Impedance ("Z score") feature is added #165
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efel/pyfeatures/pyfeatures.py
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| freq = numpy.fft.fftfreq(len(volt), d=0.0001) | ||
| Z = ((fft_volt) / (fft_cur)) | ||
| signalPhase = numpy.angle(fft_volt) | ||
| norm_Z = abs(Z[1:150]) / max(abs(Z[1:150])) |
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do we have to hardcode 150 here ? It should at least be a general eFEL setting
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I was trying to undo the _versioneer change. Let me reopen it. |
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I don't have permission to push, @mariarv did you enable the "allow contributors to make changes" option? |
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The issue was automatically getting closed when I wanted to push after a rebase while my default git push behaviour was |
Impedance feature PR BlueBrain#165 merged with master
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The only conflict with master is the presence of "impedance" feature in the |
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Sure, but that file should be changed in a way that it doesn't cause a merge conflict with getting that into master |
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It's tricky: |
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I can merge master here. I think that would be the best. |
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But I think there is something wrong with the exact line or so. I've never seen a merge conflict when adding features. |
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Previously the sorting order of lines was different and there was also the removal of duplicates. That had created the original merge conflict and after resolving it in 4117769, git still kept the conflict statement |
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That looks better :-) |
efel/pyfeatures/pyfeatures.py
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| normalized_voltage = voltage_trace - holding_voltage | ||
| current_trace = current() | ||
| if current_trace is not None: | ||
| current_base = numpy.median(current_trace[0:10]) |
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so we still need a current_base feature for this, the 0:10 should not be hardcoded
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Yes and also the "median" option for both voltage_base and current_base features.
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Now we can use the current base feature with median but how can we set the range [0:10] there?
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@mariarv should this be 0:10? Wouldn't it be better to use the same range as voltage_base?
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I started using current_base in latest commit
efel/pyfeatures/pyfeatures.py
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| Z = fft_volt / fft_cur | ||
| norm_Z = abs(Z) / max(abs(Z)) | ||
| # physiological range of frequencies range [0,100] | ||
| smooth_Z = gaussian_filter1d(norm_Z[0:100], 10) |
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this range should still become an efel setting, so that we don't hardcoded '100'
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Done in latest commit. New efel setting is impedance_max_freq and its default value is 50, to be consistent with this paper: https://pubmed.ncbi.nlm.nih.gov/1992481/
efel/pyfeatures/pyfeatures.py
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| normalized_voltage = voltage_trace - holding_voltage | ||
| current_trace = current() | ||
| if current_trace is not None: | ||
| current_base = numpy.median(current_trace[0:10]) |
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maybe this should be called holding_current to be consistent with holding_voltage?
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Done in latest commit
Codecov ReportAttention:
Additional details and impacted files@@ Coverage Diff @@
## master #165 +/- ##
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+ Coverage 53.45% 53.59% +0.14%
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Files 30 30
Lines 8394 8426 +32
Branches 3677 3677
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+ Hits 4487 4516 +29
- Misses 1261 1264 +3
Partials 2646 2646
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…-master Conflicts: efel/pyfeatures/pyfeatures.py tests/test_pyfeatures.py
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Hi there! People from BBP are starting to do single cell optimisation and they will need this feature, so I will make some changes to this PR soon. (1st plot: without 0Hz) |
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Hi @AurelienJaquier. Sure, you can get rid of 0 Hz, ideally it should not matter, as the peak of impedance shall not be at 0 Hz. |
The "impedance" feature takes the maximum of impedance of the neuron. Impedance is calculated by dividing the power spectrum of the voltage trace by the power spectrum of ZAP current. An example of impedance profile and its maximum (star symbol on the plot) for corresponding current and voltage traces is attached.
