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

Class LegacyCellpose2InferenceAlgorithm

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.LegacyCellpose2InferenceAlgorithm

All Implemented Interfaces:

JIPipeSlotConfiguration.SlotConfigurationChangedEventListener, JIPipeFunctionallyComparable, JIPipeIterationStepAlgorithm, JIPipeAdaptiveParametersAlgorithm, JIPipeParallelizedAlgorithm, JIPipeParameterCollection, JIPipeParameterCollection.ParameterChangedEventListener, JIPipeParameterCollection.ParameterStructureChangedEventListener, JIPipeParameterCollection.ParameterUIChangedEventListener, JIPipeValidatable, Cellpose2EnvironmentAccessNode

Deprecated.

@Deprecated
public class LegacyCellpose2InferenceAlgorithm
extends JIPipeSingleIterationAlgorithm
implements Cellpose2EnvironmentAccessNode

Improved version of Cellpose1InferenceAlgorithm that utilizes the Cellpose CLI

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

Modifier and Type	Field and Description
static JIPipeDataSlotInfo	INPUT_PRETRAINED_MODEL Deprecated.
static JIPipeDataSlotInfo	OUTPUT_FLOWS_D Deprecated.
static JIPipeDataSlotInfo	OUTPUT_FLOWS_XY Deprecated.
static JIPipeDataSlotInfo	OUTPUT_FLOWS_Z Deprecated.
static JIPipeDataSlotInfo	OUTPUT_LABELS Deprecated.
static JIPipeDataSlotInfo	OUTPUT_PROBABILITIES Deprecated.
static JIPipeDataSlotInfo	OUTPUT_ROI Deprecated.

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

SLOT_PARAMETERS

Constructor Summary

Constructors

Constructor and Description
LegacyCellpose2InferenceAlgorithm(JIPipeNodeInfo info) Deprecated.
LegacyCellpose2InferenceAlgorithm(LegacyCellpose2InferenceAlgorithm other) Deprecated.

Method Summary

Modifier and Type	Method and Description
Cellpose2ChannelSettings	getChannelSettings() Deprecated.
OptionalDoubleParameter	getDiameter() Deprecated.
OptionalTextAnnotationNameParameter	getDiameterAnnotation() Deprecated.
Cellpose2SegmentationTweaksSettings	getEnhancementParameters() Deprecated.
void	getEnvironmentDependencies(List<JIPipeEnvironment> target) Deprecated. Gathers all known external environments
Cellpose2GPUSettings	getGpuSettings() Deprecated.
PretrainedLegacyCellpose2InferenceModel	getModel() Deprecated.
OptionalPythonEnvironment	getOverrideEnvironment() Deprecated.
Cellpose2SegmentationOutputSettings	getSegmentationOutputSettings() Deprecated.
Cellpose2SegmentationThresholdSettings	getThresholdParameters() Deprecated.
boolean	isCleanUpAfterwards() Deprecated.
boolean	isEnable3DSegmentation() Deprecated.
boolean	isSuppressLogs() Deprecated.
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	setModel(PretrainedLegacyCellpose2InferenceModel model) Deprecated.
void	setOverrideEnvironment(OptionalPythonEnvironment overrideEnvironment) Deprecated.
void	setSuppressLogs(boolean suppressLogs) Deprecated.

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

generateDataBatchesGenerationResult, getAdaptiveParameterSettings, getDataBatchGenerationSettings, getGenerationSettingsInterface, getIgnoredAnnotationColumns, getParallelizationBatchSize, isAllowEmptyIterationStep, isParameterUIVisible, 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.plugins.cellpose.algorithms.cp2.Cellpose2EnvironmentAccessNode

getConfiguredCellposeEnvironment, reportConfiguredCellposeEnvironmentValidity

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

Field Detail

INPUT_PRETRAINED_MODEL

public static final JIPipeDataSlotInfo INPUT_PRETRAINED_MODEL

Deprecated.

OUTPUT_LABELS

public static final JIPipeDataSlotInfo OUTPUT_LABELS

Deprecated.

OUTPUT_FLOWS_XY

public static final JIPipeDataSlotInfo OUTPUT_FLOWS_XY

Deprecated.

OUTPUT_FLOWS_Z

public static final JIPipeDataSlotInfo OUTPUT_FLOWS_Z

Deprecated.

OUTPUT_FLOWS_D

public static final JIPipeDataSlotInfo OUTPUT_FLOWS_D

Deprecated.

OUTPUT_PROBABILITIES

public static final JIPipeDataSlotInfo OUTPUT_PROBABILITIES

Deprecated.

OUTPUT_ROI

public static final JIPipeDataSlotInfo OUTPUT_ROI

Deprecated.

Constructor Detail

LegacyCellpose2InferenceAlgorithm

public LegacyCellpose2InferenceAlgorithm(JIPipeNodeInfo info)

Deprecated.

LegacyCellpose2InferenceAlgorithm

public LegacyCellpose2InferenceAlgorithm(LegacyCellpose2InferenceAlgorithm other)

Deprecated.

Method Detail

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

isSuppressLogs

public boolean isSuppressLogs()

Deprecated.

setSuppressLogs

public void setSuppressLogs(boolean suppressLogs)

Deprecated.

isEnable3DSegmentation

public boolean isEnable3DSegmentation()

Deprecated.

setEnable3DSegmentation

public void setEnable3DSegmentation(boolean enable3DSegmentation)

Deprecated.

getOverrideEnvironment

public OptionalPythonEnvironment getOverrideEnvironment()

Deprecated.

Specified by:

getOverrideEnvironment in interface Cellpose2EnvironmentAccessNode

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

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.

getChannelSettings

public Cellpose2ChannelSettings getChannelSettings()

Deprecated.

getEnhancementParameters

public Cellpose2SegmentationTweaksSettings getEnhancementParameters()

Deprecated.

getThresholdParameters

public Cellpose2SegmentationThresholdSettings getThresholdParameters()

Deprecated.

getSegmentationOutputSettings

public Cellpose2SegmentationOutputSettings getSegmentationOutputSettings()

Deprecated.

getGpuSettings

public Cellpose2GPUSettings getGpuSettings()

Deprecated.

getModel

public PretrainedLegacyCellpose2InferenceModel getModel()

Deprecated.

setModel

public void setModel(PretrainedLegacyCellpose2InferenceModel model)

Deprecated.