Support fetching exact MPP resolutions #301
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ernestoarbitrio
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Aug 5, 2021
@ernestoarbitrio Thanks, all addressed. |
ernestoarbitrio
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ernestoarbitrio
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Aug 9, 2021
alessiamarcolini
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Aug 10, 2021
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This pull request introduces 1 alert when merging 7c8c93b into 6625b40 - view on LGTM.com new alerts:
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alessiamarcolini
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Aug 30, 2021
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alessiamarcolini
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Aug 30, 2021
ernestoarbitrio
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Aug 31, 2021
…edLargeImage exception to use with slide whenever large_image may be needed. This is also a bug fix, because it prevents ignoring the exception when the catch-call except ValueError is invoked in like 503 in GridTiler
… tries slide.extract_tile, only catch the specific TileSizeOrCoordinatesError class.
…sted tile_size. Testing not yet complete
…specting_given_tile_size and test_raise_error_if_mpp_and_discordant_tile_size.
Co-authored-by: Alessia Marcolini <98marcolini@gmail.com>
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This PR supports fetching exact micron-per-pixel (MPP) resolutions from the WSI using large_image as an optional dependency. The rationale here is that different WSIs have different encodings for the internal levels and different scan resolutions.
large_imagehandles this by parsing the internal metadata for a wide range of formats beyond those supported by openslide and interpolating between levels when needed to fetch exact MPP resolutions independent of the slide format, scan resolution, manufacturer etc.If the user doesn't have
large_imageinstalled but asks for an mpp resolution, they are prompted to install it.@alessiamarcolini @ernestoarbitrio @nicolebussola This is the key feature from the forked version. I added tests for (hopefully) everything, but they are skipped if
large_imageis not installed. So if you'd like all the tests to run to maintain coverage, I suggest adding thelarge_imageinstallation to test environment.Description
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