de.unihalle.informatik.MiToBo.io.images

Class ImageWriterMTB

java.lang.Object

de.unihalle.informatik.Alida.operator.ALDOperator

de.unihalle.informatik.MiToBo.core.operator.MTBOperator

de.unihalle.informatik.MiToBo.io.images.ImageWriterMTB

All Implemented Interfaces:

de.unihalle.informatik.Alida.datatypes.ALDConfigurationValidator, de.unihalle.informatik.Alida.operator.events.ALDOperatorExecutionProgressEventListener, EventListener, loci.common.StatusReporter

@ALDAOperator(genericExecutionMode=ALL,
              level=APPLICATION)
public class ImageWriterMTB
extends MTBOperator
implements loci.common.StatusReporter

Image writer operator to store MTBImage or ImagePlus to disk along with the image history (.mph) file. This writer operator is based on Bio-Formats, thus the available formats depend on Bio-Formats (and its available extension). The format is determined by the given filename extension. Different formats allow different options, e.g. compression of images or framerate of movies. If options are set by the available setter-methods that are not applicable to the current format writer, the options are simply ignored.

The ImageWriterMTB.runOp(..) throws a special OverwriteException in case that the specified file already exists, but the overwrite-flag is set to false.

Author:

Oliver Gress

Nested Class Summary

Nested classes/interfaces inherited from class de.unihalle.informatik.Alida.operator.ALDOperator

de.unihalle.informatik.Alida.operator.ALDOperator.HidingMode, de.unihalle.informatik.Alida.operator.ALDOperator.HistoryConstructionMode

Field Summary

Fields

Modifier and Type	Field and Description
private Integer	codec
private String	compression
private de.unihalle.informatik.Alida.datatypes.ALDFileString	fileName
private Integer	fps
private boolean	ignoreInvalidStackSpec
private ij.ImagePlus	inputImagePlus
private MTBImage	inputMTBImage
private boolean	overwrite
private Integer	quality
private Vector<loci.common.StatusListener>	statusListeners

Fields inherited from class de.unihalle.informatik.Alida.operator.ALDOperator

completeDAG, name, operatorExecutionEventlistenerList, portHashAccess, verbose, versionProvider

Constructor Summary

Constructors

Constructor and Description
ImageWriterMTB()
ImageWriterMTB(ij.ImagePlus imp, String filename) Image file output operator for ImagePlus objects.
ImageWriterMTB(MTBImage img, String filename) Image file output operator for MTBImage objects.

Method Summary

Modifier and Type	Method and Description
void	addStatusListener(loci.common.StatusListener listener)
HashMap<Integer,String>	getAvailableCodecs() Return available codecs for movie writers (see Bio-Formats package loci.formats.out.QTWriter) represented by a hashmap.
String[]	getAvailableCompression() Get the available compression methods for the specified file format.
HashMap<Integer,String>	getAvailableQualities() Return available qualities for quicktime movie writers (see Bio-Formats package loci.formats.out.QTWriter) represented by a hashmap.
Integer	getCodec() Get the codec (quicktime only)
String	getCompression() Get the compression type
String	getFileName() Get image filename
Integer	getFps() Get the frames per second for movie writers (*.avi,*.mov).
boolean	getIgnoreInvalidStackSpecification() Get the flag to ignore an invalid stack specification.
ij.ImagePlus	getInputImagePlus() Get ImagePlus that has to be stored to disk
MTBImage	getInputMTBImage() Get MTBImage that has to be stored to disk
boolean	getOverwrite() Get the overwrite permission flag
Integer	getQuality() Get the quality (quicktime only)
void	notifyListeners(loci.common.StatusEvent event)
protected void	operate()
protected Object	readResolve() Init function for deserialized objects.
void	removeStatusListener(loci.common.StatusListener listener)
void	setCodec(Integer codec) Set the codec (quicktime only).
void	setCompression(String compression) Set the compression type
void	setFileName(String filename) Set image filename
void	setFps(Integer fps) Set the frames per second for movie writers (*.avi,*.mov).
void	setIgnoreInvalidStackSpecification(boolean ignore) Set the flag to ignore an invalid stack specification.
void	setInputImagePlus(ij.ImagePlus imp) Set ImagePlus to store to disk
void	setInputMTBImage(MTBImage img) Set MTBImage to store to disk
void	setOverwrite(boolean overwrite) Set the overwrite permission flag
void	setQuality(Integer quality) Set the quality (quicktime only).
void	validateCustom()
protected void	writeImagePlus(String filename, ij.ImagePlus imp) Write ImagePlus to disk
protected void	writeMTBImage(String filename, MTBImage img) Write an MTBImage to disk

