Renamed the channelindex attribute to channel_index

examples/generated_data.py

@@ -35,7 +35,7 @@ def generate_block(n_segments=3, n_channels=8, n_units=3,
 
     block = neo.Block()
     block.segments = segments
-    block.channelindexes = [rcg]
+    block.channel_indexes = [rcg]
 
     # Create synthetic data
     for seg in segments:
@@ -87,7 +87,7 @@ def generate_block(n_segments=3, n_channels=8, n_units=3,
 
 # We assume that our block has only 1 ChannelIndex and each
 # RecordingChannel only has 1 AnalogSignal.
-rcg = block.channelindexes[0]
+rcg = block.channel_indexes[0]
 for rc in rcg.recordingchannels:
     print("Analysing channel %d: %s" % (rc.index, rc.name))
 
@@ -123,7 +123,7 @@ def generate_block(n_segments=3, n_channels=8, n_units=3,
 
 # By ChannelIndex. Here we calculate a PSTH averaged over trials by
 # channel location, blending all Units:
-for rcg in block.channelindexes:
+for rcg in block.channel_indexes:
     stlist = []
     for unit in rcg.units:
         stlist.extend([st - st.t_start for st in unit.spiketrains])

neo/core/analogsignal.py

@@ -185,7 +185,7 @@ def __new__(cls, signal, units=None, dtype=None, copy=True,
         obj._sampling_rate = _get_sampling_rate(sampling_rate, sampling_period)
 
         obj.segment = None
-        obj.channelindex = None
+        obj.channel_index = None
         return obj
 
     def __init__(self, signal, units=None, dtype=None, copy=True,
@@ -258,8 +258,8 @@ def __repr__(self):
     def get_channel_index(self):
         """
         """
-        if self.channelindex:
-            return self.channelindex.channel_indexes
+        if self.channel_index:
+            return self.channel_index.channel_indexes
         else:
             return None
 

neo/core/baseneo.py

@@ -126,7 +126,7 @@ def _reference_name(class_name):
     `_container_name("Block")`.
     """
     name_map = {
-        "ChannelIndex": "channelindex"
+        "ChannelIndex": "channel_index"
     }
     return name_map.get(class_name, class_name.lower())
 
@@ -141,7 +141,7 @@ def _container_name(class_name):
     obtained by calling `_container_name_plural("Segment")`.
     """
     name_map = {
-        "ChannelIndex": "channelindexes"
+        "ChannelIndex": "channel_indexes"
     }
     return name_map.get(class_name, _reference_name(class_name) + 's')
 

neo/core/block.py

@@ -41,11 +41,11 @@ class Block(Container):
         >>> for ind in range(2):
         ...     rcg = ChannelIndex(name='Array probe %d' % ind,
         ...                                 channel_indexes=np.arange(64))
-        ...     blk.channelindexes.append(rcg)
+        ...     blk.channel_indexes.append(rcg)
         ...
         >>> # Populate the Block with AnalogSignal objects
         ... for seg in blk.segments:
-        ...     for rcg in blk.channelindexes:
+        ...     for rcg in blk.channel_indexes:
         ...         a = AnalogSignal(np.random.randn(10000, 64)*nA,
         ...                               sampling_rate=10*kHz)
         ...         rcg.analogsignals.append(a)

neo/core/irregularlysampledsignal.py

@@ -148,7 +148,7 @@ def __new__(cls, times, signal, units=None, time_units=None, dtype=None,
         obj.times = pq.Quantity(times, units=time_units,
                                 dtype=float, copy=copy)
         obj.segment = None
-        obj.channelindex = None
+        obj.channel_index = None
 
         return obj
 

neo/core/recordingchannelgroup.py

@@ -44,11 +44,11 @@ class ChannelIndex(Container):
         >>> for ind in range(2):
         ...     rcg = ChannelIndex(name='Array probe %d' % ind,
         ...                                 channel_indexes=np.arange(64))
-        ...     blk.channelindexes.append(rcg)
+        ...     blk.channel_indexes.append(rcg)
         ...
         >>> # Populate the Block with AnalogSignal objects
         ... for seg in blk.segments:
-        ...     for rcg in blk.channelindexes:
+        ...     for rcg in blk.channel_indexes:
         ...         a = AnalogSignal(np.random.randn(10000, 64)*nA,
         ...                          sampling_rate=10*kHz)
         ...         rcg.analogsignals.append(a)
@@ -71,7 +71,7 @@ class ChannelIndex(Container):
         ... rcg = ChannelIndex(channel_names=np.array(['ch1', 'ch4', 'ch6']),
         ...                             channel_indexes = np.array([0, 3, 5])
         >>> rcg.analogsignals.append(sig)
-        >>> blk.channelindexes.append(rcg)
+        >>> blk.channel_indexes.append(rcg)
 
