org.hkijena.jipipe.plugins.cellpose.legacy.algorithms

Class Cellpose1InferenceAlgorithm

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

org.hkijena.jipipe.plugins.cellpose.legacy.algorithms.Cellpose1InferenceAlgorithm

All Implemented Interfaces:

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

Deprecated.

New implementation will be CellposeAlgorithm2 that is based around the Cellpose CLI

@Deprecated
public class Cellpose1InferenceAlgorithm
extends JIPipeSingleIterationAlgorithm

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
Cellpose1InferenceAlgorithm(Cellpose1InferenceAlgorithm other) Deprecated.
Cellpose1InferenceAlgorithm(JIPipeNodeInfo info) Deprecated.

Method Summary

Modifier and Type	Method and Description
static void	extractCellposeOutputs(JIPipeMultiIterationStep iterationStep, JIPipeProgressInfo progressInfo, Path outputRoiOutline, Path outputLabels, Path outputFlows, Path outputProbabilities, Path outputStyles, List<JIPipeTextAnnotation> annotationList, CellposeSegmentationOutputSettings_Old outputParameters) Deprecated.
OptionalDoubleParameter	getDiameter() Deprecated.
OptionalTextAnnotationNameParameter	getDiameterAnnotation() Deprecated.
CellposeSegmentationEnhancementSettings_Old	getEnhancementParameters() Deprecated.
void	getEnvironmentDependencies(List<JIPipeEnvironment> target) Deprecated. Gathers all known external environments
CellposeSegmentationModelSettings_Old	getModelParameters() Deprecated.
CellposeSegmentationOutputSettings_Old	getOutputParameters() Deprecated.
OptionalPythonEnvironment	getOverrideEnvironment() Deprecated.
CellposeSegmentationPerformanceSettings_Old	getPerformanceParameters() Deprecated.
CellposeSegmentationThresholdSettings_Old	getThresholdParameters() Deprecated.
boolean	isCleanUpAfterwards() Deprecated.
boolean	isEnable3DSegmentation() Deprecated.
boolean	isParameterUIVisible(JIPipeParameterTree tree, JIPipeParameterAccess access) Deprecated. Allows to override the visibility of parameters inside the UI
void	onParameterChanged(JIPipeParameterCollection.ParameterChangedEvent event) Deprecated. Triggered when a parameter is changed within the slot configuration.
void	reportValidity(JIPipeValidationReportContext reportContext, JIPipeValidationReport report) Deprecated. Generates a validity report
protected void	runIteration(JIPipeMultiIterationStep iterationStep, JIPipeIterationContext iterationContext, JIPipeGraphNodeRunContext runContext, JIPipeProgressInfo progressInfo) Deprecated. Runs code on one data row
void	setCleanUpAfterwards(boolean cleanUpAfterwards) Deprecated.
void	setDiameter(OptionalDoubleParameter diameter) Deprecated.
void	setDiameterAnnotation(OptionalTextAnnotationNameParameter diameterAnnotation) Deprecated.
void	setEnable3DSegmentation(boolean enable3DSegmentation) Deprecated.
void	setOverrideEnvironment(OptionalPythonEnvironment overrideEnvironment) Deprecated.

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

generateDataBatchesGenerationResult, getAdaptiveParameterSettings, getDataBatchGenerationSettings, getGenerationSettingsInterface, getIgnoredAnnotationColumns, getParallelizationBatchSize, isAllowEmptyIterationStep, isParameterUIVisible, runParameterSet, runPassThrough, supportsParallelization

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

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

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

canAutoPassThrough, canPassThrough, functionallyEquals, getDefaultCustomExpressionVariables, getRuntimePartition, isEnabled, isEnableDefaultCustomExpressionVariables, isPassThrough, isPostprocessor, isPreprocessor, isSkipped, loadExample, onDeserialized, 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, 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

Cellpose1InferenceAlgorithm

public Cellpose1InferenceAlgorithm(JIPipeNodeInfo info)

Deprecated.

Cellpose1InferenceAlgorithm

public Cellpose1InferenceAlgorithm(Cellpose1InferenceAlgorithm other)

Deprecated.

