org.hkijena.jipipe.extensions.imagejalgorithms.ij1.colocalization

Class Coloc2Node

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.JIPipeIteratingAlgorithm

org.hkijena.jipipe.extensions.imagejalgorithms.ij1.colocalization.Coloc2Node

All Implemented Interfaces:

JIPipeValidatable, JIPipeAdaptiveParametersAlgorithm, JIPipeDataBatchAlgorithm, JIPipeParallelizedAlgorithm, JIPipeParameterCollection

public class Coloc2Node
extends JIPipeIteratingAlgorithm

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	Coloc2Node.Settings

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

Modifier and Type	Field and Description
static JIPipeDataSlotInfo	SLOT_INPUT_MASK
static JIPipeDataSlotInfo	SLOT_INPUT_ROI
static JIPipeDataSlotInfo	SLOT_OUTPUT_WARNINGS

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

SLOT_PARAMETERS

Constructor Summary

Constructors

Constructor and Description
Coloc2Node(Coloc2Node other)
Coloc2Node(JIPipeNodeInfo info)

Method Summary

Modifier and Type	Method and Description
protected void	drawHistogramLine(Overlay overlay, Histogram2D histogram, RandomAccessibleInterval<? extends RealType<?>> img, double slope, double intercept)
String	getChannel1Name()
String	getChannel2Name()
OptionalAnnotationNameParameter	getHistogramNameAnnotation()
OptionalAnnotationNameParameter	getPlotNameAnnotation()
Coloc2Node.Settings	getSettings()
boolean	isInputMasks()
boolean	isOutputWarnings()
protected void	runIteration(JIPipeDataBatch dataBatch, JIPipeProgressInfo progressInfo) Runs code on one data row
void	setChannel1Name(String channel1Name)
void	setChannel2Name(String channel2Name)
void	setHistogramNameAnnotation(OptionalAnnotationNameParameter histogramNameAnnotation)
void	setInputMasks(boolean inputMasks)
void	setOutputWarnings(boolean outputWarnings)
void	setPlotNameAnnotation(OptionalAnnotationNameParameter plotNameAnnotation)

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

generateDataBatchesDryRun, getAdaptiveParameterSettings, getDataBatchGenerationSettings, getGenerationSettingsInterface, getParallelizationBatchSize, isParallelizationEnabled, isParameterUIVisible, isParameterUIVisible, 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, reportValidity, 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

Field Detail

SLOT_INPUT_MASK

public static final JIPipeDataSlotInfo SLOT_INPUT_MASK

SLOT_INPUT_ROI

public static final JIPipeDataSlotInfo SLOT_INPUT_ROI

SLOT_OUTPUT_WARNINGS

public static final JIPipeDataSlotInfo SLOT_OUTPUT_WARNINGS

Constructor Detail

Coloc2Node

public Coloc2Node(JIPipeNodeInfo info)

Coloc2Node

public Coloc2Node(Coloc2Node other)

Method Detail

runIteration

protected void runIteration(JIPipeDataBatch dataBatch,
                            JIPipeProgressInfo progressInfo)

Description copied from class: JIPipeIteratingAlgorithm

Runs code on one data row

Specified by:

runIteration in class JIPipeIteratingAlgorithm

Parameters:

dataBatch - The data interface

progressInfo - the progress info from the run

drawHistogramLine

protected void drawHistogramLine(Overlay overlay,
                                 Histogram2D histogram,
                                 RandomAccessibleInterval<? extends RealType<?>> img,
                                 double slope,
                                 double intercept)

getHistogramNameAnnotation

public OptionalAnnotationNameParameter getHistogramNameAnnotation()

setHistogramNameAnnotation

public void setHistogramNameAnnotation(OptionalAnnotationNameParameter histogramNameAnnotation)

getPlotNameAnnotation

public OptionalAnnotationNameParameter getPlotNameAnnotation()

setPlotNameAnnotation

public void setPlotNameAnnotation(OptionalAnnotationNameParameter plotNameAnnotation)

isOutputWarnings

public boolean isOutputWarnings()

setOutputWarnings

public void setOutputWarnings(boolean outputWarnings)

getSettings

public Coloc2Node.Settings getSettings()

isInputMasks

public boolean isInputMasks()

setInputMasks

public void setInputMasks(boolean inputMasks)

getChannel1Name

public String getChannel1Name()

setChannel1Name

public void setChannel1Name(String channel1Name)

getChannel2Name

public String getChannel2Name()

setChannel2Name

public void setChannel2Name(String channel2Name)