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Update cucim dependency for cucim transforms #2987

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bhashemian wants to merge 8 commits into from
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Update cucim dependency for cucim transforms #2987

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9229548
Update cucim dependency for cucim transforms
bhashemian Sep 21, 2021
0a4da1c
Skip rgba test if cucim>0.19.0
bhashemian Sep 21, 2021
45750c9
Fix format
bhashemian Sep 21, 2021
c35a9dc
Update skip
bhashemian Sep 21, 2021
3071e01
has_cim to has_cucim
bhashemian Sep 22, 2021
d17ab94
fall back to openslide
wyli Sep 22, 2021
ca3a094
update versions
wyli Sep 22, 2021
a102ab7
skip tests when cucim is not available
wyli Sep 22, 2021
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4 changes: 3 additions & 1 deletion monai/data/image_reader.py
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Expand Up @@ -673,8 +673,10 @@ def __init__(self, reader_lib: str = "OpenSlide"):
if has_osl:
self.wsi_reader = openslide.OpenSlide
elif self.reader_lib == "cucim":
if has_cim:
if has_cim and hasattr(cucim, "CuImage"):
self.wsi_reader = cucim.CuImage
else:
raise ImportError("Please check the cuCIM installation.")
else:
raise ValueError('`reader_lib` should be either "cuCIM" or "OpenSlide"')

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2 changes: 1 addition & 1 deletion requirements-dev.txt
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Expand Up @@ -31,7 +31,7 @@ Sphinx==3.5.3
recommonmark==0.6.0
sphinx-autodoc-typehints==1.11.1
sphinx-rtd-theme==0.5.2
cucim~=0.19.0; platform_system == "Linux"
cucim>=21.8.2; platform_system == "Linux"
openslide-python==1.1.2
pandas
requests
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4 changes: 2 additions & 2 deletions setup.cfg
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Expand Up @@ -40,7 +40,7 @@ all =
tqdm>=4.47.0
lmdb
psutil
cucim~=0.19.0
cucim>=21.8.2
openslide-python==1.1.2
pandas
einops
Expand Down Expand Up @@ -68,7 +68,7 @@ lmdb =
psutil =
psutil
cucim =
cucim~=0.19.0
cucim>=21.8.2
openslide =
openslide-python==1.1.2
pandas =
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6 changes: 4 additions & 2 deletions tests/test_cuimage_reader.py
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Expand Up @@ -21,7 +21,8 @@
from monai.data.image_reader import WSIReader
from monai.utils import optional_import

_, has_cim = optional_import("cucim")
cucim, has_cucim = optional_import("cucim")
has_cucim = has_cucim and hasattr(cucim, "CuImage")
PILImage, has_pil = optional_import("PIL.Image")

FILE_URL = "http://openslide.cs.cmu.edu/download/openslide-testdata/Generic-TIFF/CMU-1.tiff"
Expand Down Expand Up @@ -83,7 +84,7 @@


class TestCuCIMReader(unittest.TestCase):
@skipUnless(has_cim, "Requires CuCIM")
@skipUnless(has_cucim, "Requires CuCIM")
def setUp(self):
download_url(FILE_URL, FILE_PATH, "5a3cfd4fd725c50578ddb80b517b759f")

Expand Down Expand Up @@ -112,6 +113,7 @@ def test_read_patches(self, file_path, patch_info, expected_img):

@parameterized.expand([TEST_CASE_RGB_0, TEST_CASE_RGB_1])
@skipUnless(has_pil, "Requires PIL")
@skipUnless(has_cucim and cucim.__version__ == "0.19.0", "Skipped for cicum>0.19.0")
def test_read_rgba(self, img_expected):
image = {}
reader = WSIReader("cuCIM")
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3 changes: 2 additions & 1 deletion tests/test_lesion_froc.py
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Expand Up @@ -19,7 +19,8 @@
from monai.apps.pathology.metrics import LesionFROC
from monai.utils import optional_import

_, has_cucim = optional_import("cucim")
_cucim, has_cucim = optional_import("cucim")
has_cucim = has_cucim and hasattr(_cucim, "CuImage")
_, has_skimage = optional_import("skimage.measure")
_, has_sp = optional_import("scipy.ndimage")
PILImage, has_pil = optional_import("PIL.Image")
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3 changes: 2 additions & 1 deletion tests/test_patch_wsi_dataset.py
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Expand Up @@ -21,7 +21,8 @@
from monai.apps.utils import download_url
from monai.utils import optional_import

_, has_cim = optional_import("cucim")
_cucim, has_cim = optional_import("cucim")
has_cim = has_cim and hasattr(_cucim, "CuImage")
_, has_osl = optional_import("openslide")

FILE_URL = "http://openslide.cs.cmu.edu/download/openslide-testdata/Generic-TIFF/CMU-1.tiff"
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3 changes: 2 additions & 1 deletion tests/test_smartcache_patch_wsi_dataset.py
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Expand Up @@ -21,7 +21,8 @@
from monai.apps.utils import download_url
from monai.utils import optional_import

_, has_cim = optional_import("cucim")
_cucim, has_cim = optional_import("cucim")
has_cim = has_cim and hasattr(_cucim, "CuImage")

FILE_URL = "http://openslide.cs.cmu.edu/download/openslide-testdata/Generic-TIFF/CMU-1.tiff"
FILE_PATH = os.path.join(os.path.dirname(__file__), "testing_data", "temp_" + os.path.basename(FILE_URL))
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