├── .circleci ├── config.yml ├── dcm4chee │ ├── auth-docker-compose.yml │ ├── create_keycloak_token.py │ ├── docker-compose.yml │ ├── update_access_token_lifespan.py │ └── upload_example_data.py ├── make_index.py ├── make_wheels.sh └── release_pypi.sh ├── .dockerignore ├── .editorconfig ├── .git-blame-ignore-revs ├── .github ├── dependabot.yml └── workflows │ └── docker.yml ├── .gitignore ├── .pre-commit-config.yaml ├── CHANGELOG.md ├── LICENSE ├── MANIFEST.in ├── NOTICE ├── README.rst ├── codecov.yml ├── docs ├── annotations.rst ├── api_index.rst ├── caching.rst ├── conf.py ├── config_options.rst ├── development.rst ├── dicomweb_assetstore.rst ├── format_examples_datastore.py ├── formats.rst ├── generate_format_table.py ├── getting_started.rst ├── girder_annotation_config_options.rst ├── girder_caching.rst ├── girder_config_options.rst ├── girder_index.rst ├── image_conversion.rst ├── index.rst ├── make_docs.sh ├── multi_source_specification.rst ├── notebooks.rst ├── notebooks │ ├── frame_viewer_example.ipynb │ ├── large_image_examples.ipynb │ └── zarr_sink_example.ipynb ├── plottable.rst ├── static │ ├── K.png │ └── custom.css ├── tilesource_options.rst └── upgrade.rst ├── examples ├── __init__.py ├── algorithm_progression.py ├── algorithms.py ├── average_color.py └── sumsquare_color.py ├── girder ├── girder_large_image │ ├── __init__.py │ ├── constants.py │ ├── girder_tilesource.py │ ├── loadmodelcache.py │ ├── models │ │ ├── __init__.py │ │ └── image_item.py │ ├── rest │ │ ├── __init__.py │ │ ├── item_meta.py │ │ ├── large_image_resource.py │ │ └── tiles.py │ └── web_client │ │ ├── eventStream.js │ │ ├── extra │ │ └── .gitignore │ │ ├── index.js │ │ ├── main.js │ │ ├── package.json │ │ ├── routes.js │ │ ├── stylesheets │ │ ├── fileList.styl │ │ ├── imageViewerSelectWidget.styl │ │ ├── itemList.styl │ │ ├── itemView.styl │ │ ├── itemViewCodemirror.styl │ │ ├── largeImageConfig.styl │ │ └── metadataWidget.styl │ │ ├── templates │ │ ├── imageViewerSelectWidget.pug │ │ ├── itemList.pug │ │ ├── itemView.pug │ │ ├── itemViewCodemirror.pug │ │ ├── largeImageConfig.pug │ │ ├── largeImage_fileAction.pug │ │ ├── metadataWidget.pug │ │ └── metadatumEditWidget.pug │ │ ├── views │ │ ├── configView.js │ │ ├── fileList.js │ │ ├── imageViewerSelectWidget.js │ │ ├── imageViewerWidget │ │ │ ├── base.js │ │ │ ├── geojs.js │ │ │ ├── index.js │ │ │ ├── leaflet.js │ │ │ ├── openlayers.js │ │ │ ├── openseadragon.js │ │ │ ├── setFrameQuad.js │ │ │ └── slideatlas.js │ │ ├── index.js │ │ ├── itemList.js │ │ ├── itemView.js │ │ ├── itemViewCodemirror.js │ │ ├── itemViewWidget.js │ │ └── metadataWidget.js │ │ ├── vue │ │ └── components │ │ │ └── PresetsMenu.vue │ │ ├── webpack.helper.js │ │ └── widgets ├── pyproject.toml ├── setup.py └── test_girder │ ├── __init__.py │ ├── conftest.py │ ├── girder_utilities.py │ ├── test_large_image.py │ ├── test_tiles_rest.py │ ├── test_web_client.py │ └── web_client_specs │ ├── .eslintrc │ ├── imageViewerSpec.js │ ├── largeImageSpec.js │ └── otherFeatures.js ├── girder_annotation ├── docs │ ├── annotations.rst │ └── plottable.rst ├── girder_large_image_annotation │ ├── __init__.py │ ├── constants.py │ ├── handlers.py │ ├── models │ │ ├── __init__.py │ │ ├── annotation.py │ │ └── annotationelement.py │ ├── rest │ │ ├── __init__.py │ │ └── annotation.py │ ├── utils │ │ └── __init__.py │ └── web_client │ │ ├── annotations │ │ ├── convert.js │ │ ├── convertFeatures.js │ │ ├── defaults │ │ │ ├── circle.js │ │ │ ├── ellipse.js │ │ │ ├── index.js │ │ │ ├── point.js │ │ │ ├── polyline.js │ │ │ └── rectangle.js │ │ ├── geojs │ │ │ ├── common.js │ │ │ ├── convert.js │ │ │ ├── coordinates │ │ │ │ ├── array.js │ │ │ │ ├── index.js │ │ │ │ └── point.js │ │ │ ├── index.js │ │ │ └── types │ │ │ │ ├── circle.js │ │ │ │ ├── ellipse.js │ │ │ │ ├── index.js │ │ │ │ ├── line.js │ │ │ │ ├── point.js │ │ │ │ ├── polygon.js │ │ │ │ └── rectangle.js │ │ ├── geometry │ │ │ ├── circle.js │ │ │ ├── ellipse.js │ │ │ ├── index.js │ │ │ ├── point.js │ │ │ ├── polyline.js │ │ │ └── rectangle.js │ │ ├── index.js │ │ ├── rotate.js │ │ └── style.js │ │ ├── collections │ │ ├── AnnotationCollection.js │ │ ├── ElementCollection.js │ │ └── index.js │ │ ├── index.js │ │ ├── main.js │ │ ├── models │ │ ├── AnnotationModel.js │ │ ├── ElementModel.js │ │ └── index.js │ │ ├── package.json │ │ ├── routes.js │ │ ├── stylesheets │ │ ├── annotationListWidget.styl │ │ └── itemList.styl │ │ ├── templates │ │ ├── annotationListWidget.pug │ │ ├── imageViewerAnnotationList.pug │ │ └── largeImageAnnotationConfig.pug │ │ └── views │ │ ├── annotationListWidget.js │ │ ├── configView.js │ │ ├── hierarchyWidget.js │ │ ├── imageViewerSelectWidget.js │ │ ├── imageViewerWidget │ │ ├── base.js │ │ ├── geojs.js │ │ └── index.js │ │ ├── index.js │ │ └── itemList.js ├── pyproject.toml ├── setup.py └── test_annotation │ ├── __init__.py │ ├── conftest.py │ ├── girder_utilities.py │ ├── test_annotations.py │ ├── test_annotations_rest.py │ ├── test_web_client.py │ └── web_client_specs │ ├── .eslintrc │ ├── annotationListSpec.js │ ├── annotationSpec.js │ ├── geojsAnnotationSpec.js │ ├── geojsSpec.js │ └── sample_annotation.json ├── large_image ├── __init__.py ├── cache_util │ ├── __init__.py │ ├── base.py │ ├── cache.py │ ├── cachefactory.py │ ├── memcache.py │ └── rediscache.py ├── config.py ├── constants.py ├── exceptions.py ├── tilesource │ ├── __init__.py │ ├── base.py │ ├── geo.py │ ├── jupyter.py │ ├── resample.py │ ├── stylefuncs.py │ ├── tiledict.py │ ├── tileiterator.py │ └── utilities.py └── widgets │ ├── CompositeLayers.vue │ ├── DualInput.vue │ ├── FrameSelector.vue │ ├── HistogramEditor.vue │ ├── colors.json │ └── components.py ├── pyproject.toml ├── requirements-dev-osx.txt ├── requirements-dev.txt ├── requirements-test-core.txt ├── requirements-test.txt ├── setup.py ├── slim.Dockerfile ├── sources ├── bioformats │ ├── large_image_source_bioformats │ │ ├── __init__.py │ │ └── girder_source.py │ ├── pyproject.toml │ └── setup.py ├── deepzoom │ ├── large_image_source_deepzoom │ │ ├── __init__.py │ │ └── girder_source.py │ ├── pyproject.toml │ └── setup.py ├── dicom │ ├── docs │ │ └── dicomweb_assetstore.rst │ ├── large_image_source_dicom │ │ ├── __init__.py │ │ ├── assetstore │ │ │ ├── __init__.py │ │ │ ├── dicomweb_assetstore_adapter.py │ │ │ └── rest.py │ │ ├── dicom_metadata.py │ │ ├── dicom_tags.py │ │ ├── dicomweb_utils.py │ │ ├── girder_plugin.py │ │ ├── girder_source.py │ │ └── web_client │ │ │ ├── constants.js │ │ │ ├── main.js │ │ │ ├── package.json │ │ │ ├── templates │ │ │ ├── assetstoreImport.pug │ │ │ ├── dicomwebAssetstoreCreate.pug │ │ │ ├── dicomwebAssetstoreEditFields.pug │ │ │ ├── dicomwebAssetstoreImportButton.pug │ │ │ └── dicomwebAssetstoreMixins.pug │ │ │ └── views │ │ │ ├── AssetstoresView.js │ │ │ ├── AuthOptions.js │ │ │ ├── DICOMwebImportView.js │ │ │ ├── EditAssetstoreWidget.js │ │ │ └── NewAssetstoreWidget.js │ ├── pyproject.toml │ ├── setup.py │ └── test_dicom │ │ ├── __init__.py │ │ ├── test_web_client.py │ │ └── web_client_specs │ │ └── dicomWebSpec.js ├── dummy │ ├── large_image_source_dummy │ │ └── __init__.py │ ├── pyproject.toml │ └── setup.py ├── gdal │ ├── large_image_source_gdal │ │ ├── __init__.py │ │ └── girder_source.py │ ├── pyproject.toml │ └── setup.py ├── mapnik │ ├── large_image_source_mapnik │ │ ├── __init__.py │ │ └── girder_source.py │ ├── pyproject.toml │ └── setup.py ├── multi │ ├── docs │ │ └── specification.rst │ ├── large_image_source_multi │ │ ├── __init__.py │ │ └── girder_source.py │ ├── pyproject.toml │ └── setup.py ├── nd2 │ ├── large_image_source_nd2 │ │ ├── __init__.py │ │ └── girder_source.py │ ├── pyproject.toml │ └── setup.py ├── ometiff │ ├── large_image_source_ometiff │ │ ├── __init__.py │ │ └── girder_source.py │ ├── pyproject.toml │ └── setup.py ├── openjpeg │ ├── large_image_source_openjpeg │ │ ├── __init__.py │ │ └── girder_source.py │ ├── pyproject.toml │ └── setup.py ├── openslide │ ├── large_image_source_openslide │ │ ├── __init__.py │ │ └── girder_source.py │ ├── pyproject.toml │ └── setup.py ├── pil │ ├── large_image_source_pil │ │ ├── __init__.py │ │ └── girder_source.py │ ├── pyproject.toml │ └── setup.py ├── rasterio │ ├── large_image_source_rasterio │ │ ├── __init__.py │ │ └── girder_source.py │ ├── pyproject.toml │ └── setup.py ├── test │ ├── large_image_source_test │ │ └── __init__.py │ ├── pyproject.toml │ └── setup.py ├── tiff │ ├── large_image_source_tiff │ │ ├── __init__.py │ │ ├── exceptions.py │ │ ├── girder_source.py │ │ └── tiff_reader.py │ ├── pyproject.toml │ └── setup.py ├── tifffile │ ├── large_image_source_tifffile │ │ ├── __init__.py │ │ └── girder_source.py │ ├── pyproject.toml │ └── setup.py ├── vips │ ├── large_image_source_vips │ │ ├── __init__.py │ │ └── girder_source.py │ ├── pyproject.toml │ └── setup.py └── zarr │ ├── large_image_source_zarr │ ├── __init__.py │ └── girder_source.py │ ├── pyproject.toml │ └── setup.py ├── test.Dockerfile ├── test ├── __init__.py ├── datastore.py ├── lisource_compare.py ├── source_geo_base.py ├── test_cache.py ├── test_cache_source.py ├── test_cached_tiles.py ├── test_config.py ├── test_converter.py ├── test_examples.py ├── test_files │ ├── .large_image_config.yaml │ ├── README.md │ ├── geotiff_9_89_207.png │ ├── geotiff_9_89_207_py3.png │ ├── geotiff_9_89_207_py36.png │ ├── geotiff_9_89_207_v4.png │ ├── geotiff_9_89_207_v5.png │ ├── geotiff_9_89_207_v6.png │ ├── geotiff_style_7_22_51.png │ ├── geotiff_style_7_22_51_py3.png │ ├── geotiff_style_7_22_51_py36.png │ ├── geotiff_style_7_22_51_v4.png │ ├── geotiff_style_7_22_51_v5.png │ ├── geotiff_style_linear_7_22_51.png │ ├── geotiff_style_linear_7_22_51_py3.png │ ├── geotiff_style_linear_7_22_51_py36.png │ ├── geotiff_style_linear_7_22_51_v4.png │ ├── geotiff_style_linear_7_22_51_v5.png │ ├── geotiff_style_linear_7_22_51_v6.png │ ├── geotiff_style_linear_7_22_51_v7.png │ ├── global_dem.tif │ ├── grey10kx5k.tif │ ├── multi1.yml │ ├── multi2.yml │ ├── multi3.yml │ ├── multi_affine.yml │ ├── multi_band.yml │ ├── multi_channels.yml │ ├── multi_composite.yml │ ├── multi_simple_scaling.yml │ ├── multi_test_source.yml │ ├── multi_test_source3.yml │ ├── multi_test_source_axes.yml │ ├── multi_test_source_bands.yml │ ├── multi_test_source_scaling.yml │ ├── multi_test_source_style.yml │ ├── notanimage.txt │ ├── rgb_geotiff.tiff │ ├── rgba_geotiff.tiff │ ├── sample.geojson │ ├── sample.girder.cfg │ ├── sample_float32_8bit_range.zarr.zip │ ├── small_la.tiff │ ├── test_LA_16.png │ ├── test_LA_8.png │ ├── test_L_16.png │ ├── test_L_8.png │ ├── test_RGBA_16.png │ ├── test_RGBA_8.png │ ├── test_RGB_16.png │ ├── test_RGB_8.png │ ├── test_orient0.tif │ ├── test_orient1.tif │ ├── test_orient2.tif │ ├── test_orient3.tif │ ├── test_orient4.tif │ ├── test_orient5.tif │ ├── test_orient6.tif │ ├── test_orient7.tif │ ├── test_orient8.tif │ ├── yb10kx5k.png │ ├── yb10kx5k.zstd.tiff │ ├── yb10kx5ktrans.png │ └── zero_gi.tif ├── test_jupyter.py ├── test_notebooks.py ├── test_pickle.py ├── test_sink.py ├── test_source_base.py ├── test_source_bioformats.py ├── test_source_deepzoom.py ├── test_source_dicomweb.py ├── test_source_dummy.py ├── test_source_gdal.py ├── test_source_mapnik.py ├── test_source_multi.py ├── test_source_nd2.py ├── test_source_ometiff.py ├── test_source_openjpeg.py ├── test_source_openslide.py ├── test_source_pil.py ├── test_source_rasterio.py ├── test_source_tiff.py ├── test_source_vips.py ├── test_tasks.py ├── utilities.py └── utils │ ├── README.rst │ ├── compression_test.py │ └── compression_test_summary.py ├── tox.ini └── utilities ├── converter ├── README.rst ├── large_image_converter │ ├── __init__.py │ ├── __main__.py │ └── format_aperio.py ├── pyproject.toml └── setup.py └── tasks ├── README.rst ├── large_image_tasks ├── __init__.py └── tasks.py ├── pyproject.toml └── setup.py /.circleci/config.yml: -------------------------------------------------------------------------------- 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