diff --git a/commit.msg b/commit.msg
new file mode 100644
index 0000000000000000000000000000000000000000..3abb1935698a6efe63d5ea651d8c7d5c017541fe
--- /dev/null
+++ b/commit.msg
@@ -0,0 +1,9 @@
+* change `probe_sort` enum to scoped enum
+ - renamed to `probeKind`
+ - refactored out of class
+ - updated coding guidelines wiki with enum rules
+* refactor `std::pair` into structs with meaningfull name types in `cell.hpp`
+ - not just probes: stimulii and detectors too.
+* add profiling region around sampling in `cell_group`
+* change output data format for traces to json
+* remove white space at end of lines (looking at you Sam)
diff --git a/miniapp/miniapp.cpp b/miniapp/miniapp.cpp
index 4a619cf9a087dc7fa151ee9613adc6d5ff6357c4..74b551ff4f07fe795514caafde901de1721108dc 100644
--- a/miniapp/miniapp.cpp
+++ b/miniapp/miniapp.cpp
@@ -100,7 +100,10 @@ struct model {
// traces from probes
struct trace_data {
- using sample_type = std::pair<float,double>;
+ struct sample_type {
+ float time;
+ double value;
+ };
std::string name;
index_type id;
std::vector<sample_type> samples;
@@ -120,7 +123,8 @@ struct model {
float dt_ = 0;
simple_sampler_functor(std::vector<trace_data> &traces, size_t index, float dt) :
- traces_(traces), trace_index_(index), dt_(dt) {}
+ traces_(traces), trace_index_(index), dt_(dt)
+ {}
optional<float> operator()(float t, double v) {
traces_[trace_index_].samples.push_back({t,v});
@@ -128,8 +132,8 @@ struct model {
}
};
- mc::sampler make_simple_sampler(index_type probe_gid, const std::string name,
- index_type id, float dt)
+ mc::sampler make_simple_sampler(
+ index_type probe_gid, const std::string name, index_type id, float dt)
{
traces.push_back(trace_data{name, id});
return {probe_gid, simple_sampler_functor(traces, traces.size()-1, dt)};
@@ -143,15 +147,17 @@ struct model {
void dump_traces() {
// do not call during simulation: thread-unsafe access to traces.
for (const auto& trace: traces) {
- std::stringstream path;
- path << "trace_" << trace.id << "_" << trace.name << ".dat";
+ auto path = "trace_" + std::to_string(trace.id)
+ + "_" + trace.name + ".json";
- std::ofstream file(path.str());
- file << "time\t" << trace.name << "\n";
+ nlohmann::json json;
+ json["name"] = trace.name;
for (const auto& sample: trace.samples) {
- file << sample.first << "\t" << sample.second << "\n";
+ json["time"].push_back(sample.time);
+ json["value"].push_back(sample.value);
}
- file.close();
+ std::ofstream file(path);
+ file << std::setw(1) << json << std::endl;
}
}
};
@@ -403,8 +409,8 @@ mc::cell make_cell(int compartments_per_segment, int num_synapses) {
}
// add probes:
- auto probe_soma = cell.add_probe({0, 0}, mc::cell::membrane_voltage);
- auto probe_dendrite = cell.add_probe({1, 0.5}, mc::cell::membrane_voltage);
+ auto probe_soma = cell.add_probe({0, 0}, mc::probeKind::membrane_voltage);
+ auto probe_dendrite = cell.add_probe({1, 0.5}, mc::probeKind::membrane_voltage);
EXPECTS(probe_soma==0);
EXPECTS(probe_dendrite==1);
diff --git a/src/cell.hpp b/src/cell.hpp
index f53fb0592c94d76c3dfcd7552814345fde28f874..1c047e18b2b90cba58a805f66f1579723dd0ccd5 100644
--- a/src/cell.hpp
+++ b/src/cell.hpp
@@ -38,6 +38,11 @@ int find_compartment_index(
compartment_model const& graph
);
+enum class probeKind {
+ membrane_voltage,
+ membrane_current
+};
+
/// high-level abstract representation of a cell and its segments
class cell {
public:
@@ -46,8 +51,18 @@ public:
using index_type = int;
using value_type = double;
using point_type = point<value_type>;
-
- enum probe_sort { membrane_voltage, membrane_current };
+ struct probe_instance {
+ segment_location location;
+ probeKind kind;
+ };
+ struct stimulus_instance {
+ segment_location location;
+ i_clamp clamp;
+ };
+ struct detector_instance {
+ segment_location location;
+ double threshold;
+ };
// constructor
cell();
@@ -109,12 +124,12 @@ public:
//////////////////
void add_stimulus(segment_location loc, i_clamp stim);
- std::vector<std::pair<segment_location, i_clamp>>&
+ std::vector<stimulus_instance>&
stimulii() {
return stimulii_;
}
- const std::vector<std::pair<segment_location, i_clamp>>&
+ const std::vector<stimulus_instance>&
stimulii() const {
return stimulii_;
}
@@ -131,12 +146,12 @@ public:
//////////////////
void add_detector(segment_location loc, double threshold);
- std::vector<std::pair<segment_location, double>>&
+ std::vector<detector_instance>&
detectors() {
return spike_detectors_;
}
- const std::vector<std::pair<segment_location, double>>&
+ const std::vector<detector_instance>&
detectors() const {
return spike_detectors_;
}
@@ -144,12 +159,12 @@ public:
//////////////////
// probes
//////////////////
