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

Class Cellpose1TrainingAlgorithm

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.Cellpose1TrainingAlgorithm

All Implemented Interfaces:

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

Deprecated.

@Deprecated
public class Cellpose1TrainingAlgorithm
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
Cellpose1TrainingAlgorithm(Cellpose1TrainingAlgorithm other) Deprecated.
Cellpose1TrainingAlgorithm(JIPipeNodeInfo info) Deprecated.

Method Summary

Modifier and Type	Method and Description
int	getBatchSize() Deprecated.
int	getDiameter() Deprecated.
void	getEnvironmentDependencies(List<JIPipeEnvironment> target) Deprecated. Gathers all known external environments
Cellpose2GPUSettings	getGpuSettings() Deprecated.
DataAnnotationQueryExpression	getLabelDataAnnotation() Deprecated.
double	getLearningRate() Deprecated.
int	getMinTrainMasks() Deprecated.
OptionalIntegerParameter	getNuclearChannel() Deprecated.
int	getNumEpochs() Deprecated.
OptionalPythonEnvironment	getOverrideEnvironment() Deprecated.
PretrainedLegacyCellpose2TrainingModel	getPretrainedModel() Deprecated.
OptionalIntegerParameter	getSegmentedChannel() Deprecated.
double	getWeightDecay() Deprecated.
boolean	isCleanUpAfterwards() Deprecated.
boolean	isConcatenateDownsampledLayers() Deprecated.
boolean	isEnable3DSegmentation() Deprecated.
boolean	isGenerateConnectedComponents() Deprecated.
boolean	isTrainSizeModel() Deprecated.
boolean	isUseResidualConnections() Deprecated.
boolean	isUseStyleVector() Deprecated.
protected void	runIteration(JIPipeMultiIterationStep iterationStep, JIPipeIterationContext iterationContext, JIPipeGraphNodeRunContext runContext, JIPipeProgressInfo progressInfo) Deprecated. Runs code on one data row
void	setBatchSize(int batchSize) Deprecated.
void	setCleanUpAfterwards(boolean cleanUpAfterwards) Deprecated.
void	setConcatenateDownsampledLayers(boolean concatenateDownsampledLayers) Deprecated.
void	setDiameter(int diameter) Deprecated.
void	setEnable3DSegmentation(boolean enable3DSegmentation) Deprecated.
void	setGenerateConnectedComponents(boolean generateConnectedComponents) Deprecated.
void	setLabelDataAnnotation(DataAnnotationQueryExpression labelDataAnnotation) Deprecated.
void	setLearningRate(double learningRate) Deprecated.
void	setMinTrainMasks(int minTrainMasks) Deprecated.
void	setNuclearChannel(OptionalIntegerParameter nuclearChannel) Deprecated.
void	setNumEpochs(int numEpochs) Deprecated.
void	setOverrideEnvironment(OptionalPythonEnvironment overrideEnvironment) Deprecated.
void	setPretrainedModel(PretrainedLegacyCellpose2TrainingModel pretrainedModel) Deprecated.
void	setSegmentedChannel(OptionalIntegerParameter segmentedChannel) Deprecated.
void	setTrainSizeModel(boolean trainSizeModel) Deprecated.
void	setUseResidualConnections(boolean useResidualConnections) Deprecated.
void	setUseStyleVector(boolean useStyleVector) Deprecated.
void	setWeightDecay(double weightDecay) 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, 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, 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

Cellpose1TrainingAlgorithm

public Cellpose1TrainingAlgorithm(JIPipeNodeInfo info)

Deprecated.

Cellpose1TrainingAlgorithm

public Cellpose1TrainingAlgorithm(Cellpose1TrainingAlgorithm 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

getSegmentedChannel

public OptionalIntegerParameter getSegmentedChannel()

Deprecated.

setSegmentedChannel

public void setSegmentedChannel(OptionalIntegerParameter segmentedChannel)

Deprecated.

getNuclearChannel

public OptionalIntegerParameter getNuclearChannel()

Deprecated.

setNuclearChannel

public void setNuclearChannel(OptionalIntegerParameter nuclearChannel)

Deprecated.

getWeightDecay

public double getWeightDecay()

Deprecated.

setWeightDecay

public void setWeightDecay(double weightDecay)

Deprecated.

isGenerateConnectedComponents

public boolean isGenerateConnectedComponents()

Deprecated.

setGenerateConnectedComponents

public void setGenerateConnectedComponents(boolean generateConnectedComponents)

Deprecated.

getMinTrainMasks

public int getMinTrainMasks()

Deprecated.

setMinTrainMasks

public void setMinTrainMasks(int minTrainMasks)

Deprecated.

isTrainSizeModel

public boolean isTrainSizeModel()

Deprecated.

setTrainSizeModel

public void setTrainSizeModel(boolean trainSizeModel)

Deprecated.

getLearningRate

public double getLearningRate()

Deprecated.

setLearningRate

public void setLearningRate(double learningRate)

Deprecated.

getBatchSize

public int getBatchSize()

Deprecated.

setBatchSize

public void setBatchSize(int batchSize)

Deprecated.

isUseResidualConnections

public boolean isUseResidualConnections()

Deprecated.

setUseResidualConnections

public void setUseResidualConnections(boolean useResidualConnections)

Deprecated.

isUseStyleVector

public boolean isUseStyleVector()

Deprecated.

setUseStyleVector

public void setUseStyleVector(boolean useStyleVector)

Deprecated.

isConcatenateDownsampledLayers

public boolean isConcatenateDownsampledLayers()

Deprecated.

setConcatenateDownsampledLayers

public void setConcatenateDownsampledLayers(boolean concatenateDownsampledLayers)

Deprecated.

getDiameter

public int getDiameter()

Deprecated.

setDiameter

public void setDiameter(int diameter)

Deprecated.

isCleanUpAfterwards

public boolean isCleanUpAfterwards()

Deprecated.

setCleanUpAfterwards

public void setCleanUpAfterwards(boolean cleanUpAfterwards)

Deprecated.

getOverrideEnvironment

public OptionalPythonEnvironment getOverrideEnvironment()

Deprecated.

setOverrideEnvironment

public void setOverrideEnvironment(OptionalPythonEnvironment overrideEnvironment)

Deprecated.

isEnable3DSegmentation

public boolean isEnable3DSegmentation()

Deprecated.

setEnable3DSegmentation

public void setEnable3DSegmentation(boolean enable3DSegmentation)

Deprecated.

getLabelDataAnnotation

public DataAnnotationQueryExpression getLabelDataAnnotation()

Deprecated.

setLabelDataAnnotation

public void setLabelDataAnnotation(DataAnnotationQueryExpression labelDataAnnotation)

Deprecated.

getGpuSettings

public Cellpose2GPUSettings getGpuSettings()

Deprecated.

getPretrainedModel

public PretrainedLegacyCellpose2TrainingModel getPretrainedModel()

Deprecated.

setPretrainedModel

public void setPretrainedModel(PretrainedLegacyCellpose2TrainingModel pretrainedModel)

Deprecated.

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

getNumEpochs

public int getNumEpochs()

Deprecated.

setNumEpochs

public void setNumEpochs(int numEpochs)

Deprecated.