├── .github └── workflows │ ├── generate_doc.yml │ └── python-publish.yml ├── .gitignore ├── .readthedocs.yml ├── Dockerfile ├── LICENSE ├── README.md ├── docs ├── .nojekyll ├── Makefile ├── _sources │ ├── index.rst.txt │ ├── modules.rst.txt │ ├── wsiprocess.annotationparser.rst.txt │ ├── wsiprocess.converters.rst.txt │ ├── wsiprocess.pytorch.rst.txt │ └── wsiprocess.rst.txt ├── _static │ ├── _sphinx_javascript_frameworks_compat.js │ ├── basic.css │ ├── css │ │ ├── badge_only.css │ │ ├── fonts │ │ │ ├── Roboto-Slab-Bold.woff │ │ │ ├── Roboto-Slab-Bold.woff2 │ │ │ ├── Roboto-Slab-Regular.woff │ │ │ ├── Roboto-Slab-Regular.woff2 │ │ │ ├── fontawesome-webfont.eot │ │ │ ├── fontawesome-webfont.svg │ │ │ ├── fontawesome-webfont.ttf │ │ │ ├── fontawesome-webfont.woff │ │ │ ├── fontawesome-webfont.woff2 │ │ │ ├── lato-bold-italic.woff │ │ │ ├── lato-bold-italic.woff2 │ │ │ ├── lato-bold.woff │ │ │ ├── lato-bold.woff2 │ │ │ ├── lato-normal-italic.woff │ │ │ ├── lato-normal-italic.woff2 │ │ │ ├── lato-normal.woff │ │ │ └── lato-normal.woff2 │ │ └── theme.css │ ├── description.gif │ ├── doctools.js │ ├── documentation_options.js │ ├── file.png │ ├── icon.svg │ ├── jquery.js │ ├── js │ │ ├── badge_only.js │ │ ├── html5shiv-printshiv.min.js │ │ ├── html5shiv.min.js │ │ └── theme.js │ ├── language_data.js │ ├── logo.png │ ├── minus.png │ ├── plus.png │ ├── pygments.css │ ├── searchtools.js │ ├── sphinx_highlight.js │ ├── wsidissector.svg │ └── wsiprocess.svg ├── conf.py ├── genindex.html ├── index.html ├── index.rst ├── modules.html ├── modules.rst ├── objects.inv ├── py-modindex.html ├── requirements.txt ├── search.html ├── searchindex.js ├── wsiprocess.annotationparser.html ├── wsiprocess.annotationparser.rst ├── wsiprocess.converters.html ├── wsiprocess.converters.rst ├── wsiprocess.html ├── wsiprocess.pytorch.html ├── wsiprocess.pytorch.rst └── wsiprocess.rst ├── examples ├── CMU-1.txt ├── CMU-1_classification.xml ├── CMU-1_detection.xml ├── CMU-1_donwload.sh ├── CMU-1_segmentation.xml ├── README.md ├── basic_usage.py ├── basic_usage.sh ├── basic_usage_without_annotation.sh ├── classification_dataloader.py ├── classification_dataloader_with_custom_maskingfn.py ├── crop_bounding_box_after_patching.sh ├── custom_patching_function.py ├── downloader.py ├── export_annotatino_mask_with_rule.py ├── export_annotation_mask_of_a_class.py ├── export_thumbnails_with_patch.sh ├── foreground_thresholding_rule.sh ├── just_to_see_annotation_area_thumbnail.sh ├── make_mask_from_image.py ├── multiple_operations_on_foreground.py ├── on_annotation_per_classes.sh ├── override_get_patch.py ├── patching_for_object_detection.sh ├── patching_for_segmentation.sh ├── patching_with_annotation_area_rule_and_foreground_area_rule.sh ├── rule.json ├── segmentation_dataloader.py ├── sha256sum.txt ├── translate_dot_annotation_to_bounding_box.sh ├── wsidataset_for_pytorch.py └── wsisdataset_for_pytorch.py ├── images ├── description.gif ├── icon.svg ├── logo.png ├── wsidissector.svg └── wsiprocess.svg ├── setup.cfg ├── setup.py ├── tests ├── corrupted.ndpi ├── test_annotation.geojson ├── test_emptyfile.txt └── tests.py ├── utils ├── load_save_tiff.py ├── ndpi2tiff.py ├── numpy2vipsimage.py ├── showbbonimage.py ├── upload_anaconda.sh ├── upload_pypi.sh ├── vipsimage2numpy.py └── voc_to_yolo.py └── wsiprocess ├── __init__.py ├── annotation.py ├── annotationparser ├── ASAP_parser.py ├── GeoJson_parser.py ├── NDPView_parser.py ├── QuPath_parser.py ├── SlideRunner_parser.py ├── WSIDissector_parser.py ├── __init__.py └── parser_utils.py ├── cli.py ├── converter.py ├── converters ├── __init__.py ├── base_converter.py ├── wsiprocess_to_coco.py ├── wsiprocess_to_voc.py └── wsiprocess_to_yolo.py ├── error.py ├── patcher.py ├── pytorch ├── __init__.py ├── utils.py ├── wsidataloader.py └── wsidataset.py ├── rule.py ├── slide.py ├── utils.py └── verify.py /.github/workflows/generate_doc.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tand826/wsiprocess/HEAD/.github/workflows/generate_doc.yml -------------------------------------------------------------------------------- /.github/workflows/python-publish.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tand826/wsiprocess/HEAD/.github/workflows/python-publish.yml -------------------------------------------------------------------------------- /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tand826/wsiprocess/HEAD/.gitignore -------------------------------------------------------------------------------- /.readthedocs.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tand826/wsiprocess/HEAD/.readthedocs.yml -------------------------------------------------------------------------------- /Dockerfile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tand826/wsiprocess/HEAD/Dockerfile -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tand826/wsiprocess/HEAD/LICENSE -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tand826/wsiprocess/HEAD/README.md -------------------------------------------------------------------------------- /docs/.nojekyll: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /docs/Makefile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tand826/wsiprocess/HEAD/docs/Makefile -------------------------------------------------------------------------------- /docs/_sources/index.rst.