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Removal of Redundant Features in Libraries #minor #322

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merged 14 commits into from
Oct 13, 2023
Merged

Removal of Redundant Features in Libraries #minor #322

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9b6f130
remove LibV4
anilbey Oct 12, 2023
531b33e
keep only depolarized_base in LibV3
anilbey Oct 12, 2023
185d6c5
remove LibV1::peak_indices
anilbey Oct 12, 2023
ee261b2
remove commented out LibV2 pointers
anilbey Oct 12, 2023
f37cfb8
remove LibV2 E6-E40 features, not used not tested
anilbey Oct 12, 2023
0aea0a3
remove LibV1::spike_width1, use LibV5::spike_half_width
anilbey Oct 12, 2023
b2036e1
remove LibV1::rest_voltage_value, use LibV5::voltage_base
anilbey Oct 13, 2023
82c3550
remove LibV1::min_AHP_values
anilbey Oct 13, 2023
a1abcab
remove LibV1::LibV1::AHP_depth_abs
anilbey Oct 13, 2023
bddc762
remove LibV1::min_AHP_indices, LibV5 is used
anilbey Oct 13, 2023
0d63178
Merge branch 'BlueBrain:master' into removal
anilbey Oct 13, 2023
8ed9e18
test_spikecount_libv5peakindices -> test_setDependencyFileLocation
anilbey Oct 13, 2023
c903c2a
Revert "remove LibV2 E6-E40 features, not used not tested"
anilbey Oct 13, 2023
2a5ce1a
use getDependencyFileLocation in test_setDependencyFileLocation
anilbey Oct 13, 2023
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4 changes: 2 additions & 2 deletions efel/cppcore/CMakeLists.txt
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Original file line number Diff line number Diff line change
Expand Up @@ -19,7 +19,7 @@ cmake_minimum_required(VERSION 2.6)

set(CMAKE_BUILD_TYPE Debug)

set(FEATURESRCS Utils.cpp LibV1.cpp LibV2.cpp LibV3.cpp LibV4.cpp LibV5.cpp
set(FEATURESRCS Utils.cpp LibV1.cpp LibV2.cpp LibV3.cpp LibV5.cpp
FillFptrTable.cpp DependencyTree.cpp efel.cpp cfeature.cpp
mapoperations.cpp)

Expand All @@ -33,6 +33,6 @@ add_library(efel SHARED ${FEATURESRCS})
install(TARGETS efel LIBRARY DESTINATION lib)

install(FILES efel.h cfeature.h FillFptrTable.h LibV1.h LibV2.h LibV3.h
LibV4.h LibV5.h mapoperations.h Utils.h DependencyTree.h eFELLogger.h
LibV5.h mapoperations.h Utils.h DependencyTree.h eFELLogger.h
types.h
DESTINATION include)
21 changes: 0 additions & 21 deletions efel/cppcore/FillFptrTable.cpp
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Expand Up @@ -20,23 +20,17 @@
int FillFptrTable() {
//****************** for FptrTableV1 *****************************
FptrTableV1["interpolate"] = &LibV1::interpolate;
FptrTableV1["peak_indices"] = &LibV1::peak_indices;
FptrTableV1["ISI_values"] = &LibV1::ISI_values;
FptrTableV1["peak_voltage"] = &LibV1::peak_voltage;
FptrTableV1["mean_frequency"] = &LibV1::firing_rate;
FptrTableV1["peak_time"] = &LibV1::peak_time;
FptrTableV1["time_to_first_spike"] = &LibV1::first_spike_time;
FptrTableV1["min_AHP_indices"] = &LibV1::min_AHP_indices;
FptrTableV1["min_AHP_values"] = &LibV1::min_AHP_values;
FptrTableV1["voltage_base"] = &LibV1::rest_voltage_value;
FptrTableV1["burst_ISI_indices"] = &LibV1::burst_ISI_indices;
FptrTableV1["adaptation_index"] = &LibV1::adaptation_index;
FptrTableV1["trace_check"] = &LibV1::trace_check;
FptrTableV1["spike_half_width"] = &LibV1::spike_width1;
FptrTableV1["spike_width2"] = &LibV1::spike_width2;
FptrTableV1["burst_mean_freq"] = &LibV1::burst_mean_freq;
FptrTableV1["interburst_voltage"] = &LibV1::interburst_voltage;
FptrTableV1["AHP_depth_abs"] = &LibV1::AHP_depth_abs;
// passive properties
FptrTableV1["time_constant"] = &LibV1::time_constant;
FptrTableV1["voltage_deflection"] = &LibV1::voltage_deflection;
Expand Down Expand Up @@ -65,17 +59,9 @@ int FillFptrTable() {

