[ENH] use non-linear alignment as default (#234)

* use non linear alignment as default

* update changelog

* fix misc

.circleci/config.yml

@@ -185,7 +185,9 @@ workflows:
                 -   DOCKER_HUB
                 requires:
                 -   test
-
+                filters:
+                    tags:
+                        only: /.*/
 
 
 # VS Code Extension Version: 1.5.1

.github/workflows/package.yml

@@ -8,52 +8,26 @@ on:
         tags:
         -   '*'
 
-defaults:
-    run:
-        shell: bash
-
 jobs:
     package:
-        if: github.event_name == 'push' && startsWith(github.ref, 'refs/tags')
-
-    # Build packages and upload
-        runs-on: ${{ matrix.os }}
-        strategy:
-            matrix:
-                include:
-                -   os: ubuntu-latest
-                    python-version: '3.11'
-
+        runs-on: ubuntu-latest
         steps:
-
         -   uses: actions/checkout@v4
             with:
                 submodules: recursive
                 fetch-depth: 0
-
-        -   name: Set up Python ${{ matrix.python-version }}
+        -   name: Set up Python
             uses: actions/setup-python@v5
             with:
-                python-version: ${{ matrix.python-version }}
-
+                python-version: 3.11
         -   name: Display Python version
             run: python -c "import sys; print(sys.version)"
-
         -   name: Install build
             run: python -m pip install build
-
         -   name: Build sdist and wheel
             run: python -m build
-
-        -   name: Test PyPI upload
-            uses: pypa/gh-action-pypi-publish@release/v1
-            with:
-                user: __token__
-                password: ${{ secrets.TEST_PYPI_API_TOKEN }}
-                repository_url: https://test.pypi.org/legacy/
-                skip_existing: true
-
         -   name: Upload to PyPI (on tags)
+            if: github.event_name == 'push' && startsWith(github.ref, 'refs/tags')
             uses: pypa/gh-action-pypi-publish@release/v1
             with:
                 user: __token__

.github/workflows/test_and_coverage.yml

@@ -19,9 +19,9 @@ jobs:
             matrix:
                 os: [ubuntu-latest, macOS-latest] # windows-latest: do not work. antspyx is not available for windows
                 python-version: ['3.9', '3.10', '3.11']
-                exclude:
-                -   os: macOS-latest # anstpyx install is messed up with macOS and python 3.9
-                    python-version: '3.9'
+                # exclude:
+                # -   os: macOS-latest # anstpyx install is messed up with macOS and python 3.9
+                #     python-version: '3.9'
             fail-fast: false
 
         steps:

.sourcery.yaml

@@ -21,7 +21,6 @@ ignore: # A list of paths or files which Sourcery will ignore.
 -   .tox
 -   node_modules
 -   vendor
--   vendor
 -   bidsmreye/_version.py
 
 rule_settings:
@@ -32,7 +31,7 @@ rule_settings:
     -   refactoring
     -   suggestion
     -   comment
-    python_version: '3.8' # A string specifying the lowest Python version your project supports. Sourcery will not suggest refactorings requiring a higher Python version.
+    python_version: '3.9'
 
 # rules:  # A list of custom rules Sourcery will include in its analysis.
 # - id: no-print-statements
@@ -52,8 +51,8 @@ rule_settings:
 
 # rule_tags: {} # Additional rule tags.
 
-# metrics:
-#   quality_threshold: 25.0
+metrics:
+    quality_threshold: 25.0
 
 # github:
 #   labels: []

Makefile

@@ -48,19 +48,20 @@ clean-test: ## remove test and coverage artifacts
 	rm -fr htmlcov/
 	rm -fr .pytest_cache
 
+
 ## INSTALL
 
 install_dev: clean ## install the package and development dependencies to the active Python's site-packages
 	pip install -e .[dev]
 	make models
 
-release: dist ## package and upload a release
-	twine upload dist/*
-
 dist: clean ## builds source and wheel package
 	python -m build
 	ls -l dist
 
+release: dist ## package and upload a release
+	twine upload dist/*
+
 
 ## PRE-TRAINED MODELS
 .PHONY: models
@@ -83,6 +84,7 @@ models/dataset4_pursuit.h5:
 models/dataset5_free_viewing.h5:
 	bidsmreye_model --model 5_free_viewing
 
+
 ## DOC
 .PHONY: docs docs/source/FAQ.md
 
@@ -129,7 +131,7 @@ prepare: tests/data/moae_fmriprep ## demo: prepares the data of MOAE dataset
 				prepare \
 				-vv \
 				--reset_database \
-				--non_linear_coreg
+				--linear_coreg
 
 generalize: ## demo: predicts labels of MOAE dataset
 	bidsmreye 	$$PWD/tests/data/moae_fmriprep \

bidsmreye/_cli.py

@@ -54,7 +54,7 @@ def cli(argv: Any = sys.argv) -> None:
         model_weights_file=model_weights_file,
         reset_database=args.reset_database,
         bids_filter_file=args.bids_filter_file,
-        non_linear_coreg=bool(getattr(args, "non_linear_coreg", False)),
+        linear_coreg=bool(getattr(args, "linear_coreg", False)),
         log_level_name=log_level_name,
         force=bool(getattr(args, "force", False)),
     )

