Add funloc dataset to test support for session-specific anat

.circleci/config.yml

@@ -297,6 +297,25 @@ jobs:
           paths:
             - ~/mne_data/eeg_matchingpennies
 
+  cache_MNE-funloc-data:
+    <<: *imageconfig
+    steps:
+      - attach_workspace:
+          at: ~/
+      - restore_cache:
+          keys:
+            - data-cache-MNE-funloc-data-1
+      - bash_env
+      - run:
+          name: Get MNE-funloc-data
+          command: |
+            $DOWNLOAD_DATA MNE-funloc-data
+      - codecov/upload
+      - save_cache:
+          key: data-cache-MNE-funloc-data-1
+          paths:
+            - ~/mne_data/MNE-funloc-data
+
   cache_MNE-phantom-KIT-data:
     <<: *imageconfig
     steps:
@@ -784,6 +803,32 @@ jobs:
           paths:
             - mne_data/derivatives/mne-bids-pipeline/eeg_matchingpennies/*/*/*.html
 
+  test_MNE-funloc-data:
+    <<: *imageconfig
+    steps:
+      - attach_workspace:
+          at: ~/
+      - bash_env
+      - restore_cache:
+          keys:
+            - data-cache-MNE-funloc-data-1
+      - run:
+          name: test MNE-funloc-data
+          command: $RUN_TESTS MNE-funloc-data
+      - codecov/upload
+      - store_test_results:
+          path: ./test-results
+      - store_artifacts:
+          path: ./test-results
+          destination: test-results
+      - store_artifacts:
+          path: /home/circleci/reports/MNE-funloc-data
+          destination: reports/MNE-funloc-data
+      - persist_to_workspace:
+          root: ~/
+          paths:
+            - mne_data/derivatives/mne-bids-pipeline/MNE-funloc-data/*/*/*.html
+
   test_MNE-phantom-KIT-data:
     <<: *imageconfig
     steps:
@@ -1244,6 +1289,15 @@ workflows:
             - cache_eeg_matchingpennies
           <<: *filter_tags
 
+      - cache_MNE-funloc-data:
+          requires:
+            - setup_env
+          <<: *filter_tags
+      - test_MNE-funloc-data:
+          requires:
+            - cache_MNE-funloc-data
+          <<: *filter_tags
+
       - cache_MNE-phantom-KIT-data:
           requires:
             - setup_env
@@ -1304,6 +1358,7 @@ workflows:
             - test_ds003392
             - test_ds004229
             - test_eeg_matchingpennies
+            - test_MNE-funloc-data
             - test_MNE-phantom-KIT-data
             - test_ERP_CORE_N400
             - test_ERP_CORE_ERN

docs/mkdocs.yml

@@ -121,6 +121,7 @@ nav:
         - examples/ds000248_no_mri.md
         - examples/ds003104.md
         - examples/eeg_matchingpennies.md
+        - examples/MNE-funloc-data.md
         - examples/MNE-phantom-KIT-data.md
         - examples/ds001810.md
         - examples/ds000117.md

mne_bids_pipeline/_download.py

@@ -43,16 +43,18 @@ def _download_from_web(*, ds_name: str, ds_path: Path) -> None:
 
     ds_path.mkdir(parents=True, exist_ok=True)
     path = ds_path.parent.resolve(strict=True)
-    fname = f"{ds_name}.zip"
+    ext = "tar.gz" if options.get("processor") == "untar" else "zip"
+    processor = pooch.Untar if options.get("processor") == "untar" else pooch.Unzip
+    fname = f"{ds_name}.{ext}"
     pooch.retrieve(
         url=url,
         path=path,
         fname=fname,
-        processor=pooch.Unzip(extract_dir="."),  # relative to path
+        processor=processor(extract_dir="."),  # relative to path
         progressbar=True,
         known_hash=known_hash,
     )
-    (path / f"{ds_name}.zip").unlink()
+    (path / f"{ds_name}.{ext}").unlink()
 
 
 def _download_via_mne(*, ds_name: str, ds_path: Path) -> None:

