From 5478025dc94b5628daad1b481d37d1d53dfde481 Mon Sep 17 00:00:00 2001 From: Alexander Getka Date: Mon, 23 Sep 2024 23:01:45 -0400 Subject: [PATCH 1/3] Fix overlapping namespaces between DLICV/DLMUSE --- {src => DLICV}/.gitattributes | 0 {src => DLICV}/README.md | 0 {src => DLICV}/__init__.py | 0 {src => DLICV}/__main__.py | 0 .../Dataset901_Task901_dlicv/dataset.json | 0 .../dataset_fingerprint.json | 0 .../Dataset901_Task901_dlicv/nnUNetPlans.json | 0 .../splits_final.json | 0 .../Dataset901_Task901_dlicv/datalist.json | 0 .../Dataset901_Task901_dlicv/dataset.json | 0 DLICV/src/.gitattributes | 35 +++++++++++++++++++ {src => DLICV}/utils.py | 0 setup.py | 2 +- 13 files changed, 36 insertions(+), 1 deletion(-) rename {src => DLICV}/.gitattributes (100%) rename {src => DLICV}/README.md (100%) rename {src => DLICV}/__init__.py (100%) rename {src => DLICV}/__main__.py (100%) rename {src => DLICV}/nnunet_preprocessed/Dataset901_Task901_dlicv/dataset.json (100%) rename {src => DLICV}/nnunet_preprocessed/Dataset901_Task901_dlicv/dataset_fingerprint.json (100%) rename {src => DLICV}/nnunet_preprocessed/Dataset901_Task901_dlicv/nnUNetPlans.json (100%) rename {src => DLICV}/nnunet_preprocessed/Dataset901_Task901_dlicv/splits_final.json (100%) rename {src => DLICV}/nnunet_raw/Dataset901_Task901_dlicv/datalist.json (100%) rename {src => DLICV}/nnunet_raw/Dataset901_Task901_dlicv/dataset.json (100%) create mode 100644 DLICV/src/.gitattributes rename {src => DLICV}/utils.py (100%) diff --git a/src/.gitattributes b/DLICV/.gitattributes similarity index 100% rename from src/.gitattributes rename to DLICV/.gitattributes diff --git a/src/README.md b/DLICV/README.md similarity index 100% rename from src/README.md rename to DLICV/README.md diff --git a/src/__init__.py b/DLICV/__init__.py similarity index 100% rename from src/__init__.py rename to DLICV/__init__.py diff --git a/src/__main__.py b/DLICV/__main__.py similarity index 100% rename from src/__main__.py rename to DLICV/__main__.py diff --git a/src/nnunet_preprocessed/Dataset901_Task901_dlicv/dataset.json b/DLICV/nnunet_preprocessed/Dataset901_Task901_dlicv/dataset.json similarity index 100% rename from src/nnunet_preprocessed/Dataset901_Task901_dlicv/dataset.json rename to DLICV/nnunet_preprocessed/Dataset901_Task901_dlicv/dataset.json diff --git a/src/nnunet_preprocessed/Dataset901_Task901_dlicv/dataset_fingerprint.json b/DLICV/nnunet_preprocessed/Dataset901_Task901_dlicv/dataset_fingerprint.json similarity index 100% rename from src/nnunet_preprocessed/Dataset901_Task901_dlicv/dataset_fingerprint.json rename to DLICV/nnunet_preprocessed/Dataset901_Task901_dlicv/dataset_fingerprint.json diff --git a/src/nnunet_preprocessed/Dataset901_Task901_dlicv/nnUNetPlans.json b/DLICV/nnunet_preprocessed/Dataset901_Task901_dlicv/nnUNetPlans.json similarity index 100% rename from src/nnunet_preprocessed/Dataset901_Task901_dlicv/nnUNetPlans.json rename to DLICV/nnunet_preprocessed/Dataset901_Task901_dlicv/nnUNetPlans.json diff --git a/src/nnunet_preprocessed/Dataset901_Task901_dlicv/splits_final.json b/DLICV/nnunet_preprocessed/Dataset901_Task901_dlicv/splits_final.json similarity index 100% rename from src/nnunet_preprocessed/Dataset901_Task901_dlicv/splits_final.json rename to DLICV/nnunet_preprocessed/Dataset901_Task901_dlicv/splits_final.json diff --git a/src/nnunet_raw/Dataset901_Task901_dlicv/datalist.json