     *Usage 3* dealing with :class:`Unit` objects::
 
@@ -82,7 +82,7 @@ class ChannelIndex(Container):
         >>>
         >>> # Create a new ChannelIndex and add it to the Block
         >>> rcg = ChannelIndex(name='octotrode A')
-        >>> blk.channelindexes.append(rcg)
+        >>> blk.channel_indexes.append(rcg)
         >>>
         >>> # create several Unit objects and add them to the
         >>> # ChannelIndex

neo/core/segment.py

@@ -185,7 +185,7 @@ def construct_subsegment_by_unit(self, unit_list=None):
             >>>
             >>> blk = Block()
             >>> rcg = ChannelIndex(name='group0')
-            >>> blk.channelindexes = [rcg]
+            >>> blk.channel_indexes = [rcg]
             >>>
             >>> for ind in range(5):
             ...         unit = Unit(name='Unit #%s' % ind, channel_index=ind)

neo/core/unit.py

@@ -70,12 +70,12 @@ def __init__(self, name=None, description=None, file_origin=None,
         '''
         super(Unit, self).__init__(name=name, description=description,
                                    file_origin=file_origin, **annotations)
-        self.channelindex = None
+        self.channel_index = None
 
     def get_channel_indexes(self):
         """
         """
-        if self.channelindex:
-            return self.channelindex.channel_indexes
+        if self.channel_index:
+            return self.channel_index.channel_indexes
         else:
             return None

neo/io/blackrockio.py

@@ -93,8 +93,8 @@ def read_block(self, lazy=False, cascade=True, load_waveforms = False):
             channel_id = st.annotations['channel_id']
             index = None
             for sig in seg.analogsignals:
-                if channel_id in sig.channelindex.channel_ids:
-                    i = np.where(sig.channelindex.channel_ids==channel_id)[0][0]
+                if channel_id in sig.channel_index.channel_ids:
+                    i = np.where(sig.channel_index.channel_ids==channel_id)[0][0]
                     index = sig.get_channel_index()[i]
                     break
             if index is not None:
@@ -104,7 +104,7 @@ def read_block(self, lazy=False, cascade=True, load_waveforms = False):
                 unit = Unit(name=st.name)
                 unit.spiketrains.append(st)
                 rcg.units.append(unit)
-                bl.channelindexes.append(rcg)
+                bl.channel_indexes.append(rcg)
 
         bl.create_many_to_one_relationship()
 
@@ -426,7 +426,7 @@ def read_nsx(self, filename_nsx, seg, lazy, cascade):
                                         name=name,
                                         file_origin=filename_nsx)
             rcg.analogsignals.append(anasig)
-            anasig.channelindex = rcg
+            anasig.channel_index = rcg
             seg.analogsignals.append(anasig)
 
     def read_sif(self, filename_sif, seg, ):

neo/io/blackrockio_deprecated.py

@@ -114,7 +114,7 @@ def read_block(self, lazy=False, cascade=True,
         #~ # Add channel hierarchy
         #~ rcg = ChannelIndex(name='allchannels',
             #~ description='group of all channels', file_origin=self.filename)
-        #~ block.channelindexes.append(rcg)
+        #~ block.channel_indexes.append(rcg)
         #~ self.channel_number_to_recording_channel = {}
 
         #~ # Add each channel at a time to hierarchy
@@ -277,7 +277,7 @@ def channel_indexes_in_segment(seg):
         channel_indices.append(sig.recordingchannel.index)
 
     for asa in seg.analogsignals:
-        channel_indices.append(asa.channelindex.channel_indexes)
+        channel_indices.append(asa.channel_index.channel_indexes)
 
     return channel_indices
 

neo/io/brainwaredamio.py

@@ -147,7 +147,7 @@ def read_block(self, lazy=False, cascade=True, **kargs):
                                     channel_names=np.array(['Chan1'], dtype='S'))
 
