update with master

neo/rawio/axonrawio.py

@@ -158,8 +158,8 @@ def _parse_header(self):
         # Get raw data by segment
         # self._raw_signals = {}
         self._t_starts = {}
-        self._buffer_descriptions = {0 :{}}
-        self._stream_buffer_slice = {stream_id : None}
+        self._buffer_descriptions = {0: {}}
+        self._stream_buffer_slice = {stream_id: None}
         pos = 0
         for seg_index in range(nb_segment):
             length = episode_array[seg_index]["len"]
@@ -174,12 +174,12 @@ def _parse_header(self):
 
             self._buffer_descriptions[0][seg_index] = {}
             self._buffer_descriptions[0][seg_index][buffer_id] = {
-                "type" : "raw",
-                "file_path" : str(self.filename),
-                "dtype" : str(sig_dtype),
+                "type": "raw",
+                "file_path": str(self.filename),
+                "dtype": str(sig_dtype),
                 "order": "C",
-                "file_offset" : head_offset + pos * sig_dtype.itemsize,
-                "shape" : (int(length // nbchannel), int(nbchannel)),
+                "file_offset": head_offset + pos * sig_dtype.itemsize,
+                "shape": (int(length // nbchannel), int(nbchannel)),
             }
             pos += length
 
@@ -239,7 +239,9 @@ def _parse_header(self):
             else:
                 gain, offset = 1.0, 0.0
 
-            signal_channels.append((name, str(chan_id), self._sampling_rate, sig_dtype, units, gain, offset, stream_id, buffer_id))
+            signal_channels.append(
+                (name, str(chan_id), self._sampling_rate, sig_dtype, units, gain, offset, stream_id, buffer_id)
+            )
 
         signal_channels = np.array(signal_channels, dtype=_signal_channel_dtype)
 
@@ -313,7 +315,6 @@ def _get_signal_t_start(self, block_index, seg_index, stream_index):
     def _get_analogsignal_buffer_description(self, block_index, seg_index, buffer_id):
         return self._buffer_descriptions[block_index][seg_index][buffer_id]
 
-
     def _event_count(self, block_index, seg_index, event_channel_index):
         return self._raw_ev_timestamps.size
 

neo/rawio/baserawio.py

@@ -1375,7 +1375,6 @@ def _get_analogsignal_buffer_description(self, block_index, seg_index, buffer_id
         raise (NotImplementedError)
 
 
-
 class BaseRawWithBufferApiIO(BaseRawIO):
     """
     Generic class for reader that support "buffer api".
@@ -1402,7 +1401,7 @@ def _get_signal_size(self, block_index, seg_index, stream_index):
         buffer_desc = self.get_analogsignal_buffer_description(block_index, seg_index, buffer_id)
         # some hdf5 revert teh buffer
         time_axis = buffer_desc.get("time_axis", 0)
-        return buffer_desc['shape'][time_axis]
+        return buffer_desc["shape"][time_axis]
 
     def _get_analogsignal_chunk(
         self,
@@ -1413,57 +1412,63 @@ def _get_analogsignal_chunk(
         stream_index: int,
         channel_indexes: list[int] | None,
     ):
-        
+
         stream_id = self.header["signal_streams"][stream_index]["id"]
         buffer_id = self.header["signal_streams"][stream_index]["buffer_id"]
-
-        buffer_slice = self._stream_buffer_slice[stream_id]
 
+        buffer_slice = self._stream_buffer_slice[stream_id]
 
         buffer_desc = self.get_analogsignal_buffer_description(block_index, seg_index, buffer_id)
 
         i_start = i_start or 0
-        i_stop = i_stop or buffer_desc['shape'][0]
+        i_stop = i_stop or buffer_desc["shape"][0]
 
-        if buffer_desc['type'] == "raw":
+        if buffer_desc["type"] == "raw":
 
