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fix AHP_slow_time and min_AHP_values #394

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merged 7 commits into from
May 21, 2024
Merged

fix AHP_slow_time and min_AHP_values #394

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8ba9a9b
fix AHP_slow_time and min_AHP_values
May 21, 2024
434f8b3
Merge branch 'master' into fix-slowtime
AurelienJaquier May 21, 2024
e17e212
do not allow empty list as a feature value
May 21, 2024
4c54561
Merge branch 'master' of https://github.com/BlueBrain/eFEL into fix-s…
May 21, 2024
8df6372
Merge branch 'fix-slowtime' of https://github.com/AurelienJaquier/eFE…
May 21, 2024
4aa06d6
empty features should be None
May 21, 2024
e1f5966
do not hardcode return value for features computes outside of their f…
May 21, 2024
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30 changes: 24 additions & 6 deletions efel/cppcore/SpikeEvent.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -557,7 +557,10 @@ int SpikeEvent::burst_begin_indices(mapStr2intVec& IntFeatureData,
int SpikeEvent::burst_end_indices(mapStr2intVec& IntFeatureData,
mapStr2doubleVec& DoubleFeatureData,
mapStr2Str& StringData) {
return 1;
const auto& intFeatures = getFeatures(IntFeatureData, {"burst_begin_indices"});
int retVal = intFeatures.at("burst_begin_indices").size();
if (retVal <= 0) return -1;
return retVal;
}

static int __strict_burst_mean_freq(const vector<double>& PVTime,
Expand Down Expand Up @@ -695,7 +698,10 @@ int SpikeEvent::interburst_min_indices(mapStr2intVec& IntFeatureData,
int SpikeEvent::interburst_min_values(mapStr2intVec& IntFeatureData,
mapStr2doubleVec& DoubleFeatureData,
mapStr2Str& StringData) {
return 1;
const auto& intFeatures = getFeatures(IntFeatureData, {"interburst_min_indices"});
int retVal = intFeatures.at("interburst_min_indices").size();
if (retVal <= 0) return -1;
return retVal;
}

static int __postburst_min_indices(const vector<double>& t,
Expand Down Expand Up @@ -767,7 +773,10 @@ int SpikeEvent::postburst_min_indices(mapStr2intVec& IntFeatureData,
int SpikeEvent::postburst_min_values(mapStr2intVec& IntFeatureData,
mapStr2doubleVec& DoubleFeatureData,
mapStr2Str& StringData) {
return 1;
const auto& intFeatures = getFeatures(IntFeatureData, {"postburst_min_indices"});
int retVal = intFeatures.at("postburst_min_indices").size();
if (retVal <= 0) return -1;
return retVal;
}

int SpikeEvent::time_to_interburst_min(mapStr2intVec& IntFeatureData,
Expand Down Expand Up @@ -897,7 +906,10 @@ int SpikeEvent::postburst_slow_ahp_indices(mapStr2intVec& IntFeatureData,
int SpikeEvent::postburst_slow_ahp_values(mapStr2intVec& IntFeatureData,
mapStr2doubleVec& DoubleFeatureData,
mapStr2Str& StringData) {
return 1;
const auto& intFeatures = getFeatures(IntFeatureData, {"postburst_slow_ahp_indices"});
int retVal = intFeatures.at("postburst_slow_ahp_indices").size();
if (retVal <= 0) return -1;
return retVal;
}

int SpikeEvent::time_to_postburst_slow_ahp(mapStr2intVec& IntFeatureData,
Expand Down Expand Up @@ -1010,7 +1022,10 @@ int SpikeEvent::postburst_fast_ahp_indices(mapStr2intVec& IntFeatureData,
int SpikeEvent::postburst_fast_ahp_values(mapStr2intVec& IntFeatureData,
mapStr2doubleVec& DoubleFeatureData,
mapStr2Str& StringData) {
return 1;
const auto& intFeatures = getFeatures(IntFeatureData, {"postburst_fast_ahp_indices"});
int retVal = intFeatures.at("postburst_fast_ahp_indices").size();
if (retVal <= 0) return -1;
return retVal;
}

static int __postburst_adp_peak_indices(const vector<double>& t, const vector<double>& v,
Expand Down Expand Up @@ -1077,7 +1092,10 @@ int SpikeEvent::postburst_adp_peak_indices(mapStr2intVec& IntFeatureData,
int SpikeEvent::postburst_adp_peak_values(mapStr2intVec& IntFeatureData,
mapStr2doubleVec& DoubleFeatureData,
mapStr2Str& StringData) {
return 1;
const auto& intFeatures = getFeatures(IntFeatureData, {"postburst_adp_peak_indices"});
int retVal = intFeatures.at("postburst_adp_peak_indices").size();
if (retVal <= 0) return -1;
return retVal;
}

int SpikeEvent::time_to_postburst_fast_ahp(mapStr2intVec& IntFeatureData,
Expand Down
20 changes: 16 additions & 4 deletions efel/cppcore/SpikeShape.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -475,7 +475,10 @@ int SpikeShape::min_AHP_indices(mapStr2intVec& IntFeatureData,
int SpikeShape::min_AHP_values(mapStr2intVec& IntFeatureData,
mapStr2doubleVec& DoubleFeatureData,
mapStr2Str& StringData) {
return -1;
const auto& intFeatures = getFeatures(IntFeatureData, {"min_AHP_indices"});
int retVal = intFeatures.at("min_AHP_indices").size();
if (retVal <= 0) return -1;
return retVal;
}

