How to use the spikeinterface.comparison.compare_two_sorters function in spikeinterface

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github SpikeInterface / spikeinterface / tests / test_imports.py View on Github external
import spikeinterface.toolkit as st
    import spikeinterface.sorters as ss
    import spikeinterface.comparison as sc
    import spikeinterface.widgets as sw

    # se
    recording, sorting_true = se.example_datasets.toy_example(duration=60, num_channels=4, seed=0)

    # st
    rec_f = st.preprocessing.bandpass_filter(recording)

    # ss
    print(ss.available_sorters())

    # sc
    sc.compare_two_sorters(sorting_true, sorting_true)

    # sw
    sw.plot_timeseries(rec_f)
github SpikeInterface / spikeinterface / examples / getting_started / plot_getting_started.py View on Github external
##############################################################################
# Quality metrics can be also used to automatically curate the spike sorting output. For example, you can select
# sorted units with a SNR above a certain threshold:

sorting_curated_snr = st.curation.threshold_snr(sorting_KL, recording, threshold=5, threshold_sign='less')
snrs_above = st.validation.compute_snrs(sorting_curated_snr, recording_cmr)

print('Curated SNR', snrs_above)

##############################################################################
# The final part of this tutorial deals with comparing spike sorting outputs.
# We can either (1) compare the spike sorting results with the ground-truth sorting :code:`sorting_true`, (2) compare
# the output of two (Klusta and Mountainsor4), or (3) compare the output of multiple sorters:

comp_gt_KL = sc.compare_sorter_to_ground_truth(gt_sorting=sorting_true, tested_sorting=sorting_KL)
comp_KL_MS4 = sc.compare_two_sorters(sorting1=sorting_KL, sorting2=sorting_MS4)
comp_multi = sc.compare_multiple_sorters(sorting_list=[sorting_MS4, sorting_KL],
                                         name_list=['klusta', 'ms4'])


##############################################################################
# When comparing with a ground-truth sorting extractor (1), you can get the sorting performance and plot a confusion
# matrix

comp_gt_KL.get_performance()
w_conf = sw.plot_confusion_matrix(comp_gt_KL)

##############################################################################
# When comparing two sorters (2), we can see the matching of units between sorters. For example, this is how to extract
# the unit ids of Mountainsort4 (sorting2) mapped to the units of Klusta (sorting1). Units which are not mapped has -1
# as unit id.
github SpikeInterface / spikeinterface / examples / modules / comparison / plot_1_compare_two_sorters.py View on Github external
#############################################################################
# Then run two spike sorters and compare their ouput.

sorting_KL = sorters.run_klusta(recording)
sorting_MS4 = sorters.run_mountainsort4(recording)

#############################################################################
# The :code:`compare_two_sorters` function allows us to compare the spike
# sorting output. It returns a :code:`SortingComparison` object, with methods
# to inspect the comparison output easily. The comparison matches the
# units by comparing the agreement between unit spike trains.

# Let’s see how to inspect and access this matching.

cmp_KL_MS4 = sc.compare_two_sorters(sorting1=sorting_KL, sorting2=sorting_MS4, 
                                               sorting1_name='klusta', sorting2_name='ms4')

#############################################################################
# In order to check which units were matched, the :code:`get_mapped_sorting`
# methods can be used. If units are not matched they are listed as -1.

# units matched to klusta units
mapped_sorting_klusta = cmp_KL_MS4.get_mapped_sorting1()
print('Klusta units:', sorting_KL.get_unit_ids())
print('Klusta mapped units:', mapped_sorting_klusta.get_mapped_unit_ids())

# units matched to ms4 units
mapped_sorting_ms4 = cmp_KL_MS4.get_mapped_sorting2()
print('Mountainsort units:',sorting_MS4.get_unit_ids())
print('Mountainsort mapped units:',mapped_sorting_ms4.get_mapped_unit_ids())