fixes cucim compatibility

Signed-off-by: Wenqi Li <[email protected]>

Author: wyli

monai/data/image_reader.py

@@ -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"')
 

requirements-dev.txt

@@ -31,8 +31,10 @@ 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
+imagecodecs; platform_system == "Linux"
+tifffile; platform_system == "Linux"
 pandas
 requests
 einops

setup.cfg

@@ -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
@@ -68,7 +68,7 @@ lmdb =
 psutil =
     psutil
 cucim =
-    cucim~=0.19.0
+    cucim>=21.8.2
 openslide =
     openslide-python==1.1.2
 pandas =

tests/test_cuimage_reader.py

@@ -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"
@@ -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")
 
@@ -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")

tests/test_lesion_froc.py

@@ -19,18 +19,19 @@
 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")
+imwrite, has_tif = optional_import("tifffile", name="imwrite")
 
 
 def save_as_tif(filename, array):
     array = array[::-1, ...]  # Upside-down
-    img = PILImage.fromarray(array)
     if not filename.endswith(".tif"):
         filename += ".tif"
-    img.save(os.path.join("tests", "testing_data", filename))
+    file_path = os.path.join("tests", "testing_data", filename)
+    imwrite(file_path, array, compress="jpeg", tile=(16, 16))
 
 
 def around(val, interval=3):
@@ -301,7 +302,7 @@ class TestEvaluateTumorFROC(unittest.TestCase):
     @skipUnless(has_cucim, "Requires cucim")
     @skipUnless(has_skimage, "Requires skimage")
     @skipUnless(has_sp, "Requires scipy")
-    @skipUnless(has_pil, "Requires PIL")
+    @skipUnless(has_tif, "Requires tifffile")
     def setUp(self):
         prepare_test_data()
 

tests/test_patch_wsi_dataset.py

@@ -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"

tests/test_smartcache_patch_wsi_dataset.py

@@ -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))