de.unihalle.informatik.MiToBo.apps.singleCellTracking2D

Class CellSegmentationPostprocessing

java.lang.Object

de.unihalle.informatik.Alida.operator.ALDOperator

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

de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellSegmentationPostprocessing

All Implemented Interfaces:

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

@ALDAOperator(genericExecutionMode=SWING,
              level=STANDARD,
              shortDescription="Performs post-processing tasks on already segmented cell images.")
public class CellSegmentationPostprocessing
extends MTBOperator

operator for doing common postprocessing tasks on already segmented cell images

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	fg_value
private MTBImage	inImg
private Integer	maxArea
private Integer	minArea
private Boolean	objects8Connected
private Boolean	removeBorderObjects
private MTBImage	resultImg
private int	sizeC
private int	sizeT
private int	sizeX
private int	sizeY
private int	sizeZ

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

completeDAG, name, operatorExecutionEventlistenerList, portHashAccess, verbose, versionProvider

Constructor Summary

Constructors

Constructor and Description
CellSegmentationPostprocessing()
CellSegmentationPostprocessing(MTBImage inImg)

Method Summary

Modifier and Type	Method and Description
private void	drawRegions(MTBRegion2DSet keepRegions, int z, int t, int c) draw regions to the output image
private MTBRegion2DSet	excludeBorderRegions(MTBRegion2DSet regions) exclude regions that are adjacent to the image borders
private MTBRegion2DSet	excludeLargeRegions(MTBRegion2DSet regions) exclude regions that are larger than the predefined (Parameter maxArea) maximum
private MTBRegion2DSet	excludeSmallRegions(MTBRegion2DSet regions) exclude regions that are smaller than the predefined (Parameter minArea) minimum
String	getDocumentation()
MTBImage	getResultImage()
void	operate()
void	setBorderExclusion(boolean excludeBorderObjects) should border touching objects be excluded
void	setFG_Value(double val) set the intensity value of the remaining foreground regions
void	setMaximumObjectArea(int maxArea) set the maximum area (number of pixels) a region must have in order to be kept
void	setMinimumObjectArea(int minArea) set the minimum area (number of pixels) a region must have in order to be kept
void	setObjectsEightConnected(boolean eightconnected) are regions to be considered 8-connected (4-connected otherwise)

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="input image",
           required=true,
           direction=IN,
           supplemental=false,
           description="binary input image")
private transient MTBImage inImg

resultImg

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

removeBorderObjects

@Parameter(label="remove border touching objects",
           required=false,
           direction=IN,
           supplemental=false,
           description="should border touching objects be removed")
private Boolean removeBorderObjects

minArea

@Parameter(label="minimum area (pixels)",
           required=false,
           direction=IN,
           supplemental=false,
           description="minimum area (number of pixels) an object should have")
private Integer minArea

maxArea

@Parameter(label="maximum area (pixels)",
           required=false,
           direction=IN,
           supplemental=false,
           description="maximum area (number of pixels) an object should have")
private Integer maxArea

objects8Connected

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

fg_value

@Parameter(label="foreground value",
           required=false,
           direction=IN,
           supplemental=false,
           description="intensity value for remaining foreground object pixel")
private Double fg_value

sizeX

private int sizeX

sizeY

private int sizeY

sizeZ

private int sizeZ

sizeT

private int sizeT

sizeC

private int sizeC

Constructor Detail

CellSegmentationPostprocessing

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

Throws:

de.unihalle.informatik.Alida.exceptions.ALDOperatorException

CellSegmentationPostprocessing

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

Parameters:

inImg - input image

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

excludeBorderRegions

private MTBRegion2DSet excludeBorderRegions(MTBRegion2DSet regions)

exclude regions that are adjacent to the image borders

Parameters:

regions - image regions

Returns:

regions that are not touching the image borders

excludeSmallRegions

private MTBRegion2DSet excludeSmallRegions(MTBRegion2DSet regions)

exclude regions that are smaller than the predefined (Parameter minArea) minimum

Parameters:

regions - image regions

Returns:

regions that are not too small

excludeLargeRegions

private MTBRegion2DSet excludeLargeRegions(MTBRegion2DSet regions)

exclude regions that are larger than the predefined (Parameter maxArea) maximum

Parameters:

regions - image regions

Returns:

regions that are not too large

drawRegions

private void drawRegions(MTBRegion2DSet keepRegions,
                         int z,
                         int t,
                         int c)

draw regions to the output image

Parameters:

keepRegions - 2D regions to draw

z - slice number

t - frame number

c - channel number

setBorderExclusion

public void setBorderExclusion(boolean excludeBorderObjects)

should border touching objects be excluded

Parameters:

excludeBorderObjects -

setMinimumObjectArea

public void setMinimumObjectArea(int minArea)

set the minimum area (number of pixels) a region must have in order to be kept

Parameters:

minArea -

setMaximumObjectArea

public void setMaximumObjectArea(int maxArea)

set the maximum area (number of pixels) a region must have in order to be kept

Parameters:

maxArea -

setObjectsEightConnected

public void setObjectsEightConnected(boolean eightconnected)

are regions to be considered 8-connected (4-connected otherwise)

Parameters:

eightconnected -

setFG_Value

public void setFG_Value(double val)

set the intensity value of the remaining foreground regions

Parameters:

val -

getResultImage

public MTBImage getResultImage()

Returns:

result image

getDocumentation

public String getDocumentation()

Overrides:

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