org.hkijena.jipipe.extensions.cellpose.algorithms.deprecated

Class CellposeAlgorithm_Old

java.lang.Object

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.cellpose.algorithms.deprecated.CellposeAlgorithm_Old

All Implemented Interfaces:

JIPipeValidatable, JIPipeAdaptiveParametersAlgorithm, JIPipeDataBatchAlgorithm, JIPipeParallelizedAlgorithm, JIPipeParameterCollection

Deprecated.

New implementation will be CellposeAlgorithm2 that is based around the Cellpose CLI

@Deprecated
public class CellposeAlgorithm_Old
extends JIPipeSingleIterationAlgorithm

Nested Class Summary

Nested classes/interfaces inherited from class org.hkijena.jipipe.api.nodes.JIPipeAlgorithm

JIPipeAlgorithm.StateSerializer

Nested classes/interfaces inherited from class org.hkijena.jipipe.api.nodes.JIPipeGraphNode

JIPipeGraphNode.BaseDirectoryChangedEvent, JIPipeGraphNode.Serializer

Nested classes/interfaces inherited from interface org.hkijena.jipipe.api.parameters.JIPipeParameterCollection

JIPipeParameterCollection.ParameterChangedEvent, JIPipeParameterCollection.ParameterStructureChangedEvent, JIPipeParameterCollection.ParameterUIChangedEvent

Field Summary

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

SLOT_PARAMETERS

Constructor Summary

Constructors

Constructor and Description
CellposeAlgorithm_Old(CellposeAlgorithm_Old other) Deprecated.
CellposeAlgorithm_Old(JIPipeNodeInfo info) Deprecated.

Method Summary

Modifier and Type	Method and Description
OptionalDoubleParameter	getDiameter() Deprecated.
OptionalAnnotationNameParameter	getDiameterAnnotation() Deprecated.
CellposeSegmentationEnhancementSettings_Old	getEnhancementParameters() Deprecated.
CellposeSegmentationModelSettings_Old	getModelParameters() Deprecated.
CellposeSegmentationOutputSettings_Old	getOutputParameters() Deprecated.
OptionalPythonEnvironment	getOverrideEnvironment() Deprecated.
CellposeSegmentationPerformanceSettings_Old	getPerformanceParameters() Deprecated.
CellposeSegmentationThresholdSettings_Old	getThresholdParameters() Deprecated.
boolean	isCleanUpAfterwards() Deprecated.
boolean	isEnable3DSegmentation() Deprecated.
boolean	isParameterUIVisible(JIPipeParameterTree tree, JIPipeParameterAccess access) Deprecated. Allows to override the visibility of parameters inside the UI
protected void	onDeserialized(com.fasterxml.jackson.databind.JsonNode node, JIPipeIssueReport issues, JIPipeNotificationInbox notifications) Deprecated. Override this method to add operations to be run after deserialization from JSON
void	onParameterChanged(JIPipeParameterCollection.ParameterChangedEvent event) Deprecated. Triggered when a parameter is changed within the slot configuration.
void	reportValidity(JIPipeIssueReport report) Deprecated. Generates a validity report
protected void	runIteration(JIPipeMergingDataBatch dataBatch, JIPipeProgressInfo progressInfo) Deprecated. Runs code on one data row
void	setCleanUpAfterwards(boolean cleanUpAfterwards) Deprecated.
void	setDiameter(OptionalDoubleParameter diameter) Deprecated.
void	setDiameterAnnotation(OptionalAnnotationNameParameter diameterAnnotation) Deprecated.
void	setEnable3DSegmentation(boolean enable3DSegmentation) Deprecated.
void	setOverrideEnvironment(OptionalPythonEnvironment overrideEnvironment) Deprecated.

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

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

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

getDataInputSlotCount, getDataInputSlots, getFirstInputSlot, getNonParameterInputSlots, getParameterSlot, getParameterSlotAlgorithmSettings, run

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

canAutoPassThrough, canPassThrough, getStateId, getThreadPool, isEnabled, isPassThrough, isPostprocessor, isPreprocessor, loadExample, runPassThrough, setEnabled, setPassThrough, setThreadPool

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

canUserDelete, clearLocations, clearSlotData, copySlotConfiguration, duplicate, fromJson, fromJsonNode, getAliasIdInParentGraph, getBaseDirectory, getCategory, getCompartmentDisplayName, getCompartmentUUIDInGraphAsString, getCompartmentUUIDInParentGraph, getCustomDescription, getDependencies, getDisplayName, getEventBus, getFirstOutputSlot, getInfo, getInputSlot, getInputSlotMap, getInputSlotOrder, getInputSlots, getInputSlotsWithRole, getInternalStoragePath, getLastInputSlot, getLastOutputSlot, getLocations, getLocationWithin, getName, getNewScratch, getOpenInputSlots, getOutputSlot, getOutputSlotMap, getOutputSlots, getOutputSlotsWithRole, getParentGraph, getProjectCompartment, getProjectDirectory, getScratchBaseDirectory, getSlotConfiguration, getStoragePath, getUUIDInParentGraph, hasInputSlot, hasOutputSlot, isBookmarked, isVisibleIn, onParameterStructureChanged, onParameterUIChanged, onSlotConfigurationChanged, onSlotConnected, onSlotDisconnected, registerSubParameter, renderInputSlots, renderOutputSlots, setAllSlotsVirtual, setBaseDirectory, setBookmarked, setCustomDescription, setCustomName, setInfo, setInternalStoragePath, setLocations, setLocationWithin, setLocationWithin, setParentGraph, setProjectDirectory, setScratchBaseDirectory, setSlotConfiguration, setStoragePath, toggleSlot, toJson, triggerSlotsChangedEvent, updateGraphNodeSlots, updateSlotInheritance

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.JIPipeValidatable

generateValidityReport

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

addParameterChangeListener, addParameterChangeListener, getContextActions, getParameter, getParameterAccess, setParameter, triggerParameterChange, triggerParameterStructureChange, triggerParameterUIChange

Constructor Detail

CellposeAlgorithm_Old

public CellposeAlgorithm_Old(JIPipeNodeInfo info)

Deprecated.

CellposeAlgorithm_Old

public CellposeAlgorithm_Old(CellposeAlgorithm_Old other)

Deprecated.

Method Detail

isEnable3DSegmentation

public boolean isEnable3DSegmentation()

Deprecated.

setEnable3DSegmentation

public void setEnable3DSegmentation(boolean enable3DSegmentation)

Deprecated.

getOverrideEnvironment

public OptionalPythonEnvironment getOverrideEnvironment()

Deprecated.

setOverrideEnvironment

public void setOverrideEnvironment(OptionalPythonEnvironment overrideEnvironment)

Deprecated.

onParameterChanged

public void onParameterChanged(JIPipeParameterCollection.ParameterChangedEvent event)

Deprecated.

Description copied from class: JIPipeGraphNode

Triggered when a parameter is changed within the slot configuration. Triggers a JIPipeGraph.NodeSlotsChangedEvent

Overrides:

onParameterChanged in class JIPipeGraphNode

Parameters:

event - generated event

reportValidity

public void reportValidity(JIPipeIssueReport report)

Deprecated.

Description copied from interface: JIPipeValidatable

Generates a validity report

Specified by:

reportValidity in interface JIPipeValidatable

Overrides:

reportValidity in class JIPipeAlgorithm

Parameters:

report - the report to be added to

runIteration

protected void runIteration(JIPipeMergingDataBatch dataBatch,
                            JIPipeProgressInfo progressInfo)

Deprecated.

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

isCleanUpAfterwards

public boolean isCleanUpAfterwards()

Deprecated.

setCleanUpAfterwards

public void setCleanUpAfterwards(boolean cleanUpAfterwards)

Deprecated.

getDiameterAnnotation

public OptionalAnnotationNameParameter getDiameterAnnotation()

Deprecated.

setDiameterAnnotation

public void setDiameterAnnotation(OptionalAnnotationNameParameter diameterAnnotation)

Deprecated.

getDiameter

public OptionalDoubleParameter getDiameter()

Deprecated.

setDiameter

public void setDiameter(OptionalDoubleParameter diameter)

Deprecated.

getModelParameters

public CellposeSegmentationModelSettings_Old getModelParameters()

Deprecated.

getPerformanceParameters

public CellposeSegmentationPerformanceSettings_Old getPerformanceParameters()

Deprecated.

getEnhancementParameters

public CellposeSegmentationEnhancementSettings_Old getEnhancementParameters()

Deprecated.

getThresholdParameters

public CellposeSegmentationThresholdSettings_Old getThresholdParameters()

Deprecated.

getOutputParameters

public CellposeSegmentationOutputSettings_Old getOutputParameters()

Deprecated.

isParameterUIVisible

public boolean isParameterUIVisible(JIPipeParameterTree tree,
                                    JIPipeParameterAccess access)

Deprecated.

Description copied from interface: JIPipeParameterCollection

Allows to override the visibility of parameters inside the UI

Specified by:

isParameterUIVisible in interface JIPipeParameterCollection

Overrides:

isParameterUIVisible in class JIPipeSingleIterationAlgorithm

Parameters:

tree - the parameter tree that is used to access this parameter

access - the parameter

Returns:

if the parameter is visible inside the UI

onDeserialized

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

Deprecated.

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