org.hkijena.jipipe

Class JIPipe

java.lang.Object

org.scijava.AbstractContextual

org.scijava.plugin.AbstractRichPlugin

org.scijava.service.AbstractService

org.hkijena.jipipe.JIPipe

All Implemented Interfaces:

Comparable<Prioritized>, JIPipeValidatable, JIPipeService, Contextual, Disposable, Identifiable, Initializable, Locatable, Logged, HasPluginInfo, RichPlugin, SciJavaPlugin, Prioritized, Service, Versioned

public class JIPipe
extends AbstractService
implements JIPipeService

A scijava service that discovers JIPipe plugins in the classpath

Nested Class Summary

Nested classes/interfaces inherited from interface org.hkijena.jipipe.JIPipeService

JIPipeService.DatatypeRegisteredEvent, JIPipeService.DatatypeRegisteredEventEmitter, JIPipeService.DatatypeRegisteredEventListener, JIPipeService.ExtensionContentAddedEvent, JIPipeService.ExtensionContentAddedEventEmitter, JIPipeService.ExtensionContentAddedEventListener, JIPipeService.ExtensionContentRemovedEvent, JIPipeService.ExtensionContentRemovedEventEmitter, JIPipeService.ExtensionContentRemovedEventListener, JIPipeService.ExtensionDiscoveredEvent, JIPipeService.ExtensionDiscoveredEventEmitter, JIPipeService.ExtensionDiscoveredEventListener, JIPipeService.ExtensionRegisteredEvent, JIPipeService.ExtensionRegisteredEventEmitter, JIPipeService.ExtensionRegisteredEventListener, JIPipeService.NodeInfoRegisteredEvent, JIPipeService.NodeInfoRegisteredEventEmitter, JIPipeService.NodeInfoRegisteredEventListener

Field Summary

Fields

Modifier and Type	Field and Description
static JIPipeResourceManager	RESOURCES Resource manager for core JIPipe

Constructor Summary

Constructors

Constructor and Description
JIPipe()

