de.mpg.biochem.mars.image.commands

Class DNAFinderCommand

java.lang.Object

org.scijava.module.AbstractModule

org.scijava.module.DefaultMutableModule

org.scijava.command.DynamicCommand

de.mpg.biochem.mars.image.commands.DNAFinderCommand

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 DNAFinderCommand
extends org.scijava.command.DynamicCommand
implements org.scijava.command.Command, org.scijava.Initializable, org.scijava.command.Previewable

This command finds the location of vertically aligned DNA molecules.

The vertical gradient of the image is calculated and a DoG filter is applied. The resulting image is searched for pairs of positive and negative peaks. Vertically aligned pairs within the ranges provided are considered DNA molecules. Thresholds for the intensity and variance in intensity can be applied to filter the DNA molecules located and the ends can be fit with subpixel accuracy.

This command can report the number of molecules, a table with a position list, or line ROIs added to the RoiManager. Line ROIs can then be used to create a DnaMoleculeArchive using the BuildDnaArchiveCommand.

Field Summary

Fields inherited from class org.scijava.command.DynamicCommand

moduleService, pluginService

Constructor Summary

Constructors

Constructor and Description
DNAFinderCommand()

Method Summary

Modifier and Type	Method and Description
void	cancel()
boolean	getAddToRoiManager()
int	getChannel()
net.imagej.Dataset	getDataset()
MarsTable	getDNACountTable()
MarsTable	getDNATable()
boolean	getFilterByMedianIntensity()
boolean	getFilterByVariance()
boolean	getFit()
int	getFitRadius()
boolean	getFitSecondOrder()
double	getGaussianSigma()
boolean	getGenerateDNACountTable()
boolean	getGenerateDNATable()
int	getMedianIntensityLowerBound()
int	getMinimumDistance()
int	getOptimalDNALength()
boolean	getProcessAllFrames()
java.lang.String	getRegion()
ij.gui.Roi[]	getROIs()
int	getT()
int	getThreads()
double	getThreshold()
double	getVarianceUpperBound()
int	getXDNAEndSearchRadius()
int	getYDNAEndSearchRadius()
void	initialize()
protected void	openWebPage() Called when the openWebPage button is pressed.
void	preview()
protected void	previewChanged() Called when the preview parameter value changes.
void	run()
void	setAddToRoiManager(boolean addToRoiManger)
void	setChannel(int channel)
void	setDataset(net.imagej.Dataset dataset)
void	setDogFilterRadius(double dogFilterRadius)
void	setFilterByMedianIntensity(boolean medianIntensityFilter)
void	setFilterByVariance(boolean varianceFilter)
void	setFit(boolean fit)
void	setFitRadius(int fitRadius)
void	setFitSecondOrder(boolean fitSecondOrder)
void	setGaussianSigma(double gaussSigma)
void	setGenerateDNACountTable(boolean generateDNACountTable)
void	setGenerateDNATable(boolean generatePeakTable)
void	setMedianIntensityLowerBound(int medianIntensityLowerBound)
void	setMinimumDistance(int minimumDistance)
void	setOptimalDNALength(int optimalDNALength)
void	setProcessAllFrames(boolean allFrames)
void	setRegion(java.lang.String region)
void	setROIs(ij.gui.Roi[] rois)
void	setT(int theT)
void	setThreads(int nThreads)
void	setThreshold(double threshold)
void	setUseDogFiler(boolean useDogFilter)
void	setVarianceUpperBound(int varianceUpperBound)
void	setXDNAEndSearchRadius(int xDNAEndSearchRadius)
void	setYDNAEndSearchRadius(int yDNAEndSearchRadius)

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

DNAFinderCommand

public DNAFinderCommand()

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()

Called when the openWebPage button is pressed.

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.

getDNACountTable

public MarsTable getDNACountTable()

getDNATable

public MarsTable getDNATable()

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()

setGaussianSigma

public void setGaussianSigma(double gaussSigma)

getGaussianSigma

public double getGaussianSigma()

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()

setOptimalDNALength

public void setOptimalDNALength(int optimalDNALength)

getOptimalDNALength

public int getOptimalDNALength()

setYDNAEndSearchRadius

public void setYDNAEndSearchRadius(int yDNAEndSearchRadius)

getYDNAEndSearchRadius

public int getYDNAEndSearchRadius()

setXDNAEndSearchRadius

public void setXDNAEndSearchRadius(int xDNAEndSearchRadius)

getXDNAEndSearchRadius

public int getXDNAEndSearchRadius()

setFilterByVariance

public void setFilterByVariance(boolean varianceFilter)

getFilterByVariance

public boolean getFilterByVariance()

getVarianceUpperBound

public double getVarianceUpperBound()

setVarianceUpperBound

public void setVarianceUpperBound(int varianceUpperBound)

setFilterByMedianIntensity

public void setFilterByMedianIntensity(boolean medianIntensityFilter)

getFilterByMedianIntensity

public boolean getFilterByMedianIntensity()

setMedianIntensityLowerBound

public void setMedianIntensityLowerBound(int medianIntensityLowerBound)

getMedianIntensityLowerBound

public int getMedianIntensityLowerBound()

setGenerateDNACountTable

public void setGenerateDNACountTable(boolean generateDNACountTable)

getGenerateDNACountTable

public boolean getGenerateDNACountTable()

setGenerateDNATable

public void setGenerateDNATable(boolean generatePeakTable)

getGenerateDNATable

public boolean getGenerateDNATable()

setAddToRoiManager

public void setAddToRoiManager(boolean addToRoiManger)

getAddToRoiManager

public boolean getAddToRoiManager()

setProcessAllFrames

public void setProcessAllFrames(boolean allFrames)

getProcessAllFrames

public boolean getProcessAllFrames()

setFit

public void setFit(boolean fit)

getFit

public boolean getFit()

setFitSecondOrder

public void setFitSecondOrder(boolean fitSecondOrder)

getFitSecondOrder

public boolean getFitSecondOrder()

setFitRadius

public void setFitRadius(int fitRadius)

getFitRadius

public int getFitRadius()

setThreads

public void setThreads(int nThreads)

getThreads

public int getThreads()