Merge branch 'master' into neuronexus

Author: zm711

doc/source/authors.rst

@@ -95,6 +95,8 @@ and may not be the current affiliation of a contributor.
 * Rémi Proville [44]
 * Paul Adkisson [24]
 * Luiz Tauffer [24]
+* Akshaj Verma [46]
+* Letizia Signorelli [47]
 
 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
@@ -141,6 +143,8 @@ and may not be the current affiliation of a contributor.
 43. University of Genoa, Italy
 44. AquiNeuro, SAS
 45. Maxwell Biosystems AG
+46. Brain Center, University Medical Center Utrecht, Utrecht University, The Netherlands
+47. Centre for Molecular Medicine Norway (NCMM), University of Oslo, Norway
 
 
 

neo/core/spiketrainlist.py

@@ -113,8 +113,11 @@ def __init__(self, items=None, parent=None):
         self._channel_id_array = None
         self._all_channel_ids = None
         self._spiketrain_metadata = {}
-        if parent is not None and parent.__class__.__name__ != "Segment":
-            raise AttributeError("The parent class must be a Segment")
+
+        from .segment import Segment  # import here rather than at the top to avoid circular import
+
+        if parent is not None and not isinstance(parent, Segment):
+            raise AttributeError("If provided, the parent class must be a Segment")
         self.segment = parent
 
     @property

neo/rawio/axonarawio.py

@@ -377,8 +377,7 @@ def _get_analogsignal_chunk(self, block_index, seg_index, i_start, i_stop, strea
         if channel_indexes is None:
             channel_indexes = [i for i in range(bin_dict["num_channels"])]
         elif isinstance(channel_indexes, slice):
-            channel_indexes_all = [i for i in range(bin_dict["num_channels"])]
-            channel_indexes = channel_indexes_all[channel_indexes]
+            channel_indexes = self._get_active_channels()
 
         num_samples = i_stop - i_start
 
@@ -562,6 +561,20 @@ def get_active_tetrode(self):
                     active_tetrodes.append(tetrode_id)
         return active_tetrodes
 
+    def _get_active_channels(self):
+        """
+        Returns the ID numbers of the active channels as a list.
+        E.g.: [20,21,22,23] for tetrode 6 active.
+        """
+        active_tetrodes = self.get_active_tetrode()
+        active_channels = []
+
+        for tetrode in active_tetrodes:
+            chans = self._get_channel_from_tetrode(tetrode)
+            active_channels.append(chans)
+
+        return np.concatenate(active_channels)
+
     def _get_channel_from_tetrode(self, tetrode):
         """
         This function will take the tetrode number and return the Axona
@@ -632,12 +645,13 @@ def _get_signal_chan_header(self):
         gain_list = self._get_channel_gain()
         offset = 0  # What is the offset?
 
+        first_channel = (active_tetrode_set[0] - 1) * elec_per_tetrode
         sig_channels = []
         for itetr in range(num_active_tetrode):
 
             for ielec in range(elec_per_tetrode):
-                cntr = (itetr * elec_per_tetrode) + ielec
-                ch_name = f"{itetr + 1}{letters[ielec]}"
+                cntr = (itetr * elec_per_tetrode) + ielec + first_channel
+                ch_name = f"{itetr + active_tetrode_set[0]}{letters[ielec]}"
                 chan_id = str(cntr)
                 gain = gain_list[cntr]
                 stream_id = "0"

neo/rawio/micromedrawio.py

@@ -51,7 +51,6 @@ def __init__(self, filename=""):
         self.filename = filename
 
     def _parse_header(self):
-
         with open(self.filename, "rb") as fid:
             f = StructFile(fid)
 
@@ -133,7 +132,11 @@ def _parse_header(self):
             sig_grounds = []
             for c in range(Num_Chan):
                 zname2, pos, length = zones["LABCOD"]
-                f.seek(pos + code[c] * 128 + 2, 0)
+                # Force code[c] which is currently a uint16 (or u2) into a int to prevent integer overflow
+                # for the following operation -- code[c] * 128 + 2.
+                # An integer overflow below may have side - effects including but not limited
+                # to having repeated channel names.
+                f.seek(pos + int(code[c]) * 128 + 2, 0)
 
                 chan_name = f.read(6).strip(b"\x00").decode("ascii")
                 ground = f.read(6).strip(b"\x00").decode("ascii")
@@ -269,7 +272,6 @@ def _event_count(self, block_index, seg_index, event_channel_index):
         return n
 
     def _get_event_timestamps(self, block_index, seg_index, event_channel_index, t_start, t_stop):
-
         raw_event = self._raw_events[event_channel_index][seg_index]
 
         # important : all events timing are related to the first segment t_start

neo/rawio/spikeglxrawio.py

@@ -576,7 +576,7 @@ def extract_stream_info(meta_file, meta):
         if (
             "imDatPrb_type" not in meta
             or meta["imDatPrb_type"] == "0"
-            or meta["imDatPrb_type"] in ("1015", "1016", "1022", "1030", "1031", "1032", "1100", "1121", "1123","1300")
+            or meta["imDatPrb_type"] in ("1015", "1016", "1022", "1030", "1031", "1032", "1100", "1121", "1123", "1300")
         ):
             # This work with NP 1.0 case with different metadata versions
             # https://github.com/billkarsh/SpikeGLX/blob/15ec8898e17829f9f08c226bf04f46281f106e5f/Markdown/Metadata_30.md

neo/test/iotest/test_plexon2io.py

@@ -20,6 +20,7 @@
 
 TEST_PLEXON2 = bool(os.getenv("PLEXON2_TEST"))
 
+
 @unittest.skipUnless(HAVE_PYPL2 and TEST_PLEXON2, "requires pypl package and all its dependencies")
 class TestPlexon2IO(BaseTestIO, unittest.TestCase):
     entities_to_download = TestPlexon2RawIO.entities_to_download

neo/test/rawiotest/test_plexon2rawio.py

@@ -19,6 +19,7 @@
 
 TEST_PLEXON2 = bool(os.getenv("PLEXON2_TEST"))
 
+
 @unittest.skipUnless(HAVE_PYPL2 and TEST_PLEXON2, "requires pypl package and all its dependencies")
 class TestPlexon2RawIO(
     BaseTestRawIO,