Fix cucim dep compatibility

monai/data/image_reader.py

@@ -25,21 +25,17 @@
 from .utils import is_supported_format
 
 if TYPE_CHECKING:
-    import cucim
     import itk  # type: ignore
     import nibabel as nib
-    import openslide
     from nibabel.nifti1 import Nifti1Image
     from PIL import Image as PILImage
 
-    has_itk = has_nib = has_pil = has_cim = has_osl = True
+    has_itk = has_nib = has_pil = True
 else:
     itk, has_itk = optional_import("itk", allow_namespace_pkg=True)
     nib, has_nib = optional_import("nibabel")
     Nifti1Image, _ = optional_import("nibabel.nifti1", name="Nifti1Image")
     PILImage, has_pil = optional_import("PIL.Image")
-    cucim, has_cim = optional_import("cucim")
-    openslide, has_osl = optional_import("openslide")
 
 __all__ = ["ImageReader", "ITKReader", "NibabelReader", "NumpyReader", "PILReader", "WSIReader"]
 
@@ -670,11 +666,9 @@ def __init__(self, reader_lib: str = "OpenSlide"):
         super().__init__()
         self.reader_lib = reader_lib.lower()
         if self.reader_lib == "openslide":
-            if has_osl:
-                self.wsi_reader = openslide.OpenSlide
+            self.wsi_reader, *_ = optional_import("openslide", name="OpenSlide")
         elif self.reader_lib == "cucim":
-            if has_cim:
-                self.wsi_reader = cucim.CuImage
+            self.wsi_reader, *_ = optional_import("cucim", name="CuImage")
         else:
             raise ValueError('`reader_lib` should be either "cuCIM" or "OpenSlide"')
 
@@ -697,11 +691,6 @@ 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):
-            raise ImportError("No module named 'openslide'")
-        if (self.reader_lib == "cucim") and (not has_cim):
-            raise ImportError("No module named 'cucim'")
-
         img_: List = []
 
         filenames: Sequence[str] = ensure_tuple(data)

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

@@ -21,10 +21,11 @@
 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"
+FILE_URL = "https://drive.google.com/uc?id=1sGTKZlJBIz53pfqTxoTqiIQzIoEzHLAe"
 FILE_PATH = os.path.join(os.path.dirname(__file__), "testing_data", "temp_" + os.path.basename(FILE_URL))
 
 HEIGHT = 32914
@@ -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_masked_inference_wsi_dataset.py

@@ -25,7 +25,7 @@
 _, has_cim = optional_import("cucim")
 _, has_osl = optional_import("openslide")
 
-FILE_URL = "http://openslide.cs.cmu.edu/download/openslide-testdata/Generic-TIFF/CMU-1.tiff"
+FILE_URL = "https://drive.google.com/uc?id=1sGTKZlJBIz53pfqTxoTqiIQzIoEzHLAe"
 base_name, extension = os.path.splitext(os.path.basename(FILE_URL))
 FILE_NAME = "temp_" + base_name
 FILE_PATH = os.path.join(os.path.dirname(__file__), "testing_data", FILE_NAME + extension)

tests/test_openslide_reader.py

@@ -24,7 +24,7 @@
 _, has_osl = optional_import("openslide")
 
 
-FILE_URL = "http://openslide.cs.cmu.edu/download/openslide-testdata/Generic-TIFF/CMU-1.tiff"
+FILE_URL = "https://drive.google.com/uc?id=1sGTKZlJBIz53pfqTxoTqiIQzIoEzHLAe"
 FILE_PATH = os.path.join(os.path.dirname(__file__), "testing_data", "temp_" + os.path.basename(FILE_URL))
 
 HEIGHT = 32914

tests/test_patch_wsi_dataset.py

@@ -21,10 +21,11 @@
 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"
+FILE_URL = "https://drive.google.com/uc?id=1sGTKZlJBIz53pfqTxoTqiIQzIoEzHLAe"
 FILE_PATH = os.path.join(os.path.dirname(__file__), "testing_data", "temp_" + os.path.basename(FILE_URL))
 
 TEST_CASE_0 = [

tests/test_smartcache_patch_wsi_dataset.py

@@ -21,9 +21,10 @@
 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_URL = "https://drive.google.com/uc?id=1sGTKZlJBIz53pfqTxoTqiIQzIoEzHLAe"
 FILE_PATH = os.path.join(os.path.dirname(__file__), "testing_data", "temp_" + os.path.basename(FILE_URL))
 
 TEST_CASE_0 = [