Merge pull request #3299 from jonahpearl/sortingview_qms

allow quality and template metrics in sortingview's unit table

Author: alejoe91

src/spikeinterface/widgets/sorting_summary.py

@@ -43,7 +43,12 @@ class SortingSummaryWidget(BaseWidget):
         List of labels to be added to the curation table
         (sortingview backend)
     unit_table_properties : list or None, default: None
-        List of properties to be added to the unit table
+        List of properties to be added to the unit table.
+        These may be drawn from the sorting extractor, and, if available,
+        the quality_metrics and template_metrics extensions of the SortingAnalyzer.
+        See all properties available with sorting.get_property_keys(), and, if available,
+        analyzer.get_extension("quality_metrics").get_data().columns and
+        analyzer.get_extension("template_metrics").get_data().columns.
         (sortingview backend)
     """
 
@@ -151,7 +156,7 @@ def plot_sortingview(self, data_plot, **backend_kwargs):
 
         # unit ids
         v_units_table = generate_unit_table_view(
-            dp.sorting_analyzer.sorting, dp.unit_table_properties, similarity_scores=similarity_scores
+            dp.sorting_analyzer, dp.unit_table_properties, similarity_scores=similarity_scores
         )
 
         if dp.curation:

src/spikeinterface/widgets/utils_sortingview.py

@@ -3,6 +3,7 @@
 import numpy as np
 
 from ..core.core_tools import check_json
+from warnings import warn
 
 
 def make_serializable(*args):
@@ -45,9 +46,33 @@ def handle_display_and_url(widget, view, **backend_kwargs):
     return url
 
 
-def generate_unit_table_view(sorting, unit_properties=None, similarity_scores=None):
+def generate_unit_table_view(analyzer, unit_properties=None, similarity_scores=None):
     import sortingview.views as vv
 
+    sorting = analyzer.sorting
+
+    # Find available unit properties from all sources
+    sorting_props = list(sorting.get_property_keys())
+    if analyzer.get_extension("quality_metrics") is not None:
+        qm_props = list(analyzer.get_extension("quality_metrics").get_data().columns)
+        qm_data = analyzer.get_extension("quality_metrics").get_data()
+    else:
+        qm_props = []
+    if analyzer.get_extension("template_metrics") is not None:
+        tm_props = list(analyzer.get_extension("template_metrics").get_data().columns)
+        tm_data = analyzer.get_extension("template_metrics").get_data()
+    else:
+        tm_props = []
+
+    # Check for any overlaps and warn user if any
+    all_props = sorting_props + qm_props + tm_props
+    overlap_props = [prop for prop in all_props if all_props.count(prop) > 1]
+    if len(overlap_props) > 0:
+        warn(
+            f"Warning: Overlapping properties found in sorting, quality_metrics, and template_metrics: {overlap_props}"
+        )
+
+    # Get unit properties
     if unit_properties is None:
         ut_columns = []
         ut_rows = [vv.UnitsTableRow(unit_id=u, values={}) for u in sorting.unit_ids]
@@ -56,8 +81,20 @@ def generate_unit_table_view(sorting, unit_properties=None, similarity_scores=No
         ut_rows = []
         values = {}
         valid_unit_properties = []
+
+        # Create columns for each property
         for prop_name in unit_properties:
-            property_values = sorting.get_property(prop_name)
+
+            # Get property values from correct location
+            if prop_name in sorting_props:
+                property_values = sorting.get_property(prop_name)
+            elif prop_name in qm_props:
+                property_values = qm_data[prop_name].values
+            elif prop_name in tm_props:
+                property_values = tm_data[prop_name].values
+            else:
+                raise ValueError(f"Property '{prop_name}' not found in sorting, quality_metrics, or template_metrics")
+
             # make dtype available
             val0 = np.array(property_values[0])
             if val0.dtype.kind in ("i", "u"):
@@ -74,14 +111,28 @@ def generate_unit_table_view(sorting, unit_properties=None, similarity_scores=No
             ut_columns.append(vv.UnitsTableColumn(key=prop_name, label=prop_name, dtype=dtype))
             valid_unit_properties.append(prop_name)
 
+        # Create rows for each unit
         for ui, unit in enumerate(sorting.unit_ids):
             for prop_name in valid_unit_properties:
-                property_values = sorting.get_property(prop_name)
+
+                # Get property values from correct location
+                if prop_name in sorting_props:
+                    property_values = sorting.get_property(prop_name)
+                elif prop_name in qm_props:
+                    property_values = qm_data[prop_name].values
+                elif prop_name in tm_props:
+                    property_values = tm_data[prop_name].values
+                else:
+                    raise ValueError(
+                        f"Property '{prop_name}' not found in sorting, quality_metrics, or template_metrics"
+                    )
+
+                # Check for NaN values
                 val0 = np.array(property_values[0])
                 if val0.dtype.kind == "f":
                     if np.isnan(property_values[ui]):
                         continue
-                values[prop_name] = property_values[ui]
+                values[prop_name] = np.format_float_positional(property_values[ui], precision=4, fractional=False)
             ut_rows.append(vv.UnitsTableRow(unit_id=unit, values=check_json(values)))
 
     v_units_table = vv.UnitsTable(rows=ut_rows, columns=ut_columns, similarity_scores=similarity_scores)