org.hkijena.jipipe.api.nodes

Class JIPipeAlgorithm

java.lang.Object

org.hkijena.jipipe.api.parameters.AbstractJIPipeParameterCollection

org.hkijena.jipipe.api.nodes.JIPipeGraphNode

org.hkijena.jipipe.api.nodes.JIPipeAlgorithm

All Implemented Interfaces:

JIPipeSlotConfiguration.SlotConfigurationChangedEventListener, JIPipeFunctionallyComparable, JIPipeParameterCollection, JIPipeParameterCollection.ParameterChangedEventListener, JIPipeParameterCollection.ParameterStructureChangedEventListener, JIPipeParameterCollection.ParameterUIChangedEventListener, JIPipeValidatable

Direct Known Subclasses:

DefineParametersAlgorithm, DefineParametersTableAlgorithm, DefineRectangularRoiAlgorithm, DefineTablesAlgorithm, ExportDataByParameter, ExtractParametersAlgorithm, FileDataSource, FileListDataSource, FilterByAnnotation, FolderDataSource, FolderListDataSource, FormGeneratorAlgorithm, IOInterfaceAlgorithm, IteratingFormProcessorAlgorithm, JIPipeGraphWrapperAlgorithm, JIPipeParameterlessSimpleIteratingAlgorithm, JIPipeParameterSlotAlgorithm, MergeDataSlots, MergingFormProcessorAlgorithm, ModifyAndMergeTablesScript, MultiplyParametersAlgorithm, OutputFolderDataSource, PathDataSource, PathListDataSource, SimpleIteratingFormProcessorAlgorithm, SplitByAnnotation, TablesFromScript

public abstract class JIPipeAlgorithm
extends JIPipeGraphNode

An JIPipeGraphNode that contains a non-empty workload. This class contains additional parameters to control the workload behavior. Please prefer to use this class or its derivatives if you write your algorithms.

Nested Class Summary

Nested classes/interfaces inherited from class org.hkijena.jipipe.api.nodes.JIPipeGraphNode

JIPipeGraphNode.BaseDirectoryChangedEvent, JIPipeGraphNode.BaseDirectoryChangedEventEmitter, JIPipeGraphNode.BaseDirectoryChangedEventListener, JIPipeGraphNode.NodeSlotsChangedEvent, JIPipeGraphNode.NodeSlotsChangedEventEmitter, JIPipeGraphNode.NodeSlotsChangedEventListener, JIPipeGraphNode.Serializer

Nested classes/interfaces inherited from interface org.hkijena.jipipe.api.parameters.JIPipeParameterCollection

JIPipeParameterCollection.ParameterChangedEvent, JIPipeParameterCollection.ParameterChangedEventEmitter, JIPipeParameterCollection.ParameterChangedEventListener, JIPipeParameterCollection.ParameterStructureChangedEvent, JIPipeParameterCollection.ParameterStructureChangedEventEmitter, JIPipeParameterCollection.ParameterStructureChangedEventListener, JIPipeParameterCollection.ParameterUIChangedEvent, JIPipeParameterCollection.ParameterUIChangedEventEmitter, JIPipeParameterCollection.ParameterUIChangedEventListener

Constructor Summary

Constructors

Constructor and Description
JIPipeAlgorithm(JIPipeAlgorithm other) Creates a copy
JIPipeAlgorithm(JIPipeNodeInfo info) Initializes a new node type instance
JIPipeAlgorithm(JIPipeNodeInfo info, JIPipeSlotConfiguration slotConfiguration) Initializes a new node type instance and sets a custom slot configuration

Method Summary

Modifier and Type	Method and Description
protected boolean	canAutoPassThrough() Returns true if the algorithm can automatically apply pass-through This is only possible if there is at most one input and at most one output.
boolean	canPassThrough() Returns true if the algorithm can apply pass-through.
boolean	functionallyEquals(Object other) Returns true if this node and the other node are functionally equal (i.e. they have the same functional parameters).
JIPipeCustomExpressionVariablesParameter	getDefaultCustomExpressionVariables()
RuntimePartitionReferenceParameter	getRuntimePartition()
boolean	isEnabled()
boolean	isEnableDefaultCustomExpressionVariables() Returns true if the default custom expression variables are shown in the UI (defaults to true)
boolean	isParameterUIVisible(JIPipeParameterTree tree, JIPipeParameterAccess access) Allows to override the visibility of parameters inside the UI
boolean	isParameterUIVisible(JIPipeParameterTree tree, JIPipeParameterCollection subParameter) Allows to override the visibility of sub-parameters inside the UI
boolean	isPassThrough()
boolean	isPostprocessor() Indicates if the node should be run after all other nodes.
boolean	isPreprocessor() Indicates if the node should be run before all other nodes.
boolean	isSkipped() Used internally to mark an algorithm as (not) executed without triggering isFunctionallyEquals() Affects JIPipeGraph's getDeactivatedNodes This is not serialized, but copied
void	loadExample(JIPipeNodeExample example) Loads an example.
protected void	onDeserialized(com.fasterxml.jackson.databind.JsonNode node, JIPipeValidationReport issues, JIPipeNotificationInbox notifications) Override this method to add operations to be run after deserialization from JSON
void	reportValidity(JIPipeValidationReportContext reportContext, JIPipeValidationReport report) Generates a validity report
void	run(JIPipeGraphNodeRunContext runContext, JIPipeProgressInfo progressInfo) Runs the workload
protected void	runPassThrough(JIPipeGraphNodeRunContext runContext, JIPipeProgressInfo progressInfo) Runs the pass through.
void	setEnabled(boolean enabled)
void	setPassThrough(boolean passThrough)
void	setRuntimePartition(RuntimePartitionReferenceParameter runtimePartition)
void	setSkipped(boolean skipped) Used internally to mark an algorithm as (not) executed without triggering isFunctionallyEquals() Affects JIPipeGraph's getDeactivatedNodes This is not serialized, but copied

