From 10cc9097b7430005385252bf66f692814ebed7eb Mon Sep 17 00:00:00 2001 From: Marcel Rosier Date: Thu, 7 Aug 2025 11:49:40 +0200 Subject: [PATCH 01/24] Replace placeholder name with package name --- .github/ISSUE_TEMPLATE/bug_report.md | 6 +++--- .github/workflows/tests.yml | 2 +- README.md | 22 +++++++++++----------- docs/source/conf.py | 2 +- docs/source/index.rst | 2 +- pyproject.toml | 6 +++--- 6 files changed, 20 insertions(+), 20 deletions(-) diff --git a/.github/ISSUE_TEMPLATE/bug_report.md b/.github/ISSUE_TEMPLATE/bug_report.md index d1fd917..73ba72f 100644 --- a/.github/ISSUE_TEMPLATE/bug_report.md +++ b/.github/ISSUE_TEMPLATE/bug_report.md @@ -66,10 +66,10 @@ please specify your docker version, You can find it by running: docker --version ``` -### Version of !PACKAGE_NAME! ? -please specify your version of !PACKAGE_NAME! (please make sure you run the latest version): +### Version of !stroke_segmentor! ? +please specify your version of !stroke_segmentor! (please make sure you run the latest version): ```sh -pip freeze | grep !PACKAGE_NAME! +pip freeze | grep !stroke_segmentor! ``` **Additional context** diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml index 7724ad0..ce48f1c 100644 --- a/.github/workflows/tests.yml +++ b/.github/workflows/tests.yml @@ -39,7 +39,7 @@ jobs: poetry run flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics - name: Test with pytest run: | - poetry run pytest --cov=package_name --cov-report=xml --cov-report=term + poetry run pytest --cov=stroke_segmentor --cov-report=xml --cov-report=term # Add the following block to upload coverage to Codecov, requires a CODECOV_TOKEN secret to be set in the repository # - name: Upload results to Codecov # # Only upload to Codecov after a merge to the main branch diff --git a/README.md b/README.md index 5e232f2..6caea7e 100644 --- a/README.md +++ b/README.md @@ -1,10 +1,10 @@ -# PACKAGE_NAME +# stroke_segmentor -[![Python Versions](https://img.shields.io/pypi/pyversions/PACKAGE_NAME)](https://pypi.org/project/PACKAGE_NAME/) -[![Stable Version](https://img.shields.io/pypi/v/PACKAGE_NAME?label=stable)](https://pypi.python.org/pypi/PACKAGE_NAME/) -[![Documentation Status](https://readthedocs.org/projects/PACKAGE_NAME/badge/?version=latest)](http://PACKAGE_NAME.readthedocs.io/?badge=latest) -[![tests](https://github.com/BrainLesion/PACKAGE_NAME/actions/workflows/tests.yml/badge.svg)](https://github.com/BrainLesion/PACKAGE_NAME/actions/workflows/tests.yml) -[![codecov](https://codecov.io/gh/BrainLesion/PACKAGE_NAME/graph/badge.svg?token=A7FWUKO9Y4)](https://codecov.io/gh/BrainLesion/PACKAGE_NAME) +[![Python Versions](https://img.shields.io/pypi/pyversions/stroke_segmentor)](https://pypi.org/project/stroke_segmentor/) +[![Stable Version](https://img.shields.io/pypi/v/stroke_segmentor?label=stable)](https://pypi.python.org/pypi/stroke_segmentor/) +[![Documentation Status](https://readthedocs.org/projects/stroke_segmentor/badge/?version=latest)](http://stroke_segmentor.readthedocs.io/?badge=latest) +[![tests](https://github.com/BrainLesion/stroke_segmentor/actions/workflows/tests.yml/badge.svg)](https://github.com/BrainLesion/stroke_segmentor/actions/workflows/tests.yml) +[![codecov](https://codecov.io/gh/BrainLesion/stroke_segmentor/graph/badge.svg?token=A7FWUKO9Y4)](https://codecov.io/gh/BrainLesion/stroke_segmentor) [![License](https://img.shields.io/badge/License-Apache%202.0-blue.svg)](https://opensource.org/licenses/Apache-2.0) Description @@ -13,10 +13,10 @@ Description ## Installation -With a Python 3.8+ environment, you can install `PACKAGE_NAME` directly from [PyPI](https://pypi.org/project/PACKAGE_NAME/): +With a Python 3.8+ environment, you can install `stroke_segmentor` directly from [PyPI](https://pypi.org/project/stroke_segmentor/): ```bash -pip install PACKAGE_NAME +pip install stroke_segmentor ``` @@ -28,12 +28,12 @@ A minimal example to create a segmentation could look like this: # example ``` - + ## Citation -If you use PACKAGE_NAME in your research, please cite it to support the development! +If you use stroke_segmentor in your research, please cite it to support the development! ``` TODO: citation will be added asap @@ -45,7 +45,7 @@ We welcome all kinds of contributions from the community! ### Reporting Bugs, Feature Requests and Questions -Please open a new issue [here](https://github.com/BrainLesion/PACKAGE_NAME/issues). +Please open a new issue [here](https://github.com/BrainLesion/stroke_segmentor/issues). ### Code contributions diff --git a/docs/source/conf.py b/docs/source/conf.py index 7bc126f..5e91c72 100644 --- a/docs/source/conf.py +++ b/docs/source/conf.py @@ -16,7 +16,7 @@ # -- Project information ----------------------------------------------------- # https://www.sphinx-doc.org/en/master/usage/configuration.html#project-information -project = "PACKAGE_NAME" +project = "stroke_segmentor" copyright = "2024, Marcel Rosier et al." author = "Marcel Rosier, Florian Kofler" diff --git a/docs/source/index.rst b/docs/source/index.rst index ee56e5b..9fb81e3 100644 --- a/docs/source/index.rst +++ b/docs/source/index.rst @@ -1,4 +1,4 @@ -PACKAGE_NAME documentation +stroke_segmentor documentation =================== .. include:: ../README_preprocessed.md diff --git a/pyproject.toml b/pyproject.toml index f4e281a..67c32dd 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -6,12 +6,12 @@ build-backend = "poetry_dynamic_versioning.backend" enable = true [tool.poetry] -name = "package_name" +name = "stroke_segmentor" version = "0.0.0.dev" description = "" authors = ["Marcel Rosier "] -repository = "https://www.TODO.com" -homepage = "https://www.TODO.com" +repository = "https://github.com/BrainLesion/stroke_segmentor" +homepage = "https://github.com/BrainLesion/stroke_segmentor" documentation = "https://www.TODO.com" readme = "README.md" From 5382c2674e0ebc65b295531b7d5fffef70f001d2 Mon Sep 17 00:00:00 2001 From: Marcel Rosier Date: Sat, 9 Aug 2025 11:29:35 +0200 Subject: [PATCH 02/24] Rename package dir --- .gitignore | 5 +++++ {package_name => stroke_segmentor}/.gitignore | 0 {package_name => stroke_segmentor}/__init__.py | 0 3 files changed, 5 insertions(+) rename {package_name => stroke_segmentor}/.gitignore (100%) rename {package_name => stroke_segmentor}/__init__.py (100%) diff --git a/.gitignore b/.gitignore index 68bc17f..ec928a2 100644 --- a/.gitignore +++ b/.gitignore @@ -158,3 +158,8 @@ cython_debug/ # and can be added to the global gitignore or merged into this file. For a more nuclear # option (not recommended) you can uncomment the following to ignore the entire idea folder. #.idea/ + +testdata +NVAUTO +*.nii.gz +*.ipynb diff --git a/package_name/.gitignore b/stroke_segmentor/.gitignore similarity index 100% rename from package_name/.gitignore rename to stroke_segmentor/.gitignore diff --git a/package_name/__init__.py b/stroke_segmentor/__init__.py similarity index 100% rename from package_name/__init__.py rename to stroke_segmentor/__init__.py From 2b7766a23bb23d3fd785fab65b60fa3724073e67 Mon Sep 17 00:00:00 2001 From: Marcel Rosier Date: Sat, 9 Aug 2025 11:29:52 +0200 Subject: [PATCH 03/24] Add rich,monai,sitk, nibabel --- poetry.lock | 661 ++++++++++++++++++++++++++++++++++++++++++++++++- pyproject.toml | 6 +- 2 files changed, 656 insertions(+), 11 deletions(-) diff --git a/poetry.lock b/poetry.lock index 66a899d..4d31eb1 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,4 +1,4 @@ -# This file is automatically @generated by Poetry 2.1.1 and should not be changed by hand. +# This file is automatically @generated by Poetry 2.1.4 and should not be changed by hand. [[package]] name = "alabaster" @@ -281,7 +281,7 @@ description = "Backport of PEP 654 (exception groups)" optional = false python-versions = ">=3.7" groups = ["dev"] -markers = "python_version < \"3.11\"" +markers = "python_version == \"3.10\"" files = [ {file = "exceptiongroup-1.2.2-py3-none-any.whl", hash = "sha256:3111b9d131c238bec2f8f516e123e14ba243563fb135d3fe885990585aa7795b"}, {file = "exceptiongroup-1.2.2.tar.gz", hash = "sha256:47c2edf7c6738fafb49fd34290706d1a1a2f4d1c6df275526b62cbb4aa5393cc"}, @@ -290,6 +290,23 @@ files = [ [package.extras] test = ["pytest (>=6)"] +[[package]] +name = "filelock" +version = "3.18.0" +description = "A platform independent file lock." +optional = false +python-versions = ">=3.9" +groups = ["main"] +files = [ + {file = "filelock-3.18.0-py3-none-any.whl", hash = "sha256:c401f4f8377c4464e6db25fff06205fd89bdd83b65eb0488ed1b160f780e21de"}, + {file = "filelock-3.18.0.tar.gz", hash = "sha256:adbc88eabb99d2fec8c9c1b229b171f18afa655400173ddc653d5d01501fb9f2"}, +] + +[package.extras] +docs = ["furo (>=2024.8.6)", "sphinx (>=8.1.3)", "sphinx-autodoc-typehints (>=3)"] +testing = ["covdefaults (>=2.3)", "coverage (>=7.6.10)", "diff-cover (>=9.2.1)", "pytest (>=8.3.4)", "pytest-asyncio (>=0.25.2)", "pytest-cov (>=6)", "pytest-mock (>=3.14)", "pytest-timeout (>=2.3.1)", "virtualenv (>=20.28.1)"] +typing = ["typing-extensions (>=4.12.2) ; python_version < \"3.11\""] + [[package]] name = "flake8" version = "7.1.2" @@ -307,6 +324,46 @@ mccabe = ">=0.7.0,<0.8.0" pycodestyle = ">=2.12.0,<2.13.0" pyflakes = ">=3.2.0,<3.3.0" +[[package]] +name = "fsspec" +version = "2025.7.0" +description = "File-system specification" +optional = false +python-versions = ">=3.9" +groups = ["main"] +files = [ + {file = "fsspec-2025.7.0-py3-none-any.whl", hash = "sha256:8b012e39f63c7d5f10474de957f3ab793b47b45ae7d39f2fb735f8bbe25c0e21"}, + {file = "fsspec-2025.7.0.tar.gz", hash = "sha256:786120687ffa54b8283d942929540d8bc5ccfa820deb555a2b5d0ed2b737bf58"}, +] + +[package.extras] +abfs = ["adlfs"] +adl = ["adlfs"] +arrow = ["pyarrow (>=1)"] +dask = ["dask", "distributed"] +dev = ["pre-commit", "ruff (>=0.5)"] +doc = ["numpydoc", "sphinx", "sphinx-design", "sphinx-rtd-theme", "yarl"] +dropbox = ["dropbox", "dropboxdrivefs", "requests"] +full = ["adlfs", "aiohttp (!=4.0.0a0,!=4.0.0a1)", "dask", "distributed", "dropbox", "dropboxdrivefs", "fusepy", "gcsfs", "libarchive-c", "ocifs", "panel", "paramiko", "pyarrow (>=1)", "pygit2", "requests", "s3fs", "smbprotocol", "tqdm"] +fuse = ["fusepy"] +gcs = ["gcsfs"] +git = ["pygit2"] +github = ["requests"] +gs = ["gcsfs"] +gui = ["panel"] +hdfs = ["pyarrow (>=1)"] +http = ["aiohttp (!=4.0.0a0,!=4.0.0a1)"] +libarchive = ["libarchive-c"] +oci = ["ocifs"] +s3 = ["s3fs"] +sftp = ["paramiko"] +smb = ["smbprotocol"] +ssh = ["paramiko"] +test = ["aiohttp (!=4.0.0a0,!=4.0.0a1)", "numpy", "pytest", "pytest-asyncio (!=0.22.0)", "pytest-benchmark", "pytest-cov", "pytest-mock", "pytest-recording", "pytest-rerunfailures", "requests"] +test-downstream = ["aiobotocore (>=2.5.4,<3.0.0)", "dask[dataframe,test]", "moto[server] (>4,<5)", "pytest-timeout", "xarray"] +test-full = ["adlfs", "aiohttp (!=4.0.0a0,!=4.0.0a1)", "cloudpickle", "dask", "distributed", "dropbox", "dropboxdrivefs", "fastparquet", "fusepy", "gcsfs", "jinja2", "kerchunk", "libarchive-c", "lz4", "notebook", "numpy", "ocifs", "pandas", "panel", "paramiko", "pyarrow", "pyarrow (>=1)", "pyftpdlib", "pygit2", "pytest", "pytest-asyncio (!=0.22.0)", "pytest-benchmark", "pytest-cov", "pytest-mock", "pytest-recording", "pytest-rerunfailures", "python-snappy", "requests", "smbprotocol", "tqdm", "urllib3", "zarr", "zstandard ; python_version < \"3.14\""] +tqdm = ["tqdm"] + [[package]] name = "furo" version = "2024.8.6" @@ -352,6 +409,27 @@ files = [ {file = "imagesize-1.4.1.tar.gz", hash = "sha256:69150444affb9cb0d5cc5a92b3676f0b2fb7cd9ae39e947a5e11a36b4497cd4a"}, ] +[[package]] +name = "importlib-resources" +version = "6.5.2" +description = "Read resources from Python packages" +optional = false +python-versions = ">=3.9" +groups = ["main"] +markers = "python_version < \"3.12\"" +files = [ + {file = "importlib_resources-6.5.2-py3-none-any.whl", hash = "sha256:789cfdc3ed28c78b67a06acb8126751ced69a3d5f79c095a98298cd8a760ccec"}, + {file = "importlib_resources-6.5.2.tar.gz", hash = "sha256:185f87adef5bcc288449d98fb4fba07cea78bc036455dd44c5fc4a2fe78fed2c"}, +] + +[package.extras] +check = ["pytest-checkdocs (>=2.4)", "pytest-ruff (>=0.2.1) ; sys_platform != \"cygwin\""] +cover = ["pytest-cov"] +doc = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-lint"] +enabler = ["pytest-enabler (>=2.2)"] +test = ["jaraco.test (>=5.4)", "pytest (>=6,!=8.1.*)", "zipp (>=3.17)"] +type = ["pytest-mypy"] + [[package]] name = "iniconfig" version = "2.0.0" @@ -370,7 +448,7 @@ version = "3.1.4" description = "A very fast and expressive template engine." optional = false python-versions = ">=3.7" -groups = ["docs"] +groups = ["main", "docs"] files = [ {file = "jinja2-3.1.4-py3-none-any.whl", hash = "sha256:bc5dd2abb727a5319567b7a813e6a2e7318c39f4f487cfe6c89c6f9c7d25197d"}, {file = "jinja2-3.1.4.tar.gz", hash = "sha256:4a3aee7acbbe7303aede8e9648d13b8bf88a429282aa6122a993f0ac800cb369"}, @@ -388,7 +466,7 @@ version = "3.0.0" description = "Python port of markdown-it. Markdown parsing, done right!" optional = false python-versions = ">=3.8" -groups = ["docs"] +groups = ["main", "docs"] files = [ {file = "markdown-it-py-3.0.0.tar.gz", hash = "sha256:e3f60a94fa066dc52ec76661e37c851cb232d92f9886b15cb560aaada2df8feb"}, {file = "markdown_it_py-3.0.0-py3-none-any.whl", hash = "sha256:355216845c60bd96232cd8d8c40e8f9765cc86f46880e43a8fd22dc1a1a8cab1"}, @@ -413,7 +491,7 @@ version = "2.1.5" description = "Safely add untrusted strings to HTML/XML markup." optional = false python-versions = ">=3.7" -groups = ["docs"] +groups = ["main", "docs"] files = [ {file = "MarkupSafe-2.1.5-cp310-cp310-macosx_10_9_universal2.whl", hash = "sha256:a17a92de5231666cfbe003f0e4b9b3a7ae3afb1ec2845aadc2bacc93ff85febc"}, {file = "MarkupSafe-2.1.5-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:72b6be590cc35924b02c78ef34b467da4ba07e4e0f0454a2c5907f473fc50ce5"}, @@ -515,12 +593,90 @@ version = "0.1.2" description = "Markdown URL utilities" optional = false python-versions = ">=3.7" -groups = ["docs"] +groups = ["main", "docs"] files = [ {file = "mdurl-0.1.2-py3-none-any.whl", hash = "sha256:84008a41e51615a49fc9966191ff91509e3c40b939176e643fd50a5c2196b8f8"}, {file = "mdurl-0.1.2.tar.gz", hash = "sha256:bb413d29f5eea38f31dd4754dd7377d4465116fb207585f97bf925588687c1ba"}, ] +[[package]] +name = "monai" +version = "1.5.0" +description = "AI Toolkit for Healthcare Imaging" +optional = false +python-versions = ">=3.9" +groups = ["main"] +files = [ + {file = "monai-1.5.0-py3-none-any.whl", hash = "sha256:93259cfa8b68fbf006dea7c78376a46ce38f369bf8b20b36f74ab1d3f484d37b"}, + {file = "monai-1.5.0.tar.gz", hash = "sha256:8c5e4555839812fe060e13da34d9b3342d750d8ad5934f1b79f9b08eb6b35d64"}, +] + +[package.dependencies] +numpy = ">=1.24,<3.0" +torch = ">=2.4.1,<2.7.0" + +[package.extras] +all = ["clearml (>=1.10.0rc0)", "cucim-cu12 ; platform_system == \"Linux\" and python_version >= \"3.9\" and python_version <= \"3.10\"", "einops", "fire", "gdown (>=4.7.3)", "h5py", 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b/pyproject.toml index 67c32dd..5d86d6f 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,3 +1,4 @@ + [build-system] requires = ["poetry-core>=1.0.0", "poetry-dynamic-versioning>=1.0.0,<2.0.0"] build-backend = "poetry_dynamic_versioning.backend" @@ -21,7 +22,10 @@ exclude = ["examples", "benchmark"] [tool.poetry.dependencies] python = ">=3.10" - +rich = "^13.9.4" +monai = "^1.5.0" +simpleitk = ">=2.2.1" +nibabel = "^5.3.2" [tool.poetry.group.dev.dependencies] pytest = ">=8.0.0" From 59a80f350120e9dcec18acc0888d12be91896f0f Mon Sep 17 00:00:00 2001 From: Marcel Rosier Date: Sat, 9 Aug 2025 11:30:05 +0200 Subject: [PATCH 04/24] Add model handler and inferer --- stroke_segmentor/inferer.py | 80 +++++++++++++++ stroke_segmentor/model_handler.py | 159 ++++++++++++++++++++++++++++++ 2 files changed, 239 insertions(+) create