[draft] new reader for curry files, using curry-python-reader code

azure-pipelines.yml

@@ -113,7 +113,7 @@ stages:
           - bash: |
               set -e
               python -m pip install --progress-bar off --upgrade pip
-              python -m pip install --progress-bar off "mne-qt-browser[opengl] @ git+https://github.com/mne-tools/mne-qt-browser.git" pyvista scikit-learn python-picard qtpy nibabel sphinx-gallery "PySide6!=6.8.0,!=6.8.0.1,!=6.8.1.1,!=6.9.1" pandas neo pymatreader antio defusedxml
+              python -m pip install --progress-bar off "mne-qt-browser[opengl] @ git+https://github.com/mne-tools/mne-qt-browser.git" pyvista scikit-learn python-picard qtpy nibabel sphinx-gallery "PySide6!=6.8.0,!=6.8.0.1,!=6.8.1.1,!=6.9.1" pandas neo pymatreader antio defusedxml curryreader
               python -m pip uninstall -yq mne
               python -m pip install --progress-bar off --upgrade -e .[test]
             displayName: 'Install dependencies with pip'

doc/api/preprocessing.rst

@@ -41,6 +41,7 @@ Projections:
    make_dig_montage
    read_dig_polhemus_isotrak
    read_dig_captrak
+   read_dig_curry
    read_dig_dat
    read_dig_egi
    read_dig_fif

doc/changes/dev/13176.dependency.rst

@@ -0,0 +1 @@
+New reader for Neuroscan Curry files, using the curry-python-reader module, by `Dominik Welke`_.

doc/changes/dev/13176.newfeature.rst

@@ -0,0 +1 @@
+Read impedances and montage from Neuroscan Curry files, by `Dominik Welke`_.

environment.yml

@@ -5,6 +5,7 @@ channels:
 dependencies:
   - python >=3.10
   - antio >=0.5.0
+  - curryreader >=0.1.2
   - darkdetect
   - decorator
   - defusedxml

mne/channels/__init__.pyi

@@ -22,6 +22,7 @@ __all__ = [
     "read_ch_adjacency",
     "read_custom_montage",
     "read_dig_captrak",
+    "read_dig_curry",
     "read_dig_dat",
     "read_dig_egi",
     "read_dig_fif",
@@ -67,6 +68,7 @@ from .montage import (
     make_standard_montage,
     read_custom_montage,
     read_dig_captrak,
+    read_dig_curry,
     read_dig_dat,
     read_dig_egi,
     read_dig_fif,

mne/channels/_dig_montage_utils.py

@@ -94,3 +94,49 @@ def _parse_brainvision_dig_montage(fname, scale):
         ch_pos=dig_ch_pos,
         coord_frame="unknown",
     )
+
+
+def _read_dig_montage_curry(ch_names, ch_types, ch_pos, landmarks, landmarkslabels):
+    import re
+
+    # scale ch_pos to m?!
+    ch_pos /= 1000.0
+    landmarks /= 1000.0
+    # channel locations
+    # what about misc without pos? can they mess things up if unordered?
+    assert len(ch_pos) >= (ch_types.count("mag") + ch_types.count("eeg"))
+    assert len(ch_pos) == (ch_types.count("mag") + ch_types.count("eeg"))
+    ch_pos_eeg = {
+        ch_names[i]: ch_pos[i, :3] for i, t in enumerate(ch_types) if t == "eeg"
+    }
+    # landmarks and headshape
+    landmark_dict = dict(zip(landmarkslabels, landmarks))
+    for k in ["Nas", "RPA", "LPA"]:
+        if k not in landmark_dict.keys():
+            landmark_dict[k] = None
+    if len(landmarkslabels) > 0:
+        hpi_pos = landmarks[
+            [i for i, n in enumerate(landmarkslabels) if re.match("HPI[1-99]", n)], :
+        ]
+    else:
+        hpi_pos = None
+    if len(landmarkslabels) > 0:
+        hsp_pos = landmarks[
+            [i for i, n in enumerate(landmarkslabels) if re.match("H[1-99]", n)], :
+        ]
+    else:
+        hsp_pos = None
+    # compile dig montage positions for eeg
+    if len(ch_pos_eeg) > 0:
+        return dict(
+            ch_pos=ch_pos_eeg,
+            nasion=landmark_dict["Nas"],
+            lpa=landmark_dict["LPA"],
+            rpa=landmark_dict["RPA"],
+            hsp=hsp_pos,
+            hpi=hpi_pos,
+            coord_frame="head",
+        )
+    else:  # not recorded?
+        warn("No eeg sensor locations found in file.")
+        return None

