io.scif

Class AbstractWriter<M extends TypedMetadata>

java.lang.Object

org.scijava.AbstractContextual

org.scijava.plugin.AbstractRichPlugin

io.scif.AbstractSCIFIOPlugin

io.scif.AbstractHasFormat

io.scif.AbstractHasSource

io.scif.AbstractWriter<M>

Type Parameters:

M - - The Metadata type required by this Writer.

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

Direct Known Subclasses:

APNGFormat.Writer, AVIFormat.Writer, DefaultWriter, EPSFormat.Writer, ICSFormat.Writer, ImageIOFormat.Writer, JPEG2000Format.Writer, LegacyQTFormat.Writer, NativeQTFormat.Writer, TIFFFormat.Writer

public abstract class AbstractWriter<M extends TypedMetadata>
extends AbstractHasSource
implements TypedWriter<M>

Abstract superclass of all SCIFIO Writer implementations.

Author:

Mark Hiner

See Also:

Writer, HasFormat, Metadata

Constructor Summary

Constructors

Constructor and Description
AbstractWriter()

Method Summary

Modifier and Type	Method and Description
boolean	canDoStacks()
protected void	checkLocation(org.scijava.io.handle.DataHandle<org.scijava.io.location.Location> out, SCIFIOConfig config) Validate that the given output is consistent with the given configuration.
protected void	checkParams(int imageIndex, long planeIndex, byte[] buf, net.imglib2.Interval bounds) Ensure that the arguments that are being passed to saveBytes(...) are valid.
void	close(boolean fileOnly) Closes the image source(s) associated with this component, with a toggle to determine if the component itself is reset.
CodecOptions	getCodecOptions()
ColorModel	getColorModel() Gets the color model.
String	getCompression()
String[]	getCompressionTypes() Gets the available compression types.
int	getFramesPerSecond()
org.scijava.io.handle.DataHandle<org.scijava.io.location.Location>	getHandle() Retrieves a reference to the output source that will be written to during Writer.savePlane(int, long, io.scif.Plane) calls.
M	getMetadata() Gets the Metadata that will be used when saving planes.
int[]	getPixelTypes(String codec) Gets the supported pixel types for the given codec.
int	getValidBits()
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	isInitialized(int imageIndex, long planeIndex)
void	isSupportedCompression(String compression) Checks if the given compression type is supported.
boolean	isSupportedType(int type, String codec) Checks if the given pixel type is supported.
protected abstract String[]	makeCompressionTypes()
void	savePlane(int imageIndex, long planeIndex, Plane plane) Saves the provided plane to the specified image and plane index of this Writer's destination image.
void	savePlane(int imageIndex, long planeIndex, Plane plane, net.imglib2.Interval bounds) Saves the specified tile (sub-region) of the provided plane to the specified image and plane index of this Writer's destination image.
void	setColorModel(ColorModel cm) Sets the color model.
void	setDest(org.scijava.io.handle.DataHandle<org.scijava.io.location.Location> out) Sets the source that will be written to during Writer.savePlane(int, long, io.scif.Plane) calls.
void	setDest(org.scijava.io.handle.DataHandle<org.scijava.io.location.Location> out, int imageIndex) As Writer.setDest(DataHandle), with specification for source image index.
void	setDest(org.scijava.io.handle.DataHandle<org.scijava.io.location.Location> out, int imageIndex, SCIFIOConfig config) As Writer.setDest(DataHandle, int), with specification for new configuration options.
void	setDest(org.scijava.io.handle.DataHandle<org.scijava.io.location.Location> out, SCIFIOConfig config) As Writer.setDest(DataHandle), with specification for new configuration options.
void	setDest(org.scijava.io.location.Location fileName) Sets the source that will be written to during Writer.savePlane(int, long, io.scif.Plane) calls.
void	setDest(org.scijava.io.location.Location loc, int imageIndex) As Writer.setDest(Location) with specification for source image index.
void	setDest(org.scijava.io.location.Location loc, int imageIndex, SCIFIOConfig config) As Writer.setDest(Location, int) with specification for new configuration options.
void	setDest(org.scijava.io.location.Location loc, SCIFIOConfig config) As Writer.setDest(Location) with specification for new configuration options.
void	setMetadata(M meta) Generic-parameterized setMetadata method, using TypedMetadata to avoid type erasure conflicts with Writer.setMetadata(Metadata).
void	setMetadata(Metadata meta) Provides this Writer with a Metadata object to use when interpreting Planes during calls to Writer.savePlane(int, long, io.scif.Plane).
protected abstract void	writePlane(int imageIndex, long planeIndex, Plane plane, net.imglib2.Interval bounds) Helper method invoked by savePlane(int, long, io.scif.Plane) to perform actual format- specific output.
boolean	writeSequential()

