Update WSIReader with cuCIM

.github/workflows/pythonapp.yml

@@ -83,6 +83,10 @@ jobs:
         python -m pip install torch==1.8.0+cpu torchvision==0.9.0+cpu -f https://download.pytorch.org/whl/torch_stable.html
         # min. requirements for windows instances
         python -c "f=open('requirements-dev.txt', 'r'); txt=f.readlines(); f.close(); print(txt); f=open('requirements-dev.txt', 'w'); f.writelines(txt[1:12]); f.close()"
+    - if: runner.os == 'macos'
+      name: Remove cucim installation (Mac only)
+      run: |
+        python -c "f=open('requirements-dev.txt', 'r'); txt=f.readlines(); f.close(); print(txt); f=open('requirements-dev.txt', 'w'); f.writelines([t for t in txt if not t.startswith('cucim')]); f.close()"
     - name: Install the dependencies
       run: |
         python -m pip install torch==1.8.0 torchvision==0.9.0

docs/requirements.txt

@@ -4,6 +4,7 @@ pytorch-ignite==0.4.4
 numpy>=1.17
 itk>=5.0
 nibabel
+cucim==0.18.0
 openslide-python==1.1.2
 parameterized
 scikit-image>=0.14.2

monai/data/image_reader.py

@@ -25,22 +25,22 @@
 from .utils import is_supported_format
 
 if TYPE_CHECKING:
-    import cuimage
+    import cucim
     import itk  # type: ignore
     import nibabel as nib
     import openslide
     from itk import Image  # type: ignore
     from nibabel.nifti1 import Nifti1Image
     from PIL import Image as PILImage
 
-    has_itk = has_nib = has_pil = has_cux = has_osl = True
+    has_itk = has_nib = has_pil = has_cim = has_osl = True
 else:
     itk, has_itk = optional_import("itk", allow_namespace_pkg=True)
     Image, _ = optional_import("itk", allow_namespace_pkg=True, name="Image")
     nib, has_nib = optional_import("nibabel")
     Nifti1Image, _ = optional_import("nibabel.nifti1", name="Nifti1Image")
     PILImage, has_pil = optional_import("PIL.Image")
-    cuimage, has_cux = optional_import("cuimage")
+    cucim, has_cim = optional_import("cucim")
     openslide, has_osl = optional_import("openslide")
 
 __all__ = ["ImageReader", "ITKReader", "NibabelReader", "NumpyReader", "PILReader", "WSIReader"]
@@ -638,8 +638,7 @@ class WSIReader(ImageReader):
     Read whole slide imaging and extract patches.
 
     Args:
-        reader_lib: backend library to load the images, available options: "OpenSlide" or "cuClaraImage".
-            TODO: `cuClaraImage` package is unavailable so far, will enable the support later.
+        reader_lib: backend library to load the images, available options: "OpenSlide" or "cuCIM".
 
     """
 
@@ -649,11 +648,11 @@ def __init__(self, reader_lib: str = "OpenSlide"):
         if self.reader_lib == "openslide":
             if has_osl:
                 self.wsi_reader = openslide.OpenSlide
-        elif self.reader_lib == "cuclaraimage":
-            if has_cux:
-                self.wsi_reader = cuimage.CuImage
+        elif self.reader_lib == "cucim":
+            if has_cim:
+                self.wsi_reader = cucim.CuImage
         else:
-            raise ValueError('`reader_lib` should be either "cuClaraImage" or "OpenSlide"')
+            raise ValueError('`reader_lib` should be either "cuCIM" or "OpenSlide"')
 
     def verify_suffix(self, filename: Union[Sequence[str], str]) -> bool:
         """
@@ -676,8 +675,8 @@ def read(self, data: Union[Sequence[str], str, np.ndarray], **kwargs):
         """
         if (self.reader_lib == "openslide") and (not has_osl):
             raise ImportError("No module named 'openslide'")
-        elif (self.reader_lib == "cuclaraimage") and (not has_cux):
-            raise ImportError("No module named 'cuimage'")
+        elif (self.reader_lib == "cucim") and (not has_cim):
+            raise ImportError("No module named 'cucim'")
 
         img_: List = []
 

requirements-dev.txt

@@ -30,4 +30,5 @@ Sphinx==3.3.0
 recommonmark==0.6.0
 sphinx-autodoc-typehints==1.11.1
 sphinx-rtd-theme==0.5.0
+cucim==0.18.0
 openslide-python==1.1.2

setup.cfg

@@ -32,6 +32,7 @@ all =
     torchvision
     itk>=5.0
     tqdm>=4.47.0
+    cucim==0.18.0
     openslide-python==1.1.2
 nibabel =
     nibabel
@@ -55,6 +56,8 @@ lmdb =
     lmdb
 psutil =
     psutil
+cucim =
+    cucim==0.18.0
 openslide =
     openslide-python==1.1.2
 

tests/test_cuimage_reader.py

@@ -10,7 +10,7 @@
 from monai.data.image_reader import WSIReader
 from monai.utils import optional_import
 
-_, has_cui = optional_import("cuimage")
+_, has_cim = optional_import("cucim")
 
 
 FILE_URL = "http://openslide.cs.cmu.edu/download/openslide-testdata/Generic-TIFF/CMU-1.tiff"
@@ -61,31 +61,31 @@
 ]
 
 
-class TestCuClaraImageReader(unittest.TestCase):
+class TestCuCIMReader(unittest.TestCase):
     @parameterized.expand([TEST_CASE_0])
-    @skipUnless(has_cui, "Requires CuClaraImage")
+    @skipUnless(has_cim, "Requires CuCIM")
     def test_read_whole_image(self, file_url, expected_shape):
         filename = self.camelyon_data_download(file_url)
-        reader = WSIReader("CuClaraImage")
+        reader = WSIReader("cuCIM")
         img_obj = reader.read(filename)
         img = reader.get_data(img_obj)[0]
         self.assertTupleEqual(img.shape, expected_shape)
 
     @parameterized.expand([TEST_CASE_1, TEST_CASE_2])
-    @skipUnless(has_cui, "Requires CuClaraImage")
+    @skipUnless(has_cim, "Requires cuCIM")
     def test_read_region(self, file_url, patch_info, expected_img):
         filename = self.camelyon_data_download(file_url)
-        reader = WSIReader("CuClaraImage")
+        reader = WSIReader("cuCIM")
         img_obj = reader.read(filename)
         img = reader.get_data(img_obj, **patch_info)[0]
         self.assertTupleEqual(img.shape, expected_img.shape)
         self.assertIsNone(assert_array_equal(img, expected_img))
 
     @parameterized.expand([TEST_CASE_3, TEST_CASE_4])
-    @skipUnless(has_cui, "Requires CuClaraImage")
+    @skipUnless(has_cim, "Requires cuCIM")
     def test_read_patches(self, file_url, patch_info, expected_img):
         filename = self.camelyon_data_download(file_url)
-        reader = WSIReader("CuClaraImage")
+        reader = WSIReader("cuCIM")
         img_obj = reader.read(filename)
         img = reader.get_data(img_obj, **patch_info)[0]
         self.assertTupleEqual(img.shape, expected_img.shape)