Good times extension #4299
Good times extension #4299
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Depends on #4302 |
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@m-beau @samuelgarcia the parallelization makes it extremely fast. I slightly refactored the misc_metrics so I can directly call the low-level functions. Now computing good periods for a full 1 hour NP probe takes a minute or so :) The cool trick is that we can compute all fp/fn values for all chunks (a chunk is unit+segment+period) and filter it all at once with thresholds. This simplifies the logic a lot! Take a look, for me this is ready to review. I also tested the relative period mode and it works very well! @m-beau I changed some defaults and naming to something that I think is a bit less strict, but not too much |
| HAVE_NUMBA = False | ||
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| class ComputeGoodPeriodsPerUnit(AnalyzerExtension): |
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I pretty bad for english but my first react is "good" could be replace by "valid" for a clearer semantic no ?
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That was my suggestion too! I like it better as well :)
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That was my suggestion too! I like it better as well :)
| fn_threshold=fn_threshold, | ||
| minimum_n_spikes=minimum_n_spikes, | ||
| minimum_valid_period_duration=minimum_valid_period_duration, | ||
| user_defined_periods=user_defined_periods, |
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Very good point! We still have to add tests for the external periods, but what we could do is set it as a self.user_defined_period and pop in from the dict in self params, so they are not set in the JSON but the run function can still use it.
| def _merge_extension_data( | ||
| self, merge_unit_groups, new_unit_ids, new_sorting_analyzer, censor_ms=None, verbose=False, **job_kwargs | ||
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| new_extension_data = self.data |
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I guess for this we should decide the rules of merging valid period.
intersection or union or period pre merging ?
| new_extension_data = self.data | ||
| return new_extension_data |
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same here what do we want for period after a split ?
maybe remove period of this units no ?
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same here. Probably we want to recompute?
| subperiod["end_sample_index"] = end | ||
| subperiod["unit_index"] = unit_index | ||
| periods_for_unit[i] = subperiod | ||
| all_subperiods = np.concatenate((all_subperiods, periods_for_unit), axis=0) |
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I think this is better to make a final concatenate at the end of the loop and magaing this with list.
This avoid too much memory allocation
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This looks cool. Could we make a very simple matplotlib widgets for this new extension ? (in addtion to sigui f course) |
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Yes, I'll add some TODO's to the PR description so we keep track of it. |
| # TODO: in case of periods, should we use total samples only in provided periods? | ||
| total_samples = sorting_analyzer.get_total_samples() |
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@m-beau @samuelgarcia @chrishalcrow this is a critical point. I refactor the computation so that we can pass the total samples externally. This is needed both when computing in chunks for the compute_good_periods function and also when we update the metrics to use the valid periods. In that case, we will need to count the valid samples for each units, so total_samples can be a dictionary now
| "amplitude_scalings", | ||
| ), "Invalid amplitude_extension. It can be either 'spike_amplitudes' or 'amplitude_scalings'" | ||
| sorting = sorting_analyzer.sorting | ||
| total_duration = sorting_analyzer.get_total_duration() |
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Hello - do we need to be careful about stuff like this? Here the total_duration of the entire recording. It's used later to compute a firing rate, and this firing rate is the total num spikes divided by total duration, rather than num-spike-in-periods/duration-of-periods.
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In this case is the num spikes in period. So I think this is correct, but I'll double check carefully!
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In this case is the num spikes in period. So I think this is correct, but I'll double check carefully!
4 participants
Implements #4294