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

Class InternalGradientSegmentation2DAlgorithm

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.InternalGradientSegmentation2DAlgorithm

All Implemented Interfaces:

JIPipeValidatable, JIPipeAdaptiveParametersAlgorithm, JIPipeDataBatchAlgorithm, JIPipeParallelizedAlgorithm, JIPipeParameterCollection

public class InternalGradientSegmentation2DAlgorithm
extends JIPipeSimpleIteratingAlgorithm

Internal gradient segmenter

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
InternalGradientSegmentation2DAlgorithm(InternalGradientSegmentation2DAlgorithm other) Copies the algorithm
InternalGradientSegmentation2DAlgorithm(JIPipeNodeInfo info)

Method Summary

Modifier and Type	Method and Description
AutoThreshold2DAlgorithm	getAutoThresholding()
CLAHEContrastEnhancer	getContrastEnhancer()
int	getDilationIterations()
int	getErosionIterations()
double	getGaussSigma()
int	getInternalGradientRadius()
boolean	isApplyFirstCLAHE()
boolean	isApplyGaussian()
boolean	isApplySecondCLAHE()
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	setApplyFirstCLAHE(boolean applyFirstCLAHE)
void	setApplyGaussian(boolean applyGaussian)
void	setApplySecondCLAHE(boolean applySecondCLAHE)
void	setDilationIterations(int dilationIterations)
void	setErosionIterations(int erosionIterations)
void	setGaussSigma(double gaussSigma)
void	setInternalGradientRadius(int internalGradientRadius)
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

InternalGradientSegmentation2DAlgorithm

public InternalGradientSegmentation2DAlgorithm(JIPipeNodeInfo info)

Parameters:

info - the algorithm info

InternalGradientSegmentation2DAlgorithm

public InternalGradientSegmentation2DAlgorithm(InternalGradientSegmentation2DAlgorithm 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 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

getGaussSigma

public double getGaussSigma()

setGaussSigma

public void setGaussSigma(double gaussSigma)

getInternalGradientRadius

public int getInternalGradientRadius()

setInternalGradientRadius

public void setInternalGradientRadius(int internalGradientRadius)

getDilationIterations

public int getDilationIterations()

setDilationIterations

public void setDilationIterations(int dilationIterations)

getErosionIterations

public int getErosionIterations()

setErosionIterations

public void setErosionIterations(int erosionIterations)

getAutoThresholding

public AutoThreshold2DAlgorithm getAutoThresholding()

getContrastEnhancer

public CLAHEContrastEnhancer getContrastEnhancer()

isApplyFirstCLAHE

public boolean isApplyFirstCLAHE()

setApplyFirstCLAHE

public void setApplyFirstCLAHE(boolean applyFirstCLAHE)

isApplySecondCLAHE

public boolean isApplySecondCLAHE()

setApplySecondCLAHE

public void setApplySecondCLAHE(boolean applySecondCLAHE)

isApplyGaussian

public boolean isApplyGaussian()

setApplyGaussian

public void setApplyGaussian(boolean applyGaussian)

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

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