Patternstip fix : allow restore phases to provide new pattern-stim

Author: pramodk

coreneuron/mech/modfile/pattern.mod

@@ -116,6 +116,7 @@ void pattern_stim_setup_helper(int size, double* tv, int* gv, _threadargsproto_)
 	info->size = size;
 	info->tvec = tv;
 	info->gidvec = gv;
+	artcell_net_send ( _tqitem, -1, (Point_process*) _nt->_vdata[_ppvar[1*_STRIDE]], t +  0.0 , 1.0 ) ;
 }
 } // namespace coreneuron
 ENDVERBATIM

coreneuron/nrniv/main1.cpp

@@ -264,7 +264,7 @@ void nrn_init_and_load_data(int argc,
 
     // Invoke PatternStim
     if (nrnopt_get_flag("--pattern")) {
-        nrn_mkPatternStim(nrnopt_get_str("--pattern").c_str());
+        nrn_mkPatternStim(nrnopt_get_str("--pattern").c_str(), nrnopt_get_dbl("--tstop"));
     }
 
     /// Setting the timeout

coreneuron/nrniv/nrniv_decl.h

@@ -59,7 +59,7 @@ extern int nrn_setup_multiple;
 extern int nrn_setup_extracon;
 extern void nrn_cleanup(bool clean_ion_global_map = true);
 extern void BBS_netpar_solve(double);
-extern void nrn_mkPatternStim(const char* filename);
+extern void nrn_mkPatternStim(const char* filename, double tstop);
 extern int nrn_extra_thread0_vdata;
 extern void nrn_set_extra_thread0_vdata(void);
 extern Point_process* nrn_artcell_instantiate(const char* mechname);

coreneuron/nrniv/patternstim.cpp

@@ -57,7 +57,7 @@ extern void pattern_stim_setup_helper(int size,
                                       NrnThread* _nt,
                                       double v);
 
-static size_t read_raster_file(const char* fname, double** tvec, int** gidvec);
+static size_t read_raster_file(const char* fname, double** tvec, int** gidvec, double tstop);
 
 int nrn_extra_thread0_vdata;
 
@@ -76,7 +76,7 @@ void nrn_set_extra_thread0_vdata() {
 
 // fname is the filename of an output_spikes.h format raster file.
 // todo : add function for memory cleanup (to be called at the end of simulation)
-void nrn_mkPatternStim(const char* fname) {
+void nrn_mkPatternStim(const char* fname, double tstop) {
     int type = nrn_get_mechtype("PatternStim");
     if (!memb_func[type].sym) {
         printf("nrn_set_extra_thread_vdata must be called (after mk_mech, and before nrn_setup\n");
@@ -92,7 +92,7 @@ void nrn_mkPatternStim(const char* fname) {
     int* gidvec;
 
     // todo : handle when spike raster will be very large (int < size_t)
-    size_t size = read_raster_file(fname, &tvec, &gidvec);
+    size_t size = read_raster_file(fname, &tvec, &gidvec, tstop);
 
     Point_process* pnt = nrn_artcell_instantiate("PatternStim");
     NrnThread* nt = nrn_threads + pnt->_tid;
@@ -122,7 +122,8 @@ static bool spike_comparator(const spike_type& l, const spike_type& r) {
     return l.first < r.first;
 }
 
-size_t read_raster_file(const char* fname, double** tvec, int** gidvec) {
+
+size_t read_raster_file(const char* fname, double** tvec, int** gidvec, double tstop) {
     FILE* f = fopen(fname, "r");
     nrn_assert(f);
 
@@ -137,7 +138,9 @@ size_t read_raster_file(const char* fname, double** tvec, int** gidvec) {
     int gid;
 
     while (fscanf(f, "%lf %d\n", &stime, &gid) == 2) {
-        spikes.push_back(std::make_pair(stime, gid));
+        if ( stime >= t && stime <= tstop) {
+            spikes.push_back(std::make_pair(stime, gid));
+        }
     }
 
     fclose(f);