Merge branch 'master' into be_quiet

Author: alexsavulescu

coreneuron/apps/main1.cpp

@@ -465,6 +465,7 @@ extern "C" int run_solve_core(int argc, char** argv) {
 
     std::vector<ReportConfiguration> configs;
     std::vector<std::unique_ptr<ReportHandler> > report_handlers;
+    std::string spikes_population_name;
     bool reports_needs_finalize = false;
 
     if (!corenrn_param.is_quiet()) {
@@ -482,7 +483,8 @@ extern "C" int run_solve_core(int argc, char** argv) {
                 printf("\n WARNING! : Can't enable reports with model duplications feature! \n");
         } else {
             configs = create_report_configurations(corenrn_param.reportfilepath.c_str(),
-                                                   corenrn_param.outpath.c_str());
+                                                   corenrn_param.outpath.c_str(),
+                                                   spikes_population_name);
             reports_needs_finalize = configs.size();
         }
     }
@@ -596,7 +598,7 @@ extern "C" int run_solve_core(int argc, char** argv) {
     // write spike information to outpath
     {
         Instrumentor::phase p("output-spike");
-        output_spikes(output_dir.c_str());
+        output_spikes(output_dir.c_str(), spikes_population_name);
     }
 
     {

coreneuron/io/output_spikes.cpp

@@ -155,7 +155,7 @@ void sort_spikes(std::vector<double>& spikevec_time, std::vector<int>& spikevec_
  *  \todo : MPI related code should be factored into nrnmpi.c
  *          Check spike record length which is set to 64 chars
  */
-void output_spikes_parallel(const char* outpath) {
+void output_spikes_parallel(const char* outpath, const std::string& population_name) {
     std::stringstream ss;
     ss << outpath << "/out.dat";
     std::string fname = ss.str();
@@ -165,9 +165,7 @@ void output_spikes_parallel(const char* outpath) {
         remove(fname.c_str());
     }
 #ifdef ENABLE_SONATA_REPORTS
-    // TODO: Move population_name as input parameter
-    const char* population_name = "All";
-    sonata_write_spikes(population_name, spikevec_time.data(), spikevec_time.size(), spikevec_gid.data(),
+    sonata_write_spikes(population_name.data(), spikevec_time.data(), spikevec_time.size(), spikevec_gid.data(),
                         spikevec_gid.size(), outpath);
 #endif  // ENABLE_SONATA_REPORTS
     sort_spikes(spikevec_time, spikevec_gid);
@@ -253,10 +251,10 @@ void output_spikes_serial(const char* outpath) {
     fclose(f);
 }
 
-void output_spikes(const char* outpath) {
+void output_spikes(const char* outpath, const std::string& population_name) {
 #if NRNMPI
     if (nrnmpi_initialized()) {
-        output_spikes_parallel(outpath);
+        output_spikes_parallel(outpath, population_name);
     } else {
         output_spikes_serial(outpath);
     }

coreneuron/io/output_spikes.hpp

@@ -32,7 +32,7 @@ THE POSSIBILITY OF SUCH DAMAGE.
 #include <vector>
 #include <utility>
 namespace coreneuron {
-void output_spikes(const char* outpath);
+void output_spikes(const char* outpath, const std::string& population_name);
 void mk_spikevec_buffer(int);
 
 extern std::vector<double> spikevec_time;

coreneuron/io/reports/nrnreport.hpp

@@ -62,6 +62,7 @@ struct ReportConfiguration {
     char unit[REPORT_MAX_NAME_LEN];         // unit of the report
     char format[REPORT_MAX_NAME_LEN];       // format of the report (Bin, hdf5, SONATA)
     char type_str[REPORT_MAX_NAME_LEN];     // type of report string
+    char population_name[REPORT_MAX_NAME_LEN];  // population name of the report
     ReportType type;                        // type of the report
     int mech_id;                            // mechanism
     double report_dt;                       // reporting timestep
@@ -74,7 +75,8 @@ struct ReportConfiguration {
 
 void setup_report_engine(double dt_report, double mindelay);
 std::vector<ReportConfiguration> create_report_configurations(const char* filename,
-                                                              const char* output_dir);
+                                                              const char* output_dir,
+                                                              std::string& spikes_population_name);
 void finalize_report();
 void nrn_flush_reports(double t);
 void set_report_buffer_size(int n);

