org.hkijena.jipipe.plugins.imagejalgorithms.nodes.segment

Class RidgeDetector2DAlgorithm

java.lang.Object

org.hkijena.jipipe.api.parameters.AbstractJIPipeParameterCollection

org.hkijena.jipipe.api.nodes.JIPipeGraphNode

org.hkijena.jipipe.api.nodes.JIPipeAlgorithm

org.hkijena.jipipe.api.nodes.algorithm.JIPipeParameterSlotAlgorithm

org.hkijena.jipipe.api.nodes.algorithm.JIPipeSimpleIteratingAlgorithm

org.hkijena.jipipe.plugins.imagejalgorithms.nodes.segment.RidgeDetector2DAlgorithm

All Implemented Interfaces:

JIPipeSlotConfiguration.SlotConfigurationChangedEventListener, JIPipeFunctionallyComparable, JIPipeIterationStepAlgorithm, JIPipeAdaptiveParametersAlgorithm, JIPipeParallelizedAlgorithm, JIPipeParameterCollection, JIPipeParameterCollection.ParameterChangedEventListener, JIPipeParameterCollection.ParameterStructureChangedEventListener, JIPipeParameterCollection.ParameterUIChangedEventListener, JIPipeValidatable

public class RidgeDetector2DAlgorithm
extends JIPipeSimpleIteratingAlgorithm

Nested Class Summary

Nested classes/interfaces inherited from class org.hkijena.jipipe.api.nodes.JIPipeGraphNode

JIPipeGraphNode.BaseDirectoryChangedEvent, JIPipeGraphNode.BaseDirectoryChangedEventEmitter, JIPipeGraphNode.BaseDirectoryChangedEventListener, JIPipeGraphNode.NodeSlotsChangedEvent, JIPipeGraphNode.NodeSlotsChangedEventEmitter, JIPipeGraphNode.NodeSlotsChangedEventListener, JIPipeGraphNode.Serializer

Nested classes/interfaces inherited from interface org.hkijena.jipipe.api.parameters.JIPipeParameterCollection

JIPipeParameterCollection.ParameterChangedEvent, JIPipeParameterCollection.ParameterChangedEventEmitter, JIPipeParameterCollection.ParameterChangedEventListener, JIPipeParameterCollection.ParameterStructureChangedEvent, JIPipeParameterCollection.ParameterStructureChangedEventEmitter, JIPipeParameterCollection.ParameterStructureChangedEventListener, JIPipeParameterCollection.ParameterUIChangedEvent, JIPipeParameterCollection.ParameterUIChangedEventEmitter, JIPipeParameterCollection.ParameterUIChangedEventListener

Field Summary

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

SLOT_PARAMETERS

Constructor Summary

Constructors

Constructor and Description
RidgeDetector2DAlgorithm(JIPipeNodeInfo info)
RidgeDetector2DAlgorithm(RidgeDetector2DAlgorithm other)

Method Summary

Modifier and Type	Method and Description
double	getContrastHigh()
double	getContrastLow()
double	getLineWidth()
double	getLowerThreshold()
double	getMaxLength()
double	getMinLength()
de.biomedical_imaging.ij.steger.OverlapOption	getOverlapResolution()
double	getSigma()
double	getUpperThreshold()
boolean	isDarkLine()
boolean	isDoCorrectPosition()
boolean	isDoEstimateWidth()
boolean	isDoExtendLine()
boolean	isEstimateHighThreshold()
boolean	isEstimateLowThreshold()
boolean	isEstimateSigma()
boolean	isParameterUIVisible(JIPipeParameterTree tree, JIPipeParameterAccess access) Allows to override the visibility of parameters inside the UI
protected void	runIteration(JIPipeSingleIterationStep iterationStep, JIPipeIterationContext iterationContext, JIPipeGraphNodeRunContext runContext, JIPipeProgressInfo progressInfo) Runs code on one data row
void	setContrastHigh(double contrastHigh)
void	setContrastLow(double contrastLow)
void	setDarkLine(boolean darkLine)
void	setDoCorrectPosition(boolean doCorrectPosition)
void	setDoEstimateWidth(boolean doEstimateWidth)
void	setDoExtendLine(boolean doExtendLine)
void	setEstimateHighThreshold(boolean estimateHighThreshold)
void	setEstimateLowThreshold(boolean estimateLowThreshold)
void	setEstimateSigma(boolean estimateSigma)
void	setLineWidth(double lineWidth)
void	setLowerThreshold(double lowerThreshold)
void	setMaxLength(double maxLength)
void	setMinLength(double minLength)
void	setOverlapResolution(de.biomedical_imaging.ij.steger.OverlapOption overlapResolution)
void	setSigma(double sigma)
void	setUpperThreshold(double upperThreshold)

