org.hkijena.jipipe.extensions.imagejalgorithms.ij1.threshold.iterative

Class IterativeThresholdByROIStatistics2DAlgorithm

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.threshold.iterative.IterativeThresholdByROIStatistics2DAlgorithm

All Implemented Interfaces:

JIPipeValidatable, JIPipeAdaptiveParametersAlgorithm, JIPipeDataBatchAlgorithm, JIPipeParallelizedAlgorithm, JIPipeParameterCollection

public class IterativeThresholdByROIStatistics2DAlgorithm
extends JIPipeIteratingAlgorithm

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	IterativeThresholdByROIStatistics2DAlgorithm.FilteringParameters
static class	IterativeThresholdByROIStatistics2DAlgorithm.ScoreParameters
static class	IterativeThresholdByROIStatistics2DAlgorithm.ThresholdingResult

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
IterativeThresholdByROIStatistics2DAlgorithm(IterativeThresholdByROIStatistics2DAlgorithm other)
IterativeThresholdByROIStatistics2DAlgorithm(JIPipeNodeInfo info)

Method Summary

Modifier and Type	Method and Description
CustomExpressionVariablesParameter	getCustomFilterVariables()
IterativeThresholdByROIStatistics2DAlgorithm.FilteringParameters	getFilteringParameters()
ImageStatisticsSetParameter	getMeasurements()
IterativeThresholdByROIStatistics2DAlgorithm.ScoreParameters	getScoreParameters()
OptionalAnnotationNameParameter	getThresholdAnnotation()
JIPipeTextAnnotationMergeMode	getThresholdAnnotationStrategy()
DefaultExpressionParameter	getThresholdCombinationExpression()
IntegerRange	getThresholds()
boolean	isExcludeEdgeROIs()
boolean	isMeasureInPhysicalUnits()
void	run(JIPipeProgressInfo progressInfo) Runs the workload
protected void	runIteration(JIPipeDataBatch dataBatch, JIPipeProgressInfo progressInfo) Runs code on one data row
void	setExcludeEdgeROIs(boolean excludeEdgeROIs)
void	setMeasureInPhysicalUnits(boolean measureInPhysicalUnits)
void	setMeasurements(ImageStatisticsSetParameter measurements)
void	setThresholdAnnotation(OptionalAnnotationNameParameter thresholdAnnotation)
void	setThresholdAnnotationStrategy(JIPipeTextAnnotationMergeMode thresholdAnnotationStrategy)
void	setThresholdCombinationExpression(DefaultExpressionParameter thresholdCombinationExpression)
void	setThresholds(IntegerRange thresholds)

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

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

IterativeThresholdByROIStatistics2DAlgorithm

public IterativeThresholdByROIStatistics2DAlgorithm(JIPipeNodeInfo info)

IterativeThresholdByROIStatistics2DAlgorithm

public IterativeThresholdByROIStatistics2DAlgorithm(IterativeThresholdByROIStatistics2DAlgorithm other)

Method Detail

run

public void run(JIPipeProgressInfo progressInfo)

Description copied from class: JIPipeGraphNode

Runs the workload

Overrides:

run in class JIPipeParameterSlotAlgorithm

Parameters:

progressInfo - progress passed from the runner

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

getCustomFilterVariables

public CustomExpressionVariablesParameter getCustomFilterVariables()

getMeasurements

public ImageStatisticsSetParameter getMeasurements()

setMeasurements

public void setMeasurements(ImageStatisticsSetParameter measurements)

getThresholds

public IntegerRange getThresholds()

setThresholds

public void setThresholds(IntegerRange thresholds)

isMeasureInPhysicalUnits

public boolean isMeasureInPhysicalUnits()

setMeasureInPhysicalUnits

public void setMeasureInPhysicalUnits(boolean measureInPhysicalUnits)

getThresholdAnnotationStrategy

public JIPipeTextAnnotationMergeMode getThresholdAnnotationStrategy()

setThresholdAnnotationStrategy

public void setThresholdAnnotationStrategy(JIPipeTextAnnotationMergeMode thresholdAnnotationStrategy)

getThresholdCombinationExpression

public DefaultExpressionParameter getThresholdCombinationExpression()

setThresholdCombinationExpression

public void setThresholdCombinationExpression(DefaultExpressionParameter thresholdCombinationExpression)

getThresholdAnnotation

public OptionalAnnotationNameParameter getThresholdAnnotation()

setThresholdAnnotation

public void setThresholdAnnotation(OptionalAnnotationNameParameter thresholdAnnotation)

isExcludeEdgeROIs

public boolean isExcludeEdgeROIs()

setExcludeEdgeROIs

public void setExcludeEdgeROIs(boolean excludeEdgeROIs)

getFilteringParameters

public IterativeThresholdByROIStatistics2DAlgorithm.FilteringParameters getFilteringParameters()

getScoreParameters

public IterativeThresholdByROIStatistics2DAlgorithm.ScoreParameters getScoreParameters()