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

Class Cellpose3SegmentationTrainingAlgorithm

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.Cellpose3SegmentationTrainingAlgorithm

All Implemented Interfaces:

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

public class Cellpose3SegmentationTrainingAlgorithm
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_SIZE_MODEL

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

SLOT_PARAMETERS

Constructor Summary

Constructors

Constructor and Description
Cellpose3SegmentationTrainingAlgorithm(Cellpose3SegmentationTrainingAlgorithm other)
Cellpose3SegmentationTrainingAlgorithm(JIPipeNodeInfo info)

Method Summary

Modifier and Type	Method and Description
Cellpose2ChannelSettings	getChannelSettings()
OptionalDoubleParameter	getDiameter()
void	getEnvironmentDependencies(List<JIPipeEnvironment> target) Gathers all known external environments
Cellpose2GPUSettings	getGpuSettings()
DataAnnotationQueryExpression	getLabelDataAnnotation()
int	getNumEpochs()
OptionalPythonEnvironment	getOverrideEnvironment()
Cellpose3SegmentationTrainingTweaksSettings	getTweaksSettings()
boolean	isCleanUpAfterwards()
boolean	isEnable3DSegmentation()
boolean	isSuppressLogs()
boolean	isTrainSizeModel()
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	setEnable3DSegmentation(boolean enable3DSegmentation)
void	setLabelDataAnnotation(DataAnnotationQueryExpression labelDataAnnotation)
void	setNumEpochs(int numEpochs)
void	setOverrideEnvironment(OptionalPythonEnvironment overrideEnvironment)
void	setSuppressLogs(boolean suppressLogs)
void	setTrainSizeModel(boolean trainSizeModel)

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, 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, 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_SIZE_MODEL

public static final JIPipeDataSlotInfo OUTPUT_SIZE_MODEL

Constructor Detail

Cellpose3SegmentationTrainingAlgorithm

public Cellpose3SegmentationTrainingAlgorithm(JIPipeNodeInfo info)

Cellpose3SegmentationTrainingAlgorithm

public Cellpose3SegmentationTrainingAlgorithm(Cellpose3SegmentationTrainingAlgorithm other)

Method Detail

isSuppressLogs

public boolean isSuppressLogs()

setSuppressLogs

public void setSuppressLogs(boolean suppressLogs)

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

isTrainSizeModel

public boolean isTrainSizeModel()

setTrainSizeModel

public void setTrainSizeModel(boolean trainSizeModel)

getDiameter

public OptionalDoubleParameter getDiameter()

setDiameter

public void setDiameter(OptionalDoubleParameter diameter)

isCleanUpAfterwards

public boolean isCleanUpAfterwards()

setCleanUpAfterwards

public void setCleanUpAfterwards(boolean cleanUpAfterwards)

getOverrideEnvironment

public OptionalPythonEnvironment getOverrideEnvironment()

Specified by:

getOverrideEnvironment in interface Cellpose3EnvironmentAccessNode

setOverrideEnvironment

public void setOverrideEnvironment(OptionalPythonEnvironment overrideEnvironment)

isEnable3DSegmentation

public boolean isEnable3DSegmentation()

setEnable3DSegmentation

public void setEnable3DSegmentation(boolean enable3DSegmentation)

getLabelDataAnnotation

public DataAnnotationQueryExpression getLabelDataAnnotation()

setLabelDataAnnotation

public void setLabelDataAnnotation(DataAnnotationQueryExpression labelDataAnnotation)

getGpuSettings

public Cellpose2GPUSettings getGpuSettings()

getTweaksSettings

public Cellpose3SegmentationTrainingTweaksSettings getTweaksSettings()

getChannelSettings

public Cellpose2ChannelSettings getChannelSettings()

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

getNumEpochs

public int getNumEpochs()

setNumEpochs

public void setNumEpochs(int numEpochs)

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