|
||||||||
PREV CLASS NEXT CLASS | FRAMES NO FRAMES | |||||||
SUMMARY: NESTED | FIELD | CONSTR | METHOD | DETAIL: FIELD | CONSTR | METHOD |
java.lang.Objectde.unihalle.informatik.Alida.operator.ALDOperator
de.unihalle.informatik.MiToBo.core.operator.MTBOperator
de.unihalle.informatik.MiToBo.io.images.ImageReaderMTB
@ALDAOperator(genericExecutionMode=ALL, level=APPLICATION) public class ImageReaderMTB
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).
Nested Class Summary | |
---|---|
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 |
Field Summary | |
---|---|
protected de.unihalle.informatik.Alida.datatypes.ALDFileString |
fileName
|
protected int |
imageIndex
|
protected loci.formats.meta.IMetadata |
omemeta
|
protected java.lang.String |
omexml
|
protected ImageReaderMTB.OutImageType |
outImageType
|
protected loci.formats.IFormatReader |
reader
|
protected ij.ImagePlus |
resultImagePlus
|
protected MTBImage |
resultMTBImage
|
private java.util.Vector<loci.common.StatusListener> |
statusListeners
|
Fields inherited from class de.unihalle.informatik.Alida.operator.ALDOperator |
---|
completeDAG, name, portHashAccess, verbose, versionProvider |
Constructor Summary | |
---|---|
ImageReaderMTB()
|
|
ImageReaderMTB(java.lang.String filename)
Constructor of an image reader instance by filename. |
Method Summary | |
---|---|
void |
addStatusListener(loci.common.StatusListener listener)
|
java.lang.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. |
java.lang.String |
getImageID(int imageIdx)
Get the ID of the imageIdx-th image in the file, if available |
java.lang.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 java.lang.Object |
readResolve()
Init function for deserialized objects. |
void |
removeStatusListener(loci.common.StatusListener listener)
|
void |
setFileName(java.lang.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 |
---|
deserializeFromXmlFile, fieldContained, getALDPortHashAccessKey, getConstructionMode, getInInoutNames, getInInoutNames, getInNames, getInOutNames, getMissingRequiredInputs, getName, getNumParameters, getOutInoutNames, getOutNames, getParameter, getParameterDescriptor, getParameterNames, getSupplementalNames, getVerbose, getVersion, isConfigured, parametersToXmlObject, print, print, print, printInterface, printInterface, readHistory, reinitializeParameterDescriptors, runOp, runOp, runOp, serializeToXmlFile, setConstructionMode, setName, setParameter, setParametersFromXml, setParametersFromXml, setVerbose, toStringVerbose, unconfiguredItems, validate, validateGeneric, writeHistory, writeHistory, writeHistory, writeParametersToXml |
Methods inherited from class java.lang.Object |
---|
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Field Detail |
---|
@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
@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
protected transient loci.formats.meta.IMetadata omemeta
protected java.lang.String omexml
@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
protected transient loci.formats.IFormatReader reader
@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
@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
private transient java.util.Vector<loci.common.StatusListener> statusListeners
Constructor Detail |
---|
public ImageReaderMTB() throws de.unihalle.informatik.Alida.exceptions.ALDOperatorException
de.unihalle.informatik.Alida.exceptions.ALDOperatorException
public ImageReaderMTB(java.lang.String filename) throws de.unihalle.informatik.Alida.exceptions.ALDOperatorException, loci.formats.FormatException, java.io.IOException, loci.common.services.DependencyException, loci.common.services.ServiceException
filename
-
de.unihalle.informatik.Alida.exceptions.ALDOperatorException
loci.formats.FormatException
java.io.IOException
loci.common.services.DependencyException
loci.common.services.ServiceException
Method Detail |
---|
public void addStatusListener(loci.common.StatusListener listener)
addStatusListener
in interface loci.common.StatusReporter
public java.lang.String getFileName()
public int getImageCount()
public java.lang.String getImageID(int imageIdx)
public java.lang.String getImageName(int imageIdx)
public int getIndexOfImageToRead()
public ImageReaderMTB.OutImageType getOutImageType()
public ij.ImagePlus getResultImagePlus()
public MTBImage getResultMTBImage()
protected void initReader() throws loci.formats.FormatException, java.io.IOException, loci.common.services.DependencyException, loci.common.services.ServiceException
loci.formats.FormatException
java.io.IOException
loci.common.services.DependencyException
loci.common.services.ServiceException
public void notifyListeners(loci.common.StatusEvent event)
notifyListeners
in interface loci.common.StatusReporter
protected void operate() throws de.unihalle.informatik.Alida.exceptions.ALDOperatorException, de.unihalle.informatik.Alida.exceptions.ALDProcessingDAGException
operate
in class de.unihalle.informatik.Alida.operator.ALDOperator
de.unihalle.informatik.Alida.exceptions.ALDOperatorException
de.unihalle.informatik.Alida.exceptions.ALDProcessingDAGException
protected ij.ImagePlus readImagePlus(int imageIdx) throws loci.formats.FormatException, java.io.IOException, loci.common.services.DependencyException, loci.common.services.ServiceException, java.lang.IllegalArgumentException, de.unihalle.informatik.Alida.exceptions.ALDOperatorException
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.
loci.formats.FormatException
java.io.IOException
loci.common.services.DependencyException
loci.common.services.ServiceException
java.lang.IllegalArgumentException
de.unihalle.informatik.Alida.exceptions.ALDOperatorException
protected MTBImage readMTBImage(int imageIdx) throws loci.formats.FormatException, java.io.IOException, java.lang.IllegalArgumentException, loci.common.services.DependencyException, loci.common.services.ServiceException, de.unihalle.informatik.Alida.exceptions.ALDOperatorException
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.
loci.formats.FormatException
java.io.IOException
java.lang.IllegalArgumentException
loci.common.services.DependencyException
loci.common.services.ServiceException
de.unihalle.informatik.Alida.exceptions.ALDOperatorException
protected java.lang.Object readResolve()
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.
readResolve
in class MTBOperator
public void removeStatusListener(loci.common.StatusListener listener)
removeStatusListener
in interface loci.common.StatusReporter
public void setFileName(java.lang.String filename) throws loci.formats.FormatException, java.io.IOException, loci.common.services.DependencyException, loci.common.services.ServiceException
loci.formats.FormatException
java.io.IOException
loci.common.services.DependencyException
loci.common.services.ServiceException
public void setIndexOfImageToRead(int imageIdx)
public void setOutImageType(ImageReaderMTB.OutImageType outtype)
protected void setResultImagePlus(ij.ImagePlus img)
protected void setResultMTBImage(MTBImage img)
public void validateCustom() throws de.unihalle.informatik.Alida.exceptions.ALDOperatorException
validateCustom
in class de.unihalle.informatik.Alida.operator.ALDOperator
de.unihalle.informatik.Alida.exceptions.ALDOperatorException
|
||||||||
PREV CLASS NEXT CLASS | FRAMES NO FRAMES | |||||||
SUMMARY: NESTED | FIELD | CONSTR | METHOD | DETAIL: FIELD | CONSTR | METHOD |