org.hkijena.jipipe.plugins.omnipose

Class OmniposePlugin

java.lang.Object

org.scijava.AbstractContextual

org.scijava.plugin.AbstractRichPlugin

org.scijava.service.AbstractService

org.hkijena.jipipe.JIPipeDefaultJavaPlugin

org.hkijena.jipipe.plugins.JIPipePrepackagedDefaultJavaPlugin

org.hkijena.jipipe.plugins.omnipose.OmniposePlugin

All Implemented Interfaces:

Comparable<org.scijava.Prioritized>, JIPipeValidatable, JIPipeDependency, JIPipeJavaPlugin, JIPipePlugin, org.scijava.Contextual, org.scijava.Disposable, org.scijava.Identifiable, org.scijava.Initializable, org.scijava.Locatable, org.scijava.log.Logged, org.scijava.plugin.HasPluginInfo, org.scijava.plugin.RichPlugin, org.scijava.plugin.SciJavaPlugin, org.scijava.Prioritized, org.scijava.service.Service, org.scijava.Versioned

public class OmniposePlugin
extends JIPipePrepackagedDefaultJavaPlugin

Field Summary

Fields

Modifier and Type	Field and Description
static JIPipeDependency	AS_DEPENDENCY Dependency instance to be used for creating the set of dependencies
static JIPipeResourceManager	RESOURCES

Constructor Summary

Constructors

Constructor and Description
OmniposePlugin()

Method Summary

Modifier and Type	Method and Description
JIPipeAuthorMetadata.List	getAcknowledgements() Returns additionally cited authors
Set<JIPipeDependency>	getDependencies() List of JIPipe dependencies.
StringList	getDependencyCitations() Returns all dependent work
String	getDependencyId()
StringList	getDependencyProvides() The list of alternative IDs that are covered by this dependency
HTMLText	getDescription()
static PythonEnvironment	getEnvironment(JIPipeProject project, OptionalPythonEnvironment nodeEnvironment)
String	getName()
List<ImageIcon>	getSplashIcons() Returns icons that will be displayed in the splash screen.
boolean	isBeta() Returns whether this extension is in beta testing.
void	register(JIPipe jiPipe, org.scijava.Context context, JIPipeProgressInfo progressInfo) Registers custom modules into JIPipe

Methods inherited from class org.hkijena.jipipe.plugins.JIPipePrepackagedDefaultJavaPlugin

getAuthors, getCitation, getDependencyVersion, getLicense, getLogo, getWebsite

Methods inherited from class org.hkijena.jipipe.JIPipeDefaultJavaPlugin

configureDefaultImageJAdapters, configureDefaultImageJAdapters, getCategories, getDependencyLocation, getMetadata, getRegistry, getSummary, registerAnnotationNodeType, registerApplicationSettingsSheet, registerContextMenuAction, registerDatatype, registerDatatype, registerDatatypeConversion, registerDatatypeDisplayOperation, registerDatatypeImportOperation, registerDatatypeOperation, registerDefaultDataTypeViewer, registerEnumParameterType, registerEnvironment, registerEnvironmentInstaller, registerExpressionFunction, registerExpressionFunction, registerFileChooserKnownDirectoryType, registerFileChooserKnownDirectoryType, registerFileChooserKnownFileType, registerFileChooserKnownFileType, registerGraphEditorTool, registerGraphEditorToolBarButtonExtension, registerImageJDataExporter, registerImageJDataImporter, registerMenuExtension, registerMetadataObjectType, registerNodeExample, registerNodeExample, registerNodeExample, registerNodeExamplesFromResources, registerNodeExamplesFromResources, registerNodeTemplate, registerNodeTemplatesFromResources, registerNodeTemplatesFromResources, registerNodeType, registerNodeType, registerNodeType, registerNodeType, registerNodeType, registerNodeTypeCategory, registerParameterEditor, registerParameterGenerator, registerParameterType, registerParameterType, registerParameterType, registerParameterType, registerParameterType, registerParameterType, registerProjectSettingsSheet, registerProjectTemplatesFromResources, registerProjectTemplatesFromResources, registerTableColumnOperation, registerTableColumnOperationAndExpressionFunction, registerUtility, reportValidity, setRegistry

