de.unihalle.informatik.MiToBo.apps.singleCellTracking2D

Class ShapeAnalyzer

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.ShapeAnalyzer

All Implemented Interfaces:

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

public class ShapeAnalyzer
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
(package private) Hashtable<Integer,Vector<Double>>	areas
(package private) Hashtable<Integer,Vector<Double>>	circularities
(package private) Hashtable<Integer,Vector<Double>>	eccentricities
private MTBImage	labelImg
(package private) Hashtable<Integer,Vector<Double>>	lengths
(package private) Hashtable<Integer,Vector<Double>>	perimeters
private int	sizeT
private int	sizeX
private int	sizeY
(package private) Hashtable<Integer,Vector<Double>>	widths

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
ShapeAnalyzer(MTBImage labelImg) constructor

Method Summary

Modifier and Type	Method and Description
private Hashtable<Integer,Vector<Double>>	getAreaFractions(Hashtable<Integer,Vector<Double>> areas)
private Hashtable<Integer,Vector<Double>>	getOverlaps()
private void	getShapeFeatures() calculate several shape features in one method
protected 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

labelImg

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

sizeT

private int sizeT

sizeX

private int sizeX

sizeY

private int sizeY

areas

Hashtable<Integer,Vector<Double>> areas

perimeters

Hashtable<Integer,Vector<Double>> perimeters

circularities

Hashtable<Integer,Vector<Double>> circularities

eccentricities

Hashtable<Integer,Vector<Double>> eccentricities

lengths

Hashtable<Integer,Vector<Double>> lengths

widths

Hashtable<Integer,Vector<Double>> widths

Constructor Detail

ShapeAnalyzer

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

constructor

Parameters:

labelImg - input label image

Throws:

de.unihalle.informatik.Alida.exceptions.ALDOperatorException

Method Detail

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

getShapeFeatures

private void getShapeFeatures()

calculate several shape features in one method

getAreaFractions

private Hashtable<Integer,Vector<Double>> getAreaFractions(Hashtable<Integer,Vector<Double>> areas)

Parameters:

areas - areas of the objects in the distinct frames

Returns:

key: areas fractions of the objects from one frame to the next
key: object-id, value: list of areas fractions

getOverlaps

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

Returns:

key: overlap of the object pixels in the distinct frames
key: object-id, value: list of overlaps