org.hkijena.jipipe.api.nodes

Class JIPipeSimpleIteratingAlgorithm

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

All Implemented Interfaces:

JIPipeValidatable, JIPipeAdaptiveParametersAlgorithm, JIPipeDataBatchAlgorithm, JIPipeParallelizedAlgorithm, JIPipeParameterCollection

Direct Known Subclasses:

AddAnnotationColumnsAlgorithm, AddBorder2DAlgorithm, AddMissingRowsInSeriesAlgorithm, AddNoise2DAlgorithm, AddSaltAndPepperNoise2DAlgorithm, AnnotateByExpression, AnnotateByTablePropertiesAlgorithm, AnnotateWithDataString, AnnotateWithDataTableProperties, AnnotateWithPathProperties, AnnotateWithSourceSlot, AnnotationTableFromFile, AnnotationTableToPaths, AnnotationToPath, AppendRectangularRoiAlgorithm, ApplyColorMathExpression2DExpression, ApplyDistanceTransform2DAlgorithm, ApplyExpressionPerRowAlgorithm, ApplyExpressionToColumnsAlgorithm, ApplyLUTAlgorithm, ApplyMath2DAlgorithm, ApplyMathExpression2DAlgorithm, ApplyTransform2DAlgorithm, ApplyVectorMathExpression2DAlgorithm, ArrangeChannelsAlgorithm, BernsenLocalAutoThreshold2DAlgorithm, BinarizeAlgorithm, BioFormatsExporter, BioFormatsImporter, BoxFilter2DAlgorithm, BoxFilter3DAlgorithm, BrightSpotsSegmentation2DAlgorithm, CannyEdgeDetectorAlgorithm, ChamferDistanceMap2DAlgorithm, ChamferDistanceMap3DAlgorithm, ChangeRoiPropertiesAlgorithm, ChangeRoiPropertiesFromAnnotationsAlgorithm, CircularHoughSegmentation2DAlgorithm, CLAHEContrastEnhancer, Clij2ExecuteKernelSimpleIterating, Clij2PullAlgorithm, Clij2PushAlgorithm, ColorRoiByNameAlgorithm, ColorSpaceConverterAlgorithm, ColorThresholdExpression2D, ColorToGreyscaleExpression2D, ColumnsToAnnotationsAlgorithm, ColumnToNumericAlgorithm, ColumnToStringAlgorithm, CombineChannelsToRGBAlgorithm, ConcatenateByParameter, ConditionalInverterAlgorithm, ConnectedComponentsLabeling2DAlgorithm, ConnectedComponentsLabeling3DAlgorithm, ContrastLocalAutoThreshold2DAlgorithm, ConvertAnnotationTableToAnnotatedTables, ConvertColumnsAlgorithm, ConvertDataToOutputPath, ConverterAlgorithm, ConvertImageAlgorithm, ConvertImageTo16BitAlgorithm, ConvertImageTo32BitAlgorithm, ConvertImageTo8BitAlgorithm, ConvertImageToHSBAlgorithm, ConvertImageToLABAlgorithm, ConvertParametersToTableAlgorithm, ConvertSpotsToRoiNode, ConvertTracksToRoiNode, ConvexifyAlgorithm, ConvolveByParameter2DAlgorithm, CreateDirectory, CreateIJ2OutOfBoundsFactoryAlgorithm, CreateIJ2ShapeAlgorithm, CreateSpotDetectorNode, CreateSpotTrackerNode, CropLabelsAlgorithm, DataAnnotationToStringAnnotation, DataToPreviewAlgorithm, DespeckleFilter2DAlgorithm, DifferenceOfGaussian2DAlgorithm, DilateLabelsAlgorithm, DirectionalFilter2DAlgorithm, DisplayRangeCalibrationAlgorithm, DistanceTransformWatershed2DAlgorithm, DivideByMaximumAlgorithm, DownloadFilesDataSource, DownloadOMEROImageAlgorithm, DownloadOMEROTableAlgorithm, DrawScaleBarAlgorithm, ExpandLabelsAlgorithm, ExplodeRoiAlgorithm, ExpressionSlicerAlgorithm, ExtendedMaxima2DAlgorithm, ExtendedMaxima3DAlgorithm, ExtendedMinima2DAlgorithm, ExtendedMinima3DAlgorithm, ExtractAndReplaceAnnotation, ExtractDataAnnotation, ExtractFileName