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tand826/wsiprocess/HEAD/docs/_sources/index.rst.txt -------------------------------------------------------------------------------- /docs/_sources/modules.rst.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tand826/wsiprocess/HEAD/docs/_sources/modules.rst.txt -------------------------------------------------------------------------------- /docs/_sources/wsiprocess.annotationparser.rst.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tand826/wsiprocess/HEAD/docs/_sources/wsiprocess.annotationparser.rst.txt -------------------------------------------------------------------------------- /docs/_sources/wsiprocess.converters.rst.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tand826/wsiprocess/HEAD/docs/_sources/wsiprocess.converters.rst.txt -------------------------------------------------------------------------------- /docs/_sources/wsiprocess.pytorch.rst.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tand826/wsiprocess/HEAD/docs/_sources/wsiprocess.pytorch.rst.txt -------------------------------------------------------------------------------- /docs/_sources/wsiprocess.rst.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tand826/wsiprocess/HEAD/docs/_sources/wsiprocess.rst.txt -------------------------------------------------------------------------------- /docs/_static/_sphinx_javascript_frameworks_compat.js: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tand826/wsiprocess/HEAD/docs/_static/_sphinx_javascript_frameworks_compat.js -------------------------------------------------------------------------------- /docs/_static/basic.css: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tand826/wsiprocess/HEAD/docs/_static/basic.css -------------------------------------------------------------------------------- /docs/_static/css/badge_only.css: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tand826/wsiprocess/HEAD/docs/_static/css/badge_only.css -------------------------------------------------------------------------------- /docs/_static/css/fonts/Roboto-Slab-Bold.woff: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tand826/wsiprocess/HEAD/docs/_static/css/fonts/Roboto-Slab-Bold.woff -------------------------------------------------------------------------------- /docs/_static/css/fonts/Roboto-Slab-Bold.woff2: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tand826/wsiprocess/HEAD/docs/_static/css/fonts/Roboto-Slab-Bold.woff2 -------------------------------------------------------------------------------- /docs/_static/css/fonts/Roboto-Slab-Regular.woff: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tand826/wsiprocess/HEAD/docs/_static/css/fonts/Roboto-Slab-Regular.woff -------------------------------------------------------------------------------- /docs/_static/css/fonts/Roboto-Slab-Regular.woff2: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tand826/wsiprocess/HEAD/docs/_static/css/fonts/Roboto-Slab-Regular.woff2 -------------------------------------------------------------------------------- /docs/_static/css/fonts/fontawesome-webfont.eot: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tand826/wsiprocess/HEAD/docs/_static/css/fonts/fontawesome-webfont.eot -------------------------------------------------------------------------------- /docs/_static/css/fonts/fontawesome-webfont.svg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tand826/wsiprocess/HEAD/docs/_static/css/fonts/fontawesome-webfont.svg -------------------------------------------------------------------------------- /docs/_static/css/fonts/fontawesome-webfont.ttf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tand826/wsiprocess/HEAD/docs/_static/css/fonts/fontawesome-webfont.ttf -------------------------------------------------------------------------------- /docs/_static/css/fonts/fontawesome-webfont.woff: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tand826/wsiprocess/HEAD/docs/_static/css/fonts/fontawesome-webfont.woff -------------------------------------------------------------------------------- /docs/_static/css/fonts/fontawesome-webfont.woff2: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tand826/wsiprocess/HEAD/docs/_static/css/fonts/fontawesome-webfont.woff2 -------------------------------------------------------------------------------- /docs/_static/css/fonts/lato-bold-italic.woff: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tand826/wsiprocess/HEAD/docs/_static/css/fonts/lato-bold-italic.woff -------------------------------------------------------------------------------- /docs/_static/css/fonts/lato-bold-italic.woff2: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tand826/wsiprocess/HEAD/docs/_static/css/fonts/lato-bold-italic.woff2 -------------------------------------------------------------------------------- /docs/_static/css/fonts/lato-bold.woff: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tand826/wsiprocess/HEAD/docs/_static/css/fonts/lato-bold.woff -------------------------------------------------------------------------------- /docs/_static/css/fonts/lato-bold.woff2: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tand826/wsiprocess/HEAD/docs/_static/css/fonts/lato-bold.woff2 -------------------------------------------------------------------------------- /docs/_static/css/fonts/lato-normal-italic.woff: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tand826/wsiprocess/HEAD/docs/_static/css/fonts/lato-normal-italic.woff -------------------------------------------------------------------------------- /docs/_static/css/fonts/lato-normal-italic.woff2: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tand826/wsiprocess/HEAD/docs/_static/css/fonts/lato-normal-italic.woff2 -------------------------------------------------------------------------------- /docs/_static/css/fonts/lato-normal.woff: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tand826/wsiprocess/HEAD/docs/_static/css/fonts/lato-normal.woff -------------------------------------------------------------------------------- /docs/_static/css/fonts/lato-normal.woff2: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tand826/wsiprocess/HEAD/docs/_static/css/fonts/lato-normal.woff2 -------------------------------------------------------------------------------- /docs/_static/css/theme.css: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tand826/wsiprocess/HEAD/docs/_static/css/theme.css -------------------------------------------------------------------------------- /docs/_static/description.gif: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tand826/wsiprocess/HEAD/docs/_static/description.gif -------------------------------------------------------------------------------- /docs/_static/doctools.js: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tand826/wsiprocess/HEAD/docs/_static/doctools.js -------------------------------------------------------------------------------- /docs/_static/documentation_options.js: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tand826/wsiprocess/HEAD/docs/_static/documentation_options.js -------------------------------------------------------------------------------- /docs/_static/file.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tand826/wsiprocess/HEAD/docs/_static/file.png -------------------------------------------------------------------------------- /docs/_static/icon.svg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tand826/wsiprocess/HEAD/docs/_static/icon.svg -------------------------------------------------------------------------------- /docs/_static/jquery.js: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tand826/wsiprocess/HEAD/docs/_static/jquery.js -------------------------------------------------------------------------------- /docs/_static/js/badge_only.js: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tand826/wsiprocess/HEAD/docs/_static/js/badge_only.js -------------------------------------------------------------------------------- /docs/_static/js/html5shiv-printshiv.min.js: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tand826/wsiprocess/HEAD/docs/_static/js/html5shiv-printshiv.min.js -------------------------------------------------------------------------------- /docs/_static/js/html5shiv.min.js: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tand826/wsiprocess/HEAD/docs/_static/js/html5shiv.min.js -------------------------------------------------------------------------------- /docs/_static/js/theme.js: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tand826/wsiprocess/HEAD/docs/_static/js/theme.js -------------------------------------------------------------------------------- /docs/_static/language_data.js: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tand826/wsiprocess/HEAD/docs/_static/language_data.js -------------------------------------------------------------------------------- /docs/_static/logo.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tand826/wsiprocess/HEAD/docs/_static/logo.png -------------------------------------------------------------------------------- /docs/_static/minus.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tand826/wsiprocess/HEAD/docs/_static/minus.png -------------------------------------------------------------------------------- /docs/_static/plus.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tand826/wsiprocess/HEAD/docs/_static/plus.png -------------------------------------------------------------------------------- /docs/_static/pygments.css: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tand826/wsiprocess/HEAD/docs/_static/pygments.css -------------------------------------------------------------------------------- /docs/_static/searchtools.js: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tand826/wsiprocess/HEAD/docs/_static/searchtools.js -------------------------------------------------------------------------------- /docs/_static/sphinx_highlight.js: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tand826/wsiprocess/HEAD/docs/_static/sphinx_highlight.js -------------------------------------------------------------------------------- /docs/_static/wsidissector.svg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tand826/wsiprocess/HEAD/docs/_static/wsidissector.svg -------------------------------------------------------------------------------- /docs/_static/wsiprocess.svg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tand826/wsiprocess/HEAD/docs/_static/wsiprocess.svg -------------------------------------------------------------------------------- /docs/conf.