de.mpg.biochem.mars.image.commands

Class MoleculeIntegratorMultiViewCommand

java.lang.Object

org.scijava.module.AbstractModule

org.scijava.module.DefaultMutableModule

org.scijava.command.DynamicCommand

de.mpg.biochem.mars.image.commands.MoleculeIntegratorMultiViewCommand

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 MoleculeIntegratorMultiViewCommand
extends org.scijava.command.DynamicCommand
implements org.scijava.command.Command, org.scijava.Initializable

Command for integrating the fluorescence signal from spot. A list of peaks for integration can be provided as OvalRois or PointRois in the RoiManger with the format UID_REGION1, UID_REGION2, etc. for peaks in different subregions of a multiview image representing different wavelengths. The positions given are integrated for all T for all channels specified to generate a SingleMoleculeArchive in which all molecule record tables have columns for all integrated colors.

Field Summary

Fields inherited from class org.scijava.command.DynamicCommand

moduleService, pluginService

Constructor Summary

Constructors

Constructor and Description
MoleculeIntegratorMultiViewCommand()

Method Summary

Modifier and Type	Method and Description
void	addIntegrationMap(java.lang.String name, int c, net.imglib2.Interval interval, java.util.Map<java.lang.Integer,java.util.Map<java.lang.String,Peak>> integrationMap) This method accepts maps the specify peak locations that should be integrated in the form of a map first to T and then a Map From UID to Peak.
SingleMoleculeArchive	getArchive()
net.imagej.Dataset	getDataset()
int	getInnerRadius()
java.util.Map<java.lang.Integer,java.util.Map<java.lang.String,Peak>>	getIntegrationMap(java.lang.String name, int c)
net.imglib2.Interval	getInterval(java.lang.String name)
java.util.Map<java.lang.String,net.imglib2.Interval>	getIntervals()
java.lang.String	getMetadataUIDSource()
java.lang.String	getMicroscope()
int	getNumberOfIntegrationMaps()
int	getOuterRadius()
int	getThreads()
boolean	getVerbose()
void	initialize()
protected void	openWebPage()
void	run()
void	setDataset(net.imagej.Dataset dataset)
void	setInnerRadius(int innerRadius)
void	setMetadataUIDSource(java.lang.String metadataUIDSource)
void	setMicroscope(java.lang.String microscope)
void	setOuterRadius(int outerRadius)
void	setRegionBoundaries(java.lang.String name, int x0, int y0, int width, int height)
void	setRegionInterval(java.lang.String name, net.imglib2.Interval interval)
void	setThreads(int nThreads)
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

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

MoleculeIntegratorMultiViewCommand

public MoleculeIntegratorMultiViewCommand()

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

addIntegrationMap

public void addIntegrationMap(java.lang.String name,
                              int c,
                              net.imglib2.Interval interval,
                              java.util.Map<java.lang.Integer,java.util.Map<java.lang.String,Peak>> integrationMap)

This method accepts maps the specify peak locations that should be integrated in the form of a map first to T and then a Map From UID to Peak.

Parameters:

name - Name of the peaks, usually the color.

c - The channel index to integrate.

interval - The interval used for integration. Beyond will be mirrored.

integrationMap - Map from T to Map from UID to Peak.

openWebPage

protected void openWebPage()

getNumberOfIntegrationMaps

public int getNumberOfIntegrationMaps()

getIntegrationMap

public java.util.Map<java.lang.Integer,java.util.Map<java.lang.String,Peak>> getIntegrationMap(java.lang.String name,
                                                                                               int c)

getArchive

public SingleMoleculeArchive getArchive()

setDataset

public void setDataset(net.imagej.Dataset dataset)

getDataset

public net.imagej.Dataset getDataset()

setMicroscope

public void setMicroscope(java.lang.String microscope)

getMicroscope

public java.lang.String getMicroscope()

setInnerRadius

public void setInnerRadius(int innerRadius)

getInnerRadius

public int getInnerRadius()

setOuterRadius

public void setOuterRadius(int outerRadius)

getOuterRadius

public int getOuterRadius()

setRegionBoundaries

public void setRegionBoundaries(java.lang.String name,
                                int x0,
                                int y0,
                                int width,
                                int height)

setRegionInterval

public void setRegionInterval(java.lang.String name,
                              net.imglib2.Interval interval)

getIntervals

public java.util.Map<java.lang.String,net.imglib2.Interval> getIntervals()

getInterval

public net.imglib2.Interval getInterval(java.lang.String name)

setThreads

public void setThreads(int nThreads)

getThreads

public int getThreads()

setVerbose

public void setVerbose(boolean verbose)

getVerbose

public boolean getVerbose()

setMetadataUIDSource

public void setMetadataUIDSource(java.lang.String metadataUIDSource)

getMetadataUIDSource

public java.lang.String getMetadataUIDSource()