BrainVisionRawIO: read marker positions as 1-based

doc/source/authors.rst

@@ -106,6 +106,7 @@ and may not be the current affiliation of a contributor.
 * Aditya Singh (github)
 * Stanley C.
 * Axel Coiffard-Donaty
+* Aaron Kanzer [53]
 
 1. Centre de Recherche en Neuroscience de Lyon, CNRS UMR5292 - INSERM U1028 - Université Claude Bernard Lyon 1
 2. Unité de Neuroscience, Information et Complexité, CNRS UPR 3293, Gif-sur-Yvette, France
@@ -159,6 +160,7 @@ and may not be the current affiliation of a contributor.
 50. Ludwig-Maximilians-Universität München, Munich, Germany
 51. Stony Brook University, Stony Brook, NY, USA
 52. University of Sussex, Brighton, UK
+53. Scigantic, USA
 
 
 

neo/rawio/brainvisionrawio.py

@@ -166,7 +166,10 @@ def _parse_header(self):
         for i in range(len(all_info)):
             ev_type, ev_label, pos, size, channel = all_info[f"Mk{i+1}"].split(",")[:5]
             ev_types.append(ev_type)
-            ev_timestamps.append(int(pos))
+            # Marker positions are 1-based (the first data point is position 1), see
+            # section 4.3 of the BrainVision Core Data Format 1.0 specification:
+            # https://www.brainproducts.com/download/specification-of-brainvision-core-data-format-1-0/
+            ev_timestamps.append(int(pos) - 1)
             ev_labels.append(ev_label)
         ev_types = np.array(ev_types)
         ev_timestamps = np.array(ev_timestamps)

neo/test/rawiotest/test_brainvisionrawio.py

@@ -1,6 +1,10 @@
 """ """
 
+import tempfile
 import unittest
+from pathlib import Path
+
+import numpy as np
 
 from neo.rawio.brainvisionrawio import BrainVisionRawIO
 
@@ -24,5 +28,50 @@ class TestBrainVisionRawIO(
     entities_to_download = ["brainvision"]
 
 
+class TestBrainVisionRawIOMarkers(unittest.TestCase):
+    def test_marker_positions_are_one_based(self):
+        vhdr = (
+            "Brain Vision Data Exchange Header File Version 1.0\n"
+            "[Common Infos]\n"
+            "Codepage=UTF-8\n"
+            "DataFile=test.eeg\n"
+            "MarkerFile=test.vmrk\n"
+            "DataFormat=BINARY\n"
+            "DataOrientation=MULTIPLEXED\n"
+            "NumberOfChannels=1\n"
+            "SamplingInterval=1000\n"
+            "[Binary Infos]\n"
+            "BinaryFormat=INT_16\n"
+            "[Channel Infos]\n"
+            "Ch1=Fp1,,1,µV\n"
+        )
+        vmrk = (
+            "Brain Vision Data Exchange Marker File, Version 1.0\n"
+            "[Marker Infos]\n"
+            "Mk1=New Segment,,1,1,0\n"
+            "Mk2=Stimulus,S  1,11,1,0\n"
+        )
+        with tempfile.TemporaryDirectory() as tmp_dir:
+            tmp_dir = Path(tmp_dir)
+            (tmp_dir / "test.vhdr").write_text(vhdr, encoding="utf8")
+            (tmp_dir / "test.vmrk").write_text(vmrk, encoding="utf8")
+            np.arange(20, dtype="int16").tofile(tmp_dir / "test.eeg")
+
+            reader = BrainVisionRawIO(filename=tmp_dir / "test.vhdr")
+            reader.parse_header()
+            event_names = list(reader.header["event_channels"]["name"])
+
+            # position 1 is the first data point, so it is sample 0 and time 0 s
+            timestamps, _, _ = reader.get_event_timestamps(event_channel_index=event_names.index("New Segment"))
+            np.testing.assert_array_equal(timestamps, [0])
+
+            # position 11 is sample 10, 10 ms into the recording at 1 kHz
+            timestamps, _, labels = reader.get_event_timestamps(event_channel_index=event_names.index("Stimulus"))
+            np.testing.assert_array_equal(timestamps, [10])
+            np.testing.assert_array_equal(labels, ["S  1"])
+            times = reader.rescale_event_timestamp(timestamps, event_channel_index=event_names.index("Stimulus"))
+            np.testing.assert_allclose(times, [0.010])
+
+
 if __name__ == "__main__":
     unittest.main()