org.hkijena.jipipe.api.nodes.algorithm

Class JIPipeSingleIterationAlgorithm

java.lang.Object

org.hkijena.jipipe.api.parameters.AbstractJIPipeParameterCollection

org.hkijena.jipipe.api.nodes.JIPipeGraphNode

org.hkijena.jipipe.api.nodes.JIPipeAlgorithm

org.hkijena.jipipe.api.nodes.algorithm.JIPipeParameterSlotAlgorithm

org.hkijena.jipipe.api.nodes.algorithm.JIPipeSingleIterationAlgorithm

All Implemented Interfaces:

JIPipeSlotConfiguration.SlotConfigurationChangedEventListener, JIPipeFunctionallyComparable, JIPipeIterationStepAlgorithm, JIPipeAdaptiveParametersAlgorithm, JIPipeParallelizedAlgorithm, JIPipeParameterCollection, JIPipeParameterCollection.ParameterChangedEventListener, JIPipeParameterCollection.ParameterStructureChangedEventListener, JIPipeParameterCollection.ParameterUIChangedEventListener, JIPipeValidatable

Direct Known Subclasses:

AnnotateOMEROImageReferenceAlgorithm, AnnotateOMEROPlateReferenceAlgorithm, AnnotateOMEROProjectReferenceAlgorithm, AnnotateOMEROScreenReferenceAlgorithm, AnnotateOMEROWellReferenceAlgorithm, Cellpose1InferenceAlgorithm, Cellpose1TrainingAlgorithm, Cellpose2SegmentationInferenceAlgorithm, Cellpose2TrainingAlgorithm, Cellpose3DenoiseInferenceAlgorithm, Cellpose3DenoiseTrainingAlgorithm, Cellpose3SegmentationInferenceAlgorithm, Cellpose3SegmentationTrainingAlgorithm, IlastikAutoContextAlgorithm, IlastikObjectClassificationAlgorithm, IlastikPixelClassificationAlgorithm, IlastikPredictionMapsObjectClassificationAlgorithm, IlastikSegmentationImageObjectClassificationAlgorithm, LegacyCellpose2InferenceAlgorithm, LegacyCellpose2TrainingAlgorithm, LegacyOmnipose0InferenceAlgorithm, LegacyOmnipose0TrainingAlgorithm, OMEROListDatasetImagesAlgorithm, OMEROListDatasetsAlgorithm, OMEROListGroupsAlgorithm, OMEROListPlatesAlgorithm, OMEROListProjectsAlgorithm, OMEROListScreensAlgorithm, OMEROListWellImagesAlgorithm, OMEROListWellsAlgorithm, Omnipose0InferenceAlgorithm, Omnipose0TrainingAlgorithm

public abstract class JIPipeSingleIterationAlgorithm
extends JIPipeParameterSlotAlgorithm
implements JIPipeParallelizedAlgorithm, JIPipeIterationStepAlgorithm, JIPipeAdaptiveParametersAlgorithm

An JIPipeAlgorithm that applies a single iteration with a iteration step containing all data.

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

Field Summary

Fields inherited from class org.hkijena.jipipe.api.nodes.algorithm.JIPipeParameterSlotAlgorithm

SLOT_PARAMETERS

Constructor Summary

Constructors

Constructor and Description
JIPipeSingleIterationAlgorithm(JIPipeNodeInfo info) Creates a new instance
JIPipeSingleIterationAlgorithm(JIPipeNodeInfo info, JIPipeSlotConfiguration slotConfiguration) Creates a new instance
JIPipeSingleIterationAlgorithm(JIPipeSingleIterationAlgorithm other) Copies the algorithm