// Difference with SpikeShape is that this function doesn't return -1 if there are no
Expand Down Expand Up @@ -550,7 +553,10 @@ int SpikeShape::AHP_depth_abs_slow(mapStr2intVec& IntFeatureData,
int SpikeShape::AHP_slow_time(mapStr2intVec& IntFeatureData,
mapStr2doubleVec& DoubleFeatureData,
mapStr2Str& StringData) {
return -1;
const auto& doubleFeatures = getFeatures(DoubleFeatureData, {"AHP_depth_abs_slow"});
int retVal = doubleFeatures.at("AHP_depth_abs_slow").size();
if (retVal <= 0) return -1;
return retVal;
}

// *** AHP_depth_slow ***
Expand Down Expand Up @@ -818,7 +824,10 @@ int SpikeShape::ADP_peak_indices(mapStr2intVec& IntFeatureData,
int SpikeShape::ADP_peak_values(mapStr2intVec& IntFeatureData,
mapStr2doubleVec& DoubleFeatureData,
mapStr2Str& StringData) {
return 1;
const auto& intFeatures = getFeatures(IntFeatureData, {"ADP_peak_indices"});
int retVal = intFeatures.at("ADP_peak_indices").size();
if (retVal <= 0) return -1;
return retVal;
}

// strict_stiminterval should be True when using this feature
Expand Down Expand Up @@ -994,7 +1003,10 @@ int SpikeShape::min_between_peaks_indices(mapStr2intVec& IntFeatureData,
int SpikeShape::min_between_peaks_values(mapStr2intVec& IntFeatureData,
mapStr2doubleVec& DoubleFeatureData,
mapStr2Str& StringData) {
return 1;
const auto& intFeatures = getFeatures(IntFeatureData, {"min_between_peaks_indices"});
int retVal = intFeatures.at("min_between_peaks_indices").size();
if (retVal <= 0) return -1;
return retVal;
}

// *** AP_duration_half_width according to E8 and E16 ***
Expand Down
5 changes: 4 additions & 1 deletion efel/cppcore/cfeature.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -303,7 +303,10 @@ int cFeature::getFeature(string strName, vector<T>& vec) {
return -1;
}
vec = getMapData<T>(strName, *dataMap);
if (vec.empty()) GErrorStr += "Feature [" + strName + "] data is missing\n";
if (vec.empty()) {
GErrorStr += "Feature [" + strName + "] data is missing\n";
return -1;
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This will turn empty lists into None

}

logger << "Calculated feature " << strName << ":" << vec << endl;
return vec.size();
Expand Down
4 changes: 2 additions & 2 deletions efel/pyfeatures/pyfeatures.py
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Original file line number Diff line number Diff line change
Expand Up @@ -291,7 +291,7 @@ def spikes_per_burst():
burst_begin_indices = get_cpp_feature("burst_begin_indices")
burst_end_indices = get_cpp_feature("burst_end_indices")

if burst_begin_indices is None:
if burst_begin_indices is None or len(burst_begin_indices) < 1:
return None

ap_per_bursts = []
Expand All @@ -304,7 +304,7 @@ def spikes_per_burst():
def spikes_per_burst_diff():
"""Calculate the diff between the spikes in each burst and the next one"""
spikes_per_burst_values = spikes_per_burst()
if spikes_per_burst_values is None:
if spikes_per_burst_values is None or len(spikes_per_burst_values) < 2:
return None

return spikes_per_burst_values[:-1] - spikes_per_burst_values[1:]
Expand Down
16 changes: 8 additions & 8 deletions tests/testdata/allfeatures/expectedresults.json
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Original file line number Diff line number Diff line change
Expand Up @@ -435,8 +435,8 @@
"interburst_60percent_indices": null,
"interburst_60percent_values": null,
"interburst_duration": null,
"interburst_min_indices": [],
"interburst_min_values": [],
"interburst_min_indices": null,
"interburst_min_values": null,
"interburst_voltage": [
-38.820613862535545
],
Expand Down Expand Up @@ -624,7 +624,7 @@
"strict_burst_number": [
1
],
"strict_interburst_voltage": [],
"strict_interburst_voltage": null,
"time": [
0.0,
0.1,
Expand Down Expand Up @@ -30632,7 +30632,7 @@
"time_to_first_spike": [
8.000000000092427
],
"time_to_interburst_min": [],
"time_to_interburst_min": null,
"time_to_last_spike": [
1937.7999999986964
],
Expand Down Expand Up @@ -60680,7 +60680,7 @@
"spikes_per_burst": [
2
],
"spikes_per_burst_diff": [],
"spikes_per_burst_diff": null,
"spikes_in_burst1_burst2_diff": null,
"spikes_in_burst1_burstlast_diff": null,
"depol_block": null,
Expand Down Expand Up @@ -60723,7 +60723,7 @@
"strict_burst_mean_freq": [
7.99041151
],
"strict_interburst_voltage": [],
"strict_interburst_voltage": null,
"ADP_peak_amplitude": [
0.0,
2.6873666528663236,
Expand All @@ -60748,8 +60748,8 @@
-41.12299346923828,
-38.12341871769886
],
"interburst_min_indices": [],
"interburst_min_values": [],
"interburst_min_indices": null,
"interburst_min_values": null,
"postburst_min_indices": [
26465
],
Expand Down