de.mpg.biochem.mars.image.commands

Class PeakFinderCommand

java.lang.Object

org.scijava.module.AbstractModule

org.scijava.module.DefaultMutableModule

org.scijava.command.DynamicCommand

de.mpg.biochem.mars.image.commands.PeakFinderCommand

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 PeakFinderCommand
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
PeakFinderCommand()

Method Summary

Modifier and Type	Method and Description
void	cancel()
boolean	getAddToRoiManager()
int	getChannel()
net.imagej.Dataset	getDataset()
boolean	getFindNegativePeaks()
boolean	getFitPeaks()
int	getFitRadius()
boolean	getGeneratePeakCountTable()
boolean	getGeneratePeakTable()
boolean	getIntegrate()
int	getIntegrationInnerRadius()
int	getIntegrationOuterRadius()
int	getMinimumDistance()
double	getMinimumRsquared()
MarsTable	getPeakCountTable()
MarsTable	getPeakTable()
boolean	getProcessAllFrames()
java.lang.String	getRegion()
ij.plugin.frame.RoiManager	getRoiManager()
ij.gui.Roi[]	getROIs()
java.lang.String	getRoiType()
int	getT()
int	getThreads()
double	getThreshold()
boolean	getVerbose()
void	initialize()
protected void	openWebPage()
void	preview()
protected void	previewChanged() Called when the preview parameter value changes.
void	run()
void	setAddToRoiManager(boolean addToRoiManager)
void	setChannel(int channel)
void	setDataset(net.imagej.Dataset dataset)
void	setDogFilterRadius(double dogFilterRadius)
void	setFindNegativePeaks(boolean findNegativePeaks)
void	setFitPeaks(boolean fitPeaks)
void	setFitRadius(int fitRadius)
void	setGeneratePeakCountTable(boolean generatePeakCountTable)
void	setGeneratePeakTable(boolean generatePeakTable)
void	setIntegrate(boolean integrate)
void	setIntegrationInnerRadius(int integrationInnerRadius)
void	setIntegrationOuterRadius(int integrationOuterRadius)
void	setMinimumDistance(int minimumDistance)
void	setMinimumRsquared(double RsquaredMin)
void	setProcessAllFrames(boolean allFrames)
void	setRegion(java.lang.String region)
void	setRoiManager(ij.plugin.frame.RoiManager roiManager)
void	setRois(ij.gui.Roi[] rois)
void	setRoiType(java.lang.String roiType) This method specifies the type of Roi to add to the RoiManager.
void	setT(int theT)
void	setThreads(int nThreads)
void	setThreshold(double threshold)
void	setUseDogFiler(boolean useDogFilter)
void	setVerbose(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

PeakFinderCommand

public PeakFinderCommand()

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

openWebPage

protected void openWebPage()

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.

setRoiManager

public void setRoiManager(ij.plugin.frame.RoiManager roiManager)

getRoiManager

public ij.plugin.frame.RoiManager getRoiManager()

getPeakCountTable

public MarsTable getPeakCountTable()

getPeakTable

public MarsTable getPeakTable()

setDataset

public void setDataset(net.imagej.Dataset dataset)

getDataset

public net.imagej.Dataset getDataset()

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()

setT

public void setT(int theT)

getT

public int getT()

setUseDogFiler

public void setUseDogFiler(boolean useDogFilter)

setDogFilterRadius

public void setDogFilterRadius(double dogFilterRadius)

setThreshold

public void setThreshold(double 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()

setGeneratePeakCountTable

public void setGeneratePeakCountTable(boolean generatePeakCountTable)

getGeneratePeakCountTable

public boolean getGeneratePeakCountTable()

setGeneratePeakTable

public void setGeneratePeakTable(boolean generatePeakTable)

getGeneratePeakTable

public boolean getGeneratePeakTable()

setMinimumRsquared

public void setMinimumRsquared(double RsquaredMin)

getMinimumRsquared

public double getMinimumRsquared()

setAddToRoiManager

public void setAddToRoiManager(boolean addToRoiManager)

getAddToRoiManager

public boolean getAddToRoiManager()

setRoiType

public void setRoiType(java.lang.String roiType)

This method specifies the type of Roi to add to the RoiManager. The currently available types are "point" or "circle" with non-available string defaulting to points.

Parameters:

roiType - String specifying the roi type.

getRoiType

public java.lang.String getRoiType()

setProcessAllFrames

public void setProcessAllFrames(boolean allFrames)

getProcessAllFrames

public boolean getProcessAllFrames()

setFitPeaks

public void setFitPeaks(boolean fitPeaks)

getFitPeaks

public boolean getFitPeaks()

setFitRadius

public void setFitRadius(int fitRadius)

getFitRadius

public int getFitRadius()

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()

setVerbose

public void setVerbose(boolean verbose)

getVerbose

public boolean getVerbose()

setThreads

public void setThreads(int nThreads)

getThreads

public int getThreads()