//****************** for FptrTableV2 *****************************
/*
FptrTableV2["peak_indices"] = &LibV2::peak_indices;
FptrTableV2["ISI_values"] = &LibV2::ISI_values;
FptrTableV2["peak_voltage"] = &LibV2::peak_voltage;
FptrTableV2["firing_rate"] = &LibV2::firing_rate;
FptrTableV2["peak_time"] = &LibV2::peak_time;
FptrTableV2["first_spike_time"] = &LibV2::first_spike_time;
FptrTableV2["AHP_min_indices"] = &LibV2::AHP_min_indices;
FptrTableV2["AHP_values"] = &LibV2::AHP_values;
FptrTableV2["rest_voltage_value"] = &LibV2::rest_voltage_value;
FptrTableV2["burst_vector"] = &LibV2::burst_vector;
FptrTableV2["adaptation_index"] = &LibV2::adaptation_index;
*/

// AP parameter
Expand Down Expand Up @@ -137,18 +123,11 @@ int FillFptrTable() {
//****************** end of FptrTableV2 *****************************

//****************** FptrTableV3 *****************************
FptrTableV3["AP_amplitude"] = &LibV3::AP_amplitude;
FptrTableV3["AP_width"] = &LibV3::AP_width;

FptrTableV3["AP_begin_indices"] = &LibV3::AP_begin_indices;
FptrTableV3["AP_end_indices"] = &LibV3::AP_end_indices;
// eFeatures
FptrTableV3["depolarized_base"] = &LibV3::depolarized_base;

//****************** end of FptrTableV3 *****************************

FptrTableV4["peak_indices"] = &LibV4::peak_indices;

//****************** FptrTableV5 *****************************

FptrTableV5["ISI_log_slope"] = &LibV5::ISI_log_slope;
Expand Down
2 changes: 0 additions & 2 deletions efel/cppcore/FillFptrTable.h
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Original file line number Diff line number Diff line change
Expand Up @@ -24,13 +24,11 @@
#include "LibV1.h"
#include "LibV2.h"
#include "LibV3.h"
#include "LibV4.h"
#include "LibV5.h"

extern feature2function FptrTableV1;
extern feature2function FptrTableV2;
extern feature2function FptrTableV3;
extern feature2function FptrTableV4;
extern feature2function FptrTableV5;

int FillFptrTable();
Expand Down
263 changes: 0 additions & 263 deletions efel/cppcore/LibV1.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -85,66 +85,6 @@ int LibV1::interpolate(mapStr2intVec& IntFeatureData,
return retVal;
}

static int __peak_indices(double dThreshold, vector<double>& V,
vector<int>& PeakIndex) {
vector<int> upVec, dnVec;
double dtmp;
int itmp;

for (size_t i = 1; i < V.size(); i++) {
if (V[i] > dThreshold && V[i - 1] < dThreshold) {
upVec.push_back(i);
} else if (V[i] < dThreshold && V[i - 1] > dThreshold) {
dnVec.push_back(i);
}
}
if (dnVec.size() == 0) {
GErrorStr +=
"\nVoltage never goes below or above threshold in spike detection.\n";
return 0;
}

if (dnVec.size() != upVec.size()) {
GErrorStr += "\nVoltage never goes below threshold after last spike.\n";
return 0;
}

PeakIndex.clear();
int j = 0;
for (size_t i = 0; i < upVec.size(); i++) {
dtmp = -1e9;
itmp = -1;
for (j = upVec[i]; j <= dnVec[i]; j++) {
if (dtmp < V[j]) {
dtmp = V[j];
itmp = j;
}
}
if (itmp != -1) PeakIndex.push_back(itmp);
}
return PeakIndex.size();
}
int LibV1::peak_indices(mapStr2intVec& IntFeatureData,
mapStr2doubleVec& DoubleFeatureData,
mapStr2Str& StringData) {
// printf("\n LibV1 This is inside peak_indices()");
int retVal, nSize;
retVal =
CheckInMap(IntFeatureData, StringData, "peak_indices", nSize);
if (retVal)
return nSize;
vector<int> PeakIndex;
vector<double> v, Th;
retVal = getVec(DoubleFeatureData, StringData, "V", v);
if (retVal <= 0) return -1;
retVal = getDoubleParam(DoubleFeatureData, "Threshold", Th);
if (retVal <= 0) return -1;
int retval = __peak_indices(Th[0], v, PeakIndex);
if (retval >= 0)
setVec(IntFeatureData, StringData, "peak_indices", PeakIndex);
return retval;
}

// *** Spikecount ***
int LibV1::Spikecount(mapStr2intVec& IntFeatureData,
mapStr2doubleVec& DoubleFeatureData,
Expand Down Expand Up @@ -358,67 +298,6 @@ int LibV1::first_spike_time(mapStr2intVec& IntFeatureData,
return first_spike.size();
}

