Update to spikeinterface 0.102.3 (#240)

* pin neo.

* Rename 'neurpixels' to 'imec0' in get_probe.

* Always offset times.

* Update docs link.

* Update documentation.

* Troubleshooting the test.

* Fix run loading.

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

---------

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

Author: JoeZiminski

docs/source/galleries/how_to/01_preprocess_a_session.py

@@ -34,7 +34,7 @@
 
     plots = session.plot_preprocessed(
         show=True,
-        time_range=(0, 0.5),
+        time_range=(0, 0.5),  # time relative to the first sample (not absolute)
         show_channel_ids=False,  # also, "mode"="map" or "line"
     )
 

docs/source/get_started/supported_formats.md

@@ -141,7 +141,7 @@ Use [catGT](https://billkarsh.github.io/SpikeGLX/help/dmx_vs_gbl/dmx_vs_gbl) for
 
 :::{tab-item} OpenEphys
 
-Currently, the [flat binary format](https://open-ephys.github.io/gui-docs/User-Manual/Recording-data/Binary-format.html)
+Currently, the [flat binary format](https://open-ephys.github.io/gui-docs/User-Manual/Data-formats/Binary-format.html)
 (the OpenEphys default) is supported.
 
 [OpenEphys](https://open-ephys.org/) flat binary recordings

pyproject.toml

@@ -21,7 +21,8 @@ classifiers = [
 ]
 
 dependencies = [
-    "spikeinterface[full]==0.102.0",
+    "spikeinterface[full]==0.102.3",
+    "neo==0.14.1",
     "submitit",
     "slurmio",
     "psutil",

spikewrap/process/_loading.py

@@ -133,15 +133,14 @@ def get_raw_run_paths(
     if passed_run_names == "all":
         run_paths = detected_run_paths
     else:
-        detected_run_names = [path_.name for path_ in detected_run_paths]
+        detected_runs = {path_.name: path_ for path_ in detected_run_paths}
 
         for passed_name in passed_run_names:
-            if passed_name not in detected_run_names:
+            if passed_name not in detected_runs:
                 raise ValueError(f"{passed_name} not found in folder: {ses_path}")
 
-        run_paths = [
-            path_ for path_ in detected_run_paths if path_.name in detected_run_names
-        ]
+        # We need to maintain the same order as `passed_run_names`
+        run_paths = [detected_runs[name] for name in passed_run_names]
 
     if not _utils._paths_are_in_datetime_order(run_paths, "creation"):
         warnings.warn(

spikewrap/structure/_preprocess_run.py

@@ -192,6 +192,8 @@ def plot_preprocessed(
             The type of plot to generate. ``"map"`` for a heatmap and ``"line"`` for a line plot.
         time_range
             The time range (start, end) to plot the data within, in seconds.
+            This is relative to the first sample, and not the absolute time.
+            i.e. `0` is always the first timepoint.
         show_channel_ids
             If True, the plot will display channel IDs.
         show

spikewrap/structure/session.py

@@ -234,6 +234,8 @@ def plot_preprocessed(
             Determines the plotting style, a heatmap-style or line plot.
         time_range
             Time range (start, end), in seconds, to plot. e.g. (0.0, 1.0)
+            This is relative to the first sample, and not the absolute time.
+            i.e. `0` is always the first timepoint.
         show_channel_ids
             If ``True``, displays the channel identifiers on the plots.
         show

spikewrap/visualise/_visualise.py

@@ -71,16 +71,19 @@ def visualise_run_preprocessed(
             preprocessed, "last"
         )
 
+        time_range_adjusted = time_range + recording_to_plot.get_times()[0]
+
         si.plot_traces(
             recording_to_plot,
             order_channel_by_depth=True,
-            time_range=time_range,
+            time_range=time_range_adjusted,
             return_scaled=True,
             show_channel_ids=show_channel_ids,
             mode=mode,
             ax=ax,
             segment_index=0,
         )
+
         if key == canon.grouped_shankname():
             ax.set_title(f"Session: {ses_name}, Run: {run_name}")
         else:

tests/test_integration/base.py

@@ -24,6 +24,6 @@ def get_mock_probe(self):
         """
         Get an arbitrary probe to use on the test recording (16 channels).
         """
-        mock_probe = pi.get_probe("neuropixels", "NP2014")
+        mock_probe = pi.get_probe("imec", "NP2014")
         mock_probe = mock_probe.get_slice(np.arange(16))
         return mock_probe

tests/test_integration/test_sync.py

@@ -32,7 +32,9 @@ def test_run_name_matches_index(self, session):
 
         for run_idx, run_name in enumerate(session.get_raw_run_names()):
             assert session._raw_runs[run_idx]._run_name == run_name
-            assert run_name == session._passed_run_names[run_idx]
+            assert (
+                run_name == session._passed_run_names[run_idx]
+            ), f"session.get_raw_run_names(){session.get_raw_run_names()} ------  session._passed_run_names {session._passed_run_names}"
 
     def test_get_sync(self, session):
         """