de.unihalle.informatik.MiToBo.apps.neurites2D

Class NeuriteParticleDetector2D

java.lang.Object

de.unihalle.informatik.Alida.operator.ALDOperator

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

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

All Implemented Interfaces:

de.unihalle.informatik.Alida.datatypes.ALDConfigurationValidator, de.unihalle.informatik.Alida.operator.events.ALDOperatorExecutionProgressEventListener, EventListener

@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, de.unihalle.informatik.Alida.operator.ALDOperator.HistoryConstructionMode

Field Summary

Fields

Modifier and Type	Field and Description
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 Integer	particleChannel Define extractor parameters.
private ParticleDetectorUWT2D	particleDetector

Fields inherited from class de.unihalle.informatik.Alida.operator.ALDOperator

completeDAG, name, operatorExecutionEventlistenerList, portHashAccess, verbose, versionProvider

Constructor Summary

Constructors

Constructor and Description
NeuriteParticleDetector2D() Standardconstructor.
NeuriteParticleDetector2D(Integer _particleChannel, ParticleDetectorUWT2D _particleDetector, MTBNeurite2DSet _neuriteSet, Boolean _verbose) Constructor.

Method Summary

Modifier and Type	Method and Description
MTBRegion2DSet	getDetectedParticles() Get regions of detected particles.
MTBNeurite2DSet	getNeuriteSet() Get the input set of neurites.
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

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, validateCustom, validateGeneric, writeHistory, writeHistory, writeHistory

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

particleChannel

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

Define extractor parameters.

particleDetector

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

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

Constructor Detail

NeuriteParticleDetector2D

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

Standardconstructor.

Throws:

de.unihalle.informatik.Alida.exceptions.ALDOperatorException

NeuriteParticleDetector2D

public NeuriteParticleDetector2D(Integer _particleChannel,
                                 ParticleDetectorUWT2D _particleDetector,
                                 MTBNeurite2DSet _neuriteSet,
                                 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

getParticleChannel

public Integer getParticleChannel()

Get image channel including particles.

getParticleDetector

public ParticleDetectorUWT2D getParticleDetector()

Get particle detector.

setParticleImage

public void setParticleImage(MTBImage particleImage)

Set particle image for particle detector.

getNeuriteSet

public MTBNeurite2DSet getNeuriteSet()

Get the input set of neurites.

setNeuriteSet

public void setNeuriteSet(MTBNeurite2DSet _neuriteSet)

Set the input set of neurites.

getDetectedParticles

public MTBRegion2DSet getDetectedParticles()

Get regions of detected particles.

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