de.unihalle.informatik.MiToBo.apps.singleCellTracking2D

Class MigrationAnalyzer

java.lang.Object

de.unihalle.informatik.Alida.operator.ALDOperator

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

de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.MigrationAnalyzer

All Implemented Interfaces:

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

@ALDAOperator(genericExecutionMode=ALL,
              level=STANDARD,
              shortDescription="Analyzes the movement pattern of cells as well as changes in morphology and fluorescence intensity")
public class MigrationAnalyzer
extends MTBOperator

Operator for analyzing the movement pattern of cells as well as changes in morphology and fluorescence intensity

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 Boolean	analyzeIntensities
private Boolean	analyzeShapes
private Boolean	analyzeTrajectories
private Double	deltaT
private Double	deltaX
private Double	deltaY
private Double	factor
private Boolean	include
private MTBImage	intImg
private String	intReport
private MTBImage	labelImg
private MTBImage	maskImg
private Integer	minTrackLength
private Boolean	removeExcluded
private String	shapeReport
private Boolean	showOverlayImage
private Boolean	showTrajectoryMap
private String	trackReport
private String	unitT
private String	unitXY

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

completeDAG, name, operatorExecutionEventlistenerList, portHashAccess, verbose, versionProvider

Constructor Summary

Constructors

Constructor and Description
MigrationAnalyzer()
MigrationAnalyzer(MTBImage labelImg)
MigrationAnalyzer(MTBImage labelImg, MTBImage maskImg)

Method Summary

Modifier and Type	Method and Description
void	analyzeIntensities(boolean analyzeIntensities)
void	analyzeShapes(boolean analyzeShapes)
void	analyzeTrajectories(boolean analyzeTrajectories)
private void	getCalibration()
String	getDocumentation()
String	getIntensityReport()
MTBImage	getLabelImage()
String	getShapeReport()
String	getTrackReport()
void	includeMask(boolean include)
void	operate()
void	removeExcludedObjects(boolean remove)
void	setDeltaT(double deltaT)
void	setDeltaX(double deltaX)
void	setDeltaY(double deltaY)
void	setFactor(double factor)
void	setIntensityImage(MTBImage intImg)
void	setMinTrackLength(int minTrackLength)
void	setUnitT(String unitT)
void	setUnitXY(String unitXY)
private void	showMaskChannelTextbox()
void	showOverlayImage(boolean showOverlay)
void	showTrajectoryMap(boolean showTrajectories)

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

labelImg

@Parameter(label="label image",
           required=true,
           direction=INOUT,
           supplemental=false,
           description="labeled input image",
           dataIOOrder=0,
           callback="getCalibration",
           paramModificationMode=MODIFIES_INTERFACE)
private transient MTBImage labelImg

intImg

@Parameter(label="intensity image",
           required=false,
           direction=IN,
           supplemental=false,
           description="additional intensity image",
           dataIOOrder=1)
private transient MTBImage intImg

maskImg

@Parameter(label="mask image",
           required=false,
           direction=IN,
           supplemental=false,
           description="intensity image used to include or exclude certain objects",
           dataIOOrder=2,
           mode=ADVANCED,
           callback="showMaskChannelTextbox",
           paramModificationMode=MODIFIES_INTERFACE)
private transient MTBImage maskImg

include

@Parameter(label="include mask",
           required=false,
           direction=IN,
           supplemental=false,
           description="include tracks that have corresponding signals in mask image (otherwise these tracks are excluded)",
           dataIOOrder=3,
           mode=STANDARD)
private Boolean include

factor

@Parameter(label="average factor",
           required=false,
           direction=IN,
           supplemental=false,
           description="object\'s mean intensity must be at least mean image intensity multiplied with this factor to be included/ excluded",
           dataIOOrder=4,
           mode=STANDARD)
private Double factor

deltaX

@Parameter(label="pixel length, x-direction",
           required=false,
           direction=IN,
           supplemental=false,
           description="pixel length in x-direction",
           dataIOOrder=5)
private Double deltaX

deltaY

@Parameter(label="pixel length, y-direction",
           required=false,
           direction=IN,
           supplemental=false,
           description="pixel length in y-direction",
           dataIOOrder=6)
private Double deltaY

unitXY

@Parameter(label="unit space",
           required=false,
           direction=IN,
           supplemental=false,
           description="unit x/y",
           dataIOOrder=7)
private String unitXY

deltaT

@Parameter(label="time between frames",
           required=false,
           direction=IN,
           supplemental=false,
           description="time between frames",
           dataIOOrder=8)
private Double deltaT