Method Summary

Modifier and Type	Method and Description
JIPipeDataBatchGenerationResult	generateDataBatchesGenerationResult(List<JIPipeInputDataSlot> slots, JIPipeProgressInfo progressInfo) Generates iteration steps.
JIPipeAdaptiveParameterSettings	getAdaptiveParameterSettings()
JIPipeSingleIterationAlgorithmIterationStepGenerationSettings	getDataBatchGenerationSettings()
JIPipeIterationStepGenerationSettings	getGenerationSettingsInterface() Returns the batch generation settings as interface
Set<String>	getIgnoredAnnotationColumns() Returns annotation types that should be ignored by the internal logic.
int	getParallelizationBatchSize() Returns how many threads the actual algorithm requires.
protected boolean	isAllowEmptyIterationStep() If true, allow the execution of an empty iteration step if all inputs are optional and are empty
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
protected abstract void	runIteration(JIPipeMultiIterationStep iterationStep, JIPipeIterationContext iterationContext, JIPipeGraphNodeRunContext runContext, JIPipeProgressInfo progressInfo) Runs code on one data row
void	runParameterSet(JIPipeGraphNodeRunContext runContext, JIPipeProgressInfo progressInfo, List<JIPipeTextAnnotation> parameterAnnotations) Runs a parameter set iteration
protected void	runPassThrough(JIPipeProgressInfo progressInfo, JIPipeMultiIterationStep iterationStep) A pass-through variant for merging algorithms.
boolean	supportsParallelization() Indicates to the algorithm base implementation if parallelization is supported.

Methods inherited from class org.hkijena.jipipe.api.nodes.algorithm.JIPipeParameterSlotAlgorithm

createUIInputSlotIconDescriptionMenuItems, getDataInputSlotCount, getDataInputSlots, getFirstInputSlot, getNonParameterInputSlots, getParameterSlot, getParameterSlotAlgorithmSettings, getUIInputSlotIcon, getUIInputSlotIconBaseDimensions, onParameterChanged, run

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

canAutoPassThrough, canPassThrough, functionallyEquals, getDefaultCustomExpressionVariables, getRuntimePartition, isEnabled, isEnableDefaultCustomExpressionVariables, isPassThrough, isPostprocessor, isPreprocessor, isSkipped, loadExample, onDeserialized, reportValidity, runPassThrough, setEnabled, setPassThrough, setRuntimePartition, setSkipped

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

archiveTo, canUserDelete, clearLocations, clearSlotData, copySlotConfiguration, duplicate, emitNodeSlotsChangedEvent, fromJson, getAliasIdInParentGraph, getBaseDirectory, getBaseDirectoryChangedEventEmitter, getCategory, getCompartmentDisplayName, getCompartmentUUIDInGraphAsString, getCompartmentUUIDInParentGraph, getCustomDescription, getCustomName, getDependencies, getDisplayName, getEnvironmentDependencies, 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, getUUIDInParentGraph, hasInputSlot, hasOutputSlot, isBookmarked, isUiLocked, isVisibleIn, 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.nodes.iterationstep.JIPipeIterationStepAlgorithm

generateDataBatchesDryRun

Methods inherited from interface org.hkijena.jipipe.api.nodes.JIPipeAdaptiveParametersAlgorithm

installUIOverrideParameterEditor, installUIParameterOptions

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

deserializeFromJsonNode, emitParameterChangedEvent, emitParameterStructureChangedEvent, emitParameterUIChangedEvent, getContextActions, getParameter, getParameterAccess, getParameterChangedEventEmitter, getParameterStructureChangedEventEmitter, getParameterUIChangedEventEmitter, serializeToJsonFile, serializeToJsonGenerator, serializeToJsonString, setParameter

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

Constructor Detail

JIPipeSingleIterationAlgorithm

public JIPipeSingleIterationAlgorithm(JIPipeNodeInfo info,
                                      JIPipeSlotConfiguration slotConfiguration)

Creates a new instance

Parameters:

info - Algorithm info

slotConfiguration - Slot configuration override

JIPipeSingleIterationAlgorithm

public JIPipeSingleIterationAlgorithm(JIPipeNodeInfo info)

Creates a new instance

Parameters:

info - Algorithm info

JIPipeSingleIterationAlgorithm

public JIPipeSingleIterationAlgorithm(JIPipeSingleIterationAlgorithm other)

Copies the algorithm

Parameters:

other - The original

Method Detail

isAllowEmptyIterationStep

protected boolean isAllowEmptyIterationStep()

