[FIX] save models in output dir (#219)

* save models in output dir

* improve command line help

* change model_name to model

* ignore link

.circleci/config.yml

@@ -99,6 +99,7 @@ jobs:
                           --participant_label 302 307 \
                           --space MNI152NLin2009cAsym \
                           --reset_database \
+                          --model 1to5 \
                           -vv
         -   run:
                 name: rerun prepare - fast as output already exists

Makefile

@@ -70,19 +70,19 @@ clean-models: ## remove pretrained models
 	rm -fr models/
 
 models:
-	bidsmreye_model --model_name 1to6
+	bidsmreye_model --model 1to6
 models/dataset1_guided_fixations.h5:
 	bidsmreye_model
 models/dataset2_pursuit.h5:
-	bidsmreye_model --model_name 2_pursuit
+	bidsmreye_model --model 2_pursuit
 models/dataset3_openclosed.h5:
-	bidsmreye_model --model_name 3_openclosed
+	bidsmreye_model --model 3_openclosed
 models/dataset3_pursuit.h5:
-	bidsmreye_model --model_name 3_pursuit
+	bidsmreye_model --model 3_pursuit
 models/dataset4_pursuit.h5:
-	bidsmreye_model --model_name 4_pursuit
+	bidsmreye_model --model 4_pursuit
 models/dataset5_free_viewing.h5:
-	bidsmreye_model --model_name 5_free_viewing
+	bidsmreye_model --model 5_free_viewing
 
 ## DOC
 .PHONY: docs docs/source/FAQ.md
@@ -137,6 +137,7 @@ generalize: ## demo: predicts labels of MOAE dataset
 				$$PWD/outputs/moae_fmriprep/derivatives \
 				participant \
 				generalize \
+				--model 1_guided_fixations \
 				-vv
 
 
@@ -234,7 +235,7 @@ docker_build:
 docker_build_no_cache:
 	docker build --tag cpplab/bidsmreye:unstable --no-cache --file Dockerfile .
 
-docker_demo: docker_build clean-demo
+docker_demo: clean-demo
 	make docker_prepare_data
 	make docker_generalize
 
@@ -257,7 +258,7 @@ docker_generalize:
 				/home/neuro/data/ \
 				/home/neuro/outputs/ \
 				participant \
-				generalize
+				generalize --model 1_guided_fixations
 
 docker_ds002799: get_ds002799
 # datalad unlock $$PWD/tests/data/ds002799/derivatives/fmriprep/sub-30[27]/ses-*/func/*run-*preproc*bold*

bidsmreye/_cli.py

@@ -69,4 +69,4 @@ def cli_download(argv: Any = sys.argv) -> None:
     parser = download_parser(formatter_class=RichHelpFormatter)
     args = parser.parse_args(argv[1:])
 
-    download(model_name=args.model_name, output_dir=args.output_dir)
+    download(model=args.model, output_dir=args.output_dir)

bidsmreye/_parsers.py

@@ -177,7 +177,7 @@ def common_parser(formatter_class: type[HelpFormatter] = HelpFormatter) -> Argum
     # TODO make it possible to pass path to a model ?
     generalize_parser.add_argument(
         "--model",
-        help="model to use",
+        help=f"Model to use. Default model: {default_model()}.",
         choices=available_models(),
         default=default_model(),
     )
@@ -200,7 +200,7 @@ def common_parser(formatter_class: type[HelpFormatter] = HelpFormatter) -> Argum
     # TODO make it possible to pass path to a model ?
     all_parser.add_argument(
         "--model",
-        help="model to use",
+        help=f"Model to use. Default model: {default_model()}.",
         choices=available_models(),
         default=default_model(),
     )
@@ -228,10 +228,8 @@ def download_parser(
         formatter_class=formatter_class,
     )
     parser.add_argument(
-        "--model_name",
-        help="""
-Model to download.
-        """,
+        "--model",
+        help=f"Model to download. Default model: {default_model()}.",
         choices=available_models(),
         default=default_model(),
     )

bidsmreye/bidsmreye.py

@@ -75,7 +75,12 @@ def bidsmreye(
     if action in {"all", "generalize"} and isinstance(cfg.model_weights_file, str):
         from bidsmreye.download import download
 
-        cfg.model_weights_file = download(cfg.model_weights_file)
+        model_output_dir = cfg.output_dir / "models"
+        model_output_dir.mkdir(exist_ok=True, parents=True)
+
+        cfg.model_weights_file = download(
+            cfg.model_weights_file, output_dir=model_output_dir
+        )
 
     dispatch(analysis_level=analysis_level, action=action, cfg=cfg)
 

bidsmreye/download.py

@@ -16,26 +16,26 @@
 
 
 def download(
-    model_name: str | Path | None = None, output_dir: Path | str | None = None
+    model: str | Path | None = None, output_dir: Path | str | None = None
 ) -> Path | None:
     """Download the models from OSF.
 