mode 100644 stroke_segmentor/inferer.py create mode 100644 stroke_segmentor/model_handler.py diff --git a/stroke_segmentor/inferer.py b/stroke_segmentor/inferer.py new file mode 100644 index 0000000..a680784 --- /dev/null +++ b/stroke_segmentor/inferer.py @@ -0,0 +1,80 @@ +from pathlib import Path +from typing import Optional + +import SimpleITK +import numpy as np +from stroke_segmentor.model_handler import ModelHandler +from numpy.typing import NDArray + + +class Inferer: + + def __init__( + self, + ): + self.model_weights_folder = "" + self.device = "cuda" + self.model_handler = ModelHandler(device=self.device) + + def _save( + self, + dwi_path: str | Path, + prediction: NDArray, + segmentation_path: str | Path, + ) -> None: + """Save the prediction as a SimpleITK image. + + Args: + dwi_path (str | Path): Path to the DWI image. + prediction (NDArray): The predicted segmentation mask. + segmentation_path (str | Path): Path to save the segmentation mask. + + Returns: + None + """ + dwi_image = SimpleITK.ReadImage(str(dwi_path)) + + # Get origin, spacing and direction from the DWI image. + origin, spacing, direction = ( + dwi_image.GetOrigin(), + dwi_image.GetSpacing(), + dwi_image.GetDirection(), + ) + + # Build the itk object. + output_image = SimpleITK.GetImageFromArray(prediction.astype(np.uint8)) + output_image.SetOrigin(origin) + output_image.SetSpacing(spacing) + output_image.SetDirection(direction) + + Path(segmentation_path).parent.mkdir(parents=True, exist_ok=True) + SimpleITK.WriteImage(output_image, str(segmentation_path)) + + def infer( + self, + adc_path: str | Path, + dwi_path: str | Path, + segmentation_path: Optional[str | Path] = None, + ) -> NDArray: + """Run inference on the provided ADC and DWI images. + + Args: + adc_path (str | Path): Path to the ADC image. + dwi_path (str | Path): Path to the DWI image. + segmentation_path (Optional[str | Path], optional): Path to save the segmentation mask. Defaults to None. + + Returns: + NDArray: The predicted segmentation mask. + """ + + prediction = self.model_handler.infer( + adc_path=adc_path, + dwi_path=dwi_path, + ) + if segmentation_path: + self._save( + dwi_path=dwi_path, + prediction=prediction, + segmentation_path=segmentation_path, + ) + return prediction diff --git a/stroke_segmentor/model_handler.py b/stroke_segmentor/model_handler.py new file mode 100644 index 0000000..fe50ea6 --- /dev/null +++ b/stroke_segmentor/model_handler.py @@ -0,0 +1,159 @@ +from __future__ import annotations + +from pathlib import Path + +import numpy as np +import torch +from monai.data.dataloader import DataLoader +from monai.data.dataset import Dataset +from monai.data.utils import decollate_batch +from monai.inferers.inferer import SlidingWindowInferer +from monai.transforms.compose import Compose +from monai.transforms.intensity.dictionary import NormalizeIntensityd +from monai.transforms.io.dictionary import LoadImaged +from monai.transforms.post.dictionary import Invertd +from monai.transforms.spatial.dictionary import Spacingd +from monai.transforms.utility.dictionary import ( + CastToTyped, + EnsureChannelFirstd, + EnsureTyped, +) +from numpy.typing import NDArray +from torch.amp.autocast_mode import autocast + + +class ModelHandler: + """Class for model loading, inference and post processing""" + + def __init__(self, device: str) -> "ModelHandler": + """Initialize the ModelHandler class. + + Args: + device (str): Device to use for inference. + + Returns: + ModelHandler: ModelHandler instance. + """ + + self.device = torch.device(device) + # get location of model weights + self.model_weights_folder = Path( + "/home/marcelrosier/stroke_segmentor/NVAUTO" + ) # check_weights_path()# TODO zenodo download logic + self.checkpoints = [ + self.model_weights_folder / "ts" / f"model{i}.ts" for i in range(15) + ] + + self.transforms = self._get_transforms() + + def _get_transforms(self) -> Compose: + """Get the transforms to be applied to the input data. + + Returns: + Compose: Composed transforms. + """ + load_keys = ["image"] + + return Compose( + [ + LoadImaged(keys=load_keys), + EnsureChannelFirstd(keys=load_keys), + CastToTyped(keys=["image"], dtype=np.float32), + EnsureTyped(keys=load_keys, data_type="tensor"), + Spacingd(keys=["image"], pixdim=[1, 1, 1], mode=["bilinear"]), + NormalizeIntensityd(keys="image", nonzero=True, channel_wise=True), + ] + ) + + def _get_data_loader( + self, adc_path: str | Path, dwi_path: str | Path + ) -> DataLoader: + """Get the data loader for the input data. + + Args: + adc_path (str | Path): Path to the ADC image. + dwi_path (str | Path): Path to the DWI image. + + Returns: + DataLoader: DataLoader for the input data. + """ + + files = [{"image": [adc_path, dwi_path]}] + + ds = Dataset( + data=files, + transform=self.transforms, + ) + return DataLoader( + ds, + batch_size=1, + shuffle=False, + num_workers=0, + sampler=None, + ) + + def infer( + self, + adc_path: str | Path, + dwi_path: str | Path, + ) -> NDArray: + """Run inference on the provided ADC and DWI images. + + Args: + adc_path (str | Path): Path to the ADC image. + dwi_path (str | Path): Path to the DWI image. + + Returns: + NDArray: The predicted segmentation mask. + """ + + dataloader = self._get_data_loader(adc_path, dwi_path) + model_inferer = SlidingWindowInferer( + roi_size=[192, 192, 128], + overlap=0.625, + mode="gaussian", + cache_roi_weight_map=True, + sw_batch_size=2, + ) + + with torch.no_grad(): + for idx, batch_data in enumerate(dataloader): + image = batch_data["image"].cuda(0) + + all_probs = [] + for checkpoint in self.checkpoints: + + model = torch.jit.load(checkpoint) + model.cuda(0) + model.eval() + + with autocast("cuda", enabled=True): + logits = model_inferer(inputs=image, network=model) + + probs = torch.softmax(logits.float(), dim=1) + + batch_data["pred"] = probs + inverter = Invertd( + keys="pred", + transform=self.transforms, + orig_keys="image", + meta_keys="pred_meta_dict", + nearest_interp=False, + to_tensor=True, + ) + probs = [ + inverter(x)["pred"] for x in decollate_batch(batch_data) + ] # invert resampling if any + probs = torch.stack(probs, dim=0) + # print('inverted resampling', logits.shape) + + all_probs.append(probs.cpu()) + + probs = sum(all_probs) / len(all_probs) # mean + labels = torch.argmax(probs, dim=1).cpu().numpy().astype(np.int8) + + prediction = labels[0].copy() + + prediction = prediction.transpose((2, 1, 0)) + + return prediction.astype(int) From a62faf360b178e902a1139b666224a3c85d8628b Mon Sep 17 00:00:00 2001 From: Marcel Rosier Date: Sat, 9 Aug 2025 11:35:09 +0200 Subject: [PATCH 05/24] Make typing backwards compatible --- stroke_segmentor/inferer.py | 19 +++++++++++-------- stroke_segmentor/model_handler.py | 9 ++++++--- 2 files changed, 17 insertions(+), 11 deletions(-) diff --git a/stroke_segmentor/inferer.py b/stroke_segmentor/inferer.py index a680784..aa53352 100644 --- a/stroke_segmentor/inferer.py +++ b/stroke_segmentor/inferer.py @@ -1,11 +1,14 @@ +from __future__ import annotations + from pathlib import Path -from typing import Optional +from typing import Optional, Union -import SimpleITK import numpy as np -from stroke_segmentor.model_handler import ModelHandler +import SimpleITK from numpy.typing import NDArray +from stroke_segmentor.model_handler import ModelHandler + class Inferer: @@ -18,9 +21,9 @@ def __init__( def _save( self, - dwi_path: str | Path, + dwi_path: Union[str, Path], prediction: NDArray, - segmentation_path: str | Path, + segmentation_path: Union[str, Path], ) -> None: """Save the prediction as a SimpleITK image. @@ -52,9 +55,9 @@ def _save( def infer( self, - adc_path: str | Path, - dwi_path: str | Path, - segmentation_path: Optional[str | Path] = None, + adc_path: Union[str, Path], + dwi_path: Union[str, Path], + segmentation_path: Optional[Union[str, Path]] = None, ) -> NDArray: """Run inference on the provided