Merge branch 'master' into update-copyright

Author: zm711

neo/core/spiketrain.py

@@ -199,7 +199,7 @@ def normalize_times_array(times, units=None, dtype=None, copy=None):
             "In order to facilitate the deprecation copy can be set to None but will raise an "
             "error if set to True/False since this will silently do nothing. This argument will be completely "
             "removed in Neo 0.15.0. Please update your code base as necessary."
-            )
+        )
 
     if dtype is None:
         if not hasattr(times, "dtype"):

neo/rawio/blackrockrawio.py

@@ -681,8 +681,7 @@ def _get_timestamp_slice(self, timestamp, seg_index, t_start, t_stop):
             if t_start is None:
                 t_start = self._seg_t_starts[seg_index]
             if t_stop is None:
-                t_stop = self._seg_t_stops[seg_index] + 1 / float(
-                    self.__nev_basic_header['timestamp_resolution'])
+                t_stop = self._seg_t_stops[seg_index] + 1 / float(self.__nev_basic_header["timestamp_resolution"])
 
         if t_start is None:
             ind_start = None
@@ -715,15 +714,16 @@ def _get_spike_raw_waveforms(self, block_index, seg_index, unit_index, t_start,
         )
         unit_spikes = all_spikes[mask]
 
-        wf_dtype = self.__nev_params('waveform_dtypes')[channel_id]
-        wf_size = self.__nev_params('waveform_size')[channel_id]
+        wf_dtype = self.__nev_params("waveform_dtypes")[channel_id]
+        wf_size = self.__nev_params("waveform_size")[channel_id]
         wf_byte_size = np.dtype(wf_dtype).itemsize * wf_size
 
         dt1 = [
-            ('extra', 'S{}'.format(unit_spikes['waveform'].dtype.itemsize - wf_byte_size)),
-            ('ch_waveform', 'S{}'.format(wf_byte_size))]
+            ("extra", "S{}".format(unit_spikes["waveform"].dtype.itemsize - wf_byte_size)),
+            ("ch_waveform", "S{}".format(wf_byte_size)),
+        ]
 
-        waveforms = unit_spikes['waveform'].view(dt1)['ch_waveform'].flatten().view(wf_dtype)
+        waveforms = unit_spikes["waveform"].view(dt1)["ch_waveform"].flatten().view(wf_dtype)
 
         waveforms = waveforms.reshape(int(unit_spikes.size), 1, int(wf_size))
 
@@ -1365,7 +1365,9 @@ def __match_nsx_and_nev_segment_ids(self, nsx_nb):
 
                     # Show warning if spikes do not fit any segment (+- 1 sampling 'tick')
                     # Spike should belong to segment before
-                    mask_outside = (ev_ids == i) & (data["timestamp"] < int(seg["timestamp"]) - int(nsx_offset) - int(nsx_period))
+                    mask_outside = (ev_ids == i) & (
+                        data["timestamp"] < int(seg["timestamp"]) - int(nsx_offset) - int(nsx_period)
+                    )
 
                     if len(data[mask_outside]) > 0:
                         warnings.warn(f"Spikes outside any segment. Detected on segment #{i}")
@@ -1995,7 +1997,6 @@ def __get_nsx_param_variant_a(self, nsx_nb):
         else:
             units = "uV"
 
-        
         nsx_parameters = {
             "nb_data_points": int(
                 (self.__get_file_size(filename) - bytes_in_headers)

neo/rawio/intanrawio.py

@@ -92,7 +92,7 @@ class IntanRawIO(BaseRawIO):
       one long vector, which must be post-processed to extract individual digital channel information.
       See the intantech website for more information on performing this post-processing.
 
