Merge branch 'master' into fix_openephys_stream

Author: h-mayorquin

doc/source/authors.rst

@@ -90,8 +90,10 @@ and may not be the current affiliation of a contributor.
 * Xin Niu
 * Nikhil Chandra [40]
 * Luigi Petrucco [42]
+* Tommaso Lambresa [43]
+* Nina Kudryashova [37]
 
-1. Centre de Recherche en Neuroscience de Lyon, CNRS UMR5292 - INSERM U1028 - Universite Claude Bernard Lyon 1
+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
 3. University of California, Berkeley
 4. Laboratoire de Neurosciences Intégratives et Adaptatives, CNRS UMR 6149 - Université de Provence, Marseille, France
@@ -133,6 +135,7 @@ and may not be the current affiliation of a contributor.
 40. Plexon Inc.
 41. Paris Brain Institute
 42. Istituto Italiano di Tecnologia (IIT), Italy
+43. University of Genoa, Italy
 
 
 

neo/io/__init__.py

@@ -167,7 +167,7 @@
 .. autoclass:: neo.io.MaxwellIO
 
     .. autoattribute:: extensions
-    
+
 .. autoclass:: neo.io.MedIO
 
     .. autoattribute:: extensions

neo/rawio/axonrawio.py

@@ -23,7 +23,7 @@
 strings section:
 [uModifierNameIndex, uCreatorNameIndex, uProtocolPathIndex, lFileComment, lADCCChannelNames, lADCUnitsIndex
 lDACChannelNameIndex, lDACUnitIndex, lDACFilePath, nLeakSubtractADC]
-['', 'Clampex', '', 'C:/path/protocol.pro', 'some comment', 'IN 0', 'mV', 'IN 1', 'mV', 'Cmd 0', 'pA', 
+['', 'Clampex', '', 'C:/path/protocol.pro', 'some comment', 'IN 0', 'mV', 'IN 1', 'mV', 'Cmd 0', 'pA',
 'Cmd 1', 'pA', 'Cmd 2', 'mV', 'Cmd 3', 'mV']
 
 Information on abf 1 and 2 formats is available here:

neo/rawio/blackrockrawio.py

@@ -979,7 +979,7 @@ def __read_nsx_dataheader_variant_b(
             # use of `int` avoids overflow problem
             data_size = int(dh["nb_data_points"]) * int(self.__nsx_basic_header[nsx_nb]["channel_count"]) * 2
             # define new offset (to possible next data block)
-            offset = data_header[index]["offset_to_data_block"] + data_size
+            offset = int(data_header[index]["offset_to_data_block"]) + data_size
 
             index += 1
 

neo/rawio/intanrawio.py

@@ -16,7 +16,7 @@
   * http://intantech.com/files/Intan_RHD2000_data_file_formats.pdf
   * http://intantech.com/files/Intan_RHS2000_data_file_formats.pdf
 
-  
+
 Author: Samuel Garcia (Initial), Zach McKenzie & Heberto Mayorquin (Updates)
 
 """

neo/rawio/medrawio.py

@@ -1,6 +1,6 @@
 """
 Class for reading MED (Multiscale Electrophysiology Data) Format.
-    
+
 Uses the dhn-med-py python package, created by Dark Horse Neuro, Inc.
 
 Authors: Dan Crepeau, Matt Stead

neo/rawio/neuronexusrawio.py

@@ -6,13 +6,13 @@
   * The *.xdat.json metadata file
   * The *_data.xdat binary file of all raw data
   * The *_timestamps.xdat binary file of the timestamp data
-  
+
 Based on sample data is appears that the binary file is always a float32 format
 Other information can be found within the metadata json file
 
 
 The metadata file has a pretty complicated structure as far as I can tell
-a lot of which is dedicated to probe information, which won't be handle at the 
+a lot of which is dedicated to probe information, which won't be handle at the
 the Neo level.
 
 It appears that the metadata['status'] provides most of the information necessary

neo/rawio/openephysbinaryrawio.py

@@ -358,16 +358,14 @@ def _parse_header(self):
                                     rising_indices.extend(rising)
                                     falling_indices.extend(falling)
 
-                            rising_indices = np.array(rising_indices)
-                            falling_indices = np.array(falling_indices)
+                            rising_indices = np.array(rising_indices, dtype=np.int64)
+                            falling_indices = np.array(falling_indices, dtype=np.int64)
 
                             # Sort the indices to maintain chronological order
                             sorted_order = np.argsort(rising_indices)
                             rising_indices = rising_indices[sorted_order]
                             falling_indices = falling_indices[sorted_order]
 
-                            durations = None
-                            # if len(rising_indices) == len(falling_indices):
                             durations = timestamps[falling_indices] - timestamps[rising_indices]
                             if not self._use_direct_evt_timestamps:
                                 timestamps = timestamps / info["sample_rate"]

neo/test/iotest/test_openephysbinaryio.py

@@ -1,6 +1,4 @@
-"""
-
-"""
+""" """
 
 import unittest
 

neo/test/iotest/test_openephysio.py

@@ -1,6 +1,4 @@
-"""
-
-"""
+""" """
 
 import unittest