ADC and DWI images. diff --git a/stroke_segmentor/model_handler.py b/stroke_segmentor/model_handler.py index fe50ea6..550a155 100644 --- a/stroke_segmentor/model_handler.py +++ b/stroke_segmentor/model_handler.py @@ -1,6 +1,7 @@ from __future__ import annotations from pathlib import Path +from typing import Union import numpy as np import torch @@ -66,7 +67,9 @@ def _get_transforms(self) -> Compose: ) def _get_data_loader( - self, adc_path: str | Path, dwi_path: str | Path + self, + adc_path: Union[str, Path], + dwi_path: Union[str, Path], ) -> DataLoader: """Get the data loader for the input data. @@ -94,8 +97,8 @@ def _get_data_loader( def infer( self, - adc_path: str | Path, - dwi_path: str | Path, + adc_path: Union[str, Path], + dwi_path: Union[str, Path], ) -> NDArray: """Run inference on the provided ADC and DWI images. From 0835d3643bddd42b026cf1430466cc5be42b88d7 Mon Sep 17 00:00:00 2001 From: Marcel Rosier Date: Sat, 9 Aug 2025 11:40:06 +0200 Subject: [PATCH 06/24] Add intro, minimal example and part of citation info --- README.md | 27 +++++++++++++++------------ 1 file changed, 15 insertions(+), 12 deletions(-) diff --git a/README.md b/README.md index 6caea7e..8feaeaf 100644 --- a/README.md +++ b/README.md @@ -1,14 +1,13 @@ -# stroke_segmentor +# Stroke Segmentor [![Python Versions](https://img.shields.io/pypi/pyversions/stroke_segmentor)](https://pypi.org/project/stroke_segmentor/) [![Stable Version](https://img.shields.io/pypi/v/stroke_segmentor?label=stable)](https://pypi.python.org/pypi/stroke_segmentor/) [![Documentation Status](https://readthedocs.org/projects/stroke_segmentor/badge/?version=latest)](http://stroke_segmentor.readthedocs.io/?badge=latest) [![tests](https://github.com/BrainLesion/stroke_segmentor/actions/workflows/tests.yml/badge.svg)](https://github.com/BrainLesion/stroke_segmentor/actions/workflows/tests.yml) -[![codecov](https://codecov.io/gh/BrainLesion/stroke_segmentor/graph/badge.svg?token=A7FWUKO9Y4)](https://codecov.io/gh/BrainLesion/stroke_segmentor) [![License](https://img.shields.io/badge/License-Apache%202.0-blue.svg)](https://opensource.org/licenses/Apache-2.0) + -Description -## Features +State-of-the-art ischemic stroke lesion segmentation in MRI ## Installation @@ -25,19 +24,23 @@ pip install stroke_segmentor A minimal example to create a segmentation could look like this: ```python - # example +from stroke_segmentor.inferer import Inferer + +inferer = Inferer() +pred = inferer.infer( + dwi_path="path/to/dwi.nii.gz", + adc_path="path/to/adc.nii.gz", + segmentation_path="seg.nii.gz", # optional. the numpy array is always returned for direct usage +) ``` - - - ## Citation -If you use stroke_segmentor in your research, please cite it to support the development! +`stroke_segmentor` is part of the [BrainLesion](https://github.com/BrainLesion) suite. +Please cite it support the development! +https://github.com/BrainLesion#-citing-brainlesion-suite -``` -TODO: citation will be added asap -``` + > TODO: citations for deep isles and NVAUTO ## Contributing From d292fffdb41453360c7ebf15631b058b42dc3c55 Mon Sep 17 00:00:00 2001 From: Marcel Rosier Date: Thu, 21 Aug 2025 17:04:25 +0200 Subject: [PATCH 07/24] Add zenodo downloader and tests --- stroke_segmentor/zenodo.py | 191 +++++++++++++++++++++++++++++++++++++ tests/test_dummy.py | 2 - tests/test_zenodo.py | 173 +++++++++++++++++++++++++++++++++ 3 files changed, 364 insertions(+), 2 deletions(-) create mode 100644 stroke_segmentor/zenodo.py delete mode 100644 tests/test_dummy.py create mode 100644 tests/test_zenodo.py diff --git a/stroke_segmentor/zenodo.py b/stroke_segmentor/zenodo.py new file mode 100644 index 0000000..efe2880 --- /dev/null +++ b/stroke_segmentor/zenodo.py @@ -0,0 +1,191 @@ +from __future__ import annotations + +import shutil +import zipfile +from io import BytesIO +from pathlib import Path +from typing import Dict, List, Tuple + +import requests +from loguru import logger +from rich.progress import Progress, SpinnerColumn, TextColumn + +WEIGHTS_FOLDER = Path(__file__).parent / "weights" +WEIGHTS_RECORD_ID = "16920681" + + +def fetch_weights() -> Path: + """ + Ensure that the required weights are available locally, downloading them if necessary. + + Returns: + Path: The path to the folder containing the atlases. + """ + record = ZenodoRecord( + record_id=WEIGHTS_RECORD_ID, + target_dir=WEIGHTS_FOLDER, + label="weights", + ) + return record.fetch() + + +class ZenodoException(Exception): + """Raised when Zenodo cannot be reached or the request fails.""" + + pass + + +class ZenodoRecord: + BASE_URL = "https://zenodo.org/api/records" + + def __init__( + self, + record_id: str, + target_dir: Path, + label: str = "asset", + ): + self.record_id = record_id + self.target_dir = target_dir + self.label = label + + def fetch(self) -> Path: + """Fetch the latest version of the record from Zenodo or from local storage.""" + zenodo_response = self._get_metadata_and_archive_url() + + pattern = self._glob_pattern() + matching_folders = list(self.target_dir.glob(pattern)) + latest_local = self._get_latest_version_folder_name(matching_folders) + + if not latest_local: + if not zenodo_response: + msg = f"{self.label.title()} not found locally and Zenodo could not be reached." + logger.error(msg) + raise ZenodoException(msg) + + logger.info(f"{self.label.title()} not found locally.") + metadata, archive_url = zenodo_response + return self._download(metadata, archive_url) + + logger.info(f"Found local {self.label}: {latest_local}") + + if not zenodo_response: + logger.warning(f"Zenodo unreachable. Using latest downloaded {self.label}.") + return self.target_dir / latest_local + + metadata, archive_url = zenodo_response + remote_version = metadata["version"] + local_version = latest_local.split("_v")[1] + + if remote_version == local_version: + logger.info(f"Latest {self.label} ({remote_version}) already present.") + return self.target_dir / latest_local + + logger.info( + f"New version of {self.label} available on Zenodo ({remote_version}). Replacing local copy..." + ) + shutil.rmtree( + self.target_dir / latest_local, + onerror=lambda func, path, excinfo: logger.warning( + f"Failed to delete {path}: {excinfo}" + ), + ) + return self._download(metadata, archive_url) + + def _glob_pattern(self) -> str: + return f"{self.record_id}_v*.*.*" + + def _build_folder_path( + self, + version: str, + ) -> Path: + return self.target_dir / f"{self.record_id}_v{version}" + + def _get_latest_version_folder_name( + self, + folders: List[Path], + ) -> str | None: + if not folders: + return None + latest = sorted( + folders, + reverse=True, + key=lambda x: tuple(map(int, str(x.name).split("_v")[1].split("."))), + )[0] + if not list(latest.glob("*")): + return None + return latest.name + + def _get_metadata_and_archive_url(self) -> Tuple[Dict, str] | None: + try: + response = requests.get(f"{self.BASE_URL}/{self.record_id}") + if response.status_code != 200: + error_msg = ( + f"Cannot find record '{self.record_id}' on Zenodo " + f"({response.status_code=})." + ) + logger.error(error_msg) + raise ZenodoException(error_msg) + + data = response.json() + return data["metadata"], data["links"]["archive"] + + except requests.exceptions.RequestException as e: + logger.warning(f"Failed to fetch metadata from Zenodo: {e}") + return None + + def _download( + self, + metadata: Dict, + archive_url: str, + ) -> Path: + folder = self._build_folder_path(metadata["version"]) + folder.mkdir(parents=True, exist_ok=True) + + logger.info(f"Downloading {self.label} from Zenodo. This may take a while...") + + response = requests.get(archive_url, stream=True) + if response.status_code != 200: + msg = ( + f"Failed to download {self.label}. Status code: {response.status_code}" + ) + logger.error(msg) + raise ZenodoException(msg) + + self._extract_archive(response, folder) + logger.info(f"{self.label.title()} extracted