org.hkijena.jipipe.plugins.cellpose.algorithms.cp3

Class Cellpose3SegmentationInferenceAlgorithm

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.algorithms.cp3.Cellpose3SegmentationInferenceAlgorithm

All Implemented Interfaces:

JIPipeSlotConfiguration.SlotConfigurationChangedEventListener, JIPipeFunctionallyComparable, JIPipeIterationStepAlgorithm, JIPipeAdaptiveParametersAlgorithm, JIPipeParallelizedAlgorithm, JIPipeParameterCollection, JIPipeParameterCollection.ParameterChangedEventListener, JIPipeParameterCollection.ParameterStructureChangedEventListener, JIPipeParameterCollection.ParameterUIChangedEventListener, JIPipeValidatable, Cellpose3EnvironmentAccessNode

public class Cellpose3SegmentationInferenceAlgorithm
extends JIPipeSingleIterationAlgorithm
implements Cellpose3EnvironmentAccessNode

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	OUTPUT_FLOWS_D
static JIPipeDataSlotInfo	OUTPUT_FLOWS_XY
static JIPipeDataSlotInfo	OUTPUT_FLOWS_Z
static JIPipeDataSlotInfo	OUTPUT_LABELS
static JIPipeDataSlotInfo	OUTPUT_PROBABILITIES
static JIPipeDataSlotInfo	OUTPUT_ROI

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

SLOT_PARAMETERS

Constructor Summary

Constructors

Constructor and Description
Cellpose3SegmentationInferenceAlgorithm(Cellpose3SegmentationInferenceAlgorithm other)
Cellpose3SegmentationInferenceAlgorithm(JIPipeNodeInfo info)

Method Summary

Modifier and Type	Method and Description
Cellpose2ChannelSettings	getChannelSettings()
OptionalDoubleParameter	getDiameter()
OptionalTextAnnotationNameParameter	getDiameterAnnotation()
Cellpose3SegmentationTweaksSettings	getEnhancementParameters()
void	getEnvironmentDependencies(List<JIPipeEnvironment> target) Gathers all known external environments
Cellpose2GPUSettings	getGpuSettings()
OptionalPythonEnvironment	getOverrideEnvironment()
Cellpose2SegmentationOutputSettings	getSegmentationOutputSettings()
Cellpose2SegmentationThresholdSettings	getThresholdParameters()
boolean	isCleanUpAfterwards()
boolean	isEnable3D()
boolean	isEnableMultiChannel()
boolean	isSuppressLogs()
void	onParameterChanged(JIPipeParameterCollection.ParameterChangedEvent event) Triggered when a parameter is changed within the slot configuration.
void	reportValidity(JIPipeValidationReportContext reportContext, JIPipeValidationReport report) Generates a validity report
protected void	runIteration(JIPipeMultiIterationStep iterationStep, JIPipeIterationContext iterationContext, JIPipeGraphNodeRunContext runContext, JIPipeProgressInfo progressInfo) Runs code on one data row
void	setCleanUpAfterwards(boolean cleanUpAfterwards)
void	setDiameter(OptionalDoubleParameter diameter)
void	setDiameterAnnotation(OptionalTextAnnotationNameParameter diameterAnnotation)
void	setEnable3D(boolean enable3D)
void	setEnableMultiChannel(boolean enableMultiChannel)
void	setOverrideEnvironment(OptionalPythonEnvironment overrideEnvironment)
void	setSuppressLogs(boolean suppressLogs)

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.cp3.Cellpose3EnvironmentAccessNode

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

OUTPUT_LABELS

public static final JIPipeDataSlotInfo OUTPUT_LABELS

OUTPUT_FLOWS_XY

public static final JIPipeDataSlotInfo OUTPUT_FLOWS_XY

OUTPUT_FLOWS_Z

public static final JIPipeDataSlotInfo OUTPUT_FLOWS_Z

OUTPUT_FLOWS_D

public static final JIPipeDataSlotInfo OUTPUT_FLOWS_D

OUTPUT_PROBABILITIES

public static final JIPipeDataSlotInfo OUTPUT_PROBABILITIES

OUTPUT_ROI

public static final JIPipeDataSlotInfo OUTPUT_ROI

Constructor Detail

Cellpose3SegmentationInferenceAlgorithm

public Cellpose3SegmentationInferenceAlgorithm(JIPipeNodeInfo info)

Cellpose3SegmentationInferenceAlgorithm

public Cellpose3SegmentationInferenceAlgorithm(Cellpose3SegmentationInferenceAlgorithm other)

Method Detail

getEnvironmentDependencies

public void getEnvironmentDependencies(List<JIPipeEnvironment> target)

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()

setSuppressLogs

public void setSuppressLogs(boolean suppressLogs)

isEnable3D

public boolean isEnable3D()

setEnable3D

public void setEnable3D(boolean enable3D)

isEnableMultiChannel

public boolean isEnableMultiChannel()

setEnableMultiChannel

public void setEnableMultiChannel(boolean enableMultiChannel)

getOverrideEnvironment

public OptionalPythonEnvironment getOverrideEnvironment()

Specified by:

getOverrideEnvironment in interface Cellpose3EnvironmentAccessNode

setOverrideEnvironment

public void setOverrideEnvironment(OptionalPythonEnvironment overrideEnvironment)

onParameterChanged

public void onParameterChanged(JIPipeParameterCollection.ParameterChangedEvent event)

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)

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)

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()

setCleanUpAfterwards

public void setCleanUpAfterwards(boolean cleanUpAfterwards)

getDiameterAnnotation

public OptionalTextAnnotationNameParameter getDiameterAnnotation()

setDiameterAnnotation

public void setDiameterAnnotation(OptionalTextAnnotationNameParameter diameterAnnotation)

getDiameter

public OptionalDoubleParameter getDiameter()

setDiameter

public void setDiameter(OptionalDoubleParameter diameter)

getChannelSettings

public Cellpose2ChannelSettings getChannelSettings()

getEnhancementParameters

public Cellpose3SegmentationTweaksSettings getEnhancementParameters()

getThresholdParameters

public Cellpose2SegmentationThresholdSettings getThresholdParameters()

getSegmentationOutputSettings

public Cellpose2SegmentationOutputSettings getSegmentationOutputSettings()

getGpuSettings

public Cellpose2GPUSettings getGpuSettings()