mne_bids_pipeline/tests/configs/config_funloc.py

@@ -0,0 +1,36 @@
+"""Funloc data."""
+
+from pathlib import Path
+
+data_root = Path("~/mne_data").expanduser().resolve()
+bids_root = data_root / "MNE-funloc-data"
+deriv_root = data_root / "derivatives" / "mne-bids-pipeline" / "MNE-funloc-data"
+subjects_dir = bids_root / "derivatives" / "freesurfer" / "subjects"
+task = "funloc"
+ch_types = ["meg", "eeg"]
+data_type = "meg"
+
+# filter
+l_freq = None
+h_freq = 50.0
+# maxfilter
+use_maxwell_filter: bool = True
+mf_st_duration = 60.0
+# SSP
+n_proj_eog = dict(n_mag=1, n_grad=1, n_eeg=2)
+n_proj_ecg = dict(n_mag=1, n_grad=1, n_eeg=0)
+
+# Epochs
+epochs_tmin = -0.2
+epochs_tmax = 0.5
+epochs_t_adjust = -4.0e-3  # TODO is there a way to do this in MBP?
+epochs_decim = 5  # 1000 -> 200 Hz
+baseline = (None, 0)
+conditions = [
+    "auditory/standard",
+    "auditory/deviant",
+    "visual/standard",
+    "visual/deviant",
+]
+# contrasts
+contrasts = [("auditory", "visual")]

mne_bids_pipeline/tests/datasets.py

@@ -15,6 +15,7 @@ class DATASET_OPTIONS_T(TypedDict, total=False):
     include: list[str]  # []
     exclude: list[str]  # []
     hash: str  # ""
+    processor: str  # ""
 
 
 DATASET_OPTIONS: dict[str, DATASET_OPTIONS_T] = {
@@ -118,4 +119,9 @@ class DATASET_OPTIONS_T(TypedDict, total=False):
     "MNE-phantom-KIT-data": {
         "mne": "phantom_kit",
     },
+    "MNE-funloc-data": {
+        "web": "https://osf.io/2pemg/download?version=1",
+        "hash": "sha256:05a6b0e9d7a21ac3378236082de5e3b8f1a02315501b8e587179959bc5fafba2",  # noqa: E501
+        "processor": "untar",
+    },
 }

mne_bids_pipeline/tests/test_run.py

@@ -9,7 +9,9 @@
 from typing import Any, TypedDict
 
 import pytest
+from mne_bids import BIDSPath, get_bids_path_from_fname
 
+from mne_bids_pipeline._config_import import _import_config
 from mne_bids_pipeline._download import main as download_main
 from mne_bids_pipeline._main import main
 
@@ -135,6 +137,10 @@ class _TestOptionsT(TypedDict, total=False):
     "MNE-phantom-KIT-data": {
         "config": "config_MNE_phantom_KIT_data.py",
     },
+    "MNE-funloc-data": {
+        "config": "config_funloc.py",
+        "steps": ["init", "preprocessing", "sensor", "source"],
+    },
 }
 
