandle<org.scijava.io.location.Location> dest, int imageIndex, SCIFIOConfig config) As Writer.setDest(DataHandle, int), with specification for new configuration options.
void	writePlane(int imageIndex, long planeIndex, Plane plane, net.imglib2.Interval bounds) Helper method invoked by AbstractWriter.savePlane(int, long, io.scif.Plane) to perform actual format- specific output.

Methods inherited from class io.scif.AbstractWriter

checkLocation, checkParams, close, getCodecOptions, getColorModel, getCompression, getCompressionTypes, getFramesPerSecond, getHandle, getMetadata, getValidBits, isInitialized, isSupportedCompression, isSupportedType, savePlane, savePlane, setColorModel, setDest, setDest, setDest, setDest, setDest, setDest, setDest, setMetadata, setMetadata, writeSequential

Methods inherited from class io.scif.AbstractHasFormat

asBrowsableLocation, asBrowsableLocation, getFormat, getFormatName

Methods inherited from class io.scif.AbstractSCIFIOPlugin

getVersion, log

Methods inherited from class org.scijava.plugin.AbstractRichPlugin

getInfo, getPriority, setInfo, setPriority, toString

Methods inherited from class org.scijava.AbstractContextual

context, getContext

Methods inherited from class java.lang.Object

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

Methods inherited from interface io.scif.HasFormat

getFormat, getFormatName

Methods inherited from interface io.scif.SCIFIOPlugin

getVersion, log

Methods inherited from interface org.scijava.plugin.RichPlugin

getIdentifier

Methods inherited from interface org.scijava.Contextual

context, getContext, setContext

Methods inherited from interface org.scijava.Prioritized

compareTo, getPriority, setPriority

Methods inherited from interface org.scijava.plugin.HasPluginInfo

getInfo, setInfo

Methods inherited from interface org.scijava.Locatable

getLocation

Field Detail

COMPRESSION_UNCOMPRESSED

public static final String COMPRESSION_UNCOMPRESSED

COMPRESSION_LZW

public static final String COMPRESSION_LZW

COMPRESSION_ZLIB

public static final String COMPRESSION_ZLIB

COMPRESSION_J2K

public static final String COMPRESSION_J2K

COMPRESSION_J2K_LOSSY

public static final String COMPRESSION_J2K_LOSSY

COMPRESSION_JPEG

public static final String COMPRESSION_JPEG

BIG_TIFF_KEY

public static final String BIG_TIFF_KEY

See Also:

Constant Field Values

Constructor Detail

Writer

public Writer()

Method Detail

makeCompressionTypes

protected String[] makeCompressionTypes()

Specified by:

makeCompressionTypes in class AbstractWriter<M extends TIFFFormat.Metadata>

Returns:

An array of compression types supported by this format. An empty array indicates no compression.

setBigTiff

public void setBigTiff(boolean bigTiff)

Sets whether or not BigTIFF files should be written. This flag is not reset when close() is called.

isBigTiff

public boolean isBigTiff()

Returns:

Whether or not this Writer is configured to write BigTIFF data.

savePlane

public void savePlane(int imageIndex,
                      long planeIndex,
                      Plane plane,
                      IFD ifd,
                      net.imglib2.Interval bounds)
               throws IOException,
                      FormatException

Saves the given image to the specified series in the current file. The IFD hashtable allows specification of TIFF parameters such as bit depth, compression and units.

Throws:

IOException

FormatException

initialize

protected void initialize(int imageIndex,
                          long planeIndex,
                          net.imglib2.Interval bounds)
                   throws FormatException,
                          IOException

Description copied from class: AbstractWriter

Ensures this writer is prepared to write the given plane of the given image.

Overrides:

initialize in class AbstractWriter<M extends TIFFFormat.Metadata>

Throws:

FormatException

IOException

setDest

public void setDest(org.scijava.io.handle.DataHandle<org.scijava.io.location.Location> dest,
                    int imageIndex,
                    SCIFIOConfig config)
             throws FormatException,
                    IOException

Description copied from interface: Writer

As Writer.setDest(DataHandle, int), with specification for new configuration options.

Specified by:

setDest in interface Writer

Overrides:

setDest in class AbstractWriter<M extends TIFFFormat.Metadata>

Parameters:

dest - The image source to write to.

imageIndex - The index within the source that will be written.

config - Configuration information to use for this write.

Throws:

FormatException

IOException

writePlane

public void writePlane(int imageIndex,
                       long planeIndex,
                       Plane plane,
                       net.imglib2.Interval bounds)
                throws FormatException,
                       IOException

Description copied from class: AbstractWriter

Helper method invoked by AbstractWriter.savePlane(int, long, io.scif.Plane) to perform actual format- specific output.

Specified by:

writePlane in class AbstractWriter<M extends TIFFFormat.Metadata>

Throws:

FormatException

IOException

canDoStacks

public boolean canDoStacks()

Specified by:

canDoStacks in interface Writer

Overrides:

canDoStacks in class AbstractWriter<M extends TIFFFormat.Metadata>

Returns:

True if this Writer can save multiple images to a single file.

getPixelTypes

public int[] getPixelTypes(String codec)

Description copied from interface: Writer

Gets the supported pixel types for the given codec.

Specified by:

getPixelTypes in interface Writer

Overrides:

getPixelTypes in class AbstractWriter<M extends TIFFFormat.Metadata>

close

public void close()
           throws IOException

Description copied from interface: HasSource

Closes the image source(s) associated with this component and resets the component to its default state.

Equivalent to calling close(false).

Specified by:

close in interface HasSource

Overrides:

close in class AbstractHasSource

Throws:

IOException