de.unihalle.informatik.MiToBo.apps.nuclei2D

Class NucleusSeparator2DPeakSearch_RegionSeparator

java.lang.Object

de.unihalle.informatik.Alida.operator.ALDOperator

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

de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DPeakSearch_RegionSeparator

All Implemented Interfaces:

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

@ALDAOperator(genericExecutionMode=NONE)
public class NucleusSeparator2DPeakSearch_RegionSeparator
extends MTBOperator

Operator to analyze a given binary image or a set of nuclei regions.

The data will be transformed into a distance map in which the peaks are analyzed and compared to identify overlapping nuclei.

The result will be center-coordinates of all nuclei in the data. Furthermore the regions may be divided or initial regions for further analysis may be delivered.

This operator has been written as part of Jochen's project in WS 2011/12.

Author:

Jochen Luechtrath, Birgit Moeller

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 boolean[][]	blacklist
private MTBRegion2DSet	candidates
private MTBImage	distImg Calculated distance map.
private DistanceTransform.DistanceMetric	distmet Metric for distance map calculation.
private MTBImage	inImg Binary input image to be analyzed.
private MTBRegion2DSet	inputRegions Optional set of pre-segmented input regions.
private double	mad Maximal allowed discrepancy.
private double	max_d2c Maximum peak distance factor.
boolean	report
private int	res_x
private int	res_y
private MTBRegion2DSet[]	resultAreas
private MTBRegion2DSet	resultCenters Set of detected nuclei centers.
private MTBRegion2DSet[]	resultRegCenters Nuclei centers sorted according to former regions.
private double	schwelle Threshold to suppress peak analysis close to scraggy contours.
private boolean[][]	seen
private MTBPolygon2DSet	snakePrimerEllipse Set of elliptical snake polygons.
private MTBPolygon2DSet	snakePrimerVoronoi Set of snake polygons based on Voronoi tesselation.

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

completeDAG, name, operatorExecutionEventlistenerList, portHashAccess, verbose, versionProvider

Constructor Summary

Constructors

Constructor and Description
NucleusSeparator2DPeakSearch_RegionSeparator() Default constructor.
NucleusSeparator2DPeakSearch_RegionSeparator(MTBImageByte image) Constructor with input image.
NucleusSeparator2DPeakSearch_RegionSeparator(MTBRegion2DSet oset) Constructor with region set.

Method Summary

Modifier and Type	Method and Description
private void	ellipsoidSnakePrimer() Function to extract elliptical snake primers.
MTBRegion2DSet	getCandidates() Returns set of detected candidate peaks.
MTBImage	getDistImg() Returns calculated distance map.
MTBPolygon2DSet	getEllipsoidSnakePrimer() Returns set of initial snake ellipses.
MTBRegion2DSet	getInputRegs() Get set of input regions.
MTBRegion2DSet[]	getRegCenters() Returns the centers of the nuclei sorted to their original regions.
MTBRegion2DSet[]	getResultAreas() Returns separated regions sorted according to original regions.
MTBRegion2DSet	getResultCenters() Returns centers of result regions.
MTBPolygon2DSet	getVoronoidSnakePrimer() Returns set of snake polygons resulting from Voronoi tesselation.
private boolean	gratwanderung(int x, int y, MTBRegion2D tempreg) Function to travers ridges.
private void	makeline(int xstart, int ystart, int xend, int yend, Vector<Point2D.Double> line) Draws a line between two points.
protected void	operate()
private void	regionVoronoize() Function to perform Voronoi tesselation.
void	setDistmet(DistanceTransform.DistanceMetric _distmet) Specify the metric for the distance transformation.
void	setInImg(MTBImageByte _inImg) Specify binary input image.
void	setInputRegs(MTBRegion2DSet _inputRegions) Specify set of input regions.
void	setMad(double _mad) Sets maximal allowed discrepancy of direct connection to actual profile between two peaks.
void	setMax_d2c(double _max_d2c) Sets factor to adjust maximal allowed distance from lower to upper peak.
void	setSuppressor(int sup) Sets threshold to suppress peak analysis close to scraggy contours.
private void	voronoidSnakePrimer() Function to extract Voronoi primers.