Methods inherited from class org.hkijena.jipipe.api.nodes.JIPipeGraphNode

archiveTo, canUserDelete, clearLocations, clearSlotData, copySlotConfiguration, createUIInputSlotIconDescriptionMenuItems, duplicate, emitNodeSlotsChangedEvent, fromJson, getAliasIdInParentGraph, getBaseDirectory, getBaseDirectoryChangedEventEmitter, getCategory, getCompartmentDisplayName, getCompartmentUUIDInGraphAsString, getCompartmentUUIDInParentGraph, getCustomDescription, getCustomName, getDataInputSlots, getDependencies, getDisplayName, getEnvironmentDependencies, getFirstInputSlot, getFirstOutputSlot, getInfo, getInputSlot, getInputSlotMap, getInputSlotOrder, getInputSlots, getInputSlotsWithRole, getInternalStoragePath, getLastInputSlot, getLastOutputSlot, getName, getNewScratch, getNodeSlotsChangedEventEmitter, getNodeUILocationPerViewModePerCompartment, getNodeUILocationWithin, getOpenInputSlots, getOutputSlot, getOutputSlotMap, getOutputSlots, getOutputSlotsWithRole, getParentGraph, getProject, getProjectCompartment, getProjectDataDirs, getProjectDirectory, getRuntimeProject, getScratchBaseDirectory, getSlotConfiguration, getStoragePath, getTextDescription, getUIInputSlotIcon, getUIInputSlotIconBaseDimensions, getUUIDInParentGraph, hasInputSlot, hasOutputSlot, isBookmarked, isUiLocked, isVisibleIn, onParameterChanged, onSlotConfigurationChanged, renderInputSlots, renderOutputSlots, setBaseDirectory, setBookmarked, setCustomDescription, setCustomName, setInfo, setInternalStoragePath, setNodeUILocationPerViewModePerCompartment, setNodeUILocationWithin, setNodeUILocationWithin, setParentGraph, setProjectDirectory, setRuntimeProject, setScratchBaseDirectory, setSlotConfiguration, setStoragePath, setUiLocked, toggleSlot, toJson, updateGraphNodeSlots

Methods inherited from class org.hkijena.jipipe.api.parameters.AbstractJIPipeParameterCollection

getParameterChangedEventEmitter, getParameterStructureChangedEventEmitter, getParameterUIChangedEventEmitter, onParameterStructureChanged, onParameterUIChanged, registerSubParameter, registerSubParameters

Methods inherited from class java.lang.Object

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

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

generateValidityReport

Methods inherited from interface org.hkijena.jipipe.api.parameters.JIPipeParameterCollection.ParameterUIChangedEventListener

onParameterUIChanged

Methods inherited from interface org.hkijena.jipipe.api.parameters.JIPipeParameterCollection.ParameterStructureChangedEventListener

onParameterStructureChanged

Methods inherited from interface org.hkijena.jipipe.api.parameters.JIPipeParameterCollection

deserializeFromJsonNode, emitParameterChangedEvent, emitParameterStructureChangedEvent, emitParameterUIChangedEvent, getContextActions, getParameter, getParameterAccess, installUIOverrideParameterEditor, installUIParameterOptions, serializeToJsonFile, serializeToJsonGenerator, serializeToJsonString, setParameter

Constructor Detail

JIPipeAlgorithm

public JIPipeAlgorithm(JIPipeNodeInfo info,
                       JIPipeSlotConfiguration slotConfiguration)

Initializes a new node type instance and sets a custom slot configuration

Parameters:

info - The algorithm info

slotConfiguration - The slot configuration

JIPipeAlgorithm

public JIPipeAlgorithm(JIPipeNodeInfo info)

Initializes a new node type instance

Parameters:

info - The algorithm info

JIPipeAlgorithm

public JIPipeAlgorithm(JIPipeAlgorithm other)

Creates a copy

Parameters:

other - the original

Method Detail

run

public void run(JIPipeGraphNodeRunContext runContext,
                JIPipeProgressInfo progressInfo)