Method Summary

Modifier and Type	Method and Description
void	checkUpdateSites(JIPipeRegistryIssues issues, List<JIPipeDependency> extensions, Progress progressAdapter, JIPipeProgressInfo progressInfo) Checks the update sites of all extensions and stores the results in the issues
static int	comparePlugins(PluginInfo<?> p0, PluginInfo<?> p1) Compares two plugins and sorts them by priority
static <T extends JIPipeData> T	createData(Class<T> klass, Object... constructorParameters) Instantiates a data class with the provided parameters This method is helpful if output data is constructed based on slot types
static JIPipe	createInstance(Context context) Helper to create JIPipe from a context.
static <T extends JIPipeGraphNode> T	createNode(Class<T> klass) Creates a new node instance from its class.
static <T extends JIPipeGraphNode> T	createNode(String id) Creates a new node instance from its id
static <T extends JIPipeGraphNode> T	duplicateNode(T node) Duplicates a JIPipeGraphNode
static <T> T	duplicateParameter(T value) Duplicates a value that is registered as parameter
static JIPipeProjectRun	enqueueProject(JIPipeProject project, JIPipeRunSettings settings) Runs a project in the current thread.
static JIPipeProjectRun	enqueueProject(JIPipeProject project, Path outputFolder, int threads) Runs a project in a different thread.
static JIPipe	ensureInstance() Ensures that JIPipe is initialized and available.
static JIPipe	ensureInstance(Context context) Ensures that JIPipe is initialized and available.
JIPipeDependency	findExtensionById(String dependencyId)
JIPipeCustomMenuRegistry	getCustomMenuRegistry()
static JIPipeCustomMenuRegistry	getCustomMenus()
JIPipeService.DatatypeRegisteredEventEmitter	getDatatypeRegisteredEventEmitter()
JIPipeDatatypeRegistry	getDatatypeRegistry()
static JIPipeDatatypeRegistry	getDataTypes()
JIPipeExpressionRegistry	getExpressionRegistry()
JIPipeService.ExtensionContentAddedEventEmitter	getExtensionContentAddedEventEmitter()
JIPipeService.ExtensionContentRemovedEventEmitter	getExtensionContentRemovedEventEmitter()
JIPipeService.ExtensionDiscoveredEventEmitter	getExtensionDiscoveredEventEmitter()
JIPipeService.ExtensionRegisteredEventEmitter	getExtensionRegisteredEventEmitter()
JIPipeExtensionRegistry	getExtensionRegistry()
JIPipeExternalEnvironmentRegistry	getExternalEnvironmentRegistry()
List<JIPipeDependency>	getFailedExtensions()
JIPipeGraphEditorToolRegistry	getGraphEditorToolRegistry()
static JIPipeImageJAdapterRegistry	getImageJAdapters()
JIPipeImageJAdapterRegistry	getImageJDataAdapterRegistry()
FilesCollection	getImageJPlugins()
static JIPipe	getInstance()
static String	getJIPipeVersion() The current version of JIPipe according to the Maven-proved information
LogService	getLogService()
JIPipeService.NodeInfoRegisteredEventEmitter	getNodeInfoRegisteredEventEmitter()
JIPipeNodeRegistry	getNodeRegistry()
static JIPipeNodeRegistry	getNodes()
NodeTemplatesRefreshedEventEmitter	getNodeTemplatesRefreshedEventEmitter()
JIPipeParameterTypeRegistry	getParameterTypeRegistry()
static JIPipeParameterTypeRegistry	getParameterTypes()
PluginService	getPluginService()
JIPipeProgressInfo	getProgressInfo()
JIPipeProjectTemplateRegistry	getProjectTemplateRegistry()
Set<String>	getRegisteredExtensionIds()
List<JIPipeDependency>	getRegisteredExtensions()
static JIPipeSettingsRegistry	getSettings()
JIPipeSettingsRegistry	getSettingsRegistry()
JIPipeExpressionRegistry	getTableOperationRegistry()
static JIPipeExpressionRegistry	getTableOperations()
JIPipeUtilityRegistry	getUtilityRegistry()
static <T extends JIPipeData> T	importData(JIPipeReadDataStorage storage, Class<T> klass, JIPipeProgressInfo progressInfo) Imports data of given data type from its output folder.
void	initialize() Initializes JIPipe.
void	initialize(ExtensionSettings extensionSettings, JIPipeRegistryIssues issues) Initializes JIPipe
boolean	isInitializing()
static boolean	isInstantiated()
static boolean	isRestarting() Returns true if a JIPipe restart is in progress.
static boolean	isValidExtensionId(String id) Returns if the ID is a valid extension ID Must have following structure: [group]:[artifact] [group] should be lower-case and be a valid Maven group ID [artifact] should be lower-case and a valid Maven artifact ID
static JIPipeProject	loadProject(Path fileName) Loads a project
static JIPipeProject	loadProject(Path fileName, JIPipeIssueReport report) Loads a project
static JIPipeProject	loadProject(Path fileName, JIPipeIssueReport report, JIPipeNotificationInbox notifications) Loads a project
static JIPipeProject	loadProject(Path fileName, JIPipeNotificationInbox notifications) Loads a project
void	register(JIPipeJsonExtension extension, JIPipeProgressInfo progressInfo) Registers a JSON extension
void	reportValidity(JIPipeIssueReport report) Generates a validity report
static void	restartGUI()
static JIPipeProjectRun	runProject(JIPipeProject project, JIPipeRunSettings settings) Runs a project in the current thread.
static JIPipeProjectRun	runProject(JIPipeProject project, Path outputFolder, int threads) Runs a project in the current thread.

