de.unihalle.informatik.MiToBo.apps.singleCellTracking2D

Class IntensityAnalyzer

java.lang.Object

de.unihalle.informatik.Alida.operator.ALDOperator

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

de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.ReportGenerator

de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.IntensityAnalyzer

All Implemented Interfaces:

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

public class IntensityAnalyzer
extends ReportGenerator

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 MTBImage	intensityImg
private MTBImage	labelImg
private int	sizeT
private int	sizeX
private int	sizeY

Fields inherited from class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.ReportGenerator

bgLabel, deltaT, deltaX, deltaY, deltaZ, exclude, minTrackLength, naString, nf, report, unitAngle, unitSpace, unitTime

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

completeDAG, name, operatorExecutionEventlistenerList, portHashAccess, verbose, versionProvider

Constructor Summary

Constructors

Constructor and Description
IntensityAnalyzer(MTBImage intensityImg, MTBImage labelImg)

Method Summary

Modifier and Type	Method and Description
private Hashtable<Integer,Vector<Double>>	getIntensityMeans()
private Hashtable<Integer,Vector<Double>>	getIntensityStdDevs(Hashtable<Integer,Vector<Double>> intensityMeans)
private Hashtable<Integer,Vector<Double>>	getMeanBackgroundIntensity()
private Hashtable<Integer,Vector<Double>>	getStdDevBackgroundIntensity(Hashtable<Integer,Vector<Double>> meanBGIntensity)
void	operate()

Methods inherited from class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.ReportGenerator

getAverageMean, getAverageStdDev, getExcluded, getObjectsMeans, getObjectsStdDevs, getReport, getSettings, hashtableToString, hashtableToString, numberToString, pointHashtableToString, pointHashtableToStringX, pointHashtableToStringY, pointVectorToString, pointVectorToStringX, pointVectorToStringY, setDeltaT, setDeltaX, setDeltaY, setExcluded, setMinTrackLength, setUnitAngle, setUnitSpace, setUnitTime, trim, vectorToString, vectorToString

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

intensityImg

@Parameter(label="(fluorescence) intensity image",
           required=true,
           direction=IN,
           supplemental=false,
           description="(fluorescence) intensity image",
           dataIOOrder=0)
private transient MTBImage intensityImg

labelImg

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

sizeX

private int sizeX

sizeY

private int sizeY

sizeT

private int sizeT

Constructor Detail

IntensityAnalyzer

public IntensityAnalyzer(MTBImage intensityImg,
                         MTBImage labelImg)
                  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

getIntensityMeans

private Hashtable<Integer,Vector<Double>> getIntensityMeans()

Parameters:

intensityImg -

Returns:

mean intensities of each object in every frame
key: object-id, value: list of mean intensities

getIntensityStdDevs

private Hashtable<Integer,Vector<Double>> getIntensityStdDevs(Hashtable<Integer,Vector<Double>> intensityMeans)

Parameters:

intensityMeans - mean intensities of each object in every frame

Returns:

standard deviation of intensities of each object in every frame
key: object-id, value: list of standard deviations

getMeanBackgroundIntensity

private Hashtable<Integer,Vector<Double>> getMeanBackgroundIntensity()

Returns:

mean background intensity for every frame
key: object-id (= background label), value: list of mean intensities

getStdDevBackgroundIntensity

private Hashtable<Integer,Vector<Double>> getStdDevBackgroundIntensity(Hashtable<Integer,Vector<Double>> meanBGIntensity)

Parameters:

meanBGIntensity - mean intensities of background in every frame

Returns:

standard deviation of background intensity in every frame
key: object-id (= background label), value: list of standard deviations