org.hkijena.jipipe.extensions.cellpose.algorithms

Class CellposeAlgorithm

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.CellposeAlgorithm

All Implemented Interfaces:

JIPipeValidatable, JIPipeAdaptiveParametersAlgorithm, JIPipeDataBatchAlgorithm, JIPipeParallelizedAlgorithm, JIPipeParameterCollection

public class CellposeAlgorithm
extends JIPipeSingleIterationAlgorithm

Improved version of CellposeAlgorithm_Old that utilizes the Cellpose CLI

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

Modifier and Type	Field and Description
static JIPipeDataSlotInfo	INPUT_PRETRAINED_MODEL
static JIPipeDataSlotInfo	OUTPUT_FLOWS_D
static JIPipeDataSlotInfo	OUTPUT_FLOWS_XY
static JIPipeDataSlotInfo	OUTPUT_FLOWS_Z
static JIPipeDataSlotInfo	OUTPUT_LABELS
static JIPipeDataSlotInfo	OUTPUT_PROBABILITIES
static JIPipeDataSlotInfo	OUTPUT_ROI

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

SLOT_PARAMETERS

Constructor Summary

Constructors

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

Method Summary

Modifier and Type	Method and Description
CellposeChannelSettings	getChannelSettings()
OptionalDoubleParameter	getDiameter()
OptionalAnnotationNameParameter	getDiameterAnnotation()
CellposeSegmentationTweaksSettings	getEnhancementParameters()
CellposeGPUSettings	getGpuSettings()
CellposeModel	getModel()
OptionalPythonEnvironment	getOverrideEnvironment()
CellposeSegmentationOutputSettings	getSegmentationOutputSettings()
CellposeSegmentationThresholdSettings	getThresholdParameters()
boolean	isCleanUpAfterwards()
boolean	isEnable3DSegmentation()
protected void	onDeserialized(com.fasterxml.jackson.databind.JsonNode node, JIPipeIssueReport issues, JIPipeNotificationInbox notifications) Override this method to add operations to be run after deserialization from JSON
void	onParameterChanged(JIPipeParameterCollection.ParameterChangedEvent event) Triggered when a parameter is changed within the slot configuration.
void	reportValidity(JIPipeIssueReport report) Generates a validity report
protected void	runIteration(JIPipeMergingDataBatch dataBatch, JIPipeProgressInfo progressInfo) Runs code on one data row
void	setCleanUpAfterwards(boolean cleanUpAfterwards)
void	setDiameter(OptionalDoubleParameter diameter)
void	setDiameterAnnotation(OptionalAnnotationNameParameter diameterAnnotation)
void	setEnable3DSegmentation(boolean enable3DSegmentation)
void	setModel(CellposeModel model)
void	setOverrideEnvironment(OptionalPythonEnvironment overrideEnvironment)

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

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

Field Detail

INPUT_PRETRAINED_MODEL

public static final JIPipeDataSlotInfo INPUT_PRETRAINED_MODEL

OUTPUT_LABELS

public static final JIPipeDataSlotInfo OUTPUT_LABELS

OUTPUT_FLOWS_XY

public static final JIPipeDataSlotInfo OUTPUT_FLOWS_XY

OUTPUT_FLOWS_Z

public static final JIPipeDataSlotInfo OUTPUT_FLOWS_Z

OUTPUT_FLOWS_D

public static final JIPipeDataSlotInfo OUTPUT_FLOWS_D

OUTPUT_PROBABILITIES

public static final JIPipeDataSlotInfo OUTPUT_PROBABILITIES

OUTPUT_ROI

public static final JIPipeDataSlotInfo OUTPUT_ROI

Constructor Detail

CellposeAlgorithm

public CellposeAlgorithm(JIPipeNodeInfo info)

CellposeAlgorithm

public CellposeAlgorithm(CellposeAlgorithm other)

Method Detail

isEnable3DSegmentation

public boolean isEnable3DSegmentation()

setEnable3DSegmentation

public void setEnable3DSegmentation(boolean enable3DSegmentation)

getOverrideEnvironment

public OptionalPythonEnvironment getOverrideEnvironment()

setOverrideEnvironment

public void setOverrideEnvironment(OptionalPythonEnvironment overrideEnvironment)

onParameterChanged

public void onParameterChanged(JIPipeParameterCollection.ParameterChangedEvent event)

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)

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)

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()

setCleanUpAfterwards

public void setCleanUpAfterwards(boolean cleanUpAfterwards)

getDiameterAnnotation

public OptionalAnnotationNameParameter getDiameterAnnotation()

setDiameterAnnotation

public void setDiameterAnnotation(OptionalAnnotationNameParameter diameterAnnotation)

getDiameter

public OptionalDoubleParameter getDiameter()

setDiameter

public void setDiameter(OptionalDoubleParameter diameter)

getChannelSettings

public CellposeChannelSettings getChannelSettings()

getEnhancementParameters

public CellposeSegmentationTweaksSettings getEnhancementParameters()

getThresholdParameters

public CellposeSegmentationThresholdSettings getThresholdParameters()

getSegmentationOutputSettings

public CellposeSegmentationOutputSettings getSegmentationOutputSettings()

getGpuSettings

public CellposeGPUSettings getGpuSettings()

getModel

public CellposeModel getModel()

setModel

public void setModel(CellposeModel model)

onDeserialized

protected void onDeserialized(com.fasterxml.jackson.databind.JsonNode node,
                              JIPipeIssueReport 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