spikeinterface 0.100.4__tar.gz → 0.100.5__tar.gz

{spikeinterface-0.100.4/src/spikeinterface.egg-info → spikeinterface-0.100.5}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: spikeinterface
-Version: 0.100.4
+Version: 0.100.5
 Summary: Python toolkit for analysis, visualization, and comparison of spike sorting output
 Author-email: Alessio Buccino <alessiop.buccino@gmail.com>, Samuel Garcia <sam.garcia.die@gmail.com>
 Project-URL: homepage, https://github.com/SpikeInterface/spikeinterface
@@ -25,7 +25,7 @@ Requires-Dist: neo>=0.13.0
 Requires-Dist: probeinterface>=0.2.21
 Provides-Extra: extractors
 Requires-Dist: MEArec>=1.8; extra == "extractors"
-Requires-Dist: pynwb>=2.3.0; extra == "extractors"
+Requires-Dist: pynwb>=2.6.0; extra == "extractors"
 Requires-Dist: hdmf-zarr>=0.5.0; extra == "extractors"
 Requires-Dist: pyedflib>=0.1.30; extra == "extractors"
 Requires-Dist: sonpy; python_version < "3.10" and extra == "extractors"
@@ -41,7 +41,7 @@ Requires-Dist: ibllib>=2.21.0; extra == "streaming-extractors"
 Requires-Dist: fsspec; extra == "streaming-extractors"
 Requires-Dist: aiohttp; extra == "streaming-extractors"
 Requires-Dist: requests; extra == "streaming-extractors"
-Requires-Dist: pynwb>=2.3.0; extra == "streaming-extractors"
+Requires-Dist: pynwb>=2.6.0; extra == "streaming-extractors"
 Requires-Dist: hdmf-zarr>=0.5.0; extra == "streaming-extractors"
 Requires-Dist: remfile; extra == "streaming-extractors"
 Requires-Dist: s3fs; extra == "streaming-extractors"

{spikeinterface-0.100.4 → spikeinterface-0.100.5}/pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "spikeinterface"
-version = "0.100.4"
+version = "0.100.5"
 authors = [
   { name="Alessio Buccino", email="alessiop.buccino@gmail.com" },
   { name="Samuel Garcia", email="sam.garcia.die@gmail.com" },
@@ -59,7 +59,7 @@ changelog = "https://spikeinterface.readthedocs.io/en/latest/whatisnew.html"
 
 extractors = [
     "MEArec>=1.8",
-    "pynwb>=2.3.0",
+    "pynwb>=2.6.0",
     "hdmf-zarr>=0.5.0",
     "pyedflib>=0.1.30",
     "sonpy;python_version<'3.10'",
@@ -80,7 +80,7 @@ streaming_extractors = [
     "fsspec",
     "aiohttp",
     "requests",
-    "pynwb>=2.3.0",
+    "pynwb>=2.6.0",
     "hdmf-zarr>=0.5.0",
     "remfile",
     "s3fs"

{spikeinterface-0.100.4 → spikeinterface-0.100.5}/src/spikeinterface/extractors/neoextractors/openephys.py

@@ -180,6 +180,9 @@ class OpenEphysBinaryRecordingExtractor(NeoBaseRecordingExtractor):
             exp_id = exp_ids[0]
         else:
             exp_id = exp_ids[block_index]
+        rec_ids = sorted(
+            list(self.neo_reader.folder_structure[record_node]["experiments"][exp_id]["recordings"].keys())
+        )
 
         # do not load probe for NIDQ stream or if load_sync_channel is True
         if "NI-DAQmx" not in stream_name and not load_sync_channel:
@@ -229,10 +232,8 @@ class OpenEphysBinaryRecordingExtractor(NeoBaseRecordingExtractor):
         # load synchronized timestamps and set_times to recording
         recording_folder = Path(folder_path) / record_node
         stream_folders = []
-        for segment_index in range(self.get_num_segments()):
-            stream_folder = (
-                recording_folder / f"experiment{exp_id}" / f"recording{segment_index+1}" / "continuous" / oe_stream
-            )
+        for segment_index, rec_id in enumerate(rec_ids):
+            stream_folder = recording_folder / f"experiment{exp_id}" / f"recording{rec_id}" / "continuous" / oe_stream
             stream_folders.append(stream_folder)
             if load_sync_timestamps:
                 if (stream_folder / "sample_numbers.npy").is_file():
@@ -245,7 +246,7 @@ class OpenEphysBinaryRecordingExtractor(NeoBaseRecordingExtractor):
                     sync_times = None
                 try:
                     self.set_times(times=sync_times, segment_index=segment_index, with_warning=False)
-                except AssertionError:
+                except:
                     warnings.warn(f"Could not load synchronized timestamps for {stream_name}")
 
         self._stream_folders = stream_folders

{spikeinterface-0.100.4 → spikeinterface-0.100.5}/src/spikeinterface/extractors/nwbextractors.py