bidsmreye/_parsers.py

@@ -158,10 +158,13 @@ def common_parser(formatter_class: type[HelpFormatter] = HelpFormatter) -> Argum
     prepare_parser = _add_common_arguments(prepare_parser)
     # TODO make it possible to pass path to a model ?
     prepare_parser.add_argument(
-        "--non_linear_coreg",
+        "--linear_coreg",
         help="""
-Uses a more aggressive (and non-linear) alignment procedure
-to the deepmreye template.""",
+Uses a less aggressive (and linear) alignment procedure
+to the deepmreye template.
+
+May lead to worse results so check your outputs.
+""",
         action="store_true",
     )
 
@@ -190,10 +193,12 @@ def common_parser(formatter_class: type[HelpFormatter] = HelpFormatter) -> Argum
     all_parser = _add_common_arguments(all_parser)
     # TODO make it possible to pass path to a model ?
     all_parser.add_argument(
-        "--non_linear_coreg",
+        "--linear_coreg",
         help="""
-Uses a more aggressive (and non-linear) alignment procedure
+Uses a less aggressive (and linear) alignment procedure
 to the deepmreye template.
+
+May lead to worse results so check your outputs.
 """,
         action="store_true",
     )

bidsmreye/bidsmreye.py

@@ -27,7 +27,7 @@ def bidsmreye(
     model_weights_file: str | None = None,
     reset_database: bool | None = None,
     bids_filter_file: str | None = None,
-    non_linear_coreg: bool = False,
+    linear_coreg: bool = False,
     log_level_name: str | None = None,
     force: bool = False,
 ) -> None:
@@ -50,7 +50,7 @@ def bidsmreye(
         model_weights_file=model_weights_file,
         reset_database=reset_database,
         bids_filter=bids_filter,
-        non_linear_coreg=non_linear_coreg,
+        linear_coreg=linear_coreg,
         force=force,
     )  # type: ignore
 

bidsmreye/configuration.py

@@ -54,7 +54,7 @@ def _check_input_dir(self, attribute: str, value: Path) -> None:
 
     debug: str | bool | None = field(kw_only=True, default=None)
     reset_database: bool = field(kw_only=True, default=False)
-    non_linear_coreg: bool = field(kw_only=True, default=False)
+    linear_coreg: bool = field(kw_only=True, default=False)
     force: bool = field(kw_only=True, default=False)
 
     has_GPU: bool = False

bidsmreye/prepare_data.py

@@ -33,7 +33,7 @@
 log = bidsmreye_log(name="bidsmreye")
 
 
-def coregister_and_extract_data(img: str, non_linear_coreg: bool = False) -> None:
+def coregister_and_extract_data(img: str, linear_coreg: bool = False) -> None:
     """Coregister image to eye template and extract data from eye mask for one image.
 
     :param img: Image to coregister and extract data from
@@ -49,7 +49,7 @@ def coregister_and_extract_data(img: str, non_linear_coreg: bool = False) -> Non
         z_edges,
     ) = preprocess.get_masks()
 
-    transforms = ["Affine", "Affine", "SyNAggro"] if non_linear_coreg else None
+    transforms = None if linear_coreg else ["Affine", "Affine", "SyNAggro"]
 
     preprocess.run_participant(
         img,
@@ -168,7 +168,7 @@ def prepapre_image(
 
     log.info(f"Processing file: {Path(img_path).name}")
 
-    coregister_and_extract_data(img_path, non_linear_coreg=cfg.non_linear_coreg)
+    coregister_and_extract_data(img_path, linear_coreg=cfg.linear_coreg)
 
     deepmreye_mask_report = get_deepmreye_filename(
         layout_in, img=img_path, filetype="report"
@@ -205,8 +205,8 @@ def prepare_data(cfg: Config) -> None:
     subjects = list_subjects(cfg, layout_in)
 
     text = "PREPARING DATA"
-    if cfg.non_linear_coreg:
-        log.info("Using non-linear coregistration")
+    if cfg.linear_coreg:
+        log.info("Using linear coregistration")
 
     with progress_bar(text=text) as progress:
         subject_loop = progress.add_task(