Methods inherited from class io.scif.AbstractHasSource

close

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

Methods inherited from interface io.scif.HasSource

close

Constructor Detail

AbstractWriter

public AbstractWriter()

Method Detail

checkLocation

protected void checkLocation(org.scijava.io.handle.DataHandle<org.scijava.io.location.Location> out,
                             SCIFIOConfig config)
                      throws FormatException,
                             IOException

Validate that the given output is consistent with the given configuration.

Throws:

FormatException - If the output does not meet the requirements of the configuration

IOException

checkParams

protected void checkParams(int imageIndex,
                           long planeIndex,
                           byte[] buf,
                           net.imglib2.Interval bounds)
                    throws FormatException

Ensure that the arguments that are being passed to saveBytes(...) are valid.

Throws:

FormatException - if any of the arguments is invalid.

initialize

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

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

Throws:

FormatException

IOException

makeCompressionTypes

protected abstract String[] makeCompressionTypes()

Returns:

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

writePlane

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

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

Throws:

FormatException

IOException

savePlane

public void savePlane(int imageIndex,
                      long planeIndex,
                      Plane plane)
               throws FormatException,
                      IOException

Description copied from interface: Writer

Saves the provided plane to the specified image and plane index of this Writer's destination image.

Specified by:

savePlane in interface Writer

Parameters:

imageIndex - the image index within the dataset.

planeIndex - the plane index within the image.

plane - the pixels save

Throws:

FormatException - if one of the parameters is invalid.

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

savePlane

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

Description copied from interface: Writer

Saves the specified tile (sub-region) of the provided plane to the specified image and plane index of this Writer's destination image.

Specified by:

savePlane in interface Writer

Parameters:

imageIndex - the image index within the dataset.

planeIndex - the plane index within the image.

plane - the pixels save

bounds - bounds of the planar axes.

Throws:

FormatException - if one of the parameters is invalid.

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

canDoStacks

public boolean canDoStacks()

Specified by:

canDoStacks in interface Writer

Returns:

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

setMetadata

public void setMetadata(Metadata meta)
                 throws FormatException

Description copied from interface: Writer

Provides this Writer with a Metadata object to use when interpreting Planes during calls to Writer.savePlane(int, long, io.scif.Plane).

NB: This method has accepts a general Metadata so that this signature can appear in the base interface for all Writers, but behavior if provided with a Metadata instance not associated with this Writer is undefined and should throw an exception.

Specified by:

setMetadata in interface Writer

Parameters:

meta - The Metadata to associate with this Writer.

Throws:

FormatException

getMetadata

public M getMetadata()

Description copied from interface: Writer

Gets the Metadata that will be used when saving planes.

Specified by:

getMetadata in interface TypedWriter<M extends TypedMetadata>

Specified by:

getMetadata in interface Writer

Returns:

The Metadata associated with this Writer.

setDest

public void setDest(org.scijava.io.location.Location fileName)
             throws FormatException,
                    IOException

Description copied from interface: Writer

Sets the source that will be written to during Writer.savePlane(int, long, io.scif.Plane) calls. NB: resets any configuration on this writer.

Specified by:

setDest in interface Writer

Parameters:

fileName - The Location to where the image source will be written.

Throws:

FormatException

IOException

setDest

public void setDest(org.scijava.io.handle.DataHandle<org.scijava.io.location.Location> out)
             throws FormatException,
                    IOException

Description copied from interface: Writer

Sets the source that will be written to during Writer.savePlane(int, long, io.scif.Plane) calls. NB: resets any configuration on this writer.

Specified by:

setDest in interface Writer

Parameters:

out - The image source to write to.

Throws:

FormatException

IOException

setDest

public void setDest(org.scijava.io.location.Location loc,
                    int imageIndex)
             throws FormatException,
                    IOException

Description copied from interface: Writer

As Writer.setDest(Location) with specification for source image index.

