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

Class BrightSpotsSegmentation2DAlgorithm

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.BrightSpotsSegmentation2DAlgorithm

All Implemented Interfaces:

JIPipeValidatable, JIPipeAdaptiveParametersAlgorithm, JIPipeDataBatchAlgorithm, JIPipeParallelizedAlgorithm, JIPipeParameterCollection

public class BrightSpotsSegmentation2DAlgorithm
extends JIPipeSimpleIteratingAlgorithm

Applies Bright spots segmentation

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
BrightSpotsSegmentation2DAlgorithm(BrightSpotsSegmentation2DAlgorithm other) Copies the algorithm
BrightSpotsSegmentation2DAlgorithm(JIPipeNodeInfo info)

Method Summary

Modifier and Type	Method and Description
AutoThreshold2DAlgorithm	getAutoThresholding()
int	getDilationErodeSteps()
double	getGaussianSigma()
int	getRollingBallRadius()
boolean	isParameterUIVisible(JIPipeParameterTree tree, JIPipeParameterAccess access) Allows to override the visibility of parameters inside the UI
protected void	runIteration(JIPipeDataBatch dataBatch, JIPipeProgressInfo progressInfo) Runs code on one data row
void	setDilationErodeSteps(int dilationErodeSteps)
void	setGaussianSigma(double gaussianSigma)
void	setRollingBallRadius(int rollingBallRadius)
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, reportValidity, 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

BrightSpotsSegmentation2DAlgorithm

public BrightSpotsSegmentation2DAlgorithm(JIPipeNodeInfo info)

Parameters:

info - the info

BrightSpotsSegmentation2DAlgorithm

public BrightSpotsSegmentation2DAlgorithm(BrightSpotsSegmentation2DAlgorithm 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

getRollingBallRadius

public int getRollingBallRadius()

setRollingBallRadius

public void setRollingBallRadius(int rollingBallRadius)

getDilationErodeSteps

public int getDilationErodeSteps()

setDilationErodeSteps

public void setDilationErodeSteps(int dilationErodeSteps)

getGaussianSigma

public double getGaussianSigma()

setGaussianSigma

public void setGaussianSigma(double gaussianSigma)

getAutoThresholding

public AutoThreshold2DAlgorithm getAutoThresholding()