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java.lang.Objectde.unihalle.informatik.Alida.operator.ALDOperator
de.unihalle.informatik.MiToBo.core.operator.MTBOperator
de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteMolProfExtractor2D
@ALDAOperator(genericExecutionMode=NONE, level=STANDARD, allowBatchMode=false) public class NeuriteMolProfExtractor2D
The Neurite Molecular Profile Extractor 2D application offers advanced functionality to extract molecular intensity profiles of multichannel fluorescence images along detected neurite regions. The profiles are stored in a vector of profile sets. Each set includes the profiles for one neurite region over all protein stains (image channels).
Nested Class Summary |
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Nested classes/interfaces inherited from class de.unihalle.informatik.Alida.operator.ALDOperator |
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de.unihalle.informatik.Alida.operator.ALDOperator.HidingMode |
Field Summary |
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Fields inherited from class de.unihalle.informatik.Alida.operator.ALDOperator |
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completeDAG, name, operatorExecutionEventlistenerList, portHashAccess, verbose, versionProvider |
Constructor Summary | |
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NeuriteMolProfExtractor2D()
Standard constructor |
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NeuriteMolProfExtractor2D(MTBImage _moleculeImage,
Integer[] _moleculeChannels,
MTBNeurite2DSet _neuriteSet,
Boolean _verbose)
Constructor to create a new neurite profile extraction operator. |
Method Summary | |
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int |
getImageSizeX()
Get the image size in x-direction. |
int |
getImageSizeY()
Get the image size in y-direction. |
MTBImage |
getMoelculeImg()
Get the input image with the fluorescence labeled molecules. |
Integer[] |
getMoleculeChannles()
Get molecule channels, used for extraction. |
MTBNeurite2DSet |
getNeuriteSet()
Get the input set of neurites. |
Vector<MTBNeurite2DProfileSet> |
getProfiles()
Get the resulting set of neurite profiles. |
protected void |
operate()
This method does the actual work. |
void |
validateCustom()
Custom validation of some input parameters. |
Methods inherited from class de.unihalle.informatik.MiToBo.core.operator.MTBOperator |
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readResolve |
Methods inherited from class de.unihalle.informatik.Alida.operator.ALDOperator |
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addOperatorExecutionProgressEventListener, fieldContained, fireOperatorExecutionProgressEvent, getALDPortHashAccessKey, getConstructionMode, getHidingMode, getInInoutNames, getInInoutNames, getInNames, getInOutNames, getMissingRequiredInputs, getName, getNumParameters, getOutInoutNames, getOutNames, getParameter, getParameterDescriptor, getParameterNames, getSupplementalNames, getVerbose, getVersion, handleOperatorExecutionProgressEvent, isConfigured, print, print, print, printInterface, printInterface, readHistory, reinitializeParameterDescriptors, removeOperatorExecutionProgressEventListener, runOp, runOp, runOp, setConstructionMode, setHidingMode, setName, setParameter, setVerbose, toStringVerbose, unconfiguredItems, validate, validateGeneric, writeHistory, writeHistory, writeHistory |
Methods inherited from class java.lang.Object |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Constructor Detail |
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public NeuriteMolProfExtractor2D() throws de.unihalle.informatik.Alida.exceptions.ALDOperatorException
de.unihalle.informatik.Alida.exceptions.ALDOperatorException
public NeuriteMolProfExtractor2D(MTBImage _moleculeImage, Integer[] _moleculeChannels, MTBNeurite2DSet _neuriteSet, Boolean _verbose) throws de.unihalle.informatik.Alida.exceptions.ALDOperatorException
_moleculeImage
- multichannel fluorescence image with stained molecules_moleculeChannels
- channles including molecule stains_neuriteSet
- set of MTBNeurite2D objects_molecules
- _verbose
- flag for standard console outputs
de.unihalle.informatik.Alida.exceptions.ALDOperatorException
Method Detail |
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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
public MTBImage getMoelculeImg()
public Integer[] getMoleculeChannles()
public MTBNeurite2DSet getNeuriteSet()
public int getImageSizeX()
public int getImageSizeY()
public Vector<MTBNeurite2DProfileSet> getProfiles()
protected void operate() throws de.unihalle.informatik.Alida.exceptions.ALDOperatorException
operate
in class de.unihalle.informatik.Alida.operator.ALDOperator
de.unihalle.informatik.Alida.exceptions.ALDOperatorException
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