From e0886601009834703ba2da711b9e676321551648 Mon Sep 17 00:00:00 2001 From: Spiros Maggioros Date: Sun, 10 Nov 2024 02:18:24 +0200 Subject: [PATCH] Added pre-commit configuration and pre-commit bot | Some small fixes on setup.py(nothing special) | Remove nnunet_* subfolders --- .github/workflows/pre-commit.yml | 19 + .pre-commit-config.yaml | 20 + DLWMLS/__main__.py | 41 +- .../dataset.json | 11 - .../dataset_fingerprint.json | 2818 --------------- .../nnUNetPlans.json | 175 - .../splits_final.json | 1432 -------- .../datalist.json | 3086 ----------------- .../dataset.json | 11 - setup.py | 18 +- 10 files changed, 63 insertions(+), 7568 deletions(-) create mode 100644 .github/workflows/pre-commit.yml create mode 100644 .pre-commit-config.yaml delete mode 100644 DLWMLS/nnunet_preprocessed/Dataset002_Dataset002_dlwmlsICVAll/dataset.json delete mode 100644 DLWMLS/nnunet_preprocessed/Dataset002_Dataset002_dlwmlsICVAll/dataset_fingerprint.json delete mode 100644 DLWMLS/nnunet_preprocessed/Dataset002_Dataset002_dlwmlsICVAll/nnUNetPlans.json delete mode 100644 DLWMLS/nnunet_preprocessed/Dataset002_Dataset002_dlwmlsICVAll/splits_final.json delete mode 100644 DLWMLS/nnunet_raw/Dataset002_Dataset002_dlwmlsICVAll/datalist.json delete mode 100644 DLWMLS/nnunet_raw/Dataset002_Dataset002_dlwmlsICVAll/dataset.json diff --git a/.github/workflows/pre-commit.yml b/.github/workflows/pre-commit.yml new file mode 100644 index 0000000..0e42715 --- /dev/null +++ b/.github/workflows/pre-commit.yml @@ -0,0 +1,19 @@ +name: pre-commit + +on: + pull_request: + push: + branches: [main, spiros-dev] + +jobs: + pre-commit: + runs-on: macos-latest + steps: + - uses: actions/checkout@v4 + - uses: actions/setup-python@v5 + with: + python-version: "3.12" + - name: install pre commit + run: pip install pre-commit && pre-commit install + - name: pre-commit + uses: pre-commit/action@v3.0.1 diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml new file mode 100644 index 0000000..47b9452 --- /dev/null +++ b/.pre-commit-config.yaml @@ -0,0 +1,20 @@ +repos: + - repo: https://github.com/ambv/black + rev: 24.3.0 + hooks: + - id: black + - repo: https://github.com/pycqa/isort + rev: 5.11.5 + hooks: + - id: isort + args: ["--profile", "black"] + - repo: https://github.com/pycqa/flake8 + rev: 5.0.4 + hooks: + - id: flake8 + - repo: https://github.com/pre-commit/mirrors-mypy + rev: v0.991 + hooks: + - id: mypy + args: ["--ignore-missing-imports"] + diff --git a/DLWMLS/__main__.py b/DLWMLS/__main__.py index 30d50d2..caf2d39 100644 --- a/DLWMLS/__main__.py +++ b/DLWMLS/__main__.py @@ -1,10 +1,10 @@ import argparse import json import os -from pathlib import Path import shutil import sys import warnings +from pathlib import Path import torch @@ -15,15 +15,16 @@ VERSION = 1.0 + def main() -> None: - prog="DLWMLS" + prog = "DLWMLS" parser = argparse.ArgumentParser( prog=prog, description="DLWMLS - MUlti-atlas region Segmentation utilizing Ensembles of registration algorithms and parameters.", usage=""" DLWMLS v{VERSION} Segment White Matter Lesions from the ICV-segmented (see DLICV method), LPS oriented brain image (Nifti/.nii.gz format). - + Required arguments: [-i, --in_dir] The filepath of the input directory [-o, --out_dir] The filepath of the output directory @@ -36,8 +37,10 @@ def main() -> None: -o /path/to/output \ -device cpu|cuda|mps - """.format(VERSION=VERSION), - add_help=False + """.format( + VERSION=VERSION + ), + add_help=False, ) # Required Arguments @@ -53,7 +56,7 @@ def main() -> None: required=True, help="[REQUIRED] Output folder for the segmentation results in Nifti format (nii.gz).", ) - + # Optional Arguments parser.add_argument( "-device", @@ -99,7 +102,7 @@ def main() -> None: action="store_true", required=False, default=False, - help="Set this flag to clear any cached models before running. This is recommended if a previous download failed." + help="Set this flag to clear any cached models before running. This is recommended if a previous download failed.", ) parser.add_argument( "--disable_tta", @@ -109,13 +112,6 @@ def main() -> None: help="[nnUnet Arg] Set this flag to disable test time data augmentation in the form of mirroring. " "Faster, but less accurate inference. Not recommended.", ) - ### DEPRECIATED #### - # parser.add_argument( - # "-m", - # type=str, - # required=True, - # help="Model folder path. The model folder should be named nnunet_results.", - # ) parser.add_argument( "-d", type=str, @@ -208,25 +204,17 @@ def main() -> None: required=False, default=0, help="[nnUnet Arg] If multiple nnUNetv2_predict exist, which one is this? IDs start with 0 " - "can end with num_parts - 1. So when you submit 5 nnUNetv2_predict calls you need to set " + "can end with num_parts - 1. So when you submit 5 nnUNetv2_predict calls you need to set " "-num_parts 5 and use -part_id 0, 1, 2, 3 and 4. Note: You are yourself responsible to make these run on separate GPUs! " "Use CUDA_VISIBLE_DEVICES.", ) - - args = parser.parse_args() args.f = [args.f] if args.clear_cache: - shutil.rmtree(os.path.join( - Path(__file__).parent, - "nnunet_results" - )) - shutil.rmtree(os.path.join( - Path(__file__).parent, - ".cache" - )) + shutil.rmtree(os.path.join(Path(__file__).parent, "nnunet_results")) + shutil.rmtree(os.path.join(Path(__file__).parent, ".cache")) if not args.i or not args.o: print("Cache cleared and missing either -i / -o. Exiting.") sys.exit(0) @@ -263,7 +251,6 @@ def main() -> None: % (args.d, args.d, args.c), ) - # Check if model exists. If not exist, download using HuggingFace print(f"Using model folder: {model_folder}") if not os.path.exists(model_folder): @@ -271,6 +258,7 @@ def main() -> None: print("DLWMLS model not found, downloading...") from huggingface_hub import snapshot_download + local_src = Path(__file__).parent snapshot_download(repo_id="nichart/DLWMLS", local_dir=local_src) @@ -292,6 +280,7 @@ def main() -> None: if args.device == "cpu": import multiprocessing + # use half of the available threads in the system. torch.set_num_threads(multiprocessing.cpu_count() // 2) device = torch.device("cpu") diff --git a/DLWMLS/nnunet_preprocessed/Dataset002_Dataset002_dlwmlsICVAll/dataset.json b/DLWMLS/nnunet_preprocessed/Dataset002_Dataset002_dlwmlsICVAll/dataset.json deleted file mode 100644 index fdf5bfc..0000000 --- a/DLWMLS/nnunet_preprocessed/Dataset002_Dataset002_dlwmlsICVAll/dataset.json +++ /dev/null @@ -1,11 +0,0 @@ -{ - "channel_names": { - "0": "FLAIR" - }, - "file_ending": ".nii.gz", - "labels": { - "background": 0, - "class1": 1 - }, - "numTraining": 280 -} \ No newline at end of file diff --git a/DLWMLS/nnunet_preprocessed/Dataset002_Dataset002_dlwmlsICVAll/dataset_fingerprint.json b/DLWMLS/nnunet_preprocessed/Dataset002_Dataset002_dlwmlsICVAll/dataset_fingerprint.json deleted file mode 100644 