-    
+
     Examples
     --------
     >>> import neo.rawio

neo/rawio/micromedrawio.py

@@ -52,7 +52,6 @@ def __init__(self, filename=""):
 
     def _parse_header(self):
 
-
         with open(self.filename, "rb") as fid:
             f = StructFile(fid)
 
@@ -99,7 +98,6 @@ def _parse_header(self):
                 if zname != zname2.decode("ascii").strip(" "):
                     raise NeoReadWriteError("expected the zone name to match")
 
-
             # "TRONCA" zone define segments
             zname2, pos, length = zones["TRONCA"]
             f.seek(pos)
@@ -114,7 +112,7 @@ def _parse_header(self):
                     break
                 else:
                     self.info_segments.append((seg_start, trace_offset))
-            
+
             if len(self.info_segments) == 0:
                 # one unique segment = general case
                 self.info_segments.append((0, 0))
@@ -152,8 +150,9 @@ def _parse_header(self):
                 (sampling_rate,) = f.read_f("H")
                 sampling_rate *= Rate_Min
                 chan_id = str(c)
-                signal_channels.append((chan_name, chan_id, sampling_rate, sig_dtype, units, gain, offset, stream_id, buffer_id))
-
+                signal_channels.append(
+                    (chan_name, chan_id, sampling_rate, sig_dtype, units, gain, offset, stream_id, buffer_id)
+                )
 
             signal_channels = np.array(signal_channels, dtype=_signal_channel_dtype)
 
@@ -166,31 +165,31 @@ def _parse_header(self):
             self._sampling_rate = float(np.unique(signal_channels["sampling_rate"])[0])
 
             # memmap traces buffer
-            full_signal_shape = get_memmap_shape(self.filename, sig_dtype, num_channels=Num_Chan, offset=Data_Start_Offset)
+            full_signal_shape = get_memmap_shape(
+                self.filename, sig_dtype, num_channels=Num_Chan, offset=Data_Start_Offset
+            )
             seg_limits = [trace_offset for seg_start, trace_offset in self.info_segments] + [full_signal_shape[0]]
             self._t_starts = []
-            self._buffer_descriptions = {0 :{}}
+            self._buffer_descriptions = {0: {}}
             for seg_index in range(nb_segment):
                 seg_start, trace_offset = self.info_segments[seg_index]
                 self._t_starts.append(seg_start / self._sampling_rate)
 
                 start = seg_limits[seg_index]
                 stop = seg_limits[seg_index + 1]
-                
+
                 shape = (stop - start, Num_Chan)
-                file_offset = Data_Start_Offset + ( start * np.dtype(sig_dtype).itemsize * Num_Chan)
+                file_offset = Data_Start_Offset + (start * np.dtype(sig_dtype).itemsize * Num_Chan)
                 self._buffer_descriptions[0][seg_index] = {}
                 self._buffer_descriptions[0][seg_index][buffer_id] = {
-                    "type" : "raw",
-                    "file_path" : str(self.filename),
-                    "dtype" : sig_dtype,
+                    "type": "raw",
+                    "file_path": str(self.filename),
+                    "dtype": sig_dtype,
                     "order": "C",
-                    "file_offset" : file_offset,
-                    "shape" : shape,
+                    "file_offset": file_offset,
+                    "shape": shape,
                 }
 
-
-
             # Event channels
             event_channels = []
             event_channels.append(("Trigger", "", "event"))
@@ -217,14 +216,9 @@ def _parse_header(self):
                 for seg_index in range(nb_segment):
                     left_lim = seg_limits[seg_index]
                     right_lim = seg_limits[seg_index + 1]
-                    keep = (
-                        (rawevent["start"] >= left_lim)
-                        & (rawevent["start"] < right_lim)
-                        & (rawevent["start"] != 0)
-                    )
+                    keep = (rawevent["start"] >= left_lim) & (rawevent["start"] < right_lim) & (rawevent["start"] != 0)
                     self._raw_events[-1].append(rawevent[keep])
 
-
             # No spikes
             spike_channels = []
             spike_channels = np.array(spike_channels, dtype=_spike_channel_dtype)

neo/rawio/neuronexusrawio.py

@@ -73,7 +73,7 @@ def __init__(self, filename: str | Path = ""):
             * The *.xdat.json metadata file
             * The *_data.xdat binary file of all raw data
             * The *_timestamps.xdat binary file of the timestamp data
-            
+
         From the metadata the other two files are located within the same directory
         and loaded.
 