Method Detail

extractCellposeOutputs

public static void extractCellposeOutputs(JIPipeMultiIterationStep iterationStep,
                                          JIPipeProgressInfo progressInfo,
                                          Path outputRoiOutline,
                                          Path outputLabels,
                                          Path outputFlows,
                                          Path outputProbabilities,
                                          Path outputStyles,
                                          List<JIPipeTextAnnotation> annotationList,
                                          CellposeSegmentationOutputSettings_Old outputParameters)

Deprecated.

isEnable3DSegmentation

public boolean isEnable3DSegmentation()

Deprecated.

setEnable3DSegmentation

public void setEnable3DSegmentation(boolean enable3DSegmentation)

Deprecated.

getOverrideEnvironment

public OptionalPythonEnvironment getOverrideEnvironment()

Deprecated.

setOverrideEnvironment

public void setOverrideEnvironment(OptionalPythonEnvironment overrideEnvironment)

Deprecated.

onParameterChanged

public void onParameterChanged(JIPipeParameterCollection.ParameterChangedEvent event)

Deprecated.

Description copied from class: JIPipeGraphNode

Triggered when a parameter is changed within the slot configuration. Triggers a JIPipeGraphNode.NodeSlotsChangedEvent

Specified by:

onParameterChanged in interface JIPipeParameterCollection.ParameterChangedEventListener

Overrides:

onParameterChanged in class JIPipeParameterSlotAlgorithm

Parameters:

event - generated event

reportValidity

public void reportValidity(JIPipeValidationReportContext reportContext,
                           JIPipeValidationReport report)

Deprecated.

Description copied from interface: JIPipeValidatable

Generates a validity report

Specified by:

reportValidity in interface JIPipeValidatable

Overrides:

reportValidity in class JIPipeAlgorithm

Parameters:

reportContext - the report context

report - the report to be added to

getEnvironmentDependencies

public void getEnvironmentDependencies(List<JIPipeEnvironment> target)

Deprecated.

Description copied from class: JIPipeGraphNode

Gathers all known external environments

Overrides:

getEnvironmentDependencies in class JIPipeGraphNode

Parameters:

target - the list where the external environments will be gathered

runIteration

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

Deprecated.

Description copied from class: JIPipeSingleIterationAlgorithm

Runs code on one data row

Specified by:

runIteration in class JIPipeSingleIterationAlgorithm

Parameters:

iterationStep - The data interface

iterationContext - The iteration context

runContext - the run context

progressInfo - the progress from the run

isCleanUpAfterwards

public boolean isCleanUpAfterwards()

Deprecated.

setCleanUpAfterwards

public void setCleanUpAfterwards(boolean cleanUpAfterwards)

Deprecated.

getDiameterAnnotation

public OptionalTextAnnotationNameParameter getDiameterAnnotation()

Deprecated.

setDiameterAnnotation

public void setDiameterAnnotation(OptionalTextAnnotationNameParameter diameterAnnotation)

Deprecated.

getDiameter

public OptionalDoubleParameter getDiameter()

Deprecated.

setDiameter

public void setDiameter(OptionalDoubleParameter diameter)

Deprecated.

getModelParameters

public CellposeSegmentationModelSettings_Old getModelParameters()

Deprecated.

getPerformanceParameters

public CellposeSegmentationPerformanceSettings_Old getPerformanceParameters()

Deprecated.

getEnhancementParameters

public CellposeSegmentationEnhancementSettings_Old getEnhancementParameters()

Deprecated.

getThresholdParameters

public CellposeSegmentationThresholdSettings_Old getThresholdParameters()

Deprecated.

getOutputParameters

public CellposeSegmentationOutputSettings_Old getOutputParameters()

Deprecated.

isParameterUIVisible

public boolean isParameterUIVisible(JIPipeParameterTree tree,
                                    JIPipeParameterAccess access)

Deprecated.

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 JIPipeSingleIterationAlgorithm

Parameters:

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

access - the parameter

Returns:

if the parameter is visible inside the UI