initial commit

mne/io/ctf/eeg.py

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+"""Read .eeg files."""
+
+# Authors: The MNE-Python contributors.
+# License: BSD-3-Clause
+# Copyright the MNE-Python contributors.
+
+from os import listdir
+from os.path import join
+
+import numpy as np
+
+from ..._fiff.constants import FIFF
+from ...transforms import apply_trans
+from ...utils import logger, warn
+from .res4 import _make_ctf_name
+
+_cardinal_dict = dict(
+    nasion=FIFF.FIFFV_POINT_NASION,
+    lpa=FIFF.FIFFV_POINT_LPA,
+    left=FIFF.FIFFV_POINT_LPA,
+    rpa=FIFF.FIFFV_POINT_RPA,
+    right=FIFF.FIFFV_POINT_RPA,
+)
+
+
+def _read_eeg(directory):
+    """Read the .eeg file."""
+    # Missing file is ok
+    fname, found = _make_ctf_name(directory, "eeg", raise_error=False)
+    if not found:
+        logger.info("    Separate EEG position data file not present.")
+        return
+    eeg = dict(
+        labels=list(),
+        kinds=list(),
+        ids=list(),
+        rr=list(),
+        np=0,
+        assign_to_chs=True,
+        coord_frame=FIFF.FIFFV_MNE_COORD_CTF_HEAD,
+    )
+    with open(fname, "rb") as fid:
+        for line in fid:
+            line = line.strip()
+            if len(line) > 0:
+                parts = line.decode("utf-8").split()
+                if len(parts) != 5:
+                    raise RuntimeError(f"Illegal data in EEG position file: {line}")
+                r = np.array([float(p) for p in parts[2:]]) / 100.0
+                if (r * r).sum() > 1e-4:
+                    label = parts[1]
+                    eeg["labels"].append(label)
+                    eeg["rr"].append(r)
+                    id_ = _cardinal_dict.get(label.lower(), int(parts[0]))
+                    if label.lower() in _cardinal_dict:
+                        kind = FIFF.FIFFV_POINT_CARDINAL
+                    else:
+                        kind = FIFF.FIFFV_POINT_EXTRA
+                    eeg["ids"].append(id_)
+                    eeg["kinds"].append(kind)
+                    eeg["np"] += 1
+    logger.info("    Separate EEG position data file read.")
+    return eeg
+
+
+def _read_pos(directory, transformations):
+    """Read the .pos file and return eeg positions as dig extra points."""
+    fname = [join(directory, f) for f in listdir(directory) if f.endswith(".pos")]
+    if len(fname) < 1:
+        return list()
+    elif len(fname) > 1:
+        warn("    Found multiple pos files. Extra digitizer points not added.")
+        return list()
+    logger.info(f"    Reading digitizer points from {fname}...")
+    if transformations["t_ctf_head_head"] is None:
+        warn("    No transformation found. Extra digitizer points not added.")
+        return list()
+    fname = fname[0]
+    digs = list()
+    i = 2000
+    with open(fname) as fid:
+        for line in fid:
+            line = line.strip()
+            if len(line) > 0:
+                parts = line.split()
+                # The lines can have 4 or 5 parts. First part is for the id,
+                # which can be an int or a string. The last three are for xyz
+                # coordinates. The extra part is for additional info
+                # (e.g. 'Pz', 'Cz') which is ignored.
+                if len(parts) not in [4, 5]:
+                    continue
+                try:
+                    ident = int(parts[0]) + 1000
+                except ValueError:  # if id is not an int
+                    ident = i
+                    i += 1
+                dig = dict(
+                    kind=FIFF.FIFFV_POINT_EXTRA,
+                    ident=ident,
+                    r=list(),
+                    coord_frame=FIFF.FIFFV_COORD_HEAD,
+                )
+                r = np.array([float(p) for p in parts[-3:]]) / 100.0  # cm to m
+                if (r * r).sum() > 1e-4:
+                    r = apply_trans(transformations["t_ctf_head_head"], r)
+                    dig["r"] = r
+                    digs.append(dig)
+    return digs