Methods inherited from class org.hkijena.jipipe.api.nodes.algorithm.JIPipeSimpleIteratingAlgorithm

createUIInputSlotIconDescriptionMenuItems, generateDataBatchesGenerationResult, getAdaptiveParameterSettings, getDataBatchGenerationSettings, getGenerationSettingsInterface, getParallelizationBatchSize, isAllowEmptyIterationStep, isParameterUIVisible, reportValidity, runParameterSet, runPassThrough, supportsParallelization

Methods inherited from class org.hkijena.jipipe.api.nodes.algorithm.JIPipeParameterSlotAlgorithm

getDataInputSlotCount, getDataInputSlots, getFirstInputSlot, getNonParameterInputSlots, getParameterSlot, getParameterSlotAlgorithmSettings, getUIInputSlotIcon, getUIInputSlotIconBaseDimensions, onParameterChanged, run

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

canAutoPassThrough, canPassThrough, functionallyEquals, getDefaultCustomExpressionVariables, getRuntimePartition, isEnabled, isEnableDefaultCustomExpressionVariables, isPassThrough, isPostprocessor, isPreprocessor, isSkipped, loadExample, onDeserialized, runPassThrough, setEnabled, setPassThrough, setRuntimePartition, setSkipped

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

archiveTo, canUserDelete, clearLocations, clearSlotData, copySlotConfiguration, duplicate, emitNodeSlotsChangedEvent, fromJson, getAliasIdInParentGraph, getBaseDirectory, getBaseDirectoryChangedEventEmitter, getCategory, getCompartmentDisplayName, getCompartmentUUIDInGraphAsString, getCompartmentUUIDInParentGraph, getCustomDescription, getCustomName, getDependencies, getDisplayName, getEnvironmentDependencies, getFirstOutputSlot, getInfo, getInputSlot, getInputSlotMap, getInputSlotOrder, getInputSlots, getInputSlotsWithRole, getInternalStoragePath, getLastInputSlot, getLastOutputSlot, getName, getNewScratch, getNodeSlotsChangedEventEmitter, getNodeUILocationPerViewModePerCompartment, getNodeUILocationWithin, getOpenInputSlots, getOutputSlot, getOutputSlotMap, getOutputSlots, getOutputSlotsWithRole, getParentGraph, getProject, getProjectCompartment, getProjectDataDirs, getProjectDirectory, getRuntimeProject, getScratchBaseDirectory, getSlotConfiguration, getStoragePath, getTextDescription, getUUIDInParentGraph, hasInputSlot, hasOutputSlot, isBookmarked, isUiLocked, isVisibleIn, onSlotConfigurationChanged, renderInputSlots, renderOutputSlots, setBaseDirectory, setBookmarked, setCustomDescription, setCustomName, setInfo, setInternalStoragePath, setNodeUILocationPerViewModePerCompartment, setNodeUILocationWithin, setNodeUILocationWithin, setParentGraph, setProjectDirectory, setRuntimeProject, setScratchBaseDirectory, setSlotConfiguration, setStoragePath, setUiLocked, toggleSlot, toJson, updateGraphNodeSlots

Methods inherited from class org.hkijena.jipipe.api.parameters.AbstractJIPipeParameterCollection

getParameterChangedEventEmitter, getParameterStructureChangedEventEmitter, getParameterUIChangedEventEmitter, onParameterStructureChanged, onParameterUIChanged, registerSubParameter, registerSubParameters

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.nodes.iterationstep.JIPipeIterationStepAlgorithm

generateDataBatchesDryRun

Methods inherited from interface org.hkijena.jipipe.api.nodes.JIPipeAdaptiveParametersAlgorithm

installUIOverrideParameterEditor, installUIParameterOptions

Methods inherited from interface org.hkijena.jipipe.api.parameters.JIPipeParameterCollection

deserializeFromJsonNode, emitParameterChangedEvent, emitParameterStructureChangedEvent, emitParameterUIChangedEvent, getContextActions, getParameter, getParameterAccess, getParameterChangedEventEmitter, getParameterStructureChangedEventEmitter, getParameterUIChangedEventEmitter, serializeToJsonFile, serializeToJsonGenerator, serializeToJsonString, setParameter

