Strip out vendor specific formats into separate packages

.github/workflows/ci-cd.yml

@@ -29,10 +29,6 @@ jobs:
     steps:
     - name: Checkout
       uses: actions/checkout@v6
-    - name: Unset header
-      # checkout@v2 adds a header that makes branch protection report errors
-      # because the Github action bot is not a collaborator on the repo
-      run: git config --local --unset http.https://github.com/.extraheader
     - name: Fetch tags
       run: git fetch --prune --unshallow
     - name: Disable etelemetry
@@ -87,10 +83,7 @@ jobs:
       with:
         submodules: recursive
         fetch-depth: 0
-    - name: Unset header
-      # checkout@v2 adds a header that makes branch protection report errors
-      # because the Github action bot is not a collaborator on the repo
-      run: git config --local --unset http.https://github.com/.extraheader
+
     - name: Set up Python
       uses: actions/setup-python@v6
       with:

extras/fileformats/extras/biosig/__init__.py

@@ -1,5 +1,4 @@
 from ._version import __version__
-from . import eeg
-from . import meg
+from . import edf
 
-__all__ = ["__version__", "eeg", "meg"]
+__all__ = ["__version__", "edf"]

extras/fileformats/extras/biosig/eeg.py → extras/fileformats/extras/biosig/edf.py

@@ -1,5 +1,4 @@
 import os
-import configparser
 import typing as ty
 import tempfile
 from pathlib import Path
@@ -8,7 +7,7 @@
 import mne.export
 
 from fileformats.core import extra_implementation, FileSet
-from fileformats.biosig import Biosig, BrainVision, Edf, EdfPlus
+from fileformats.biosig import Biosig, Edf, EdfPlus
 
 from .utils import mne_deidentify
 
@@ -31,17 +30,6 @@ def edf_plus_read_metadata(edf: EdfPlus, **kwargs: ty.Any) -> ty.Mapping[str, ty
     }
 
 
-@extra_implementation(FileSet.read_metadata)
-def brain_vision_read_metadata(
-    bv: BrainVision, **kwargs: ty.Any
-) -> ty.Mapping[str, ty.Any]:
-    raw = mne.io.read_raw_brainvision(bv.header_file, preload=False, verbose=False)
-    return {
-        **raw.info.to_json_dict(),
-        **_parse_vhdr(bv.header_file),
-    }
-
-
 @extra_implementation(Biosig.deidentify)
 def edf_deidentify(
     edf: Edf,
@@ -58,22 +46,6 @@ def edf_deidentify(
     return type(edf)(deid_fspath), reid
 
 
-@extra_implementation(Biosig.deidentify)
-def brain_vision_deidentify(
-    bv: BrainVision,
-    spec: ty.Any = None,
-    out_dir: os.PathLike[str] | None = None,
-) -> tuple[BrainVision, dict[str, ty.Any]]:
-    out_dir = Path(tempfile.mkdtemp() if out_dir is None else out_dir)
-    out_dir.mkdir(parents=True, exist_ok=True)
-    raw = mne.io.read_raw_brainvision(bv.header_file, preload=True, verbose=False)
-    deidentified_info, reid = mne_deidentify(raw, spec)
-    raw.info = deidentified_info
-    deid_vhdr = out_dir / "eeg.vhdr"
-    mne.export.export_raw(deid_vhdr, raw, fmt="brainvision", overwrite=True)
-    return BrainVision(out_dir / "eeg.eeg"), reid
-
-
 def _parse_edf_header(path: os.PathLike[str]) -> dict[str, ty.Any]:
     """
     Parse EDF/EDF+ header bytes directly for patient and recording fields
@@ -112,42 +84,3 @@ def _parse_edf_header(path: os.PathLike[str]) -> dict[str, ty.Any]:
         "edf_start_time": start_time,
         "edf_subtype": reserved if reserved.startswith("EDF+") else None,
     }
-
-
-def _parse_vhdr(path: os.PathLike[str]) -> dict[str, ty.Any]:
-    """
-    Parse a BrainVision .vhdr file (INI format) for fields not exposed by MNE.
-    Extracts acquisition settings and the free-text Comment section.
-    """
-    parser = configparser.RawConfigParser()
-    # vhdr files start with a magic line before the first INI section — skip it
-    with open(path, encoding="utf-8-sig", errors="replace") as f:
-        lines = f.readlines()
-    ini_lines = [line for line in lines if not line.startswith("Brain Vision")]
-    parser.read_string("".join(ini_lines))
-
-    def get(
-        section: ty.Any,
-        key: str,
-        fallback: ty.Any = None,
-    ) -> ty.Any:
-        try:
-            return parser.get(section, key)
-        except (configparser.NoSectionError, configparser.NoOptionError):
-            return fallback
-
-    # [Common Infos] uses inconsistent casing across BrainVision versions
-    common = next((s for s in parser.sections() if s.lower() == "common infos"), None)
-
-    comment_lines = []
-    if parser.has_section("Comment"):
-        comment_lines = [v for _, v in parser.items("Comment") if v.strip()]
-
-    return {
-        "bv_data_format": get(common, "DataFormat") if common else None,
-        "bv_data_orientation": get(common, "DataOrientation") if common else None,
-        "bv_n_channels": get(common, "NumberOfChannels") if common else None,
-        "bv_sampling_interval_us": get(common, "SamplingInterval") if common else None,
-        "bv_binary_format": get("Binary Infos", "BinaryFormat"),
-        "bv_comment": "\n".join(comment_lines) if comment_lines else None,
-    }