Description copied from class: JIPipeGraphNode

Runs the workload

Specified by:

run in class JIPipeGraphNode

Parameters:

runContext - the context of the run process

progressInfo - progress passed from the runner

reportValidity

public void reportValidity(JIPipeValidationReportContext reportContext,
                           JIPipeValidationReport report)

Description copied from interface: JIPipeValidatable

Generates a validity report

Parameters:

reportContext - the report context

report - the report to be added to

runPassThrough

protected void runPassThrough(JIPipeGraphNodeRunContext runContext,
                              JIPipeProgressInfo progressInfo)

Runs the pass through. Override this for custom implementations if you want

Parameters:

runContext - the context of the running operation

progressInfo - the progress

canAutoPassThrough

protected boolean canAutoPassThrough()

Returns true if the algorithm can automatically apply pass-through This is only possible if there is at most one input and at most one output. Input must be compatible to the output.

Returns:

if the algorithm can automatically apply pass-through

canPassThrough

public boolean canPassThrough()

Returns true if the algorithm can apply pass-through. Override this method to implement your own checks

Returns:

true if the algorithm can apply pass-through

isSkipped

public boolean isSkipped()

Used internally to mark an algorithm as (not) executed without triggering isFunctionallyEquals() Affects JIPipeGraph's getDeactivatedNodes This is not serialized, but copied

Returns:

if the node should be skipped in the next runs

setSkipped

public void setSkipped(boolean skipped)

Used internally to mark an algorithm as (not) executed without triggering isFunctionallyEquals() Affects JIPipeGraph's getDeactivatedNodes This is not serialized, but copied

Parameters:

skipped - if the node should be skipped in the next runs

isEnabled

public boolean isEnabled()

setEnabled

public void setEnabled(boolean enabled)

getRuntimePartition

public RuntimePartitionReferenceParameter getRuntimePartition()

setRuntimePartition

public void setRuntimePartition(RuntimePartitionReferenceParameter runtimePartition)

isPassThrough

public boolean isPassThrough()

setPassThrough

public void setPassThrough(boolean passThrough)

getDefaultCustomExpressionVariables

public JIPipeCustomExpressionVariablesParameter getDefaultCustomExpressionVariables()

onDeserialized

protected void onDeserialized(com.fasterxml.jackson.databind.JsonNode node,
                              JIPipeValidationReport issues,
                              JIPipeNotificationInbox notifications)

Description copied from class: JIPipeGraphNode

Override this method to add operations to be run after deserialization from JSON

Overrides:

onDeserialized in class JIPipeGraphNode

Parameters:

node - the JSON node where the data was loaded

issues - issues during deserialization. if you want to notify the user about potential issues that can be acted upon, use the notification inbox

notifications - additional notifications for the user. these can be acted upon

isEnableDefaultCustomExpressionVariables

public boolean isEnableDefaultCustomExpressionVariables()

Returns true if the default custom expression variables are shown in the UI (defaults to true)

Returns:

if the custom expression variables are shown in the UI

isParameterUIVisible

public boolean isParameterUIVisible(JIPipeParameterTree tree,
                                    JIPipeParameterAccess access)

Description copied from interface: JIPipeParameterCollection

Allows to override the visibility of parameters inside the UI

Specified by:

isParameterUIVisible in interface JIPipeParameterCollection

Overrides:

isParameterUIVisible in class JIPipeGraphNode

Parameters:

tree - the parameter tree that is used to access this parameter

access - the parameter

Returns:

if the parameter is visible inside the UI

isParameterUIVisible

public boolean isParameterUIVisible(JIPipeParameterTree tree,
                                    JIPipeParameterCollection subParameter)

Description copied from interface: JIPipeParameterCollection

Allows to override the visibility of sub-parameters inside the UI

Parameters:

tree - the parameter tree that is used to access this parameter

subParameter - a sub parameter

Returns:

if the parameter is visible inside the UI

functionallyEquals

public boolean functionallyEquals(Object other)

Description copied from class: JIPipeGraphNode

Returns true if this node and the other node are functionally equal (i.e. they have the same functional parameters). For non-functional nodes, this determines if the JIPipeNodeInfo is equal

Specified by:

functionallyEquals in interface JIPipeFunctionallyComparable

Overrides:

functionallyEquals in class JIPipeGraphNode

Parameters:

other - the other node

Returns:

if the nodes are functionally equal

isPreprocessor

public boolean isPreprocessor()

Indicates if the node should be run before all other nodes. Only applies if there is no input. Defaults to false.

Returns:

If the node should behave like a preprocessor.

isPostprocessor

public boolean isPostprocessor()

Indicates if the node should be run after all other nodes. Only applies if the output is not used or there is no output. Defaults to false

Returns:

If the node should behave like a postprocessor.

loadExample

public void loadExample(JIPipeNodeExample example)

Loads an example. Warning: This method will not ask for confirmation

Parameters:

example - the example