de.unihalle.informatik.MiToBo.apps.singleCellTracking2D

Class CellTrackerBipartite

java.lang.Object

de.unihalle.informatik.Alida.operator.ALDOperator

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

de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellTrackerBipartite

All Implemented Interfaces:

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

@ALDAOperator(genericExecutionMode=ALL,
              level=STANDARD,
              shortDescription="Assigns unique labels to regions representing individual cells in the input binary image sequence.")
public class CellTrackerBipartite
extends MTBOperator

This operator assigns unique labels to regions representing individual cells in the input binary image sequence

Author:

glass

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 double	currentMax
private int	DISAPPEARED
private static double	inf
private MTBImage	inImg
(package private) MTBImage	labelImg
private double	maxAreaChange
private double	maxDist
private Vector<Integer>	objectLabels
private Boolean	objects8Connected
private MTBImage	resultImg
private int	sizeT
private int	sizeX
private int	sizeY
private int	totalNumberOfObjects
private boolean	useAutoDistance

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

completeDAG, name, operatorExecutionEventlistenerList, portHashAccess, verbose, versionProvider

Constructor Summary

Constructors

Constructor and Description
CellTrackerBipartite()
CellTrackerBipartite(MTBImage inImg)

Method Summary

Modifier and Type	Method and Description
private byte[][]	assign(MTBRegion2DSet currentRegions, MTBRegion2DSet nextRegions) assign regions from one frame to regions from another frame
private int	determineGatingDistance() automatic gating distance determination according to: "Automated and semi-automated cell tracking: addressing portability challenges" KAN, A. and CHAKRAVORTY, R. and BAILEY, J. and LECKIE, C. and MARKHAM, J. and DOWLING, M.R.
private MTBImage	drawRegions(MTBRegion2DSet regions)
private double[][]	getAreaFracMatrix(MTBRegion2DSet currRegions, MTBRegion2DSet nextRegions)
private double	getAreaFraction(MTBRegion2D r, MTBRegion2D s)
private double	getDistance(MTBRegion2D r, MTBRegion2D s)
private double[][]	getDistMatrix(MTBRegion2DSet currRegions, MTBRegion2DSet nextRegions)
String	getDocumentation()
MTBImage	getResultImage()
private MTBRegion2DSet	label(MTBImage img)
void	operate()
private MTBImage	relabel(byte[][] a, int n, int m, MTBRegion2DSet nextRegions) find and assign object labels to segmented objects in two frames
void	setMaxAreaChange(double t)
void	setMaxDistance(double t)
void	setObjectsEightConnected(boolean eightconnected)
private void	showMaxDistTextbox()
private void	track() the actual tracking method
void	useAutoDistanceDetermination(boolean useAutoDistance)
private void	verbosePrintln(String s) prints the given text if the verbose flag is set

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

inImg

@Parameter(label="binary input image",
           required=true,
           direction=IN,
           supplemental=false,
           description="binary input image",
           dataIOOrder=0)
private transient MTBImage inImg

useAutoDistance

@Parameter(label="determine gating distance automatically",
           required=false,
           direction=IN,
           supplemental=false,
           description="determine gating distance automatically",
           dataIOOrder=1,
           callback="showMaxDistTextbox",
           paramModificationMode=MODIFIES_INTERFACE)
private boolean useAutoDistance

maxDist

@Parameter(label="maximum distance (pixels)",
           required=false,
           direction=IN,
           supplemental=false,
           description="maximum distance for two objects to be assigned to each other",
           dataIOOrder=2)
private double maxDist

maxAreaChange

@Parameter(label="maximum area change",
           required=false,
           direction=IN,
           supplemental=false,
           description="maximum change in area (fraction) for two objects to be assigned to each other",
           dataIOOrder=3)
private double maxAreaChange

objects8Connected

@Parameter(label="are objects 8-connected",
           required=false,
           direction=IN,
           supplemental=false,
           description="are objects 8-connected",
           dataIOOrder=4)
private Boolean objects8Connected

resultImg

@Parameter(label="result image",
           required=true,
           direction=OUT,
           supplemental=false,
           description="result image")
private transient MTBImage resultImg

DISAPPEARED

private final int DISAPPEARED

See Also:

Constant Field Values

inf

private static double inf

sizeX

private int sizeX

sizeY

private int sizeY

sizeT

private int sizeT

totalNumberOfObjects

private int totalNumberOfObjects

labelImg

MTBImage labelImg

objectLabels

private Vector<Integer> objectLabels

currentMax

private double currentMax

Constructor Detail

CellTrackerBipartite

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

Throws:

de.unihalle.informatik.Alida.exceptions.ALDOperatorException

CellTrackerBipartite

public CellTrackerBipartite(MTBImage inImg)
                     throws de.unihalle.informatik.Alida.exceptions.ALDOperatorException

