Fix spike finding #21
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neuroanalysis/event_detection.py
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| @@ -95,45 +95,175 @@ def zero_crossing_events(data, min_length=3, min_peak=0.0, min_sum=0.0, noise_th | |||
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| return events | |||
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| def deal_unbalanced_initial_off(omit_ends, on_inds, off_inds): | |||
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Start function names with _ if you don't intend then to be used externally.
| data = trace.data | ||
| data1 = data - baseline | ||
| # convert threshold array | ||
| if isinstance(threshold, float): | ||
| threshold = np.ones(len(data)) * abs(threshold) |
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why convert to array? this just slows down the comparisons that come later.
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I made it so that the input threshold could be an array so that it doesn't need to be constant (see line 130). For current clamp I alter the threshold across the duration of the stimulation pulse. (See spike_detection.py line 154)
neuroanalysis/event_detection.py
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| masks = [(data1 > threshold).astype(np.byte), (data1 < -threshold).astype(np.byte)] | ||
| ## find all positive and negative threshold crossings of baseline adjusted data | ||
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| if debug: |
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I'm not so keen on merging debugging code unless there's a good reason to keep it here?
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Yes I figured, you would want it removed, but I didn't want to do it before you looked at the rest of the code incase I needed to look at stuff again. The debug plots are particularly insightful for your questions below about removing the +1 on line 191. Once you are happy it can be removed before merge along with the 'debug' argument into the functions.
neuroanalysis/event_detection.py
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| # TODO: It might be a good idea to make offindexes one less so that region above threshold looks symmetrical | ||
| # find start and end inicies (above threshold) where waveform is above threshold | ||
| on_inds = list(np.argwhere(diff==1)[:,0] + 1) #where crosses from below to above threshold Note taking index after this happens | ||
| off_inds = list(np.argwhere(diff==-1)[:,0]) #where crosses from above to below threshold. Note taking index before this happens |
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Why did you remove the +1 here? The idea is you could take data[on_ind:off_ind] and get exactly the region above threshold.
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The last index was actually below the threshold and I only wanted to use indexes above threshold. The +1 includes an area and a value below threshold in the sum and the area.
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I will also remove the #TODO on 188 as I did implement that here.
neuroanalysis/event_detection.py
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| # sometimes an event happens at the beginning of the pulse window and the trace hasn't |
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This is a generic function for detecting threshold crossings; not a good place for comments that require an understanding of your specific use case.
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I can make this statement more generic. But this if statement is here for the case when an event happens at the beginning.
neuroanalysis/event_detection.py
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| if on_inds[i] == off_inds[i]: | ||
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| # remove any point where an on off is seperated by less than 2 indicies | ||
| if (on_inds[i] + 1) == off_inds[i]: |
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Why? Again, this is a generic threshold-crossing function; we shouldn't make assumptions about the use case here.
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This was useful in the downstream stream code, I can pull it out and put in the other function.
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@campagnola I tried to use the new event_detection code I checked out from master with the changes you made. I am not sure why but the changes you made to master are not showing up in this PR but you can see them on the master branch if opened outside not this PR.... In any case at https://github.com/aiephys/neuroanalysis/blob/master/neuroanalysis/event_detection.py#L118 causes an out of range index error. So I used my code again.
@campagnola here is the current code; 53 failed, 519 passed. This pull request so that you can checkout the code (and my current data test set) and look at my current failures which I had difficulty making calls manually and want more eyes on to see if worth it. The current clamp is pretty good. Voltage clamp could have a bit more time.