org.hkijena.jipipe.extensions.imagejalgorithms.ij1.analyze

Class FindParticles2D

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.analyze.FindParticles2D

All Implemented Interfaces:

JIPipeValidatable, JIPipeAdaptiveParametersAlgorithm, JIPipeDataBatchAlgorithm, JIPipeParallelizedAlgorithm, JIPipeParameterCollection

public class FindParticles2D
extends JIPipeSimpleIteratingAlgorithm

Converts a mask to ROI and ROI measurements

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
FindParticles2D(FindParticles2D other) Copies the algorithm
FindParticles2D(JIPipeNodeInfo info)

Method Summary

Modifier and Type	Method and Description
OptionalStringParameter	getAnnotationType()
double	getMaxParticleCircularity()
double	getMaxParticleSize()
double	getMinParticleCircularity()
double	getMinParticleSize()
Neighborhood2D	getNeighborhood()
ImageStatisticsSetParameter	getStatisticsParameters()
boolean	isBlackBackground()
boolean	isExcludeEdges()
boolean	isIncludeHoles()
boolean	isMeasureInPhysicalUnits()
boolean	isSplitSlices()
protected void	runIteration(JIPipeDataBatch dataBatch, JIPipeProgressInfo progressInfo) Runs code on one data row
void	setAnnotationType(OptionalStringParameter annotationType)
void	setBlackBackground(boolean blackBackground)
void	setExcludeEdges(boolean excludeEdges)
void	setIncludeHoles(boolean includeHoles)
boolean	setMaxParticleCircularity(double maxParticleCircularity)
void	setMaxParticleSize(double maxParticleSize)
void	setMeasureInPhysicalUnits(boolean measureInPhysicalUnits)
boolean	setMinParticleCircularity(double minParticleCircularity)
void	setMinParticleSize(double minParticleSize)
void	setNeighborhood(Neighborhood2D neighborhood)
void	setSplitSlices(boolean splitSlices)
void	setStatisticsParameters(ImageStatisticsSetParameter statisticsParameters)

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

generateDataBatchesDryRun, getAdaptiveParameterSettings, getDataBatchGenerationSettings, getGenerationSettingsInterface, getParallelizationBatchSize, isParallelizationEnabled, isParameterUIVisible, isParameterUIVisible, reportValidity, runParameterSet, runPassThrough, setParallelizationEnabled, supportsParallelization

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

FindParticles2D

public FindParticles2D(JIPipeNodeInfo info)

Parameters:

info - algorithm info

FindParticles2D

public FindParticles2D(FindParticles2D other)

Copies the algorithm

Parameters:

other - the original

Method Detail

getStatisticsParameters

public ImageStatisticsSetParameter getStatisticsParameters()

setStatisticsParameters

public void setStatisticsParameters(ImageStatisticsSetParameter statisticsParameters)

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

isMeasureInPhysicalUnits

public boolean isMeasureInPhysicalUnits()

setMeasureInPhysicalUnits

public void setMeasureInPhysicalUnits(boolean measureInPhysicalUnits)

getMinParticleSize

public double getMinParticleSize()

setMinParticleSize

public void setMinParticleSize(double minParticleSize)

getMaxParticleSize

public double getMaxParticleSize()

setMaxParticleSize

public void setMaxParticleSize(double maxParticleSize)

getMinParticleCircularity

public double getMinParticleCircularity()

setMinParticleCircularity

public boolean setMinParticleCircularity(double minParticleCircularity)

Parameters:

minParticleCircularity - value from 0 to 1

Returns:

if setting the value was successful

getMaxParticleCircularity

public double getMaxParticleCircularity()

setMaxParticleCircularity

public boolean setMaxParticleCircularity(double maxParticleCircularity)

Parameters:

maxParticleCircularity - value from 0 to 1

Returns:

if setting the value was successful

isExcludeEdges

public boolean isExcludeEdges()

setExcludeEdges

public void setExcludeEdges(boolean excludeEdges)

isSplitSlices

public boolean isSplitSlices()

setSplitSlices

public void setSplitSlices(boolean splitSlices)

getAnnotationType

public OptionalStringParameter getAnnotationType()

setAnnotationType

public void setAnnotationType(OptionalStringParameter annotationType)

isBlackBackground

public boolean isBlackBackground()

setBlackBackground

public void setBlackBackground(boolean blackBackground)

isIncludeHoles

public boolean isIncludeHoles()

setIncludeHoles

public void setIncludeHoles(boolean includeHoles)

getNeighborhood

public Neighborhood2D getNeighborhood()

setNeighborhood

public void setNeighborhood(Neighborhood2D neighborhood)