to {folder}") + return folder + + def _extract_archive( + self, + response: requests.Response, + folder: Path, + ): + chunk_size = 1024 # 1KB + buffer = BytesIO() + + with Progress( + SpinnerColumn(), + TextColumn(f"[cyan]Downloading {self.label}..."), + TextColumn("[cyan]{task.completed:.2f} MB"), + transient=True, + ) as progress: + task = progress.add_task("", total=None) + for chunk in response.iter_content(chunk_size=chunk_size): + buffer.write(chunk) + progress.update(task, advance=len(chunk) / (chunk_size**2)) + + with zipfile.ZipFile(buffer) as z: + z.extractall(folder) + + for file in folder.iterdir(): + if file.is_file() and file.suffix == ".zip": + with zipfile.ZipFile(file) as inner_zip: + files = inner_zip.namelist() + with Progress(transient=True) as progress: + task = progress.add_task( + f"[cyan]Extracting inner zip...", total=len(files) + ) + for i, f in enumerate(files): + inner_zip.extract(f, folder) + progress.update(task, completed=i + 1) + file.unlink() # Remove inner zip after extraction diff --git a/tests/test_dummy.py b/tests/test_dummy.py deleted file mode 100644 index f4f5361..0000000 --- a/tests/test_dummy.py +++ /dev/null @@ -1,2 +0,0 @@ -def test_dummy(): - assert True diff --git a/tests/test_zenodo.py b/tests/test_zenodo.py new file mode 100644 index 0000000..fab7080 --- /dev/null +++ b/tests/test_zenodo.py @@ -0,0 +1,173 @@ +from pathlib import Path +from unittest.mock import MagicMock, patch + +import pytest +import requests + +from stroke_segmentor.zenodo import ( + ZenodoException, + ZenodoRecord, + fetch_weights, +) + +# ---- Fixtures ---- + + +@pytest.fixture +def dummy_metadata(): + return { + "version": "1.2.3", + "title": "Test Record", + } + + +@pytest.fixture +def dummy_archive_url(): + return "https://zenodo.org/record/dummy/archive.zip" + + +@pytest.fixture +def dummy_zenodo_response(dummy_metadata, dummy_archive_url): + return dummy_metadata, dummy_archive_url + + +# ---- Tests for _get_metadata_and_archive_url ---- + + +def test_get_metadata_and_archive_url_success( + monkeypatch, dummy_metadata, dummy_archive_url +): + response_mock = MagicMock() + response_mock.status_code = 200 + response_mock.json.return_value = { + "metadata": dummy_metadata, + "links": {"archive": dummy_archive_url}, + } + + monkeypatch.setattr("requests.get", lambda *args, **kwargs: response_mock) + record = ZenodoRecord("123", Path("/tmp"), "test") + + metadata, url = record._get_metadata_and_archive_url() + + assert metadata == dummy_metadata + assert url == dummy_archive_url + + +def test_get_metadata_and_archive_url_failure(monkeypatch): + response_mock = MagicMock() + response_mock.status_code = 404 + + monkeypatch.setattr("requests.get", lambda *args, **kwargs: response_mock) + record = ZenodoRecord("invalid", Path("/tmp"), "test") + + with pytest.raises(ZenodoException): + record._get_metadata_and_archive_url() + + +@patch( + "requests.get", side_effect=requests.exceptions.RequestException("Connection error") +) +def test_get_metadata_and_archive_url_connection_error(mock_get): + record = ZenodoRecord("123", Path("/tmp"), "test") + + assert record._get_metadata_and_archive_url() is None + + +# ---- Tests for _get_latest_version_folder_name ---- + + +def test_get_latest_version_folder_name(tmp_path): + folder = tmp_path / "123_v1.2.3" + folder.mkdir() + (folder / "dummy.txt").touch() + + record = ZenodoRecord("123", tmp_path, "test") + result = record._get_latest_version_folder_name(list(tmp_path.glob("*"))) + + assert result == "123_v1.2.3" + + +def test_get_latest_version_folder_name_empty(tmp_path): + record = ZenodoRecord("123", tmp_path, "test") + assert record._get_latest_version_folder_name([]) is None + + +def test_get_latest_version_folder_name_ignores_empty_folder(tmp_path): + folder = tmp_path / "123_v1.2.3" + folder.mkdir() + record = ZenodoRecord("123", tmp_path, "test") + assert record._get_latest_version_folder_name([folder]) is None + + +# ---- Tests for fetch() method ---- + + +@patch.object(ZenodoRecord, "_get_metadata_and_archive_url") +@patch.object(ZenodoRecord, "_download") +def test_fetch_downloads_new_if_no_local( + mock_download, mock_metadata, tmp_path, dummy_zenodo_response +): + mock_metadata.return_value = dummy_zenodo_response + mock_download.return_value = tmp_path / "123_v1.2.3" + + record = ZenodoRecord("123", tmp_path, "test") + result = record.fetch() + + assert result.name == "123_v1.2.3" + mock_download.assert_called_once() + + +@patch.object(ZenodoRecord, "_get_metadata_and_archive_url", return_value=None) +def test_fetch_zenodo_unreachable_raises(mock_metadata, tmp_path): + record = ZenodoRecord("123", tmp_path, "test") + + with pytest.raises(ZenodoException): + record.fetch() + + +@patch.object(ZenodoRecord, "_get_metadata_and_archive_url") +@patch.object(ZenodoRecord, "_download") +def test_fetch_skips_if_latest_present( + mock_download, mock_metadata, tmp_path, dummy_zenodo_response +): + local_folder = tmp_path / "123_v1.2.3" + local_folder.mkdir() + (local_folder / "dummy.txt").touch() + + mock_metadata.return_value = dummy_zenodo_response + record = ZenodoRecord("123", tmp_path, "test") + + result = record.fetch() + assert result.name == "123_v1.2.3" + mock_download.assert_not_called() + + +@patch.object(ZenodoRecord, "_get_metadata_and_archive_url") +@patch.object(ZenodoRecord, "_download") +def test_fetch_replaces_old_version( + mock_download, mock_metadata, tmp_path, dummy_zenodo_response +): + old_folder = tmp_path / "123_v1.0.0" + old_folder.mkdir() + (old_folder / "dummy.txt").touch() + + mock_metadata.return_value = dummy_zenodo_response + mock_download.return_value = tmp_path / "123_v1.2.3" + + record = ZenodoRecord("123", tmp_path, "test") + + result = record.fetch() + assert result.name == "123_v1.2.3" + assert not old_folder.exists() + mock_download.assert_called_once() + + +# ---- fetch_weights ---- + + +@patch("stroke_segmentor.zenodo.ZenodoRecord.fetch") +def test_fetch_weights_calls_fetch(mock_fetch): + mock_fetch.return_value = Path("/fake/path") + result = fetch_weights() + assert result == Path("/fake/path") + mock_fetch.assert_called_once() From 08c15af13bf7dcbb2c9145c45bef8d157bc49a49 Mon Sep 17 00:00:00 2001 From: Marcel Rosier Date: Thu, 21 Aug 2025 17:04:54 +0200 Subject: [PATCH 08/24] Integrate zenodo downloader and fix type issues Remove unnecessary loop --- stroke_segmentor/model_handler.py | 74 ++++++++++++++++--------------- 1 file changed, 38 insertions(+), 36 deletions(-) diff --git a/stroke_segmentor/model_handler.py b/stroke_segmentor/model_handler.py index 550a155..9dc11a5 100644 --- a/stroke_segmentor/model_handler.py +++ b/stroke_segmentor/model_handler.py @@ -1,7 +1,7 @@ from __future__ import annotations from pathlib import Path -from typing import Union +from typing import Any, Dict, List, Union import numpy as np import torch @@ -22,11 +22,13 @@ from numpy.typing import NDArray from torch.amp.autocast_mode import autocast +from stroke_segmentor.zenodo import fetch_weights + class ModelHandler: """Class for model loading, inference and post processing""" - def __init__(self, device: str) -> "ModelHandler": + def __init__(self, device: str): """Initialize the ModelHandler class. Args: @@ -38,11 +40,9 @@ def __init__(self, device: str) -> "ModelHandler": self.device = torch.device(device) # get location of model weights - self.model_weights_folder = Path( - "/home/marcelrosier/stroke_segmentor/NVAUTO" - ) # check_weights_path()# TODO zenodo download logic + self.model_weights_folder = fetch_weights() self.checkpoints = [ - self.model_weights_folder / "ts" / f"model{i}.ts" for i in range(15) + self.model_weights_folder / f"model{i}.ts" for i in range(15) ] self.transforms = self._get_transforms() @@ -120,43 +120,45 @@ def infer( ) with torch.no_grad(): - for idx, batch_data in enumerate(dataloader): - image = batch_data["image"].cuda(0) + batch_data: