de.unihalle.informatik.MiToBo.io.images

Class ImageReaderMTB

java.lang.Object

de.unihalle.informatik.Alida.operator.ALDOperator

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

de.unihalle.informatik.MiToBo.io.images.ImageReaderMTB

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 ImageReaderMTB
extends MTBOperator
implements loci.common.StatusReporter

Image reader operator to create MTBImage or ImagePlus objects from image files while reading and restoring image history from corresponding history files (.mph). This reader operator is based on Bio-Formats, thus the available formats depend on Bio-Formats (and its available extension).

Author:

Oliver Gress

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	ImageReaderMTB.OutImageType Specifies the image object that is constructed by the reader

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
protected de.unihalle.informatik.Alida.datatypes.ALDFileString	fileName
protected int	imageIndex
protected loci.formats.meta.IMetadata	omemeta
protected String	omexml
protected ImageReaderMTB.OutImageType	outImageType
protected loci.formats.IFormatReader	reader
protected ij.ImagePlus	resultImagePlus
protected MTBImage	resultMTBImage
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
ImageReaderMTB()
ImageReaderMTB(String filename) Constructor of an image reader instance by filename.

Method Summary

Modifier and Type	Method and Description
void	addStatusListener(loci.common.StatusListener listener)
String	getFileName() Get the filename of the image that has to be read.
int	getImageCount() Get the number of (multi-dimensional) images stored in the specified file.
String	getImageID(int imageIdx) Get the ID of the imageIdx-th image in the file, if available
String	getImageName(int imageIdx) Get the name of the imageIdx-th image in the file, if available
int	getIndexOfImageToRead() Get the index of the image that has to be read from the file.
ImageReaderMTB.OutImageType	getOutImageType() Get the type of image object that is created as result image.
ij.ImagePlus	getResultImagePlus() Get resulting image that was read from disk.
MTBImage	getResultMTBImage() Get resulting image that was read from disk.
protected void	initReader() Initialize the reader (this method is called in the constructor)
void	notifyListeners(loci.common.StatusEvent event)
protected void	operate()
protected ij.ImagePlus	readImagePlus(int imageIdx) Read image imageIdx from the specified file and return it as ImagePlus object.
protected MTBImage	readMTBImage(int imageIdx) Read image imageIdx from the specified file and return it as MTBImage object.
protected Object	readResolve() Init function for deserialized objects.
void	removeStatusListener(loci.common.StatusListener listener)
void	setFileName(String filename) Set the filename of the image that has to be read.
void	setIndexOfImageToRead(int imageIdx) Set the index of the image that has to be read from the file.
void	setOutImageType(ImageReaderMTB.OutImageType outtype) Set the type of image object that is created as result image.
protected void	setResultImagePlus(ij.ImagePlus img) Set resulting image
protected void	setResultMTBImage(MTBImage img) Set resulting image
void	validateCustom()

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

reader

protected transient loci.formats.IFormatReader reader

omexml

protected String omexml

omemeta

protected transient loci.formats.meta.IMetadata omemeta

imageIndex

@Parameter(label="Image index",
           required=true,
           direction=IN,
           mode=ADVANCED,
           dataIOOrder=2,
           description="Index of the image (aka series) in the file that has to be read")
protected int imageIndex

outImageType

@Parameter(label="Output image type",
           required=true,
           direction=IN,
           mode=STANDARD,
           dataIOOrder=3,
           description="Determines the image object class that is created as result image")
protected ImageReaderMTB.OutImageType outImageType

fileName

@Parameter(label="Filename",
           required=true,
           direction=IN,
           mode=STANDARD,
           dataIOOrder=1,
           description="Filename of the image to be read")
protected de.unihalle.informatik.Alida.datatypes.ALDFileString fileName

resultImagePlus

@Parameter(label="Result ImagePlus",
           required=false,
           direction=OUT,
           mode=STANDARD,
           dataIOOrder=2,
           description="Image that has been read from disk returned as ImagePlus")
protected transient ij.ImagePlus resultImagePlus

resultMTBImage

@Parameter(label="Result MTBImage",
           required=false,
           direction=OUT,
           mode=STANDARD,
           dataIOOrder=1,
           description="Image that has been read from disk returned as MTBImage")
protected transient MTBImage resultMTBImage

Constructor Detail

ImageReaderMTB

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

Throws:

de.unihalle.informatik.Alida.exceptions.ALDOperatorException

ImageReaderMTB

public ImageReaderMTB(String filename)
               throws de.unihalle.informatik.Alida.exceptions.ALDOperatorException,
                      loci.formats.FormatException,
                      IOException,
                      loci.common.services.DependencyException,
                      loci.common.services.ServiceException

Constructor of an image reader instance by filename.