extras/fileformats/extras/biosig/tests/test_eeg_extras.py → extras/fileformats/extras/biosig/tests/test_edf_extras.py

@@ -10,10 +10,7 @@
 - miaocao@swin.edu.au
 """
 
-from fileformats.biosig import (
-    BrainVision,
-    EdfPlus,
-)
+from fileformats.biosig import EdfPlus
 
 # ------------------------------
 # EEG: EDF
@@ -25,15 +22,3 @@ def test_edf_plus_read_metadata(edf_plus_path):
     assert isinstance(metadata, dict)
     assert metadata["sfreq"] is not None
     assert "edf_patient_code" in metadata
-
-
-# ------------------------------
-# EEG: BrainVision
-# ------------------------------
-
-
-def test_brainvision_read_metadata(bv_vhdr_path):
-    metadata = BrainVision(bv_vhdr_path.with_suffix(".eeg")).metadata
-    assert isinstance(metadata, dict)
-    assert metadata["sfreq"] is not None
-    assert "bv_n_channels" in metadata

fileformats/biosig/__init__.py

@@ -10,26 +10,10 @@
 - miaocao@swin.edu.au
 """
 
-from .base import Biosig
-from .eeg import (
-    Eeg,
+from .base import Biosig, Eeg, Meg
+from .edf import (
     Edf,
     EdfPlus,
-    BrainVisionHeader,
-    BrainVisionMarker,
-    BrainVision,
-)
-from .meg import (
-    Meg,
-    CtfMeg4,
-    CtfRes4,
-    CtfInfo,
-    Ctf,
-    Fif,
-    KitMark,
-    KitHeadPosition,
-    KitSensorInfo,
-    Kit,
 )
 
 from ._version import __version__
@@ -38,20 +22,7 @@
     "__version__",
     "Biosig",
     "Eeg",
-    "Fif",
-    "FifGz",
     "Edf",
     "EdfPlus",
-    "BrainVisionHeader",
-    "BrainVisionMarker",
-    "BrainVision",
     "Meg",
-    "CtfMeg4",
-    "CtfRes4",
-    "CtfInfo",
-    "Ctf",
-    "KitMark",
-    "KitHeadPosition",
-    "KitSensorInfo",
-    "Kit",
 ]

fileformats/biosig/base.py

@@ -35,3 +35,19 @@ def deidentify(
             were stripped/modified during the deidentification process.
         """
         raise NotImplementedError
+
+
+class Eeg(Biosig):
+    """Base class for all Electroencephalography recordings"""
+
+    pass
+
+
+# ------------------------------
+# Base MEG Type (Abstract Class)
+# ------------------------------
+class Meg(Biosig):
+    """
+    Base class for MEG data formats
+    All specific MEG formats inherit from this class with unified validation logic
+    """