@@ -842,7 +842,8 @@ class NwbRecordingExtractor(BaseRecording):
         data_attributes = self.electrical_series["data"].attrs
         electrical_series_conversion = data_attributes["conversion"]
         gains = electrical_series_conversion * 1e6
-        if "channel_conversion" in data_attributes:
+        channel_conversion = self.electrical_series.get("channel_conversion", None)
+        if channel_conversion:
             gains *= self.electrical_series["channel_conversion"][:]
 
         # Channel offsets

{spikeinterface-0.100.4 → spikeinterface-0.100.5}/src/spikeinterface/widgets/spikes_on_traces.py

@@ -183,8 +183,7 @@ class SpikesOnTracesWidget(BaseWidget):
                 spike_times_to_plot = sorting.get_unit_spike_train(
                     unit, segment_index=segment_index, return_times=True
                 )[spike_start:spike_end]
-                unit_y_loc = min_y + max_y - dp.unit_locations[unit][1]
-                # markers = np.ones_like(spike_frames_to_plot) * (min_y + max_y - dp.unit_locations[unit][1])
+                unit_y_loc = dp.unit_locations[unit][1]
                 width = 2 * 1e-3
                 ellipse_kwargs = dict(width=width, height=10, fc="none", ec=dp.unit_colors[unit], lw=2)
                 patches = [Ellipse((s, unit_y_loc), **ellipse_kwargs) for s in spike_times_to_plot]

{spikeinterface-0.100.4 → spikeinterface-0.100.5/src/spikeinterface.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: spikeinterface
-Version: 0.100.4
+Version: 0.100.5
 Summary: Python toolkit for analysis, visualization, and comparison of spike sorting output
 Author-email: Alessio Buccino <alessiop.buccino@gmail.com>, Samuel Garcia <sam.garcia.die@gmail.com>
 Project-URL: homepage, https://github.com/SpikeInterface/spikeinterface
@@ -25,7 +25,7 @@ Requires-Dist: neo>=0.13.0
 Requires-Dist: probeinterface>=0.2.21
 Provides-Extra: extractors
 Requires-Dist: MEArec>=1.8; extra == "extractors"
-Requires-Dist: pynwb>=2.3.0; extra == "extractors"
+Requires-Dist: pynwb>=2.6.0; extra == "extractors"
 Requires-Dist: hdmf-zarr>=0.5.0; extra == "extractors"
 Requires-Dist: pyedflib>=0.1.30; extra == "extractors"
 Requires-Dist: sonpy; python_version < "3.10" and extra == "extractors"
@@ -41,7 +41,7 @@ Requires-Dist: ibllib>=2.21.0; extra == "streaming-extractors"
 Requires-Dist: fsspec; extra == "streaming-extractors"
 Requires-Dist: aiohttp; extra == "streaming-extractors"
 Requires-Dist: requests; extra == "streaming-extractors"
-Requires-Dist: pynwb>=2.3.0; extra == "streaming-extractors"
+Requires-Dist: pynwb>=2.6.0; extra == "streaming-extractors"
 Requires-Dist: hdmf-zarr>=0.5.0; extra == "streaming-extractors"
 Requires-Dist: remfile; extra == "streaming-extractors"
 Requires-Dist: s3fs; extra == "streaming-extractors"

{spikeinterface-0.100.4 → spikeinterface-0.100.5}/src/spikeinterface.egg-info/requires.txt

@@ -26,7 +26,7 @@ numba
 
 [extractors]
 MEArec>=1.8
-pynwb>=2.3.0
+pynwb>=2.6.0
 hdmf-zarr>=0.5.0
 pyedflib>=0.1.30
 lxml
@@ -67,7 +67,7 @@ ibllib>=2.21.0
 fsspec
 aiohttp
 requests
-pynwb>=2.3.0
+pynwb>=2.6.0
 hdmf-zarr>=0.5.0
 remfile
 s3fs