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Support fetching exact MPP resolutions#301

Merged

alessiamarcolini merged 47 commits intomasterfrom

Nov 16, 2021

Commits on Nov 16, 2021

[WIP] - use large_image as an optional dependency to handle a wide range of wsi formats beyond openslide and to accomodate fetching exact MPP resolutions rather than being restricted of internal re…

kheffah
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alessiamarcolini
committed
[WIP] - allow control of large_image usage for Slide even if large_image is installed

kheffah
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alessiamarcolini
committed
[WIP] - allow control of large_image usage for Slide even if large_image is installed

kheffah
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alessiamarcolini
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[WIP] - fix testing now that large_image usage is an option

kheffah
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alessiamarcolini
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revert tests/expectations/svs-images/small-region-svs-resampled-array.npy -- let's change the default up and downsampling method in a future pull request instead of doign two things at once. Turns …

kheffah
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alessiamarcolini
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OK now all tests pass without large_image usage. next, we'll incorporate tests for large_image usage

kheffah
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alessiamarcolini
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Unit tests for Slide module with large_image usage

kheffah
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alessiamarcolini
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[WIP] - Unit tests for tiler modules with large_image usage

kheffah
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alessiamarcolini
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Unit tests for tiler modules with large_image usage

kheffah
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alessiamarcolini
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minor style change for linting

kheffah
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alessiamarcolini
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minor style change for linting

kheffah
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alessiamarcolini
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minor style change for linting

kheffah
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alessiamarcolini
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catch miscellaneous errors from openslide other than PIL.UnidentifiedImageError

kheffah
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alessiamarcolini
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unit tests assume large_image is installed to make sure any future development triggers all tests

kheffah
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alessiamarcolini
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reorder slide and tiler methods alphabetically for consistency

kheffah
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alessiamarcolini
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address comments from code review

kheffah
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alessiamarcolini
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additional unit tests for slide

kheffah
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alessiamarcolini
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fix additional unit tests for slide

kheffah
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alessiamarcolini
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better exception messages when large_image is needed for slide module

kheffah
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alessiamarcolini
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use getters and setters for updating tile size depening on slide if mpp

kheffah
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alessiamarcolini
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linting and better naming

kheffah
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alessiamarcolini
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reorder exceptions alphabetically

kheffah
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alessiamarcolini
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instead of using exception types that dont really fit, create a MayneedLargeImage exception to use with slide whenever large_image may be needed. This is also a bug fix, because it prevents ignorin…

kheffah
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alessiamarcolini
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bug fix: instead of catching all ValueErrors in _tiles_generator when tries slide.extract_tile, only catch the specific TileSizeOrCoordinatesError class.

kheffah
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alessiamarcolini
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add docstring for base_mpp

kheffah
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alessiamarcolini
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get rid of extra magnif variable in _resample

kheffah
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alessiamarcolini
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fix extract signature to be compliant with the abstractmethod

ernestoarbitrio
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alessiamarcolini
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add large-image in CI

ernestoarbitrio
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alessiamarcolini
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test fix python3.6 on the CI

ernestoarbitrio
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alessiamarcolini
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simplyfy all(tile_size[i] == j for i, j in enumerate(image.size))

ernestoarbitrio
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alessiamarcolini
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add use_largeimage param documentation

kheffah
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alessiamarcolini
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handle if unknown mpp despite using large_image

kheffah
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alessiamarcolini
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linting and more descriptive docs

kheffah
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alessiamarcolini
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Only resize tiles fetched by mpp if within certain tolerance of requested tile_size. Testing not yet complete

kheffah
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alessiamarcolini
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Try to reach full test coverage. Add test_extract_tiles_at_mpp_not_respecting_given_tile_size and test_raise_error_if_mpp_and_discordant_tile_size.

kheffah
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alessiamarcolini
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Apply suggestions from code review

kheffah
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alessiamarcolini
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improve docstrings

kheffah
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alessiamarcolini
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fix broken tests

ernestoarbitrio
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alessiamarcolini
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address alessia's comments and fix dirty tests

ernestoarbitrio
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alessiamarcolini
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refactor tiler tile_size and pixel_overlap

ernestoarbitrio
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alessiamarcolini
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tiny slide.py reformat

ernestoarbitrio
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alessiamarcolini
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fix flake8 failures

ernestoarbitrio
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alessiamarcolini
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fix other weird tests

ernestoarbitrio
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alessiamarcolini
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fix lgtm alert

ernestoarbitrio
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alessiamarcolini
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address alessia's comments pt 2

ernestoarbitrio
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alessiamarcolini
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address alessia's comments pt3

ernestoarbitrio
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alessiamarcolini
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Fix error message
alessiamarcolini
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