mne/channels/montage.py

@@ -773,6 +773,7 @@ def read_dig_dat(fname):
     See Also
     --------
     read_dig_captrak
+    read_dig_curry
     read_dig_dat
     read_dig_egi
     read_dig_fif
@@ -842,6 +843,7 @@ def read_dig_fif(fname, *, verbose=None):
     read_dig_dat
     read_dig_egi
     read_dig_captrak
+    read_dig_curry
     read_dig_polhemus_isotrak
     read_dig_hpts
     read_dig_localite
@@ -892,6 +894,7 @@ def read_dig_hpts(fname, unit="mm"):
     --------
     DigMontage
     read_dig_captrak
+    read_dig_curry
     read_dig_dat
     read_dig_egi
     read_dig_fif
@@ -985,6 +988,7 @@ def read_dig_egi(fname):
     --------
     DigMontage
     read_dig_captrak
+    read_dig_curry
     read_dig_dat
     read_dig_fif
     read_dig_hpts
@@ -1017,6 +1021,7 @@ def read_dig_captrak(fname):
     See Also
     --------
     DigMontage
+    read_dig_curry
     read_dig_dat
     read_dig_egi
     read_dig_fif
@@ -1031,6 +1036,50 @@ def read_dig_captrak(fname):
     return make_dig_montage(**data)
 
 
+def read_dig_curry(fname):
+    """Read electrode locations from Neuroscan Curry files.
+
+    Parameters
+    ----------
+    fname : path-like
+        A valid Curry file.
+
+    Returns
+    -------
+    montage : instance of DigMontage | None
+        The montage.
+
+    See Also
+    --------
+    DigMontage
+    read_dig_captrak
+    read_dig_dat
+    read_dig_egi
+    read_dig_fif
+    read_dig_hpts
+    read_dig_localite
+    read_dig_polhemus_isotrak
+    make_dig_montage
+    """
+    from ..io.curry.curry import (
+        _check_curry_filename,
+        _extract_curry_info,
+    )
+    from ._dig_montage_utils import _read_dig_montage_curry
+
+    # TODO - REVIEW NEEDED
+    # API? do i need to add this in the docs somewhere?
+    fname = _check_curry_filename(fname)
+    (_, _, ch_names, ch_types, ch_pos, landmarks, landmarkslabels, _, _, _, _, _, _) = (
+        _extract_curry_info(fname)
+    )
+    data = _read_dig_montage_curry(
+        ch_names, ch_types, ch_pos, landmarks, landmarkslabels
+    )
+    mont = make_dig_montage(**data) if data else None
+    return mont
+
+
 def read_dig_localite(fname, nasion=None, lpa=None, rpa=None):
     """Read Localite .csv file.
 
@@ -1054,6 +1103,7 @@ def read_dig_localite(fname, nasion=None, lpa=None, rpa=None):
     --------
     DigMontage
     read_dig_captrak
+    read_dig_curry
     read_dig_dat
     read_dig_egi
     read_dig_fif
@@ -1455,6 +1505,7 @@ def read_dig_polhemus_isotrak(fname, ch_names=None, unit="m"):
     make_dig_montage
     read_polhemus_fastscan
     read_dig_captrak
+    read_dig_curry
     read_dig_dat
     read_dig_egi
     read_dig_fif
@@ -1815,8 +1866,8 @@ def make_standard_montage(kind, head_size="auto"):
     Notes
     -----
     Individualized (digitized) electrode positions should be read in using
-    :func:`read_dig_captrak`, :func:`read_dig_dat`, :func:`read_dig_egi`,
-    :func:`read_dig_fif`, :func:`read_dig_polhemus_isotrak`,
+    :func:`read_dig_captrak`, :func:`read_dig_curry`, :func:`read_dig_dat`,
+    :func:`read_dig_egi`, :func:`read_dig_fif`, :func:`read_dig_polhemus_isotrak`,
     :func:`read_dig_hpts`, or manually made with :func:`make_dig_montage`.
 
     .. versionadded:: 0.19.0

mne/datasets/config.py

@@ -87,7 +87,7 @@
 # update the checksum in the MNE_DATASETS dict below, and change version
 # here: ↓↓↓↓↓↓↓↓
 RELEASES = dict(
-    testing="0.161",
+    testing="0.164",
     misc="0.27",
     phantom_kit="0.2",
     ucl_opm_auditory="0.2",
@@ -115,7 +115,7 @@
 # Testing and misc are at the top as they're updated most often
 MNE_DATASETS["testing"] = dict(
     archive_name=f"{TESTING_VERSIONED}.tar.gz",
-    hash="md5:a32cfb9e098dec39a5f3ed6c0833580d",
+    hash="md5:7b9ac40783f8131f5cefa3a103be2daf",
     url=(
         "https://codeload.github.com/mne-tools/mne-testing-data/"
         f"tar.gz/{RELEASES['testing']}"

mne/io/curry/__init__.py

@@ -5,3 +5,4 @@
 # Copyright the MNE-Python contributors.
 
 from .curry import read_raw_curry
+from .curry import read_impedances_curry