Dict[str, Any] = next(iter(dataloader)) + image = batch_data["image"].cuda(0) + + all_probs = [] + for checkpoint in self.checkpoints: - all_probs = [] - for checkpoint in self.checkpoints: + model = torch.jit.load(checkpoint) + model.cuda(0) + model.eval() - model = torch.jit.load(checkpoint) - model.cuda(0) - model.eval() + with autocast("cuda", enabled=True): + logits = model_inferer(inputs=image, network=model) - with autocast("cuda", enabled=True): - logits = model_inferer(inputs=image, network=model) + assert isinstance(logits, torch.Tensor) - probs = torch.softmax(logits.float(), dim=1) + probs = torch.softmax(logits.float(), dim=1) - batch_data["pred"] = probs - inverter = Invertd( - keys="pred", - transform=self.transforms, - orig_keys="image", - meta_keys="pred_meta_dict", - nearest_interp=False, - to_tensor=True, - ) - probs = [ - inverter(x)["pred"] for x in decollate_batch(batch_data) - ] # invert resampling if any - probs = torch.stack(probs, dim=0) - # print('inverted resampling', logits.shape) + batch_data["pred"] = probs + inverter = Invertd( + keys="pred", + transform=self.transforms, + orig_keys="image", + meta_keys="pred_meta_dict", + nearest_interp=False, + to_tensor=True, + ) + probs = [ + inverter(x)["pred"] for x in decollate_batch(batch_data) + ] # invert resampling if any + probs = torch.stack(probs, dim=0) + # print('inverted resampling', logits.shape) - all_probs.append(probs.cpu()) + all_probs.append(probs.cpu()) - probs = sum(all_probs) / len(all_probs) # mean - labels = torch.argmax(probs, dim=1).cpu().numpy().astype(np.int8) + avg_probs = torch.mean(torch.stack(all_probs), dim=0) + labels = torch.argmax(avg_probs, dim=1).cpu().numpy().astype(np.int8) - prediction = labels[0].copy() + prediction = labels[0].copy() - prediction = prediction.transpose((2, 1, 0)) + prediction = prediction.transpose((2, 1, 0)) - return prediction.astype(int) + return prediction.astype(int) From c42c30e39c9ce7b8c215ac5c6f86323c5246fe1b Mon Sep 17 00:00:00 2001 From: Marcel Rosier Date: Thu, 21 Aug 2025 17:05:14 +0200 Subject: [PATCH 09/24] Add weights --- .gitignore | 2 ++ 1 file changed, 2 insertions(+) diff --git a/.gitignore b/.gitignore index ec928a2..77b0594 100644 --- a/.gitignore +++ b/.gitignore @@ -163,3 +163,5 @@ testdata NVAUTO *.nii.gz *.ipynb + +stroke_segmentor/weights \ No newline at end of file From 2611b2697afa115905cc1d24c5f94c714508c586 Mon Sep 17 00:00:00 2001 From: Marcel Rosier Date: Thu, 21 Aug 2025 17:05:33 +0200 Subject: [PATCH 10/24] Add loguru, limit python to <4.0 --- pyproject.toml | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/pyproject.toml b/pyproject.toml index 5d86d6f..523d164 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -21,11 +21,12 @@ readme = "README.md" exclude = ["examples", "benchmark"] [tool.poetry.dependencies] -python = ">=3.10" +python = "^3.10" rich = "^13.9.4" monai = "^1.5.0" simpleitk = ">=2.2.1" nibabel = "^5.3.2" +loguru = "^0.7.3" [tool.poetry.group.dev.dependencies] pytest = ">=8.0.0" From 6eb47d3d68cb300303c6c1ebbeb8e94b946c7247 Mon Sep 17 00:00:00 2001 From: Marcel Rosier Date: Thu, 21 Aug 2025 17:05:43 +0200 Subject: [PATCH 11/24] Add citation info --- README.md | 10 ++++++---- 1 file changed, 6 insertions(+), 4 deletions(-) diff --git a/README.md b/README.md index 8feaeaf..054fa2b 100644 --- a/README.md +++ b/README.md @@ -36,11 +36,13 @@ pred = inferer.infer( ## Citation -`stroke_segmentor` is part of the [BrainLesion](https://github.com/BrainLesion) suite. -Please cite it support the development! -https://github.com/BrainLesion#-citing-brainlesion-suite +> [!IMPORTANT] +> `stroke_segmentor` is part of the [BrainLesion](https://github.com/BrainLesion) suite. +> Please cite it support the development! +> https://github.com/BrainLesion#-citing-brainlesion-suite - > TODO: citations for deep isles and NVAUTO + This project is based on [DeepISLES](https://github.com/ezequieldlrosa/DeepIsles) and offers its NVAUTO algorithm. + Please cite the [original manuscript](https://github.com/ezequieldlrosa/DeepIsles?tab=readme-ov-file#citations). ## Contributing From eb4ba8b7abe22400b215f19e87d164939c2fcdef Mon Sep 17 00:00:00 2001 From: Marcel Rosier Date: Thu, 21 Aug 2025 17:16:19 +0200 Subject: [PATCH 12/24] Disable logger by default --- stroke_segmentor/__init__.py | 3 +++ 1 file changed, 3 insertions(+) diff --git a/stroke_segmentor/__init__.py b/stroke_segmentor/__init__.py index e69de29..bb35ec8 100644 --- a/stroke_segmentor/__init__.py +++ b/stroke_segmentor/__init__.py @@ -0,0 +1,3 @@ +from loguru import logger + +logger.disable("stroke_segmentor") From 1ac260b3d66b170afec5d685394746a58d80ba0c Mon Sep 17 00:00:00 2001 From: Marcel Rosier Date: Thu, 21 Aug 2025 17:32:16 +0200 Subject: [PATCH 13/24] Add CPU support --- stroke_segmentor/inferer.py | 5 ++--- stroke_segmentor/model_handler.py | 22 +++++++++++++--------- 2 files changed, 15 insertions(+), 12 deletions(-) diff --git a/stroke_segmentor/inferer.py b/stroke_segmentor/inferer.py index aa53352..7b7b82b 100644 --- a/stroke_segmentor/inferer.py +++ b/stroke_segmentor/inferer.py @@ -14,10 +14,9 @@ class Inferer: def __init__( self, + force_cpu: bool = False, ): - self.model_weights_folder = "" - self.device = "cuda" - self.model_handler = ModelHandler(device=self.device) + self.model_handler = ModelHandler(force_cpu=force_cpu) def _save( self, diff --git a/stroke_segmentor/model_handler.py b/stroke_segmentor/model_handler.py index 9dc11a5..6b9fab1 100644 --- a/stroke_segmentor/model_handler.py +++ b/stroke_segmentor/model_handler.py @@ -1,5 +1,6 @@ from __future__ import annotations +from contextlib import nullcontext from pathlib import Path from typing import Any, Dict, List, Union @@ -28,17 +29,19 @@ class ModelHandler: """Class for model loading, inference and post processing""" - def __init__(self, device: str): + def __init__(self, force_cpu: bool = False): """Initialize the ModelHandler class. Args: - device (str): Device to use for inference. + force_cpu (bool): Whether to force the use of CPU for inference. Returns: ModelHandler: ModelHandler instance. """ - self.device = torch.device(device) + self.device = torch.device( + "cuda" if torch.cuda.is_available() and not force_cpu else "cpu" + ) # get location of model weights self.model_weights_folder = fetch_weights() self.checkpoints = [ @@ -121,20 +124,21 @@ def infer( with torch.no_grad(): batch_data: Dict[str, Any] = next(iter(dataloader)) - image = batch_data["image"].cuda(0) + image = batch_data["image"].to(self.device) all_probs = [] for checkpoint in self.checkpoints: - model = torch.jit.load(checkpoint) - model.cuda(0) + model = torch.jit.load(checkpoint).to(self.device) model.eval() - with autocast("cuda", enabled=True): + with ( + autocast("cuda", enabled=True) + if self.device.type == "cuda" + else nullcontext() + ): logits = model_inferer(inputs=image, network=model) - assert isinstance(logits, torch.Tensor) - probs = torch.softmax(logits.float(), dim=1) batch_data["pred"] = probs From 20eb65f73c6290b3141fee3f56312ee1c6dba230 Mon Sep 17 00:00:00 2001 From: Marcel Rosier Date: Thu, 21 Aug 2025 17:36:22 +0200 Subject: [PATCH 14/24] Add basic RTD page --- Makefile | 20 ++++++++++++ docs/README_preprocessed.md | 57 +++++++++++++++++++++++++++++++++++ docs/source/conf.py | 2 +- docs/source/index.rst | 3 ++ docs/source/inferer.rst | 5 +++ docs/source/model_handler.rst | 5 +++ make.bat | 35 +++++++++++++++++++++ 7 files changed, 126 insertions(+), 1 deletion(-) create mode 100644 Makefile create mode 100644 docs/README_preprocessed.md create mode 100644 docs/source/inferer.rst create mode 100644 docs/source/model_handler.rst create mode 100644 make.bat diff --git a/Makefile b/Makefile new file mode 100644 index 0000000..d0c3cbf --- /dev/null +++ b/Makefile @@ -0,0 +1,20 @@ +# Minimal makefile for Sphinx documentation +# + +# You can set these variables from the command line, and also +# from the environment for the first two. +SPHINXOPTS ?