com.github.celldynamics.quimp.plugin.binaryseg

Class BinarySegmentation_

java.lang.Object

com.github.celldynamics.quimp.plugin.AbstractOptionsParser

com.github.celldynamics.quimp.plugin.AbstractPluginBase

com.github.celldynamics.quimp.plugin.AbstractPluginTemplate

com.github.celldynamics.quimp.plugin.binaryseg.BinarySegmentation_

All Implemented Interfaces:

IQuimpPlugin, IQuimpPluginAttachImage, IQuimpPluginAttachImagePlus, IQuimpPluginAttachNest, IQuimpPluginExchangeData, IQuimpPluginSynchro, ij.plugin.PlugIn

Direct Known Subclasses:

BinarySegmentation_Runner

public class BinarySegmentation_
extends AbstractPluginTemplate
implements IQuimpPluginSynchro, IQuimpPluginAttachNest, IQuimpPluginExchangeData, IQuimpPluginAttachImagePlus

Binary segmentation plugin called from Fiji.

Use BinarySegmentation for API calls or AbstractPluginBase.run(String)

This is front-end of BinarySegmentation used as stand alone plugin and BOA component.

Author:

p.baniukiewicz

See Also:

BinarySegmentationView

Field Summary

Fields inherited from class com.github.celldynamics.quimp.plugin.AbstractOptionsParser

apiCall, errorSink, logger, options

Constructor Summary

Constructors

Constructor and Description
BinarySegmentation_() Default constructor.
BinarySegmentation_(AbstractPluginOptions options) Constructor for API calls.

Method Summary

Modifier and Type	Method and Description
String	about() Return plugin description.
void	attachContext(ViewUpdater b) Pass to plugin ViewUpdater object which is accessor to selected methods from QuimP interface.
void	attachImage(ij.process.ImageProcessor img) Attach image to filter.
void	attachImagePlus(ij.ImagePlus img) Attach image plus to filter.
void	attachNest(Nest data) Attach processed data to plugin.
ParamList	getPluginConfig() Retrieve plugin configuration data as pairs (key,value>=).
boolean	isWindowVisible() Return true if window is visible.
protected void	runPlugin() Main plugin logic.
void	setPluginConfig(ParamList par) Pass to plugin its configuration data as pairs (key,value).
void	showUi(boolean val) Open plugin UI.

Methods inherited from class com.github.celldynamics.quimp.plugin.AbstractPluginTemplate

executer

Methods inherited from class com.github.celldynamics.quimp.plugin.AbstractPluginBase

run, setPluginName

Methods inherited from class com.github.celldynamics.quimp.plugin.AbstractOptionsParser

getOptions, parseArgumentString, publishMacroString

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

BinarySegmentation_

public BinarySegmentation_()

Default constructor.

BinarySegmentation_

public BinarySegmentation_(AbstractPluginOptions options)

Constructor for API calls.

Call runPlugin() afterwards. Note that AbstractOptionsParser.apiCall is set to true and sink to Console.

Parameters:

options - configuration options

Method Detail

runPlugin

protected void runPlugin()
                  throws QuimpPluginException

Main plugin logic.

Specified by:

runPlugin in class AbstractPluginTemplate

Throws:

QuimpPluginException - on any error, handled by AbstractPluginBase.run(String)

isWindowVisible

public boolean isWindowVisible()

Return true if window is visible.

Returns:

true if window is visible

attachNest

public void attachNest(Nest data)

Description copied from interface: IQuimpPluginAttachNest

Attach processed data to plugin.

This method allows to process data by plugin without running it what is important e.g. for visualizing.

warning

data may be passed as null from QuimP. Plugin must deal with this.

Specified by:

attachNest in interface IQuimpPluginAttachNest

Parameters:

data - nest to connect

attachContext

public void attachContext(ViewUpdater b)

Description copied from interface: IQuimpPluginSynchro

Pass to plugin ViewUpdater object which is accessor to selected methods from QuimP interface.

The main role of ViewUpdater is to limit methods that plugin can call to avoid accidental data destruction.

Specified by:

attachContext in interface IQuimpPluginSynchro

Parameters:

b - Reference to ViewUpdater that holds selected methods from main QuimP object

See Also:

to check what methods are exposed to plugin.

showUi

public void showUi(boolean val)

Description copied from class: AbstractPluginBase

Open plugin UI.

Executed if AbstractPluginBase.run(String) could not parse parameters.

Specified by:

showUi in class AbstractPluginBase

Parameters:

val - true to show UI

getPluginConfig

public ParamList getPluginConfig()

Description copied from interface: IQuimpPluginExchangeData

Retrieve plugin configuration data as pairs (key,value>=).

This configuration is not used by QuimP but it may be stored in QuimP configuration.

Specified by:

getPluginConfig in interface IQuimpPluginExchangeData

Returns:

Plugin configuration

See Also:

IQuimpPluginExchangeData.setPluginConfig(ParamList)

setPluginConfig

public void setPluginConfig(ParamList par)
                     throws QuimpPluginException

Description copied from interface: IQuimpPluginExchangeData

Pass to plugin its configuration data as pairs (key,value).

This method is used for restoring configuration from config files maintained by caller. Caller do not modify these values and only stores them as the were returned by getPluginConfig() method.

Numerical values should be passed as Double. setPluginConfig(ParamList) and getPluginConfig() should use the same convention of key naming and parameters casting

Specified by:

setPluginConfig in interface IQuimpPluginExchangeData

Parameters:

par - plugin configuration.

Throws:

QuimpPluginException - on problems with understanding parameters by plugin e.g. \b key is not understood or converting from \c String \b value to other type has not been successful.

attachImage

public void attachImage(ij.process.ImageProcessor img)

Description copied from interface: IQuimpPluginAttachImage

Attach image to filter.

Specified by:

attachImage in interface IQuimpPluginAttachImage

Parameters:

img - image to attach.

attachImagePlus

public void attachImagePlus(ij.ImagePlus img)

Description copied from interface: IQuimpPluginAttachImagePlus

Attach image plus to filter.

Specified by:

attachImagePlus in interface IQuimpPluginAttachImagePlus

Parameters:

img - image to attach.

about

public String about()

Description copied from interface: IQuimpPlugin

Return plugin description.

Specified by:

about in interface IQuimpPlugin

Returns:

Plugin description