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tand826/wsiprocess/HEAD/docs/conf.py -------------------------------------------------------------------------------- /docs/genindex.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tand826/wsiprocess/HEAD/docs/genindex.html -------------------------------------------------------------------------------- /docs/index.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tand826/wsiprocess/HEAD/docs/index.html -------------------------------------------------------------------------------- /docs/index.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tand826/wsiprocess/HEAD/docs/index.rst -------------------------------------------------------------------------------- /docs/modules.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tand826/wsiprocess/HEAD/docs/modules.html -------------------------------------------------------------------------------- /docs/modules.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tand826/wsiprocess/HEAD/docs/modules.rst -------------------------------------------------------------------------------- /docs/objects.inv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tand826/wsiprocess/HEAD/docs/objects.inv -------------------------------------------------------------------------------- /docs/py-modindex.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tand826/wsiprocess/HEAD/docs/py-modindex.html -------------------------------------------------------------------------------- /docs/requirements.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tand826/wsiprocess/HEAD/docs/requirements.txt -------------------------------------------------------------------------------- /docs/search.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tand826/wsiprocess/HEAD/docs/search.html -------------------------------------------------------------------------------- /docs/searchindex.js: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tand826/wsiprocess/HEAD/docs/searchindex.js -------------------------------------------------------------------------------- /docs/wsiprocess.annotationparser.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tand826/wsiprocess/HEAD/docs/wsiprocess.annotationparser.html -------------------------------------------------------------------------------- /docs/wsiprocess.annotationparser.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tand826/wsiprocess/HEAD/docs/wsiprocess.annotationparser.rst -------------------------------------------------------------------------------- /docs/wsiprocess.converters.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tand826/wsiprocess/HEAD/docs/wsiprocess.converters.html -------------------------------------------------------------------------------- /docs/wsiprocess.converters.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tand826/wsiprocess/HEAD/docs/wsiprocess.converters.rst -------------------------------------------------------------------------------- /docs/wsiprocess.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tand826/wsiprocess/HEAD/docs/wsiprocess.html -------------------------------------------------------------------------------- /docs/wsiprocess.pytorch.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tand826/wsiprocess/HEAD/docs/wsiprocess.pytorch.html -------------------------------------------------------------------------------- /docs/wsiprocess.pytorch.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tand826/wsiprocess/HEAD/docs/wsiprocess.pytorch.rst -------------------------------------------------------------------------------- /docs/wsiprocess.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tand826/wsiprocess/HEAD/docs/wsiprocess.rst -------------------------------------------------------------------------------- /examples/CMU-1.txt: -------------------------------------------------------------------------------- 1 | malignant benign -------------------------------------------------------------------------------- /examples/CMU-1_classification.xml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tand826/wsiprocess/HEAD/examples/CMU-1_classification.xml -------------------------------------------------------------------------------- /examples/CMU-1_detection.xml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tand826/wsiprocess/HEAD/examples/CMU-1_detection.xml -------------------------------------------------------------------------------- /examples/CMU-1_donwload.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tand826/wsiprocess/HEAD/examples/CMU-1_donwload.sh -------------------------------------------------------------------------------- /examples/CMU-1_segmentation.xml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tand826/wsiprocess/HEAD/examples/CMU-1_segmentation.xml -------------------------------------------------------------------------------- /examples/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tand826/wsiprocess/HEAD/examples/README.md -------------------------------------------------------------------------------- /examples/basic_usage.