b/DLICV/nnunet_raw/Dataset901_Task901_dlicv/datalist.json similarity index 100% rename from src/nnunet_raw/Dataset901_Task901_dlicv/datalist.json rename to DLICV/nnunet_raw/Dataset901_Task901_dlicv/datalist.json diff --git a/src/nnunet_raw/Dataset901_Task901_dlicv/dataset.json b/DLICV/nnunet_raw/Dataset901_Task901_dlicv/dataset.json similarity index 100% rename from src/nnunet_raw/Dataset901_Task901_dlicv/dataset.json rename to DLICV/nnunet_raw/Dataset901_Task901_dlicv/dataset.json diff --git a/DLICV/src/.gitattributes b/DLICV/src/.gitattributes new file mode 100644 index 0000000..a6344aa --- /dev/null +++ b/DLICV/src/.gitattributes @@ -0,0 +1,35 @@ +*.7z filter=lfs diff=lfs merge=lfs -text +*.arrow filter=lfs diff=lfs merge=lfs -text +*.bin filter=lfs diff=lfs merge=lfs -text +*.bz2 filter=lfs diff=lfs merge=lfs -text +*.ckpt filter=lfs diff=lfs merge=lfs -text +*.ftz filter=lfs diff=lfs merge=lfs -text +*.gz filter=lfs diff=lfs merge=lfs -text +*.h5 filter=lfs diff=lfs merge=lfs -text +*.joblib filter=lfs diff=lfs merge=lfs -text +*.lfs.* filter=lfs diff=lfs merge=lfs -text +*.mlmodel filter=lfs diff=lfs merge=lfs -text +*.model filter=lfs diff=lfs merge=lfs -text +*.msgpack filter=lfs diff=lfs merge=lfs -text +*.npy filter=lfs diff=lfs merge=lfs -text +*.npz filter=lfs diff=lfs merge=lfs -text +*.onnx filter=lfs diff=lfs merge=lfs -text +*.ot filter=lfs diff=lfs merge=lfs -text +*.parquet filter=lfs diff=lfs merge=lfs -text +*.pb filter=lfs diff=lfs merge=lfs -text +*.pickle filter=lfs diff=lfs merge=lfs -text +*.pkl filter=lfs diff=lfs merge=lfs -text +*.pt filter=lfs diff=lfs merge=lfs -text +*.pth filter=lfs diff=lfs merge=lfs -text +*.rar filter=lfs diff=lfs merge=lfs -text +*.safetensors filter=lfs diff=lfs merge=lfs -text +saved_model/**/* filter=lfs diff=lfs merge=lfs -text +*.tar.* filter=lfs diff=lfs merge=lfs -text +*.tar filter=lfs diff=lfs merge=lfs -text +*.tflite filter=lfs diff=lfs merge=lfs -text +*.tgz filter=lfs diff=lfs merge=lfs -text +*.wasm filter=lfs diff=lfs merge=lfs -text +*.xz filter=lfs diff=lfs merge=lfs -text +*.zip filter=lfs diff=lfs merge=lfs -text +*.zst filter=lfs diff=lfs merge=lfs -text +*tfevents* filter=lfs diff=lfs merge=lfs -text diff --git a/src/utils.py b/DLICV/utils.py similarity index 100% rename from src/utils.py rename to DLICV/utils.py diff --git a/setup.py b/setup.py index a176087..17d2cad 100644 --- a/setup.py +++ b/setup.py @@ -27,7 +27,7 @@ python_requires=">=3.8", install_requires=required, entry_points={ - "console_scripts": ["DLICV = src.__main__:main"] + "console_scripts": ["DLICV = DLICV.__main__:main"] }, classifiers=[ "Intended Audience :: Developers", From 522e0d41e762062dde7e9e26bafd061f1af8a167 Mon Sep 17 00:00:00 2001 From: KyleB Date: Tue, 24 Sep 2024 11:24:37 -0400 Subject: [PATCH 2/3] Update requirements.txt --- requirements.txt | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/requirements.txt b/requirements.txt index e3eae65..6b8132b 100644 --- a/requirements.txt +++ b/requirements.txt @@ -1,4 +1,4 @@ -torch==2.2.1 +torch>=2.2.1 nnunetv2==2.5.1 argparse -huggingface_hub \ No newline at end of file +huggingface_hub From 216a392da57b9764f931b7a59a1f72cf52e7c0de Mon Sep 17 00:00:00 2001 From: Alexander Getka Date: Tue, 24 Sep 2024 11:46:25 -0400 Subject: [PATCH 3/3] setup and readme fixes --- README.md | 24 +++++++++--------------- setup.py | 8 ++++---- 2 files changed, 13 insertions(+), 19 deletions(-) diff --git a/README.md b/README.md index bd6c95e..c299c2b 100644 --- a/README.md +++ b/README.md @@ -1,4 +1,4 @@ -### DLICV - Deep Learning Intra Cranial Volume +# DLICV - Deep Learning Intra Cranial Volume ## Overview @@ -6,37 +6,31 @@ DLICV uses a trained [nnUNet](https://github.com/MIC-DKFZ/nnUNet) model to compu ## Installation -# As a python package +### As a python package ```bash pip install DLICV ``` -# Directly from this repository +### Directly from this repository ```bash git clone https://github.com/CBICA/DLICV cd DLICV pip install -e . ``` +### Installing PyTorch +Depending on your system configuration and supported CUDA version, you may need to follow the [PyTorch Installation Instructions](https://pytorch.org/get-started/locally/). + ## Usage -A pre-trained nnUNet model can be found at our [hugging face account](https://huggingface.co/nichart/DLICV) or at [DLICV-V2 v1.0.0 release](https://github.com/CBICA/DLMUSE/releases/tag/v1.0.0). +A pre-trained nnUNet model can be found at our [hugging face account](https://huggingface.co/nichart/DLICV). Feel free to use it under the package's [licence](LICENCE) ```bash -DLICV -i "input_folder" -o "output_folder" -device cuda/cpu/mps +DLICV -i "input_folder" -o "output_folder" -device cpu ``` -You can perform one example test run using the test input folder by running -```bash -DLICV -i test_input/DLICV_test_images -o test_input/DLICV_test_results -device cuda -``` ## Contact For more information, please contact [CBICA Software](mailto:software@cbica.upenn.edu). ## For developers Contributions are welcome! Please refer to our [CONTRIBUTING.md](CONTRIBUTING.md) for more information on how to report bugs, suggest enhancements, and contribute code. -If you're a developer looking to contribute, you'll first need to set up a development environment. After cloning the repository, you can install the development dependencies with: - -```bash -pip install -r requirements.txt -``` -This will install the packages required for running tests and formatting code. Please make sure to write tests for new code and run them before submitting a pull request. +Please make sure to write tests for new code and run them before submitting a pull request. diff --git a/setup.py b/setup.py index 17d2cad..65d24e0 100644 --- a/setup.py +++ b/setup.py @@ -13,14 +13,14 @@ setup( name="DLICV", - version="1.0.0", + version="1.0.1", description="DLICV - Deep Learning Intra Cranial Volume.", long_description=long_description, long_description_content_type="text/markdown", - author="Ashish Singh, Guray Erus, Vishnu Bashyam, George Aidinis", + author="Ashish Singh, Guray Erus, Vishnu Bashyam, George Aidinis, Alexander Getka", author_email="software@cbica.upenn.edu", - maintainer="George Aidinis, Spiros Maggioros, Kyunglok Baik", - maintainer_email="aidinisg@pennmedicine.upenn.edu, Spiros.Maggioros@pennmedicine.upenn.edu, kyunglok.baik@pennmedicine.upenn.edu", + maintainer="George Aidinis, Spiros Maggioros, Kyunglok Baik, Alexander Getka", + maintainer_email="aidinisg@pennmedicine.upenn.edu, Spiros.Maggioros@pennmedicine.upenn.edu, kyunglok.baik@pennmedicine.upenn.edu, alexander.getka@pennmedicine.upenn.edu", download_url="https://github.com/CBICA/DLICV/", url="https://github.com/CBICA/DLICV/", packages=find_packages(exclude=["tests", ".github"]),