Methods inherited from class de.unihalle.informatik.Alida.operator.ALDOperator

addOperatorExecutionProgressEventListener, addParameter, addParameter, addParameterUnconditioned, fieldContained, fireOperatorExecutionProgressEvent, getALDPortHashAccessKey, getConstructionMode, getDocumentation, getHidingMode, getInactiveParameterNames, getInInoutNames, getInInoutNames, getInNames, getInOutNames, getMissingRequiredInputs, getName, getNumParameters, getOutInoutNames, getOutNames, getParameter, getParameterDescriptor, getParameterDescriptorUnconditioned, getParameterNames, getParameterUnconditioned, getSupplementalNames, getVerbose, getVersion, handleOperatorExecutionProgressEvent, hasInOutParameters, hasParameter, isAnnotatedParameter, isConfigured, print, print, print, printInterface, printInterface, readHistory, reinitializeParameterDescriptors, removeOperatorExecutionProgressEventListener, removeParameter, runOp, runOp, runOp, setConstructionMode, setConstructionMode, setConstructionMode, setHidingMode, setName, setParameter, setParameterUnconditioned, setVerbose, toStringVerbose, unconfiguredItems, validate, validateGeneric, writeHistory, writeHistory, writeHistory

Methods inherited from class java.lang.Object

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

Field Detail

statusListeners

private transient Vector<loci.common.StatusListener> statusListeners

compression

@Parameter(label="Image compression",
           required=false,
           direction=IN,
           mode=ADVANCED,
           dataIOOrder=6,
           description="Image compression")
private String compression

overwrite

@Parameter(label="overwrite",
           required=true,
           direction=IN,
           mode=STANDARD,
           dataIOOrder=4,
           description="Overwrite permission flag")
private boolean overwrite

codec

@Parameter(label="Video codec",
           required=false,
           direction=IN,
           mode=ADVANCED,
           dataIOOrder=8,
           description="Video codec (quicktime only)")
private Integer codec

fps

@Parameter(label="Fps",
           required=false,
           direction=IN,
           mode=ADVANCED,
           dataIOOrder=7,
           description="Frames per second for movies")
private Integer fps

ignoreInvalidStackSpec

@Parameter(label="Ignore stack specifications",
           required=true,
           direction=IN,
           mode=ADVANCED,
           dataIOOrder=5,
           description="Flag to ignore an invalid specification of the stack")
private boolean ignoreInvalidStackSpec

quality

@Parameter(label="Video quality",
           required=false,
           direction=IN,
           mode=ADVANCED,
           dataIOOrder=9,
           description="Video quality (quicktime only)")
private Integer quality

fileName

@Parameter(label="Filename",
           required=true,
           direction=IN,
           mode=STANDARD,
           dataIOOrder=3,
           description="Image filename")
private de.unihalle.informatik.Alida.datatypes.ALDFileString fileName

inputMTBImage

@Parameter(label="Input MTBImage",
           required=false,
           direction=IN,
           mode=STANDARD,
           dataIOOrder=1,
           description="MTBImage to save")
private transient MTBImage inputMTBImage

inputImagePlus

@Parameter(label="Input ImagePlus",
           required=false,
           direction=IN,
           mode=STANDARD,
           dataIOOrder=2,
           description="ImagePlus to save")
private transient ij.ImagePlus inputImagePlus

Constructor Detail

ImageWriterMTB

public ImageWriterMTB()
               throws de.unihalle.informatik.Alida.exceptions.ALDOperatorException

Throws:

de.unihalle.informatik.Alida.exceptions.ALDOperatorException

ImageWriterMTB

public ImageWriterMTB(MTBImage img,
                      String filename)
               throws de.unihalle.informatik.Alida.exceptions.ALDOperatorException

Image file output operator for MTBImage objects.

