Add SEClamp to LFP calculation (#2360)

* Add SEClamp to LFP calculation in coreneuron * Create function to avoid code repetition
neuronsimulator · May 17, 2023 · c685dfc · c685dfc
1 parent d8e07da
commit c685dfc
Showing 1 changed file with 21 additions and 12 deletions.
diff --git a/src/coreneuron/io/reports/report_handler.cpp b/src/coreneuron/io/reports/report_handler.cpp
@@ -353,6 +353,24 @@ VarsToReport ReportHandler::get_synapse_vars_to_report(
     return vars_to_report;
 }
 
+void add_clamp_current(const char* clamp,
+                       const NrnThread& nt,
+                       std::unordered_map<size_t, std::vector<std::pair<double*, int>>>& currents,
+                       int gid,
+                       const std::vector<int>& nodes_to_gids) {
+    auto mech_id = nrn_get_mechtype(clamp);
+    Memb_list* ml = nt._ml_list[mech_id];
+    if (ml) {
+        for (int i = 0; i < ml->nodecount; i++) {
+            auto segment_id = ml->nodeindices[i];
+            if ((nodes_to_gids[segment_id] == gid)) {
+                double* var_value = get_var_location_from_var_name(mech_id, "i", ml, i);
+                currents[segment_id].push_back(std::make_pair(var_value, -1));
+            }
+        }
+    }
+}
+
 VarsToReport ReportHandler::get_lfp_vars_to_report(const NrnThread& nt,
                                                    const std::vector<int>& gids_to_report,
                                                    ReportConfiguration& report,
@@ -368,18 +386,9 @@ VarsToReport ReportHandler::get_lfp_vars_to_report(const NrnThread& nt,
     VarsToReport vars_to_report;
     off_t offset_lfp = 0;
     for (const auto& gid: gids_to_report) {
-        // IClamp is needed for the LFP calculation
-        auto mech_id = nrn_get_mechtype("IClamp");
-        Memb_list* ml = nt._ml_list[mech_id];
-        if (ml) {
-            for (int j = 0; j < ml->nodecount; j++) {
-                auto segment_id = ml->nodeindices[j];
-                if ((nodes_to_gids[segment_id] == gid)) {
-                    double* var_value = get_var_location_from_var_name(mech_id, "i", ml, j);
-                    summation_report.currents_[segment_id].push_back(std::make_pair(var_value, -1));
-                }
-            }
-        }
+        // IClamp & SEClamp are needed for the LFP calculation
+        add_clamp_current("IClamp", nt, summation_report.currents_, gid, nodes_to_gids);
+        add_clamp_current("SEClamp", nt, summation_report.currents_, gid, nodes_to_gids);
         const auto& cell_mapping = mapinfo->get_cell_mapping(gid);
         if (cell_mapping == nullptr) {
             std::cerr << "[LFP] Error : Compartment mapping information is missing for gid " << gid