Methods inherited from interface org.hkijena.jipipe.api.validation.JIPipeValidatable

generateValidityReport

Methods inherited from interface org.hkijena.jipipe.api.parameters.JIPipeParameterCollection.ParameterUIChangedEventListener

onParameterUIChanged

Methods inherited from interface org.hkijena.jipipe.api.parameters.JIPipeParameterCollection.ParameterStructureChangedEventListener

onParameterStructureChanged

Constructor Detail

RidgeDetector2DAlgorithm

public RidgeDetector2DAlgorithm(JIPipeNodeInfo info)

RidgeDetector2DAlgorithm

public RidgeDetector2DAlgorithm(RidgeDetector2DAlgorithm other)

Method Detail

runIteration

protected void runIteration(JIPipeSingleIterationStep iterationStep,
                            JIPipeIterationContext iterationContext,
                            JIPipeGraphNodeRunContext runContext,
                            JIPipeProgressInfo progressInfo)

Description copied from class: JIPipeSimpleIteratingAlgorithm

Runs code on one data row

Specified by:

runIteration in class JIPipeSimpleIteratingAlgorithm

Parameters:

iterationStep - The data interface

iterationContext - the iteration context

runContext - the run context

progressInfo - the progress info from the run

getMinLength

public double getMinLength()

setMinLength

public void setMinLength(double minLength)

getMaxLength

public double getMaxLength()

setMaxLength

public void setMaxLength(double maxLength)

isDoCorrectPosition

public boolean isDoCorrectPosition()

setDoCorrectPosition

public void setDoCorrectPosition(boolean doCorrectPosition)

isDoEstimateWidth

public boolean isDoEstimateWidth()

setDoEstimateWidth

public void setDoEstimateWidth(boolean doEstimateWidth)

isDoExtendLine

public boolean isDoExtendLine()

setDoExtendLine

public void setDoExtendLine(boolean doExtendLine)

getOverlapResolution

public de.biomedical_imaging.ij.steger.OverlapOption getOverlapResolution()

setOverlapResolution

public void setOverlapResolution(de.biomedical_imaging.ij.steger.OverlapOption overlapResolution)

getSigma

public double getSigma()

setSigma

public void setSigma(double sigma)

getLowerThreshold

public double getLowerThreshold()

setLowerThreshold

public void setLowerThreshold(double lowerThreshold)

getUpperThreshold

public double getUpperThreshold()

setUpperThreshold

public void setUpperThreshold(double upperThreshold)

isDarkLine

public boolean isDarkLine()

setDarkLine

public void setDarkLine(boolean darkLine)

getLineWidth

public double getLineWidth()

setLineWidth

public void setLineWidth(double lineWidth)

getContrastHigh

public double getContrastHigh()

setContrastHigh

public void setContrastHigh(double contrastHigh)

getContrastLow

public double getContrastLow()

setContrastLow

public void setContrastLow(double contrastLow)

isEstimateSigma

public boolean isEstimateSigma()

setEstimateSigma

public void setEstimateSigma(boolean estimateSigma)

isEstimateLowThreshold

public boolean isEstimateLowThreshold()

setEstimateLowThreshold

public void setEstimateLowThreshold(boolean estimateLowThreshold)

isEstimateHighThreshold

public boolean isEstimateHighThreshold()

setEstimateHighThreshold

public void setEstimateHighThreshold(boolean estimateHighThreshold)

isParameterUIVisible

public boolean isParameterUIVisible(JIPipeParameterTree tree,
                                    JIPipeParameterAccess access)

Description copied from interface: JIPipeParameterCollection

Allows to override the visibility of parameters inside the UI

Specified by:

isParameterUIVisible in interface JIPipeParameterCollection

Overrides:

isParameterUIVisible in class JIPipeSimpleIteratingAlgorithm

Parameters:

tree - the parameter tree that is used to access this parameter

access - the parameter

Returns:

if the parameter is visible inside the UI