├── .github ├── build.sh ├── setup.sh └── workflows │ └── build.yml ├── .gitignore ├── .mailmap ├── LICENSE.txt ├── README.md ├── pom.xml └── src ├── it ├── ij1-quit │ ├── pom.xml │ └── src │ │ └── main │ │ └── java │ │ └── SystemExitIT.java └── settings.xml ├── main ├── java │ └── net │ │ └── imagej │ │ └── legacy │ │ ├── DefaultLegacyHooks.java │ │ ├── IJ1Helper.java │ │ ├── ImageJ2Options.java │ │ ├── LegacyCodeRunner.java │ │ ├── LegacyCommandline.java │ │ ├── LegacyImageJApp.java │ │ ├── LegacyImageMap.java │ │ ├── LegacyService.java │ │ ├── Macros.java │ │ ├── OptionsSynchronizer.java │ │ ├── SingleInstance.java │ │ ├── SingleInstanceArgument.java │ │ ├── command │ │ ├── LegacyCommand.java │ │ ├── LegacyCommandFinder.java │ │ └── LegacyCommandInfo.java │ │ ├── convert │ │ ├── AbstractImagePlusLegacyConverter.java │ │ ├── AbstractLegacyConverter.java │ │ ├── DatasetToImagePlusConverter.java │ │ ├── DoubleToImagePlusConverter.java │ │ ├── ImageDisplayToImagePlusConverter.java │ │ ├── ImagePlusToDatasetConverter.java │ │ ├── ImagePlusToImageDisplayConverter.java │ │ ├── ImagePlusToImgPlusConverter.java │ │ ├── ImageTitleToImagePlusConverter.java │ │ ├── ImgPlusToImagePlusConverter.java │ │ ├── OverlayToROITreeConverter.java │ │ ├── ROITreeToOverlayConverter.java │ │ ├── ResultsTableColumnWrapper.java │ │ ├── ResultsTableToGenericTableConverter.java │ │ ├── ResultsTableUnwrapper.java │ │ ├── ResultsTableWrapper.java │ │ ├── StringToDatasetConverter.java │ │ ├── StringToImagePlusConverter.java │ │ ├── TableListWrapper.java │ │ ├── TableToResultsTableConverters.java │ │ ├── TableUnwrapper.java │ │ ├── TableWrapper.java │ │ └── roi │ │ │ ├── AbstractMaskPredicateToRoiConverter.java │ │ │ ├── AbstractMaskPredicateUnwrapConverter.java │ │ │ ├── AbstractPolygonRoiWrapper.java │ │ │ ├── AbstractRoiToMaskPredicateConverter.java │ │ │ ├── AbstractRoiUnwrapConverter.java │ │ │ ├── BinaryCompositeMaskPredicateToShapeRoiConverter.java │ │ │ ├── DefaultRoiWrapper.java │ │ │ ├── IJRealRoiWrapper.java │ │ │ ├── IJRoiWrapper.java │ │ │ ├── MaskPredicateUnwrappers.java │ │ │ ├── MaskPredicateWrapper.java │ │ │ ├── RealMaskRealIntervalToImageRoiConverter.java │ │ │ ├── RoiToMaskIntervalConverter.java │ │ │ ├── RoiUnwrappers.java │ │ │ ├── Rois.java │ │ │ ├── ShapeRoiToMaskRealIntervalConverter.java │ │ │ ├── ShapeRoiWrapper.java │ │ │ ├── box │ │ │ ├── BoxToRoiConverter.java │ │ │ ├── BoxWrapper.java │ │ │ ├── RoiToBoxConverter.java │ │ │ ├── RoiWrapper.java │ │ │ └── WritableBoxToRoiConverter.java │ │ │ ├── ellipsoid │ │ │ ├── EllipsoidToOvalRoiConverter.java │ │ │ ├── EllipsoidWrapper.java │ │ │ ├── OvalRoiToEllipsoidConverter.java │ │ │ ├── OvalRoiWrapper.java │ │ │ └── WritableEllipsoidToOvalRoiConverter.java │ │ │ ├── line │ │ │ ├── IJLineToLineConverter.java │ │ │ ├── IJLineWrapper.java │ │ │ ├── LineToIJLineConverter.java │ │ │ ├── LineWrapper.java │ │ │ └── WritableLineToIJLineConverter.java │ │ │ ├── point │ │ │ ├── PointMaskToPointRoiConverter.java │ │ │ ├── PointMaskWrapper.java │ │ │ ├── PointRoiToRealPointCollectionConverter.java │ │ │ ├── PointRoiWrapper.java │ │ │ ├── RealPointCollectionToPointRoiConverter.java │ │ │ ├── RealPointCollectionWrapper.java │ │ │ ├── WritablePointMaskToPointRoiConverter.java │ │ │ └── WritableRealPointCollectionToPointRoiConverter.java │ │ │ ├── polygon2d │ │ │ ├── Polygon2DToPolygonRoiConverter.java │ │ │ ├── Polygon2DWrapper.java │ │ │ ├── PolygonRoiToPolygon2DConverter.java │ │ │ ├── PolygonRoiWrapper.java │ │ │ ├── UnmodifiablePolygonRoiWrapper.java │ │ │ └── WritablePolygon2DToPolygonRoiConverter.java │ │ │ └── polyline │ │ │ ├── IrregularPolylineRoiWrapper.java │ │ │ ├── PolylineRoiToPolylineConverter.java │ │ │ ├── PolylineRoiToRealMaskRealIntervalConverter.java │ │ │ ├── PolylineRoiWrapper.java │ │ │ ├── PolylineToPolylineRoiConverter.java │ │ │ ├── PolylineWrapper.java │ │ │ ├── UnmodifiablePolylineRoiWrapper.java │ │ │ └── WritablePolylineToPolylineRoiConverter.java │ │ ├── display │ │ ├── DefaultImagePlusDisplay.java │ │ ├── ImagePlusDisplay.java │ │ ├── ImagePlusDisplayViewer.java │ │ ├── LegacyDisplayViewer.java │ │ ├── LegacyImageDisplayService.java │ │ └── LegacyImageDisplayViewer.java │ │ ├── plugin │ │ ├── ActiveImagePlusPreprocessor.java │ │ ├── DefaultLegacyEditor.java │ │ ├── DefaultLegacyOpener.java │ │ ├── GetPath.java │ │ ├── IJ1MacroEngine.java │ │ ├── IJ1MacroLanguage.java │ │ ├── LegacyAppConfiguration.java │ │ ├── LegacyAutoImporter.java │ │ ├── LegacyEditor.java │ │ ├── LegacyInitializer.java │ │ ├── LegacyOpener.java │ │ ├── LegacyPostRefreshMenus.java │ │ ├── MacroAutoCompletionProvider.java │ │ ├── MacroExtensionAutoCompletionPlugin.java │ │ ├── MacroExtensionAutoCompletionService.java │ │ ├── MacroLanguageSupportPlugin.java │ │ ├── MacroPreprocessor.java │ │ ├── MacroRecorderExcludedInputs.java │ │ ├── MacroRecorderPostprocessor.java │ │ ├── MacroRecorderPreprocessor.java │ │ ├── OverlayPreprocessor.java │ │ ├── ResultsTablePreprocessor.java │ │ └── RoiManagerPreprocessor.java │ │ ├── search │ │ ├── FocusSearchBar.java │ │ ├── LegacyHelpSearchActionFactory.java │ │ ├── LegacySourceSearchActionFactory.java │ │ ├── OpenTemplateSearchActionFactory.java │ │ ├── SearchBarHacker.java │ │ └── SearchOptions.java │ │ ├── task │ │ ├── TaskMonitorButtonHacker.java │ │ └── TaskMonitorOptions.java │ │ ├── translate │ │ ├── ColorTableHarmonizer.java │ │ ├── CompositeHarmonizer.java │ │ ├── DataHarmonizer.java │ │ ├── DatasetUtils.java │ │ ├── DisplayCreator.java │ │ ├── DisplayHarmonizer.java │ │ ├── Harmonizer.java │ │ ├── ImagePlusCreator.java │ │ ├── ImagePlusCreatorUtils.java │ │ ├── ImageTranslator.java │ │ ├── LegacyUtils.java │ │ ├── MetadataHarmonizer.java │ │ ├── NameHarmonizer.java │ │ ├── OverlayHarmonizer.java │ │ ├── PositionHarmonizer.java │ │ └── ResultsTableHarmonizer.java │ │ └── ui │ │ ├── AbstractLegacyAdapter.java │ │ ├── LegacyAdapter.java │ │ ├── LegacyApplicationFrame.java │ │ ├── LegacyDialogPrompt.java │ │ ├── LegacyInputHarvester.java │ │ ├── LegacyStatusBar.java │ │ ├── LegacyToolBar.java │ │ └── LegacyUI.java └── resources │ ├── doc │ └── ij1macro │ │ ├── functions.html │ │ └── functions_extd.html │ ├── icons │ ├── imagej-256.png │ └── legacy.png │ ├── script_templates │ └── ImageJ_1.x │ │ ├── Batch │ │ ├── Process_Folder.groovy │ │ ├── Process_Folder.ijm │ │ ├── Process_Folder.py │ │ └── Process_Open_Images.ijm │ │ ├── Examples │ │ ├── Advanced_overlap_analysis.ijm │ │ ├── Debugging.bsh │ │ ├── ImgLib2_Plugin.java │ │ ├── Invert_Selection.py │ │ ├── JFreeChart_Example.java │ │ ├── Loop_over_slices.py │ │ ├── Modify_Image_Properties.py │ │ ├── OpsThresholdIJ1Analyze.py │ │ ├── Optimization_Example.java │ │ ├── Overlap_analysis_by_channel.ijm │ │ ├── Plot_Example.java │ │ ├── Process_Pixels.java │ │ ├── Rotate_ROI.py │ │ ├── Scale_All_ROIs.ijm │ │ ├── Specify_Roi.py │ │ └── Straighten.py │ │ ├── Intro │ │ ├── Greeting.ijm │ │ ├── Hello_World.ijm │ │ ├── Invert_Image.py │ │ ├── New_Image.py │ │ ├── Open_Image.py │ │ ├── Open_Sample.py │ │ ├── Select_All.py │ │ └── Select_None.py │ │ └── Skeletons │ │ ├── Bare_PlugIn.java │ │ ├── Bare_PlugInFilter.java │ │ ├── Bare_Reader_PlugIn.java │ │ ├── Bare_Tool.java │ │ └── Bare_Tracking_Tool.java │ └── scripts │ └── Image │ └── Adjust │ └── Manual_Threshold.js └── test ├── java └── net │ └── imagej │ └── legacy │ ├── BatchModeTest.java │ ├── Helper.java │ ├── ImageJ1EncapsulationTest.java │ ├── LegacyEditorTestDrive.java │ ├── LegacyImageMapTest.java │ ├── LegacyOpenerTest.java │ ├── LegacyServiceTest.java │ ├── MacroTest.java │ ├── Main.java │ ├── OverlayHarmonizerTest.java │ ├── ShutdownTest.java │ ├── TestDrive.java │ ├── convert │ ├── ImagePlusConversionTest.java │ ├── ResultsTableConversionTest.java │ ├── StringToDatasetConverterTest.java │ ├── StringToImagePlusConverterTest.java │ └── roi │ │ ├── DefaultRoiConversionTest.java │ │ ├── RealMaskRealIntervalToImageRoiConverterTest.java │ │ ├── ShapeRoiConversionTest.java │ │ ├── box │ │ ├── BoxWrapperTest.java │ │ ├── RoiConversionTest.java │ │ └── RoiWrapperTest.java │ │ ├── ellipsoid │ │ ├── EllipsoidWrapperTest.java │ │ ├── OvalRoiConversionTest.java │ │ └── OvalRoiWrapperTest.java │ │ ├── line │ │ ├── IJLineWrapperTest.java │ │ ├── LineConversionTest.java │ │ └── LineWrapperTest.java │ │ ├── point │ │ ├── PointMaskWrapperTest.java │ │ ├── PointRoiConversionTest.java │ │ ├── PointRoiWrapperTest.java │ │ └── RealPointCollectionWrapperTest.java │ │ ├── polygon2d │ │ ├── Polygon2DWrapperTest.java │ │ ├── PolygonRoiConversionTest.java │ │ ├── PolygonRoiWrapperTest.java │ │ └── UnmodifiablePolygonRoiWrapperTest.java │ │ └── polyline │ │ ├── IrregularPolylineRoiConversionTest.java │ │ ├── IrregularPolylineRoiWrapperTest.java │ │ ├── PolylineRoiConversionTest.java │ │ ├── PolylineRoiWrapperTest.java │ │ ├── PolylineWrapperTest.java │ │ └── UnmodifiablePolylineRoiWrapperTest.java │ ├── plugin │ ├── IJ1MacroLanguageTest.java │ ├── MacroRecorderPostprocessorTest.java │ ├── ResultsTablePreprocessorTest.java │ └── RoiManagerPreprocessorTest.java │ └── translate │ ├── DisplayCreatorBenchmark.java │ ├── DisplayCreatorTest.java │ ├── ImagePlusCreatorBenchmark.java │ ├── ImagePlusCreatorTest.java │ └── LegacyUtilsTest.java └── resources └── with-slice-label.tif /.github/build.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/imagej/imagej-legacy/HEAD/.github/build.sh -------------------------------------------------------------------------------- /.github/setup.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/imagej/imagej-legacy/HEAD/.github/setup.sh -------------------------------------------------------------------------------- /.github/workflows/build.yml: -------------------------------------------------------------------------------- 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