Merge pull request #1933 from aaronkanzer/fix/brainvision-marker-positions

BrainVisionRawIO: read marker positions as 1-based

Author: h-mayorquin

doc/source/authors.rst

@@ -107,6 +107,7 @@ and may not be the current affiliation of a contributor.
 * Stanley C.
 * Axel Coiffard-Donaty
 * Anthony Mercer
+* 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
@@ -160,6 +161,7 @@ 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

@@ -2,6 +2,8 @@
 
 import unittest
 
+import numpy as np
+
 from neo.rawio.brainvisionrawio import BrainVisionRawIO
 
 from neo.test.rawiotest.common_rawio_test import BaseTestRawIO
@@ -23,6 +25,14 @@ class TestBrainVisionRawIO(
 
     entities_to_download = ["brainvision"]
 
+    def test_marker_positions_are_one_based(self):
+        # SegmentDataPoints=294 in the .vhdr and a "New Segment" marker on the first sample of each of the 34 segments
+        reader = BrainVisionRawIO(self.get_local_path("brainvision/File_brainvision_3_int16.vhdr"))
+        reader.parse_header()
+        event_names = list(reader.header["event_channels"]["name"])
+        timestamps, _, _ = reader.get_event_timestamps(event_channel_index=event_names.index("New Segment"))
+        np.testing.assert_array_equal(timestamps, np.arange(34) * 294)
+
 
 if __name__ == "__main__":
     unittest.main()