.coveragerc
.pre-commit-config.yaml
AUTHORS
CONTRIBUTING.md
LICENSE.txt
MANIFEST.in
Makefile
README.md
bandit.yaml
pyproject.toml
readthedocs.yml
requirements-dev.txt
requirements.txt
setup.cfg
setup.py
histolab/__init__.py
histolab/exceptions.py
histolab/masks.py
histolab/scorer.py
histolab/slide.py
histolab/tile.py
histolab/tiler.py
histolab/types.py
histolab/util.py
histolab.egg-info/PKG-INFO
histolab.egg-info/SOURCES.txt
histolab.egg-info/dependency_links.txt
histolab.egg-info/requires.txt
histolab.egg-info/top_level.txt
histolab.egg-info/zip-safe
histolab/data/__init__.py
histolab/data/_registry.py
histolab/data/cmu_small_region.svs
histolab/filters/__init__.py
histolab/filters/compositions.py
histolab/filters/image_filters.py
histolab/filters/image_filters_functional.py
histolab/filters/morphological_filters.py
histolab/filters/morphological_filters_functional.py
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/arrays/diagnostic-slide-thumb-rgb-to-hed.npy
tests/expectations/arrays/diagnostic-slide-thumb-rgb-to-hsv.npy
tests/expectations/arrays/diagnostic-slide-thumb-rgb-to-lab.npy
tests/expectations/arrays/diagnostic-slide-thumb-rgb-to-od.npy
tests/expectations/arrays/tcga-lung-rgb-to-od.npy
tests/expectations/mask-arrays/biggest-tissue-box-cmu-1-small-region.npy
tests/expectations/mask-arrays/biggest-tissue-box-kidney-48-5.npy
tests/expectations/mask-arrays/biggest-tissue-box-tcga-cr-7395.npy
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-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-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/regions-to-binary-mask.npy
tests/expectations/mask-arrays/tcga-lung-rgb-pen-marks-mask.npy
tests/expectations/mask-arrays/tissue-mask-cmu-1-small-region.npy
tests/expectations/mask-arrays/tissue-mask-diagnostic-slide-thumb-rgb.npy
tests/expectations/mask-arrays/tissue-mask-kidney-48-5.npy
tests/expectations/mask-arrays/tissue-mask-tcga-cr-7395.npy
tests/expectations/mask-arrays/tissue-mask-tcga-lung-rgb.npy
tests/expectations/mask-arrays/tissue-mask-tissue-level2-3000-7666-7096-11763.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/mask-location-images/cmu-1-small-region-bbox-location-tissue-mask-false.png
tests/expectations/mask-location-images/cmu-1-small-region-bbox-location-tissue-mask-true.png
tests/expectations/mask-location-images/cmu-1-small-region-tissue-location-tissue-mask-false.png
tests/expectations/mask-location-images/cmu-1-small-region-tissue-location-tissue-mask-true.png
tests/expectations/mask-location-images/tcga-cr-7395-01a-01-ts1-bbox-location-tissue-mask-false.png
tests/expectations/mask-location-images/tcga-cr-7395-01a-01-ts1-bbox-location-tissue-mask-true.png
tests/expectations/mask-location-images/tcga-cr-7395-01a-01-ts1-tissue-location-tissue-mask-false.png
tests/expectations/mask-location-images/tcga-cr-7395-01a-01-ts1-tissue-location-tissue-mask-true.png
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-local-equalization.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-gs-kmeans-segmentation.png
tests/expectations/pil-images-rgb/diagnostic-slide-thumb-gs-rag-threshold.png
tests/expectations/pil-images-rgb/diagnostic-slide-thumb-hed-to-rgb.png
tests/expectations/pil-images-rgb/diagnostic-slide-thumb-lab-to-rgb.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-hsv.png
tests/expectations/pil-images-rgb/tcga-lung-rgb-dab-channel.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-dab-channel.png
