de.unihalle.informatik.MiToBo.apps.neurites2D
Class NeuriteParticleDetector2D

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.NeuriteParticleDetector2D
All Implemented Interfaces:
de.unihalle.informatik.Alida.datatypes.ALDConfigurationValidator

@ALDAOperator(genericExecutionMode=ALL,
              level=APPLICATION,
              allowBatchMode=true)
public class NeuriteParticleDetector2D
extends MTBOperator

This operator detects particles of a neuron image, for example from FISH analysis. Particles in the complete image or inside the neurite regions of a given neurite set can be detected.

Author:
Danny Misiak
See Also:
ParticleDetectorUWT2D

Nested Class Summary
 
Nested classes/interfaces inherited from class de.unihalle.informatik.Alida.operator.ALDOperator
de.unihalle.informatik.Alida.operator.ALDOperator.HidingMode
 
Field Summary
private  MTBRegion2DSet detectedParticles
           
private  MTBNeurite2DSet neuriteSet
          Set of neurite regions for detecting particle only inside these regions, an be null for detection all particles in the complete image
private  java.lang.Integer particleChannel
          Define extractor parameters.
private  ParticleDetectorUWT2D particleDetector
           
 
Fields inherited from class de.unihalle.informatik.Alida.operator.ALDOperator
completeDAG, name, portHashAccess, verbose, versionProvider
 
Constructor Summary
NeuriteParticleDetector2D()
          Standardconstructor.
NeuriteParticleDetector2D(java.lang.Integer _particleChannel, ParticleDetectorUWT2D _particleDetector, MTBNeurite2DSet _neuriteSet, java.lang.Boolean _verbose)
          Constructor.
 
Method Summary
 MTBRegion2DSet getDetectedParticles()
          Get regions of detected particles.
 MTBNeurite2DSet getNeuriteSet()
          Get the input set of neurites.
 java.lang.Integer getParticleChannel()
          Get image channel including particles.
 ParticleDetectorUWT2D getParticleDetector()
          Get particle detector.
protected  void operate()
           
 void setNeuriteSet(MTBNeurite2DSet _neuriteSet)
          Set the input set of neurites.
 void setParticleImage(MTBImage particleImage)
          Set particle image for particle detector.
 
Methods inherited from class de.unihalle.informatik.MiToBo.core.operator.MTBOperator
readResolve
 
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, validateCustom, 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

detectedParticles

@Parameter(label="Detected Particle Regions",
           direction=OUT,
           required=true,
           description="Regions of detected particles.")
private transient MTBRegion2DSet detectedParticles

neuriteSet

private transient MTBNeurite2DSet neuriteSet
Set of neurite regions for detecting particle only inside these regions, an be null for detection all particles in the complete image


particleChannel

@Parameter(label="Particle Channel",
           direction=IN,
           required=true,
           description="Image channel including particles (1 labels first channel).",
           mode=STANDARD,
           dataIOOrder=0)
private java.lang.Integer particleChannel
Define extractor parameters.


particleDetector

@Parameter(label="Particle Detector",
           required=true,
           direction=IN,
           description="Particle detector.",
           mode=STANDARD,
           dataIOOrder=1)
private ParticleDetectorUWT2D particleDetector
Constructor Detail

NeuriteParticleDetector2D

public NeuriteParticleDetector2D()
                          throws de.unihalle.informatik.Alida.exceptions.ALDOperatorException
Standardconstructor.

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

NeuriteParticleDetector2D

public NeuriteParticleDetector2D(java.lang.Integer _particleChannel,
                                 ParticleDetectorUWT2D _particleDetector,
                                 MTBNeurite2DSet _neuriteSet,
                                 java.lang.Boolean _verbose)
                          throws de.unihalle.informatik.Alida.exceptions.ALDOperatorException
Constructor.

Parameters:
_particleChannel - channel number of particles in the multi-fluorescence image (1 labels first channel)
_particleDetector - detector for particle detection
_neuriteSet - set of neurite regions for detecting particle only inside these regions, can be null for detection all particles in the complete image
_verbose - flag for standard console outputs
Throws:
de.unihalle.informatik.Alida.exceptions.ALDOperatorException
Method Detail

getDetectedParticles

public MTBRegion2DSet getDetectedParticles()
Get regions of detected particles.


getNeuriteSet

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


getParticleChannel

public java.lang.Integer getParticleChannel()
Get image channel including particles.


getParticleDetector

public ParticleDetectorUWT2D getParticleDetector()
Get particle detector.


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

setNeuriteSet

public void setNeuriteSet(MTBNeurite2DSet _neuriteSet)
Set the input set of neurites.


setParticleImage

public void setParticleImage(MTBImage particleImage)
Set particle image for particle detector.