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.scijava.service.Service

registerEventHandlers

Methods inherited from interface org.scijava.plugin.RichPlugin

getIdentifier, log

Methods inherited from interface org.scijava.Contextual

context, getContext, setContext

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

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

generateValidityReport

Field Detail

RESOURCES

public static final JIPipeResourceManager RESOURCES

Resource manager for core JIPipe

Constructor Detail

JIPipe

public JIPipe()

Method Detail

importData

public static <T extends JIPipeData> T importData(JIPipeReadDataStorage storage,
                                                  Class<T> klass,
                                                  JIPipeProgressInfo progressInfo)

Imports data of given data type from its output folder. Generally, the output folder should conform to the data type's saveTo() function without 'forceName' enabled

Type Parameters:

T - the data type

Parameters:

storage - the storage that contains the serialized data

klass - the data type

progressInfo - the progress info

Returns:

imported data

isRestarting

public static boolean isRestarting()

Returns true if a JIPipe restart is in progress. Can be utilized by methods to prevent the closing of the Java app

Returns:

if JIPipe is restarting

getParameterTypes

public static JIPipeParameterTypeRegistry getParameterTypes()

getTableOperations

public static JIPipeExpressionRegistry getTableOperations()

getCustomMenus

public static JIPipeCustomMenuRegistry getCustomMenus()

getImageJAdapters

public static JIPipeImageJAdapterRegistry getImageJAdapters()

getSettings

public static JIPipeSettingsRegistry getSettings()

getNodes

public static JIPipeNodeRegistry getNodes()

getDataTypes

public static JIPipeDatatypeRegistry getDataTypes()

getNodeTemplatesRefreshedEventEmitter

public NodeTemplatesRefreshedEventEmitter getNodeTemplatesRefreshedEventEmitter()

getDatatypeRegisteredEventEmitter

public JIPipeService.DatatypeRegisteredEventEmitter getDatatypeRegisteredEventEmitter()

Specified by:

getDatatypeRegisteredEventEmitter in interface JIPipeService

getExtensionContentAddedEventEmitter

public JIPipeService.ExtensionContentAddedEventEmitter getExtensionContentAddedEventEmitter()

Specified by:

getExtensionContentAddedEventEmitter in interface JIPipeService

getExtensionContentRemovedEventEmitter

public JIPipeService.ExtensionContentRemovedEventEmitter getExtensionContentRemovedEventEmitter()

Specified by:

getExtensionContentRemovedEventEmitter in interface JIPipeService

getExtensionDiscoveredEventEmitter

public JIPipeService.ExtensionDiscoveredEventEmitter getExtensionDiscoveredEventEmitter()

Specified by:

getExtensionDiscoveredEventEmitter in interface JIPipeService

getExtensionRegisteredEventEmitter

public JIPipeService.ExtensionRegisteredEventEmitter getExtensionRegisteredEventEmitter()

Specified by:

getExtensionRegisteredEventEmitter in interface JIPipeService

getNodeInfoRegisteredEventEmitter

public JIPipeService.NodeInfoRegisteredEventEmitter getNodeInfoRegisteredEventEmitter()

Specified by:

getNodeInfoRegisteredEventEmitter in interface JIPipeService

getInstance

public static JIPipe getInstance()

Returns:

Singleton instance

restartGUI

public static void restartGUI()

ensureInstance

public static JIPipe ensureInstance()

Ensures that JIPipe is initialized and available. Creates a new ImageJ instance to obtain a Context if JIPipe is not initialized already.

Returns:

the current instance

ensureInstance

public static JIPipe ensureInstance(Context context)

Ensures that JIPipe is initialized and available.

Parameters:

context - the context to initialize JIPipe

Returns:

the current instance

createInstance

public static JIPipe createInstance(Context context)

Helper to create JIPipe from a context. Will create a new JIPipe instance, so be careful. We recommend using the ensureInstance() method.

Parameters:

context - the context

isInstantiated

public static boolean isInstantiated()

comparePlugins

public static int comparePlugins(PluginInfo<?> p0,
                                 PluginInfo<?> p1)

Compares two plugins and sorts them by priority

Parameters:

p0 - Plugin

p1 - Plugin

Returns:

Comparator result

loadProject

public static JIPipeProject loadProject(Path fileName)
                                 throws IOException

Loads a project

Parameters:

fileName - Project file

Returns:

the project

Throws:

IOException - thrown if the file could not be read or the file is corrupt

loadProject

public static JIPipeProject loadProject(Path fileName,
                                        JIPipeNotificationInbox notifications)
                                 throws IOException

