de.unihalle.informatik.MiToBo.apps.particles2D

Class MultiChannelParticleAnalyzer2D

java.lang.Object

de.unihalle.informatik.Alida.operator.ALDOperator

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

de.unihalle.informatik.MiToBo.apps.particles2D.MultiChannelParticleAnalyzer2D

All Implemented Interfaces:

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

@ALDAOperator(genericExecutionMode=ALL,
              level=APPLICATION)
public class MultiChannelParticleAnalyzer2D
extends MTBOperator

Operator for detecting sub-cellular structures in a given image.

This operator allows to configure a particle detector for each channel of the image separately. If a proper nucleus channel is given that one is skipped. The first detector in the vector of detectors is applied to the first non-nucleus channel, the second to the second, etc. It is important that for all channels to be processed detectors are provided.

Author:

moeller

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	MultiChannelParticleAnalyzer2D.ResultImageMode Display mode of the result image.

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 MTBImageByte	excludeMask Optional mask to exclude particles in certain regions.
private int	height Height of the processed image.
private MTBImage	inImg Multi-channel input image to be processed.
private SegResultEnums.MeasureUnit	measureUnits Units for measurements.
private ParticleDetector	particleDetector_1
private ParticleDetector	particleDetector_2
private ParticleDetector	particleDetector_3
private ParticleDetector	particleDetector_4
private ParticleDetector	particleDetector_5
private SegResult_ParticlesMultiChannel	resultData Vector of result data objects.
private MultiChannelParticleAnalyzer2D.ResultImageMode	resultDisplayMode Mode of how to display result image.
private MTBImageRGB	resultImg Stack with result overlays corresponding to channels.
private int	stackSize Number of channels in image.
private int	width Width of the processed image.

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

completeDAG, name, operatorExecutionEventlistenerList, portHashAccess, verbose, versionProvider

Constructor Summary

Constructors

Constructor and Description
MultiChannelParticleAnalyzer2D() Empty constructor.
MultiChannelParticleAnalyzer2D(MTBImage image, Vector<ParticleDetector> pOps) Default constructor.

Method Summary

Modifier and Type	Method and Description
Vector<ParticleDetector>	getDetectors() Get a reference to configured detectors' vector.
SegResult_ParticlesMultiChannel	getResultDataArray() Returns extracted result data.
MTBImageRGB	getResultImage() Returns result image, i.e. the segmentation mask.
protected void	operate()
private void	prepareResultImage() Prepare visualization of result data by overlay on input image.
private MTBImageRGB	prepareResultImageStack(Vector<MTBImage> imgvec) Initialize result image stack.
void	setInputImage(MTBImage img) Specify input image.
void	setMeasureUnits(SegResultEnums.MeasureUnit mu) Specify units in which to measure areas.
void	setNucleiMask(MTBImageByte mask) Specify nuclei mask.

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

inImg

@Parameter(label="Input image",
           required=true,
           mode=STANDARD,
           direction=IN,
           description="Input image.",
           dataIOOrder=-20)
private transient MTBImage inImg

Multi-channel input image to be processed.

resultData

@Parameter(label="Result statistics",
           direction=OUT,
           description="Result data.")
private transient SegResult_ParticlesMultiChannel resultData

Vector of result data objects.

particleDetector_1

@Parameter(label="Particle detector channel 1",
           required=false,
           direction=IN,
           dataIOOrder=-15,
           mode=STANDARD,
           description="Particle detector operator(s) for channels.")
private ParticleDetector particleDetector_1

particleDetector_2

@Parameter(label="Particle detector channel 2",
           required=false,
           direction=IN,
           dataIOOrder=-14,
           mode=STANDARD,
           description="Particle detector operator(s) for channels.")
private ParticleDetector particleDetector_2

particleDetector_3

@Parameter(label="Particle detector channel 3",
           required=false,
           direction=IN,
           dataIOOrder=-13,
           mode=STANDARD,
           description="Particle detector operator(s) for channels.")
private ParticleDetector particleDetector_3

particleDetector_4

@Parameter(label="Particle detector channel 4",
           required=false,
           direction=IN,
           dataIOOrder=-12,
           mode=STANDARD,
           description="Particle detector operator(s) for channels.")
private ParticleDetector particleDetector_4

particleDetector_5

@Parameter(label="Particle detector channel 5",
           required=false,
           direction=IN,
           dataIOOrder=-11,
           mode=STANDARD,
           description="Particle detector operator(s) for channels.")
private ParticleDetector particleDetector_5

excludeMask

@Parameter(label="Region exclude mask",
           direction=IN,
           mode=ADVANCED,
           required=false,
           description="Region exclude mask.")
private transient MTBImageByte excludeMask

Optional mask to exclude particles in certain regions.

Particles in exclude regions are ignored if mask is non-null.

measureUnits

@Parameter(label="Measure units",
           required=false,
           dataIOOrder=20,
           mode=ADVANCED,
           direction=IN,
           description="Units for area measurements.")
private SegResultEnums.MeasureUnit measureUnits

Units for measurements.

resultImg

@Parameter(label="Result image",
           direction=OUT,
           description="Result image",
           supplemental=true)
private transient MTBImageRGB resultImg

Stack with result overlays corresponding to channels.

resultDisplayMode

@Parameter(label="Result image display mode",
           required=false,
           mode=ADVANCED,
           direction=IN,
           supplemental=true,
           description="Mode how result image is displayed.")
private MultiChannelParticleAnalyzer2D.ResultImageMode resultDisplayMode

Mode of how to display result image.

height

private transient int height

Height of the processed image.

width

private transient int width

Width of the processed image.

stackSize

private transient int stackSize

Number of channels in image.

Constructor Detail

MultiChannelParticleAnalyzer2D

public MultiChannelParticleAnalyzer2D()
                               throws de.unihalle.informatik.Alida.exceptions.ALDOperatorException

Empty constructor.

Throws:

de.unihalle.informatik.Alida.exceptions.ALDOperatorException

MultiChannelParticleAnalyzer2D

public MultiChannelParticleAnalyzer2D(MTBImage image,
                                      Vector<ParticleDetector> pOps)
                               throws de.unihalle.informatik.Alida.exceptions.ALDOperatorException

Default constructor.

Parameters:

image - Image to be processed.

pOps - List of detectors.

Throws:

de.unihalle.informatik.Alida.exceptions.ALDOperatorException

Method Detail

setInputImage

public void setInputImage(MTBImage img)

Specify input image.

setNucleiMask

public void setNucleiMask(MTBImageByte mask)

Specify nuclei mask.

setMeasureUnits

public void setMeasureUnits(SegResultEnums.MeasureUnit mu)

Specify units in which to measure areas.

getResultDataArray

public SegResult_ParticlesMultiChannel getResultDataArray()

Returns extracted result data.

getDetectors

public Vector<ParticleDetector> getDetectors()

Get a reference to configured detectors' vector.

Returns:

Reference to vector of detectors.

getResultImage

public MTBImageRGB getResultImage()

Returns result image, i.e. the segmentation mask.

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

prepareResultImage

private void prepareResultImage()

Prepare visualization of result data by overlay on input image.

prepareResultImageStack

private MTBImageRGB prepareResultImageStack(Vector<MTBImage> imgvec)

Initialize result image stack.

Transfers result images to a multi-channel RGB image.