 
@@ -274,3 +280,98 @@ def test_missing_sessions(
         print()
         with context:
             main()
+
+
+@pytest.mark.dataset_test
+@pytest.mark.parametrize("dataset", ["MNE-funloc-data"])
+def test_session_specific_mri(
+    dataset: str,
+    monkeypatch: pytest.MonkeyPatch,
+    dataset_test: Any,
+    tmp_path: Path,
+    capsys: pytest.CaptureFixture[str],
+) -> None:
+    """Test of (faked) session-specific MRIs."""
+    test_options = TEST_SUITE[dataset]
+    config = test_options.get("config", f"config_{dataset}.py")
+    config_path = BIDS_PIPELINE_DIR / "tests" / "configs" / config
+    # copy the dataset to a tmpdir
+    config_obj = _import_config(config_path=config_path)
+    # make it seem like there's only one subj with different MRIs for different sessions
+    new_bids_path = BIDSPath(root=tmp_path / dataset, subject="01", session="a")
+    # sub-01/* → sub-01/ses-a/*
+    src_dir = config_obj.bids_root / "sub-01"
+    dst_dir = new_bids_path.root / "sub-01" / "ses-a"
+    for root, dirs, files in src_dir.walk():
+        offset = root.relative_to(src_dir)
+        for _dir in dirs:
+            (dst_dir / offset / _dir).mkdir(parents=True)
+        for _file in files:
+            bp = get_bids_path_from_fname(root / _file)
+            bp.update(root=new_bids_path.root, session="a")
+            shutil.copyfile(src=root / _file, dst=dst_dir / offset / bp.basename)
+    # sub-02/* → sub-01/ses-b/*
+    src_dir = config_obj.bids_root / "sub-02"
+    dst_dir = new_bids_path.root / "sub-01" / "ses-b"
+    for root, dirs, files in src_dir.walk():
+        offset = root.relative_to(src_dir)
+        for _dir in dirs:
+            (dst_dir / offset / _dir).mkdir(parents=True)
+        for _file in files:
+            bp = get_bids_path_from_fname(root / _file)
+            bp.update(root=new_bids_path.root, subject="01", session="b")
+            shutil.copyfile(src=root / _file, dst=dst_dir / offset / bp.basename)
+    # emptyroom
+    src_dir = config_obj.bids_root / "sub-emptyroom"
+    dst_dir = new_bids_path.root / "sub-emptyroom"
+    shutil.copytree(src=src_dir, dst=dst_dir)
+    # root-level files (dataset description, etc)
+    src_dir = config_obj.bids_root
+    dst_dir = new_bids_path.root
+    files = [f for f in src_dir.iterdir() if f.is_file()]
+    for _file in files:
+        shutil.copyfile(src=_file, dst=dst_dir / _file.name)
+    # now move derivatives (freesurfer files)
+    src_dir = config_obj.bids_root / "derivatives" / "freesurfer" / "subjects"
+    dst_dir = new_bids_path.root / "derivatives" / "freesurfer" / "subjects"
+    dst_dir.mkdir(parents=True)
+    for root, dirs, files in src_dir.walk():
+        new_root = root
+        if "sub01" in root.parts:
+            new_root = Path(
+                *["sub-01_ses-a" if p == "sub01" else p for p in new_root.parts]
+            )
+        elif "sub02" in root.parts:
+            new_root = Path(
+                *["sub-01_ses-b" if p == "sub02" else p for p in new_root.parts]
+            )
+        offset = new_root.relative_to(src_dir)
+        for _dir in dirs:
+            if _dir == "sub01":
+                _dir = "sub-01_ses-a"
+            elif _dir == "sub02":
+                _dir = "sub-01_ses-b"
+            (dst_dir / offset / _dir).mkdir()
+        for _file in files:
+            dst_file = _file
+            if _file.startswith("sub01"):
+                dst_file = dst_file.replace("sub01", "sub-01_ses-a")
+            elif _file.startswith("sub02"):
+                dst_file = dst_file.replace("sub02", "sub-01_ses-b")
+            shutil.copyfile(src=root / _file, dst=dst_dir / offset / dst_file)
+    # print_dir_tree(new_bids_path.root)  # for debugging
+    # hack in the new bids_root
+    extra_config = dict(bids_root=str(new_bids_path.root))
+    extra_path = tmp_path / "extra_config.py"
+    extra_path.write_text(str(extra_config))
+    monkeypatch.setenv("_MNE_BIDS_STUDY_TESTING_EXTRA_CONFIG", str(extra_path))
+    # Run the tests.
+    steps = test_options.get("steps", ())
+    command = ["mne_bids_pipeline", str(config_path), f"--steps={','.join(steps)}"]
+    if "--pdb" in sys.argv:
+        command.append("--n_jobs=1")
+    monkeypatch.setenv("_MNE_BIDS_STUDY_TESTING", "true")
+    monkeypatch.setattr(sys, "argv", command)
+    with capsys.disabled():
+        print()
+        main()