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Merged
kaeldai merged 2 commits into from
Jul 17, 2025
Merged

Update/workshop 2025 #432

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9e10a25
adding brain_observatory code
kaeldai Jul 8, 2025
a38ca74
fixing issue with bob_cache
kaeldai Jul 17, 2025
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4 changes: 2 additions & 2 deletions bmtk/analyzer/spike_trains.py
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Original file line number Diff line number Diff line change
Expand Up @@ -331,7 +331,7 @@ def calc_stats(r):

return pd.Series(d, index=['count', 'isi'])

spike_counts_df = spike_trains.to_dataframe().groupby(['population', 'node_ids']).apply(calc_stats)
spike_counts_df = spike_trains.to_dataframe().groupby(['population', 'node_ids'])[['timestamps']].apply(calc_stats)
spike_counts_df = spike_counts_df.rename({'timestamps': 'counts'}, axis=1)
spike_counts_df.index.names = ['population', 'node_id']

Expand All @@ -343,7 +343,7 @@ def calc_stats(r):
vals_df = pd.merge(nodes_df, spike_counts_df, left_index=True, right_index=True, how='left')
vals_df = vals_df.fillna({'count': 0.0, 'firing_rate': 0.0, 'isi': 0.0})

vals_df = vals_df.groupby(group_by)[['firing_rate', 'count', 'isi']].agg([np.mean, np.std])
vals_df = vals_df.groupby(group_by)[['firing_rate', 'count', 'isi']].agg(['mean', 'std'])
return vals_df
else:
return spike_counts_df
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Empty file added bmtk/utils/brain_observatory/__init__.py
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