neo/rawio/spikeglxrawio.py

@@ -85,7 +85,7 @@ class SpikeGLXRawIO(BaseRawWithBufferApiIO):
     * This IO reads the entire folder and subfolders locating the `.bin` and `.meta` files
     * Handles gates and triggers as segments (based on the `_gt0`, `_gt1`, `_t0` , `_t1` in filenames)
     * Handles all signals coming from different acquisition cards ("imec0", "imec1", etc) in a typical
-        PXIe chassis setup and also external signal like "nidq". 
+        PXIe chassis setup and also external signal like "nidq".
     * For imec devices both "ap" and "lf" are extracted so even a one device setup will have several "streams"
 
     Examples
@@ -227,22 +227,19 @@ def _parse_header(self):
 
         self._t_starts = {stream_name: {} for stream_name in stream_names}
         self._t_stops = {seg_index: 0.0 for seg_index in range(nb_segment)}
-        
+
         for stream_name in stream_names:
             for seg_index in range(nb_segment):
                 info = self.signals_info_dict[seg_index, stream_name]
 
                 frame_start = float(info["meta"]["firstSample"])
                 sampling_frequency = info["sampling_rate"]
                 t_start = frame_start / sampling_frequency
-                                
-                self._t_starts[stream_name][seg_index] = t_start 
+
+                self._t_starts[stream_name][seg_index] = t_start
                 t_stop = info["sample_length"] / info["sampling_rate"]
                 self._t_stops[seg_index] = max(self._t_stops[seg_index], t_stop)
 
-                
-
-
         # fille into header dict
         self.header = {}
         self.header["nb_block"] = 1
@@ -361,24 +358,23 @@ def scan_files(dirname):
         raise FileNotFoundError(f"No appropriate combination of .meta and .bin files were detected in {dirname}")
 
     # This sets non-integers values before integers
-    normalize = lambda x: x if isinstance(x, int) else -1  
+    normalize = lambda x: x if isinstance(x, int) else -1
 
     # Segment index is determined by the gate_num and trigger_num in that order
     def get_segment_tuple(info):
         # Create a key from the normalized gate_num and trigger_num
         gate_num = normalize(info.get("gate_num"))
         trigger_num = normalize(info.get("trigger_num"))
         return (gate_num, trigger_num)
-    
+
     unique_segment_tuples = {get_segment_tuple(info) for info in info_list}
     sorted_keys = sorted(unique_segment_tuples)
 
     # Map each unique key to a corresponding index
     segment_tuple_to_segment_index = {key: idx for idx, key in enumerate(sorted_keys)}
 
     for info in info_list:
-        info["seg_index"] = segment_tuple_to_segment_index[get_segment_tuple(info)]    
-    
+        info["seg_index"] = segment_tuple_to_segment_index[get_segment_tuple(info)]
 
     # Probe index calculation
     # The calculation is ordered by slot, port, dock in that order, this is the number that appears in the filename
@@ -409,7 +405,7 @@ def get_probe_tuple(info):
         stream_name = f"{device_kind}{device_index}{stream_kind}"
 
         info["stream_name"] = stream_name
-        
+
     return info_list
 
 

neo/test/rawiotest/test_micromedrawio.py

@@ -10,6 +10,7 @@
 
 import numpy as np
 
+
 class TestMicromedRawIO(
     BaseTestRawIO,
     unittest.TestCase,
@@ -25,15 +26,15 @@ class TestMicromedRawIO(
     def test_micromed_multi_segments(self):
         file_full = self.get_local_path("micromed/File_mircomed2.TRC")
         file_splitted = self.get_local_path("micromed/File_mircomed2_2segments.TRC")
-        
+
         # the second file contains 2 pieces of the first file
         # so it is 2 segments with the same traces but reduced
         # note that traces in the splited can differ at the very end of the cut
 
         reader1 = MicromedRawIO(file_full)
         reader1.parse_header()
         assert reader1.segment_count(block_index=0) == 1
-        assert reader1.get_signal_t_start(block_index=0, seg_index=0, stream_index=0) == 0.
+        assert reader1.get_signal_t_start(block_index=0, seg_index=0, stream_index=0) == 0.0
         traces1 = reader1.get_analogsignal_chunk(stream_index=0)
 
         reader2 = MicromedRawIO(file_splitted)
@@ -48,11 +49,10 @@ def test_micromed_multi_segments(self):
             sr = reader2.get_signal_sampling_rate(stream_index=0)
             ind_start = int(t_start * sr)
             traces2 = reader2.get_analogsignal_chunk(block_index=0, seg_index=seg_index, stream_index=0)
-            traces1_chunk = traces1[ind_start: ind_start+traces2.shape[0]]
+            traces1_chunk = traces1[ind_start : ind_start + traces2.shape[0]]
             # we remove the last 100 sample because tools that cut traces is truncating the last buffer
             assert np.array_equal(traces2[:-100], traces1_chunk[:-100])
 
 
-
 if __name__ == "__main__":
     unittest.main()

neo/test/rawiotest/test_spikeglxrawio.py

@@ -114,63 +114,40 @@ def test_nidq_digital_channel(self):
 
     def test_t_start_reading(self):
         """Test that t_start values are correctly read for all streams and segments."""
-        
+
         # Expected t_start values for each stream and segment
         expected_t_starts = {
-            'imec0.ap': {
-                0: 15.319535472007237,
-                1: 15.339535431281986,
-                2: 21.284723325294053,
-                3: 21.3047232845688
-            },
-            'imec1.ap': {
-                0: 15.319554693264516,
-                1: 15.339521518106308,
-                2: 21.284735282142822,
-                3: 21.304702106984614
-            },
-            'imec0.lf': {
-                0: 15.3191688060872,
-                1: 15.339168765361949,
-                2: 21.284356659374016,
-                3: 21.304356618648765
-            },
-            'imec1.lf': {
-                0: 15.319321358082725,
-                1: 15.339321516521915,
-                2: 21.284568614155827,
-                3: 21.30456877259502
-            }
+            "imec0.ap": {0: 15.319535472007237, 1: 15.339535431281986, 2: 21.284723325294053, 3: 21.3047232845688},
+            "imec1.ap": {0: 15.319554693264516, 1: 15.339521518106308, 2: 21.284735282142822, 3: 21.304702106984614},
+            "imec0.lf": {0: 15.3191688060872, 1: 15.339168765361949, 2: 21.284356659374016, 3: 21.304356618648765},
+            "imec1.lf": {0: 15.319321358082725, 1: 15.339321516521915, 2: 21.284568614155827, 3: 21.30456877259502},
         }
-        
+
         # Initialize the RawIO
         rawio = SpikeGLXRawIO(self.get_local_path("spikeglx/multi_trigger_multi_gate/SpikeGLX/5-19-2022-CI4"))
         rawio.parse_header()
-        
+
         # Get list of stream names
         stream_names = rawio.header["signal_streams"]["name"]
-        
+
         # Test t_start for each stream and segment
         for stream_name, expected_values in expected_t_starts.items():
             # Get stream index
             stream_index = list(stream_names).index(stream_name)
-            
+
             # Check each segment
             for seg_index, expected_t_start in expected_values.items():
-                actual_t_start = rawio.get_signal_t_start(
-                    block_index=0,
-                    seg_index=seg_index,
-                    stream_index=stream_index
-                )
-                
+                actual_t_start = rawio.get_signal_t_start(block_index=0, seg_index=seg_index, stream_index=stream_index)
+
                 # Use numpy.testing for proper float comparison
                 np.testing.assert_allclose(
                     actual_t_start,
                     expected_t_start,
                     rtol=1e-9,
                     atol=1e-9,
-                    err_msg=f"Mismatch in t_start for stream '{stream_name}', segment {seg_index}"
+                    err_msg=f"Mismatch in t_start for stream '{stream_name}', segment {seg_index}",
                 )
 
+
 if __name__ == "__main__":
     unittest.main()