.coveragerc
.pre-commit-config.yaml
CONTRIBUTING.md
LICENSE.txt
MANIFEST.in
Makefile
README.md
pyproject.toml
readthedocs.yml
requirements-dev.txt
requirements.txt
setup.cfg
setup.py
src/__init__.py
src/histolab/__init__.py
src/histolab/exceptions.py
src/histolab/scorer.py
src/histolab/slide.py
src/histolab/tile.py
src/histolab/tiler.py
src/histolab/types.py
src/histolab/util.py
src/histolab.egg-info/PKG-INFO
src/histolab.egg-info/SOURCES.txt
src/histolab.egg-info/dependency_links.txt
src/histolab.egg-info/requires.txt
src/histolab.egg-info/top_level.txt
src/histolab.egg-info/zip-safe
src/histolab/data/__init__.py
src/histolab/data/_registry.py
src/histolab/data/cmu_small_region.svs
src/histolab/filters/__init__.py
src/histolab/filters/compositions.py
src/histolab/filters/image_filters.py
src/histolab/filters/image_filters_functional.py
src/histolab/filters/morphological_filters.py
src/histolab/filters/morphological_filters_functional.py
src/histolab/filters/util.py
tests/__init__.py
tests/base.py
tests/conftest.py
tests/unitutil.py
tests/util.py
tests/benchmarks/__init__.py
tests/benchmarks/test_benchmarks.py
tests/expectations/tcga-cr-7395-01a-01-ts1-tl-scored-false.png
tests/expectations/bbox-location-images/cmu-1-small-region-bbox-location-tissue-mask-false.png
tests/expectations/bbox-location-images/cmu-1-small-region-bbox-location-tissue-mask-true.png
tests/expectations/bbox-location-images/tcga-cr-7395-01a-01-ts1-bbox-location-tissue-mask-false.png
tests/expectations/bbox-location-images/tcga-cr-7395-01a-01-ts1-bbox-location-tissue-mask-true.png
tests/expectations/mask-arrays/diagnostic-slide-thumb-blue-pen-filter-mask.npy
tests/expectations/mask-arrays/diagnostic-slide-thumb-grays-mask.npy
tests/expectations/mask-arrays/diagnostic-slide-thumb-green-pen-filter-mask.npy
tests/expectations/mask-arrays/diagnostic-slide-thumb-gs-canny-edges-mask.npy
tests/expectations/mask-arrays/diagnostic-slide-thumb-gs-filter-entropy-mask.npy
tests/expectations/mask-arrays/diagnostic-slide-thumb-gs-otsu-threshold-mask.npy
tests/expectations/mask-arrays/diagnostic-slide-thumb-gs-yen-threshold-mask.npy
tests/expectations/mask-arrays/diagnostic-slide-thumb-gs1-hysteresis-threshold-mask.npy
tests/expectations/mask-arrays/diagnostic-slide-thumb-gs2-hysteresis-threshold-mask.npy
tests/expectations/mask-arrays/diagnostic-slide-thumb-gs3-hysteresis-threshold-mask.npy
tests/expectations/mask-arrays/diagnostic-slide-thumb-gs4-hysteresis-threshold-mask.npy
tests/expectations/mask-arrays/diagnostic-slide-thumb-hsv-blue-filter-mask.npy
tests/expectations/mask-arrays/diagnostic-slide-thumb-hsv-blue-pen-filter-mask.npy
tests/expectations/mask-arrays/diagnostic-slide-thumb-hsv-grays-mask.npy
tests/expectations/mask-arrays/diagnostic-slide-thumb-hsv-green-filter-mask.npy
tests/expectations/mask-arrays/diagnostic-slide-thumb-hsv-green-pen-filter-mask.npy
tests/expectations/mask-arrays/diagnostic-slide-thumb-hsv-hysteresis-threshold-mask.npy
tests/expectations/mask-arrays/diagnostic-slide-thumb-hsv-otsu-threshold-mask.npy
