AP_phaseslope_range (#400)

* add AP_phaseslope_range to efel settings with a default value of 2

* add AP_phaseslope default value in documentation

* fix tests

* added change to changelog

* let range be an int

---------

Co-authored-by: Jaquier Aurélien Tristan <aurelien.jaquier@epfl.ch>

CHANGELOG.rst

@@ -5,10 +5,15 @@ All notable changes to this project will be documented in this file.
 The format is based on `Keep a Changelog <https://keepachangelog.com/en/1.0.0/>`_,
 and this project adheres to `Semantic Versioning <https://semver.org/spec/v2.0.0.html>`_.
 
+5.6.29 - 2024-06
+----------------
+
+- Added AP_phaseslope_range to efel.settings as int with default value of 2
+
 5.6.27 - 2024-05
 ----------------
 
-- FIxed edge case (1 spike and no min_AHP_indices dependency) in AP_begin_indices
+- Fixed edge case (1 spike and no min_AHP_indices dependency) in AP_begin_indices
 
 5.6.20 - 2024-05
 ----------------

docs/source/eFeatures.rst

@@ -1549,7 +1549,7 @@ AP_phaseslope
 (at the point where the derivative crosses the DerivativeThreshold)
 
 - **Required features**: AP_begin_indices
-- **Parameters**: AP_phaseslope_range
+- **Parameters**: AP_phaseslope_range (default=2)
 - **Units**: 1/(ms)
 - **Pseudocode**: ::
 

efel/cppcore/SpikeShape.cpp

@@ -2279,7 +2279,7 @@ int SpikeShape::AP_fall_rate_change(mapStr2intVec& IntFeatureData,
 static int __AP_phaseslope(const vector<double>& v, const vector<double>& t,
                            double stimStart, double stimEnd,
                            vector<double>& ap_phaseslopes, vector<int> apbi,
-                           double range) {
+                           int range) {
   vector<double> dvdt(v.size());
   vector<double> dv;
   vector<double> dt;
@@ -2292,8 +2292,8 @@ static int __AP_phaseslope(const vector<double>& v, const vector<double>& t,
 
   for (size_t i = 0; i < apbi.size(); i++) {
     apbegin_index = apbi[i];
-    range_min_index = apbegin_index - int(range);
-    range_max_index = apbegin_index + int(range);
+    range_min_index = apbegin_index - range;
+    range_max_index = apbegin_index + range;
     if (range_min_index < 0 || range_max_index < 0) return -1;
     if (range_min_index > (int)t.size() || range_max_index > (int)t.size())
       return -1;
@@ -2316,14 +2316,16 @@ int SpikeShape::AP_phaseslope(mapStr2intVec& IntFeatureData,
                          mapStr2Str& StringData) {
   const auto& doubleFeatures =
       getFeatures(DoubleFeatureData,
-                  {"V", "T", "stim_start", "stim_end", "AP_phaseslope_range"});
-  const auto& intFeatures = getFeatures(IntFeatureData, {"AP_begin_indices"});
+                  {"V", "T", "stim_start", "stim_end"});
+  const auto& intFeatures = 
+      getFeatures(IntFeatureData,
+                  {"AP_begin_indices", "AP_phaseslope_range"});
   vector<double> ap_phaseslopes;
   int retVal = __AP_phaseslope(doubleFeatures.at("V"), doubleFeatures.at("T"),
                                doubleFeatures.at("stim_start")[0],
                                doubleFeatures.at("stim_end")[0], ap_phaseslopes,
                                intFeatures.at("AP_begin_indices"),
-                               doubleFeatures.at("AP_phaseslope_range")[0]);
+                               intFeatures.at("AP_phaseslope_range")[0]);
 
   if (retVal > 0) {
     setVec(DoubleFeatureData, StringData, "AP_phaseslope", ap_phaseslopes);

efel/settings.py

@@ -98,6 +98,7 @@ class Settings:
     sahp_start: float = 5.0
     ignore_first_ISI: bool = True
     impedance_max_freq: float = 50.0
+    AP_phaseslope_range: int = 2
 
     def set_setting(self,
                     setting_name: str,

tests/test_settings.py

@@ -161,6 +161,7 @@ def test_str_method():
         "precision_threshold: 1e-10\n"
         "sahp_start: 5.0\n"
         "ignore_first_ISI: True\n"
-        "impedance_max_freq: 50.0"
+        "impedance_max_freq: 50.0\n"
+        "AP_phaseslope_range: 2"
     )
     assert str(settings) == expected_output

tests/testdata/allfeatures/expectedresults.json

@@ -280,7 +280,14 @@
         40.51507371451861,
         40.98143755958056
     ],
-    "AP_phaseslope": null,
+    "AP_phaseslope": [
+        8.368063428797635,
+        8.205484762938424,
+        5.729511888356036,
+        5.224282360605566,
+        3.887601463053442,
+        4.872345425348057
+    ],
     "AP_rise_indices": [
         7074,
         9104,