         # load objects into their containers
-        block.channelindexes.append(rcg)
+        block.channel_indexes.append(rcg)
 
         # open the file
         with open(self._path, 'rb') as fobject:
@@ -159,7 +159,7 @@ def read_block(self, lazy=False, cascade=True, **kargs):
                     break
 
                 # store the segment and signals
-                seg.analogsignals[0].channelindex = rcg
+                seg.analogsignals[0].channel_index = rcg
                 block.segments.append(seg)
 
         # remove the file object

neo/io/brainwaref32io.py

@@ -163,7 +163,7 @@ def read_block(self, lazy=False, cascade=True, **kargs):
         self.__unit = Unit(file_origin=self._filename)
 
         # load objects into their containers
-        block.channelindexes.append(rcg)
+        block.channel_indexes.append(rcg)
         rcg.units.append(self.__unit)
 
         # initialize values

neo/io/brainwaresrcio.py

@@ -164,7 +164,7 @@ def __init__(self, filename=None):
         self._blk = None
 
         # This stores the current ChannelIndex for easy access
-        # It is equivalent to self._blk.channelindexes[0]
+        # It is equivalent to self._blk.channel_indexes[0]
         self._rcg = None
 
         # This stores the current Segment for easy access
@@ -296,7 +296,7 @@ def read_next_block(self, cascade=True, lazy=False, **kargs):
                            file_origin=self._file_origin,
                            elliptic=[], boundaries=[],
                            timestamp=[], max_valid=[])
-        self._blk.channelindexes.append(self._rcg)
+        self._blk.channel_indexes.append(self._rcg)
         self._rcg.units.append(self._unit0)
         self._blk.segments.append(self._seg0)
 

neo/io/elphyio.py

@@ -4203,7 +4203,7 @@ def read_channelindex( self, episode ):
         )
         for spk in range(0, n_spikes) :
             channel = self.read_channelindex(episode, spk)
-            group.channelindexes.append(channel)
+            group.channel_indexes.append(channel)
         return group
 
 

neo/io/hdf5io.py

@@ -534,7 +534,7 @@ def _get_parent(self, path, ref, parent_type):
 
         if parent_type.lower() in ('recordingchannel', 'unit'):
             # We need to search all recording channels
-            path = block_path + '/channelindexes'
+            path = block_path + '/channel_indexes'
             for n in self._data.iterNodes(path):
                 if not '_type' in n._v_attrs:
                     continue
@@ -547,9 +547,9 @@ def _get_parent(self, path, ref, parent_type):
 
         if parent_type.lower() == 'segment':
             path = block_path + '/segments'
-        elif parent_type.lower() in ('channelindex',
-                                     'channelindexes'):
-            path = block_path + '/channelindexes'
+        elif parent_type.lower() in ('channel_index',
+                                     'channel_indexes'):
+            path = block_path + '/channel_indexes'
         else:
             return ''
 
@@ -561,7 +561,7 @@ def _get_rcgs(self, path, ref):
         parts = path.split('/')
         object_folder = parts[-2]
         block_path = '/'.join(parts[:-4])
-        path = block_path + '/channelindexes'
+        path = block_path + '/channel_indexes'
         return self._search_parent(path, object_folder, ref, True)
 
     def _search_parent(self, path, object_folder, ref, multi=False):
@@ -616,17 +616,17 @@ def load_lazy_cascade(self, path, lazy):
                         ppaths.append(None)
                 self.parent_paths[path] = ppaths
             elif t == 'RecordingChannel':
-                if 'channelindexes' in node._v_attrs:
+                if 'channel_indexes' in node._v_attrs:
                     self.parent_paths[path] = node._f_getAttr(
-                        'channelindexes')
+                        'channel_indexes')
 