tests/expectations/mask-arrays/diagnostic-slide-thumb-hsv-otsu-threshold-remove-small-objects-mask.npy
tests/expectations/mask-arrays/diagnostic-slide-thumb-hsv-otsu-threshold-remove-small-objects2-mask.npy
tests/expectations/mask-arrays/diagnostic-slide-thumb-hsv-pen-marks-mask.npy
tests/expectations/mask-arrays/diagnostic-slide-thumb-hsv-red-filter-mask.npy
tests/expectations/mask-arrays/diagnostic-slide-thumb-hsv-red-pen-filter-mask.npy
tests/expectations/mask-arrays/diagnostic-slide-thumb-hsv-yen-threshold-mask.npy
tests/expectations/mask-arrays/diagnostic-slide-thumb-hysteresis-threshold-mask.npy
tests/expectations/mask-arrays/diagnostic-slide-thumb-otsu-threshold-mask.npy
tests/expectations/mask-arrays/diagnostic-slide-thumb-red-pen-filter-mask.npy
tests/expectations/mask-arrays/diagnostic-slide-thumb-rgb-blue-filter-mask.npy
tests/expectations/mask-arrays/diagnostic-slide-thumb-rgb-blue-pen-filter-mask.npy
tests/expectations/mask-arrays/diagnostic-slide-thumb-rgb-grays-mask.npy
tests/expectations/mask-arrays/diagnostic-slide-thumb-rgb-green-filter-mask.npy
tests/expectations/mask-arrays/diagnostic-slide-thumb-rgb-green-pen-filter-mask.npy
tests/expectations/mask-arrays/diagnostic-slide-thumb-rgb-pen-marks-mask.npy
tests/expectations/mask-arrays/diagnostic-slide-thumb-rgb-red-filter-mask.npy
tests/expectations/mask-arrays/diagnostic-slide-thumb-rgb-red-pen-filter-mask.npy
tests/expectations/mask-arrays/diagnostic-slide-thumb-rgb-yen-threshold-mask.npy
tests/expectations/mask-arrays/diagnostic-slide-thumb-rgb1-hysteresis-threshold-mask.npy
tests/expectations/mask-arrays/diagnostic-slide-thumb-rgb1-hysteresis-threshold-remove-small-objects-mask.npy
tests/expectations/mask-arrays/diagnostic-slide-thumb-rgb1-hysteresis-threshold-remove-small-objects2-mask.npy
tests/expectations/mask-arrays/diagnostic-slide-thumb-rgb2-hysteresis-threshold-mask.npy
tests/expectations/mask-arrays/diagnostic-slide-thumb-rgba1-blue-filter-mask.npy
tests/expectations/mask-arrays/diagnostic-slide-thumb-rgba1-green-ch-filter-mask.npy
tests/expectations/mask-arrays/diagnostic-slide-thumb-rgba1-green-filter-mask.npy
tests/expectations/mask-arrays/diagnostic-slide-thumb-rgba1-red-filter-mask.npy
tests/expectations/mask-arrays/diagnostic-slide-thumb-rgba2-blue-filter-mask.npy
tests/expectations/mask-arrays/diagnostic-slide-thumb-rgba2-green-ch-filter-mask.npy
tests/expectations/mask-arrays/diagnostic-slide-thumb-rgba2-green-filter-mask.npy
tests/expectations/mask-arrays/diagnostic-slide-thumb-rgba2-red-filter-mask.npy
tests/expectations/mask-arrays/diagnostic-slide-thumb-rgba3-blue-filter-mask.npy
tests/expectations/mask-arrays/diagnostic-slide-thumb-rgba3-green-ch-filter-mask.npy
tests/expectations/mask-arrays/diagnostic-slide-thumb-rgba3-green-filter-mask.npy
tests/expectations/mask-arrays/diagnostic-slide-thumb-rgba3-red-filter-mask.npy
tests/expectations/mask-arrays/diagnostic-slide-thumb-rgba4-green-ch-filter-mask.npy
tests/expectations/mask-arrays/diagnostic-slide-thumb-ycbcr-blue-filter-mask.npy
