de.unihalle.informatik.MiToBo.apps.nuclei2D

Class NucleusSeparator2DBeamCut

java.lang.Object

de.unihalle.informatik.Alida.operator.ALDOperator

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

de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DAlgos

de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DBeamCut

All Implemented Interfaces:

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

@ALDAOperator(genericExecutionMode=ALL,
              shortDescription="Routines for separating conglomerates of cell nuclei in 2D.")
 @ALDDerivedClass
public class NucleusSeparator2DBeamCut
extends NucleusSeparator2DAlgos

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

This operator is not supposed to be directly executed in a generic fashion. Use the operator NucleusSeparator2D instead.

Author:

posch

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	NucleusSeparator2DBeamCut.NuclSeparateMode Available modes for nuclei separation in 2D images.

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 int	debug
private boolean	doErosion
private int	erodeSize
private int	minSize
private double	minSizeFraction
private NucleusSeparator2DBeamCut.NuclSeparateMode	opMode Operation mode of this separator.
private int	sizeDilation
private int	sizeOpening
private int	sizeTH
private double	thresTH
(package private) MTBImage	tmpImg temp. binary image

Fields inherited from class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DAlgos

inputImg, labelImg, resultImg

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

completeDAG, name, operatorExecutionEventlistenerList, portHashAccess, verbose, versionProvider

Constructor Summary

Constructors

Constructor and Description
NucleusSeparator2DBeamCut() Default constructor
NucleusSeparator2DBeamCut(MTBImage labelImg) Constructor.
NucleusSeparator2DBeamCut(MTBImage labelImg, NucleusSeparator2DBeamCut.NuclSeparateMode opMode) Constructor.

Method Summary

Modifier and Type	Method and Description
private double[]	dilate1D(double[] x, int size)
private double[]	erode1D(double[] x, int size)
private void	erodeComponent(int label, int size) erode one component with given label
private int[]	estimateMean(int label) Suche nach bestem Mittelpunkt des Embryos: ueberpruefe kreisfoermige Raster (8 Punkte +Mittelpunkt des Bildes) um Bildmittelpunkt aus Kriterium: max. min.
private double	euklidDist(double x1, double y1, double x2, double y2) Hilfsmethode zur Bestimmung der euklidischen Distanz zw. 2 Punkten
private double[]	getCentroid(MTBImage img, int label) auxiliary method to determine the centroid (x,y) and width/heigth of compoment with label in a double array of length 4 (should go in class/record)
int	getDebug() Get value of debug.
String	getDocumentation()
boolean	getDoErosion() Get value of doErosion.
int	getErodeSize() Get value of erodeSize.
MTBImage	getLabelImg() Get value of labelImg.
int	getMinSize() Get value of minSize.
double	getMinSizeFraction() Get value of minSizeFraction.
NucleusSeparator2DBeamCut.NuclSeparateMode	getOpMode() Get value of opMode.
private int	getSize(int label)
int	getSizeDilation() Get value of sizeDilation.
int	getSizeOpening() Get value of sizeOpening.
int	getSizeTH() Get value of sizeTH.
double	getThresTH() Get value of thresTH.
private void	keepLargestCC(MTBImage img, int label) remove all but the largest connected component with label from
private double[]	open1D(double[] x, int size)
protected void	operate()
private int	resetLabel(int fromLabel, int toLabel)
private int	separate(int label, int nextLabel) try to separate component with label 2.
void	setDebug(int value) Set value of debug.
void	setDoErosion(boolean value) Set value of doErosion.
void	setErodeSize(int value) Set value of erodeSize.
void	setLabelImg(MTBImage value) Set value of labelImg.
void	setMinSize(int value) Set value of minSize.
void	setMinSizeFraction(double value) Set value of minSizeFraction.
void	setOpMode(NucleusSeparator2DBeamCut.NuclSeparateMode value) Set value of opMode.
void	setSizeDilation(int value) Set value of sizeDilation.
void	setSizeOpening(int value) Set value of sizeOpening.
void	setSizeTH(int value) Set value of sizeTH.
void	setThresTH(double value) Set value of thresTH.
private double[]	topHat1D(double[] x, int size)

Methods inherited from class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DAlgos

getResultImg, setInputGrayScaleImage, setInputLabelImage, setResultImg

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

opMode

@Parameter(label="Operator mode",
           required=true,
           direction=IN,
           description="Operator separation mode.")
private NucleusSeparator2DBeamCut.NuclSeparateMode opMode

Operation mode of this separator.