// min_AHP_indices
// find the minimum between two spikes,
// and the minimum between the last spike and the time the stimulus ends
int LibV1::min_AHP_indices(mapStr2intVec& IntFeatureData,
mapStr2doubleVec& DoubleFeatureData,
mapStr2Str& StringData) {
int retVal, nSize;
retVal = CheckInMap(IntFeatureData, StringData, "min_AHP_indices", nSize);
if (retVal)
return nSize;

vector<int> peak_indices_plus;
vector<int> min_ahp_indices;
vector<double> v;
vector<double> min_ahp_values;
vector<double> stim_end;
vector<double> t;
retVal = getVec(DoubleFeatureData, StringData, "V", v);
if (retVal <= 0) return -1;
retVal = getVec(IntFeatureData, StringData, "peak_indices",
peak_indices_plus);
if (retVal < 1) {
GErrorStr += "\n At least one spike required for calculation of "
"min_AHP_indices.\n";
return -1;
}
retVal = getVec(DoubleFeatureData, StringData, "stim_end", stim_end);
if (retVal <= 0) return -1;
retVal = getVec(DoubleFeatureData, StringData, "T", t);
if (retVal <= 0) return -1;

int end_index = distance(
t.begin(), find_if(t.begin(), t.end(),
bind2nd(greater_equal<double>(), stim_end[0])));
// if the last spike happens to be close to the end of the stimulus
// there will not be a proper AHP, this case is not properly dealt with here
if (end_index > peak_indices_plus.back() + 5) {
peak_indices_plus.push_back(end_index);
}
for (size_t i = 0; i < peak_indices_plus.size() - 1; i++) {
int ahpindex = distance(
v.begin(), min_element(v.begin() + peak_indices_plus[i],
v.begin() + peak_indices_plus[i + 1]));
min_ahp_indices.push_back(ahpindex);
min_ahp_values.push_back(v[ahpindex]);
}
setVec(IntFeatureData, StringData, "min_AHP_indices", min_ahp_indices);
setVec(DoubleFeatureData, StringData, "min_AHP_values", min_ahp_values);
return min_ahp_indices.size();
}

int LibV1::min_AHP_values(mapStr2intVec& IntFeatureData,
mapStr2doubleVec& DoubleFeatureData,
mapStr2Str& StringData) {
int retVal, nSize;
retVal = CheckInMap(DoubleFeatureData, StringData,
"min_AHP_values", nSize);
if (retVal) return nSize;
return -1;
}

int LibV1::AP_height(mapStr2intVec& IntFeatureData,
mapStr2doubleVec& DoubleFeatureData,
mapStr2Str& StringData) {
Expand Down Expand Up @@ -517,29 +396,6 @@ int LibV1::AP_amplitude(mapStr2intVec& IntFeatureData,
return apamplitude.size();
}

// AHP_depth_abs
// naming conflict here AHP_depth_abs does the same as min_AHP_values.
// In my opinion the should not be a feature called 'AHP_depth_abs',
// use min_AHP_values instead.
// A more interesting feature would be 'AHP_depth' anyways, which calculates the
// depth of the AHP relative to the voltage base
int LibV1::AHP_depth_abs(mapStr2intVec& IntFeatureData,
mapStr2doubleVec& DoubleFeatureData,
mapStr2Str& StringData) {
int retVal, nSize;
retVal = CheckInMap(DoubleFeatureData, StringData,
"AHP_depth_abs", nSize);
if (retVal)
return nSize;

vector<double> vAHP;
retVal = getVec(DoubleFeatureData, StringData,
"min_AHP_values", vAHP);
if (retVal <= 0) return -1;
setVec(DoubleFeatureData, StringData, "AHP_depth_abs", vAHP);
return vAHP.size();
}

// *** AHP_depth_abs_slow ***
// same as AHP_depth_abs but the minimum search starts
// 5 ms (or custom duration) after the spike,
Expand Down Expand Up @@ -625,43 +481,6 @@ int LibV1::AHP_slow_time(mapStr2intVec& IntFeatureData,
return -1;
}

int LibV1::rest_voltage_value(mapStr2intVec& IntFeatureData,
mapStr2doubleVec& DoubleFeatureData,
mapStr2Str& StringData) {
int retVal, nSize;
retVal = CheckInMap(DoubleFeatureData, StringData,
"voltage_base", nSize);
if (retVal)
return nSize;