Methods inherited from class org.scijava.service.AbstractService

getContext, setContext, toString

Methods inherited from class org.scijava.plugin.AbstractRichPlugin

getInfo, getPriority, setInfo, setPriority

Methods inherited from class org.scijava.AbstractContextual

context

Methods inherited from class java.lang.Object

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

Methods inherited from interface org.hkijena.jipipe.JIPipeJavaPlugin

postprocess

Methods inherited from interface org.hkijena.jipipe.JIPipePlugin

canActivate, isActivated, isCorePlugin, isScheduledForActivation, isScheduledForDeactivation

Methods inherited from interface org.hkijena.jipipe.JIPipeDependency

getAllDependencies, getAllDependencies, getAllImageJUpdateSiteDependencies, getImageJUpdateSiteDependencies, getImageJUpdateSites, simplifyAndMinimize, toHtmlElement

Methods inherited from interface org.hkijena.jipipe.api.validation.JIPipeValidatable

generateValidityReport

Methods inherited from interface org.scijava.service.Service

initialize, registerEventHandlers

Methods inherited from interface org.scijava.plugin.RichPlugin

getIdentifier, log

Methods inherited from interface org.scijava.Contextual

context

Methods inherited from interface org.scijava.Prioritized

compareTo, getPriority, setPriority

Methods inherited from interface org.scijava.plugin.HasPluginInfo

getInfo, setInfo

Methods inherited from interface org.scijava.Locatable

getLocation

Methods inherited from interface org.scijava.Versioned

getVersion

Methods inherited from interface org.scijava.Disposable

dispose

Field Detail

AS_DEPENDENCY

public static final JIPipeDependency AS_DEPENDENCY

Dependency instance to be used for creating the set of dependencies

RESOURCES

public static final JIPipeResourceManager RESOURCES

Constructor Detail

OmniposePlugin

public OmniposePlugin()

Method Detail

getEnvironment

public static PythonEnvironment getEnvironment(JIPipeProject project,
                                               OptionalPythonEnvironment nodeEnvironment)

getDependencyProvides

public StringList getDependencyProvides()

Description copied from interface: JIPipeDependency

The list of alternative IDs that are covered by this dependency

Returns:

alternative IDs

getDependencies

public Set<JIPipeDependency> getDependencies()

Description copied from interface: JIPipeDependency

List of JIPipe dependencies. This can contain nested or even cyclic dependencies. The storage of dependencies into JSON format is handled by getTraversedDependencies()

Specified by:

getDependencies in interface JIPipeDependency

Overrides:

getDependencies in class JIPipeDefaultJavaPlugin

Returns:

the set of JIPipe dependencies

isBeta

public boolean isBeta()

Description copied from interface: JIPipePlugin

Returns whether this extension is in beta testing. If true, users should expect significant changes in how the extension and its nodes work.

Returns:

if the extension is in beta

getAcknowledgements

public JIPipeAuthorMetadata.List getAcknowledgements()

Description copied from class: JIPipeDefaultJavaPlugin

Returns additionally cited authors

Overrides:

getAcknowledgements in class JIPipeDefaultJavaPlugin

Returns:

the authors

getDependencyCitations

public StringList getDependencyCitations()

Description copied from class: JIPipeDefaultJavaPlugin

Returns all dependent work

Specified by:

getDependencyCitations in class JIPipeDefaultJavaPlugin

Returns:

dependent work

getName

public String getName()

Specified by:

getName in class JIPipeDefaultJavaPlugin

Returns:

The extension name

getDescription

public HTMLText getDescription()

Specified by:

getDescription in class JIPipeDefaultJavaPlugin

Returns:

The extension description

getDependencyId

public String getDependencyId()

Returns:

The unique dependency ID

getSplashIcons

public List<ImageIcon> getSplashIcons()

Description copied from interface: JIPipeJavaPlugin

Returns icons that will be displayed in the splash screen. They must have a size of 32x32. There can only be at most 45 icons, so please do not over-do it

Returns:

the icons

register

public void register(JIPipe jiPipe,
                     org.scijava.Context context,
                     JIPipeProgressInfo progressInfo)

Description copied from interface: JIPipeJavaPlugin

Registers custom modules into JIPipe

Parameters:

jiPipe - the JIPipe instance that calls this function

context - the SciJava Context

progressInfo - the progress info