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Raise import error for openslide and cuimage #1699

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Merged
bhashemian merged 2 commits into from
Mar 7, 2021
Merged

Raise import error for openslide and cuimage #1699

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Raise import error for openslide and cuimage
bhashemian Mar 5, 2021
6bc94b5
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bhashemian Mar 5, 2021
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7 changes: 6 additions & 1 deletion monai/data/image_reader.py
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Original file line number Diff line number Diff line change
Expand Up @@ -639,7 +639,7 @@ class WSIReader(ImageReader):

"""

def __init__(self, reader_lib: str = "cuClaraImage"):
def __init__(self, reader_lib: str = "OpenSlide"):
super().__init__()
self.reader_lib = reader_lib.lower()
if self.reader_lib == "openslide":
Expand Down Expand Up @@ -672,6 +672,11 @@ def read(self, data: Union[Sequence[str], str, np.ndarray], **kwargs):
data: file name or a list of file names to read.

"""
if (self.reader_lib == "openslide") and (not has_osl):

@wyli wyli Mar 5, 2021

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could have these logics even earlier for example between line 646 and 652?

@bhashemian bhashemian Mar 5, 2021

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Actually no, Nic is instantiating this class in LoadImage, so the error shouldn't be raised in __init__ (it used to be raise without having has_osl and has_cux). The first place that it can be raised here.

I agree that the best place would be when the class is instantiating but for that purpose LoadImage need to be changed:

MONAI/monai/transforms/io/array.py

Line 93 in 6bc94b5

self.readers: List[ImageReader] = [ITKReader(), NumpyReader(), PILReader(), NibabelReader(), WSIReader()]

@wyli wyli Mar 7, 2021

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sure you're right!

(@Nic-Ma I'm approving this for now, perhaps we need another iteration to revise the base API?)

raise ImportError("No module named 'openslide'")
elif (self.reader_lib == "cuclaraimage") and (not has_cux):
raise ImportError("No module named 'cuimage'")

img_: List = []

filenames: Sequence[str] = ensure_tuple(data)
Expand Down