tests/expectations/pil-images-rgba/tcga-lung-eosin-channel.png
tests/expectations/pil-images-rgba/tcga-lung-hematoxylin-channel.png
tests/expectations/pil-images-rgba/tcga-lung-rgb-to-od.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-BTB-false-512x512.png
tests/expectations/tiles-location-images/cmu-1-small-region-tl-grid-TM-false-128x120.png
tests/expectations/tiles-location-images/cmu-1-small-region-tl-grid-TM-true-128x120.png
tests/expectations/tiles-location-images/cmu-1-small-region-tl-grid-TM-true-128x128.png
tests/expectations/tiles-location-images/cmu-1-small-region-tl-random-BTB-false-512x512.png
tests/expectations/tiles-location-images/cmu-1-small-region-tl-random-TM-true-512x530.png
tests/expectations/tiles-location-images/cmu-1-small-region-tl-score-false-512x512.png
tests/expectations/tiles-location-images/cmu-1-small-region-tl-score-true-120x128.png
tests/expectations/tiles-location-images/external-cmu-3-grid-BTB-false-512x512.png
tests/expectations/tiles-location-images/external-cmu-3-grid-TM-false-512x512.png
tests/expectations/tiles-location-images/kidney-48-5-grid-TM-false-20x20.png
tests/expectations/tiles-location-images/kidney-48-5-grid-TM-true-10x10.png
tests/expectations/tiles-location-images/kidney-48-5-grid-TM-true-15x10.png
tests/expectations/tiles-location-images/kidney-48-5-random-TM-false-20x20.png
tests/expectations/tiles-location-images/kidney-48-5-random-TM-true-10x10.png
tests/expectations/tiles-location-images/tcga-cr-7395-01a-01-ts1-tl-grid-BTB-f-512x512.png
tests/expectations/tiles-location-images/tcga-cr-7395-01a-01-ts1-tl-grid-TM-f-512x550.png
tests/expectations/tiles-location-images/tcga-cr-7395-01a-01-ts1-tl-grid-TM-true-128x128.png
tests/expectations/tiles-location-images/tcga-cr-7395-01a-01-ts1-tl-random-BTB-f-128x530.png
tests/expectations/tiles-location-images/tcga-cr-7395-01a-01-ts1-tl-random-TM-f-512x512.png
tests/expectations/tiles-location-images/tcga-cr-7395-01a-01-ts1-tl-random-TM-t-128x128.png
tests/expectations/tiles-location-images/tcga-cr-7395-01a-01-ts1-tl-score-f-512x512.png
tests/expectations/tiles-location-images/tcga-cr-7395-01a-01-ts1-tl-score-f-512x530.png
tests/expectations/tiles-location-images/tcga-cr-7395-01a-01-ts1-tl-score-t-128x128.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/diagnostic-slide-thumb-hed.npy
tests/fixtures/arrays/diagnostic-slide-thumb-lab.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-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-rgb.png
tests/fixtures/pil-images-rgb/tcga-green-pen.png
tests/fixtures/pil-images-rgb/tcga-lung-rgb.png
tests/fixtures/pil-images-rgb/tcga-red-pen.png
tests/fixtures/pil-images-rgb/wsi-blue-pen.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/tiff-images/kidney-48-5.tif
tests/fixtures/tiles/almost-white-1.png
tests/fixtures/tiles/almost-white-2.png
tests/fixtures/tiles/almost-white-ihc.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/kidney-ihc-level0-310-500-360-530.png
tests/fixtures/tiles/kidney-ihc-level0-330-480-380-510.png
tests/fixtures/tiles/kidney-ihc-level0-340-520-390-550.png
tests/fixtures/tiles/kidney-ihc-level0-350-530-360-540.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_masks.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/integration/test_util.py
tests/unit/__init__.py
tests/unit/test_compositions.py
tests/unit/test_exceptions.py
tests/unit/test_masks.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