diff --git a/example/probe-demo/probe-demo.cpp b/example/probe-demo/probe-demo.cpp
index 585ea25436ac3d0391acdaf44747723df6e273fe..9e9f785430e0da57daa17b0f2801c835d652456f 100644
--- a/example/probe-demo/probe-demo.cpp
+++ b/example/probe-demo/probe-demo.cpp
@@ -32,7 +32,7 @@ const char* help_msg =
" --until=TIME simulate until TIME [ms]\n"
" -n, --n-cv=N discretize with N CVs\n"
" -t, --sample=TIME take a sample every TIME [ms]\n"
- " -x, --at=X take sample at relative position X along cable\n"
+ " -x, --at=X take sample at relative position X along cable or index of synapse\n"
" --exact use exact time sampling\n"
" -h, --help print extended usage information and exit\n"
"\n"
@@ -56,6 +56,7 @@ const char* help_msg =
" hh_m HH state variable m at X\n"
" hh_h HH state variable h at X\n"
" hh_n HH state variable n at X\n"
+ " expsyn_g expsyn state variable g at X"
"\n"
"where X is the relative position along the cable as described above, or else:\n"
"\n"
@@ -68,7 +69,8 @@ const char* help_msg =
" all_c_k internal potassium concentration [mmol/L] in each CV\n"
" all_hh_m HH state variable m in each CV\n"
" all_hh_h HH state variable h in each CV\n"
- " all_hh_n HH state variable n in each CV\n";
+ " all_hh_n HH state variable n in each CV\n"
+ " all_expsyn_g expsyn state variable g for all synapses\n";
struct options {
double sim_end = 100.0; // [ms]
@@ -121,9 +123,17 @@ struct cable_recipe: public arb::recipe {
arb::decor decor;
decor.paint(arb::reg::all(), arb::density("hh")); // HH mechanism over whole cell.
decor.place(arb::mlocation{0, 0.}, arb::i_clamp{1.}, "iclamp"); // Inject a 1 nA current indefinitely.
+ decor.place(arb::mlocation{0, 0.}, arb::synapse("expsyn"), "synapse1"); // a synapse
+ decor.place(arb::mlocation{0, 0.5}, arb::synapse("expsyn"), "synapse2"); // another synapse
return arb::cable_cell(tree, {}, decor);
}
+
+ virtual std::vector<arb::event_generator> event_generators(arb::cell_gid_type) const override {
+ return {arb::poisson_generator({"synapse1"}, .005, 0., 0.1, std::minstd_rand{}),
+ arb::poisson_generator({"synapse2"}, .1, 0., 0.1, std::minstd_rand{})};
+ }
+
};
int main(int argc, char** argv) {
@@ -160,7 +170,10 @@ int main(int argc, char** argv) {
void scalar_sampler(arb::probe_metadata pm, std::size_t n, const arb::sample_record* samples) {
auto* loc = any_cast<const arb::mlocation*>(pm.meta);
- assert(loc);
+ auto* point_info = any_cast<const arb::cable_probe_point_info*>(pm.meta);
+ assert((loc != nullptr) || (point_info != nullptr));
+
+ loc = loc ? loc : &(point_info->loc);
std::cout << std::fixed << std::setprecision(4);
for (std::size_t i = 0; i<n; ++i) {
@@ -173,21 +186,29 @@ void scalar_sampler(arb::probe_metadata pm, std::size_t n, const arb::sample_rec
void vector_sampler(arb::probe_metadata pm, std::size_t n, const arb::sample_record* samples) {
auto* cables_ptr = any_cast<const arb::mcable_list*>(pm.meta);
- assert(cables_ptr);
- unsigned n_cable = cables_ptr->size();
+ auto* point_info_ptr = any_cast<const std::vector<arb::cable_probe_point_info>*>(pm.meta);
+
+ assert((cables_ptr != nullptr) || (point_info_ptr != nullptr));
+
+ unsigned n_entities = cables_ptr ? cables_ptr->size() : point_info_ptr->size();
std::cout << std::fixed << std::setprecision(4);
for (std::size_t i = 0; i<n; ++i) {
auto* value_range = any_cast<const arb::cable_sample_range*>(samples[i].data);
assert(value_range);
- assert(n_cable==value_range->second-value_range->first);
-
- for (unsigned j = 0; j<n_cable; ++j) {
- arb::mcable where = (*cables_ptr)[j];
- std::cout << samples[i].time << ", "
- << where.prox_pos << ", "
- << where.dist_pos << ", "
- << value_range->first[j] << '\n';
+ const auto& [lo, hi] = *value_range;
+ assert(n_entities==hi-lo);
+
+ for (unsigned j = 0; j<n_entities; ++j) {
+ std::cout << samples[i].time << ", ";
+ if (cables_ptr) {
+ arb::mcable where = (*cables_ptr)[j];
+ std::cout << where.prox_pos << ", " << where.dist_pos << ", ";
+ } else {
+ arb::mlocation loc = (*point_info_ptr)[j].loc;
+ std::cout << loc.pos << ", ";
+ }
+ std::cout << lo[j] << '\n';
}
}
}
@@ -213,6 +234,7 @@ bool parse_options(options& opt, int& argc, char** argv) {
{"hh_m", {"hh_m", true, [](double x) { return arb::cable_probe_density_state{L{0, x}, "hh", "m"}; }}},
{"hh_h", {"hh_h", true, [](double x) { return arb::cable_probe_density_state{L{0, x}, "hh", "h"}; }}},
{"hh_n", {"hh_n", true, [](double x) { return arb::cable_probe_density_state{L{0, x}, "hh", "n"}; }}},
+ {"expsyn_g", {"expsyn_ g", true, [](arb::cell_lid_type i) { return arb::cable_probe_point_state{i, "expsyn", "g"}; }}},
// all-of-cell probes
{"all_v", {"v", false, [](double) { return arb::cable_probe_membrane_voltage_cell{}; }}},
{"all_i_ion", {"i_ion", false, [](double) { return arb::cable_probe_total_ion_current_cell{}; }}},
@@ -223,7 +245,8 @@ bool parse_options(options& opt, int& argc, char** argv) {
{"all_c_k", {"c_k", false, [](double) { return arb::cable_probe_ion_int_concentration_cell{"k"}; }}},
{"all_hh_m", {"hh_m", false, [](double) { return arb::cable_probe_density_state_cell{"hh", "m"}; }}},
{"all_hh_h", {"hh_h", false, [](double) { return arb::cable_probe_density_state_cell{"hh", "h"}; }}},
- {"all_hh_n", {"hh_n", false, [](double) { return arb::cable_probe_density_state_cell{"hh", "n"}; }}}
+ {"all_hh_n", {"hh_n", false, [](double) { return arb::cable_probe_density_state_cell{"hh", "n"}; }}},
+ {"all_expsyn_g", {"expsyn_ g", false, [](arb::cell_lid_type) { return arb::cable_probe_point_state_cell{"expsyn", "g"}; }}},
};
std::tuple<const char*, bool, std::function<any (double)>> probe_spec;