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Commits

Commits on Nov 16, 2021

improve docstrings

kheffah
authored and
alessiamarcolini
committed
Apply suggestions from code review

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

kheffah
authored and
alessiamarcolini
committed
linting and more descriptive docs

kheffah
authored and
alessiamarcolini
committed
handle if unknown mpp despite using large_image

kheffah
authored and
alessiamarcolini
committed
add use_largeimage param documentation

kheffah
authored and
alessiamarcolini
committed
get rid of extra magnif variable in _resample

kheffah
authored and
alessiamarcolini
committed
add docstring for base_mpp

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

kheffah
authored and
alessiamarcolini
committed
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
authored and
alessiamarcolini
committed
reorder exceptions alphabetically

kheffah
authored and
alessiamarcolini
committed
linting and better naming

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

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

kheffah
authored and
alessiamarcolini
committed
fix additional unit tests for slide

kheffah
authored and
alessiamarcolini
committed
additional unit tests for slide

kheffah
authored and
alessiamarcolini
committed
address comments from code review

kheffah
authored and
alessiamarcolini
committed
reorder slide and tiler methods alphabetically for consistency

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

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

kheffah
authored and
alessiamarcolini
committed
minor style change for linting

kheffah
authored and
alessiamarcolini
committed
minor style change for linting

kheffah
authored and
alessiamarcolini
committed
minor style change for linting

kheffah
authored and
alessiamarcolini
committed
Unit tests for tiler modules with large_image usage

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

kheffah
authored and
alessiamarcolini
committed
Unit tests for Slide module with large_image usage

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

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

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

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

kheffah
authored and
alessiamarcolini
committed
[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
authored and
alessiamarcolini
committed

Commits on Nov 15, 2021

stylistic changes from code review

kheffah
authored and
alessiamarcolini
committed
Fix RAG threshold returns

kheffah
and
alessiamarcolini
committed