initial commit

mne/io/ctf/markers.py

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+# Authors: The MNE-Python contributors.
+# License: BSD-3-Clause
+# Copyright the MNE-Python contributors.
+
+import os.path as op
+from io import BytesIO
+
+import numpy as np
+
+from ...annotations import Annotations
+from .info import _convert_time
+from .res4 import _read_res4
+
+
+def _get_markers(fname):
+    def consume(fid, predicate):  # just a consumer to move around conveniently
+        while predicate(fid.readline()):
+            pass
+
+    def parse_marker(string):  # XXX: there should be a nicer way to do that
+        data = np.genfromtxt(
+            BytesIO(string.encode()), dtype=[("trial", int), ("sync", float)]
+        )
+        return int(data["trial"]), float(data["sync"])
+
+    markers = dict()
+    with open(fname) as fid:
+        consume(fid, lambda line: not line.startswith("NUMBER OF MARKERS:"))
+        num_of_markers = int(fid.readline())
+
+        for _ in range(num_of_markers):
+            consume(fid, lambda line: not line.startswith("NAME:"))
+            label = fid.readline().strip("\n")
+
+            consume(fid, lambda line: not line.startswith("NUMBER OF SAMPLES:"))
+            n_markers = int(fid.readline())
+
+            consume(fid, lambda line: not line.startswith("LIST OF SAMPLES:"))
+            next(fid)  # skip the samples header
+            markers[label] = [parse_marker(next(fid)) for _ in range(n_markers)]
+
+    return markers
+
+
+def _get_res4_info_needed_by_markers(directory):
+    """Get required information from CTF res4 information file."""
+    # we only need a few values from res4. Maybe we can read them directly
+    # instead of parsing the entire res4 file.
+    res4 = _read_res4(directory)
+
+    total_offset_duration = res4["pre_trig_pts"] / res4["sfreq"]
+    trial_duration = res4["nsamp"] / res4["sfreq"]
+
+    meas_date = (_convert_time(res4["data_date"], res4["data_time"]), 0)
+    return total_offset_duration, trial_duration, meas_date
+
+
+def _read_annotations_ctf(directory):
+    total_offset, trial_duration, meas_date = _get_res4_info_needed_by_markers(
+        directory
+    )
+    return _read_annotations_ctf_call(
+        directory, total_offset, trial_duration, meas_date
+    )
+
+
+def _read_annotations_ctf_call(directory, total_offset, trial_duration, meas_date):
+    fname = op.join(directory, "MarkerFile.mrk")
+    if not op.exists(fname):
+        return Annotations(list(), list(), list(), orig_time=meas_date)
+    else:
+        markers = _get_markers(fname)
+
+        onset = [
+            synctime + (trialnum * trial_duration) + total_offset
+            for _, m in markers.items()
+            for (trialnum, synctime) in m
+        ]
+
+        description = np.concatenate(
+            [np.repeat(label, len(m)) for label, m in markers.items()]
+        )
+
+        return Annotations(
+            onset=onset,
+            duration=np.zeros_like(onset),
+            description=description,
+            orig_time=meas_date,
+        )