Specified by:

setDest in interface Writer

Parameters:

loc - The Location of an image source to be written.

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

Throws:

FormatException

IOException

setDest

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

Description copied from interface: Writer

As Writer.setDest(DataHandle), with specification for source image index.

Specified by:

setDest in interface Writer

Parameters:

out - The image source to write to.

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

Throws:

FormatException

IOException

setDest

public void setDest(org.scijava.io.location.Location loc,
                    SCIFIOConfig config)
             throws FormatException,
                    IOException

Description copied from interface: Writer

As Writer.setDest(Location) with specification for new configuration options.

Specified by:

setDest in interface Writer

Parameters:

loc - The Location of an image source to be written.

config - Configuration information to use for this write.

Throws:

FormatException

IOException

setDest

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

Description copied from interface: Writer

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

Specified by:

setDest in interface Writer

Parameters:

out - The image source to write to.

config - Configuration information to use for this write.

Throws:

FormatException

IOException

setDest

public void setDest(org.scijava.io.location.Location loc,
                    int imageIndex,
                    SCIFIOConfig config)
             throws FormatException,
                    IOException

Description copied from interface: Writer

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

Specified by:

setDest in interface Writer

Parameters:

loc - The Location of an image source to be written.

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

config - Configuration information to use for this write.

Throws:

FormatException

IOException

setDest

public void setDest(org.scijava.io.handle.DataHandle<org.scijava.io.location.Location> out,
                    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

Parameters:

out - 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

getHandle

public org.scijava.io.handle.DataHandle<org.scijava.io.location.Location> getHandle()

Description copied from interface: Writer

Retrieves a reference to the output source that will be written to during Writer.savePlane(int, long, io.scif.Plane) calls.

Specified by:

getHandle in interface Writer

Returns:

The DataHandle} associated with this Writer.

setColorModel

public void setColorModel(ColorModel cm)

Description copied from interface: Writer

Sets the color model.

NB: the color model should be set before the output destination.

Specified by:

setColorModel in interface Writer

getColorModel

public ColorModel getColorModel()

Description copied from interface: Writer

Gets the color model.

Specified by:

getColorModel in interface Writer

getCompressionTypes

public String[] getCompressionTypes()

Description copied from interface: Writer

Gets the available compression types.

Specified by:

getCompressionTypes in interface Writer

getFramesPerSecond

public int getFramesPerSecond()

Specified by:

getFramesPerSecond in interface Writer

Returns:

The current frames per second being used by the writer.

getCodecOptions

public CodecOptions getCodecOptions()

Specified by:

getCodecOptions in interface Writer

Returns:

CodecOptions used by this writer, if applicable.

writeSequential

public boolean writeSequential()

Specified by:

writeSequential in interface Writer

Returns:

True if this writer should output planes sequentially.

getValidBits

public int getValidBits()

Specified by:

getValidBits in interface Writer

Returns:

Number of valid bits per pixel.

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

isSupportedType

public boolean isSupportedType(int type,
                               String codec)

Description copied from interface: Writer

Checks if the given pixel type is supported.

Specified by:

isSupportedType in interface Writer

isSupportedCompression

public void isSupportedCompression(String compression)
                            throws FormatException

Description copied from interface: Writer

Checks if the given compression type is supported.

Specified by:

isSupportedCompression in interface Writer

Throws:

FormatException

setMetadata

public void setMetadata(M meta)
                 throws FormatException

Description copied from interface: TypedWriter

Generic-parameterized setMetadata method, using TypedMetadata to avoid type erasure conflicts with Writer.setMetadata(Metadata).

Specified by:

setMetadata in interface TypedWriter<M extends TypedMetadata>

Throws:

FormatException

See Also:

Parser.parse(Location, Metadata)

isInitialized

public boolean isInitialized(int imageIndex,
                             long planeIndex)

Specified by:

isInitialized in interface Writer

Returns:

True iff this writer is prepared to write the given plane of the given image index.

getCompression

public String getCompression()

Specified by:

getCompression in interface Writer

Returns:

The current compression being used by the writer, or null if not set.

close

public void close(boolean fileOnly)
           throws IOException

Description copied from interface: HasSource

Closes the image source(s) associated with this component, with a toggle to determine if the component itself is reset.

Specified by:

close in interface HasSource

Parameters:

fileOnly - - If true, only the associated source(s) are closed.

Throws:

IOException