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tand826/wsiprocess/HEAD/examples/basic_usage.py -------------------------------------------------------------------------------- /examples/basic_usage.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tand826/wsiprocess/HEAD/examples/basic_usage.sh -------------------------------------------------------------------------------- /examples/basic_usage_without_annotation.sh: -------------------------------------------------------------------------------- 1 | wsiprocess evaluation CMU-1.ndpi -ve 2 | -------------------------------------------------------------------------------- /examples/classification_dataloader.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tand826/wsiprocess/HEAD/examples/classification_dataloader.py -------------------------------------------------------------------------------- /examples/classification_dataloader_with_custom_maskingfn.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tand826/wsiprocess/HEAD/examples/classification_dataloader_with_custom_maskingfn.py -------------------------------------------------------------------------------- /examples/crop_bounding_box_after_patching.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tand826/wsiprocess/HEAD/examples/crop_bounding_box_after_patching.sh -------------------------------------------------------------------------------- /examples/custom_patching_function.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tand826/wsiprocess/HEAD/examples/custom_patching_function.py -------------------------------------------------------------------------------- /examples/downloader.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tand826/wsiprocess/HEAD/examples/downloader.py -------------------------------------------------------------------------------- /examples/export_annotatino_mask_with_rule.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tand826/wsiprocess/HEAD/examples/export_annotatino_mask_with_rule.py -------------------------------------------------------------------------------- /examples/export_annotation_mask_of_a_class.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tand826/wsiprocess/HEAD/examples/export_annotation_mask_of_a_class.py -------------------------------------------------------------------------------- /examples/export_thumbnails_with_patch.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tand826/wsiprocess/HEAD/examples/export_thumbnails_with_patch.sh -------------------------------------------------------------------------------- /examples/foreground_thresholding_rule.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tand826/wsiprocess/HEAD/examples/foreground_thresholding_rule.sh -------------------------------------------------------------------------------- /examples/just_to_see_annotation_area_thumbnail.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tand826/wsiprocess/HEAD/examples/just_to_see_annotation_area_thumbnail.sh -------------------------------------------------------------------------------- /examples/make_mask_from_image.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tand826/wsiprocess/HEAD/examples/make_mask_from_image.py -------------------------------------------------------------------------------- /examples/multiple_operations_on_foreground.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tand826/wsiprocess/HEAD/examples/multiple_operations_on_foreground.py -------------------------------------------------------------------------------- /examples/on_annotation_per_classes.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tand826/wsiprocess/HEAD/examples/on_annotation_per_classes.sh -------------------------------------------------------------------------------- /examples/override_get_patch.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tand826/wsiprocess/HEAD/examples/override_get_patch.py -------------------------------------------------------------------------------- /examples/patching_for_object_detection.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tand826/wsiprocess/HEAD/examples/patching_for_object_detection.sh -------------------------------------------------------------------------------- /examples/patching_for_segmentation.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tand826/wsiprocess/HEAD/examples/patching_for_segmentation.sh -------------------------------------------------------------------------------- /examples/patching_with_annotation_area_rule_and_foreground_area_rule.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tand826/wsiprocess/HEAD/examples/patching_with_annotation_area_rule_and_foreground_area_rule.sh -------------------------------------------------------------------------------- /examples/rule.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tand826/wsiprocess/HEAD/examples/rule.json -------------------------------------------------------------------------------- /examples/segmentation_dataloader.