- index_type add_probe(segment_location loc, enum probe_sort sort) {
- probes_.push_back({loc, sort});
+ index_type add_probe(segment_location loc, probeKind kind) {
+ probes_.push_back({loc, kind});
return probes_.size()-1;
}
- const std::vector<std::pair<segment_location, enum probe_sort>>&
+ const std::vector<probe_instance>&
probes() const { return probes_; }
private:
@@ -161,16 +176,16 @@ private:
std::vector<segment_ptr> segments_;
// the stimulii
- std::vector<std::pair<segment_location, i_clamp>> stimulii_;
+ std::vector<stimulus_instance> stimulii_;
// the synapses
std::vector<segment_location> synapses_;
// the sensors
- std::vector<std::pair<segment_location, double>> spike_detectors_;
+ std::vector<detector_instance> spike_detectors_;
// the probes
- std::vector<std::pair<segment_location, enum probe_sort>> probes_;
+ std::vector<probe_instance> probes_;
};
// Checks that two cells have the same
diff --git a/src/cell_group.hpp b/src/cell_group.hpp
index 922b7b197091af6cf4ba7ecc345030bcff3e380e..70bfdeb13123c780744c5875ae125bf631bf6142 100644
--- a/src/cell_group.hpp
+++ b/src/cell_group.hpp
@@ -24,7 +24,7 @@ struct sampler {
index_type probe_gid; // samplers are attached to probes
std::function<util::optional<time_type>(time_type, value_type)> sample;
};
-
+
template <typename Cell>
class cell_group {
public:
@@ -49,7 +49,7 @@ public:
for (auto& d : c.detectors()) {
spike_sources_.push_back( {
- 0u, spike_detector_type(cell_, d.first, d.second, 0.f)
+ 0u, spike_detector_type(cell_, d.location, d.threshold, 0.f)
});
}
}
@@ -76,23 +76,14 @@ public:
return { first_probe_gid_, first_probe_gid_+cell_.num_probes() };
}
-#ifdef SPLAT
- void splat(std::string fname) {
- char buffer[128];
- std::ofstream fid(fname);
- for (auto i=0u; i<tt.size(); ++i) {
- sprintf(buffer, "%8.4f %16.8f %16.8f\n", tt[i], vs[i], vd[i]);
- fid << buffer;
- }
- }
-#endif
-
void advance(double tfinal, double dt) {
while (cell_.time()<tfinal) {
// take any pending samples
float cell_time = cell_.time();
+
+ nest::mc::util::profiler_enter("sampling");
while (auto m = sample_events_.pop_if_before(cell_time)) {
- auto &sampler = samplers_[m->sampler_index];
+ auto& sampler = samplers_[m->sampler_index];
EXPECTS((bool)sampler.sample);
index_type probe_index = sampler.probe_gid-first_probe_gid_;
@@ -102,12 +93,8 @@ public:
sample_events_.push(*m);
}
}
+ nest::mc::util::profiler_leave();
-#ifdef SPLAT
- tt.push_back(cell_.time());
- vs.push_back(cell_.voltage({0,0.0}));
- vd.push_back(cell_.voltage({1,0.5}));
-#endif
// look for events in the next time step
auto tstep = std::min(tfinal, cell_.time()+dt);
auto next = events_.pop_if_before(tstep);
@@ -164,20 +151,14 @@ public:
spikes_.clear();
}
- void add_sampler(const sampler &s, float start_time = 0) {
- unsigned sampler_index = samplers_.size();
+ void add_sampler(const sampler& s, float start_time = 0) {
+ auto sampler_index = uint32_t(samplers_.size());
samplers_.push_back(s);
sample_events_.push({sampler_index, start_time});
}
-
+
private:
-#ifdef SPLAT
- // REMOVE as soon as we have a better way to probe cell state
- std::vector<float> tt;
- std::vector<float> vs;
- std::vector<float> vd;
-#endif
/// the lowered cell state (e.g. FVM) of the cell
cell_type cell_;
diff --git a/src/fvm_cell.hpp b/src/fvm_cell.hpp
index 947b7a7ba233340274f5113c12d075d7851a1ea1..90e7f7be0d373274aba0b4ff28b908465e674cb5 100644
--- a/src/fvm_cell.hpp
+++ b/src/fvm_cell.hpp
@@ -382,8 +382,8 @@ fvm_cell<T, I>::fvm_cell(nest::mc::cell const& cell)
// add the stimulii
for(const auto& stim : cell.stimulii()) {
- auto idx = find_compartment_index(stim.first, graph);
- stimulii_.push_back( {idx, stim.second} );
+ auto idx = find_compartment_index(stim.location, graph);
+ stimulii_.push_back( {idx, stim.clamp} );
}
// add the synapses
@@ -406,16 +406,16 @@ fvm_cell<T, I>::fvm_cell(nest::mc::cell const& cell)
// record probe locations by index into corresponding state vector
for (auto probe : cell.probes()) {
- uint32_t comp = find_compartment_index(probe.first, graph);
- switch (probe.second) {
- case nest::mc::cell::membrane_voltage:
- probes_.push_back({&fvm_cell::voltage_, comp});
- break;
- case nest::mc::cell::membrane_current:
- probes_.push_back({&fvm_cell::current_, comp});
- break;
- default:
- throw std::logic_error("unrecognized probe sort");
+ uint32_t comp = find_compartment_index(probe.location, graph);
+ switch (probe.kind) {
+ case probeKind::membrane_voltage:
+ probes_.push_back({&fvm_cell::voltage_, comp});
+ break;
+ case probeKind::membrane_current:
+ probes_.push_back({&fvm_cell::current_, comp});
+ break;
+ default:
+ throw std::logic_error("unrecognized probeKind");
}
}
}