= +SPHINXBUILD ?= sphinx-build +SOURCEDIR = source +BUILDDIR = build + +# Put it first so that "make" without argument is like "make help". +help: + @$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O) + +.PHONY: help Makefile + +# Catch-all target: route all unknown targets to Sphinx using the new +# "make mode" option. $(O) is meant as a shortcut for $(SPHINXOPTS). +%: Makefile + @$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O) diff --git a/docs/README_preprocessed.md b/docs/README_preprocessed.md new file mode 100644 index 0000000..590ea1d --- /dev/null +++ b/docs/README_preprocessed.md @@ -0,0 +1,57 @@ +# Stroke Segmentor + +[![Python Versions](https://img.shields.io/pypi/pyversions/stroke_segmentor)](https://pypi.org/project/stroke_segmentor/) +[![Stable Version](https://img.shields.io/pypi/v/stroke_segmentor?label=stable)](https://pypi.python.org/pypi/stroke_segmentor/) +[![Documentation Status](https://readthedocs.org/projects/stroke_segmentor/badge/?version=latest)](http://stroke_segmentor.readthedocs.io/?badge=latest) +[![tests](https://github.com/BrainLesion/stroke_segmentor/actions/workflows/tests.yml/badge.svg)](https://github.com/BrainLesion/stroke_segmentor/actions/workflows/tests.yml) +[![License](https://img.shields.io/badge/License-Apache%202.0-blue.svg)](https://opensource.org/licenses/Apache-2.0) + + +State-of-the-art ischemic stroke lesion segmentation in MRI + + +## Installation + +With a Python 3.8+ environment, you can install `stroke_segmentor` directly from [PyPI](https://pypi.org/project/stroke_segmentor/): + +```bash +pip install stroke_segmentor +``` + + +## Use Cases and Tutorials + +A minimal example to create a segmentation could look like this: + +```python +from stroke_segmentor.inferer import Inferer + +inferer = Inferer() +pred = inferer.infer( + dwi_path="path/to/dwi.nii.gz", + adc_path="path/to/adc.nii.gz", + segmentation_path="seg.nii.gz", # optional. the numpy array is always returned for direct usage +) +``` + +## Citation + +```{IMPORTANT} +`stroke_segmentor` is part of the [BrainLesion](https://github.com/BrainLesion) suite. +Please cite it support the development! +https://github.com/BrainLesion#-citing-brainlesion-suite +``` + This project is based on [DeepISLES](https://github.com/ezequieldlrosa/DeepIsles) and offers its NVAUTO algorithm. + Please cite the [original manuscript](https://github.com/ezequieldlrosa/DeepIsles?tab=readme-ov-file#citations). + +## Contributing + +We welcome all kinds of contributions from the community! + +### Reporting Bugs, Feature Requests and Questions + +Please open a new issue [here](https://github.com/BrainLesion/stroke_segmentor/issues). + +### Code contributions + +Nice to have you on board! Please have a look at our [CONTRIBUTING.md](CONTRIBUTING.md) file. diff --git a/docs/source/conf.py b/docs/source/conf.py index 5e91c72..9240b8f 100644 --- a/docs/source/conf.py +++ b/docs/source/conf.py @@ -17,7 +17,7 @@ # https://www.sphinx-doc.org/en/master/usage/configuration.html#project-information project = "stroke_segmentor" -copyright = "2024, Marcel Rosier et al." +copyright = "2025, Marcel Rosier et al." author = "Marcel Rosier, Florian Kofler" # -- General configuration --------------------------------------------------- diff --git a/docs/source/index.rst b/docs/source/index.rst index 9fb81e3..93b29e3 100644 --- a/docs/source/index.rst +++ b/docs/source/index.rst @@ -20,3 +20,6 @@ Sections :maxdepth: 2 :caption: API Reference: + inferer + model_handler + diff --git a/docs/source/inferer.rst b/docs/source/inferer.rst new file mode 100644 index 0000000..0755b21 --- /dev/null +++ b/docs/source/inferer.rst @@ -0,0 +1,5 @@ +Inferer +=================== + +.. automodule:: stroke_segmentor.inferer + :members: diff --git a/docs/source/model_handler.rst b/docs/source/model_handler.rst new file mode 100644 index 0000000..c632a04 --- /dev/null +++ b/docs/source/model_handler.rst @@ -0,0 +1,5 @@ +Model Handler +=================== + +.. automodule:: stroke_segmentor.model_handler + :members: diff --git a/make.bat b/make.bat new file mode 100644 index 0000000..747ffb7 --- /dev/null +++ b/make.bat @@ -0,0 +1,35 @@ +@ECHO OFF + +pushd %~dp0 + +REM Command file for Sphinx documentation + +if "%SPHINXBUILD%" == "" ( + set SPHINXBUILD=sphinx-build +) +set SOURCEDIR=source +set BUILDDIR=build + +%SPHINXBUILD% >NUL 2>NUL +if errorlevel 9009 ( + echo. + echo.The 'sphinx-build' command was not found. Make sure you have Sphinx + echo.installed, then set the SPHINXBUILD environment variable to point + echo.to the full path of the 'sphinx-build' executable. Alternatively you + echo.may add the Sphinx directory to PATH. + echo. + echo.If you don't have Sphinx installed, grab it from + echo.https://www.sphinx-doc.org/ + exit /b 1 +) + +if "%1" == "" goto help + +%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O% +goto end + +:help +%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O% + +:end +popd From 713f48749564c33aa96adec6b7aa12a8fb845310 Mon Sep 17 00:00:00 2001 From: Marcel Rosier Date: Thu, 21 Aug 2025 17:48:02 +0200 Subject: [PATCH 15/24] Support py3.9 --- pyproject.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pyproject.toml b/pyproject.toml index 523d164..88b140c 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -21,7 +21,7 @@ readme = "README.md" exclude = ["examples", "benchmark"] [tool.poetry.dependencies] -python = "^3.10" +python = "^3.9" rich = "^13.9.4" monai = "^1.5.0" simpleitk = ">=2.2.1" From 902e82bc8224538bb64c1e9dfff0901ab9699411 Mon Sep 17 00:00:00 2001 From: Marcel Rosier Date: Thu, 21 Aug 2025 18:20:35 +0200 Subject: [PATCH 16/24] Add extremely basic tests --- pyproject.toml | 1 + tests/test_inferer.py | 62 +++++++++++++++++++++++++++++++++++++ tests/test_model_handler.py | 19 ++++++++++++ 3 files changed, 82 insertions(+) create mode 100644 tests/test_inferer.py create mode 100644 tests/test_model_handler.py diff --git a/pyproject.toml b/pyproject.toml index 88b140c..f4fd5f5 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -32,6 +32,7 @@ loguru = "^0.7.3" pytest = ">=8.0.0" pytest-cov = ">=5.0.0" flake8 = ">=5.0.1" +pytest-mock = "^3.14.1" [tool.pytest.ini_options] pythonpath = ["."] diff --git a/tests/test_inferer.py b/tests/test_inferer.py new file mode 100644 index 0000000..7b55e88 --- /dev/null +++ b/tests/test_inferer.py @@ -0,0 +1,62 @@ +import numpy as np +import pytest +from pathlib import Path + +import SimpleITK +from stroke_segmentor.inferer import Inferer + + +@pytest.fixture +def mock_model_handler(mocker): + """Fixture to mock ModelHandler inside Inferer.""" + mock = mocker.patch("stroke_segmentor.inferer.ModelHandler") + instance = mock.return_value + instance.infer.return_value = np.array([[1, 0], [0, 1]], dtype=np.uint8) + return instance + + +def test_infer_without_save(mock_model_handler): + inferer = Inferer(force_cpu=True) + + # Run inference + adc = "fake_adc.nii.gz" + dwi = "fake_dwi.nii.gz" + result = inferer.infer(adc_path=adc, dwi_path=dwi) + + # Assertions + assert isinstance(result, np.ndarray) + np.testing.assert_array_equal(result, np.array([[1, 0], [0, 1]], dtype=np.uint8)) + mock_model_handler.infer.assert_called_once_with(adc_path=adc, dwi_path=dwi) + + +def test_infer_with_save(tmp_path, mocker, mock_model_handler): + inferer = Inferer(force_cpu=False) + + adc = "adc_fake.nii.gz" + dwi = "dwi_fake.nii.gz" + seg_out = tmp_path / "segmentation.nii.gz" + + # Mock SimpleITK functions + mock_image = mocker.Mock() + mock_image.GetOrigin.return_value = (0, 0, 0) + mock_image.GetSpacing.return_value = (1, 1, 1) + mock_image.GetDirection.return_value = (1, 0, 0, 0, 1, 0, 0, 0, 1) + + mocker.patch( + "stroke_segmentor.inferer.SimpleITK.ReadImage", return_value=mock_image + ) + mocker.patch( + "stroke_segmentor.inferer.SimpleITK.GetImageFromArray", + return_value=mocker.Mock(), + ) + write_mock = mocker.patch("stroke_segmentor.inferer.SimpleITK.WriteImage") + + # Run inference with save path + result = inferer.infer(adc_path=adc, dwi_path=dwi, segmentation_path=seg_out) + + # Assertions + assert isinstance(result, np.ndarray) + write_mock.assert_called_once() + # Check if file got written to correct path + args, kwargs = write_mock.call_args + assert str(seg_out) in args or kwargs.values() diff --git a/tests/test_model_handler.py b/tests/test_model_handler.py new file mode 100644 index 0000000..739b4e0 --- /dev/null +++ b/tests/test_model_handler.py @@ -0,0 +1,19 @@ +from pathlib import Path + +import numpy as np +import torch + +from stroke_segmentor.model_handler import ModelHandler + + +def test_modelhandler_init_cpu(mocker): + """Check that ModelHandler initializes on CPU if force_cpu=True.""" + mocker.patch( + "stroke_segmentor.model_handler.fetch_weights", + return_value=Path("/fake/weights"), + ) + handler = ModelHandler(force_cpu=True) + + assert handler.device.type == "cpu" + assert len(handler.checkpoints) == 15 + assert all(str(c).startswith("/fake/weights/model") for c in handler.checkpoints) From ca6129cfecd0820ca1ddef4e9bbad96d4e046b37 Mon Sep 17 00:00:00 2001 From: Marcel Rosier Date: Thu, 21 Aug 2025 18:23:50 +0200 Subject: [PATCH 17/24] Add py 3.9, 3.13 to tests --- .github/workflows/tests.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml index ce48f1c..910814e 100644 --- a/.github/workflows/tests.yml +++ b/.github/workflows/tests.yml @@ -16,7 +16,7 @@ jobs: fail-fast: false matrix: os: [ubuntu-latest] #, windows-latest, macos-latest] # Extend to your needs - 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"pytest-ignore-flaky"] +type = ["pytest-mypy"] + +[metadata] +lock-version = "2.1" +python-versions = "^3.9" +content-hash = "4b1a69becdf0da073344a45a30b93f609b5c2cb2a75e9f846b8358db54531469" From d6d14d9d557fe26a85229ec7c9caf57e4d31c6eb Mon Sep 17 00:00:00 2001 From: Marcel Rosier Date: Thu, 21 Aug 2025 18:34:11 +0200 Subject: [PATCH 21/24] Add requests lib --- poetry.lock | 12 ++++++------ pyproject.toml | 1 + 2 files changed, 7 insertions(+), 6 deletions(-) diff --git a/poetry.lock b/poetry.lock index be2d497..dc1d0e1 100644 --- a/poetry.lock +++ b/poetry.lock @@ -75,7 +75,7 @@ version = "2025.8.3" description = "Python package for providing Mozilla's CA Bundle." optional = false python-versions = ">=3.7" -groups = ["docs"] +groups = ["main", "docs"] files = [ {file = "certifi-2025.8.3-py3-none-any.whl", hash = "sha256:f6c12493cfb1b06ba2ff328595af9350c65d6644968e5d3a2ffd78699af217a5"}, {file = "certifi-2025.8.3.tar.gz", hash = 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Open, modern and actively maintained alternative to Chardet." optional = false python-versions = ">=3.7" -groups = ["docs"] +groups = ["main", "docs"] files = [ {file = "charset_normalizer-3.4.3-cp310-cp310-macosx_10_9_universal2.whl", hash = "sha256:fb7f67a1bfa6e40b438170ebdc8158b78dc465a5a67b6dde178a46987b244a72"}, {file = "charset_normalizer-3.4.3-cp310-cp310-manylinux2014_aarch64.manylinux_2_17_aarch64.manylinux_2_28_aarch64.whl", hash = "sha256:cc9370a2da1ac13f0153780040f465839e6cccb4a1e44810124b4e22483c93fe"}, @@ -412,7 +412,7 @@ version = "3.10" description = "Internationalized Domain Names in Applications (IDNA)" optional = false python-versions = ">=3.6" -groups = ["docs"] +groups = ["main", "docs"] files = [ {file = "idna-3.10-py3-none-any.whl", hash = "sha256:946d195a0d259cbba61165e88e65941f16e9b36ea6ddb97f00452bae8b1287d3"}, {file = "idna-3.10.tar.gz", hash = "sha256:12f65c9b470abda6dc35cf8e63cc574b1c52b11df2c86030af0ac09b01b13ea9"}, @@ -1273,7 +1273,7 @@ version = "2.32.5" description = "Python HTTP for Humans." optional = false python-versions = ">=3.9" -groups = ["docs"] +groups = ["main", "docs"] files = [ {file = "requests-2.32.5-py3-none-any.whl", hash = "sha256:2462f94637a34fd532264295e186976db0f5d453d1cdd31473c85a6a161affb6"}, {file = "requests-2.32.5.tar.gz", hash = "sha256:dbba0bac56e100853db0ea71b82b4dfd5fe2bf6d3754a8893c3af500cec7d7cf"}, @@ -1712,7 +1712,7 @@ version = "2.5.0" description = "HTTP library with thread-safe connection pooling, file post, and more." optional = false python-versions = ">=3.9" -groups = ["docs"] +groups = ["main", "docs"] files = [ {file = "urllib3-2.5.0-py3-none-any.whl", hash = "sha256:e6b01673c0fa6a13e374b50871808eb3bf7046c4b125b216f6bf1cc604cff0dc"}, {file = "urllib3-2.5.0.tar.gz", hash = "sha256:3fc47733c7e419d4bc3f6b3dc2b4f890bb743906a30d56ba4a5bfa4bbff92760"}, @@ -1764,4 +1764,4 @@ type = ["pytest-mypy"] [metadata] lock-version = "2.1" python-versions = "^3.9" -content-hash = "4b1a69becdf0da073344a45a30b93f609b5c2cb2a75e9f846b8358db54531469" +content-hash = "4a76a34d7ce2f096c2c4bb8eb20752ee62412020b9bcff2da98ba50d87d82a69" diff --git a/pyproject.toml b/pyproject.toml index f4fd5f5..8cf8a9b 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -27,6 +27,7 @@ monai = "^1.5.0" simpleitk = ">=2.2.1" nibabel = "^5.3.2" loguru = "^0.7.3" +requests = "^2.32.5" [tool.poetry.group.dev.dependencies] pytest = ">=8.0.0" From 7e32464394de1e67479733c43b9fd3e84d435eb5 Mon Sep 17 00:00:00 2001 From: neuronflow <7048826+neuronflow@users.noreply.github.com> Date: Sat, 23 Aug 2025 09:42:31 +0200 Subject: [PATCH 22/24] Update stroke_segmentor/zenodo.py Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> --- stroke_segmentor/zenodo.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/stroke_segmentor/zenodo.py b/stroke_segmentor/zenodo.py index efe2880..ec7397f 100644 --- a/stroke_segmentor/zenodo.py +++ b/stroke_segmentor/zenodo.py @@ -19,7 +19,7 @@ def fetch_weights() -> Path: Ensure that the required weights are available locally, downloading them if necessary. Returns: - Path: The path to the folder containing the atlases. + Path: The path to the folder containing the model weights. """ record = ZenodoRecord( record_id=WEIGHTS_RECORD_ID, From 75971137372f2487fad8ca7a7a17b92c28344d3e Mon Sep 17 00:00:00 2001 From: Marcel Rosier Date: Sat, 23 Aug 2025 13:52:28 +0200 Subject: [PATCH 23/24] Add .vscode --- .gitignore | 1 + 1 file changed, 1 insertion(+) diff --git a/.gitignore b/.gitignore index 77b0594..0694516 100644 --- a/.gitignore +++ b/.gitignore @@ -163,5 +163,6 @@ testdata NVAUTO *.nii.gz *.ipynb +.vscode stroke_segmentor/weights \ No newline at end of file From dab7c01fd703d3d7ea54e2a1f3d6b30873b57744 Mon Sep 17 00:00:00 2001 From: Marcel Rosier Date: Sat, 23 Aug 2025 13:52:50 +0200 Subject: [PATCH 24/24] Add docstring, fix differing type casts --- stroke_segmentor/inferer.py | 13 +++++++++++++ stroke_segmentor/model_handler.py | 4 ++-- 2 files changed, 15 insertions(+), 2 deletions(-) diff --git a/stroke_segmentor/inferer.py b/stroke_segmentor/inferer.py index 7b7b82b..0838ee6 100644 --- a/stroke_segmentor/inferer.py +++ b/stroke_segmentor/inferer.py @@ -11,6 +11,19 @@ class Inferer: + """ + Handles inference for stroke segmentation using DWI and ADC images. + This class wraps a model handler to perform inference on given images and can optionally + save the resulting segmentation mask to disk. + + Basic usage: + ``` + .. code-block:: python + + inferer = Inferer() + prediction = inferer.infer(adc_path, dwi_path, segmentation_path) + ``` + """ def __init__( self, diff --git a/stroke_segmentor/model_handler.py b/stroke_segmentor/model_handler.py index 9427423..f7e99cd 100644 --- a/stroke_segmentor/model_handler.py +++ b/stroke_segmentor/model_handler.py @@ -158,10 +158,10 @@ def infer( all_probs.append(probs.cpu()) avg_probs = torch.mean(torch.stack(all_probs), dim=0) - labels = torch.argmax(avg_probs, dim=1).cpu().numpy().astype(np.int8) + labels = torch.argmax(avg_probs, dim=1).cpu().numpy() prediction = labels[0].copy() prediction = prediction.transpose((2, 1, 0)) - return prediction.astype(int) + return prediction.astype(np.int8)