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,
           direction=IN,
           dataIOOrder=1,
           mode=STANDARD,
           description="Binary input image.")
private transient MTBImage inImg

Binary input image to be analyzed.

inputRegions

@Parameter(label="Input Regions",
           required=false,
           direction=INOUT,
           dataIOOrder=1,
           mode=ADVANCED,
           description="Input nuclei regions.")
private transient MTBRegion2DSet inputRegions

Optional set of pre-segmented input regions.

schwelle

@Parameter(label="Significance Threshold for Peaks",
           required=false,
           direction=IN,
           mode=ADVANCED,
           description="Threshold to suppress peak analysis close to scraggy contours (should be >4).")
private double schwelle

Threshold to suppress peak analysis close to scraggy contours.

max_d2c

@Parameter(label="Maximum Peak Distance Factor",
           required=false,
           direction=IN,
           mode=ADVANCED,
           description="Factor to adjust maximal allowed distance from lower to upper peak.")
private double max_d2c

Maximum peak distance factor.

mad

@Parameter(label="Maximal Allowed Discrepancy",
           required=false,
           direction=IN,
           mode=ADVANCED,
           description="Max. allowed discrepancy of direct connection to actual profile.")
private double mad

Maximal allowed discrepancy.

distmet

@Parameter(label="Distance Metric",
           required=false,
           direction=IN,
           mode=ADVANCED,
           description="Distance metric.")
private DistanceTransform.DistanceMetric distmet

Metric for distance map calculation.

distImg

@Parameter(label="Distance Map",
           required=false,
           direction=OUT,
           description="Distance Map.")
private transient MTBImage distImg

Calculated distance map.

resultCenters

@Parameter(label="Nuclei Centers",
           required=false,
           direction=OUT,
           description="Centers of all detected nuclei.")
private transient MTBRegion2DSet resultCenters

Set of detected nuclei centers.

resultRegCenters

@Parameter(label="Nuclei Centers of former regions",
           required=false,
           direction=OUT,
           description="Centers of detected nuclei seperated in their former regions")
private transient MTBRegion2DSet[] resultRegCenters

Nuclei centers sorted according to former regions.

snakePrimerEllipse

@Parameter(label="Elliptic Snake Initialisations",
           required=false,
           direction=OUT,
           description="Set of elliptical snake polygons.")
private transient MTBPolygon2DSet snakePrimerEllipse

Set of elliptical snake polygons.

snakePrimerVoronoi

@Parameter(label="Snake Initialisation by Voronoi",
           required=false,
           direction=OUT,
           description="Snake polygons from Voronoi-tesselated regions.")
private transient MTBPolygon2DSet snakePrimerVoronoi

Set of snake polygons based on Voronoi tesselation.

res_x

private transient int res_x

res_y

private transient int res_y

blacklist

private transient boolean[][] blacklist

seen

private transient boolean[][] seen

report

public transient boolean report

resultAreas

private transient MTBRegion2DSet[] resultAreas

candidates

private transient MTBRegion2DSet candidates

Constructor Detail

NucleusSeparator2DPeakSearch_RegionSeparator

public NucleusSeparator2DPeakSearch_RegionSeparator()
                                             throws de.unihalle.informatik.Alida.exceptions.ALDOperatorException

Default constructor.

Throws:

de.unihalle.informatik.Alida.exceptions.ALDOperatorException

NucleusSeparator2DPeakSearch_RegionSeparator

public NucleusSeparator2DPeakSearch_RegionSeparator(MTBImageByte image)
                                             throws de.unihalle.informatik.Alida.exceptions.ALDOperatorException

Constructor with input image.

Parameters:

image - Binary input image.

Throws:

de.unihalle.informatik.Alida.exceptions.ALDOperatorException

NucleusSeparator2DPeakSearch_RegionSeparator

public NucleusSeparator2DPeakSearch_RegionSeparator(MTBRegion2DSet oset)
                                             throws de.unihalle.informatik.Alida.exceptions.ALDOperatorException

Constructor with region set.