, ExtractOverlayAlgorithm, ExtractParent, ExtractROIMetadataAlgorithm, FastCircularHoughSegmentation2DAlgorithm, FFT2DForwardTransform, FFT2DInverseTransform, FFT2DSwapQuadrants, FilterLabelsByExpression2DAlgorithm, FilterLabelsByExpression3DAlgorithm, FilterLabelsByIdAlgorithm, FilterPaths, FilterRoiByNameAlgorithm, FilterROIListsAlgorithm, FilterTableRowsAlgorithm, FilterTablesAlgorithm, FindHoles2DAlgorithm, FindParticles2D, FrangiVesselnessFeatures, GaussianBlur2DAlgorithm, GaussianBlur3DAlgorithm, GenerateColumnAlgorithm, GenerateFromMathExpression2D, GenerateLUTImageFromColorMap, GenerateParametersFromExpressionAlgorithm, GenerateStructureElement2DAlgorithm, GenerateStructureElement3DAlgorithm, GenerateTableFromExpressionAlgorithm, GenerateUniqueAnnotation, GenerateVectorFromMathExpression, GenerateZeroImage, GetJIPipeSlotFolderAlgorithm, GetLabelBoundariesAlgorithm, Hessian2DAlgorithm, HessianSegmentation2DAlgorithm, HistogramAlgorithm, HistogramContrastEnhancerAlgorithm, HistogramGenerator, HyperstackSlicerAlgorithm, IlluminationCorrection2DAlgorithm, ImageFromMatrix2DAlgorithm, ImagePlusFromFile, ImagePlusFromGUI, ImagePlusToGUI, ImagePropertiesToAnnotationAlgorithm, ImageStackFromFolder, ImageToMatrixAlgorithm, ImageToTableAlgorithm, ImportCellposeModelAlgorithm, ImportCellposeSizeModelAlgorithm, ImportDataRowFolder, ImportDataTableArchive, ImportDataTableDirectory, ImportLUTAsRGBFromFile, ImportRDatasetAlgorithm, IntegrateColumnsAlgorithm, InternalGradientSegmentation2DAlgorithm, InvertColorsAlgorithm, KeepLargestLabelAlgorithm, KeepLargestRegionAlgorithm, LabelChamferDistanceMap3DAlgorithm, LabelsToRGBAlgorithm, LabelsToROIAlgorithm, LaplacianEdgeDetectorAlgorithm, LaplacianOfGaussian2DAlgorithm, LaplacianSharpen2DAlgorithm, LinesHoughDetection2DAlgorithm, ListFiles, ListSubfolders, LocalAutoThreshold2DAlgorithm, LocalMaxima2DAlgorithm, LocalMaximumFilter2DAlgorithm, LocalMaximumFilter3DAlgorithm, LocalMinimumFilter2DAlgorithm, LocalMinimumFilter3DAlgorithm, LocalVarianceFilter2DAlgorithm, LocalVarianceFilter3DAlgorithm, LUTInverterAlgorithm, ManualHSBThreshold2DAlgorithm, ManualLABThreshold2DAlgorithm, ManualRGBThreshold2DAlgorithm, ManualThreshold16U2DAlgorithm, ManualThreshold32F2DAlgorithm, ManualThreshold8U2DAlgorithm, MaskToRoiAlgorithm, MatrixToImageAlgorithm, MeasureBranchesNode, MeasureEdgesNode, MeasureSpotsNode, MeasureTracksNode, MedianBlurFilter2DAlgorithm, MedianBlurFilter3DAlgorithm, MedianBlurGreyscale8U2DAlgorithm, MedianBlurRGB2DAlgorithm, MeijeringVesselness2DFeatures, MeltTableAlgorithm, ModifyAnnotationScript, ModifyPath, ModifyTableColumnNamesAlgorithm, ModifyTablesScript, Morphology2DAlgorithm, Morphology3DAlgorithm, MorphologyBinary2DAlgorithm, MorphologyFillHoles2DAlgorithm, MorphologyInternalGradient2DAlgorithm, MorphologyOutline2DAlgorithm, MorphologySkeletonize2DAlgorithm, MorphologySkeletonize3DAlgorithm, MSEBlockFlowAlgorithm, MSEGaussianFlowAlgorithm, NewSplitChannelsAlgorithm, NewZProjectorAlgorithm, NiblackLocalAutoThreshold2DAlgorithm, OMERODatasetReferenceDataSource, OMEROFindProjectAlgorithm, OMEROGroupReferenceDataSource, OMEROImageReferenceDataSource, OMEROProjectReferenceDataSource, OutlineRoiAlgorithm, PathFromUserDataSource, PercentileThreshold8U2DAlgorithm, PhansalkarLocalAutoThreshold2DAlgorithm, PMCCBlockFlowAlgorithm, PullDataTableAnnotations, PushDataTableAnnotations, RegionalMaxima2DAlgorithm, RegionalMaxima3DAlgorithm, RegionalMinima2DAlgorithm, RegionalMinima3DAlgorithm, RelativizeByParameter, RemapLabelsAlgorithm, RemoveAnnotationAlgorithm, RemoveBorderLabelsAlgorithm, RemoveColumnAlgorithm, RemoveDataAnnotations, RemoveLargestLabelAlgorithm, RemoveLargestRegionAlgorithm, RemoveLUTAlgorithm, RemoveNaNFilter2DAlgorithm, RemoveOutliersFilter2DAlgorithm, RemoveOverlayAlgorithm, RemoveROIMetadataAlgorithm, RenameAnnotation, RenameByString, RenameDataAnnotation, RenameSingleColumnsAlgorithm, RenameTableColumnsAlgorithm, RenameTableColumnsToAnnotationAlgorithm, RenderImageToRGBAlgorithm, RenderJIPipeProjectAlgorithm, RenderOverlayAlgorithm, ReorderDimensionsAlgorithm, ReorderRoiDimensionsAlgorithm, ReplaceLabelsAlgorithm, ResliceAlgorithm, ResultsTableFromFile, ResultsTableFromGUI, ResultsTableToGUI, RidgeDetector2DAlgorithm, RoiCalculatorAlgorithm, ROIDataFromFile, ROIDataFromOMEImage, ROIFromGUI, RoiPropertiesToAnnotationsAlgorithm, RoiToCentroidAlgorithm, ROIToGUI, RollingBallBackgroundEstimator2DAlgorithm, RoundFloatImageAlgorithm, RunExpressionAlgorithm, RunImageJImporterAlgorithm, RunJIPipeProjectAlgorithm, SauvolaLocalAutoThreshold2DAlgorithm, ScaleRoiAlgorithm, SetBioFormatsExporterSettings, SetLUTFromColorMapAlgorithm, SetLUTFromColorsAlgorithm, SetPhysicalDimensionsAlgorithm, SetPhysicalDimensionsByAnnotationsAlgorithm, SetPhysicalDimensionsByExpressionsAlgorithm, SetSingleAnnotation, SetVirtualStateAlgorithm, SimpleFileAnnotationGenerator, SimpleFolderAnnotationGenerator, SimpleIteratingJythonScriptAlgorithm, SimplePathAnnotationGenerator, SimplifyAnnotationsAlgorithm, SliceROIListAlgorithm, SliceTableRowsAlgorithm, SobelEdgeDetectorAlgorithm, SortTableColumnsAlgorithm, SortTableRowsAlgorithm, SplitByAnnotationScript, SplitByDimensionAlgorithm, SplitChannelsAlgorithm, SplitRGBChannelsAlgorithm, SplitRoiAlgorithm, SplitSpotsNode, SplitTableByColumnsAlgorithm, SplitTableIntoColumnsAlgorithm, SplitTableIntoRowsAlgorithm, SplitTracksNode, SpotFilterNode, StackInverterAlgorithm, StackSplitterAlgorithm, StackTo2DAlgorithm, StringDefinitionDataSource, TableToCircularROIAlgorithm, TableToImageAlgorithm, TableToRectangularROIAlgorithm, ThresholdByAnnotation2DAlgorithm, TileImage2DAlgorithm, ToDataStringAlgorithm, TrackFilterNode, TrackSchemeRendererNode, TransformCrop2DAlgorithm, TransformFlip2DAlgorithm, TransformRotate2DAlgorithm, TransformRotateFree2DAlgorithm, TransformScale2DAlgorithm, TransformScale3DAlgorithm, TransformSetHyperstackDimensionsAlgorithm, UltimateErodedPoints2DAlgorithm, UnMeltTableAlgorithm, UnreferencedRoiToMaskAlgorithm, UnreferencedRoiToRGBAlgorithm, UnsetRoiImageAlgorithm, VolumeOpening2DAlgorithm, VolumeOpening3DAlgorithm, Voronoi2DAlgorithm, ZProjectorAlgorithm

