Issue1883

doc/source/authors.rst

@@ -102,6 +102,7 @@ and may not be the current affiliation of a contributor.
 * LizzyMcKay (github)
 * Reema Gupta [50]
 * Sai Asish Yamani [51]
+* Kevin Doran [52]
 
 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
@@ -154,6 +155,7 @@ and may not be the current affiliation of a contributor.
 49. Swartz Center for Computational Neuroscience, University of California, San Diego
 50. Ludwig-Maximilians-Universität München, Munich, Germany
 51. Stony Brook University, Stony Brook, NY, USA
+52. University of Sussex, Brighton, UK
 
 
 

neo/rawio/biocamrawio.py

@@ -213,7 +213,9 @@ def open_biocam_file_header(filename) -> dict:
     if "3BRecInfo" in rf.keys():  # brw v3.x
         # Read recording variables
         rec_vars = rf.require_group("3BRecInfo/3BRecVars/")
-        bit_depth = rec_vars["BitDepth"][0]
+        # Biocam v3.x stores BitDepth as a np.uint8.
+        # Convert to int to avoid overflow when calculating gain.
+        bit_depth = int(rec_vars["BitDepth"][0])
         max_uv = rec_vars["MaxVolt"][0]
         min_uv = rec_vars["MinVolt"][0]
         num_frames = rec_vars["NRecFrames"][0]

neo/test/rawiotest/test_biocamrawio.py

@@ -3,6 +3,10 @@
 """
 
 import unittest
+import pytest
+
+import numpy as np
+import h5py
 
 from neo.rawio.biocamrawio import BiocamRawIO
 from neo.test.rawiotest.common_rawio_test import BaseTestRawIO
@@ -23,5 +27,39 @@ class TestBiocamRawIO(
     ]
 
 
+def test_biocamrawio_gain(tmp_path):
+    """Test that BiocamRawIO correctly reads the gain from a Biocam HDF5 file.
+
+    A test case, from Issue #1883 (https://github.com/NeuralEnsemble/python-neo/issues/1883).
+    Previously, BiocamRawIO would return a gain of `inf`, due to a numpy dtype
+    overflow bug.
+    """
+    # Setup
+    n_ch = 4
+    n_frames = 10
+    path = tmp_path / "minimal_v3.brw"
+    bit_depth = 12
+    max_volt = 4125.0
+    min_volt = -4125.0
+    with h5py.File(path, "w") as f:
+        rv = f.create_group("3BRecInfo/3BRecVars")
+        rv.create_dataset("BitDepth", data=np.array([bit_depth], dtype=np.uint8))
+        rv.create_dataset("MaxVolt", data=np.array([max_volt]))
+        rv.create_dataset("MinVolt", data=np.array([min_volt]))
+        rv.create_dataset("NRecFrames", data=np.array([n_frames], dtype=np.int64))
+        rv.create_dataset("SamplingRate", data=np.array([17852.77]))
+        rv.create_dataset("SignalInversion", data=np.array([1], dtype=np.int32))
+        f.create_dataset("3BRecInfo/3BMeaStreams/Raw/Chs", data=np.arange(2 * n_ch, dtype=np.int32).reshape(n_ch, 2))
+        f.create_dataset("3BData/Raw", data=np.zeros(n_ch * n_frames, dtype=np.uint16))
+        f["3BData"].attrs["Version"] = 102
+
+    # Test
+    r = BiocamRawIO(filename=path)
+    r.parse_header()
+    expected_gain = (max_volt - min_volt) / 2**bit_depth  # ~ 2.014
+    gain = r.header["signal_channels"]["gain"][0]
+    assert expected_gain == pytest.approx(gain)
+
+
 if __name__ == "__main__":
     unittest.main()