Parameters:

img - image to write to disk

filename - filename to write the image to. The extension specifies the output format.

Throws:

de.unihalle.informatik.Alida.exceptions.ALDOperatorException

ImageWriterMTB

public ImageWriterMTB(ij.ImagePlus imp,
                      String filename)
               throws de.unihalle.informatik.Alida.exceptions.ALDOperatorException

Image file output operator for ImagePlus objects.

Parameters:

imp - image to write to disk

filename - filename to write the image to. The extension specifies the output format.

Throws:

de.unihalle.informatik.Alida.exceptions.ALDOperatorException

Method Detail

operate

protected void operate()
                throws de.unihalle.informatik.Alida.exceptions.ALDOperatorException,
                       de.unihalle.informatik.Alida.exceptions.ALDProcessingDAGException,
                       OverwriteException

Specified by:

operate in class de.unihalle.informatik.Alida.operator.ALDOperator

Throws:

de.unihalle.informatik.Alida.exceptions.ALDOperatorException

de.unihalle.informatik.Alida.exceptions.ALDProcessingDAGException

OverwriteException

validateCustom

public void validateCustom()
                    throws de.unihalle.informatik.Alida.exceptions.ALDOperatorException

Overrides:

validateCustom in class de.unihalle.informatik.Alida.operator.ALDOperator

Throws:

de.unihalle.informatik.Alida.exceptions.ALDOperatorException

writeMTBImage

protected void writeMTBImage(String filename,
                             MTBImage img)
                      throws loci.common.services.DependencyException,
                             loci.common.services.ServiceException,
                             de.unihalle.informatik.Alida.exceptions.ALDOperatorException,
                             RuntimeException,
                             loci.formats.FormatException,
                             IOException,
                             ome.xml.model.enums.EnumerationException,
                             de.unihalle.informatik.Alida.exceptions.ALDProcessingDAGException

Write an MTBImage to disk

Throws:

loci.common.services.DependencyException

loci.common.services.ServiceException

de.unihalle.informatik.Alida.exceptions.ALDOperatorException

RuntimeException

loci.formats.FormatException

IOException

ome.xml.model.enums.EnumerationException

de.unihalle.informatik.Alida.exceptions.ALDProcessingDAGException

writeImagePlus

protected void writeImagePlus(String filename,
                              ij.ImagePlus imp)
                       throws RuntimeException,
                              loci.formats.FormatException,
                              IOException,
                              loci.common.services.DependencyException,
                              loci.common.services.ServiceException,
                              ome.xml.model.enums.EnumerationException,
                              de.unihalle.informatik.Alida.exceptions.ALDOperatorException,
                              de.unihalle.informatik.Alida.exceptions.ALDProcessingDAGException

Write ImagePlus to disk

Throws:

RuntimeException

loci.formats.FormatException

IOException

loci.common.services.DependencyException

loci.common.services.ServiceException

ome.xml.model.enums.EnumerationException

de.unihalle.informatik.Alida.exceptions.ALDOperatorException

de.unihalle.informatik.Alida.exceptions.ALDProcessingDAGException

getAvailableCompression

public String[] getAvailableCompression()
                                 throws loci.formats.FormatException

Get the available compression methods for the specified file format. Returns null if no compression options are available or the filename has not been specified yet.

Throws:

loci.formats.FormatException

getAvailableCodecs

public HashMap<Integer,String> getAvailableCodecs()
                                           throws loci.formats.FormatException

Return available codecs for movie writers (see Bio-Formats package loci.formats.out.QTWriter) represented by a hashmap. The key is the integer codec ID and the value a string with the codec's name. Only quicktime writers have the codec option, for any other writers (.avi or any non-movie format), this method returns null. This method will also return null, if the filename has not been specified yet.

Throws:

loci.formats.FormatException

getAvailableQualities

public HashMap<Integer,String> getAvailableQualities()
                                              throws loci.formats.FormatException

Return available qualities for quicktime movie writers (see Bio-Formats package loci.formats.out.QTWriter) represented by a hashmap. The key is the integer quality ID and the value a string specifying the quality. Only quicktime writers have this option, for any other writers (.avi or any non-movie format), this method returns null. This method will also return null, if the filename has not been specified yet.

