Implement select_sorting_periods in metrics
#4302
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This is OK for me. |
| rng = np.random.default_rng() | ||
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| # number of random periods | ||
| n_periods = 10_000 |
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duration, num_units and n_periods are all quite large for a test. Is it slow??
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I agree we should put a small number
Co-authored-by: Chris Halcrow <[email protected]>
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| base_period_dtype = [ |
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move all dtypes to base
Co-authored-by: Chris Halcrow <[email protected]>
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@chrishalcrow I refactored a few metrics to make sure durations, spike counts, and bins are properly accounted for when slicing with periods. Happy to discuss about this! |
alejoe91
changed the title
select_sorting_periodsselect_sorting_periods in metrics
yger
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yger
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This looks good to me, I think this is a great extension to be able to compute metrics on sub_periods only. A couple of minor comments, and I think everything is not too slow, but good work!
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| # Check that all spikes in the sliced sorting are within the periods | ||
| for segment_index in range(sorting.get_num_segments()): | ||
| periods_in_segment = periods[periods["segment_index"] == segment_index] |
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do we assume not too many periods, just to be sure that all these masks won't take too long?
| spike_vector = sorting.to_spike_vector() | ||
| spike_vector_list = sorting.to_spike_vector(concatenated=False) | ||
| keep_mask = np.zeros(len(spike_vector), dtype=bool) | ||
| all_global_indices = spike_vector_to_indices(spike_vector_list, unit_ids=sorting.unit_ids, absolute_index=True) |
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why not using self.sorting_analyzer.sorting.get_spike_vector_to_indices(), and thus make use of a possible cache?
| for segment_index in range(sorting.get_num_segments()): | ||
| global_indices_segment = all_global_indices[segment_index] | ||
| # filter periods by segment | ||
| periods_in_segment = periods[periods["segment_index"] == segment_index] |
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assuming not too many periods, these masks would be fine. Otherwise, we'll need to optimize
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We don't want to extend these quality metrics to the extension() ? What if someone wants to only get the ISI, CCG or anything else only on the periods? Would it be easy to slice the sorting, and then compute only on the sub sorting? Are the extension robust w.r.t. periods? |
4 participants
Depends on #4316
Slices a sorting object based on an array ov valid periods. Periods are defined as a structured dtype as:
EDIT:
Refactored computation of spike train metrics, to make sure that periods are consistently taken into account. Added 2 utils functions to compute durations per unit and bin edges per unit, that optionally use the provided periods