public abstract class JIPipeSimpleIteratingAlgorithm
extends JIPipeParameterSlotAlgorithm
implements JIPipeParallelizedAlgorithm, JIPipeDataBatchAlgorithm, JIPipeAdaptiveParametersAlgorithm

An JIPipeAlgorithm that iterates through each data row. This is a simplified version of JIPipeIteratingAlgorithm that assumes that there is only one or zero input slots. An error is thrown if there are more than one input slots.

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
JIPipeSimpleIteratingAlgorithm(JIPipeNodeInfo info) Creates a new instance
JIPipeSimpleIteratingAlgorithm(JIPipeNodeInfo info, JIPipeSlotConfiguration slotConfiguration) Creates a new instance
JIPipeSimpleIteratingAlgorithm(JIPipeSimpleIteratingAlgorithm other) Copies the algorithm

Method Summary

Modifier and Type	Method and Description
List<JIPipeMergingDataBatch>	generateDataBatchesDryRun(List<JIPipeInputDataSlot> slots, JIPipeProgressInfo progressInfo) Generates data batches.
JIPipeAdaptiveParameterSettings	getAdaptiveParameterSettings()
JIPipeSimpleIteratingAlgorithmDataBatchGenerationSettings	getDataBatchGenerationSettings()
JIPipeDataBatchGenerationSettings	getGenerationSettingsInterface() Returns the batch generation settings as interface
int	getParallelizationBatchSize() Returns how many threads the actual algorithm requires.
boolean	isParallelizationEnabled()
boolean	isParameterUIVisible(JIPipeParameterTree tree, JIPipeParameterAccess access) Allows to override the visibility of parameters inside the UI
boolean	isParameterUIVisible(JIPipeParameterTree tree, JIPipeParameterCollection subParameter) Allows to override the visibility of sub-parameters inside the UI
void	reportValidity(JIPipeIssueReport report) Generates a validity report
protected abstract void	runIteration(JIPipeDataBatch dataBatch, JIPipeProgressInfo progressInfo) Runs code on one data row
void	runParameterSet(JIPipeProgressInfo progressInfo, List<JIPipeTextAnnotation> parameterAnnotations) Runs a parameter set iteration
protected void	runPassThrough(JIPipeProgressInfo progressInfo, JIPipeDataBatch dataBatch) A pass-through variant for iterating algorithms.
void	setParallelizationEnabled(boolean parallelizationEnabled) User-defined parameter to control if parallelization is enabled
boolean	supportsParallelization() Indicates to the algorithm base implementation if parallelization is supported.

