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V1.2.1 dev #37

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Apr 29, 2024
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V1.2.1 dev #37

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ca790d7
Return attentions from inference.py:inference
jsilter Apr 24, 2024
5cc0ac1
Upgrade the versions of some dependencies, including torch and pydicom.
jsilter Apr 24, 2024
485d6d1
Add dependency on pylibjpeg, so that we can process DICOMs which stor…
jsilter Apr 29, 2024
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5 changes: 3 additions & 2 deletions scripts/inference.py
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Original file line number Diff line number Diff line change
Expand Up @@ -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:
Expand All @@ -124,7 +125,7 @@ def inference(
gain=3,
)

return pred_dict
return pred_dict, series_with_attention


def main():
Expand All @@ -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,
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18 changes: 10 additions & 8 deletions setup.cfg
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Expand Up @@ -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
Expand All @@ -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

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2 changes: 1 addition & 1 deletion tox.ini
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Expand Up @@ -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
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