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2baa344
Redesign BaseWSIReader, WSIReader, CuCIMWSIReader
bhashemian Apr 12, 2022
e46fea0
Add unittests for WSIReader
bhashemian Apr 12, 2022
f946a63
Add image mode for output validation
bhashemian Apr 12, 2022
9b41019
Merge branch 'dev' into new-wsireader
bhashemian Apr 12, 2022
9c15ea3
Update docs
bhashemian Apr 13, 2022
e004538
Update references to new WSIReader
bhashemian Apr 13, 2022
df0a61e
Remove legacy WSIReader
bhashemian Apr 13, 2022
b64c087
Update unittests
bhashemian Apr 13, 2022
7f09e73
Update docs
bhashemian Apr 13, 2022
d95e1c2
sort imports
bhashemian Apr 13, 2022
025376b
Clean up imports
bhashemian Apr 13, 2022
3e6fb27
Update docstrings
bhashemian Apr 13, 2022
b8a2444
Update docs and docstrings
bhashemian Apr 13, 2022
0268a03
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Apr 13, 2022
f2b14aa
Fix a typo
bhashemian Apr 13, 2022
aed0ac5
Remove redundant checking
bhashemian Apr 13, 2022
272d11f
Merge branch 'new-wsireader' of github.com:drbeh/MONAI into new-wsire…
bhashemian Apr 13, 2022
ae4ff17
Update read and other methods
bhashemian Apr 14, 2022
e0bad98
Merge branch 'pathology' of github.com:Project-MONAI/MONAI into new-w…
bhashemian Apr 14, 2022
e5a7a18
Update wsireader to support multi image and update docstrings
bhashemian Apr 18, 2022
da6b675
Make workaround for CuImage objects
bhashemian Apr 18, 2022
1ed8154
Add unittests for multi image reading
bhashemian Apr 18, 2022
77f8747
Update a note about cucim
bhashemian Apr 18, 2022
36e5b17
Update type hints and docstrings
bhashemian Apr 19, 2022
0328fe6
Merge branch 'pathology' of github.com:Project-MONAI/MONAI into new-w…
bhashemian Apr 19, 2022
78340a9
Redesign whole slide image reading (#4107)
bhashemian Apr 19, 2022
a0ddd3f
Merge branch 'pathology' of github.com:Project-MONAI/MONAI into new-w…
bhashemian Apr 19, 2022
a592482
Bring back previous WSIReader for backward compatibility
bhashemian Apr 19, 2022
41337db
Revert to legacy WSIReader
bhashemian Apr 19, 2022
daec9c7
Rename test files
bhashemian Apr 19, 2022
124477e
Rename test files
bhashemian Apr 19, 2022
5aa59b3
Merge branch 'dev' into new-wsireader
bhashemian Apr 19, 2022
f848288
Merge branch 'dev' into new-wsireader
Nic-Ma Apr 19, 2022
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13 changes: 13 additions & 0 deletions docs/source/data.rst
Original file line number Diff line number Diff line change
Expand Up @@ -152,11 +152,24 @@ PILReader
.. autoclass:: PILReader
:members:

Whole slide image reader
------------------------

BaseWSIReader
~~~~~~~~~~~~~
.. autoclass:: BaseWSIReader
:members:

WSIReader
~~~~~~~~~
.. autoclass:: WSIReader
:members:

CuCIMWSIReader
~~~~~~~~~~~~~~
.. autoclass:: CuCIMWSIReader
:members:

Image writer
------------

Expand Down
3 changes: 2 additions & 1 deletion monai/data/__init__.py
Original file line number Diff line number Diff line change
Expand Up @@ -34,7 +34,7 @@
from .folder_layout import FolderLayout
from .grid_dataset import GridPatchDataset, PatchDataset, PatchIter, PatchIterd
from .image_dataset import ImageDataset
from .image_reader import ImageReader, ITKReader, NibabelReader, NumpyReader, PILReader, WSIReader
from .image_reader import ImageReader, ITKReader, NibabelReader, NumpyReader, PILReader
from .image_writer import (
SUPPORTED_WRITERS,
ImageWriter,
Expand Down Expand Up @@ -87,3 +87,4 @@
worker_init_fn,
zoom_affine,
)
from .wsi_reader import BaseWSIReader, CuCIMWSIReader, WSIReader
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