org.hkijena.jipipe.extensions.imagejalgorithms.ij1.labels

Class AnnotateWithOverlapMeasureLabelsAlgorithm

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.JIPipeIteratingAlgorithm

org.hkijena.jipipe.extensions.imagejalgorithms.ij1.labels.AnnotateWithOverlapMeasureLabelsAlgorithm

All Implemented Interfaces:

JIPipeValidatable, JIPipeAdaptiveParametersAlgorithm, JIPipeDataBatchAlgorithm, JIPipeParallelizedAlgorithm, JIPipeParameterCollection

public class AnnotateWithOverlapMeasureLabelsAlgorithm
extends JIPipeIteratingAlgorithm

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
AnnotateWithOverlapMeasureLabelsAlgorithm(AnnotateWithOverlapMeasureLabelsAlgorithm other)
AnnotateWithOverlapMeasureLabelsAlgorithm(JIPipeNodeInfo info)

Method Summary

Modifier and Type	Method and Description
OptionalAnnotationNameParameter	getDiceCoefficientAnnotation()
OptionalAnnotationNameParameter	getFalseNegativeErrorAnnotation()
OptionalAnnotationNameParameter	getFalsePositiveErrorAnnotation()
OptionalAnnotationNameParameter	getJaccardIndexAnnotation()
OptionalAnnotationNameParameter	getTotalOverlapAnnotation()
OptionalAnnotationNameParameter	getVolumeSimilarityAnnotation()
protected void	runIteration(JIPipeDataBatch dataBatch, JIPipeProgressInfo progressInfo) Runs code on one data row
void	setDiceCoefficientAnnotation(OptionalAnnotationNameParameter diceCoefficientAnnotation)
void	setFalseNegativeErrorAnnotation(OptionalAnnotationNameParameter falseNegativeErrorAnnotation)
void	setFalsePositiveErrorAnnotation(OptionalAnnotationNameParameter falsePositiveErrorAnnotation)
void	setJaccardIndexAnnotation(OptionalAnnotationNameParameter jaccardIndexAnnotation)
void	setTotalOverlapAnnotation(OptionalAnnotationNameParameter totalOverlapAnnotation)
void	setVolumeSimilarityAnnotation(OptionalAnnotationNameParameter volumeSimilarityAnnotation)

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

generateDataBatchesDryRun, getAdaptiveParameterSettings, getDataBatchGenerationSettings, getGenerationSettingsInterface, 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, reportValidity, 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, onDeserialized, onParameterChanged, 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

AnnotateWithOverlapMeasureLabelsAlgorithm

public AnnotateWithOverlapMeasureLabelsAlgorithm(JIPipeNodeInfo info)

AnnotateWithOverlapMeasureLabelsAlgorithm

public AnnotateWithOverlapMeasureLabelsAlgorithm(AnnotateWithOverlapMeasureLabelsAlgorithm other)

Method Detail

getTotalOverlapAnnotation

public OptionalAnnotationNameParameter getTotalOverlapAnnotation()

setTotalOverlapAnnotation

public void setTotalOverlapAnnotation(OptionalAnnotationNameParameter totalOverlapAnnotation)

getJaccardIndexAnnotation

public OptionalAnnotationNameParameter getJaccardIndexAnnotation()

setJaccardIndexAnnotation

public void setJaccardIndexAnnotation(OptionalAnnotationNameParameter jaccardIndexAnnotation)

getDiceCoefficientAnnotation

public OptionalAnnotationNameParameter getDiceCoefficientAnnotation()

setDiceCoefficientAnnotation

public void setDiceCoefficientAnnotation(OptionalAnnotationNameParameter diceCoefficientAnnotation)

getVolumeSimilarityAnnotation

public OptionalAnnotationNameParameter getVolumeSimilarityAnnotation()

setVolumeSimilarityAnnotation

public void setVolumeSimilarityAnnotation(OptionalAnnotationNameParameter volumeSimilarityAnnotation)

getFalseNegativeErrorAnnotation

public OptionalAnnotationNameParameter getFalseNegativeErrorAnnotation()

setFalseNegativeErrorAnnotation

public void setFalseNegativeErrorAnnotation(OptionalAnnotationNameParameter falseNegativeErrorAnnotation)

getFalsePositiveErrorAnnotation

public OptionalAnnotationNameParameter getFalsePositiveErrorAnnotation()

setFalsePositiveErrorAnnotation

public void setFalsePositiveErrorAnnotation(OptionalAnnotationNameParameter falsePositiveErrorAnnotation)

runIteration

protected void runIteration(JIPipeDataBatch dataBatch,
                            JIPipeProgressInfo progressInfo)

Description copied from class: JIPipeIteratingAlgorithm

Runs code on one data row

Specified by:

runIteration in class JIPipeIteratingAlgorithm

Parameters:

dataBatch - The data interface

progressInfo - the progress info from the run