Absolute/RelativeShotNoise input: replace amp_cv with relative_skew (#…

…361)

include/bbp/sonata/config.h

@@ -549,8 +549,6 @@ class SONATA_API SimulationConfig
         double reversal{};
         /// Timestep of generated signal in ms. Default is 0.25 ms
         double dt{};
-        /// The coefficient of variation (sd/mean) of gamma-distributed amplitudes
-        double ampCv{};
         /// Signal mean as percentage of a cell’s threshold current (current_clamp) or inverse input
         /// resistance (conductance)
         double meanPercent{};
@@ -559,6 +557,10 @@ class SONATA_API SimulationConfig
         double sdPercent{};
         /// Whether this input represents a physical electrode. Default is false
         bool representsPhysicalElectrode = false;
+        /// Signal skewness as a fraction in [0, 1] representing a value between the minimum and
+        /// maximum skewness values compatible with the given signal mean and std dev. Default is
+        /// 0.5.
+        double relativeSkew{};
     };
 
     struct InputAbsoluteShotNoise: public InputBase {
@@ -572,14 +574,16 @@ class SONATA_API SimulationConfig
         double reversal{};
         /// Timestep of generated signal in ms. Default is 0.25 ms
         double dt{};
-        /// The coefficient of variation (sd/mean) of gamma-distributed amplitudes
-        double ampCv{};
         /// Signal mean in nA (current_clamp) or uS (conductance).
         double mean{};
         /// signal std dev in nA (current_clamp) or uS (conductance).
         double sigma{};
         /// Whether this input represents a physical electrode. Default is false
         bool representsPhysicalElectrode = false;
+        /// Signal skewness as a fraction in [0, 1] representing a value between the minimum and
+        /// maximum skewness values compatible with the given signal mean and std dev. Default is
+        /// 0.5.
+        double relativeSkew{};
     };
 
     struct InputOrnsteinUhlenbeck: public InputBase {

python/bindings.cpp

@@ -695,15 +695,20 @@ PYBIND11_MODULE(_libsonata, m) {
         .def_readonly("mechanisms",
                       &SimulationConfig::Conditions::mechanisms,
                       DOC_SIMULATIONCONFIG(Conditions, mechanisms))
-        .def("modifications", &SimulationConfig::Conditions::getModifications);
+        .def("modifications",
+             &SimulationConfig::Conditions::getModifications,
+             DOC_SIMULATIONCONFIG(Conditions, getModifications));
 
 
     py::enum_<SimulationConfig::Conditions::SpikeLocation>(conditions, "SpikeLocation")
         .value("soma", SimulationConfig::Conditions::SpikeLocation::soma)
         .value("AIS", SimulationConfig::Conditions::SpikeLocation::AIS);
 
     py::class_<SimulationConfig::ModificationBase> modificationBase(simConf, "ModificationBase");
-    modificationBase.def_readonly("name", &SimulationConfig::ModificationBase::name)
+    modificationBase
+        .def_readonly("name",
+                      &SimulationConfig::ModificationBase::name,
+                      DOC_SIMULATIONCONFIG(ModificationBase, name))
         .def_readonly("node_set",
                       &SimulationConfig::ModificationBase::nodeSet,
                       DOC_SIMULATIONCONFIG(ModificationBase, nodeSet))
@@ -937,9 +942,6 @@ PYBIND11_MODULE(_libsonata, m) {
         .def_readonly("dt",
                       &SimulationConfig::InputRelativeShotNoise::dt,
                       DOC_SIMULATIONCONFIG(InputRelativeShotNoise, dt))
-        .def_readonly("amp_cv",
-                      &SimulationConfig::InputRelativeShotNoise::ampCv,
-                      DOC_SIMULATIONCONFIG(InputRelativeShotNoise, ampCv))
         .def_readonly("sd_percent",
                       &SimulationConfig::InputRelativeShotNoise::sdPercent,
                       DOC_SIMULATIONCONFIG(InputRelativeShotNoise, sdPercent))
@@ -948,7 +950,10 @@ PYBIND11_MODULE(_libsonata, m) {
                       DOC_SIMULATIONCONFIG(InputRelativeShotNoise, meanPercent))
         .def_readonly("represents_physical_electrode",
                       &SimulationConfig::InputRelativeShotNoise::representsPhysicalElectrode,
-                      DOC_SIMULATIONCONFIG(InputRelativeShotNoise, representsPhysicalElectrode));
+                      DOC_SIMULATIONCONFIG(InputRelativeShotNoise, representsPhysicalElectrode))
+        .def_readonly("relative_skew",
+                      &SimulationConfig::InputRelativeShotNoise::relativeSkew,
+                      DOC_SIMULATIONCONFIG(InputRelativeShotNoise, relativeSkew));
 
