de.mpg.biochem.mars.object.commands

Class ObjectTrackerCommand

java.lang.Object

org.scijava.module.AbstractModule

org.scijava.module.DefaultMutableModule

org.scijava.command.DynamicCommand

de.mpg.biochem.mars.object.commands.ObjectTrackerCommand

All Implemented Interfaces:

java.lang.Runnable, org.scijava.Cancelable, org.scijava.command.Command, org.scijava.command.Previewable, org.scijava.Contextual, org.scijava.Initializable, org.scijava.module.Module, org.scijava.module.MutableModule, org.scijava.plugin.SciJavaPlugin

public class ObjectTrackerCommand
extends org.scijava.command.DynamicCommand
implements org.scijava.command.Command, org.scijava.Initializable, org.scijava.command.Previewable

Field Summary

Fields inherited from class org.scijava.command.DynamicCommand

moduleService, pluginService

Constructor Summary

Constructors

Constructor and Description
ObjectTrackerCommand()

Method Summary

Modifier and Type	Method and Description
void	cancel()
ObjectArchive	getArchive()
int	getChannel()
net.imagej.Dataset	getDataset()
java.lang.String	getExcludedTimePointsList()
ij.ImagePlus	getImagePlus()
double	getInterpolationFactor()
double	getLocalOtsuRadius()
int	getMaxDifferenceT()
double	getMaxDifferenceX()
double	getMaxDifferenceY()
java.lang.String	getMetadataUIDSource()
java.lang.String	getMicroscope()
double	getMinimumArea()
int	getMinimumDistance()
int	getMinimumTrackLength()
double	getPixelLength()
java.lang.String	getPixelUnits()
java.lang.String	getRegion()
ij.gui.Roi[]	getROIs()
int	getThreads()
boolean	getUseAreaFilter()
boolean	getUseLocalOstu()
boolean	getVerboseOutput()
void	initialize()
void	preview()
protected void	previewChanged() Called when the preview parameter value changes.
void	run()
void	setChannel(int channel)
void	setDataset(net.imagej.Dataset dataset)
void	setExcludedTimePointsList(java.lang.String excludeTimePointList)
void	setImagePlus(ij.ImagePlus image)
void	setInterpolationFactor(double interpolationFactor)
void	setLocalOtsuRadius(int otsuRadius)
void	setMaxDifferenceT(int maxDifferenceT)
void	setMaxDifferenceX(double PeakTracker_maxDifferenceX)
void	setMaxDifferenceY(double maxDifferenceY)
void	setMetadataUIDSource(java.lang.String metadataUIDSource)
void	setMicroscope(java.lang.String microscope)
void	setMinimumArea(double minArea)
void	setMinimumDistance(int minimumDistance)
void	setMinimumTrackLength(int minTrajectoryLength)
void	setPixelLength(double pixelLength)
void	setPixelUnits(java.lang.String pixelUnits)
void	setRegion(java.lang.String region)
void	setRois(ij.gui.Roi[] rois)
void	setThreads(int nThreads)
void	setUseAreaFilter(boolean useAreaFilter)
void	setUseLocalOstu(boolean useLocalOstu)
void	setVerboseOutput(boolean verbose)

Methods inherited from class org.scijava.command.DynamicCommand

cancel, context, getCancelReason, getContext, getInfo, getInput, getOutput, isCanceled, saveInputs, setContext, setInput, setOutput, uncancel

Methods inherited from class org.scijava.module.AbstractModule

getDelegateObject, getInputs, getOutputs, isInputResolved, isOutputResolved, resolveInput, resolveOutput, setInputs, setOutputs, unresolveInput, unresolveOutput

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Methods inherited from interface org.scijava.module.MutableModule

addInput, addInput, addOutput, addOutput, removeInput, removeOutput

Methods inherited from interface org.scijava.module.Module

getDelegateObject, getInputs, getOutputs, isInputResolved, isOutputResolved, isResolved, resolveInput, resolveOutput, setInputs, setOutputs, setResolved, unresolveInput, unresolveOutput