Parameters:

filename -

Throws:

de.unihalle.informatik.Alida.exceptions.ALDOperatorException

loci.formats.FormatException

IOException

loci.common.services.DependencyException

loci.common.services.ServiceException

Method Detail

readResolve

protected Object readResolve()

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:

Initialized deserialized object.

operate

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

Specified by:

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

Throws:

de.unihalle.informatik.Alida.exceptions.ALDOperatorException

de.unihalle.informatik.Alida.exceptions.ALDProcessingDAGException

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

initReader

protected void initReader()
                   throws loci.formats.FormatException,
                          IOException,
                          loci.common.services.DependencyException,
                          loci.common.services.ServiceException

Initialize the reader (this method is called in the constructor)

Throws:

loci.formats.FormatException

IOException

loci.common.services.DependencyException

loci.common.services.ServiceException

readMTBImage

protected MTBImage readMTBImage(int imageIdx)
                         throws loci.formats.FormatException,
                                IOException,
                                IllegalArgumentException,
                                loci.common.services.DependencyException,
                                loci.common.services.ServiceException,
                                de.unihalle.informatik.Alida.exceptions.ALDOperatorException

Read image imageIdx from the specified file and return it as MTBImage object. Some formats can store a series of image, e.g. different experiment runs (not to confuse with a time series). The imageIdx specifies which image of a series has to be read.

Throws:

loci.formats.FormatException

IOException

IllegalArgumentException

loci.common.services.DependencyException

loci.common.services.ServiceException

de.unihalle.informatik.Alida.exceptions.ALDOperatorException

readImagePlus

protected ij.ImagePlus readImagePlus(int imageIdx)
                              throws loci.formats.FormatException,
                                     IOException,
                                     loci.common.services.DependencyException,
                                     loci.common.services.ServiceException,
                                     IllegalArgumentException,
                                     de.unihalle.informatik.Alida.exceptions.ALDOperatorException

Read image imageIdx from the specified file and return it as ImagePlus object. Some formats can store a series of image, e.g. different experiment runs (not to confuse with a time series). The imageIdx specifies which image of a series has to be read.

Throws:

loci.formats.FormatException

IOException

loci.common.services.DependencyException

loci.common.services.ServiceException

IllegalArgumentException

de.unihalle.informatik.Alida.exceptions.ALDOperatorException

setResultMTBImage

protected void setResultMTBImage(MTBImage img)

Set resulting image

setResultImagePlus

protected void setResultImagePlus(ij.ImagePlus img)

Set resulting image

getResultMTBImage

public MTBImage getResultMTBImage()

Get resulting image that was read from disk.

getResultImagePlus

public ij.ImagePlus getResultImagePlus()

Get resulting image that was read from disk.

setFileName

public void setFileName(String filename)
                 throws loci.formats.FormatException,
                        IOException,
                        loci.common.services.DependencyException,
                        loci.common.services.ServiceException

Set the filename of the image that has to be read.

Throws:

loci.formats.FormatException

IOException

loci.common.services.DependencyException

loci.common.services.ServiceException

getFileName

public String getFileName()

Get the filename of the image that has to be read.

setOutImageType

public void setOutImageType(ImageReaderMTB.OutImageType outtype)

Set the type of image object that is created as result image. Default is OutImageType.MTB_IMAGE

getOutImageType

public ImageReaderMTB.OutImageType getOutImageType()

Get the type of image object that is created as result image. Default is OutImageType.MTB_IMAGE

getImageCount

public int getImageCount()

Get the number of (multi-dimensional) images stored in the specified file.

getImageName

public String getImageName(int imageIdx)

Get the name of the imageIdx-th image in the file, if available

getImageID

public String getImageID(int imageIdx)

Get the ID of the imageIdx-th image in the file, if available

setIndexOfImageToRead

public void setIndexOfImageToRead(int imageIdx)

Set the index of the image that has to be read from the file. Some files may contain more than one multi-dimensional image. Default is 0.

getIndexOfImageToRead

public int getIndexOfImageToRead()

Get the index of the image that has to be read from the file. Some files may contain more than one multi-dimensional image. Default is 0.

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