de.unihalle.informatik.MiToBo.apps.singleCellTracking2D

Class ReportGenerator

java.lang.Object

de.unihalle.informatik.Alida.operator.ALDOperator

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

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

All Implemented Interfaces:

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

Direct Known Subclasses:

IntensityAnalyzer, ShapeAnalyzer, TrackAnalyzer

public abstract class ReportGenerator
extends MTBOperator

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
protected int	bgLabel
protected double	deltaT
protected double	deltaX
protected double	deltaY
protected double	deltaZ
protected Vector<Integer>	exclude
protected int	minTrackLength
protected String	naString
protected NumberFormat	nf
protected String	report
protected String	unitAngle
protected String	unitSpace
protected String	unitTime

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

completeDAG, name, operatorExecutionEventlistenerList, portHashAccess, verbose, versionProvider

Constructor Summary

Constructors

Constructor and Description
ReportGenerator()

Method Summary

Modifier and Type	Method and Description
protected double	getAverageMean(Hashtable<Integer,Vector<Double>> meanValues)
protected double	getAverageStdDev(Hashtable<Integer,Vector<Double>> meanValues)
protected String	getExcluded()
protected Hashtable<Integer,Vector<Double>>	getObjectsMeans(Hashtable<Integer,Vector<Double>> values)
protected Hashtable<Integer,Vector<Double>>	getObjectsStdDevs(Hashtable<Integer,Vector<Double>> values)
String	getReport()
protected String	getSettings()
protected String	hashtableToString(Hashtable<Integer,Vector<Double>> table, String caption)
protected String	hashtableToString(Hashtable<Integer,Vector<Double>> table, String caption, Hashtable<Integer,Integer> offsets)
protected String	numberToString(double num)
protected String	pointHashtableToString(Hashtable<Integer,Vector<Point2D.Double>> table, String caption)
protected String	pointHashtableToStringX(Hashtable<Integer,Vector<Point2D.Double>> table, String caption)
protected String	pointHashtableToStringY(Hashtable<Integer,Vector<Point2D.Double>> table, String caption)
protected StringBuffer	pointVectorToString(Vector<Point2D.Double> values)
protected StringBuffer	pointVectorToStringX(Vector<Point2D.Double> values)
protected StringBuffer	pointVectorToStringY(Vector<Point2D.Double> values)
void	setDeltaT(double dt) set the time between two frames
void	setDeltaX(double dx) set pixel length in x-direction
void	setDeltaY(double dy) set pixel length in y-direction
void	setExcluded(Vector<Integer> exclude)
void	setMinTrackLength(int minTrackLength) set minimum track length
void	setUnitAngle(String unitAngle) set unit of angles
void	setUnitSpace(String unitXY) set unit of space
void	setUnitTime(String unitT) set unit of time
protected Hashtable<Integer,Vector<Double>>	trim(Hashtable<Integer,Vector<Double>> values, int minLength)
protected StringBuffer	vectorToString(int offset, Vector<Double> values)
protected StringBuffer	vectorToString(Vector<Double> values)

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, operate, 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

deltaX

@Parameter(label="\u0394 x",
           required=false,
           direction=IN,
           supplemental=false,
           description="pixel length in x-direction",
           dataIOOrder=5)
protected double deltaX

deltaY

@Parameter(label="\u0394 y",
           required=false,
           direction=IN,
           supplemental=false,
           description="pixel length in y-direction",
           dataIOOrder=6)
protected double deltaY

deltaZ

@Parameter(label="\u0394 z",
           required=false,
           direction=IN,
           supplemental=false,
           description="pixel length in z-direction",
           dataIOOrder=7)
protected double deltaZ

deltaT

@Parameter(label="\u0394 t",
           required=false,
           direction=IN,
           supplemental=false,
           description="time between consecutive frames",
           dataIOOrder=8)
protected double deltaT

unitSpace

@Parameter(label="unit of space",
           required=false,
           direction=IN,
           supplemental=false,
           description="unit of space",
           dataIOOrder=9)
protected String unitSpace

unitTime

@Parameter(label="unit of time",
           required=false,
           direction=IN,
           supplemental=false,
           description="unit of time",
           dataIOOrder=10)
protected String unitTime

unitAngle

@Parameter(label="unit of angles",
           required=false,
           direction=IN,
           supplemental=false,
           description="unit of angles",
           dataIOOrder=11)
protected String unitAngle

minTrackLength

@Parameter(label="minimum track length",
           required=false,
           direction=IN,
           supplemental=false,
           description="minimum length a track must have to be considered",
           dataIOOrder=12)
protected int minTrackLength

report

@Parameter(label="report",
           required=true,
           direction=OUT,
           supplemental=false,
           description="resulting report")
protected String report

nf

protected NumberFormat nf

naString

protected final String naString

See Also:

Constant Field Values

exclude

protected Vector<Integer> exclude

bgLabel

protected int bgLabel

Constructor Detail

ReportGenerator

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

Throws:

de.unihalle.informatik.Alida.exceptions.ALDOperatorException

Method Detail

getObjectsMeans

protected Hashtable<Integer,Vector<Double>> getObjectsMeans(Hashtable<Integer,Vector<Double>> values)

Parameters:

values - hash table containing object id-value list pairs

Returns:

means of the values for the distinct objects

getObjectsStdDevs

protected Hashtable<Integer,Vector<Double>> getObjectsStdDevs(Hashtable<Integer,Vector<Double>> values)

Parameters:

values - hash table containing object id-value list pairs

Returns:

standard deviations of the values for the distinct objects

trim

protected Hashtable<Integer,Vector<Double>> trim(Hashtable<Integer,Vector<Double>> values,
                                                 int minLength)

Parameters:

values - hash table containing object id-value list pairs

minLength - minimum length a track must have to be kept

Returns:

trimmed hash table containing only those id-value lists that have at least minTrackLength entries

getAverageMean

protected double getAverageMean(Hashtable<Integer,Vector<Double>> meanValues)

Parameters:

meanValues -

Returns:

average of the mean values

getAverageStdDev

protected double getAverageStdDev(Hashtable<Integer,Vector<Double>> meanValues)

Parameters:

meanValues -

Returns:

average of the standard deviations

hashtableToString

protected String hashtableToString(Hashtable<Integer,Vector<Double>> table,
                                   String caption)

Parameters:

table -

caption - heading for the data

Returns:

string representation of the input hash table

hashtableToString

protected String hashtableToString(Hashtable<Integer,Vector<Double>> table,
                                   String caption,
                                   Hashtable<Integer,Integer> offsets)

Parameters:

table - data to print

caption - heading for the data

offsets - number of time points where no data are available for the respective objects

Returns:

string representation of the input hash table

pointHashtableToString

protected String pointHashtableToString(Hashtable<Integer,Vector<Point2D.Double>> table,
                                        String caption)

Parameters:

table -

caption - heading for the data

Returns:

string representation of the input hash table

pointHashtableToStringX

protected String pointHashtableToStringX(Hashtable<Integer,Vector<Point2D.Double>> table,
                                         String caption)

Parameters:

table -

caption - heading for the data

Returns:

string representation of the input hash table

pointHashtableToStringY

protected String pointHashtableToStringY(Hashtable<Integer,Vector<Point2D.Double>> table,
                                         String caption)

Parameters:

table -

caption - heading for the data

Returns:

string representation of the input hash table

vectorToString

protected StringBuffer vectorToString(Vector<Double> values)

Parameters:

values -

Returns:

string representation of the input vector

vectorToString

protected StringBuffer vectorToString(int offset,
                                      Vector<Double> values)

Parameters:

offset -

values -

Returns:

string representation of the input vector

pointVectorToString

protected StringBuffer pointVectorToString(Vector<Point2D.Double> values)

Parameters:

values -

Returns:

string representation of the input vector

pointVectorToStringX

protected StringBuffer pointVectorToStringX(Vector<Point2D.Double> values)

Parameters:

values -

Returns:

string representation of the x-coordinates of the input vector

pointVectorToStringY

protected StringBuffer pointVectorToStringY(Vector<Point2D.Double> values)

Parameters:

values -

Returns:

string representation of the y-coordinates of the input vector

numberToString

protected String numberToString(double num)

Parameters:

num - input number

Returns:

formatted String representation of the input number

getSettings

protected String getSettings()

Returns:

String containing information about parameter settings used

getExcluded

protected String getExcluded()

setDeltaT

public void setDeltaT(double dt)

set the time between two frames

Parameters:

dt -

setDeltaX

public void setDeltaX(double dx)

set pixel length in x-direction

Parameters:

dx -

setDeltaY

public void setDeltaY(double dy)

set pixel length in y-direction

Parameters:

dy -

setUnitTime

public void setUnitTime(String unitT)

set unit of time

Parameters:

unitT -

setUnitSpace

public void setUnitSpace(String unitXY)

set unit of space

Parameters:

unitXY -

setUnitAngle

public void setUnitAngle(String unitAngle)

set unit of angles

Parameters:

unitAngle -

setMinTrackLength

public void setMinTrackLength(int minTrackLength)

set minimum track length

Parameters:

minTrackLength -

setExcluded

public void setExcluded(Vector<Integer> exclude)

getReport

public String getReport()