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tand826/wsiprocess/HEAD/examples/segmentation_dataloader.py -------------------------------------------------------------------------------- /examples/sha256sum.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tand826/wsiprocess/HEAD/examples/sha256sum.txt -------------------------------------------------------------------------------- /examples/translate_dot_annotation_to_bounding_box.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tand826/wsiprocess/HEAD/examples/translate_dot_annotation_to_bounding_box.sh -------------------------------------------------------------------------------- /examples/wsidataset_for_pytorch.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tand826/wsiprocess/HEAD/examples/wsidataset_for_pytorch.py -------------------------------------------------------------------------------- /examples/wsisdataset_for_pytorch.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tand826/wsiprocess/HEAD/examples/wsisdataset_for_pytorch.py -------------------------------------------------------------------------------- /images/description.gif: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tand826/wsiprocess/HEAD/images/description.gif -------------------------------------------------------------------------------- /images/icon.svg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tand826/wsiprocess/HEAD/images/icon.svg -------------------------------------------------------------------------------- /images/logo.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tand826/wsiprocess/HEAD/images/logo.png -------------------------------------------------------------------------------- /images/wsidissector.svg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tand826/wsiprocess/HEAD/images/wsidissector.svg -------------------------------------------------------------------------------- /images/wsiprocess.svg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tand826/wsiprocess/HEAD/images/wsiprocess.svg -------------------------------------------------------------------------------- /setup.cfg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tand826/wsiprocess/HEAD/setup.cfg -------------------------------------------------------------------------------- /setup.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tand826/wsiprocess/HEAD/setup.py -------------------------------------------------------------------------------- /tests/corrupted.ndpi: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /tests/test_annotation.geojson: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tand826/wsiprocess/HEAD/tests/test_annotation.geojson -------------------------------------------------------------------------------- /tests/test_emptyfile.txt: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /tests/tests.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tand826/wsiprocess/HEAD/tests/tests.py -------------------------------------------------------------------------------- /utils/load_save_tiff.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tand826/wsiprocess/HEAD/utils/load_save_tiff.py -------------------------------------------------------------------------------- /utils/ndpi2tiff.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tand826/wsiprocess/HEAD/utils/ndpi2tiff.py -------------------------------------------------------------------------------- /utils/numpy2vipsimage.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tand826/wsiprocess/HEAD/utils/numpy2vipsimage.py -------------------------------------------------------------------------------- /utils/showbbonimage.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tand826/wsiprocess/HEAD/utils/showbbonimage.py -------------------------------------------------------------------------------- /utils/upload_anaconda.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tand826/wsiprocess/HEAD/utils/upload_anaconda.sh -------------------------------------------------------------------------------- /utils/upload_pypi.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tand826/wsiprocess/HEAD/utils/upload_pypi.sh -------------------------------------------------------------------------------- /utils/vipsimage2numpy.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tand826/wsiprocess/HEAD/utils/vipsimage2numpy.py -------------------------------------------------------------------------------- /utils/voc_to_yolo.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tand826/wsiprocess/HEAD/utils/voc_to_yolo.py -------------------------------------------------------------------------------- /wsiprocess/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tand826/wsiprocess/HEAD/wsiprocess/__init__.py -------------------------------------------------------------------------------- /wsiprocess/annotation.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tand826/wsiprocess/HEAD/wsiprocess/annotation.py -------------------------------------------------------------------------------- /wsiprocess/annotationparser/ASAP_parser.