Merge branch 'spikesorting_v1' of github.com:khl02007/nwb_datajoint i…

…nto spikesorting_v1

src/spyglass/spikesorting/v1/artifact.py

@@ -393,11 +393,10 @@ def _check_artifact_thresholds(
     ValueError: if signal thresholds are negative
     """
     # amplitude or zscore thresholds should be negative, as they are applied to an absolute signal
-    signal_thresholds = [
-        t for t in [amplitude_thresh_uV, zscore_thresh] if t is not None
-    ]
-    for t in signal_thresholds:
-        if t < 0:
+    def is_negative(value):
+        return value < 0 if value is not None else False
+
+    if is_negative(amplitude_thresh_uV) or is_negative(zscore_thresh):
             raise ValueError(
                 "Amplitude and Z-Score thresholds must be >= 0, or None"
             )

src/spyglass/spikesorting/v1/figurl_curation.py

@@ -58,7 +58,7 @@ def insert_selection(cls, key: dict):
 
     @staticmethod
     def generate_curation_uri(key: Dict) -> str:
-        """Generates a kachery-cloud URI containing curation info from a row in CurationV1 table
+        """Generates a kachery-cloud URI from a row in CurationV1 table
 
         Parameters
         ----------
@@ -82,30 +82,29 @@ def generate_curation_uri(key: Dict) -> str:
 
         unit_ids = [str(unit_id) for unit_id in unit_ids]
 
-        if labels:
-            labels_dict = {
-                unit_id: list(label) for unit_id, label in zip(unit_ids, labels)
-            }
-        else:
-            labels_dict = {}
+        labels_dict = (
+            {unit_id: list(label) for unit_id, label in zip(unit_ids, labels)}
+            if labels
+            else {}
+        )
 
-        if merge_groups:
-            merge_groups_dict = dict(zip(unit_ids, merge_groups))
-            merge_groups_list = _merge_dict_to_list(merge_groups_dict)
-            merge_groups_list = [
+        merge_groups_list = (
+            [
                 [str(unit_id) for unit_id in merge_group]
-                for merge_group in merge_groups_list
+                for merge_group in _merge_dict_to_list(
+                    dict(zip(unit_ids, merge_groups))
+                )
             ]
-        else:
-            merge_groups_list = []
-
-        curation_dict = {
-            "labelsByUnit": labels_dict,
-            "mergeGroups": merge_groups_list,
-        }
-        curation_uri = kcl.store_json(curation_dict)
+            if merge_groups
+            else []
+        )
 
-        return curation_uri
+        return kcl.store_json(
+            {
+                "labelsByUnit": labels_dict,
+                "mergeGroups": merge_groups_list,
+            }
+        )
 
 
 @schema
@@ -279,18 +278,16 @@ def _generate_figurl(
 
 
 def _reformat_metrics(metrics: Dict[str, Dict[str, float]]) -> List[Dict]:
-    for metric_name in metrics:
-        metrics[metric_name] = {
-            str(unit_id): metric_value
-            for unit_id, metric_value in metrics[metric_name].items()
-        }
-    new_external_metrics = [
+    return [
         {
             "name": metric_name,
             "label": metric_name,
             "tooltip": metric_name,
-            "data": metric,
+            "data": {
+                str(unit_id): metric_value
+                for unit_id, metric_value in metric.items()
+            },
         }
         for metric_name, metric in metrics.items()
     ]
-    return new_external_metrics
+

src/spyglass/spikesorting/v1/metric_curation.py

@@ -575,12 +575,10 @@ def _write_metric_curation_to_nwb(
             )
         if metrics is not None:
             for metric, metric_dict in metrics.items():
-                metric_values = []
-                for unit_id in unit_ids:
-                    if unit_id not in metric_dict:
-                        metric_values.append([])
-                    else:
-                        metric_values.append(metric_dict[unit_id])
+                metric_values = [
+                    metric_dict[unit_id] if unit_id in metric_dict else []
+                    for unit_id in unit_ids
+                ]
                 nwbf.add_unit_column(
                     name=metric,
                     description=metric,

src/spyglass/spikesorting/v1/metric_utils.py

@@ -61,11 +61,9 @@ def get_peak_channel(
         peak_sign=peak_sign,
         **metric_params,
     )
-    peak_channel = {key: int(val) for key, val in peak_channel_dict.items()}
-    return peak_channel
+    return {key: int(val) for key, val in peak_channel_dict.items()}
 
 
 def get_num_spikes(waveform_extractor: si.WaveformExtractor, this_unit_id: str):
     """Computes the number of spikes for each unit."""
-    num_spikes = sq.compute_num_spikes(waveform_extractor)
-    return num_spikes[this_unit_id]
+    return sq.compute_num_spikes(waveform_extractor)[this_unit_id]

src/spyglass/spikesorting/v1/recording.py

@@ -176,7 +176,7 @@ def set_group_by_shank(
 @schema
 class SpikeSortingPreprocessingParameters(dj.Lookup):
     definition = """
-    # Parameters for denoising (filtering and referencing/whitening) a recording prior to spike sorting.
+    # Parameters for denoising a recording prior to spike sorting.
     preproc_param_name: varchar(200)
     ---
     preproc_params: blob