Loads a project

Parameters:

fileName - Project file

notifications - notifications for the user

Returns:

the project

Throws:

IOException - thrown if the file could not be read or the file is corrupt

loadProject

public static JIPipeProject loadProject(Path fileName,
                                        JIPipeIssueReport report,
                                        JIPipeNotificationInbox notifications)
                                 throws IOException

Loads a project

Parameters:

fileName - Project file

report - Report whether the project is valid

notifications - notifications for the user

Returns:

the project

Throws:

IOException - thrown if the file could not be read or the file is corrupt

loadProject

public static JIPipeProject loadProject(Path fileName,
                                        JIPipeIssueReport report)
                                 throws IOException

Loads a project

Parameters:

fileName - Project file

report - Report whether the project is valid

Returns:

the project

Throws:

IOException - thrown if the file could not be read or the file is corrupt

runProject

public static JIPipeProjectRun runProject(JIPipeProject project,
                                          Path outputFolder,
                                          int threads)

Runs a project in the current thread. The progress will be put into the stdout This will block the current thread.

Parameters:

project - the project

outputFolder - the output folder

threads - the number of threads (set to zero for using the default value)

Returns:

the result

runProject

public static JIPipeProjectRun runProject(JIPipeProject project,
                                          JIPipeRunSettings settings)

Runs a project in the current thread. The progress will be put into the stdout This will block the current thread.

Parameters:

project - the project

settings - settings for the run

Returns:

the result

enqueueProject

public static JIPipeProjectRun enqueueProject(JIPipeProject project,
                                              Path outputFolder,
                                              int threads)

Runs a project in a different thread. The progress will be put into the stdout

Parameters:

project - the project

outputFolder - the output folder

threads - the number of threads (set to zero for using the default value)

Returns:

the future result. You have to check the JIPipeRunnerQueue to see if the run is finished.

enqueueProject

public static JIPipeProjectRun enqueueProject(JIPipeProject project,
                                              JIPipeRunSettings settings)

Runs a project in the current thread. The progress will be put into the stdout

Parameters:

project - the project

settings - settings for the run

Returns:

the future result. You have to check the JIPipeRunnerQueue to see if the run is finished.

createNode

public static <T extends JIPipeGraphNode> T createNode(String id)

Creates a new node instance from its id

Type Parameters:

T - Algorithm class

Parameters:

id - Algorithm ID

Returns:

Algorithm instance

createNode

public static <T extends JIPipeGraphNode> T createNode(Class<T> klass)

Creates a new node instance from its class. Please note that this might not work for all node types, as there is no 1:1 relation between node classes and their Ids

Type Parameters:

T - node class

Parameters:

klass - node class

Returns:

the node

duplicateNode

public static <T extends JIPipeGraphNode> T duplicateNode(T node)

Duplicates a JIPipeGraphNode

Type Parameters:

T - the node class

Parameters:

node - the node

Returns:

a deep copy

duplicateParameter

public static <T> T duplicateParameter(T value)

Duplicates a value that is registered as parameter

Type Parameters:

T - the type of the value

Parameters:

value - the value. can be null

Returns:

duplicate of the value

createData

public static <T extends JIPipeData> T createData(Class<T> klass,
                                                  Object... constructorParameters)

Instantiates a data class with the provided parameters This method is helpful if output data is constructed based on slot types

Type Parameters:

T - Data class

Parameters:

klass - The data class

constructorParameters - Constructor parameters

Returns:

Data instance

getJIPipeVersion

public static String getJIPipeVersion()

The current version of JIPipe according to the Maven-proved information

Returns:

the version string or 'Development' if none is available

isValidExtensionId

public static boolean isValidExtensionId(String id)

Returns if the ID is a valid extension ID Must have following structure: [group]:[artifact] [group] should be lower-case and be a valid Maven group ID [artifact] should be lower-case and a valid Maven artifact ID

Parameters:

id - the ID

Returns:

if the id is a valid extension id

getTableOperationRegistry

public JIPipeExpressionRegistry getTableOperationRegistry()