tests/expectations/mask-arrays/diagnostic-slide-thumb-ycbcr-blue-pen-filter-mask.npy
tests/expectations/mask-arrays/diagnostic-slide-thumb-ycbcr-grays-mask.npy
tests/expectations/mask-arrays/diagnostic-slide-thumb-ycbcr-green-filter-mask.npy
tests/expectations/mask-arrays/diagnostic-slide-thumb-ycbcr-green-pen-filter-mask.npy
tests/expectations/mask-arrays/diagnostic-slide-thumb-ycbcr-hysteresis-threshold-mask.npy
tests/expectations/mask-arrays/diagnostic-slide-thumb-ycbcr-otsu-threshold-mask.npy
tests/expectations/mask-arrays/diagnostic-slide-thumb-ycbcr-pen-marks-mask.npy
tests/expectations/mask-arrays/diagnostic-slide-thumb-ycbcr-red-filter-mask.npy
tests/expectations/mask-arrays/diagnostic-slide-thumb-ycbcr-red-pen-filter-mask.npy
tests/expectations/mask-arrays/diagnostic-slide-thumb-ycbcr-yen-threshold-mask.npy
tests/expectations/mask-arrays/diagnostic-slide-thumb-yen-threshold-mask.npy
tests/expectations/mask-arrays/polygon-to-mask-array-0325.npy
tests/expectations/mask-arrays/polygon-to-mask-array-1020.npy
tests/expectations/mask-arrays/polygon-to-mask-array-2143.npy
tests/expectations/mask-arrays/tcga-lung-rgb-pen-marks-mask.npy
tests/expectations/mask-arrays/ytma1-watershed-segmentation-region3.npy
tests/expectations/mask-arrays/ytma1-watershed-segmentation-region6.npy
tests/expectations/mask-arrays/ytma2-watershed-segmentation-region3.npy
tests/expectations/mask-arrays/ytma2-watershed-segmentation-region6.npy
tests/expectations/pil-images-gs/diagnostic-slide-thumb-gs-adaptive-equalization.png
tests/expectations/pil-images-gs/diagnostic-slide-thumb-gs-histogram-equalization.png
tests/expectations/pil-images-gs/diagnostic-slide-thumb-gs-hysteresis-threshold.png
tests/expectations/pil-images-gs/diagnostic-slide-thumb-gs-inverted.png
tests/expectations/pil-images-gs/diagnostic-slide-thumb-gs-kmeans-segmentation.png
tests/expectations/pil-images-gs/diagnostic-slide-thumb-gs-local-equalization.png
tests/expectations/pil-images-gs/diagnostic-slide-thumb-gs-rag-threshold.png
tests/expectations/pil-images-gs/diagnostic-slide-thumb-gs-stretch-contrast.png
tests/expectations/pil-images-gs/diagnostic-slide-thumb-gs1-local-otsu.png
tests/expectations/pil-images-gs/diagnostic-slide-thumb-gs2-local-otsu.png
tests/expectations/pil-images-gs/diagnostic-slide-thumb-gs3-local-otsu.png
tests/expectations/pil-images-gs/diagnostic-slide-thumb-gs4-local-otsu.png
tests/expectations/pil-images-rgb/diagnostic-slide-thumb-hsv-adaptive-equalization.png
tests/expectations/pil-images-rgb/diagnostic-slide-thumb-hsv-blue-pen-filter.png
tests/expectations/pil-images-rgb/diagnostic-slide-thumb-hsv-green-pen-filter.png
tests/expectations/pil-images-rgb/diagnostic-slide-thumb-hsv-histogram-equalization.png
tests/expectations/pil-images-rgb/diagnostic-slide-thumb-hsv-hysteresis-threshold.png
tests/expectations/pil-images-rgb/diagnostic-slide-thumb-hsv-inverted.png
tests/expectations/pil-images-rgb/diagnostic-slide-thumb-hsv-kmeans-segmentation.png
tests/expectations/pil-images-rgb/diagnostic-slide-thumb-hsv-rag-threshold.png
