add optional save path argument for spikesorting metrics

Author: mayofaulkner

ibllib/ephys/ephysqc.py

@@ -389,15 +389,18 @@ def _single_test(assertion, str_ok, str_ko):
     return ok
 
 
-def spike_sorting_metrics_ks2(ks2_path=None, m=None, save=True):
+def spike_sorting_metrics_ks2(ks2_path=None, m=None, save=True, save_path=None):
     """
     Given a path containing kilosort 2 output, compute quality metrics and optionally save them
     to a clusters_metric.csv file
     :param ks2_path:
     :param save
+    :param save_path: If not given will save into the path given as ks2_path
     :return:
     """
 
+    save_path = save_path or ks2_path
+
     # ensure that either a ks2_path or a phylib `TemplateModel` object with unit info is given
     assert not(ks2_path is None and m is None), 'Must either specify a path to a ks2 output ' \
                                                 'directory, or a phylib `TemplateModel` object'
@@ -419,8 +422,9 @@ def spike_sorting_metrics_ks2(ks2_path=None, m=None, save=True):
         c = c.set_index('cluster_id', drop=False).join(ks2_labels.set_index('cluster_id'))
 
     if save:
+        Path(save_path).mkdir(exist_ok=True, parents=True)
         #  the file name contains the label of the probe (directory name in this case)
-        c.to_csv(ks2_path.joinpath('cluster_metrics.csv'))
+        c.to_csv(Path(save_path).joinpath('cluster_metrics.csv'))
 
     return c
 

ibllib/ephys/sync_probes.py

@@ -146,6 +146,9 @@ def version3B(ses_path, display=True, type=None, tol=2.5):
             raise Neuropixel3BSyncFrontsNonMatching(f"{ses_path}")
 
         # Find the indexes in case the sizes don't match
+        if sync_nidq.times.size != sync_probe.times.size:
+            _logger.warning(f'Sync mismatch by {np.abs(sync_nidq.times.size - sync_probe.times.size)} '
+                            f'NIDQ sync times: {sync_nidq.times.size}, Probe sync times {sync_probe.times.size}')
         sync_idx = np.min([sync_nidq.times.size, sync_probe.times.size])
 
         # if the qc of the diff finds anomalies, do not attempt to smooth the interp function

release_notes.md

@@ -1,5 +1,7 @@
 ## To be added to next release
 - Fix in EphysDLC task to not return multiple copies of outputs
+- Loading examples for different IBL data types
+- Fix for probe syncing when Nidq and probe pulses don't match
 
 ## Release Note 2.9