unitT

@Parameter(label="unit time",
           required=false,
           direction=IN,
           supplemental=false,
           description="unit time",
           dataIOOrder=9)
private String unitT

minTrackLength

@Parameter(label="minimum track length",
           required=false,
           direction=IN,
           supplemental=false,
           description="minimum track length to be considered",
           dataIOOrder=10)
private Integer minTrackLength

analyzeTrajectories

@Parameter(label="analyze trajectories",
           required=false,
           direction=IN,
           supplemental=false,
           description="should the objects\' trajectories be analyzed",
           dataIOOrder=11)
private Boolean analyzeTrajectories

analyzeShapes

@Parameter(label="analyze shapes",
           required=false,
           direction=IN,
           supplemental=false,
           description="should the objects\' shapes be analyzed",
           dataIOOrder=12)
private Boolean analyzeShapes

analyzeIntensities

@Parameter(label="analyze intensities",
           required=false,
           direction=IN,
           supplemental=false,
           description="should the objects\' intensities be analyzed",
           dataIOOrder=13)
private Boolean analyzeIntensities

showTrajectoryMap

@Parameter(label="show trajectory map",
           required=false,
           direction=IN,
           supplemental=false,
           description="should a 2D map of the extracted trajectories be shown",
           dataIOOrder=14)
private Boolean showTrajectoryMap

showOverlayImage

@Parameter(label="show overlay image",
           required=false,
           direction=IN,
           supplemental=false,
           description="should the extracted trajectories be shown overlayed on the cells",
           dataIOOrder=15)
private Boolean showOverlayImage

removeExcluded

@Parameter(label="remove excluded objects",
           required=false,
           direction=IN,
           supplemental=false,
           description="should objects that weren\'t analyzed be removed from the label image",
           dataIOOrder=16)
private Boolean removeExcluded

trackReport

@Parameter(label="track report",
           required=true,
           direction=OUT,
           supplemental=false,
           description="track report")
private String trackReport

shapeReport

@Parameter(label="shape report",
           required=true,
           direction=OUT,
           supplemental=false,
           description="shape report")
private String shapeReport

intReport

@Parameter(label="intensity report",
           required=true,
           direction=OUT,
           supplemental=false,
           description="intensity report")
private String intReport

Constructor Detail

MigrationAnalyzer

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

Throws:

de.unihalle.informatik.Alida.exceptions.ALDOperatorException

MigrationAnalyzer

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

Throws:

de.unihalle.informatik.Alida.exceptions.ALDOperatorException

MigrationAnalyzer

public MigrationAnalyzer(MTBImage labelImg,
                         MTBImage maskImg)
                  throws de.unihalle.informatik.Alida.exceptions.ALDOperatorException

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

setIntensityImage

public void setIntensityImage(MTBImage intImg)

Parameters:

intImg -

setDeltaX

public void setDeltaX(double deltaX)

Parameters:

deltaX -

setDeltaY

public void setDeltaY(double deltaY)

Parameters:

deltaY -

setDeltaT

public void setDeltaT(double deltaT)

Parameters:

deltaT -

setUnitXY

public void setUnitXY(String unitXY)

Parameters:

unitXY -

setUnitT

public void setUnitT(String unitT)

Parameters:

unitT -

setMinTrackLength

public void setMinTrackLength(int minTrackLength)

Parameters:

minTrackLength -

includeMask

public void includeMask(boolean include)

removeExcludedObjects

public void removeExcludedObjects(boolean remove)

setFactor

public void setFactor(double factor)

analyzeTrajectories

public void analyzeTrajectories(boolean analyzeTrajectories)

Parameters:

analyzeTrajectories -

analyzeShapes

public void analyzeShapes(boolean analyzeShapes)

Parameters:

analyzeShapes -

analyzeIntensities

public void analyzeIntensities(boolean analyzeIntensities)

Parameters:

analyzeIntensities -

showTrajectoryMap

public void showTrajectoryMap(boolean showTrajectories)

Parameters:

showTrajectories -

showOverlayImage

public void showOverlayImage(boolean showOverlay)

Parameters:

showOverlay -

getLabelImage

public MTBImage getLabelImage()

Returns:

label image

getTrackReport

public String getTrackReport()

Returns:

tracking report

getShapeReport

public String getShapeReport()

Returns:

shape report

getIntensityReport

public String getIntensityReport()

Returns:

intensity report

getCalibration

private void getCalibration()

showMaskChannelTextbox

private void showMaskChannelTextbox()

getDocumentation

public String getDocumentation()

Overrides:

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