de.mpg.biochem.mars.image.commands

Class MoleculeIntegratorCommand

java.lang.Object

org.scijava.module.AbstractModule

org.scijava.module.DefaultMutableModule

org.scijava.command.DynamicCommand

de.mpg.biochem.mars.image.commands.MoleculeIntegratorCommand

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

Command for integrating the fluorescence signal from peaks. Input - A list of peaks for integration can be provided as OvalRois or PointRois in the RoiManger. Names should be UIDs. The positions given are integrated for all T for all colors 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
MoleculeIntegratorCommand()

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)
java.lang.String	getMetadataUIDSource()
java.lang.String	getMicroscope()
int	getNumberOfIntegrationMaps()
int	getOuterRadius()
ij.plugin.frame.RoiManager	getRoiManager()
int	getThreads()
boolean	getVerbose()
void	initialize()
protected void	openWebPage()
void	run()
void	setDataset(net.imagej.Dataset dataset)
void	setInnerRadius(int innerRadius)
void	setIntegrationChannel(int channel, java.lang.String integrationType) Method used to set the channels that will be integrated in a script.
void	setIntegrationChannel(java.lang.String channelName, java.lang.String integrationType) Method used to set the channels that will be integrated in a script.
void	setMetadataUIDSource(java.lang.String metadataUIDSource) Determines whether the metadata UID is taken directly from the image metadata or randomly generated.
void	setMicroscope(java.lang.String microscope)
void	setOuterRadius(int outerRadius)
void	setRoiManager(ij.plugin.frame.RoiManager roiManager)
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

MoleculeIntegratorCommand

public MoleculeIntegratorCommand()

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.

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)

openWebPage

protected void openWebPage()

getArchive

public SingleMoleculeArchive getArchive()

setRoiManager

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

getRoiManager

public ij.plugin.frame.RoiManager getRoiManager()

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()

setIntegrationChannel

public void setIntegrationChannel(int channel,
                                  java.lang.String integrationType)

Method used to set the channels that will be integrated in a script. Integration types are "Do not integrate" or "Integrate"

Parameters:

channel - Index of the channel to integrate.

integrationType - The type of integration to perform.

setIntegrationChannel

public void setIntegrationChannel(java.lang.String channelName,
                                  java.lang.String integrationType)

Method used to set the channels that will be integrated in a script. Integration types are "Do not integrate" or "Integrate"

Parameters:

channelName - Name of the channel to integrate.

integrationType - The type of integration to perform.

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)

Determines whether the metadata UID is taken directly from the image metadata or randomly generated. Options are "unique from dataset" or "random"

Parameters:

metadataUIDSource - The metadata UID source.

getMetadataUIDSource

public java.lang.String getMetadataUIDSource()