coreneuron/io/reports/report_configuration_parser.cpp

@@ -58,11 +58,13 @@ void parse_filter_string(char* filter, ReportConfiguration& config) {
 }
 
 std::vector<ReportConfiguration> create_report_configurations(const char* conf_file,
-                                                              const char* output_dir) {
+                                                              const char* output_dir,
+                                                              std::string& spikes_population_name) {
     std::vector<ReportConfiguration> reports;
     int num_reports = 0;
     char report_on[REPORT_MAX_NAME_LEN] = "";
     char raw_line[REPORT_MAX_FILEPATH_LEN] = "";
+    char spikes_population[REPORT_MAX_NAME_LEN] = "";
     int is_soma;
     int* gids;
 
@@ -82,10 +84,10 @@ std::vector<ReportConfiguration> create_report_configurations(const char* conf_f
         report.mech_id = -1;
         report.buffer_size = 4;  // default size to 4 Mb
         fgets(raw_line, REPORT_MAX_FILEPATH_LEN, fp);
-        sscanf(raw_line, "\n%s %s %s %s %s %s %d %lf %lf %lf %d %d\n", report.name,
+        sscanf(raw_line, "\n%s %s %s %s %s %s %d %lf %lf %lf %d %d %s\n", report.name,
                report.target_name, report.type_str, report_on, report.unit, report.format, &is_soma,
                &report.report_dt, &report.start, &report.stop, &report.num_gids,
-               &report.buffer_size);
+               &report.buffer_size, report.population_name);
         for (int i = 0; i < REPORT_MAX_NAME_LEN; i++) {
             report.type_str[i] = tolower(report.type_str[i]);
         }
@@ -119,6 +121,9 @@ std::vector<ReportConfiguration> create_report_configurations(const char* conf_f
             free(gids);
         }
     }
+    fgets(raw_line, REPORT_MAX_NAME_LEN, fp);
+    sscanf(raw_line, "%s\n", spikes_population);
+    spikes_population_name = spikes_population;
     fclose(fp);
     return reports;
 }

coreneuron/io/reports/report_event.hpp

@@ -10,7 +10,7 @@
 
 namespace coreneuron {
 
-#if defined(ENABLE_REPORTINGLIB) || defined(ENABLE_SONATA_REPORTS)
+#if defined(ENABLE_BIN_REPORTS) || defined(ENABLE_SONATA_REPORTS)
 struct VarWithMapping {
     int id;
     double* var_value;
@@ -36,6 +36,6 @@ class ReportEvent : public DiscreteEvent {
     std::vector<int> gids_to_report;
     double tstart;
 };
-#endif  // defined(ENABLE_REPORTINGLIB) || defined(ENABLE_SONATA_REPORTS)
+#endif  // defined(ENABLE_BIN_REPORTS) || defined(ENABLE_SONATA_REPORTS)
 
 }  // Namespace coreneuron

coreneuron/io/reports/sonata_report_handler.cpp

@@ -42,17 +42,16 @@ void SonataReportHandler::register_report(const NrnThread& nt,
                          config.type_str);
     sonata_set_report_max_buffer_size_hint(config.output_path, config.buffer_size);
 
-    const char* population_name = "All";
     for (const auto& kv : vars_to_report) {
         int gid = kv.first;
         const std::vector<VarWithMapping>& vars = kv.second;
         if (!vars.size())
             continue;
 
-        sonata_add_node(config.output_path, population_name, gid);
+        sonata_add_node(config.output_path, config.population_name, gid);
         sonata_set_report_max_buffer_size_hint(config.output_path, config.buffer_size);
         for (const auto& variable : vars) {
-            sonata_add_element(config.output_path, population_name, gid, variable.id, variable.var_value);
+            sonata_add_element(config.output_path, config.population_name, gid, variable.id, variable.var_value);
         }
     }
 }

coreneuron/sim/fadvance_core.cpp

@@ -81,7 +81,7 @@ void nrn_fixed_step_minimal() { /* not so minimal anymore with gap junctions */
     }
 #endif
 
-#ifdef ENABLE_REPORTING
+#if defined(ENABLE_BIN_REPORTS) || defined(ENABLE_SONATA_REPORTS)
     nrn_flush_reports(nrn_threads[0]._t);
 #endif
     t = nrn_threads[0]._t;