         # Set parent objects
         if path in self.parent_paths:
             paths = self.parent_paths[path]
 
             if t == 'RecordingChannel':  # Set list of parnet channel groups
                 for rcg in self.parent_paths[path]:
-                    o.channelindexes.append(
+                    o.channel_indexes.append(
                         self.get(rcg, cascade='lazy', lazy=lazy))
             else:  # Set parents: Segment and another parent
                 if paths[0] is None:
@@ -650,7 +650,7 @@ def load_lazy_cascade(self, path, lazy):
             if t == 'RecordingChannel':
                 rcg_paths = self._get_rcgs(path, ref)
                 for rcg in rcg_paths:
-                    o.channelindexes.append(self.get(
+                    o.channel_indexes.append(self.get(
                         rcg, cascade='lazy', lazy=lazy))
                 self.parent_paths[path] = rcg_paths
             else:
@@ -812,15 +812,15 @@ def get_lazy_shape(obj, node):
                     # create at least One-to-Many
                     if obj_type == 'ChannelIndex' and not object_ref:
                         for r in relatives:
-                            r.channelindexes = [obj]
+                            r.channel_indexes = [obj]
             # special processor for RC -> RCG
             if obj_type == 'RecordingChannel':
                 if hasattr(node, '_v_parent'):
                     parent = node._v_parent
                     if hasattr(parent, '_v_parent'):
                         parent = parent._v_parent
                         if 'object_ref' in parent._v_attrs:
-                            obj.channelindexes.append(self.get(
+                            obj.channel_indexes.append(self.get(
                                 parent._v_pathname, lazy=lazy))
         return obj
 

neo/io/kwikio.py

@@ -142,12 +142,12 @@ def read_block(self,
 
             rcg = ChannelIndex(name='all channels',
                                  channel_indexes=channel_index)
-            blk.channelindexes.append(rcg)
+            blk.channel_indexes.append(rcg)
 
             ana = self.read_analogsignal(channel_index=channel_index,
                                          lazy=lazy,
                                          cascade=cascade)
-            ana.channelindex = rcg
+            ana.channel_index = rcg
             seg.duration = (self._attrs['shape'][0]
                           / self._attrs['kwik']['sample_rate']) * pq.s
 

neo/io/neuroscopeio.py

@@ -104,7 +104,7 @@ def read_block(self,
                                             channel_indexes=np.arange(n_channels, dtype = int))
                 rcg.channel_ids = np.array([int(xml_rc.text) for xml_rc in xml_rcg])
                 rcg.channel_names = np.array(['Channel{0}'.format(id) for id in rcg.channel_ids], dtype = 'S')
-                bl.channelindexes.append(rcg)
+                bl.channel_indexes.append(rcg)
 
             # AnalogSignals
             reader = RawBinarySignalIO(filename = self.filename.replace('.xml', '.dat'))

neo/io/tools.py

@@ -22,7 +22,7 @@
 
     # Special case this tricky many-to-many relationship
     # we still need links from recordingchannel to analogsignal
-#    for rcg in block.channelindexes:
+#    for rcg in block.channel_indexes:
 #        for rc in rcg.recordingchannels:
 #            rc.create_many_to_one_relationship()
 
@@ -65,11 +65,11 @@
 #     rcg = ChannelIndex(name='all channels',
 #                                 channel_indexes=indexes,
 #                                 channel_names=names)
-#     bl.channelindexes.append(rcg)
+#     bl.channel_indexes.append(rcg)
 #     for ind in indexes:
 #         # many to many relationship
 #         rcg.recordingchannels.append(recordingchannels[ind])
-#         recordingchannels[ind].channelindexes.append(rcg)
+#         recordingchannels[ind].channel_indexes.append(rcg)
 
 
 def iteritems(D):

neo/test/coretest/test_analogsignalarray.py

@@ -206,13 +206,13 @@ def test__children(self):
         self.assertEqual(signal._multi_parent_objects, ())
 
         self.assertEqual(signal._single_parent_containers,
-                         ('segment', 'channelindex'))
+                         ('segment', 'channel_index'))
         self.assertEqual(signal._multi_parent_containers, ())
 
         self.assertEqual(signal._parent_objects,
                          ('Segment', 'ChannelIndex'))
         self.assertEqual(signal._parent_containers,
-                         ('segment', 'channelindex'))
+                         ('segment', 'channel_index'))
 
         self.assertEqual(len(signal.parents), 2)
         self.assertEqual(signal.parents[0].name, 'seg1')