de.unihalle.informatik.MiToBo.apps.nuclei2D

Class NucleusSeparator2D

java.lang.Object

de.unihalle.informatik.Alida.operator.ALDOperator

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

de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2D

All Implemented Interfaces:

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

@ALDAOperator(genericExecutionMode=ALL,
              level=APPLICATION,
              shortDescription="Routines for separating conglomerates of cell nuclei in 2D.")
public class NucleusSeparator2D
extends MTBOperator

Class provides routines for separating conglomerates of cell nuclei in 2D.

Author:

moeller, posch

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	NucleusSeparator2D.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 MTBImage	inputImg Input image to be processed.
private MTBImage	labelImg Binary nuclei image to be processed.
private NucleusSeparator2DAlgos	nucSepOp Operation mode of the operator.
private NucleusSeparator2D.ResultImageMode	resultDisplayMode Mode of how to display result image.
private MTBImageShort	resultImg Result label image of separated nuclei.

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

completeDAG, name, operatorExecutionEventlistenerList, portHashAccess, verbose, versionProvider

Constructor Summary

Constructors

Constructor and Description
NucleusSeparator2D() Empty constructor.
NucleusSeparator2D(MTBImage label, NucleusSeparator2DAlgos op) Default constructor.

Method Summary

Modifier and Type	Method and Description
String	getDocumentation()
MTBImageShort	getResultImage() Returns result image, i.e. the segmentation mask.
protected void	operate()
private void	prepareResultImage(MTBImageShort labelImage) Prepare visualization of result.
void	setInputGrayScaleImage(MTBImage img) Specify input gray-scale image.
void	setInputLabelImage(MTBImage img) Specify label input image.

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, 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

inputImg

@Parameter(label="Greyscale Input Image",
           required=true,
           direction=IN,
           dataIOOrder=-21,
           mode=STANDARD,
           description="Greyscale input image to be analyzed.")
private transient MTBImage inputImg

Input image to be processed.

labelImg

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

Binary nuclei image to be processed.

resultImg

@Parameter(label="Result image",
           direction=OUT,
           description="Label image of separated nuclei.")
private transient MTBImageShort resultImg

Result label image of separated nuclei.

nucSepOp

@Parameter(label="Operator Mode",
           required=true,
           mode=STANDARD,
           direction=IN,
           description="Operator separation mode.")
private NucleusSeparator2DAlgos nucSepOp

Operation mode of the operator.

resultDisplayMode

@Parameter(label="Result image display mode",
           required=false,
           mode=STANDARD,
           direction=IN,
           supplemental=true,
           description="Mode how result image is displayed.")
private NucleusSeparator2D.ResultImageMode resultDisplayMode

Mode of how to display result image.

Constructor Detail

NucleusSeparator2D

public NucleusSeparator2D()
                   throws de.unihalle.informatik.Alida.exceptions.ALDOperatorException

Empty constructor.

Throws:

de.unihalle.informatik.Alida.exceptions.ALDOperatorException

NucleusSeparator2D

public NucleusSeparator2D(MTBImage label,
                          NucleusSeparator2DAlgos op)
                   throws de.unihalle.informatik.Alida.exceptions.ALDOperatorException

Default constructor.

Parameters:

label - Label image to be processed.

mode - Operator mode to be applied.

Throws:

de.unihalle.informatik.Alida.exceptions.ALDOperatorException

Method Detail

setInputLabelImage

public void setInputLabelImage(MTBImage img)

Specify label input image.

setInputGrayScaleImage

public void setInputGrayScaleImage(MTBImage img)

Specify input gray-scale image.

getResultImage

public MTBImageShort getResultImage()

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

Returns:

Returns the result label image.

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(MTBImageShort labelImage)

Prepare visualization of result.

getDocumentation

public String getDocumentation()

Overrides:

getDocumentation in class de.unihalle.informatik.Alida.operator.ALDOperator