public class OmniposeTrainingAlgorithm extends JIPipeSingleIterationAlgorithm
JIPipeGraphNode.BaseDirectoryChangedEvent, JIPipeGraphNode.BaseDirectoryChangedEventEmitter, JIPipeGraphNode.BaseDirectoryChangedEventListener, JIPipeGraphNode.NodeSlotsChangedEvent, JIPipeGraphNode.NodeSlotsChangedEventEmitter, JIPipeGraphNode.NodeSlotsChangedEventListener, JIPipeGraphNode.Serializer
JIPipeParameterCollection.ParameterChangedEvent, JIPipeParameterCollection.ParameterChangedEventEmitter, JIPipeParameterCollection.ParameterChangedEventListener, JIPipeParameterCollection.ParameterStructureChangedEvent, JIPipeParameterCollection.ParameterStructureChangedEventEmitter, JIPipeParameterCollection.ParameterStructureChangedEventListener, JIPipeParameterCollection.ParameterUIChangedEvent, JIPipeParameterCollection.ParameterUIChangedEventEmitter, JIPipeParameterCollection.ParameterUIChangedEventListener
Modifier and Type | Field and Description |
---|---|
static JIPipeDataSlotInfo |
INPUT_PRETRAINED_MODEL |
static JIPipeDataSlotInfo |
OUTPUT_SIZE_MODEL |
SLOT_PARAMETERS
Constructor and Description |
---|
OmniposeTrainingAlgorithm(JIPipeNodeInfo info) |
OmniposeTrainingAlgorithm(OmniposeTrainingAlgorithm other) |
generateDataBatchesGenerationResult, getAdaptiveParameterSettings, getDataBatchGenerationSettings, getGenerationSettingsInterface, getIgnoredAnnotationColumns, getParallelizationBatchSize, isParameterUIVisible, isParameterUIVisible, runParameterSet, runPassThrough, supportsParallelization
createUIInputSlotIconDescriptionMenuItems, getDataInputSlotCount, getDataInputSlots, getFirstInputSlot, getNonParameterInputSlots, getParameterSlot, getParameterSlotAlgorithmSettings, getUIInputSlotIcon, getUIInputSlotIconBaseDimensions, onParameterChanged, run
canAutoPassThrough, canPassThrough, functionallyEquals, getDefaultCustomExpressionVariables, getRuntimePartition, isEnabled, isEnableDefaultCustomExpressionVariables, isPassThrough, isPostprocessor, isPreprocessor, isSkipped, loadExample, reportValidity, runPassThrough, setEnabled, setPassThrough, setRuntimePartition, setSkipped
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, onSlotConfigurationChanged, renderInputSlots, renderOutputSlots, setBaseDirectory, setBookmarked, setCustomDescription, setCustomName, setInfo, setInternalStoragePath, setLocations, setLocationWithin, setLocationWithin, setParentGraph, setProjectDirectory, setRuntimeProject, setScratchBaseDirectory, setSlotConfiguration, setStoragePath, setUiLocked, toggleSlot, toJson, updateGraphNodeSlots
getParameterChangedEventEmitter, getParameterStructureChangedEventEmitter, getParameterUIChangedEventEmitter, onParameterStructureChanged, onParameterUIChanged, registerSubParameter, registerSubParameters
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
generateDataBatchesDryRun
installUIOverrideParameterEditor, installUIParameterOptions
emitParameterChangedEvent, emitParameterStructureChangedEvent, emitParameterUIChangedEvent, getContextActions, getParameter, getParameterAccess, getParameterChangedEventEmitter, getParameterStructureChangedEventEmitter, getParameterUIChangedEventEmitter, setParameter
generateValidityReport
onParameterUIChanged
onParameterStructureChanged
public static final JIPipeDataSlotInfo INPUT_PRETRAINED_MODEL
public static final JIPipeDataSlotInfo OUTPUT_SIZE_MODEL
public OmniposeTrainingAlgorithm(JIPipeNodeInfo info)
public OmniposeTrainingAlgorithm(OmniposeTrainingAlgorithm other)
public void getExternalEnvironments(List<JIPipeEnvironment> target)
JIPipeGraphNode
getExternalEnvironments
in class JIPipeGraphNode
target
- the list where the external environments will be gatheredpublic boolean isTrainSizeModel()
public void setTrainSizeModel(boolean trainSizeModel)
public OptionalDoubleParameter getDiameter()
public void setDiameter(OptionalDoubleParameter diameter)
public boolean isCleanUpAfterwards()
public void setCleanUpAfterwards(boolean cleanUpAfterwards)
public OptionalPythonEnvironment getOverrideEnvironment()
public void setOverrideEnvironment(OptionalPythonEnvironment overrideEnvironment)
public boolean isEnable3DSegmentation()
public void setEnable3DSegmentation(boolean enable3DSegmentation)
public DataAnnotationQueryExpression getLabelDataAnnotation()
public void setLabelDataAnnotation(DataAnnotationQueryExpression labelDataAnnotation)
public CellposeGPUSettings getGpuSettings()
public OmniposeTrainingTweaksSettings getTweaksSettings()
public CellposeChannelSettings getChannelSettings()
public OmniposePretrainedModel getPretrainedModel()
public void setPretrainedModel(OmniposePretrainedModel pretrainedModel)
protected void runIteration(JIPipeMultiIterationStep iterationStep, JIPipeIterationContext iterationContext, JIPipeGraphNodeRunContext runContext, JIPipeProgressInfo progressInfo)
JIPipeSingleIterationAlgorithm
runIteration
in class JIPipeSingleIterationAlgorithm
iterationStep
- The data interfaceiterationContext
- The iteration contextrunContext
- the run contextprogressInfo
- the progress from the runpublic int getNumEpochs()
public void setNumEpochs(int numEpochs)
protected void onDeserialized(com.fasterxml.jackson.databind.JsonNode node, JIPipeValidationReport issues, JIPipeNotificationInbox notifications)
JIPipeGraphNode
onDeserialized
in class JIPipeAlgorithm
node
- the JSON node where the data was loadedissues
- issues during deserialization. if you want to notify the user about potential issues that can be acted upon, use the notification inboxnotifications
- additional notifications for the user. these can be acted uponCopyright © 2020–2024 Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute (HKI). All rights reserved.