Merge branch 'nipreps:main' into automated-releases

docs/conf.py

@@ -39,6 +39,7 @@
     "sphinx.ext.napoleon",
     "sphinx.ext.viewcode",
     "sphinxcontrib.apidoc",
+    "sphinxarg.ext",
 ]
 
 autodoc_mock_imports = [

docs/developers.rst

@@ -28,6 +28,7 @@ Information on specific functions, classes, and methods.
 .. toctree::
    :glob:
 
+   api/eddymotion.cli
    api/eddymotion.data
    api/eddymotion.data.dmri
    api/eddymotion.estimator

docs/index.rst

@@ -14,5 +14,6 @@ Contents
     :maxdepth: 3
 
     installation
+    running
     developers
     changes

docs/running.rst

@@ -0,0 +1,11 @@
+.. _running_eddymotion:
+
+Running *Eddymotion*
+********************
+Command line interface
+----------------------
+.. argparse::
+   :ref: eddymotion.cli.parser._build_parser
+   :prog: eddymotion
+   :nodefault:
+   :nodefaultconst:

pyproject.toml

@@ -51,7 +51,8 @@ doc = [
     "sphinx_rtd_theme",
     "sphinxcontrib-apidoc ~= 0.3.0",
     "sphinxcontrib-napoleon",
-    "sphinxcontrib-versioning"
+    "sphinxcontrib-versioning",
+    "sphinx-argparse",
 ]
 
 dev = [
@@ -79,6 +80,9 @@ docs = ["eddymotion[doc]"]
 tests = ["eddymotion[test]"]
 all = ["eddymotion[doc,test,dev,plotting,resmon,popylar]"]
 
+[project.scripts]
+eddymotion = "eddymotion.cli.run:main"
+
 #
 # Hatch configurations
 #

src/eddymotion/__main__.py

@@ -0,0 +1,33 @@
+# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
+# vi: set ft=python sts=4 ts=4 sw=4 et:
+#
+# Copyright 2024 The NiPreps Developers <[email protected]>
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+#
+# We support and encourage derived works from this project, please read
+# about our expectations at
+#
+#     https://www.nipreps.org/community/licensing/
+#
+"""Entry point for Eddymotion."""
+
+import sys
+
+from . import __name__ as module
+from .cli.run import main
+
+if __name__ == "__main__":
+    if "__main__.py" in sys.argv[0]:
+        sys.argv[0] = f"{sys.executable} -m {module}"
+    main()

src/eddymotion/cli/parser.py

@@ -0,0 +1,134 @@
+# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
+# vi: set ft=python sts=4 ts=4 sw=4 et:
+#
+# Copyright 2024 The NiPreps Developers <[email protected]>
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+#
+# We support and encourage derived works from this project, please read
+# about our expectations at
+#
+#     https://www.nipreps.org/community/licensing/
+#
+"""Parser module."""
+
+from argparse import ArgumentDefaultsHelpFormatter, ArgumentParser, Namespace
+from pathlib import Path
+from typing import Optional
+
+import yaml
+
+
+def _parse_yaml_config(file_path: Path) -> dict:
+    """
+    Parse YAML configuration file.
+
+    Parameters
+    ----------
+    file_path : Path
+        Path to the YAML configuration file.
+
+    Returns
+    -------
+    dict
+        A dictionary containing the parsed YAML configuration.
+    """
+    with open(file_path, "r") as file:
+        config = yaml.safe_load(file)
+    return config
+
+
+def _build_parser() -> ArgumentParser:
+    """
+    Build parser object.
+
+    Returns
+    -------
+    :obj:`~argparse.ArgumentParser`
+        The parser object defining the interface for the command-line.
+    """
+    parser = ArgumentParser(
+        description="A model-based algorithm for the realignment of 4D brain images.",
+        formatter_class=ArgumentDefaultsHelpFormatter,
+    )
+
+    parser.add_argument(
+        "input_file",
+        action="store",
+        type=Path,
+        help="Path to the HDF5 file containing the original DWI data.",
+    )
+    parser.add_argument(
+        "--align_config",
+        action="store",
+        type=_parse_yaml_config,
+        default=None,
+        help="Path to the yaml file containing the parameters to configure the image registration process.",
+    )
+    parser.add_argument(
+        "--models",
+        action="store",
+        nargs="+",
+        default=["b0"],
+        help="Select the diffusion model for registration targets.",
+    )
+    parser.add_argument(
+        "--nthreads",
+        action="store",
+        type=int,
+        default=None,
+        help="Maximum number of threads an individual process may use.",
+    )
+    parser.add_argument(
+        "--njobs",
+        action="store",
+        type=int,
+        default=None,
+        help="Number of parallel jobs.",
+    )
+    parser.add_argument(
+        "--seed",
+        action="store",
+        type=int,
+        default=None,
+        help="Seed the random number generator for deterministic estimation.",
+    )
+    parser.add_argument(
+        "--output_dir",
+        action="store",
+        type=Path,
+        default=Path.cwd(),
+        help="Path to the output directory. Defaults to the current directory. The output file will have the same name as the input file.",
+    )
+
+    return parser
+
+
+def parse_args(args: Optional[list] = None, namespace: Optional[Namespace] = None) -> Namespace:
+    """
+    Parse args and run further checks on the command line.
+
+    Parameters
+    ----------
+    args : list of str, optional
+        List of strings representing the command line arguments. Defaults to None.
+    namespace : :class:`~argparse.Namespace`, optional
+        An object to parse the arguments into. Defaults to None.
+
+    Returns
+    -------
+    :class:`~argparse.Namespace`
+        An object holding the parsed arguments.
+    """
+    parser = _build_parser()
+    return parser.parse_args(args, namespace)

src/eddymotion/cli/run.py

@@ -0,0 +1,65 @@
+# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
+# vi: set ft=python sts=4 ts=4 sw=4 et:
+#
+# Copyright 2024 The NiPreps Developers <[email protected]>
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+#
+# We support and encourage derived works from this project, please read
+# about our expectations at
+#
+#     https://www.nipreps.org/community/licensing/
+#
+"""Eddymotion runner."""
+
+from pathlib import Path
+
+from eddymotion.cli.parser import parse_args
+from eddymotion.data.dmri import DWI
+from eddymotion.estimator import EddyMotionEstimator
+
+
+def main() -> None:
+    """
+    Entry point.
+
+    Returns
+    -------
+    None
+    """
+    args = parse_args()
+
+    # Open the data with the given file path
+    dwi_dataset: DWI = DWI.from_filename(args.input_file)
+
+    estimator: EddyMotionEstimator = EddyMotionEstimator()
+
+    _ = estimator.estimate(
+        dwi_dataset,
+        align_kwargs=args.align_config,
+        models=args.models,
+        omp_nthreads=args.nthreads,
+        njobs=args.njobs,
+        seed=args.seed,
+    )
+
+    # Set the output filename to be the same as the input filename
+    output_filename: str = Path(args.input_file).name
+    output_path: Path = Path(args.output_dir) / output_filename
+
+    # Save the DWI dataset to the output path
+    dwi_dataset.to_filename(output_path)
+
+
+if __name__ == "__main__":
+    main()