Constructor Detail

ObjectTrackerCommand

public ObjectTrackerCommand()

Method Detail

initialize

public void initialize()

Specified by:

initialize in interface org.scijava.Initializable

Specified by:

initialize in interface org.scijava.module.Module

Overrides:

initialize in class org.scijava.module.AbstractModule

run

public void run()

Specified by:

run in interface java.lang.Runnable

Specified by:

run in interface org.scijava.module.MutableModule

preview

public void preview()

Specified by:

preview in interface org.scijava.command.Previewable

Specified by:

preview in interface org.scijava.module.Module

Overrides:

preview in class org.scijava.module.AbstractModule

cancel

public void cancel()

Specified by:

cancel in interface org.scijava.command.Previewable

Specified by:

cancel in interface org.scijava.module.Module

Overrides:

cancel in class org.scijava.module.AbstractModule

previewChanged

protected void previewChanged()

Called when the preview parameter value changes.

getArchive

public ObjectArchive getArchive()

setDataset

public void setDataset(net.imagej.Dataset dataset)

getDataset

public net.imagej.Dataset getDataset()

setImagePlus

public void setImagePlus(ij.ImagePlus image)

getImagePlus

public ij.ImagePlus getImagePlus()

setRegion

public void setRegion(java.lang.String region)

getRegion

public java.lang.String getRegion()

setRois

public void setRois(ij.gui.Roi[] rois)

getROIs

public ij.gui.Roi[] getROIs()

setChannel

public void setChannel(int channel)

getChannel

public int getChannel()

setUseLocalOstu

public void setUseLocalOstu(boolean useLocalOstu)

getUseLocalOstu

public boolean getUseLocalOstu()

setLocalOtsuRadius

public void setLocalOtsuRadius(int otsuRadius)

getLocalOtsuRadius

public double getLocalOtsuRadius()

setMinimumDistance

public void setMinimumDistance(int minimumDistance)

getMinimumDistance

public int getMinimumDistance()

setInterpolationFactor

public void setInterpolationFactor(double interpolationFactor)

getInterpolationFactor

public double getInterpolationFactor()

setUseAreaFilter

public void setUseAreaFilter(boolean useAreaFilter)

getUseAreaFilter

public boolean getUseAreaFilter()

setMinimumArea

public void setMinimumArea(double minArea)

getMinimumArea

public double getMinimumArea()

setVerboseOutput

public void setVerboseOutput(boolean verbose)

getVerboseOutput

public boolean getVerboseOutput()

setMaxDifferenceX

public void setMaxDifferenceX(double PeakTracker_maxDifferenceX)

getMaxDifferenceX

public double getMaxDifferenceX()

setMaxDifferenceY

public void setMaxDifferenceY(double maxDifferenceY)

getMaxDifferenceY

public double getMaxDifferenceY()

setMaxDifferenceT

public void setMaxDifferenceT(int maxDifferenceT)

getMaxDifferenceT

public int getMaxDifferenceT()

setMinimumTrackLength

public void setMinimumTrackLength(int minTrajectoryLength)

getMinimumTrackLength

public int getMinimumTrackLength()

setMicroscope

public void setMicroscope(java.lang.String microscope)

getMicroscope

public java.lang.String getMicroscope()

setPixelLength

public void setPixelLength(double pixelLength)

getPixelLength

public double getPixelLength()

setPixelUnits

public void setPixelUnits(java.lang.String pixelUnits)

getPixelUnits

public java.lang.String getPixelUnits()

setExcludedTimePointsList

public void setExcludedTimePointsList(java.lang.String excludeTimePointList)

getExcludedTimePointsList

public java.lang.String getExcludedTimePointsList()

setThreads

public void setThreads(int nThreads)

getThreads

public int getThreads()

setMetadataUIDSource

public void setMetadataUIDSource(java.lang.String metadataUIDSource)

getMetadataUIDSource

public java.lang.String getMetadataUIDSource()