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

JIPipeSimpleIteratingAlgorithm

public JIPipeSimpleIteratingAlgorithm(JIPipeNodeInfo info,
                                      JIPipeSlotConfiguration slotConfiguration)

Creates a new instance

Parameters:

info - Algorithm info

slotConfiguration - Slot configuration override

JIPipeSimpleIteratingAlgorithm

public JIPipeSimpleIteratingAlgorithm(JIPipeNodeInfo info)

Creates a new instance

Parameters:

info - Algorithm info

JIPipeSimpleIteratingAlgorithm

public JIPipeSimpleIteratingAlgorithm(JIPipeSimpleIteratingAlgorithm other)

Copies the algorithm

Parameters:

other - The original

Method Detail

runPassThrough

protected void runPassThrough(JIPipeProgressInfo progressInfo,
                              JIPipeDataBatch dataBatch)

A pass-through variant for iterating algorithms. Passes the data batch to the single output

Parameters:

progressInfo - progress info

dataBatch - the data batch

runParameterSet

public void runParameterSet(JIPipeProgressInfo progressInfo,
                            List<JIPipeTextAnnotation> parameterAnnotations)

Description copied from class: JIPipeParameterSlotAlgorithm

Runs a parameter set iteration

Specified by:

runParameterSet in class JIPipeParameterSlotAlgorithm

Parameters:

progressInfo - progress info from the run

parameterAnnotations - parameter annotations

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 JIPipeAlgorithm

Parameters:

report - the report to be added to

runIteration

protected abstract void runIteration(JIPipeDataBatch dataBatch,
                                     JIPipeProgressInfo progressInfo)

Runs code on one data row

Parameters:

dataBatch - The data interface

progressInfo - the progress info from the run

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

Returns:

If the algorithm supports automated parallelization.

getParallelizationBatchSize

public int getParallelizationBatchSize()

Description copied from interface: JIPipeParallelizedAlgorithm

Returns how many threads the actual algorithm requires. Based on this value, the base algorithm creates batches.

Specified by:

getParallelizationBatchSize in interface JIPipeParallelizedAlgorithm

Returns:

number of threads used by the workload

isParallelizationEnabled

public boolean isParallelizationEnabled()

Specified by:

isParallelizationEnabled in interface JIPipeParallelizedAlgorithm

Returns:

if parallelization is enabled by user

setParallelizationEnabled

public void setParallelizationEnabled(boolean parallelizationEnabled)

Description copied from interface: JIPipeParallelizedAlgorithm

User-defined parameter to control if parallelization is enabled

Specified by:

setParallelizationEnabled in interface JIPipeParallelizedAlgorithm

Parameters:

parallelizationEnabled - if parallelization is enabled

getDataBatchGenerationSettings

public JIPipeSimpleIteratingAlgorithmDataBatchGenerationSettings getDataBatchGenerationSettings()

isParameterUIVisible

public boolean isParameterUIVisible(JIPipeParameterTree tree,
                                    JIPipeParameterCollection subParameter)

Description copied from interface: JIPipeParameterCollection

Allows to override the visibility of sub-parameters inside the UI

Specified by:

isParameterUIVisible in interface JIPipeParameterCollection

Overrides:

isParameterUIVisible in class JIPipeParameterSlotAlgorithm

Parameters:

tree - the parameter tree that is used to access this parameter

subParameter - a sub parameter

Returns:

if the parameter is visible inside the UI

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 JIPipeAlgorithm

Parameters:

tree - the parameter tree that is used to access this parameter

access - the parameter

Returns:

if the parameter is visible inside the UI

getGenerationSettingsInterface

public JIPipeDataBatchGenerationSettings getGenerationSettingsInterface()

Description copied from interface: JIPipeDataBatchAlgorithm

Returns the batch generation settings as interface

Specified by:

getGenerationSettingsInterface in interface JIPipeDataBatchAlgorithm

Returns:

batch generation settings as interface

getAdaptiveParameterSettings

public JIPipeAdaptiveParameterSettings getAdaptiveParameterSettings()

Specified by:

getAdaptiveParameterSettings in interface JIPipeAdaptiveParametersAlgorithm

generateDataBatchesDryRun

public List<JIPipeMergingDataBatch> generateDataBatchesDryRun(List<JIPipeInputDataSlot> slots,
                                                              JIPipeProgressInfo progressInfo)

Description copied from interface: JIPipeDataBatchAlgorithm

Generates data batches. This is a dry-run function that should never throw errors

Specified by:

generateDataBatchesDryRun in interface JIPipeDataBatchAlgorithm

Parameters:

slots - the data slots

progressInfo - the progress

Returns:

the batches