sizeTH

@Parameter(label="Tophat size",
           required=false,
           direction=IN,
           description="Size of structuring element for top hat on distances.")
private int sizeTH

thresTH

@Parameter(label="Tophat threshold",
           required=false,
           direction=IN,
           description="Threshold for result from top hat.")
private double thresTH

sizeOpening

@Parameter(label="Opening mask size",
           required=false,
           direction=IN,
           description="Size of structuring element for opening on cutpoint hypotheses.")
private int sizeOpening

sizeDilation

@Parameter(label="Dilation mask size",
           required=false,
           direction=IN,
           description="Size of structuring element for dilation on cutpoint hypotheses.")
private int sizeDilation

minSize

@Parameter(label="Minimum nuclei size",
           required=false,
           direction=IN,
           description="Minimum size of each nucleus after separation, otherwise undo separation")
private int minSize

minSizeFraction

@Parameter(label="Minimum fraction size",
           required=false,
           direction=IN,
           description="Minimum size fraction of each nucleus after separation, otherwise undo separation.")
private double minSizeFraction

doErosion

@Parameter(label="Do erosion",
           required=false,
           direction=IN,
           description="Erode each nucleus resulting from a separation.")
private boolean doErosion

erodeSize

@Parameter(label="Erode mask size",
           required=false,
           direction=IN,
           description="Size of structuring element for eroding a nucleus from a separation.")
private int erodeSize

debug

@Parameter(label="Debug mode.",
           required=false,
           direction=IN,
           supplemental=true,
           description="Flag for debugging output.")
private int debug

tmpImg

transient MTBImage tmpImg

temp. binary image

Constructor Detail

NucleusSeparator2DBeamCut

public NucleusSeparator2DBeamCut()
                          throws de.unihalle.informatik.Alida.exceptions.ALDOperatorException

Default constructor

Throws:

de.unihalle.informatik.Alida.exceptions.ALDOperatorException

NucleusSeparator2DBeamCut

public NucleusSeparator2DBeamCut(MTBImage labelImg)
                          throws de.unihalle.informatik.Alida.exceptions.ALDOperatorException

Constructor.

Throws:

de.unihalle.informatik.Alida.exceptions.ALDOperatorException

NucleusSeparator2DBeamCut

public NucleusSeparator2DBeamCut(MTBImage labelImg,
                                 NucleusSeparator2DBeamCut.NuclSeparateMode opMode)
                          throws de.unihalle.informatik.Alida.exceptions.ALDOperatorException

Constructor.

Throws:

de.unihalle.informatik.Alida.exceptions.ALDOperatorException

Method Detail

operate

protected void operate()
                throws de.unihalle.informatik.Alida.exceptions.ALDOperatorException,
                       de.unihalle.informatik.Alida.exceptions.ALDProcessingDAGException

Specified by:

operate in class NucleusSeparator2DAlgos

Throws:

de.unihalle.informatik.Alida.exceptions.ALDOperatorException

de.unihalle.informatik.Alida.exceptions.ALDProcessingDAGException

separate

private int separate(int label,
                     int nextLabel)
              throws de.unihalle.informatik.Alida.exceptions.ALDOperatorException,
                     de.unihalle.informatik.Alida.exceptions.ALDProcessingDAGException

try to separate component with label 2. Mittelpunktschaetzung: Details in Methode unten 3. kreisfoermige Abtastung des Embryos mit Strahlen und Berechnung von 360 Schnittpunkten zw. Strahl und Embryorand 4. euklid. Differenz zwischen benachbarten Schnittpunkten berechnen und daraus relevante Schnittpunkte als Abtrennpunkte erkennen 5. Fallunterscheidung je nach Anzahl der gefundenen Trennpunkte

Throws:

de.unihalle.informatik.Alida.exceptions.ALDOperatorException

de.unihalle.informatik.Alida.exceptions.ALDProcessingDAGException

estimateMean

private int[] estimateMean(int label)

Suche nach bestem Mittelpunkt des Embryos: ueberpruefe kreisfoermige Raster (8 Punkte +Mittelpunkt des Bildes) um Bildmittelpunkt aus Kriterium: max. min. Abstand zum Embryorand

Returns:

int[]

euklidDist

private double euklidDist(double x1,
                          double y1,
                          double x2,
                          double y2)

Hilfsmethode zur Bestimmung der euklidischen Distanz zw. 2 Punkten

Parameters:

x1 - double

y1 - double

x2 - double

y2 - double

Returns:

double

getCentroid

private double[] getCentroid(MTBImage img,
                             int label)

auxiliary method to determine the centroid (x,y) and width/heigth of compoment with label in a double array of length 4 (should go in class/record)

