Read lfp factors from neurodamus

Author: jorblancoa

coreneuron/io/nrn_filehandler.hpp

@@ -14,6 +14,7 @@
 #include <sys/stat.h>
 
 #include "coreneuron/utils/nrn_assert.h"
+#include "coreneuron/io/nrnsection_mapping.hpp"
 
 namespace coreneuron {
 /** Encapsulate low-level reading of coreneuron input data files.
@@ -110,7 +111,7 @@ class FileHandler {
      * Read count no of mappings for section to segment
      */
     template <typename T>
-    int read_mapping_info(T* mapinfo) {
+    int read_mapping_info(T* mapinfo, NrnThreadMappingInfo* ntmapping) {
         int nsec, nseg, n_scan;
         char line_buf[max_line_length], name[max_line_length];
 
@@ -123,14 +124,19 @@ class FileHandler {
 
         if (nseg) {
             std::vector<int> sec, seg;
+            std::vector<double> lfp_factors;
             sec.reserve(nseg);
             seg.reserve(nseg);
+            lfp_factors.reserve(nseg);
 
             read_array<int>(&sec[0], nseg);
             read_array<int>(&seg[0], nseg);
+            read_array<double>(&lfp_factors[0], nseg);
 
             for (int i = 0; i < nseg; i++) {
                 mapinfo->add_segment(sec[i], seg[i]);
+                ntmapping->add_segment_id(seg[i]);
+                ntmapping->add_segment_lfp_factor(seg[i], lfp_factors[i]);
             }
         }
         return nseg;

coreneuron/io/nrn_setup.cpp

@@ -947,7 +947,7 @@ void read_phase3(NrnThread& nt, UserParams& userParams) {
         // read section-segment mapping for every section list
         for (int j = 0; j < nseclist; j++) {
             SecMapping* smap = new SecMapping();
-            F.read_mapping_info(smap);
+            F.read_mapping_info(smap, ntmapping);
             cmap->add_sec_map(smap);
         }
 

coreneuron/io/nrnsection_mapping.hpp

@@ -14,6 +14,7 @@
 #include <vector>
 #include <map>
 #include <iostream>
+#include <unordered_map>
 
 namespace coreneuron {
 
@@ -153,6 +154,12 @@ struct NrnThreadMappingInfo {
     /** list of cells mapping */
     std::vector<CellMapping*> mappingvec;
 
+    /** list of segment ids */
+    std::vector<int> segment_ids;
+
+    /** map containing segment ids an its respective lfp factors */
+    std::unordered_map<int, double> lfp_factors;
+
     /** @brief number of cells */
     size_t size() const {
         return mappingvec.size();
@@ -181,5 +188,15 @@ struct NrnThreadMappingInfo {
     void add_cell_mapping(CellMapping* c) {
         mappingvec.push_back(c);
     }
+
+    /** @brief add a new segment */
+    void add_segment_id(const int segment_id) {
+        segment_ids.push_back(segment_id);
+    }
+
+    /** @brief add the lfp factor of a segment_id */
+    void add_segment_lfp_factor(const int segment_id, double factor) {
+        lfp_factors.insert({segment_id, factor});
+    }
 };
 }  // namespace coreneuron