If true, allow the execution of an empty iteration step if all inputs are optional and are empty

Returns:

whether empty iteration steps are allowed

getGenerationSettingsInterface

public JIPipeIterationStepGenerationSettings getGenerationSettingsInterface()

Description copied from interface: JIPipeIterationStepAlgorithm

Returns the batch generation settings as interface

Specified by:

getGenerationSettingsInterface in interface JIPipeIterationStepAlgorithm

Returns:

batch generation settings as interface

getIgnoredAnnotationColumns

public Set<String> getIgnoredAnnotationColumns()

Returns annotation types that should be ignored by the internal logic. Use this if you have some counting/sorting annotation that should not be included into the set of annotations used to match data.

Returns:

annotation types that should be ignored by the internal logic

generateDataBatchesGenerationResult

public JIPipeDataBatchGenerationResult generateDataBatchesGenerationResult(List<JIPipeInputDataSlot> slots,
                                                                           JIPipeProgressInfo progressInfo)

Description copied from interface: JIPipeIterationStepAlgorithm

Generates iteration steps. This is a dry-run function that should never throw errors

Specified by:

generateDataBatchesGenerationResult in interface JIPipeIterationStepAlgorithm

Parameters:

slots - the data slots

progressInfo - the progress

Returns:

the batches

runPassThrough

protected void runPassThrough(JIPipeProgressInfo progressInfo,
                              JIPipeMultiIterationStep iterationStep)

A pass-through variant for merging algorithms. Passes the iteration step to the single output

Parameters:

progressInfo - progress info

iterationStep - the iteration step

runParameterSet

public void runParameterSet(JIPipeGraphNodeRunContext runContext,
                            JIPipeProgressInfo progressInfo,
                            List<JIPipeTextAnnotation> parameterAnnotations)

Description copied from class: JIPipeParameterSlotAlgorithm

Runs a parameter set iteration

Specified by:

runParameterSet in class JIPipeParameterSlotAlgorithm

Parameters:

runContext - the run context

progressInfo - progress info from the run

parameterAnnotations - parameter annotations

runIteration

protected abstract void runIteration(JIPipeMultiIterationStep iterationStep,
                                     JIPipeIterationContext iterationContext,
                                     JIPipeGraphNodeRunContext runContext,
                                     JIPipeProgressInfo progressInfo)

Runs code on one data row

Parameters:

iterationStep - The data interface

iterationContext - The iteration context

runContext - the run context

progressInfo - the progress from the run

supportsParallelization

public boolean supportsParallelization()

Description copied from interface: JIPipeParallelizedAlgorithm

Indicates to the algorithm base implementation if parallelization is supported. Use this function to indicate to the algorithm to conditionally enable/disable parallelization.

Specified by:

supportsParallelization in interface JIPipeParallelizedAlgorithm

Returns:

If the algorithm supports automated parallelization.

getParallelizationBatchSize

public int getParallelizationBatchSize()

Description copied from interface: JIPipeParallelizedAlgorithm

Returns how many threads the actual algorithm requires. Based on this value, the base algorithm creates batches.

Specified by:

getParallelizationBatchSize in interface JIPipeParallelizedAlgorithm

Returns:

number of threads used by the workload

isParameterUIVisible

public boolean isParameterUIVisible(JIPipeParameterTree tree,
                                    JIPipeParameterCollection subParameter)

Description copied from interface: JIPipeParameterCollection

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

Specified by:

isParameterUIVisible in interface JIPipeParameterCollection

Overrides:

isParameterUIVisible in class JIPipeParameterSlotAlgorithm

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

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 JIPipeAlgorithm

Parameters:

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

access - the parameter

Returns:

if the parameter is visible inside the UI

getDataBatchGenerationSettings

public JIPipeSingleIterationAlgorithmIterationStepGenerationSettings getDataBatchGenerationSettings()

getAdaptiveParameterSettings

public JIPipeAdaptiveParameterSettings getAdaptiveParameterSettings()

Specified by:

getAdaptiveParameterSettings in interface JIPipeAdaptiveParametersAlgorithm