de.mpg.biochem.mars.image.commands

Class BeamProfileCorrectionCommand

java.lang.Object

org.scijava.module.AbstractModule

org.scijava.module.DefaultMutableModule

org.scijava.command.DynamicCommand

de.mpg.biochem.mars.image.commands.BeamProfileCorrectionCommand

All Implemented Interfaces:

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

public class BeamProfileCorrectionCommand
extends org.scijava.command.DynamicCommand
implements org.scijava.command.Command

This command corrects images collected with uneven illumination. The most common use is to correct images collected using a fluorescence microscope with a gaussian beam profile that is maximum in the middle and lowest at the edges.

The command requires two images: a 2D background image with the beam profile and the video that should be corrected. For each pixel at position x, y the following is calculated:

(Image(x,y) - electronic_offset) / ((Background(x,y) - electronic_offset) / (maximum_pixel_background - electronic_offset)).

When finished the active image or image provided will be corrected.

Field Summary

Fields inherited from class org.scijava.command.DynamicCommand

moduleService, pluginService

Constructor Summary

Constructors

Constructor and Description
BeamProfileCorrectionCommand()

Method Summary

Modifier and Type	Method and Description
void	correctFrame(int channel, int t)
ij.ImagePlus	getBackgroundImage()
int	getChannel()
net.imagej.Dataset	getDataset()
double	getElectronicOffset()
ij.ImagePlus	getImage()
java.lang.String	getRegion()
int	getThreads()
void	initialize()
void	run()
void	setBackgroundImage(ij.ImagePlus backgroundImage)
void	setChannel(int channel)
void	setDataset(net.imagej.Dataset dataset)
void	setElectronicOffset(double electronicOffset)
void	setImage(ij.ImagePlus image)
void	setRegion(java.lang.String region)
void	setThreads(int nThreads)

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

cancel, getDelegateObject, getInputs, getOutputs, isInputResolved, isOutputResolved, preview, 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

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

Constructor Detail

BeamProfileCorrectionCommand

public BeamProfileCorrectionCommand()

Method Detail

initialize

public void initialize()

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

correctFrame

public void correctFrame(int channel,
                         int t)

getDataset

public net.imagej.Dataset getDataset()

setDataset

public void setDataset(net.imagej.Dataset dataset)

setRegion

public void setRegion(java.lang.String region)

getRegion

public java.lang.String getRegion()

setChannel

public void setChannel(int channel)

getChannel

public int getChannel()

setImage

public void setImage(ij.ImagePlus image)

getImage

public ij.ImagePlus getImage()

setBackgroundImage

public void setBackgroundImage(ij.ImagePlus backgroundImage)

getBackgroundImage

public ij.ImagePlus getBackgroundImage()

setElectronicOffset

public void setElectronicOffset(double electronicOffset)

getElectronicOffset

public double getElectronicOffset()

setThreads

public void setThreads(int nThreads)

getThreads

public int getThreads()