diff --git a/examples/modules_gallery/qualitymetrics/plot_4_curation.py b/examples/modules_gallery/qualitymetrics/plot_4_curation.py index 8953a5a835..edd7a85ce5 100644 --- a/examples/modules_gallery/qualitymetrics/plot_4_curation.py +++ b/examples/modules_gallery/qualitymetrics/plot_4_curation.py @@ -6,6 +6,8 @@ quality metrics. """ +############################################################################# +# Import the modules and/or functions necessary from spikeinterface import spikeinterface as si import spikeinterface.extractors as se @@ -15,22 +17,21 @@ ############################################################################## -# First, let's download a simulated dataset -# from the repo 'https://gin.g-node.org/NeuralEnsemble/ephy_testing_data' +# Let's download a simulated dataset +# from the repo 'https://gin.g-node.org/NeuralEnsemble/ephy_testing_data' # # Let's imagine that the ground-truth sorting is in fact the output of a sorter. -# local_path = si.download_dataset(remote_path='mearec/mearec_test_10s.h5') -recording, sorting = se.read_mearec(local_path) +recording, sorting = se.read_mearec(file_path=local_path) print(recording) print(sorting) ############################################################################## -# First, we extract waveforms and compute their PC scores: +# First, we extract waveforms (to be saved in the folder 'wfs_mearec') and +# compute their PC scores: -folder = 'wfs_mearec' -we = si.extract_waveforms(recording, sorting, folder, +we = si.extract_waveforms(recording, sorting, folder='wfs_mearec', ms_before=1, ms_after=2., max_spikes_per_unit=500, n_jobs=1, chunk_size=30000) print(we) @@ -47,12 +48,15 @@ ############################################################################## # We can now threshold each quality metric and select units based on some rules. # -# The easiest and most intuitive way is to use boolean masking with dataframe: +# The easiest and most intuitive way is to use boolean masking with a dataframe. +# +# Then create a list of unit ids that we want to keep keep_mask = (metrics['snr'] > 7.5) & (metrics['isi_violations_ratio'] < 0.2) & (metrics['nn_hit_rate'] > 0.90) print(keep_mask) keep_unit_ids = keep_mask[keep_mask].index.values +keep_unit_ids = [unit_id for unit_id in keep_unit_ids] print(keep_unit_ids) ############################################################################## @@ -61,4 +65,5 @@ curated_sorting = sorting.select_units(keep_unit_ids) print(curated_sorting) -se.NpzSortingExtractor.write_sorting(curated_sorting, 'curated_sorting.npz') + +se.NpzSortingExtractor.write_sorting(sorting=curated_sorting, save_path='curated_sorting.npz')