vector<double> v, t, stimStart, vRest;
double startTime, endTime;
retVal = getVec(DoubleFeatureData, StringData, "V", v);
if (retVal < 0) return -1;
retVal = getVec(DoubleFeatureData, StringData, "T", t);
if (retVal < 0) return -1;
retVal = getVec(DoubleFeatureData, StringData, "stim_start", stimStart);
if (retVal < 0) return -1;
startTime = stimStart[0] * .25; // It is 25% from start (0), so if stimulus
// starts at 100ms then StartTime will be
// 25mS
// as in above case end time will be 25% less than startTime
endTime = stimStart[0] * .75;
int nCount = 0;
double vSum = 0;
// calculte the mean of voltage between startTime and endTime
for (size_t i = 0; i < t.size(); i++) {
if (t[i] >= startTime) {
vSum = vSum + v[i];
nCount++;
}
if (t[i] > endTime) break;
}
vRest.push_back(vSum / nCount);
setVec(DoubleFeatureData, StringData, "voltage_base", vRest);
return 1;
}

static int __burst_ISI_indices(double BurstFactor, vector<int>& PeakIndex,
vector<double>& ISIValues,
vector<int>& BurstIndex) {
Expand Down Expand Up @@ -1220,88 +1039,6 @@ int LibV1::spike_width2(mapStr2intVec& IntFeatureData,
return retVal;
}

// spike half width
// for spike amplitude = v_peak - v_AHP
static int __spike_width1(const vector<double>& t, const vector<double>& v,
const vector<int>& peak_indices,
const vector<int>& min_ahp_indices, double stim_start,
vector<double>& spike_width1) {
int start_index = distance(
t.begin(), find_if(t.begin(), t.end(),
bind2nd(greater_equal<double>(), stim_start)));
vector<int> min_ahp_indices_plus(min_ahp_indices.size() + 1, start_index);
copy(min_ahp_indices.begin(), min_ahp_indices.end(),
min_ahp_indices_plus.begin() + 1);
for (size_t i = 1; i < min_ahp_indices_plus.size(); i++) {
double v_half = (v[peak_indices[i - 1]] + v[min_ahp_indices_plus[i]]) / 2.;
// interpolate this one time step where the voltage is close to v_half in
// the rising and in the falling edge
double v_dev;
double delta_v;
double t_dev_rise;
double t_dev_fall;
double delta_t;
int rise_index =
distance(v.begin(), find_if(v.begin() + min_ahp_indices_plus[i - 1],
v.begin() + peak_indices[i - 1],
bind2nd(greater_equal<double>(), v_half)));
v_dev = v_half - v[rise_index];
delta_v = v[rise_index] - v[rise_index - 1];
delta_t = t[rise_index] - t[rise_index - 1];
t_dev_rise = delta_t * v_dev / delta_v;
int fall_index =
distance(v.begin(), find_if(v.begin() + peak_indices[i - 1],
v.begin() + min_ahp_indices_plus[i],
bind2nd(less_equal<double>(), v_half)));
v_dev = v_half - v[fall_index];
delta_v = v[fall_index] - v[fall_index - 1];
delta_t = t[fall_index] - t[fall_index - 1];
t_dev_fall = delta_t * v_dev / delta_v;
spike_width1.push_back(t[fall_index] + t_dev_rise - t[rise_index] +
t_dev_fall);
}
return spike_width1.size();
}

int LibV1::spike_width1(mapStr2intVec& IntFeatureData,
mapStr2doubleVec& DoubleFeatureData,
mapStr2Str& StringData) {
int retVal, nSize;
retVal = CheckInMap(DoubleFeatureData, StringData,
"spike_half_width", nSize);
if (retVal)
return nSize;

vector<int> PeakIndex, minAHPIndex;
vector<double> V, t, dv1, dv2, spike_width1;
vector<double> stim_start;
retVal = getVec(DoubleFeatureData, StringData, "V", V);
if (retVal < 0) return -1;
retVal = getVec(DoubleFeatureData, StringData, "T", t);
if (retVal < 0) return -1;
retVal = getVec(DoubleFeatureData, StringData, "stim_start", stim_start);
if (retVal < 0) return -1;
retVal = getVec(IntFeatureData, StringData, "min_AHP_indices", minAHPIndex);
if (retVal < 0) return -1;
retVal = getVec(IntFeatureData, StringData, "peak_indices", PeakIndex);
if (retVal < 0) return -1;
if (PeakIndex.size() <= 1) {
GErrorStr += "\nError: More than one spike is needed for spikewidth "
"calculation.\n";
return -1;
}
//
// Take derivative of voltage from 1st AHPmin to the peak of the spike
// Using Central difference derivative vec1[i] = ((vec[i+1]+vec[i-1])/2)/dx
retVal = __spike_width1(t, V, PeakIndex, minAHPIndex, stim_start[0],
spike_width1);
if (retVal >= 0) {
setVec(DoubleFeatureData, StringData, "spike_half_width",
spike_width1);
}
return retVal;
}

// passive properties implementation
//
// *** timeconstant ***
Expand Down
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