-            # open files on demand and keep reference to opened file 
-            if not hasattr(self, '_memmap_analogsignal_buffers'):
+            # open files on demand and keep reference to opened file
+            if not hasattr(self, "_memmap_analogsignal_buffers"):
                 self._memmap_analogsignal_buffers = {}
             if block_index not in self._memmap_analogsignal_buffers:
                 self._memmap_analogsignal_buffers[block_index] = {}
             if seg_index not in self._memmap_analogsignal_buffers[block_index]:
                 self._memmap_analogsignal_buffers[block_index][seg_index] = {}
             if buffer_id not in self._memmap_analogsignal_buffers[block_index][seg_index]:
-                fid = open(buffer_desc['file_path'], mode='rb')
+                fid = open(buffer_desc["file_path"], mode="rb")
                 self._memmap_analogsignal_buffers[block_index][seg_index][buffer_id] = fid
             else:
                 fid = self._memmap_analogsignal_buffers[block_index][seg_index][buffer_id]
-
-            num_channels = buffer_desc['shape'][1]
-
-            raw_sigs = get_memmap_chunk_from_opened_file(fid, num_channels,  i_start, i_stop, np.dtype(buffer_desc['dtype']), file_offset=buffer_desc['file_offset'])
 
-
-        elif buffer_desc['type'] == 'hdf5':
+            num_channels = buffer_desc["shape"][1]
+
+            raw_sigs = get_memmap_chunk_from_opened_file(
+                fid,
+                num_channels,
+                i_start,
+                i_stop,
+                np.dtype(buffer_desc["dtype"]),
+                file_offset=buffer_desc["file_offset"],
+            )
+
+        elif buffer_desc["type"] == "hdf5":
 
-            # open files on demand and keep reference to opened file 
-            if not hasattr(self, '_hdf5_analogsignal_buffers'):
+            # open files on demand and keep reference to opened file
+            if not hasattr(self, "_hdf5_analogsignal_buffers"):
                 self._hdf5_analogsignal_buffers = {}
             if block_index not in self._hdf5_analogsignal_buffers:
                 self._hdf5_analogsignal_buffers[block_index] = {}
             if seg_index not in self._hdf5_analogsignal_buffers[block_index]:
                 self._hdf5_analogsignal_buffers[block_index][seg_index] = {}
             if buffer_id not in self._hdf5_analogsignal_buffers[block_index][seg_index]:
                 import h5py
-                h5file = h5py.File(buffer_desc['file_path'], mode="r")
+
+                h5file = h5py.File(buffer_desc["file_path"], mode="r")
                 self._hdf5_analogsignal_buffers[block_index][seg_index][buffer_id] = h5file
             else:
                 h5file = self._hdf5_analogsignal_buffers[block_index][seg_index][buffer_id]
 
             hdf5_path = buffer_desc["hdf5_path"]
             full_raw_sigs = h5file[hdf5_path]
-            
+
             time_axis = buffer_desc.get("time_axis", 0)
             if time_axis == 0:
                 raw_sigs = full_raw_sigs[i_start:i_stop, :]
@@ -1475,31 +1480,28 @@ def _get_analogsignal_chunk(
             if buffer_slice is not None:
                 raw_sigs = raw_sigs[:, buffer_slice]
 
-
-
         else:
             raise NotImplementedError()
 
         # this is a pre slicing when the stream do not contain all channels (for instance spikeglx when load_sync_channel=False)
         if buffer_slice is not None:
             raw_sigs = raw_sigs[:, buffer_slice]
-        
+
         # channel slice requested
         if channel_indexes is not None:
             raw_sigs = raw_sigs[:, channel_indexes]
 
-
         return raw_sigs
 
     def __del__(self):
-        if hasattr(self, '_memmap_analogsignal_buffers'):
+        if hasattr(self, "_memmap_analogsignal_buffers"):
             for block_index in self._memmap_analogsignal_buffers.keys():
                 for seg_index in self._memmap_analogsignal_buffers[block_index].keys():
                     for buffer_id, fid in self._memmap_analogsignal_buffers[block_index][seg_index].items():
                         fid.close()
             del self._memmap_analogsignal_buffers
 