tests/expectations/pil-images-rgb/diagnostic-slide-thumb-hsv-red-pen-filter.png
tests/expectations/pil-images-rgb/diagnostic-slide-thumb-hsv-rgb-to-hed.png
tests/expectations/pil-images-rgb/diagnostic-slide-thumb-hsv-rgb-to-lab.png
tests/expectations/pil-images-rgb/diagnostic-slide-thumb-hsv-stretch-contrast.png
tests/expectations/pil-images-rgb/diagnostic-slide-thumb-rgb-adaptive-equalization.png
tests/expectations/pil-images-rgb/diagnostic-slide-thumb-rgb-blue-pen-filter.png
tests/expectations/pil-images-rgb/diagnostic-slide-thumb-rgb-green-pen-filter.png
tests/expectations/pil-images-rgb/diagnostic-slide-thumb-rgb-histogram-equalization.png
tests/expectations/pil-images-rgb/diagnostic-slide-thumb-rgb-hysteresis-threshold.png
tests/expectations/pil-images-rgb/diagnostic-slide-thumb-rgb-inverted.png
tests/expectations/pil-images-rgb/diagnostic-slide-thumb-rgb-kmeans-segmentation.png
tests/expectations/pil-images-rgb/diagnostic-slide-thumb-rgb-rag-threshold.png
tests/expectations/pil-images-rgb/diagnostic-slide-thumb-rgb-red-pen-filter.png
tests/expectations/pil-images-rgb/diagnostic-slide-thumb-rgb-stretch-contrast.png
tests/expectations/pil-images-rgb/diagnostic-slide-thumb-rgb-to-hed.png
tests/expectations/pil-images-rgb/diagnostic-slide-thumb-rgb-to-hsv.png
tests/expectations/pil-images-rgb/diagnostic-slide-thumb-rgb-to-lab.png
tests/expectations/pil-images-rgb/diagnostic-slide-thumb-ycbcr-adaptive-equalization.png
tests/expectations/pil-images-rgb/diagnostic-slide-thumb-ycbcr-blue-pen-filter.png
tests/expectations/pil-images-rgb/diagnostic-slide-thumb-ycbcr-green-pen-filter.png
tests/expectations/pil-images-rgb/diagnostic-slide-thumb-ycbcr-histogram-equalization.png
tests/expectations/pil-images-rgb/diagnostic-slide-thumb-ycbcr-hysteresis-threshold.png
tests/expectations/pil-images-rgb/diagnostic-slide-thumb-ycbcr-inverted.png
tests/expectations/pil-images-rgb/diagnostic-slide-thumb-ycbcr-kmeans-segmentation.png
tests/expectations/pil-images-rgb/diagnostic-slide-thumb-ycbcr-rag-threshold.png
tests/expectations/pil-images-rgb/diagnostic-slide-thumb-ycbcr-red-pen-filter.png
tests/expectations/pil-images-rgb/diagnostic-slide-thumb-ycbcr-rgb-to-hed.png
tests/expectations/pil-images-rgb/diagnostic-slide-thumb-ycbcr-rgb-to-hsv.png
tests/expectations/pil-images-rgb/diagnostic-slide-thumb-ycbcr-rgb-to-lab.png
tests/expectations/pil-images-rgb/diagnostic-slide-thumb-ycbcr-stretch-contrast.png
tests/expectations/pil-images-rgb/tcga-lung-rgb-eosin-channel.png
tests/expectations/pil-images-rgb/tcga-lung-rgb-hematoxylin-channel.png
tests/expectations/pil-images-rgba/diagnostic-slide-thumb-adaptive-equalization.png
tests/expectations/pil-images-rgba/diagnostic-slide-thumb-blue-pen-filter.png
tests/expectations/pil-images-rgba/diagnostic-slide-thumb-green-pen-filter.png
tests/expectations/pil-images-rgba/diagnostic-slide-thumb-histogram-equalization.png
tests/expectations/pil-images-rgba/diagnostic-slide-thumb-hysteresis-threshold.png
tests/expectations/pil-images-rgba/diagnostic-slide-thumb-inverted.png