boutiques/bidsmreye_0.4.0.json

@@ -3,7 +3,7 @@
     "description": "bids app using deepMReye to decode eye motion for fMRI time series data",
     "tool-version": "0.4.0",
     "schema-version": "0.5",
-    "command-line": "bidsmreye [VERSION] [BIDS_DIR] [OUTPUT_DIR] [ANALYSIS_LEVEL] [COMMAND] [PARTICIPANT_LABEL] [TASK] [RUN] [SPACE] [LOG_LEVEL] [DEBUG] [RESET_DATABASE] [BIDS_FILTER_FILE] [FORCE] [NON_LINEAR_COREG] [MODEL]",
+    "command-line": "bidsmreye [VERSION] [BIDS_DIR] [OUTPUT_DIR] [ANALYSIS_LEVEL] [COMMAND] [PARTICIPANT_LABEL] [TASK] [RUN] [SPACE] [LOG_LEVEL] [DEBUG] [RESET_DATABASE] [BIDS_FILTER_FILE] [FORCE] [LINEAR_COREG] [MODEL]",
     "inputs": [
         {
             "name": "version",
@@ -132,13 +132,13 @@
             "value-key": "[FORCE]"
         },
         {
-            "name": "non_linear_coreg",
-            "id": "non_linear_coreg",
-            "description": "Uses a more aggressive (and non-linear) alignment procedure to the deepmreye template.",
+            "name": "linear_coreg",
+            "id": "linear_coreg",
+            "description": "Uses a less aggressive (linear) alignment procedure to the deepmreye template.",
             "type": "Flag",
             "optional": true,
-            "command-line-flag": "--non_linear_coreg",
-            "value-key": "[NON_LINEAR_COREG]"
+            "command-line-flag": "--linear_coreg",
+            "value-key": "[LINEAR_COREG]"
         },
         {
             "name": "model",
@@ -187,7 +187,7 @@
                     "reset_database",
                     "debug",
                     "force",
-                    "non_linear_coreg",
+                    "linear_coreg",
                     "log_level",
                     "run",
                     "space",
@@ -199,7 +199,6 @@
                     "reset_database",
                     "debug",
                     "force",
-                    "non_linear_coreg",
                     "log_level",
                     "model",
                     "run",
@@ -212,13 +211,12 @@
                     "reset_database",
                     "debug",
                     "force",
-                    "non_linear_coreg",
+                    "linear_coreg",
                     "log_level",
                     "model",
                     "run",
                     "space",
                     "bids_filter_file",
-                    "participant_label",
                     "task"
                 ]
             }

boutiques/invocation.json

@@ -13,6 +13,6 @@
     "debug": false,
     "reset_database": true,
     "force": false,
-    "non_linear_coreg": true,
+    "linear_coreg": true,
     "model": "1_guided_fixations"
 }

docs/source/CHANGELOG.md

@@ -23,22 +23,21 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### Added
 
-* [ENH] Extra metadata have been added to the output of the `generalize` step to better align with BIDS BEP20 @Remi-Gau in https://github.com/cpp-lln-lab/bidsMReye/pull/232
+* [ENH] Extra metadata have been added to the output of the `generalize` step to better align with BIDS BEP20 by @Remi-Gau in https://github.com/cpp-lln-lab/bidsMReye/pull/232
 
 ### Changed
 
-* [ENH] Output filenames of the prepare step has been changed to use the `timeseries` suffix and the output of the `generalize` step now include the name of the Deepmreye model used to compute them @Remi-Gau in https://github.com/cpp-lln-lab/bidsMReye/pull/232
+* [ENH] Output filenames of the prepare step has been changed to use the `timeseries` suffix and the output of the `generalize` step now include the name of the Deepmreye model used to compute them by @Remi-Gau in https://github.com/cpp-lln-lab/bidsMReye/pull/232
 
-### Deprecated
+* [ENH] use non-linear alignment as default by @Remi-Gau in https://github.com/cpp-lln-lab/bidsMReye/pull/234
 
 ### Removed
 
-### Fixed
-
-* [FIX] do not apply run found for one task to all tasks by @Remi-Gau in https://github.com/cpp-lln-lab/bidsMReye/pull/228
+* [ENH] the `--non_linear_coreg` CLI argument was replaced by the `--linear_coreg` by @Remi-Gau in https://github.com/cpp-lln-lab/bidsMReye/pull/234
 
-### Security
+### Fixed
 
+* [FIX] do not apply `run` found for one task to all tasks by @Remi-Gau in https://github.com/cpp-lln-lab/bidsMReye/pull/228
 
 ## [0.4.0] - 20234-08-05
 

tests/data/derivatives/bidsmreye/dataset_description.json

@@ -66,7 +66,7 @@
                 },
                 "debug": false,
                 "reset_database": false,
-                "non_linear_coreg": false
+                "linear_coreg": false
             }
         }
     ],

tests/test_configuration.py

@@ -17,7 +17,7 @@ def test_Config(data_dir, pybids_test_dataset):
         data_dir,
     )
     assert not cfg.debug
-    assert not cfg.non_linear_coreg
+    assert not cfg.linear_coreg
     assert cfg.input_dir == pybids_test_dataset
     assert cfg.output_dir == data_dir / "bidsmreye"
     assert sorted(cfg.subjects) == ["01", "02", "03", "04", "05"]

tests/test_parsers.py

@@ -14,12 +14,12 @@ def test_parser() -> None:
             "--task",
             "foo",
             "bar",
-            "--non_linear_coreg",
+            "--linear_coreg",
         ]
     )
 
     assert args.task == ["foo", "bar"]
-    assert args.non_linear_coreg
+    assert args.linear_coreg
 
 
 def test_parser_basic() -> None:
@@ -43,7 +43,7 @@ def test_parser_basic() -> None:
     )
 
     assert args.task == ["foo", "bar"]
-    assert args.non_linear_coreg is False
+    assert args.linear_coreg is False
 
 
 def test_download_parser():