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Allow SlideData to use existing h5path files #337

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Allow SlideData to use existing h5path files #337

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cab0409
Store masks as bools
tddough98 Oct 4, 2022
6e6f802
Use dtype from SlideData constructor
tddough98 Oct 4, 2022
6dbf069
Merge branch 'merge-master' into change-dtypes
tddough98 Oct 14, 2022
be5ed26
Update h5path documentation
tddough98 Oct 14, 2022
8b2b202
Enable running pipelines on existing tiles
tddough98 Oct 20, 2022
6a08690
Debug tests
tddough98 Oct 20, 2022
201b60d
Debug tests
tddough98 Oct 20, 2022
40e8260
Debug tests
tddough98 Oct 20, 2022
ba9cfe0
Add test to exercise pipeline on h5path
tddough98 Oct 20, 2022
f7814ac
Merge branch 'change-dtypes' into use-existing-tiles
tddough98 Oct 20, 2022
6d4cc11
Debug test
tddough98 Oct 20, 2022
84a5071
Fix tile behavior
tddough98 Oct 20, 2022
1ea497f
Remove private _add_tiles
tddough98 Oct 20, 2022
8572d49
Fix syntax
tddough98 Oct 20, 2022
98b611b
Remove pdb
tddough98 Oct 20, 2022
c7c28a8
Add missing not
tddough98 Oct 20, 2022
8c78593
Revert making all masks boolean
tddough98 Oct 20, 2022
27e3db8
Merge branch 'change-dtypes' into use-existing-tiles
tddough98 Oct 20, 2022
bd3b154
Change test to not expect KeyError
tddough98 Oct 20, 2022
b0b3b98
Merge branch 'load-data-in-workers' into use-existing-tiles
tddough98 Oct 25, 2022
0662001
Add noqa: F811 for _caplog
tddough98 Oct 25, 2022
9d2bc28
Merge branch 'merge-master' into use-existing-tiles
tddough98 Oct 25, 2022
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Update h5path documentation
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@tddough98
tddough98 committed Oct 14, 2022
commit be5ed26f852a49ac6098e1f1c94fd797d1b49c72
5 changes: 4 additions & 1 deletion docs/source/h5path.rst
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Expand Up @@ -141,7 +141,10 @@ Whole-slide masks are stored in the ``masks/`` Group. All masks are enforced to
However, when running a pipeline, these masks are moved to the tile-level and stored within the tile groups.
The slide-level masks are therefore not saved when calling :meth:`SlideData.write() <pathml.core.SlideData.write>`.

We use ``float16`` as the data type for all Datasets.
By default, we use ``float16`` as the data type for all Datasets and HDF5's
`ENUM type <https://docs.h5py.org/en/stable/special.html#enumerated-types>`
for masks, which are stored as 8-bit integers. Changing the `dtype` in
the Slide constructor changes the data type used to store images.

.. note:: Be aware that the ``h5path`` format specification may change between major versions

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