Merge pull request #37 from reginabarzilaygroup/v1.2.1_dev

V1.2.1 dev

scripts/inference.py

@@ -112,6 +112,7 @@ def inference(
     with open(prediction_path, "w") as f:
         json.dump(pred_dict, f, indent=2)
 
+    series_with_attention = None
     if return_attentions:
         attention_path = os.path.join(output_dir, "attention_scores.pkl")
         with open(attention_path, "wb") as f:
@@ -124,7 +125,7 @@ def inference(
             gain=3,
         )
 
-    return pred_dict
+    return pred_dict, series_with_attention
 
 
 def main():
@@ -133,7 +134,7 @@ def main():
 
     os.makedirs(args.output_dir, exist_ok=True)
 
-    pred_dict = inference(
+    pred_dict, series_with_attention = inference(
         args.image_dir,
         args.output_dir,
         args.model_name,

setup.cfg

@@ -7,7 +7,7 @@ author_email =
 license_file = LICENSE.txt
 long_description = file: README.md
 long_description_content_type = text/markdown; charset=UTF-8; variant=GFM
-version = 1.2.0
+version = 1.2.1
 # url = 
 project_urls =
     ; Documentation = https://.../docs
@@ -32,22 +32,24 @@ python_requires = >=3.8
 # Version specifiers like >=2.2,<3.0 avoid problems due to API changes in
 # new major versions. This works if the required packages follow Semantic Versioning.
 # For more information, check out https://semver.org/.
-# Use --find-links https://download.pytorch.org/whl/cu113/torch_stable.html for torch libraries
+# Use --find-links https://download.pytorch.org/whl/cu117/torch_stable.html for torch libraries
 install_requires =
     importlib-metadata; python_version>="3.8"
     numpy==1.24.1
-    torch==1.11.0+cu113; sys_platform != "darwin"
-    torch==1.11.0; sys_platform == "darwin"
-    torchvision==0.12.0+cu113; sys_platform != "darwin"
-    torchvision==0.12.0; sys_platform == "darwin"
-    pytorch_lightning==1.5.6
+    torch==1.13.1+cu117; sys_platform != "darwin"
+    torch==1.13.1; sys_platform == "darwin"
+    torchvision==0.14.1+cu117; sys_platform != "darwin"
+    torchvision==0.14.1; sys_platform == "darwin"
+    pytorch_lightning==1.6.0
     scikit-learn==1.0.2
     tqdm==4.62.3
     lifelines==0.26.4
     opencv-python==4.5.4.60
     opencv-python-headless==4.5.4.60
     albumentations==1.1.0
-    pydicom==2.2.2
+    pillow>=10.2.0
+    pydicom==2.3.0
+    pylibjpeg[all]==2.0.0
     torchio==0.18.74
     gdown==4.6.0
 

tox.ini

@@ -17,7 +17,7 @@ deps =
     # flake8
     # mypy
     # black
-install_command = pip install --pre --find-links https://download.pytorch.org/whl/cu113/torch_stable.html {opts} {packages}
+install_command = pip install --pre --find-links https://download.pytorch.org/whl/cu117/torch_stable.html {opts} {packages}
 commands =
     pytest {posargs}
     # black {toxinidir}/sybil --check