de.unihalle.informatik.MiToBo.apps.neurites2D
Class NeuriteMolProfExtractor2D

java.lang.Object
  extended by de.unihalle.informatik.Alida.operator.ALDOperator
      extended by de.unihalle.informatik.MiToBo.core.operator.MTBOperator
          extended by de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteMolProfExtractor2D
All Implemented Interfaces:
de.unihalle.informatik.Alida.datatypes.ALDConfigurationValidator, de.unihalle.informatik.Alida.operator.events.ALDOperatorExecutionProgressEventListener, EventListener

@ALDAOperator(genericExecutionMode=NONE,
              level=STANDARD,
              allowBatchMode=false)
public class NeuriteMolProfExtractor2D
extends MTBOperator

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).

Author:
Birgit Moeller, Danny Misiak

Nested Class Summary
 
Nested classes/interfaces inherited from class de.unihalle.informatik.Alida.operator.ALDOperator
de.unihalle.informatik.Alida.operator.ALDOperator.HidingMode
 
Field Summary
 
Fields inherited from class de.unihalle.informatik.Alida.operator.ALDOperator
completeDAG, name, operatorExecutionEventlistenerList, portHashAccess, verbose, versionProvider
 
Constructor Summary
NeuriteMolProfExtractor2D()
          Standard constructor
NeuriteMolProfExtractor2D(MTBImage _moleculeImage, Integer[] _moleculeChannels, MTBNeurite2DSet _neuriteSet, Boolean _verbose)
          Constructor to create a new neurite profile extraction operator.
 
Method Summary
 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
readResolve
 
Methods inherited from class de.unihalle.informatik.Alida.operator.ALDOperator
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
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Constructor Detail

NeuriteMolProfExtractor2D

public NeuriteMolProfExtractor2D()
                          throws de.unihalle.informatik.Alida.exceptions.ALDOperatorException
Standard constructor

Throws:
de.unihalle.informatik.Alida.exceptions.ALDOperatorException

NeuriteMolProfExtractor2D

public NeuriteMolProfExtractor2D(MTBImage _moleculeImage,
                                 Integer[] _moleculeChannels,
                                 MTBNeurite2DSet _neuriteSet,
                                 Boolean _verbose)
                          throws de.unihalle.informatik.Alida.exceptions.ALDOperatorException
Constructor to create a new neurite profile extraction operator.

Parameters:
_moleculeImage - multichannel fluorescence image with stained molecules
_moleculeChannels - channles including molecule stains
_neuriteSet - set of MTBNeurite2D objects
_molecules -
_verbose - flag for standard console outputs
Throws:
de.unihalle.informatik.Alida.exceptions.ALDOperatorException
Method Detail

validateCustom

public void validateCustom()
                    throws de.unihalle.informatik.Alida.exceptions.ALDOperatorException
Custom validation of some input parameters.

Overrides:
validateCustom in class de.unihalle.informatik.Alida.operator.ALDOperator
Throws:
de.unihalle.informatik.Alida.exceptions.ALDOperatorException

getMoelculeImg

public MTBImage getMoelculeImg()
Get the input image with the fluorescence labeled molecules.

Returns:
Gray value molecule image.

getMoleculeChannles

public Integer[] getMoleculeChannles()
Get molecule channels, used for extraction.


getNeuriteSet

public MTBNeurite2DSet getNeuriteSet()
Get the input set of neurites.

Returns:
Neurite set.

getImageSizeX

public int getImageSizeX()
Get the image size in x-direction.

Returns:
Image size in x.

getImageSizeY

public int getImageSizeY()
Get the image size in y-direction.

Returns:
Image size in y.

getProfiles

public Vector<MTBNeurite2DProfileSet> getProfiles()
Get the resulting set of neurite profiles.

Returns:
Neurite profiles.

operate

protected void operate()
                throws de.unihalle.informatik.Alida.exceptions.ALDOperatorException
This method does the actual work.

Specified by:
operate in class de.unihalle.informatik.Alida.operator.ALDOperator
Throws:
de.unihalle.informatik.Alida.exceptions.ALDOperatorException


Copyright © 2010–2015 Martin Luther University Halle-Wittenberg. All rights reserved.