Specified by:

getTableOperationRegistry in interface JIPipeService

getGraphEditorToolRegistry

public JIPipeGraphEditorToolRegistry getGraphEditorToolRegistry()

Specified by:

getGraphEditorToolRegistry in interface JIPipeService

getProjectTemplateRegistry

public JIPipeProjectTemplateRegistry getProjectTemplateRegistry()

Specified by:

getProjectTemplateRegistry in interface JIPipeService

getProgressInfo

public JIPipeProgressInfo getProgressInfo()

getFailedExtensions

public List<JIPipeDependency> getFailedExtensions()

initialize

public void initialize()

Initializes JIPipe. Uses the default extension settings and discards any detected issues.

Specified by:

initialize in interface Initializable

Specified by:

initialize in interface Service

initialize

public void initialize(ExtensionSettings extensionSettings,
                       JIPipeRegistryIssues issues)

Initializes JIPipe

Parameters:

extensionSettings - extension settings

issues - if no windows should be opened

isInitializing

public boolean isInitializing()

checkUpdateSites

public void checkUpdateSites(JIPipeRegistryIssues issues,
                             List<JIPipeDependency> extensions,
                             Progress progressAdapter,
                             JIPipeProgressInfo progressInfo)

Checks the update sites of all extensions and stores the results in the issues

Parameters:

issues - the results

extensions - list of known extensions

progressAdapter - the adapter that takes the progress

progressInfo - the progress info

register

public void register(JIPipeJsonExtension extension,
                     JIPipeProgressInfo progressInfo)

Registers a JSON extension

Parameters:

extension - The extension

progressInfo - the progress info

getExtensionRegistry

public JIPipeExtensionRegistry getExtensionRegistry()

Specified by:

getExtensionRegistry in interface JIPipeService

getNodeRegistry

public JIPipeNodeRegistry getNodeRegistry()

Specified by:

getNodeRegistry in interface JIPipeService

getDatatypeRegistry

public JIPipeDatatypeRegistry getDatatypeRegistry()

Specified by:

getDatatypeRegistry in interface JIPipeService

getImageJDataAdapterRegistry

public JIPipeImageJAdapterRegistry getImageJDataAdapterRegistry()

Specified by:

getImageJDataAdapterRegistry in interface JIPipeService

getRegisteredExtensions

public List<JIPipeDependency> getRegisteredExtensions()

Specified by:

getRegisteredExtensions in interface JIPipeService

getCustomMenuRegistry

public JIPipeCustomMenuRegistry getCustomMenuRegistry()

Specified by:

getCustomMenuRegistry in interface JIPipeService

getRegisteredExtensionIds

public Set<String> getRegisteredExtensionIds()

Specified by:

getRegisteredExtensionIds in interface JIPipeService

reportValidity

public void reportValidity(JIPipeIssueReport report)

Description copied from interface: JIPipeValidatable

Generates a validity report

Specified by:

reportValidity in interface JIPipeValidatable

Parameters:

report - the report to be added to

findExtensionById

public JIPipeDependency findExtensionById(String dependencyId)

Specified by:

findExtensionById in interface JIPipeService

getPluginService

public PluginService getPluginService()

getParameterTypeRegistry

public JIPipeParameterTypeRegistry getParameterTypeRegistry()

Specified by:

getParameterTypeRegistry in interface JIPipeService

getSettingsRegistry

public JIPipeSettingsRegistry getSettingsRegistry()

Specified by:

getSettingsRegistry in interface JIPipeService

getExpressionRegistry

public JIPipeExpressionRegistry getExpressionRegistry()

Specified by:

getExpressionRegistry in interface JIPipeService

getImageJPlugins

public FilesCollection getImageJPlugins()

getLogService

public LogService getLogService()

getExternalEnvironmentRegistry

public JIPipeExternalEnvironmentRegistry getExternalEnvironmentRegistry()

Specified by:

getExternalEnvironmentRegistry in interface JIPipeService

getUtilityRegistry

public JIPipeUtilityRegistry getUtilityRegistry()

Specified by:

getUtilityRegistry in interface JIPipeService