Throws:

loci.formats.FormatException

setInputMTBImage

public void setInputMTBImage(MTBImage img)

Set MTBImage to store to disk

getInputMTBImage

public MTBImage getInputMTBImage()

Get MTBImage that has to be stored to disk

setInputImagePlus

public void setInputImagePlus(ij.ImagePlus imp)

Set ImagePlus to store to disk

getInputImagePlus

public ij.ImagePlus getInputImagePlus()

Get ImagePlus that has to be stored to disk

setFileName

public void setFileName(String filename)

Set image filename

getFileName

public String getFileName()

Get image filename

setCompression

public void setCompression(String compression)

Set the compression type

getCompression

public String getCompression()
                      throws de.unihalle.informatik.Alida.exceptions.ALDOperatorException

Get the compression type

Throws:

de.unihalle.informatik.Alida.exceptions.ALDOperatorException

setQuality

public void setQuality(Integer quality)
                throws loci.formats.FormatException

Set the quality (quicktime only). If the writer is not quicktime, the parameter is not assigned.

Parameters:

quality - quicktime movie quality ID (see Bio-Formats package loci.formats.out.QTWriter)

Throws:

loci.formats.FormatException

getQuality

public Integer getQuality()

Get the quality (quicktime only)

Returns:

quicktime movie quality ID(see Bio-Formats package loci.formats.out.QTWriter) or null

setCodec

public void setCodec(Integer codec)
              throws loci.formats.FormatException

Set the codec (quicktime only). If the writer is not quicktime, the parameter is not assigned.

Parameters:

codec - the quicktime codec ID (see Bio-Formats package loci.formats.out.QTWriter)

Throws:

loci.formats.FormatException

getCodec

public Integer getCodec()

Get the codec (quicktime only)

Returns:

quicktime movie codec ID (see Bio-Formats package loci.formats.out.QTWriter) or null

setFps

public void setFps(Integer fps)
            throws loci.formats.FormatException

Set the frames per second for movie writers (*.avi,*.mov). If the filename has not been specified yet or the writer is not a movie writer, the parameter is not assigned!

Parameters:

fps - frames per second of the written movie file (fps must be larger 0, otherwise validation fails)

Throws:

loci.formats.FormatException

getFps

public Integer getFps()

Get the frames per second for movie writers (*.avi,*.mov). Null for non-movie writers

Returns:

frames per second or null

setOverwrite

public void setOverwrite(boolean overwrite)

Set the overwrite permission flag

getOverwrite

public boolean getOverwrite()

Get the overwrite permission flag

setIgnoreInvalidStackSpecification

public void setIgnoreInvalidStackSpecification(boolean ignore)

Set the flag to ignore an invalid stack specification. This might happen if slices are added or removed from an image stack, then the stack size does not match the product of size in Z, T and C dimension. If the flag is set to 'ignore'(true), then the image stack is simply written as a stack, not a hyperstack. Default is false.

getIgnoreInvalidStackSpecification

public boolean getIgnoreInvalidStackSpecification()

Get the flag to ignore an invalid stack specification. See the setIgnoreInvalidStackSpecification(.)-method for more explanation

addStatusListener

public void addStatusListener(loci.common.StatusListener listener)

Specified by:

addStatusListener in interface loci.common.StatusReporter

notifyListeners

public void notifyListeners(loci.common.StatusEvent event)

Specified by:

notifyListeners in interface loci.common.StatusReporter

removeStatusListener

public void removeStatusListener(loci.common.StatusListener listener)

Specified by:

removeStatusListener in interface loci.common.StatusReporter

readResolve

protected Object readResolve()

Description copied from class: MTBOperator

Init function for deserialized objects.

This function is called on an instance of this class being deserialized from file, prior to handing the instance over to the user. It takes care of a proper initialization of transient member variables as they are not initialized to the default values during deserialization.

Overrides:

readResolve in class MTBOperator

Returns:

Updated deserialized object.