Parameters:

img -

label -

Returns:

double[]

erode1D

private double[] erode1D(double[] x,
                         int size)

dilate1D

private double[] dilate1D(double[] x,
                          int size)

open1D

private double[] open1D(double[] x,
                        int size)

topHat1D

private double[] topHat1D(double[] x,
                          int size)

getSize

private int getSize(int label)

resetLabel

private int resetLabel(int fromLabel,
                       int toLabel)

keepLargestCC

private void keepLargestCC(MTBImage img,
                           int label)
                    throws de.unihalle.informatik.Alida.exceptions.ALDOperatorException,
                           de.unihalle.informatik.Alida.exceptions.ALDProcessingDAGException

remove all but the largest connected component with label from

Throws:

de.unihalle.informatik.Alida.exceptions.ALDOperatorException

de.unihalle.informatik.Alida.exceptions.ALDProcessingDAGException

getThresTH

public double getThresTH()

Get value of thresTH. Explanation: Threshold for result from tophat.

Returns:

value of thresTH

setThresTH

public void setThresTH(double value)

Set value of thresTH. Explanation: Threshold for result from tophat.

Parameters:

value - New value of thresTH

getMinSizeFraction

public double getMinSizeFraction()

Get value of minSizeFraction. Explanation: ??? Minimum size of ????.

Returns:

value of minSizeFraction

setMinSizeFraction

public void setMinSizeFraction(double value)

Set value of minSizeFraction. Explanation: ??? Minimum size of ????.

Parameters:

value - New value of minSizeFraction

getSizeOpening

public int getSizeOpening()

Get value of sizeOpening. Explanation: Size of structuring element for opening.

Returns:

value of sizeOpening

setSizeOpening

public void setSizeOpening(int value)

Set value of sizeOpening. Explanation: Size of structuring element for opening.

Parameters:

value - New value of sizeOpening

getSizeTH

public int getSizeTH()

Get value of sizeTH. Explanation: Size of structuring element for tophat.

Returns:

value of sizeTH

setSizeTH

public void setSizeTH(int value)

Set value of sizeTH. Explanation: Size of structuring element for tophat.

Parameters:

value - New value of sizeTH

getMinSize

public int getMinSize()

Get value of minSize. Explanation: Minimum size of ????.

Returns:

value of minSize

setMinSize

public void setMinSize(int value)

Set value of minSize. Explanation: Minimum size of ????.

Parameters:

value - New value of minSize

getSizeDilation

public int getSizeDilation()

Get value of sizeDilation. Explanation: Size of structuring element for dilation.

Returns:

value of sizeDilation

setSizeDilation

public void setSizeDilation(int value)

Set value of sizeDilation. Explanation: Size of structuring element for dilation.

Parameters:

value - New value of sizeDilation

getOpMode

public NucleusSeparator2DBeamCut.NuclSeparateMode getOpMode()

Get value of opMode. Explanation: Operator sepration mode.

Returns:

value of opMode

setOpMode

public void setOpMode(NucleusSeparator2DBeamCut.NuclSeparateMode value)

Set value of opMode. Explanation: Operator sepration mode.

Parameters:

value - New value of opMode

getLabelImg

public MTBImage getLabelImg()

Get value of labelImg. Explanation: Label input image of nuclei.

Returns:

value of labelImg

setLabelImg

public void setLabelImg(MTBImage value)

Set value of labelImg. Explanation: Label input image of nuclei.

Parameters:

value - New value of labelImg

getDebug

public int getDebug()

Get value of debug. Explanation: Flag for debugging output..

Returns:

value of debug

setDebug

public void setDebug(int value)

Set value of debug. Explanation: Flag for debugging output..

Parameters:

value - New value of debug

getErodeSize

public int getErodeSize()

Get value of erodeSize. Explanation: Size of structuring element for eroding a nucleus from a separation.

Returns:

value of erodeSize

setErodeSize

public void setErodeSize(int value)

Set value of erodeSize. Explanation: Size of structuring element for eroding a nucleus from a separation.

Parameters:

value - New value of erodeSize

getDoErosion

public boolean getDoErosion()

Get value of doErosion. Explanation: Erode each nucleus resulting from a separation.

Returns:

value of doErosion

setDoErosion

public void setDoErosion(boolean value)

Set value of doErosion. Explanation: Erode each nucleus resulting from a separation.

Parameters:

value - New value of doErosion

erodeComponent

private void erodeComponent(int label,
                            int size)
                     throws de.unihalle.informatik.Alida.exceptions.ALDOperatorException,
                            de.unihalle.informatik.Alida.exceptions.ALDProcessingDAGException

erode one component with given label

Throws:

de.unihalle.informatik.Alida.exceptions.ALDOperatorException

de.unihalle.informatik.Alida.exceptions.ALDProcessingDAGException

getDocumentation

public String getDocumentation()

Overrides:

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