public class CellposeAlgorithm extends JIPipeSingleIterationAlgorithm
CellposeAlgorithm_Old
that utilizes the Cellpose CLIJIPipeGraphNode.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_FLOWS_D |
static JIPipeDataSlotInfo |
OUTPUT_FLOWS_XY |
static JIPipeDataSlotInfo |
OUTPUT_FLOWS_Z |
static JIPipeDataSlotInfo |
OUTPUT_LABELS |
static JIPipeDataSlotInfo |
OUTPUT_PROBABILITIES |
static JIPipeDataSlotInfo |
OUTPUT_ROI |
SLOT_PARAMETERS
Constructor and Description |
---|
CellposeAlgorithm(CellposeAlgorithm other) |
CellposeAlgorithm(JIPipeNodeInfo info) |
generateDataBatchesGenerationResult, getAdaptiveParameterSettings, getDataBatchGenerationSettings, getGenerationSettingsInterface, getIgnoredAnnotationColumns, getParallelizationBatchSize, isParameterUIVisible, isParameterUIVisible, runParameterSet, runPassThrough, supportsParallelization
createUIInputSlotIconDescriptionMenuItems, getDataInputSlotCount, getDataInputSlots, getFirstInputSlot, getNonParameterInputSlots, getParameterSlot, getParameterSlotAlgorithmSettings, getUIInputSlotIcon, getUIInputSlotIconBaseDimensions, run
canAutoPassThrough, canPassThrough, functionallyEquals, getDefaultCustomExpressionVariables, getRuntimePartition, isEnabled, isEnableDefaultCustomExpressionVariables, isPassThrough, isPostprocessor, isPreprocessor, isSkipped, loadExample, 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_LABELS
public static final JIPipeDataSlotInfo OUTPUT_FLOWS_XY
public static final JIPipeDataSlotInfo OUTPUT_FLOWS_Z
public static final JIPipeDataSlotInfo OUTPUT_FLOWS_D
public static final JIPipeDataSlotInfo OUTPUT_PROBABILITIES
public static final JIPipeDataSlotInfo OUTPUT_ROI
public CellposeAlgorithm(JIPipeNodeInfo info)
public CellposeAlgorithm(CellposeAlgorithm other)
public void getExternalEnvironments(List<JIPipeEnvironment> target)
JIPipeGraphNode
getExternalEnvironments
in class JIPipeGraphNode
target
- the list where the external environments will be gatheredpublic boolean isEnable3DSegmentation()
public void setEnable3DSegmentation(boolean enable3DSegmentation)
public OptionalPythonEnvironment getOverrideEnvironment()
public void setOverrideEnvironment(OptionalPythonEnvironment overrideEnvironment)
public void onParameterChanged(JIPipeParameterCollection.ParameterChangedEvent event)
JIPipeGraphNode
JIPipeGraphNode.NodeSlotsChangedEvent
onParameterChanged
in interface JIPipeParameterCollection.ParameterChangedEventListener
onParameterChanged
in class JIPipeParameterSlotAlgorithm
event
- generated eventpublic void reportValidity(JIPipeValidationReportContext reportContext, JIPipeValidationReport report)
JIPipeValidatable
reportValidity
in interface JIPipeValidatable
reportValidity
in class JIPipeAlgorithm
reportContext
- the report contextreport
- the report to be added toprotected 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 boolean isCleanUpAfterwards()
public void setCleanUpAfterwards(boolean cleanUpAfterwards)
public OptionalTextAnnotationNameParameter getDiameterAnnotation()
public void setDiameterAnnotation(OptionalTextAnnotationNameParameter diameterAnnotation)
public OptionalDoubleParameter getDiameter()
public void setDiameter(OptionalDoubleParameter diameter)
public CellposeChannelSettings getChannelSettings()
public CellposeSegmentationTweaksSettings getEnhancementParameters()
public CellposeSegmentationThresholdSettings getThresholdParameters()
public CellposeSegmentationOutputSettings getSegmentationOutputSettings()
public CellposeGPUSettings getGpuSettings()
public CellposeModel getModel()
public void setModel(CellposeModel model)
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.