org.hkijena.jipipe.plugins.imagejalgorithms.nodes.analyze

Class AnalyzeSkeleton2D3DAlgorithm

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.JIPipeIteratingAlgorithm

org.hkijena.jipipe.plugins.imagejalgorithms.nodes.analyze.AnalyzeSkeleton2D3DAlgorithm

All Implemented Interfaces:

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

public class AnalyzeSkeleton2D3DAlgorithm
extends JIPipeIteratingAlgorithm

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	AnalyzeSkeleton2D3DAlgorithm.CycleRemovalMethod
static class	AnalyzeSkeleton2D3DAlgorithm.EndRemovalMethod
static class	AnalyzeSkeleton2D3DAlgorithm.OutputParameters

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

Modifier and Type	Field and Description
static JIPipeDataSlotInfo	BRANCHES_TABLE_OUTPUT_SLOT
static JIPipeDataSlotInfo	LABELS_IMAGE_OUTPUT_SLOT
static JIPipeDataSlotInfo	LSP_IMAGE_OUTPUT_SLOT
static JIPipeDataSlotInfo	REFERENCE_INPUT_SLOT
static JIPipeDataSlotInfo	ROI_INPUT_SLOT
static JIPipeDataSlotInfo	SKELETONS_TABLE_OUTPUT_SLOT
static JIPipeDataSlotInfo	TAGGED_SKELETONS_IMAGE_OUTPUT_SLOT

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

SLOT_PARAMETERS

Constructor Summary

Constructors

Constructor and Description
AnalyzeSkeleton2D3DAlgorithm(AnalyzeSkeleton2D3DAlgorithm other)
AnalyzeSkeleton2D3DAlgorithm(JIPipeNodeInfo info)

Method Summary

Modifier and Type	Method and Description
AnalyzeSkeleton2D3DAlgorithm.OutputParameters	getOutputParameters()
AnalyzeSkeleton2D3DAlgorithm.CycleRemovalMethod	getPruneCyclesMethod()
AnalyzeSkeleton2D3DAlgorithm.EndRemovalMethod	getPruneEndsMethod()
protected void	runIteration(JIPipeSingleIterationStep iterationStep, JIPipeIterationContext iterationContext, JIPipeGraphNodeRunContext runContext, JIPipeProgressInfo progressInfo) Runs code on one data row
void	setPruneCyclesMethod(AnalyzeSkeleton2D3DAlgorithm.CycleRemovalMethod pruneCyclesMethod)
void	setPruneEndsMethod(AnalyzeSkeleton2D3DAlgorithm.EndRemovalMethod pruneEndsMethod)

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

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

Field Detail

ROI_INPUT_SLOT

public static final JIPipeDataSlotInfo ROI_INPUT_SLOT

REFERENCE_INPUT_SLOT

public static final JIPipeDataSlotInfo REFERENCE_INPUT_SLOT

SKELETONS_TABLE_OUTPUT_SLOT

public static final JIPipeDataSlotInfo SKELETONS_TABLE_OUTPUT_SLOT

BRANCHES_TABLE_OUTPUT_SLOT

public static final JIPipeDataSlotInfo BRANCHES_TABLE_OUTPUT_SLOT

TAGGED_SKELETONS_IMAGE_OUTPUT_SLOT

public static final JIPipeDataSlotInfo TAGGED_SKELETONS_IMAGE_OUTPUT_SLOT

LABELS_IMAGE_OUTPUT_SLOT

public static final JIPipeDataSlotInfo LABELS_IMAGE_OUTPUT_SLOT

LSP_IMAGE_OUTPUT_SLOT

public static final JIPipeDataSlotInfo LSP_IMAGE_OUTPUT_SLOT

Constructor Detail

AnalyzeSkeleton2D3DAlgorithm

public AnalyzeSkeleton2D3DAlgorithm(JIPipeNodeInfo info)

AnalyzeSkeleton2D3DAlgorithm

public AnalyzeSkeleton2D3DAlgorithm(AnalyzeSkeleton2D3DAlgorithm other)

Method Detail

runIteration

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

Description copied from class: JIPipeIteratingAlgorithm

Runs code on one data row

Specified by:

runIteration in class JIPipeIteratingAlgorithm

Parameters:

iterationStep - The data interface

iterationContext - The iteration context

runContext - the run context

progressInfo - the progress info from the run

getOutputParameters

public AnalyzeSkeleton2D3DAlgorithm.OutputParameters getOutputParameters()

getPruneCyclesMethod

public AnalyzeSkeleton2D3DAlgorithm.CycleRemovalMethod getPruneCyclesMethod()

setPruneCyclesMethod

public void setPruneCyclesMethod(AnalyzeSkeleton2D3DAlgorithm.CycleRemovalMethod pruneCyclesMethod)

getPruneEndsMethod

public AnalyzeSkeleton2D3DAlgorithm.EndRemovalMethod getPruneEndsMethod()

setPruneEndsMethod

public void setPruneEndsMethod(AnalyzeSkeleton2D3DAlgorithm.EndRemovalMethod pruneEndsMethod)