tests/expectations/pil-images-rgba/diagnostic-slide-thumb-kmeans-segmentation.png
tests/expectations/pil-images-rgba/diagnostic-slide-thumb-red-pen-filter.png
tests/expectations/pil-images-rgba/diagnostic-slide-thumb-rgba-to-hed.png
tests/expectations/pil-images-rgba/diagnostic-slide-thumb-stretch-contrast.png
tests/expectations/pil-images-rgba/tcga-lung-eosin-channel.png
tests/expectations/pil-images-rgba/tcga-lung-hematoxylin-channel.png
tests/expectations/python-expr/5-x-5-ones.py
tests/expectations/python-expr/5-x-5-x-3-ones.py
tests/expectations/python-expr/5-x-5-x-3-zeros.py
tests/expectations/python-expr/5-x-5-x-4-ones.py
tests/expectations/python-expr/5-x-5-x-4-zeros.py
tests/expectations/python-expr/5-x-5-zeros.py
tests/expectations/python-expr/apply-mask-image-exp1.py
tests/expectations/python-expr/apply-mask-image-exp2.py
tests/expectations/python-expr/apply-mask-image-exp3.py
tests/expectations/python-expr/apply-mask-image-exp4.py
tests/expectations/python-expr/np-to-pil-l.py
tests/expectations/python-expr/np-to-pil-la.py
tests/expectations/python-expr/np-to-pil-rgba.py
tests/expectations/python-expr/slide_properties_dict.py
tests/expectations/python-expr/threshold-to-mask-140.py
tests/expectations/python-expr/threshold-to-mask-160.py
tests/expectations/python-expr/threshold-to-mask-178.py
tests/expectations/python-expr/threshold-to-mask-200.py
tests/expectations/python-expr/threshold-to-mask-37.py
tests/expectations/python-expr/threshold-to-mask-39.py
tests/expectations/svs-images/small-region-svs-resampled-array.npy
tests/expectations/tiles-location-images/cmu-1-small-region-tl-grid-false.png
tests/expectations/tiles-location-images/cmu-1-small-region-tl-grid-true.png
tests/expectations/tiles-location-images/cmu-1-small-region-tl-random-false.png
tests/expectations/tiles-location-images/cmu-1-small-region-tl-random-true.png
tests/expectations/tiles-location-images/cmu-1-small-region-tl-scored-false.png
tests/expectations/tiles-location-images/cmu-1-small-region-tl-scored-true.png
tests/expectations/tiles-location-images/tcga-cr-7395-01a-01-ts1-tl-grid-false.png
tests/expectations/tiles-location-images/tcga-cr-7395-01a-01-ts1-tl-grid-true.png
tests/expectations/tiles-location-images/tcga-cr-7395-01a-01-ts1-tl-random-false.png
tests/expectations/tiles-location-images/tcga-cr-7395-01a-01-ts1-tl-random-true.png
tests/expectations/tiles-location-images/tcga-cr-7395-01a-01-ts1-tl-scored-false-1.png
tests/expectations/tiles-location-images/tcga-cr-7395-01a-01-ts1-tl-scored-false.png
tests/expectations/tiles-location-images/tcga-cr-7395-01a-01-ts1-tl-scored-true.png
tests/fixtures/__init__.py
tests/fixtures/arrays/apply-mask-image-f1.npy
tests/fixtures/arrays/apply-mask-image-f2.npy
tests/fixtures/arrays/apply-mask-image-f3.npy
tests/fixtures/arrays/apply-mask-image-f4.npy
tests/fixtures/arrays/np-to-pil-l.npy
tests/fixtures/arrays/np-to-pil-la.npy
tests/fixtures/arrays/np-to-pil-rgba.npy
tests/fixtures/mask-arrays/apply-mask-image-f1.npy
tests/fixtures/mask-arrays/apply-mask-image-f2.npy
