de.mpg.biochem.mars.roi.commands

Class TransformROIsCommand

java.lang.Object

org.scijava.module.AbstractModule

org.scijava.module.DefaultMutableModule

org.scijava.command.DynamicCommand

de.mpg.biochem.mars.roi.commands.TransformROIsCommand

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 TransformROIsCommand
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
TransformROIsCommand()

Method Summary

Modifier and Type	Method and Description
void	cancel()
<T extends net.imglib2.type.numeric.RealType<T> & net.imglib2.type.NativeType<T>> java.util.List<java.lang.Integer>	colocalize(java.util.List<ij.gui.Roi> transformedROIs, double threshold, int channel, int t)
boolean	getApplyInverseTransformation()
int	getChannel()
boolean	getColocalize()
net.imagej.Dataset	getDataset()
boolean	getFilterColocalizingRois()
boolean	getFilterOriginalRois()
ij.plugin.frame.RoiManager	getRoiManager()
int	getT()
double	getThreshold()
java.lang.String	getTransformFromRegion()
java.lang.String	getTransformToRegion()
void	initialize()
void	preview()
protected void	previewChanged() Called when the preview parameter value changes.
void	run()
void	setApplyInverseTransformation(boolean inverseTransform)
void	setChannel(int channel)
void	setColocalize(boolean colocalize)
void	setColocalizeSearchRadius(int colocalizeRadius)
void	setDataset(net.imagej.Dataset dataset)
void	setDogFilterRadius(double dogFilterRadius)
void	setFilterColocalizingRois(boolean filterColocalizingRois)
void	setFilterOriginalRois(boolean filterOriginalRois)
void	setM00(double m00)
void	setM01(double m01)
void	setM02(double m02)
void	setM10(double m10)
void	setM11(double m11)
void	setM12(double m12)
void	setRoiManager(ij.plugin.frame.RoiManager roiManager)
void	setT(int theT)
void	setThreshold(double threshold)
void	setTransformFromRegion(java.lang.String transformFrom)
void	setTransformToRegion(java.lang.String transformTo)
void	setUseDogFilter(boolean useDogFilter)

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

TransformROIsCommand

public TransformROIsCommand()

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

colocalize

public <T extends net.imglib2.type.numeric.RealType<T> & net.imglib2.type.NativeType<T>> java.util.List<java.lang.Integer> colocalize(java.util.List<ij.gui.Roi> transformedROIs,
                                                                                                                                      double threshold,
                                                                                                                                      int channel,
                                                                                                                                      int t)

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.

setRoiManager

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

getRoiManager

public ij.plugin.frame.RoiManager getRoiManager()

setM00

public void setM00(double m00)

setM01

public void setM01(double m01)

setM02

public void setM02(double m02)

setM10

public void setM10(double m10)

setM11

public void setM11(double m11)

setM12

public void setM12(double m12)

setApplyInverseTransformation

public void setApplyInverseTransformation(boolean inverseTransform)

getApplyInverseTransformation

public boolean getApplyInverseTransformation()

setDataset

public void setDataset(net.imagej.Dataset dataset)

getDataset

public net.imagej.Dataset getDataset()

setChannel

public void setChannel(int channel)

getChannel

public int getChannel()

setT

public void setT(int theT)

getT

public int getT()

setTransformFromRegion

public void setTransformFromRegion(java.lang.String transformFrom)

getTransformFromRegion

public java.lang.String getTransformFromRegion()

setTransformToRegion

public void setTransformToRegion(java.lang.String transformTo)

getTransformToRegion

public java.lang.String getTransformToRegion()

setColocalize

public void setColocalize(boolean colocalize)

getColocalize

public boolean getColocalize()

setUseDogFilter

public void setUseDogFilter(boolean useDogFilter)

setDogFilterRadius

public void setDogFilterRadius(double dogFilterRadius)

setThreshold

public void setThreshold(double threshold)

getThreshold

public double getThreshold()

setFilterOriginalRois

public void setFilterOriginalRois(boolean filterOriginalRois)

getFilterOriginalRois

public boolean getFilterOriginalRois()

setFilterColocalizingRois

public void setFilterColocalizingRois(boolean filterColocalizingRois)

getFilterColocalizingRois

public boolean getFilterColocalizingRois()

setColocalizeSearchRadius

public void setColocalizeSearchRadius(int colocalizeRadius)