de.mpg.biochem.mars.image.commands

Class PeakTrackerCommand

java.lang.Object

org.scijava.module.AbstractModule

org.scijava.module.DefaultMutableModule

org.scijava.command.DynamicCommand

de.mpg.biochem.mars.image.commands.PeakTrackerCommand

All Implemented Interfaces:

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

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

Field Summary

Fields inherited from class org.scijava.command.DynamicCommand

moduleService, pluginService

Constructor Summary

Constructors

Constructor and Description
PeakTrackerCommand()

Method Summary

Modifier and Type	Method and Description
void	cancel()
SingleMoleculeArchive	getArchive()
int	getChannel()
net.imagej.Dataset	getDataset()
java.lang.String	getExcludedTimePointsList()
boolean	getFindNegativePeaks()
int	getFitRadius()
boolean	getGridProcess()
int	getHorizontalGridRegions()
ij.ImagePlus	getImagePlus()
boolean	getIntegrate()
int	getIntegrationInnerRadius()
int	getIntegrationOuterRadius()
int	getMaxDifferenceT()
double	getMaxDifferenceX()
double	getMaxDifferenceY()
java.lang.String	getMetadataUIDSource()
java.lang.String	getMicroscope()
int	getMinimumDistance()
double	getMinimumRsquared()
int	getMinimumTrackLength()
double	getPixelLength()
java.lang.String	getPixelUnits()
java.lang.String	getRegion()
ij.gui.Roi[]	getROIs()
int	getThreads()
double	getThreshold()
boolean	getVerboseOutput()
int	getVerticalGridRegions()
void	initialize()
protected void	openWebPage()
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	setDogFilterRadius(double dogFilterRadius)
void	setExcludedTimePointsList(java.lang.String excludeTimePointList)
void	setFindNegativePeaks(boolean findNegativePeaks)
void	setFitRadius(int fitRadius)
void	setGridProcess(boolean gridProcess)
void	setHorizontalGridRegions(int horizontalGridRegions)
void	setImagePlus(ij.ImagePlus image)
void	setIntegrate(boolean integrate)
void	setIntegrationInnerRadius(int integrationInnerRadius)
void	setIntegrationOuterRadius(int integrationOuterRadius)
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	setMinimumDistance(int minimumDistance)
void	setMinimumRsquared(double Rsquared)
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	setThreshold(int threshold)
void	setUseDogFiler(boolean useDogFilter)
void	setVerboseOutput(boolean verbose)
void	setVerticalGridRegions(int verticalGridRegions)

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

PeakTrackerCommand

public PeakTrackerCommand()

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.module.Module

Overrides:

preview in class org.scijava.module.AbstractModule

openWebPage

protected void openWebPage()

cancel

public void cancel()

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 SingleMoleculeArchive 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()

setUseDogFiler

public void setUseDogFiler(boolean useDogFilter)

setDogFilterRadius

public void setDogFilterRadius(double dogFilterRadius)

setThreshold

public void setThreshold(int threshold)

getThreshold

public double getThreshold()

setMinimumDistance

public void setMinimumDistance(int minimumDistance)

getMinimumDistance

public int getMinimumDistance()

setFindNegativePeaks

public void setFindNegativePeaks(boolean findNegativePeaks)

getFindNegativePeaks

public boolean getFindNegativePeaks()

setFitRadius

public void setFitRadius(int fitRadius)

getFitRadius

public int getFitRadius()

setMinimumRsquared

public void setMinimumRsquared(double Rsquared)

getMinimumRsquared

public double getMinimumRsquared()

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()

setIntegrate

public void setIntegrate(boolean integrate)

getIntegrate

public boolean getIntegrate()

setIntegrationInnerRadius

public void setIntegrationInnerRadius(int integrationInnerRadius)

getIntegrationInnerRadius

public int getIntegrationInnerRadius()

setIntegrationOuterRadius

public void setIntegrationOuterRadius(int integrationOuterRadius)

getIntegrationOuterRadius

public int getIntegrationOuterRadius()

setGridProcess

public void setGridProcess(boolean gridProcess)

getGridProcess

public boolean getGridProcess()

setHorizontalGridRegions

public void setHorizontalGridRegions(int horizontalGridRegions)

getHorizontalGridRegions

public int getHorizontalGridRegions()

setVerticalGridRegions

public void setVerticalGridRegions(int verticalGridRegions)

getVerticalGridRegions

public int getVerticalGridRegions()

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()