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

Class HessianSegmentation2DAlgorithm

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.JIPipeSimpleIteratingAlgorithm

org.hkijena.jipipe.extensions.imagejalgorithms.ij1.threshold.HessianSegmentation2DAlgorithm

All Implemented Interfaces:

JIPipeValidatable, JIPipeAdaptiveParametersAlgorithm, JIPipeDataBatchAlgorithm, JIPipeParallelizedAlgorithm, JIPipeParameterCollection

public class HessianSegmentation2DAlgorithm
extends JIPipeSimpleIteratingAlgorithm

Segments using a Hessian

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
HessianSegmentation2DAlgorithm(HessianSegmentation2DAlgorithm other) Copies the algorithm
HessianSegmentation2DAlgorithm(JIPipeNodeInfo info)

Method Summary

Modifier and Type	Method and Description
AutoThreshold2DAlgorithm	getAutoThresholding()
int	getDespeckleIterations()
EigenvalueSelection2D	getEigenvalueSelection()
double	getGradientRadius()
double	getSmoothing()
boolean	isApplyDespeckle()
boolean	isApplyInternalGradient()
boolean	isCompareAbsolute()
boolean	isParameterUIVisible(JIPipeParameterTree tree, JIPipeParameterAccess access) Allows to override the visibility of parameters inside the UI
void	reportValidity(JIPipeIssueReport report) Generates a validity report
protected void	runIteration(JIPipeDataBatch dataBatch, JIPipeProgressInfo progressInfo) Runs code on one data row
void	setApplyDespeckle(boolean applyDespeckle)
void	setApplyInternalGradient(boolean applyInternalGradient)
void	setCompareAbsolute(boolean compareAbsolute)
void	setDespeckleIterations(int despeckleIterations)
void	setEigenvalueSelection(EigenvalueSelection2D eigenvalueSelection)
void	setGradientRadius(double gradientRadius)
void	setSmoothing(double smoothing)
boolean	supportsParallelization() Indicates to the algorithm base implementation if parallelization is supported.

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

generateDataBatchesDryRun, getAdaptiveParameterSettings, getDataBatchGenerationSettings, getGenerationSettingsInterface, getParallelizationBatchSize, isParallelizationEnabled, 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, 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

HessianSegmentation2DAlgorithm

public HessianSegmentation2DAlgorithm(JIPipeNodeInfo info)

Parameters:

info - the algorithm info

HessianSegmentation2DAlgorithm

public HessianSegmentation2DAlgorithm(HessianSegmentation2DAlgorithm other)

Copies the algorithm

Parameters:

other - the original

Method Detail

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

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 JIPipeSimpleIteratingAlgorithm

Returns:

If the algorithm supports automated parallelization.

runIteration

protected void runIteration(JIPipeDataBatch dataBatch,
                            JIPipeProgressInfo progressInfo)

Description copied from class: JIPipeSimpleIteratingAlgorithm

Runs code on one data row

Specified by:

runIteration in class JIPipeSimpleIteratingAlgorithm

Parameters:

dataBatch - The data interface

progressInfo - the progress info from the run

getSmoothing

public double getSmoothing()

setSmoothing

public void setSmoothing(double smoothing)

getGradientRadius

public double getGradientRadius()

setGradientRadius

public void setGradientRadius(double gradientRadius)

getAutoThresholding

public AutoThreshold2DAlgorithm getAutoThresholding()

reportValidity

public void reportValidity(JIPipeIssueReport report)

Description copied from interface: JIPipeValidatable

Generates a validity report

Specified by:

reportValidity in interface JIPipeValidatable

Overrides:

reportValidity in class JIPipeSimpleIteratingAlgorithm

Parameters:

report - the report to be added to

isCompareAbsolute

public boolean isCompareAbsolute()

setCompareAbsolute

public void setCompareAbsolute(boolean compareAbsolute)

getEigenvalueSelection

public EigenvalueSelection2D getEigenvalueSelection()

setEigenvalueSelection

public void setEigenvalueSelection(EigenvalueSelection2D eigenvalueSelection)

isApplyInternalGradient

public boolean isApplyInternalGradient()

setApplyInternalGradient

public void setApplyInternalGradient(boolean applyInternalGradient)

isApplyDespeckle

public boolean isApplyDespeckle()

setApplyDespeckle

public void setApplyDespeckle(boolean applyDespeckle)

getDespeckleIterations

public int getDespeckleIterations()

setDespeckleIterations

public void setDespeckleIterations(int despeckleIterations)