     py::class_<SimulationConfig::InputAbsoluteShotNoise, SimulationConfig::InputBase>(
         simConf, "AbsoluteShotNoise")
@@ -967,9 +972,6 @@ PYBIND11_MODULE(_libsonata, m) {
         .def_readonly("dt",
                       &SimulationConfig::InputAbsoluteShotNoise::dt,
                       DOC_SIMULATIONCONFIG(InputAbsoluteShotNoise, dt))
-        .def_readonly("amp_cv",
-                      &SimulationConfig::InputAbsoluteShotNoise::ampCv,
-                      DOC_SIMULATIONCONFIG(InputAbsoluteShotNoise, ampCv))
         .def_readonly("mean",
                       &SimulationConfig::InputAbsoluteShotNoise::mean,
                       DOC_SIMULATIONCONFIG(InputAbsoluteShotNoise, mean))
@@ -978,7 +980,11 @@ PYBIND11_MODULE(_libsonata, m) {
                       DOC_SIMULATIONCONFIG(InputAbsoluteShotNoise, sigma))
         .def_readonly("represents_physical_electrode",
                       &SimulationConfig::InputAbsoluteShotNoise::representsPhysicalElectrode,
-                      DOC_SIMULATIONCONFIG(InputAbsoluteShotNoise, representsPhysicalElectrode));
+                      DOC_SIMULATIONCONFIG(InputAbsoluteShotNoise, representsPhysicalElectrode))
+        .def_readonly("relative_skew",
+                      &SimulationConfig::InputAbsoluteShotNoise::relativeSkew,
+                      DOC_SIMULATIONCONFIG(InputAbsoluteShotNoise, relativeSkew));
+    ;
 
     py::class_<SimulationConfig::InputOrnsteinUhlenbeck, SimulationConfig::InputBase>(
         simConf, "OrnsteinUhlenbeck")

python/generated/docstrings.h

@@ -778,8 +778,6 @@ static const char *__doc_bbp_sonata_SimulationConfig_ConnectionOverride_weight =
 
 static const char *__doc_bbp_sonata_SimulationConfig_InputAbsoluteShotNoise = R"doc()doc";
 
-static const char *__doc_bbp_sonata_SimulationConfig_InputAbsoluteShotNoise_ampCv = R"doc(The coefficient of variation (sd/mean) of gamma-distributed amplitudes)doc";
-
 static const char *__doc_bbp_sonata_SimulationConfig_InputAbsoluteShotNoise_decayTime = R"doc(The decay time of the bi-exponential shots (ms))doc";
 
 static const char *__doc_bbp_sonata_SimulationConfig_InputAbsoluteShotNoise_dt = R"doc(Timestep of generated signal in ms. Default is 0.25 ms)doc";
@@ -790,6 +788,11 @@ static const char *__doc_bbp_sonata_SimulationConfig_InputAbsoluteShotNoise_rand
 R"doc(Override the random seed to introduce correlations between cells,
 default = None)doc";
 
+static const char *__doc_bbp_sonata_SimulationConfig_InputAbsoluteShotNoise_relativeSkew =
+R"doc(Signal skewness as a fraction in [0, 1] representing a value between
+the minimum and maximum skewness values compatible with the given
+signal mean and std dev. Default is 0.5.)doc";
+
 static const char *__doc_bbp_sonata_SimulationConfig_InputAbsoluteShotNoise_representsPhysicalElectrode = R"doc(Whether this input represents a physical electrode. Default is false)doc";
 
 static const char *__doc_bbp_sonata_SimulationConfig_InputAbsoluteShotNoise_reversal = R"doc(Reversal potential for conductance injection in mV. Default is 0)doc";
@@ -940,8 +943,6 @@ static const char *__doc_bbp_sonata_SimulationConfig_InputRelativeOrnsteinUhlenb
 
 static const char *__doc_bbp_sonata_SimulationConfig_InputRelativeShotNoise = R"doc()doc";
 
-static const char *__doc_bbp_sonata_SimulationConfig_InputRelativeShotNoise_ampCv = R"doc(The coefficient of variation (sd/mean) of gamma-distributed amplitudes)doc";
-
 static const char *__doc_bbp_sonata_SimulationConfig_InputRelativeShotNoise_decayTime = R"doc(The decay time of the bi-exponential shots (ms))doc";
 
 static const char *__doc_bbp_sonata_SimulationConfig_InputRelativeShotNoise_dt = R"doc(Timestep of generated signal in ms. Default is 0.25 ms)doc";
@@ -954,6 +955,11 @@ static const char *__doc_bbp_sonata_SimulationConfig_InputRelativeShotNoise_rand
 R"doc(Override the random seed to introduce correlations between cells,
 default = None)doc";
 
