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Fix plot_sorting_summary widget #3627

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merged 3 commits into from
Jan 20, 2025
Merged

Fix plot_sorting_summary widget #3627

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4831ad0
Use pd.concat instead of df.append
alejoe91 Jan 18, 2025
2ba92b7
Fix template metrics sv
alejoe91 Jan 18, 2025
6cf86f9
Fix tests and warning
alejoe91 Jan 18, 2025
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2 changes: 1 addition & 1 deletion src/spikeinterface/widgets/sorting_summary.py
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Original file line number Diff line number Diff line change
Expand Up @@ -16,7 +16,7 @@
from ..core import SortingAnalyzer


_default_displayed_unit_properties = ["firing_rate", "num_spikes", "x", "y", "amplitude", "snr", "rp_violation"]
_default_displayed_unit_properties = ["firing_rate", "num_spikes", "x", "y", "amplitude_median", "snr", "rp_violation"]


class SortingSummaryWidget(BaseWidget):
Expand Down
25 changes: 19 additions & 6 deletions src/spikeinterface/widgets/tests/test_widgets.py
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Expand Up @@ -73,7 +73,9 @@ def setUpClass(cls):
spike_amplitudes=dict(),
unit_locations=dict(),
spike_locations=dict(),
quality_metrics=dict(metric_names=["snr", "isi_violation", "num_spikes", "amplitude_cutoff"]),
quality_metrics=dict(
metric_names=["snr", "isi_violation", "num_spikes", "firing_rate", "amplitude_cutoff"]
),
template_metrics=dict(),
correlograms=dict(),
template_similarity=dict(),
Expand Down Expand Up @@ -531,26 +533,37 @@ def test_plot_sorting_summary(self):
possible_backends = list(sw.SortingSummaryWidget.get_possible_backends())
for backend in possible_backends:
if backend not in self.skip_backends:
sw.plot_sorting_summary(self.sorting_analyzer_dense, backend=backend, **self.backend_kwargs[backend])
sw.plot_sorting_summary(self.sorting_analyzer_sparse, backend=backend, **self.backend_kwargs[backend])
sw.plot_sorting_summary(
self.sorting_analyzer_dense,
displayed_unit_properties=[],
backend=backend,
**self.backend_kwargs[backend],
)
sw.plot_sorting_summary(
self.sorting_analyzer_sparse,
displayed_unit_properties=[],
backend=backend,
**self.backend_kwargs[backend],
)
sw.plot_sorting_summary(
self.sorting_analyzer_sparse,
sparsity=self.sparsity_strict,
displayed_unit_properties=[],
backend=backend,
**self.backend_kwargs[backend],
)
# add unit_properties
# select unit_properties
sw.plot_sorting_summary(
self.sorting_analyzer_sparse,
unit_table_properties=["firing_rate", "snr"],
displayed_unit_properties=["firing_rate", "snr"],
backend=backend,
**self.backend_kwargs[backend],
)
# adding a missing property should raise a warning
with self.assertWarns(UserWarning):
sw.plot_sorting_summary(
self.sorting_analyzer_sparse,
unit_table_properties=["missing_property"],
displayed_unit_properties=["missing_property"],
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is there a reason we changed the naming? this is a breaking change? I never use this argument but do others?

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I think Alessio wants to test if a properties is not present. We decided to not raise an error make user life easier.

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@samuelgarcia I think he means the argument!!!

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I did the change in another PR.
I prefer this one which more easy to understand.
It is back compatible.
Few users I think were using it (only for sorting view).
Now it will be usable with spikeinterface-gui.

backend=backend,
**self.backend_kwargs[backend],
)
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2 changes: 1 addition & 1 deletion src/spikeinterface/widgets/utils.py
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Expand Up @@ -316,7 +316,7 @@ def make_units_table_from_analyzer(
all_df.append(df)

if analyzer.get_extension("template_metrics") is not None:
all_df = analyzer.get_extension("template_metrics").get_data()
df = analyzer.get_extension("template_metrics").get_data()
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all_df.append(df)

if len(all_df) > 0:
Expand Down
6 changes: 2 additions & 4 deletions src/spikeinterface/widgets/utils_sortingview.py
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Expand Up @@ -72,15 +72,15 @@ def generate_unit_table_view(
# keep only selected columns
unit_properties = np.array(unit_properties)
keep = np.isin(unit_properties, units_tables.columns)
if sum(keep) < len(unit_properties):
warn(f"Some unit properties are not in the sorting: {unit_properties[~keep]}")
unit_properties = unit_properties[keep]
units_tables = units_tables.loc[:, unit_properties]

dtype_convertor = {"i": "int", "u": "int", "f": "float", "U": "str", "S": "str", "b": "bool"}

ut_columns = []
for col in unit_properties:
if col not in units_tables.columns:
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continue
values = units_tables[col].to_numpy()
if values.dtype.kind in dtype_convertor:
txt_dtype = dtype_convertor[values.dtype.kind]
Expand All @@ -90,8 +90,6 @@ def generate_unit_table_view(
for unit_index, unit_id in enumerate(sorting.unit_ids):
row_values = {}
for col in unit_properties:
if col not in units_tables.columns:
continue
values = units_tables[col].to_numpy()
if values.dtype.kind in dtype_convertor:
value = values[unit_index]
Expand Down
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