org.hkijena.jipipe.api.nodes

Interface JIPipeDataBatchAlgorithm

All Known Implementing Classes:

AddAnnotationColumnsAlgorithm, AddBorder2DAlgorithm, AddMissingRowsInSeriesAlgorithm, AddNoise2DAlgorithm, AddRoiListsAlgorithm, AddSaltAndPepperNoise2DAlgorithm, AnalyzeSkeleton2D3DAlgorithm, AnnotateByExpression, AnnotateByImageStatisticsExpressionAlgorithm, AnnotateByTablePropertiesAlgorithm, AnnotateDataWithTableValues, AnnotateWithData, AnnotateWithDataString, AnnotateWithDataTableProperties, AnnotateWithOverlapMeasureLabelsAlgorithm, AnnotateWithPathProperties, AnnotateWithSourceSlot, AnnotationsToParametersAlgorithm, AnnotationTableFromFile, AnnotationTableToPaths, AnnotationToPath, AppendRectangularRoiAlgorithm, ApplyColorMathExpression2DExpression, ApplyDistanceTransform2DAlgorithm, ApplyExpressionPerRowAlgorithm, ApplyExpressionToColumnsAlgorithm, ApplyLUTAlgorithm, ApplyMath2DAlgorithm, ApplyMathExpression2DAlgorithm, ApplyTransform2DAlgorithm, ApplyVectorMathExpression2DAlgorithm, ArrangeChannelsAlgorithm, AssembleExtractedROIAlgorithm, AutoThreshold2DAlgorithm, AverageKeyValueThresholdStatisticsGenerator, BernsenLocalAutoThreshold2DAlgorithm, BinarizeAlgorithm, BioFormatsExporter, BioFormatsImporter, BitwiseLogicalOperationAlgorithm, BlendImagesAlgorithm, BoxFilter2DAlgorithm, BoxFilter3DAlgorithm, BrightSpotsSegmentation2DAlgorithm, CannyEdgeDetectorAlgorithm, CellposeAlgorithm, CellposeAlgorithm_Old, CellposeTrainingAlgorithm, CellposeTrainingAlgorithm_Old, ChamferDistanceMap2DAlgorithm, ChamferDistanceMap3DAlgorithm, ChangeRoiNameFromExpressionsAndMeasurementsAlgorithm, ChangeRoiPropertiesAlgorithm, ChangeRoiPropertiesFromAnnotationsAlgorithm, ChangeRoiPropertiesFromExpressionsAlgorithm, CircularHoughSegmentation2DAlgorithm, CLAHEContrastEnhancer, ClassicWatershedSegmentationAlgorithm, Clij2ExecuteKernelIterating, Clij2ExecuteKernelSimpleIterating, Clij2PullAlgorithm, Clij2PushAlgorithm, CLIJCommandNode, Coloc2Node, ColorRoiByNameAlgorithm, ColorRoiByStatisticsAlgorithm, ColorSpaceConverterAlgorithm, ColorThresholdExpression2D, ColorToGreyscaleExpression2D, ColumnsToAnnotationsAlgorithm, ColumnToNumericAlgorithm, ColumnToStringAlgorithm, CombineChannelsToRGBAlgorithm, ConcatenateByParameter, ConcatenatePaths, ConditionalInverterAlgorithm, ConnectedComponentsLabeling2DAlgorithm, ConnectedComponentsLabeling3DAlgorithm, ContrastLocalAutoThreshold2DAlgorithm, ConvertAnnotationTableToAnnotatedTables, ConvertColumnsAlgorithm, ConvertDataToOutputPath, ConverterAlgorithm, ConvertImageAlgorithm, ConvertImageTo16BitAlgorithm, ConvertImageTo32BitAlgorithm, ConvertImageTo8BitAlgorithm, ConvertImageToHSBAlgorithm, ConvertImageToLABAlgorithm, ConvertParametersToTableAlgorithm, ConvertSpotsToRoiNode, ConvertToAnnotationTable, ConvertTracksToRoiNode, ConvexifyAlgorithm, ConvolveByImage2DAlgorithm, ConvolveByParameter2DAlgorithm, CopyPath, CountROIAlgorithm, CreateDirectory, CreateIJ2OutOfBoundsFactoryAlgorithm, CreateIJ2ShapeAlgorithm, CreateSpotDetectorNode, CreateSpotTrackerNode, CreateStackAlgorithm, CropLabelsAlgorithm, CropToRoiAlgorithm, CustomAutoThreshold2D16UAlgorithm, CustomAutoThreshold2D32FAlgorithm, CustomAutoThreshold2D8UAlgorithm, DataAnnotationToStringAnnotation, DataBatchSlicer, DataToPreviewAlgorithm, DespeckleFilter2DAlgorithm, DifferenceOfGaussian2DAlgorithm, DilateLabelsAlgorithm, DirectionalFilter2DAlgorithm, DisplayRangeCalibrationAlgorithm, DistanceTransformWatershed2DAlgorithm, DistributeDataRandomlyByCountAlgorithm, DistributeDataRandomlyByPercentageAlgorithm, DivideByMaximumAlgorithm, DownloadFilesDataSource, DownloadOMEROImageAlgorithm, DownloadOMEROTableAlgorithm, DrawMaskAlgorithm, DrawOvalRoiAlgorithm, DrawRectangleRoiAlgorithm, DrawROIAlgorithm, DrawScaleBarAlgorithm, DrawScaleBarRoiAlgorithm, DrawTextRoiAlgorithm, ExpandLabelsAlgorithm, ExplodeRoiAlgorithm, ExportData, ExportDataTable, ExportDataTableByParameter, ExportImage2Algorithm, ExportImageAlgorithm, ExportROIAlgorithm, ExportTableAlgorithm, ExportTableAsXLSXAlgorithm, ExpressionSlicerAlgorithm, ExtendedMaxima2DAlgorithm, ExtendedMaxima3DAlgorithm, ExtendedMinima2DAlgorithm, ExtendedMinima3DAlgorithm, ExtractAndReplaceAnnotation, ExtractDataAnnotation, ExtractFileName, ExtractFromROIAlgorithm, ExtractImageInRoiAlgorithm, ExtractLabelStatisticsAlgorithm, ExtractOverlayAlgorithm, ExtractParent, ExtractROIMetadataAlgorithm, FastCircularHoughSegmentation2DAlgorithm, FastKeyValueThresholdStatisticsGenerator, FFT2DForwardTransform, FFT2DInverseTransform, FFT2DSwapQuadrants, FilterAndMergeRoiByStatisticsScriptAlgorithm, FilterLabelsByExpression2DAlgorithm, FilterLabelsByExpression3DAlgorithm, FilterLabelsByIdAlgorithm, FilterLabelsByMaskAlgorithm, FilterLabelsByOverlapAlgorithm, FilterLabelsByStatisticsAlgorithm, FilterPaths, FilterRoiByNameAlgorithm, FilterROIByOverlapAlgorithm, FilterRoiByStatisticsAlgorithm, FilterRoiByStatisticsScriptAlgorithm, FilterROIListsAlgorithm, FilterTableRowsAlgorithm, FilterTablesAlgorithm, FindHoles2DAlgorithm, FindParticles2D, FollowSpotsPerTrackNode, FrangiVesselnessFeatures, GaussianBlur2DAlgorithm, GaussianBlur3DAlgorithm, GenerateColumnAlgorithm, GenerateFromMathExpression2D, GenerateLUTImageFromColorMap, GenerateMissingImageFromMathExpression2D, GenerateMissingRoiListsAlgorithm, GenerateMissingTablesAlgorithm, GenerateMissingZeroImage, GenerateParametersFromExpressionAlgorithm, GenerateStructureElement2DAlgorithm, GenerateStructureElement3DAlgorithm, GenerateTableFromExpressionAlgorithm, GenerateUniqueAnnotation, GenerateVectorFromMathExpression, GenerateZeroImage, GeodesicDistanceMap2DAlgorithm, GetJIPipeSlotFolderAlgorithm, GetLabelBoundariesAlgorithm, GetRoiImageAlgorithm, GraphWrapperAlgorithm, GrayscaleAttributeFiltering2DAlgorithm, GrayscaleAttributeFiltering3DAlgorithm, Hessian2DAlgorithm, HessianSegmentation2DAlgorithm, HistogramAlgorithm, HistogramContrastEnhancerAlgorithm, HistogramGenerator, HyperstackSlicerAlgorithm, IlluminationCorrection2DAlgorithm, ImageCalculator2DAlgorithm, ImageCalculator2DExpression, ImageFromMatrix2DAlgorithm, ImageJ2OpNode, ImagePlusFromFile, ImagePlusFromGUI, ImagePlusToGUI, ImagePropertiesToAnnotationAlgorithm, ImageStackFromFolder, ImageStatisticsAlgorithm, ImageStatisticsExpressionAlgorithm, ImageToMatrixAlgorithm, ImageToTableAlgorithm, ImportCellposeModelAlgorithm, ImportCellposeSizeModelAlgorithm, ImportDataRowFolder, ImportDataTableArchive, ImportDataTableDirectory, ImportJIPipeSlotFolderAlgorithm, ImportLUTAsRGBFromFile, ImportRDatasetAlgorithm, ImportWekaModelFromFileAlgorithm, ImposeMaxima2DAlgorithm, ImposeMaxima3DAlgorithm, InputImagesToMontage, IntegrateColumnsAlgorithm, InternalGradientSegmentation2DAlgorithm, InvertColorsAlgorithm, IteratingFormProcessorAlgorithm, IteratingJythonScriptAlgorithm, IteratingPythonScriptAlgorithm, IteratingRScriptAlgorithm, IterativeThresholdByROIStatistics2DAlgorithm, JIPipeIteratingAlgorithm, JIPipeIteratingMissingDataGeneratorAlgorithm, JIPipeMergingAlgorithm, JIPipeMissingDataGeneratorAlgorithm, JIPipeParameterlessSimpleIteratingAlgorithm, JIPipeSimpleIteratingAlgorithm, JIPipeSingleIterationAlgorithm, JsonAlgorithm, KeepLargestLabelAlgorithm, KeepLargestRegionAlgorithm, KeyValueAveragesGenerator, KeyValueHistogramGenerator, KeyValueThresholdPartitionAveragesGenerator, KeyValueThresholdPartitionGenerator, KeyValueThresholdStatisticsGenerator, LabelChamferDistanceMap3DAlgorithm, LabelsToRGBAlgorithm, LabelsToROIAlgorithm, LaplacianEdgeDetectorAlgorithm, LaplacianOfGaussian2DAlgorithm, LaplacianSharpen2DAlgorithm, LinesHoughDetection2DAlgorithm, ListFiles, ListSubfolders, LocalAutoThreshold2DAlgorithm, LocalImageCalculator2DExpression, LocalMaxima2DAlgorithm, LocalMaximumFilter2DAlgorithm, LocalMaximumFilter3DAlgorithm, LocalMinimumFilter2DAlgorithm, LocalMinimumFilter3DAlgorithm, LocalVarianceFilter2DAlgorithm, LocalVarianceFilter3DAlgorithm, LoopStartNode, LUTInverterAlgorithm, MacroWrapperAlgorithm, ManualHSBThreshold2DAlgorithm, ManualLABThreshold2DAlgorithm, ManualRGBThreshold2DAlgorithm, ManualThreshold16U2DAlgorithm, ManualThreshold32F2DAlgorithm, ManualThreshold8U2DAlgorithm, MaskToRoiAlgorithm, MatrixToImageAlgorithm, MeasureBranchesNode, MeasureEdgesNode, MeasureSpotsNode, MeasureTracksNode, MedianBlurFilter2DAlgorithm, MedianBlurFilter3DAlgorithm, MedianBlurGreyscale8U2DAlgorithm, MedianBlurRGB2DAlgorithm, MeijeringVesselness2DFeatures, MeltTableAlgorithm, Merge2DToHyperstackAlgorithm, MergeAnnotations, MergeChannelsAlgorithm, MergeColumnsAlgorithm, MergeDataToTableAlgorithm, MergeImagesAlgorithm, MergeLabelsAlgorithm, MergeParametersAlgorithm, MergeRoiListsAlgorithm, MergeSmallLabelsAlgorithm, MergeSpotsNode, MergeTableColumnsSimpleAlgorithm, MergeTableColumnsSupplementAlgorithm, MergeTableRowsAlgorithm, MergeTracksNode, MergingFormProcessorAlgorithm, MergingJythonScriptAlgorithm, MergingPythonScriptAlgorithm, MergingRScriptAlgorithm, ModifyAnnotationScript, ModifyPath, ModifyTableColumnNamesAlgorithm, ModifyTablesScript, MontageToStackAlgorithm, MorphologicalReconstruction2DAlgorithm, MorphologicalReconstruction3DAlgorithm, Morphology2DAlgorithm, Morphology3DAlgorithm, MorphologyBinary2DAlgorithm, MorphologyFillHoles2DAlgorithm, MorphologyInternalGradient2DAlgorithm, MorphologyOutline2DAlgorithm, MorphologySkeletonize2DAlgorithm, MorphologySkeletonize3DAlgorithm, MSEBlockFlowAlgorithm, MSEGaussianFlowAlgorithm, MultiTemplateMatchingAlgorithm, NewSplitChannelsAlgorithm, NewZProjectorAlgorithm, NiblackLocalAutoThreshold2DAlgorithm, NodeGroup, OMEImageFromImagePlus, OMERODatasetReferenceDataSource, OMEROFindProjectAlgorithm, OMEROGroupReferenceDataSource, OMEROImageReferenceDataSource, OMEROProjectReferenceDataSource, OmniposeAlgorithm, OmniposeTrainingAlgorithm, OutlineRoiAlgorithm, OverlapMeasureLabelsAlgorithm, OverlayImagesAlgorithm, OverwriteAnnotations, ParametersToAnnotationsAlgorithm, PathFromUserDataSource, PathsToJIPipeProjectParametersAlgorithm, PercentileThreshold8U2DAlgorithm, PhansalkarLocalAutoThreshold2DAlgorithm, PlotTables2Algorithm, PlotTablesAlgorithm, PMCCBlockFlowAlgorithm, PullDataTableAnnotations, PushDataTableAnnotations, ReferencedAppendRectangularRoiAlgorithm, ReferencedDefineRectangularRoiAlgorithm, RegionalMaxima2DAlgorithm, RegionalMaxima3DAlgorithm, RegionalMinima2DAlgorithm, RegionalMinima3DAlgorithm, RelativizeByParameter, RelativizePaths, RemapLabelsAlgorithm, RemoveAnnotationAlgorithm, RemoveBorderLabelsAlgorithm, RemoveBorderRoisAlgorithm, 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, RoiFloodFillAlgorithm, ROIFromGUI, RoiPropertiesToAnnotationsAlgorithm, RoiStatisticsAlgorithm, RoiToCentroidAlgorithm, ROIToGUI, ROIToLabelsByNameAlgorithm, ROIToLabelsExpressionAlgorithm, RoiToMaskAlgorithm, RoiToRGBAlgorithm, RollingBallBackgroundEstimator2DAlgorithm, RoundFloatImageAlgorithm, RunExpressionAlgorithm, RunImageJExporterAlgorithm, RunImageJImporterAlgorithm, RunJIPipeProjectAlgorithm, RunProcessIteratingAlgorithm, RunProcessMergingAlgorithm, SauvolaLocalAutoThreshold2DAlgorithm, ScaleRoiAlgorithm, SeededWatershedSegmentationAlgorithm, SetBioFormatsExporterSettings, SetLUTFromColorMapAlgorithm, SetLUTFromColorsAlgorithm, SetLUTFromImageAlgorithm, SetOverlayAlgorithm, SetPhysicalDimensionsAlgorithm, SetPhysicalDimensionsByAnnotationsAlgorithm, SetPhysicalDimensionsByExpressionsAlgorithm, SetRoiImageAlgorithm, SetRoiMetadataByStatisticsAlgorithm, SetROIMetadataFromTableAlgorithm, SetSingleAnnotation, SetToColorAlgorithm, SetToValueAlgorithm, SetVirtualStateAlgorithm, SimpleFileAnnotationGenerator, SimpleFolderAnnotationGenerator, SimpleImageAndRoiIteratingAlgorithm, SimpleIteratingFormProcessorAlgorithm, SimpleIteratingJythonScriptAlgorithm, SimplePathAnnotationGenerator, SimplifyAnnotationsAlgorithm, SliceROIListAlgorithm, SliceTableRowsAlgorithm, SobelEdgeDetectorAlgorithm, SortAndExtractRoiByStatisticsAlgorithm, SortAndExtractRoiByStatisticsAlgorithm2, SortRoiListByExpressionsAndMeasurementsAlgorithm, SortTableColumnsAlgorithm, SortTableRowsAlgorithm, SplitByAnnotationScript, SplitByDimensionAlgorithm, SplitChannelsAlgorithm, SplitRGBChannelsAlgorithm, SplitRoiAlgorithm, SplitRoiConnectedComponentsAlgorithm, SplitSpotsNode, SplitTableByColumnsAlgorithm, SplitTableIntoColumnsAlgorithm, SplitTableIntoRowsAlgorithm, SplitTracksNode, SpotDetectorNode, SpotFilterNode, SpotsToRGBNode, StackCombinerAlgorithm, StackInverterAlgorithm, StackSplitterAlgorithm, StackTo2DAlgorithm, StackToDimensionMergerAlgorithm, StackToMontageAlgorithm, StringDefinitionDataSource, TableToCircularROIAlgorithm, TableToImageAlgorithm, TableToRectangularROIAlgorithm, ThresholdByAnnotation2DAlgorithm, TileImage2DAlgorithm, ToDataStringAlgorithm, ToHSBColorSpaceConverterAlgorithm, ToLABColorSpaceConverterAlgorithm, ToRGBColorSpaceConverterAlgorithm, TrackFilterNode, TrackingNode, TrackSchemeRendererNode, TracksToRGBNode, TransformCrop2DAlgorithm, TransformEqualCanvasSize2DAlgorithm, TransformEqualizeDimensionsAlgorithm, TransformExpandCanvas2DAlgorithm, TransformFlip2DAlgorithm, TransformRotate2DAlgorithm, TransformRotateFree2DAlgorithm, TransformScale2DAlgorithm, TransformScale3DAlgorithm, TransformSetHyperstackDimensionsAlgorithm, UltimateErodedPoints2DAlgorithm, UnMeltTableAlgorithm, UnreferencedRoiToMaskAlgorithm, UnreferencedRoiToRGBAlgorithm, UnsetRoiImageAlgorithm, UnTileImage2DAlgorithm, UploadOMEROImageAlgorithm, UploadOMEROTableAlgorithm, UsePlaceholderForMissingDataAlgorithm, VolumeOpening2DAlgorithm, VolumeOpening3DAlgorithm, Voronoi2DAlgorithm, Warp2DAlgorithm, WekaClassification2DAlgorithm, WekaClassification3DAlgorithm, WekaTrainingLabels2DAlgorithm, WekaTrainingMask2DAlgorithm, WekaTrainingROI2DAlgorithm, WekaTrainingROI3DAlgorithm, ZProjectorAlgorithm

public interface JIPipeDataBatchAlgorithm

Methods shared across all JIPipeAlgorithm that generate data batches

Method Summary

Modifier and Type	Method and Description
List<JIPipeMergingDataBatch>	generateDataBatchesDryRun(List<JIPipeInputDataSlot> slots, JIPipeProgressInfo progressInfo) Generates data batches.
JIPipeDataBatchGenerationSettings	getGenerationSettingsInterface() Returns the batch generation settings as interface

Method Detail

getGenerationSettingsInterface

JIPipeDataBatchGenerationSettings getGenerationSettingsInterface()

Returns the batch generation settings as interface

Returns:

batch generation settings as interface

generateDataBatchesDryRun

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

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

Parameters:

slots - the data slots

progressInfo - the progress

Returns:

the batches