+static const char *__doc_bbp_sonata_SimulationConfig_InputRelativeShotNoise_relativeSkew =
+R"doc(Signal skewness as a fraction in [0, 1] representing a value between
+the minimum and maximum skewness values compatible with the given
+signal mean and std dev. Default is 0.5.)doc";
+
 static const char *__doc_bbp_sonata_SimulationConfig_InputRelativeShotNoise_representsPhysicalElectrode = R"doc(Whether this input represents a physical electrode. Default is false)doc";
 
 static const char *__doc_bbp_sonata_SimulationConfig_InputRelativeShotNoise_reversal = R"doc(Reversal potential for conductance injection in mV. Default is 0)doc";

python/tests/test_config.py

@@ -547,6 +547,7 @@ def test_basic(self):
         self.assertEqual(self.config.input('ex_rel_shotnoise').random_seed, 230522)
         self.assertEqual(self.config.input('ex_rel_shotnoise').dt, 0.25)
         self.assertEqual(self.config.input('ex_rel_shotnoise').reversal, 0)
+        self.assertEqual(self.config.input('ex_rel_shotnoise').relative_skew, 0.5)
 
         self.assertEqual(self.config.input('ex_replay').input_type.name, 'spikes')
         self.assertEqual(self.config.input('ex_replay').module.name, 'synapse_replay')
@@ -558,12 +559,12 @@ def test_basic(self):
         self.assertEqual(self.config.input('ex_extracellular_stimulation').node_set, 'Column')
 
         self.assertEqual(self.config.input('ex_abs_shotnoise').input_type.name, "conductance")
-        self.assertEqual(self.config.input('ex_abs_shotnoise').amp_cv, 0.63)
         self.assertEqual(self.config.input('ex_abs_shotnoise').mean, 50)
         self.assertEqual(self.config.input('ex_abs_shotnoise').sigma, 5)
         self.assertEqual(self.config.input('ex_abs_shotnoise').reversal, 10)
         self.assertEqual(self.config.input('ex_abs_shotnoise').random_seed, None)
         self.assertEqual(self.config.input('ex_abs_shotnoise').represents_physical_electrode, True)
+        self.assertEqual(self.config.input('ex_abs_shotnoise').relative_skew, 0.1)
 
         self.assertEqual(self.config.input('ex_OU').module.name, "ornstein_uhlenbeck")
         self.assertEqual(self.config.input('ex_OU').input_type.name, "conductance")

src/config.cpp

@@ -506,9 +506,9 @@ SimulationConfig::Input parseInputModule(const nlohmann::json& valueIt,
                       "represents_physical_electrode",
                       ret.representsPhysicalElectrode,
                       {false});
-        parseMandatory(valueIt, "amp_cv", debugStr, ret.ampCv);
         parseMandatory(valueIt, "mean_percent", debugStr, ret.meanPercent);
         parseMandatory(valueIt, "sd_percent", debugStr, ret.sdPercent);
+        parseOptional(valueIt, "relative_skew", ret.relativeSkew, {0.5});
         return ret;
     }
     case Module::absolute_shot_noise: {
@@ -524,9 +524,9 @@ SimulationConfig::Input parseInputModule(const nlohmann::json& valueIt,
                       "represents_physical_electrode",
                       ret.representsPhysicalElectrode,
                       {false});
-        parseMandatory(valueIt, "amp_cv", debugStr, ret.ampCv);
         parseMandatory(valueIt, "mean", debugStr, ret.mean);
         parseMandatory(valueIt, "sigma", debugStr, ret.sigma);
+        parseOptional(valueIt, "relative_skew", ret.relativeSkew, {0.5});
         return ret;
     }
     case Module::hyperpolarizing: {

tests/data/config/simulation_config.json

@@ -153,7 +153,6 @@
             "duration": 1000,
             "decay_time": 4,
             "rise_time": 0.4,
-            "amp_cv": 0.63,
             "mean_percent": 70,
             "sd_percent": 40,
             "node_set": "L5E",
@@ -167,7 +166,7 @@
             "decay_time": 4,
             "reversal": 10,
             "rise_time": 0.4,
-            "amp_cv": 0.63,
+            "relative_skew": 0.1,
             "mean": 50,
             "sigma": 5,
             "represents_physical_electrode": true,

tests/test_config.cpp

@@ -482,13 +482,13 @@ TEST_CASE("SimulationConfig") {
             CHECK(input.delay == 0);
             CHECK(input.duration == 1000);
             CHECK(input.nodeSet == "L5E");
-            CHECK(input.ampCv == 0.63);
             CHECK(input.meanPercent == 70);
             CHECK(input.sdPercent == 40);
             CHECK(input.randomSeed == 230522);
             CHECK(input.riseTime == 0.4);
             CHECK(input.decayTime == 4);
             CHECK(input.reversal == 0);
+            CHECK(input.relativeSkew == 0.5);
         }
         {
             const auto input = nonstd::get<SimulationConfig::InputHyperpolarizing>(config.getInput("ex_hyperpolarizing"));
@@ -522,12 +522,12 @@ TEST_CASE("SimulationConfig") {
                 config.getInput("ex_abs_shotnoise"));
             CHECK(input.inputType == InputType::conductance);
             CHECK(input.module == Module::absolute_shot_noise);
-            CHECK(input.ampCv == 0.63);
             CHECK(input.mean == 50);
             CHECK(input.sigma == 5);
             CHECK(input.reversal == 10);
             CHECK(input.randomSeed == nonstd::nullopt);
             CHECK(input.representsPhysicalElectrode == true);
+            CHECK(input.relativeSkew == 0.1);
         }
         {
             const auto input = nonstd::get<SimulationConfig::InputOrnsteinUhlenbeck>(