Note: the set needs correct referenced dimensions!

Parameters:

oset - Set of input regions.

Throws:

de.unihalle.informatik.Alida.exceptions.ALDOperatorException

Method Detail

setInImg

public void setInImg(MTBImageByte _inImg)

Specify binary input image.

Parameters:

inImg - Binary input image.

getInputRegs

public MTBRegion2DSet getInputRegs()

Get set of input regions.

Returns:

Set of input regions.

setInputRegs

public void setInputRegs(MTBRegion2DSet _inputRegions)

Specify set of input regions.

Parameters:

inputRegions - Set of input regions.

getDistImg

public MTBImage getDistImg()

Returns calculated distance map.

Returns:

Image distance map.

getResultCenters

public MTBRegion2DSet getResultCenters()

Returns centers of result regions.

Returns:

Centers of all detected nuclei.

getCandidates

public MTBRegion2DSet getCandidates()

Returns set of detected candidate peaks.

Returns:

Set of all possible peaks.

setMax_d2c

public void setMax_d2c(double _max_d2c)

Sets factor to adjust maximal allowed distance from lower to upper peak.

Parameters:

max_d2c - Adjustment factor, default is 1.5.

setMad

public void setMad(double _mad)

Sets maximal allowed discrepancy of direct connection to actual profile between two peaks.

Parameters:

mad - Max. discrepancy, default is 0.11.

setDistmet

public void setDistmet(DistanceTransform.DistanceMetric _distmet)

Specify the metric for the distance transformation.

Parameters:

distmet - Distance metric, default is Chessboard-Distance.

setSuppressor

public void setSuppressor(int sup)

Sets threshold to suppress peak analysis close to scraggy contours.

Parameters:

sup - Threshold, should be >4.

getRegCenters

public MTBRegion2DSet[] getRegCenters()

Returns the centers of the nuclei sorted to their original regions.

Returns:

Set of nuclei centers sorted according to their original regions.

getResultAreas

public MTBRegion2DSet[] getResultAreas()

Returns separated regions sorted according to original regions.

Returns:

Splitted regions of their actual centers.

getVoronoidSnakePrimer

public MTBPolygon2DSet getVoronoidSnakePrimer()
                                       throws de.unihalle.informatik.Alida.exceptions.ALDOperatorException,
                                              de.unihalle.informatik.Alida.exceptions.ALDProcessingDAGException

Returns set of snake polygons resulting from Voronoi tesselation.

Returns:

Initial snake polygons of voronoi divided regions.

Throws:

de.unihalle.informatik.Alida.exceptions.ALDOperatorException

de.unihalle.informatik.Alida.exceptions.ALDProcessingDAGException

getEllipsoidSnakePrimer

public MTBPolygon2DSet getEllipsoidSnakePrimer()

Returns set of initial snake ellipses.

Returns:

Elliptical snake polygons.

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

voronoidSnakePrimer

private void voronoidSnakePrimer()
                          throws de.unihalle.informatik.Alida.exceptions.ALDOperatorException,
                                 de.unihalle.informatik.Alida.exceptions.ALDProcessingDAGException

Function to extract Voronoi primers.

Throws:

de.unihalle.informatik.Alida.exceptions.ALDOperatorException

de.unihalle.informatik.Alida.exceptions.ALDProcessingDAGException

regionVoronoize

private void regionVoronoize()

Function to perform Voronoi tesselation.

ellipsoidSnakePrimer

private void ellipsoidSnakePrimer()

Function to extract elliptical snake primers.

gratwanderung

private boolean gratwanderung(int x,
                              int y,
                              MTBRegion2D tempreg)

Function to travers ridges.

Parameters:

x - x-coordinate to check.

y - y-coordinate to check.

tempreg - Region to check.

Returns:

True if pixel refers to peak.

makeline

private void makeline(int xstart,
                      int ystart,
                      int xend,
                      int yend,
                      Vector<Point2D.Double> line)

Draws a line between two points.

Parameters:

xstart - Start point x-coordinate.

ystart - Start point x-coordinate.

xend - End point x-coordinate.

yend - End point y-coordinate.

line - Points in between.