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

Class AutoThreshold2DAlgorithm

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.AutoThreshold2DAlgorithm

All Implemented Interfaces:

JIPipeValidatable, JIPipeAdaptiveParametersAlgorithm, JIPipeDataBatchAlgorithm, JIPipeParallelizedAlgorithm, JIPipeParameterCollection

public class AutoThreshold2DAlgorithm
extends JIPipeIteratingAlgorithm

Thresholding node that thresholds via an auto threshold

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	AutoThreshold2DAlgorithm.SliceThresholdMode

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
AutoThreshold2DAlgorithm(AutoThreshold2DAlgorithm other) Copies the algorithm
AutoThreshold2DAlgorithm(JIPipeNodeInfo info)

Method Summary

Modifier and Type	Method and Description
ij.process.AutoThresholder.Method	getMethod()
ImageROITargetArea	getSourceArea()
OptionalAnnotationNameParameter	getThresholdAnnotation()
JIPipeTextAnnotationMergeMode	getThresholdAnnotationStrategy()
DefaultExpressionParameter	getThresholdCombinationExpression()
AutoThreshold2DAlgorithm.SliceThresholdMode	getThresholdMode()
boolean	isDarkBackground()
protected void	runIteration(JIPipeDataBatch dataBatch, JIPipeProgressInfo progressInfo) Runs code on one data row
void	setDarkBackground(boolean darkBackground)
void	setMethod(ij.process.AutoThresholder.Method method)
void	setSourceArea(ImageROITargetArea sourceArea)
void	setThresholdAnnotation(OptionalAnnotationNameParameter thresholdAnnotation)
void	setThresholdAnnotationStrategy(JIPipeTextAnnotationMergeMode thresholdAnnotationStrategy)
void	setThresholdCombinationExpression(DefaultExpressionParameter thresholdCombinationExpression)
void	setThresholdMode(AutoThreshold2DAlgorithm.SliceThresholdMode thresholdMode)
boolean	supportsParallelization() Indicates to the algorithm base implementation if parallelization is supported.

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

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

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

AutoThreshold2DAlgorithm

public AutoThreshold2DAlgorithm(JIPipeNodeInfo info)

Parameters:

info - the info

AutoThreshold2DAlgorithm

public AutoThreshold2DAlgorithm(AutoThreshold2DAlgorithm other)

Copies the algorithm

Parameters:

other - the original

Method Detail

supportsParallelization

public boolean supportsParallelization()

Description copied from interface: JIPipeParallelizedAlgorithm

Indicates to the algorithm base implementation if parallelization is supported. Use this function to indicate to the algorithm to conditionally enable/disable parallelization.

Specified by:

supportsParallelization in interface JIPipeParallelizedAlgorithm

Overrides:

supportsParallelization in class JIPipeIteratingAlgorithm

Returns:

If the algorithm supports automated parallelization.

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

getThresholdAnnotationStrategy

public JIPipeTextAnnotationMergeMode getThresholdAnnotationStrategy()

setThresholdAnnotationStrategy

public void setThresholdAnnotationStrategy(JIPipeTextAnnotationMergeMode thresholdAnnotationStrategy)

getMethod

public ij.process.AutoThresholder.Method getMethod()

setMethod

public void setMethod(ij.process.AutoThresholder.Method method)

isDarkBackground

public boolean isDarkBackground()

setDarkBackground

public void setDarkBackground(boolean darkBackground)

getThresholdAnnotation

public OptionalAnnotationNameParameter getThresholdAnnotation()

setThresholdAnnotation

public void setThresholdAnnotation(OptionalAnnotationNameParameter thresholdAnnotation)

getThresholdMode

public AutoThreshold2DAlgorithm.SliceThresholdMode getThresholdMode()

setThresholdMode

public void setThresholdMode(AutoThreshold2DAlgorithm.SliceThresholdMode thresholdMode)

getThresholdCombinationExpression

public DefaultExpressionParameter getThresholdCombinationExpression()

setThresholdCombinationExpression

public void setThresholdCombinationExpression(DefaultExpressionParameter thresholdCombinationExpression)

getSourceArea

public ImageROITargetArea getSourceArea()

setSourceArea

public void setSourceArea(ImageROITargetArea sourceArea)