-        if hasattr(self, '_hdf5_analogsignal_buffers'):
+        if hasattr(self, "_hdf5_analogsignal_buffers"):
             for block_index in self._hdf5_analogsignal_buffers.keys():
                 for seg_index in self._hdf5_analogsignal_buffers[block_index].keys():
                     for buffer_id, h5_file in self._hdf5_analogsignal_buffers[block_index][seg_index].items():

neo/rawio/brainvisionrawio.py

@@ -80,19 +80,18 @@ def _parse_header(self):
 
         sig_dtype = np.dtype(fmts[fmt])
 
-
         stream_id = "0"
         buffer_id = "0"
-        self._buffer_descriptions = {0 :{0 : {}}}
+        self._buffer_descriptions = {0: {0: {}}}
         self._stream_buffer_slice = {}
         shape = get_memmap_shape(binary_filename, sig_dtype, num_channels=nb_channel, offset=0)
         self._buffer_descriptions[0][0][buffer_id] = {
-            "type" : "raw",
-            "file_path" : binary_filename,
-            "dtype" : str(sig_dtype),
+            "type": "raw",
+            "file_path": binary_filename,
+            "dtype": str(sig_dtype),
             "order": "C",
-            "file_offset" : 0,
-            "shape" : shape,
+            "file_offset": 0,
+            "shape": shape,
         }
         self._stream_buffer_slice[stream_id] = None
 

neo/rawio/edfrawio.py

@@ -173,14 +173,17 @@ def _parse_header(self):
         for array_key in array_keys:
             array_anno = {array_key: [h[array_key] for h in self.signal_headers]}
         seg_ann["signals"].append({"__array_annotations__": array_anno})
-        
+
         # We store the following attributes for rapid access without needing the reader
-        
+
         self._t_stop = self.edf_reader.datarecord_duration * self.edf_reader.datarecords_in_file
         # use sample count of first signal in stream
-        self._stream_index_samples = {stream_index : self.edf_reader.getNSamples()[chidx][0] for stream_index, chidx in self.stream_idx_to_chidx.items()}
+        self._stream_index_samples = {
+            stream_index: self.edf_reader.getNSamples()[chidx][0]
+            for stream_index, chidx in self.stream_idx_to_chidx.items()
+        }
         self._number_of_events = len(self.edf_reader.readAnnotations()[0])
-        
+
         self.close()
 
     def _get_stream_channels(self, stream_index):

neo/rawio/elanrawio.py

@@ -163,7 +163,7 @@ def _parse_header(self):
         buffer_id = "0"
         signal_buffers = np.array([("Signals", buffer_id)], dtype=_signal_buffer_dtype)
         signal_streams = np.array([("Signals", stream_id, buffer_id)], dtype=_signal_stream_dtype)
-        
+
         sig_channels = []
         for c, chan_info in enumerate(channel_infos):
             chan_name = chan_info["label"]
@@ -197,16 +197,16 @@ def _parse_header(self):
         sig_channels = np.array(sig_channels, dtype=_signal_channel_dtype)
 
         # raw data
-        self._buffer_descriptions = {0 :{0 : {}}}
+        self._buffer_descriptions = {0: {0: {}}}
         self._stream_buffer_slice = {}
         shape = get_memmap_shape(self.filename, sig_dtype, num_channels=nb_channel + 2, offset=0)
         self._buffer_descriptions[0][0][buffer_id] = {
-            "type" : "raw",
-            "file_path" : self.filename,
-            "dtype" : sig_dtype,
+            "type": "raw",
+            "file_path": self.filename,
+            "dtype": sig_dtype,
             "order": "C",
-            "file_offset" : 0,
-            "shape" : shape,
+            "file_offset": 0,
+            "shape": shape,
         }
         self._stream_buffer_slice["0"] = slice(0, -2)
 

neo/rawio/maxwellrawio.py

@@ -119,12 +119,12 @@ def _parse_header(self):
 