Parameters:

inImg -

Throws:

de.unihalle.informatik.Alida.exceptions.ALDOperatorException

Method Detail

operate

public 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

track

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

the actual tracking method

Throws:

de.unihalle.informatik.Alida.exceptions.ALDOperatorException

de.unihalle.informatik.Alida.exceptions.ALDProcessingDAGException

assign

private byte[][] assign(MTBRegion2DSet currentRegions,
                        MTBRegion2DSet nextRegions)
                 throws de.unihalle.informatik.Alida.exceptions.ALDOperatorException,
                        de.unihalle.informatik.Alida.exceptions.ALDProcessingDAGException

assign regions from one frame to regions from another frame

Parameters:

currentRegions - vector containing the n regions from one frame

nextRegions - vector containing the m regions from another frame

Returns:

((n+m) x (n+m))-table containing assignments (entry == 1) of the input regions
rows: regions from the first frame, columns: regions from the second frame

Throws:

de.unihalle.informatik.Alida.exceptions.ALDOperatorException

de.unihalle.informatik.Alida.exceptions.ALDProcessingDAGException

label

private MTBRegion2DSet label(MTBImage img)
                      throws de.unihalle.informatik.Alida.exceptions.ALDOperatorException,
                             de.unihalle.informatik.Alida.exceptions.ALDProcessingDAGException

Parameters:

img - binary image

Returns:

set of regions from the binary image

Throws:

de.unihalle.informatik.Alida.exceptions.ALDOperatorException

de.unihalle.informatik.Alida.exceptions.ALDProcessingDAGException

relabel

private MTBImage relabel(byte[][] a,
                         int n,
                         int m,
                         MTBRegion2DSet nextRegions)

find and assign object labels to segmented objects in two frames

Parameters:

a - assignment table

n - number of objects from the current frame

m - number of objects from the next frame

nextRegions - regions from the next frame

Returns:

frame where all connected components are labeled according to the assignments contained in a

getDistMatrix

private double[][] getDistMatrix(MTBRegion2DSet currRegions,
                                 MTBRegion2DSet nextRegions)

Parameters:

currRegions -

nextRegions -

Returns:

distance matrix for the given region sets

getAreaFracMatrix

private double[][] getAreaFracMatrix(MTBRegion2DSet currRegions,
                                     MTBRegion2DSet nextRegions)

Parameters:

currRegions -

nextRegions -

Returns:

matrix containing the fractions of the areas of the input regions

drawRegions

private MTBImage drawRegions(MTBRegion2DSet regions)

Parameters:

regions -

Returns:

image where the regions are drawn with an intensity value corresponding to their ids + 1

getDistance

private double getDistance(MTBRegion2D r,
                           MTBRegion2D s)

Parameters:

r -

s -

Returns:

euclidean distance (pixels) between the centroids of r and s

getAreaFraction

private double getAreaFraction(MTBRegion2D r,
                               MTBRegion2D s)

getResultImage

public MTBImage getResultImage()

useAutoDistanceDetermination

public void useAutoDistanceDetermination(boolean useAutoDistance)

setMaxDistance

public void setMaxDistance(double t)

setMaxAreaChange

public void setMaxAreaChange(double t)

setObjectsEightConnected

public void setObjectsEightConnected(boolean eightconnected)

verbosePrintln

private void verbosePrintln(String s)

prints the given text if the verbose flag is set

Parameters:

s - text to print

determineGatingDistance

private int determineGatingDistance()
                             throws de.unihalle.informatik.Alida.exceptions.ALDOperatorException,
                                    de.unihalle.informatik.Alida.exceptions.ALDProcessingDAGException

automatic gating distance determination according to:

"Automated and semi-automated cell tracking: addressing portability challenges"
KAN, A. and CHAKRAVORTY, R. and BAILEY, J. and LECKIE, C. and MARKHAM, J. and DOWLING, M.R.
Journal of Microscopy. Vol 244. Number 2. 2011

Throws:

de.unihalle.informatik.Alida.exceptions.ALDProcessingDAGException

de.unihalle.informatik.Alida.exceptions.ALDOperatorException

showMaxDistTextbox

private void showMaxDistTextbox()

getDocumentation

public String getDocumentation()

Overrides:

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