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Remove copy-pasted code in LibV2-LibV3 #314

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Sep 14, 2023
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Remove copy-pasted code in LibV2-LibV3 #314

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23 changes: 0 additions & 23 deletions efel/cppcore/FillFptrTable.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -79,9 +79,7 @@ int FillFptrTable() {
*/

// AP parameter
FptrTableV2["AP_begin_indices"] = &LibV2::AP_begin_indices;
FptrTableV2["AP_rise_indices"] = &LibV2::AP_rise_indices;
FptrTableV2["AP_end_indices"] = &LibV2::AP_end_indices;
FptrTableV2["AP_fall_indices"] = &LibV2::AP_fall_indices;
// eFeatures
FptrTableV2["AP_duration"] = &LibV2::AP_duration;
Expand Down Expand Up @@ -139,33 +137,12 @@ int FillFptrTable() {
//****************** end of FptrTableV2 *****************************

//****************** FptrTableV3 *****************************
FptrTableV3["interpolate"] = &LibV3::interpolate;
FptrTableV3["trace_check"] = &LibV3::trace_check;
FptrTableV3["peak_indices"] = &LibV3::peak_indices;
FptrTableV3["ISI_values"] = &LibV3::ISI_values;
FptrTableV3["ISI_CV"] = &LibV3::ISI_CV;
FptrTableV3["peak_voltage"] = &LibV3::peak_voltage;
FptrTableV3["mean_frequency"] = &LibV3::firing_rate;
FptrTableV3["peak_time"] = &LibV3::peak_time;
FptrTableV3["time_to_first_spike"] = &LibV3::first_spike_time;
FptrTableV3["spike_half_width"] = &LibV3::spike_width1;
FptrTableV3["min_AHP_indices"] = &LibV3::min_AHP_indices;
FptrTableV3["min_AHP_values"] = &LibV3::min_AHP_values;
FptrTableV3["AHP_depth_abs"] = &LibV3::AHP_depth_abs;
FptrTableV3["voltage_base"] = &LibV3::rest_voltage_value;
FptrTableV3["adaptation_index2"] = &LibV3::adaptation_index2;
FptrTableV3["AP_height"] = &LibV3::AP_height;
FptrTableV3["AP_amplitude"] = &LibV3::AP_amplitude;
FptrTableV3["AP_width"] = &LibV3::AP_width;
FptrTableV3["doublet_ISI"] = &LibV3::doublet_ISI;

FptrTableV3["AP_begin_indices"] = &LibV3::AP_begin_indices;
FptrTableV3["AP_rise_indices"] = &LibV3::AP_rise_indices;
FptrTableV3["AP_end_indices"] = &LibV3::AP_end_indices;
FptrTableV3["AP_fall_indices"] = &LibV3::AP_fall_indices;
// eFeatures
FptrTableV3["AP_duration"] = &LibV3::AP_duration;

FptrTableV3["depolarized_base"] = &LibV3::depolarized_base;

//****************** end of FptrTableV3 *****************************
Expand Down
149 changes: 0 additions & 149 deletions efel/cppcore/LibV2.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -33,155 +33,6 @@ using std::transform;

// AP parameters
//
// *** AP begin indices ***
//
static int __AP_begin_indices(const vector<double>& t, const vector<double>& v,
double stimstart, double stimend,
const vector<int>& ahpi, vector<int>& apbi) {
// derivative at peak start according to eCode specification 10mV/ms
// according to Shaul 12mV/ms
const double derivativethreshold = 12.;
// constant time steps due to 'interpolate'
vector<double> dvdt(v.size());
vector<double> dv;
vector<double> dt;
getCentralDifferenceDerivative(1., v, dv);
getCentralDifferenceDerivative(1., t, dt);
transform(dv.begin(), dv.end(), dt.begin(), dvdt.begin(), std::divides<double>());