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tand826/wsiprocess/HEAD/wsiprocess/annotationparser/ASAP_parser.py -------------------------------------------------------------------------------- /wsiprocess/annotationparser/GeoJson_parser.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tand826/wsiprocess/HEAD/wsiprocess/annotationparser/GeoJson_parser.py -------------------------------------------------------------------------------- /wsiprocess/annotationparser/NDPView_parser.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tand826/wsiprocess/HEAD/wsiprocess/annotationparser/NDPView_parser.py -------------------------------------------------------------------------------- /wsiprocess/annotationparser/QuPath_parser.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tand826/wsiprocess/HEAD/wsiprocess/annotationparser/QuPath_parser.py -------------------------------------------------------------------------------- /wsiprocess/annotationparser/SlideRunner_parser.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tand826/wsiprocess/HEAD/wsiprocess/annotationparser/SlideRunner_parser.py -------------------------------------------------------------------------------- /wsiprocess/annotationparser/WSIDissector_parser.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tand826/wsiprocess/HEAD/wsiprocess/annotationparser/WSIDissector_parser.py -------------------------------------------------------------------------------- /wsiprocess/annotationparser/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tand826/wsiprocess/HEAD/wsiprocess/annotationparser/__init__.py -------------------------------------------------------------------------------- /wsiprocess/annotationparser/parser_utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tand826/wsiprocess/HEAD/wsiprocess/annotationparser/parser_utils.py -------------------------------------------------------------------------------- /wsiprocess/cli.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tand826/wsiprocess/HEAD/wsiprocess/cli.py -------------------------------------------------------------------------------- /wsiprocess/converter.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tand826/wsiprocess/HEAD/wsiprocess/converter.py -------------------------------------------------------------------------------- /wsiprocess/converters/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /wsiprocess/converters/base_converter.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tand826/wsiprocess/HEAD/wsiprocess/converters/base_converter.py -------------------------------------------------------------------------------- /wsiprocess/converters/wsiprocess_to_coco.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tand826/wsiprocess/HEAD/wsiprocess/converters/wsiprocess_to_coco.py -------------------------------------------------------------------------------- /wsiprocess/converters/wsiprocess_to_voc.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tand826/wsiprocess/HEAD/wsiprocess/converters/wsiprocess_to_voc.py -------------------------------------------------------------------------------- /wsiprocess/converters/wsiprocess_to_yolo.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tand826/wsiprocess/HEAD/wsiprocess/converters/wsiprocess_to_yolo.py -------------------------------------------------------------------------------- /wsiprocess/error.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tand826/wsiprocess/HEAD/wsiprocess/error.py -------------------------------------------------------------------------------- /wsiprocess/patcher.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tand826/wsiprocess/HEAD/wsiprocess/patcher.py -------------------------------------------------------------------------------- /wsiprocess/pytorch/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tand826/wsiprocess/HEAD/wsiprocess/pytorch/__init__.py -------------------------------------------------------------------------------- /wsiprocess/pytorch/utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tand826/wsiprocess/HEAD/wsiprocess/pytorch/utils.py -------------------------------------------------------------------------------- /wsiprocess/pytorch/wsidataloader.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /wsiprocess/pytorch/wsidataset.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tand826/wsiprocess/HEAD/wsiprocess/pytorch/wsidataset.py -------------------------------------------------------------------------------- /wsiprocess/rule.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tand826/wsiprocess/HEAD/wsiprocess/rule.py -------------------------------------------------------------------------------- /wsiprocess/slide.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tand826/wsiprocess/HEAD/wsiprocess/slide.py -------------------------------------------------------------------------------- /wsiprocess/utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tand826/wsiprocess/HEAD/wsiprocess/utils.py -------------------------------------------------------------------------------- /wsiprocess/verify.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tand826/wsiprocess/HEAD/wsiprocess/verify.py --------------------------------------------------------------------------------