org.hkijena.jipipe.extensions.imagejalgorithms.ij1.datasources

Class ImageStackFromFolder

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.datasources.ImageStackFromFolder

All Implemented Interfaces:

JIPipeValidatable, JIPipeAdaptiveParametersAlgorithm, JIPipeDataBatchAlgorithm, JIPipeParallelizedAlgorithm, JIPipeParameterCollection

public class ImageStackFromFolder
extends JIPipeSimpleIteratingAlgorithm

Loads an image data from a file via IJ.openFile()

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

Method Summary

Modifier and Type	Method and Description
PathQueryExpression	getFilterExpression()
JIPipeDataInfoRef	getGeneratedImageType()
HyperstackDimension	getOutputDimension()
IntegerRange	getSlicesToImport()
boolean	isIgnoreInvalidSlices()
boolean	isRemoveLut()
boolean	isSortFilesNumerically()
protected void	runIteration(JIPipeDataBatch dataBatch, JIPipeProgressInfo progressInfo) Runs code on one data row
void	setFilterExpression(PathQueryExpression filterExpression)
void	setGeneratedImageType(JIPipeDataInfoRef generatedImageType)
void	setIgnoreInvalidSlices(boolean ignoreInvalidSlices)
void	setOutputDimension(HyperstackDimension outputDimension)
void	setRemoveLut(boolean removeLut)
void	setSlicesToImport(IntegerRange slicesToImport)
void	setSortFilesNumerically(boolean sortFilesNumerically)

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

ImageStackFromFolder

public ImageStackFromFolder(JIPipeNodeInfo info)

Parameters:

info - algorithm info

ImageStackFromFolder

public ImageStackFromFolder(ImageStackFromFolder other)

Copies the algorithm

Parameters:

other - the original

Method Detail

isRemoveLut

public boolean isRemoveLut()

setRemoveLut

public void setRemoveLut(boolean removeLut)

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

getGeneratedImageType

public JIPipeDataInfoRef getGeneratedImageType()

setGeneratedImageType

public void setGeneratedImageType(JIPipeDataInfoRef generatedImageType)

getOutputDimension

public HyperstackDimension getOutputDimension()

setOutputDimension

public void setOutputDimension(HyperstackDimension outputDimension)

isSortFilesNumerically

public boolean isSortFilesNumerically()

setSortFilesNumerically

public void setSortFilesNumerically(boolean sortFilesNumerically)

getFilterExpression

public PathQueryExpression getFilterExpression()

setFilterExpression

public void setFilterExpression(PathQueryExpression filterExpression)

getSlicesToImport

public IntegerRange getSlicesToImport()

setSlicesToImport

public void setSlicesToImport(IntegerRange slicesToImport)

isIgnoreInvalidSlices

public boolean isIgnoreInvalidSlices()

setIgnoreInvalidSlices

public void setIgnoreInvalidSlices(boolean ignoreInvalidSlices)