// restrict to time interval where stimulus is applied
vector<int> minima;
int stimbeginindex = distance(
t.begin(),
find_if(t.begin(), t.end(), bind2nd(greater_equal<double>(), stimstart)));
minima.push_back(stimbeginindex);
for (size_t i = 0; i < ahpi.size(); i++) {
if (ahpi[i] > stimbeginindex) {
minima.push_back(ahpi[i]);
}
if (t[ahpi[i]] > stimend) {
break;
}
}
// if the AHP_indices are already restricted make sure that we do not miss
// the last spike
if (t[minima.back()] < stimend) {
int stimendindex =
distance(t.begin(), find_if(t.begin() + minima.back(), t.end(),
bind2nd(greater_equal<double>(), stimend)));
minima.push_back(stimendindex);
}
for (size_t i = 0; i < minima.size() - 1; i++) {
// assure that the width of the slope is bigger than 4
int newbegin = minima[i];
int begin = minima[i];
int width = 5;
bool skip = false;
do {
begin = distance(
dvdt.begin(),
find_if(dvdt.begin() + newbegin, dvdt.begin() + minima[i + 1],
bind2nd(greater_equal<double>(), derivativethreshold)));
if (begin == minima[i + 1]) {
// could not find a spike in between these minima
skip = true;
break;
}
newbegin = begin + 1;
} while (find_if(dvdt.begin() + begin, dvdt.begin() + begin + width,
bind2nd(std::less<double>(), derivativethreshold)) !=
dvdt.begin() + begin + width);
if (skip) {
continue;
}
apbi.push_back(begin);
}
return apbi.size();
}
int LibV2::AP_begin_indices(mapStr2intVec& IntFeatureData,
mapStr2doubleVec& DoubleFeatureData,
mapStr2Str& StringData) {
int retVal;
int nSize;
retVal = CheckInMap(IntFeatureData, StringData, "AP_begin_indices",
nSize);
if (retVal) {
return nSize;
}
vector<double> t;
retVal = getVec(DoubleFeatureData, StringData, "T", t);
if (retVal < 0) return -1;
vector<double> v;
retVal = getVec(DoubleFeatureData, StringData, "V", v);
if (retVal < 0) return -1;
vector<double> stimstart;
retVal = getVec(DoubleFeatureData, StringData, "stim_start", stimstart);
if (retVal < 0) return -1;
vector<double> stimend;
retVal = getVec(DoubleFeatureData, StringData, "stim_end", stimend);
if (retVal < 0) return -1;
vector<int> ahpi;
retVal = getVec(IntFeatureData, StringData, "min_AHP_indices", ahpi);
if (retVal < 0) return -1;
vector<int> apbi;
retVal = __AP_begin_indices(t, v, stimstart[0], stimend[0], ahpi, apbi);
if (retVal >= 0) {
setVec(IntFeatureData, StringData, "AP_begin_indices", apbi);
}
return retVal;
}

// *** AP end indices ***
//
static int __AP_end_indices(const vector<double>& t, const vector<double>& v,
const vector<int>& pi, vector<int>& apei) {
// derivative at peak end according to eCode specification -10mV/ms
// according to Shaul -12mV/ms
const double derivativethreshold = -12.;
// assume constant time steps
double timestep = t[1] - t[0];
vector<double> dvdt;
getCentralDifferenceDerivative(timestep, v, dvdt);

apei.resize(pi.size());
vector<int> picopy(pi.begin(), pi.end());
picopy.push_back(v.size() - 1);
for (size_t i = 0; i < apei.size(); i++) {
// assure that the width of the slope is bigger than 4
apei[i] = distance(
dvdt.begin(),
find_if(dvdt.begin() + picopy[i] + 1, dvdt.begin() + picopy[i + 1],
bind2nd(greater_equal<double>(), derivativethreshold)));
}
return apei.size();
}
int LibV2::AP_end_indices(mapStr2intVec& IntFeatureData,
mapStr2doubleVec& DoubleFeatureData,
mapStr2Str& StringData) {
int retVal;
int nSize;
retVal = CheckInMap(IntFeatureData, StringData, "AP_end_indices", nSize);
if (retVal) {
return nSize;
}

vector<double> t;
retVal = getVec(DoubleFeatureData, StringData, "T", t);
if (retVal < 0) return -1;
vector<double> v;
retVal = getVec(DoubleFeatureData, StringData, "V", v);
if (retVal < 0) return -1;
vector<int> pi;
retVal = getVec(IntFeatureData, StringData, "peak_indices", pi);
if (retVal < 0) return -1;
vector<int> apei;
retVal = __AP_end_indices(t, v, pi, apei);
if (retVal >= 0) {
setVec(IntFeatureData, StringData, "AP_end_indices", apei);
}
return retVal;
}

// *** AP rise indices ***
//
static int __AP_rise_indices(const vector<double>& v, const vector<int>& apbi,
Expand Down
7 changes: 0 additions & 7 deletions efel/cppcore/LibV2.h
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Original file line number Diff line number Diff line change
Expand Up @@ -30,10 +30,6 @@ namespace LibV2 {
// AP parameters of eCode Specification 1.04
// partly reimplemented Shaul's matlab code ap_points.m
//
int AP_begin_indices(mapStr2intVec& IntFeatureData,
mapStr2doubleVec& DoubleFeatureData,
mapStr2Str& StringData);

int AP_rise_indices(mapStr2intVec& IntFeatureData,
mapStr2doubleVec& DoubleFeatureData,
mapStr2Str& StringData);
Expand All @@ -42,9 +38,6 @@ int AP_fall_indices(mapStr2intVec& IntFeatureData,
mapStr2doubleVec& DoubleFeatureData,
mapStr2Str& StringData);

int AP_end_indices(mapStr2intVec& IntFeatureData,
mapStr2doubleVec& DoubleFeatureData, mapStr2Str& StringData);

// eFeatures
int AP_duration(mapStr2intVec& IntFeatureData,
mapStr2doubleVec& DoubleFeatureData, mapStr2Str& StringData);
Expand Down
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