index 3fb4392..0000000 --- a/DLWMLS/nnunet_preprocessed/Dataset002_Dataset002_dlwmlsICVAll/dataset_fingerprint.json +++ /dev/null @@ -1,2818 +0,0 @@ -{ - "foreground_intensity_properties_per_channel": { - "0": { - "max": 22371.0, - "mean": 843.6339111328125, - "median": 162.0, - "min": 0.0, - "percentile_00_5": 0.0, - "percentile_99_5": 14186.0, - "std": 2414.174560546875 - } - }, - "median_relative_size_after_cropping": 0.33991004680765086, - "shapes_after_crop": [ - [ - 128, - 158, - 125 - ], - [ - 38, - 272, - 225 - ], - [ - 44, - 177, - 157 - ], - [ - 133, - 156, - 132 - ], - [ - 135, - 170, - 123 - ], - [ - 26, - 190, - 147 - ], - [ - 41, - 177, - 141 - ], - [ - 145, - 172, - 137 - ], - [ - 44, - 199, - 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"new_name": "case_275" - }, - { - "fold": 0, - "image": "/cbica/home/baikk/Projects/nnUnetv2_WMLS/Data/Vikas_280_ExtractedBrains/images/1000341956-20021104_FL_LPS_dlicv.nii.gz", - "label": "/cbica/home/baikk/Projects/nnUnetv2_WMLS/Data/Vikas_280_ExtractedBrains/wml/1000341956-20021104_wml.nii.gz", - "new_name": "case_276" - }, - { - "fold": 0, - "image": "/cbica/home/baikk/Projects/nnUnetv2_WMLS/Data/Vikas_280_ExtractedBrains/images/Amsterdam_GE3T_100_FL_LPS_dlicv.nii.gz", - "label": "/cbica/home/baikk/Projects/nnUnetv2_WMLS/Data/Vikas_280_ExtractedBrains/wml/Amsterdam_GE3T_100_wml.nii.gz", - "new_name": "case_277" - }, - { - "fold": 0, - "image": "/cbica/home/baikk/Projects/nnUnetv2_WMLS/Data/Vikas_280_ExtractedBrains/images/150046515-20130918_FL_LPS_dlicv.nii.gz", - "label": "/cbica/home/baikk/Projects/nnUnetv2_WMLS/Data/Vikas_280_ExtractedBrains/wml/150046515-20130918_wml.nii.gz", - "new_name": "case_278" - }, - { - "fold": 0, - "image": "/cbica/home/baikk/Projects/nnUnetv2_WMLS/Data/Vikas_280_ExtractedBrains/images/119152_20161013_FL_LPS_dlicv.nii.gz", - "label": "/cbica/home/baikk/Projects/nnUnetv2_WMLS/Data/Vikas_280_ExtractedBrains/wml/119152_20161013_wml.nii.gz", - "new_name": "case_279" - } - ] -} \ No newline at end of file diff --git a/DLWMLS/nnunet_raw/Dataset002_Dataset002_dlwmlsICVAll/dataset.json b/DLWMLS/nnunet_raw/Dataset002_Dataset002_dlwmlsICVAll/dataset.json deleted file mode 100644 index fdf5bfc..0000000 --- a/DLWMLS/nnunet_raw/Dataset002_Dataset002_dlwmlsICVAll/dataset.json +++ /dev/null @@ -1,11 +0,0 @@ -{ - "channel_names": { - "0": "FLAIR" - }, - "file_ending": ".nii.gz", - "labels": { - "background": 0, - "class1": 1 - }, - "numTraining": 280 -} \ No newline at end of file diff --git a/setup.py b/setup.py index 83eda7b..384973f 100644 --- a/setup.py +++ b/setup.py @@ -7,10 +7,6 @@ this_directory = Path(__file__).parent long_description = (this_directory / "README.md").read_text() -with open('requirements.txt') as f: - required = f.read().splitlines() - - setup( name="DLWMLS", version="0.0.1", @@ -25,7 +21,13 @@ url="https://github.com/CBICA/DLWMLS/", packages=find_packages(exclude=["tests", ".github"]), python_requires=">=3.8", - install_requires=required, + install_requires=[ + "torch>=2.2.1", + "nnunetv2>=2.2.1", + "argparse", + "huggingface_hub", + "pathlib", + ], entry_points={"console_scripts": ["DLWMLS = DLWMLS.__main__:main"]}, classifiers=[ "Intended Audience :: Developers", @@ -45,9 +47,7 @@ "medical image segmentation", "nnU-Net", "nnunet", - "nnunetv2" + "nnunetv2", ], - package_data={ - "DLWMLS": ["VERSION"] - }, + package_data={"DLWMLS": ["VERSION"]}, )