-    :param model_name: Model to download. defaults to None
-    :type model_name: str, optional
+    :param model: Model to download. defaults to None
+    :type model: str, optional
 
     :param output_dir: Path where to save the model. Defaults to None.
     :type output_dir: Path, optional
 
     :return: Path to the downloaded model.
     :rtype: Path
     """
-    if not model_name:
-        model_name = default_model()
-    if isinstance(model_name, Path):
-        assert model_name.is_file()
-        return model_name.absolute()
-    if model_name not in available_models():
-        warnings.warn(f"{model_name} is not a valid model name.", stacklevel=3)
+    if not model:
+        model = default_model()
+    if isinstance(model, Path):
+        assert model.is_file()
+        return model.absolute()
+    if model not in available_models():
+        warnings.warn(f"{model} is not a valid model name.", stacklevel=3)
         return None
 
     if output_dir is None:
@@ -52,10 +52,10 @@ def download(
     with resources.as_file(source) as registry_file:
         POOCH.load_registry(registry_file)
 
-    output_file = output_dir / f"dataset_{model_name}"
+    output_file = output_dir / f"dataset_{model}"
 
     if not output_file.is_file():
-        file_idx = available_models().index(model_name)
+        file_idx = available_models().index(model)
         filename = f"dataset_{available_models()[file_idx]}.h5"
         output_file = POOCH.fetch(filename, progressbar=True)
         if isinstance(output_file, str):

bidsmreye/methods.py

@@ -15,16 +15,16 @@
 
 def methods(
     output_dir: str | Path | None = None,
-    model_name: str | None = None,
+    model: str | None = None,
     qc_only: bool = False,
 ) -> Path:
     """Write method section.
 
     :param output_dir: Defaults to Path(".")
     :type  output_dir: Union[str, Path], optional
 
-    :param model_name: Defaults to None.
-    :type  model_name: str, optional
+    :param model: Defaults to None.
+    :type  model: str, optional
 
     :return: Output file name.
     :rtype: Path
@@ -41,26 +41,26 @@ def methods(
     bib_file = str(Path(__file__).parent / "templates" / "CITATION.bib")
     shutil.copy(bib_file, output_dir)
 
-    if not model_name:
-        model_name = default_model()
+    if not model:
+        model = default_model()
 
     is_known_models = False
     is_default_model = False
-    if model_name in available_models():
+    if model in available_models():
         is_known_models = True
-        if model_name == default_model():
+        if model == default_model():
             is_default_model = True
 
     if not is_known_models:
-        warnings.warn(f"{model_name} is not a known model name.", stacklevel=3)
+        warnings.warn(f"{model} is not a known model name.", stacklevel=3)
 
     template_file = str(Path(__file__).parent / "templates" / "CITATION.mustache")
     with open(template_file) as template:
         output = chevron.render(
             template=template,
             data={
                 "version": __version__,
-                "model_name": model_name,
+                "model": model,
                 "is_default_model": is_default_model,
                 "is_known_models": is_known_models,
                 "qc_only": qc_only,

bidsmreye/templates/CITATION.mustache

@@ -29,7 +29,7 @@ across voxels (spatial normalization).
 Voxels time series were used as inputs for generalization decoding
 using a
 {{#is_known_models}}
-pre-trained model {{ model_name }} from deepMReye from [OSF](https://osf.io/23t5v).
+pre-trained model {{ model }} from deepMReye from [OSF](https://osf.io/23t5v).
     {{#is_default_model}}
 This model was trained on the following datasets:
 guided fixations (@alexander_open_2017),

mlc_config.json

@@ -2,6 +2,9 @@
   "ignorePatterns": [
     {
       "pattern": "^https://doi.org\/"
+    },
+    {
+      "pattern": "^./faq.md#.*"
     }
   ],
   "timeout": "20s",

tests/test_download.py

@@ -9,7 +9,7 @@
 
 
 def test_download(tmp_path):
-    download(model_name="1_guided_fixations", output_dir=str(tmp_path))
+    download(model="1_guided_fixations", output_dir=str(tmp_path))
 
     assert tmp_path.is_dir()
     assert (tmp_path / "dataset_1_guided_fixations.h5").is_file()
@@ -29,4 +29,4 @@ def test_download_basic():
 
 def test_download_unknown_model():
     with pytest.warns(UserWarning):
-        download(model_name="foo")
+        download(model="foo")

tests/test_methods.py

@@ -10,7 +10,7 @@ def test_methods(tmp_path):
 
 
 def test_methods_calibration_data(tmp_path):
-    output_file = methods(output_dir=tmp_path, model_name="calibration_data")
+    output_file = methods(output_dir=tmp_path, model="calibration_data")
     assert output_file.is_file()
 
 

tests/test_parsers.py

@@ -53,7 +53,7 @@ def test_download_parser():
 
     args, _ = parser.parse_known_args(
         [
-            "--model_name",
+            "--model",
             "1_guided_fixations",
             "--output_dir",
             "/home/bob/models",