de.unihalle.informatik.MiToBo.apps.singleCellTracking2D

Class TrackAnalyzer

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.TrackAnalyzer

All Implemented Interfaces:

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

public class TrackAnalyzer
extends ReportGenerator

class for analyzing movement and shape of already tracked objects in a given label image

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 Hashtable<Integer,Vector<Point2D.Double>>	centroids
private double	maxDist
private Hashtable<Integer,Integer>	offsets
private Vector<Trajectory2D>	trajectories

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
TrackAnalyzer(Vector<Trajectory2D> trajectories)

Method Summary

Modifier and Type	Method and Description
private double	angle(Point2D.Double p, Point2D.Double q)
private double	distance(Point2D.Double p, Point2D.Double q, double deltaX, double deltaY)
private void	extractTrajectoriesWithOffsets() extract Hashtables containing the centroid locations of each trajectory and the offsets for the starting time of each trajectory
private Hashtable<Integer,Vector<Double>>	getDirectionalDifferences(Hashtable<Integer,Vector<Double>> directions)
private Hashtable<Integer,Vector<Double>>	getDirectionalities(Hashtable<Integer,Vector<Double>> netDistances, Hashtable<Integer,Vector<Double>> totalDistances)
private Hashtable<Integer,Vector<Double>>	getDirections()
private Hashtable<Integer,Vector<Double>>	getDistances()
private Hashtable<Integer,Vector<Double>>	getNetDirections()
private Hashtable<Integer,Vector<Double>>	getNetDistances()
private Hashtable<Integer,Vector<Double>>	getNumberOfFrames()
private Hashtable<Integer,Vector<Double>>	getPersistences(Hashtable<Integer,Vector<Double>> speeds, Hashtable<Integer,Vector<Double>> dirDiffs)
private Hashtable<Integer,Vector<Double>>	getSpeeds(Hashtable<Integer,Vector<Double>> distances)
private Hashtable<Integer,Vector<Double>>	getTotalDistances(Hashtable<Integer,Vector<Double>> distances)
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

trajectories

@Parameter(label="trajectories",
           required=true,
           direction=IN,
           supplemental=false,
           description="trajectories",
           dataIOOrder=0)
private Vector<Trajectory2D> trajectories

centroids

private Hashtable<Integer,Vector<Point2D.Double>> centroids

offsets

private Hashtable<Integer,Integer> offsets

maxDist

private double maxDist

Constructor Detail

TrackAnalyzer

public TrackAnalyzer(Vector<Trajectory2D> trajectories)
              throws de.unihalle.informatik.Alida.exceptions.ALDOperatorException

Parameters:

trajectories -

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

extractTrajectoriesWithOffsets

private void extractTrajectoriesWithOffsets()

extract Hashtables containing the centroid locations of each trajectory
and the offsets for the starting time of each trajectory

getDistances

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

Returns:

distances that the objects moved from one frame to another
key: object-id, value: list of distances

getSpeeds

private Hashtable<Integer,Vector<Double>> getSpeeds(Hashtable<Integer,Vector<Double>> distances)

Parameters:

distances - distances the objects moved

Returns:

key: speeds of the objects between consecutive frames
key: object-id, value: list of speeds

getNumberOfFrames

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

Returns:

number of frames each object is available

getDirections

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

Returns:

directions of movement (degree [0, 359]) of each object from one frame to another
key: object-id, value: list of directions

getDirectionalDifferences

private Hashtable<Integer,Vector<Double>> getDirectionalDifferences(Hashtable<Integer,Vector<Double>> directions)

Parameters:

directions -

Returns:

differences in directions of movement (degree [0, 180]) of each object from one frame to another
key: object-id, value: list of directions

getPersistences

private Hashtable<Integer,Vector<Double>> getPersistences(Hashtable<Integer,Vector<Double>> speeds,
                                                          Hashtable<Integer,Vector<Double>> dirDiffs)

Parameters:

speeds -

dirDiffs -

Returns:

persistence values of each object in every frame calculated as speed / (1 + (100 / 360) * directional change) key: object-id, value: list of persistences

getTotalDistances

private Hashtable<Integer,Vector<Double>> getTotalDistances(Hashtable<Integer,Vector<Double>> distances)

Parameters:

distances - distances that the objects moved from one frame to another

Returns:

total (euclidean) distances the objects moved
key: object-id, value: total distance

getNetDistances

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

Returns:

net (euclidean) distances the objects moved
key: object-id, value: net distance

getDirectionalities

private Hashtable<Integer,Vector<Double>> getDirectionalities(Hashtable<Integer,Vector<Double>> netDistances,
                                                              Hashtable<Integer,Vector<Double>> totalDistances)

Parameters:

netDistances - net distance the objects moved

totalDistances - total distance the objects moved

Returns:

directionalities of the distinct objects
key: object-id, value: directionality

getNetDirections

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

Returns:

net directions (degree [0, 359]) of the single objects,
i.e. the angle between the vector formed by the first and the last position of an object and the x-axis
key: object-id, value: net direction

distance

private double distance(Point2D.Double p,
                        Point2D.Double q,
                        double deltaX,
                        double deltaY)

Parameters:

p -

q -

deltaX -

deltaY -

Returns:

euclidean distance between p an q scaled by parameters deltaX and deltaY

angle

private double angle(Point2D.Double p,
                     Point2D.Double q)

Parameters:

p -

q -

Returns:

angle (degree [0, 359]) between the vector formed by the points p and q and the x-axis (vector (1,0))