org.hkijena.jipipe.extensions.omnipose.algorithms

Class OmniposeTrainingAlgorithm

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.JIPipeParameterSlotAlgorithm

org.hkijena.jipipe.api.nodes.JIPipeSingleIterationAlgorithm

org.hkijena.jipipe.extensions.omnipose.algorithms.OmniposeTrainingAlgorithm

All Implemented Interfaces:

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

public class OmniposeTrainingAlgorithm
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

Modifier and Type	Field and Description
static JIPipeDataSlotInfo	INPUT_PRETRAINED_MODEL
static JIPipeDataSlotInfo	OUTPUT_SIZE_MODEL

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

SLOT_PARAMETERS

Constructor Summary

Constructors

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

Method Summary

Modifier and Type	Method and Description
CellposeChannelSettings	getChannelSettings()
OptionalDoubleParameter	getDiameter()
void	getExternalEnvironments(List<JIPipeExternalEnvironment> target) Gathers all known external environments
CellposeGPUSettings	getGpuSettings()
DataAnnotationQueryExpression	getLabelDataAnnotation()
int	getNumEpochs()
OptionalPythonEnvironment	getOverrideEnvironment()
OmniposePretrainedModel	getPretrainedModel()
OmniposeTrainingTweaksSettings	getTweaksSettings()
boolean	isCleanUpAfterwards()
boolean	isEnable3DSegmentation()
boolean	isTrainSizeModel()
protected void	onDeserialized(com.fasterxml.jackson.databind.JsonNode node, JIPipeValidationReport issues, JIPipeNotificationInbox notifications) Override this method to add operations to be run after deserialization from JSON
protected void	runIteration(JIPipeMergingDataBatch dataBatch, 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	setPretrainedModel(OmniposePretrainedModel pretrainedModel)
void	setTrainSizeModel(boolean trainSizeModel)

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

generateDataBatchesDryRun, getAdaptiveParameterSettings, getDataBatchGenerationSettings, getGenerationSettingsInterface, getIgnoredAnnotationColumns, getParallelizationBatchSize, isParallelizationEnabled, isParameterUIVisible, isParameterUIVisible, runParameterSet, runPassThrough, setParallelizationEnabled, supportsParallelization

Methods inherited from class org.hkijena.jipipe.api.nodes.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, getThreadPool, isEnabled, isPassThrough, isPostprocessor, isPreprocessor, loadExample, reportValidity, runPassThrough, setEnabled, setPassThrough, setThreadPool

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, getLocations, getLocationWithin, getName, getNewScratch, getNodeSlotsChangedEventEmitter, getOpenInputSlots, getOutputSlot, getOutputSlotMap, getOutputSlots, getOutputSlotsWithRole, getParentGraph, getProjectCompartment, getProjectDataDirs, getProjectDirectory, getRuntimeProject, getScratchBaseDirectory, getSlotConfiguration, getStoragePath, getTextDescription, getUUIDInParentGraph, hasInputSlot, hasOutputSlot, isBookmarked, isUiLocked, isVisibleIn, onParameterStructureChanged, onParameterUIChanged, onSlotConfigurationChanged, registerSubParameter, renderInputSlots, renderOutputSlots, setBaseDirectory, setBookmarked, setCustomDescription, setCustomName, setInfo, setInternalStoragePath, setLocations, setLocationWithin, setLocationWithin, setParentGraph, setProjectDirectory, setRuntimeProject, setScratchBaseDirectory, setSlotConfiguration, setStoragePath, setUiLocked, toggleSlot, toJson, updateGraphNodeSlots

Methods inherited from class org.hkijena.jipipe.api.parameters.AbstractJIPipeParameterCollection

getParameterChangedEventEmitter, getParameterStructureChangedEventEmitter, getParameterUIChangedEventEmitter

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.JIPipeAdaptiveParametersAlgorithm

installUIOverrideParameterEditor, installUIParameterOptions

Methods inherited from interface org.hkijena.jipipe.api.parameters.JIPipeParameterCollection

emitParameterChangedEvent, emitParameterStructureChangedEvent, emitParameterUIChangedEvent, getContextActions, getParameter, getParameterAccess, getParameterChangedEventEmitter, getParameterStructureChangedEventEmitter, getParameterUIChangedEventEmitter, setParameter

Methods inherited from interface org.hkijena.jipipe.api.validation.JIPipeValidatable

generateValidityReport

Field Detail

INPUT_PRETRAINED_MODEL

public static final JIPipeDataSlotInfo INPUT_PRETRAINED_MODEL

OUTPUT_SIZE_MODEL

public static final JIPipeDataSlotInfo OUTPUT_SIZE_MODEL

Constructor Detail

OmniposeTrainingAlgorithm

public OmniposeTrainingAlgorithm(JIPipeNodeInfo info)

OmniposeTrainingAlgorithm

public OmniposeTrainingAlgorithm(OmniposeTrainingAlgorithm other)

Method Detail

getExternalEnvironments

public void getExternalEnvironments(List<JIPipeExternalEnvironment> target)

Description copied from class: JIPipeGraphNode

Gathers all known external environments

Overrides:

getExternalEnvironments 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()

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 CellposeGPUSettings getGpuSettings()

getTweaksSettings

public OmniposeTrainingTweaksSettings getTweaksSettings()

getChannelSettings

public CellposeChannelSettings getChannelSettings()

getPretrainedModel

public OmniposePretrainedModel getPretrainedModel()

setPretrainedModel

public void setPretrainedModel(OmniposePretrainedModel pretrainedModel)

runIteration

protected void runIteration(JIPipeMergingDataBatch dataBatch,
                            JIPipeProgressInfo progressInfo)

Description copied from class: JIPipeSingleIterationAlgorithm

Runs code on one data row

Specified by:

runIteration in class JIPipeSingleIterationAlgorithm

Parameters:

dataBatch - The data interface

progressInfo - the progress from the run

getNumEpochs

public int getNumEpochs()

setNumEpochs

public void setNumEpochs(int numEpochs)

onDeserialized

protected void onDeserialized(com.fasterxml.jackson.databind.JsonNode node,
                              JIPipeValidationReport issues,
                              JIPipeNotificationInbox notifications)

Description copied from class: JIPipeGraphNode

Override this method to add operations to be run after deserialization from JSON

Overrides:

onDeserialized in class JIPipeGraphNode

Parameters:

node - the JSON node where the data was loaded

issues - issues during deserialization. if you want to notify the user about potential issues that can be acted upon, use the notification inbox

notifications - additional notifications for the user. these can be acted upon