tests/fixtures/mask-arrays/apply-mask-image-f3.npy
tests/fixtures/mask-arrays/apply-mask-image-f4.npy
tests/fixtures/mask-arrays/diagnostic-slide-thumb-hsv-otsu-threshold-mask.npy
tests/fixtures/mask-arrays/diagnostic-slide-thumb-rgb1-hysteresis-threshold-mask.npy
tests/fixtures/mask-arrays/ytma1.npy
tests/fixtures/mask-arrays/ytma2.npy
tests/fixtures/pil-images-gs/diagnostic-slide-thumb-gs.png
tests/fixtures/pil-images-rgb/diagnostic-slide-thumb-hsv.png
tests/fixtures/pil-images-rgb/diagnostic-slide-thumb-rgb.png
tests/fixtures/pil-images-rgb/diagnostic-slide-thumb-ycbcr.png
tests/fixtures/pil-images-rgb/tcga-lung-rgb.png
tests/fixtures/pil-images-rgba/diagnostic-slide-thumb.png
tests/fixtures/pil-images-rgba/tcga-lung.png
tests/fixtures/svs-images/broken.svs
tests/fixtures/svs-images/cmu-1-small-region.svs
tests/fixtures/svs-images/tcga-cr-7395-01a-01-ts1.svs
tests/fixtures/tiles/almost-white-1.png
tests/fixtures/tiles/almost-white-2.png
tests/fixtures/tiles/high-nuclei-score-level0.png
tests/fixtures/tiles/high-nuclei-score-level2.png
tests/fixtures/tiles/high-nuclei-score-red-pen-level1.png
tests/fixtures/tiles/liver-level2-10907-7808-11707-8608.png
tests/fixtures/tiles/liver-level2-20914-13715-21714-14515.png
tests/fixtures/tiles/liver-level2-38626-13514-39426-14315.png
tests/fixtures/tiles/liver-level2-57138-8209-57938-9009.png
tests/fixtures/tiles/low-nuclei-score-level0.png
tests/fixtures/tiles/low-nuclei-score-level1.png
tests/fixtures/tiles/medium-nuclei-score-green-pen-level1.png
tests/fixtures/tiles/medium-nuclei-score-level0.png
tests/fixtures/tiles/medium-nuclei-score-level1-2.png
tests/fixtures/tiles/medium-nuclei-score-level1.png
tests/fixtures/tiles/medium-nuclei-score-level2.png
tests/fixtures/tiles/no-tissue-green-pen.png
tests/fixtures/tiles/no-tissue-line.png
tests/fixtures/tiles/no-tissue-red-pen.png
tests/fixtures/tiles/no-tissue.png
tests/fixtures/tiles/no-tissue2.png
tests/fixtures/tiles/tissue-level0-4302-10273-4814-10785.png
tests/fixtures/tiles/tissue-level0-7352-11762-7864-12274.png
tests/fixtures/tiles/tissue-level2-1784-6289-5880-10386.png
tests/fixtures/tiles/tissue-level2-3000-7666-7096-11763.png
tests/fixtures/tiles/tissue-level2-4640-4649-8736-8746.png
tests/fixtures/tiles/tissue-level2-4760-5241-8856-9338.png
tests/fixtures/tiles/very-low-nuclei-score-level0.png
tests/fixtures/tiles/very-low-nuclei-score-red-pen-level1.png
tests/integration/__init__.py
tests/integration/test_image_filters.py
tests/integration/test_morphological_filters.py
tests/integration/test_scorer.py
tests/integration/test_slide.py
tests/integration/test_tile.py
tests/integration/test_tiler.py
tests/unit/__init__.py
tests/unit/test_compositions.py
tests/unit/test_exceptions.py
tests/unit/test_scorer.py
tests/unit/test_slide.py
tests/unit/test_tile.py
tests/unit/test_tiler.py
tests/unit/test_util.py
tests/unit/data/__init__.py
tests/unit/data/test_data.py
tests/unit/filters/__init__.py
tests/unit/filters/test_image_filters.py
tests/unit/filters/test_morphological_filters.py
tests/unit/filters/test_util.py