Change image_utils.py to work with nnunetv2 (#17)

* Change `image_utils.py` to work with nnunetv2 predictions and ground truth labels with multi-class segmentations. (#17)
* Update supported Python versions to 3.8 - 3.11
* Increase version to 1.4.6

---------

Co-authored-by: Joeran Bosma <[email protected]>

.github/workflows/tests.yml

@@ -10,7 +10,7 @@ jobs:
     strategy:
       matrix:
         os: [ubuntu-latest, windows-latest]
-        python-version: ['3.7', '3.8', '3.9']
+        python-version: ['3.8', '3.11']
 
     steps:
     - uses: actions/checkout@v2

setup.cfg

@@ -8,10 +8,10 @@ platforms = unix, linux, osx, cygwin, win32
 classifiers =
     Programming Language :: Python :: 3
     Programming Language :: Python :: 3 :: Only
-    Programming Language :: Python :: 3.6
-    Programming Language :: Python :: 3.7
     Programming Language :: Python :: 3.8
     Programming Language :: Python :: 3.9
+    Programming Language :: Python :: 3.10
+    Programming Language :: Python :: 3.11
 
 [options]
 packages =

setup.py

@@ -63,7 +63,7 @@ def run(self):
         long_description = fh.read()
 
     setuptools.setup(
-        version='1.4.5',  # also update version in metrics.py -> version
+        version='1.4.6',  # also update version in metrics.py -> version
         author_email='[email protected]',
         long_description=long_description,
         long_description_content_type="text/markdown",

src/picai_eval/image_utils.py

@@ -69,7 +69,10 @@ def read_image(path: PathLike):
     elif '.nii' in path or '.mha' in path or 'mhd' in path:
         return sitk.GetArrayFromImage(sitk.ReadImage(path))
     elif '.npz' in path:
-        return np.load(path)['softmax'].astype('float32')[1]  # nnUnet format
+        # read the nnU-Net format
+        data = np.load(path)
+        data = data["softmax"] if "softmax" in data else data["probabilities"]
+        return data.astype("float32")[1]
     else:
         raise ValueError(f"Unexpected file path. Supported file formats: .nii(.gz), .mha, .npy and .npz. Got: {path}.")