         # create signal channels
         max_sig_length = 0
-        self._buffer_descriptions = {0 :{0 :{}}}
+        self._buffer_descriptions = {0: {0: {}}}
         self._stream_buffer_slice = {}
         sig_channels = []
         well_indices_to_remove = []
         for stream_index, stream_id in enumerate(signal_streams["id"]):
-            
+
             if int(version) == 20160704:
                 sr = 20000.0
                 settings = h5file["settings"]
@@ -163,14 +163,14 @@ def _parse_header(self):
                     continue
 
                 self._stream_buffer_slice[stream_id] = None
-            
+
             buffer_id = stream_id
             shape = h5file[hdf5_path].shape
             self._buffer_descriptions[0][0][buffer_id] = {
-                "type" : "hdf5",
-                "file_path" : str(self.filename),
-                "hdf5_path" : hdf5_path,
-                "shape" : shape,
+                "type": "hdf5",
+                "file_path": str(self.filename),
+                "hdf5_path": hdf5_path,
+                "shape": shape,
                 "time_axis": 1,
             }
             self._stream_buffer_slice[stream_id] = slice(None)
@@ -232,7 +232,9 @@ def _get_signal_t_start(self, block_index, seg_index, stream_index):
 
     def _get_analogsignal_chunk(self, block_index, seg_index, i_start, i_stop, stream_index, channel_indexes):
         try:
-            return super()._get_analogsignal_chunk(block_index, seg_index, i_start, i_stop, stream_index, channel_indexes)
+            return super()._get_analogsignal_chunk(
+                block_index, seg_index, i_start, i_stop, stream_index, channel_indexes
+            )
         except OSError as e:
             print("*" * 10)
             print(_hdf_maxwell_error)

neo/rawio/micromedrawio.py

@@ -46,15 +46,13 @@ class MicromedRawIO(BaseRawWithBufferApiIO):
     extensions = ["trc", "TRC"]
     rawmode = "one-file"
 
-
     def __init__(self, filename=""):
         BaseRawWithBufferApiIO.__init__(self)
         self.filename = filename
 
     def _parse_header(self):
 
 
-
         with open(self.filename, "rb") as fid:
             f = StructFile(fid)
 
@@ -156,7 +154,7 @@ def _parse_header(self):
 
 
             signal_channels = np.array(signal_channels, dtype=_signal_channel_dtype)
-            
+
             self._stream_buffer_slice = {"0": slice(None)}
             signal_buffers = np.array([("Signals", buffer_id)], dtype=_signal_buffer_dtype)
             signal_streams = np.array([("Signals", stream_id, buffer_id)], dtype=_signal_stream_dtype)

neo/rawio/neuronexusrawio.py

@@ -136,14 +136,14 @@ def _parse_header(self):
 
         # the will cretae a memory map with teh generic mechanism
         buffer_id = "0"
-        self._buffer_descriptions = {0 :{0 :{}}}
+        self._buffer_descriptions = {0: {0: {}}}
         self._buffer_descriptions[0][0][buffer_id] = {
-            "type" : "raw",
-            "file_path" : str(binary_file),
-            "dtype" : BINARY_DTYPE,
+            "type": "raw",
+            "file_path": str(binary_file),
+            "dtype": BINARY_DTYPE,
             "order": "C",
-            "file_offset" : 0,
-            "shape" : (self._n_samples, self._n_channels),
+            "file_offset": 0,
+            "shape": (self._n_samples, self._n_channels),
         }
         # Make the memory map for timestamp
         self._timestamps = np.memmap(

neo/rawio/neuroscoperawio.py

@@ -112,16 +112,16 @@ def _parse_header(self):
         shape = get_memmap_shape(self.data_file_path, sig_dtype, num_channels=nb_channel, offset=0)
         buffer_id = "0"
         stream_id = "0"
-        self._buffer_descriptions = {0: {0:{}}}
+        self._buffer_descriptions = {0: {0: {}}}
         self._buffer_descriptions[0][0][buffer_id] = {
-            "type" : "raw",
-            "file_path" : str(self.data_file_path),
-            "dtype" : sig_dtype,
+            "type": "raw",
+            "file_path": str(self.data_file_path),
+            "dtype": sig_dtype,
             "order": "C",
-            "file_offset" : 0,
-            "shape" : shape,
+            "file_offset": 0,
+            "shape": shape,
         }
-        self._stream_buffer_slice = {stream_id : None}
+        self._stream_buffer_slice = {stream_id: None}
 
         # one unique stream and buffer
         signal_buffers = np.array([("Signals", buffer_id)], dtype=_signal_buffer_dtype)