Merge branch 'NeuralEnsemble:master' into matlabio

Author: zm711

neo/core/group.py

@@ -51,7 +51,7 @@ class Group(Container):
         'AnalogSignal', 'IrregularlySampledSignal', 'SpikeTrain',
         'Event', 'Epoch', 'ChannelView', 'ImageSequence'
     )
-    _container_child_objects = ('Segment', 'Group')
+    _container_child_objects = ('Group',)
     _parent_objects = ('Block',)
 
     def __init__(self, objects=None, name=None, description=None, file_origin=None,

neo/rawio/blackrockrawio.py

@@ -61,6 +61,7 @@
 import os
 import re
 import warnings
+import math
 
 import numpy as np
 import quantities as pq
@@ -646,7 +647,7 @@ def _get_timestamp_slice(self, timestamp, seg_index, t_start, t_stop):
         if t_start is None:
             ind_start = None
         else:
-            ts = np.math.ceil(t_start * self.__nev_basic_header['timestamp_resolution'])
+            ts = math.ceil(t_start * self.__nev_basic_header['timestamp_resolution'])
             ind_start = np.searchsorted(timestamp, ts)
 
         if t_stop is None:

neo/rawio/plexon2rawio/plexon2rawio.py

@@ -23,6 +23,8 @@
 """
 import pathlib
 import warnings
+import platform
+
 from collections import namedtuple
 from urllib.request import urlopen
 from datetime import datetime
@@ -74,14 +76,19 @@ def __init__(self, filename, pl2_dll_file_path=None):
 
         # download default PL2 dll once if not yet available
         if pl2_dll_file_path is None:
-            pl2_dll_folder = pathlib.Path .home() / '.plexon_dlls_for_neo'
+            architecture = platform.architecture()[0]
+            if architecture == '64bit' and platform.system() == 'Windows':
+                file_name = "PL2FileReader64.dll"
+            else:  # Apparently wine uses the 32 bit version in linux
+                file_name = "PL2FileReader.dll"
+            pl2_dll_folder = pathlib.Path.home() / '.plexon_dlls_for_neo'
             pl2_dll_folder.mkdir(exist_ok=True)
-            pl2_dll_file_path = pl2_dll_folder / 'PL2FileReader.dll'
+            pl2_dll_file_path = pl2_dll_folder / file_name
+
+            if not pl2_dll_file_path.exists():
+                url = f'https://raw.githubusercontent.com/Neuralensemble/pypl2/master/bin/{file_name}'
+                dist = urlopen(url=url)
 
-            if pl2_dll_file_path.exists():
-                warnings.warn(f'Using cached plexon dll at {pl2_dll_file_path}')
-            else:
-                dist = urlopen('https://raw.githubusercontent.com/Neuralensemble/pypl2/master/bin/PL2FileReader.dll')
                 with open(pl2_dll_file_path, 'wb') as f:
                     print(f'Downloading plexon dll to {pl2_dll_file_path}')
                     f.write(dist.read())
@@ -288,7 +295,7 @@ def _get_signal_size(self, block_index, seg_index, stream_index):
         stream_id = self.header['signal_streams'][stream_index]['id']
         stream_characteristic = list(self.signal_stream_characteristics.values())[stream_index]
         assert stream_id == stream_characteristic.id
-        return stream_characteristic.n_samples
+        return int(stream_characteristic.n_samples)  # Avoids returning a numpy.int64 scalar
 
     def _get_signal_t_start(self, block_index, seg_index, stream_index):
         # This returns the t_start of signals as a float value in seconds

neo/test/coretest/test_group.py

@@ -41,7 +41,7 @@ def setUp(self):
         self.test_segment.spiketrains.extend(self.test_spiketrains)
 
     def test_create_group(self):
-        objects = [self.test_view, self.test_signal, self.test_segment]
+        objects = [self.test_view, self.test_signal]
         objects.extend(self.test_spiketrains)
         group = Group(objects)
 
@@ -50,21 +50,19 @@ def test_create_group(self):
         assert group.spiketrains[1] is self.test_spiketrains[1]
         assert group.channelviews[0] is self.test_view
         assert len(group.irregularlysampledsignals) == 0
-        assert group.segments[0].analogsignals[0] is self.test_signal
 
     def test_create_empty_group(self):
         group = Group()
 
     def test_children(self):
         group = Group(self.test_spiketrains + [self.test_view]
-                      + [self.test_signal] + [self.test_segment])
+                      + [self.test_signal])
 
         # note: ordering is by class name for data children (AnalogSignal, SpikeTrain),
         #       then container children (Segment)
         assert group.children == (self.test_signal,
                                   *self.test_spiketrains,
-                                  self.test_view,
-                                  self.test_segment)
+                                  self.test_view)
 
     def test_with_allowed_types(self):
         objects = [self.test_signal] + self.test_spiketrains