diff --git a/mechanisms/mod/exp2syn.mod b/mechanisms/mod/exp2syn.mod
index da2d2ae639143b1732b714b20f5ce0c2cf1f2216..ea0cf025e9228216b4699161a2e574ca1d1dda6e 100755
--- a/mechanisms/mod/exp2syn.mod
+++ b/mechanisms/mod/exp2syn.mod
@@ -1,5 +1,5 @@
NEURON {
- POINT_PROCESS Exp2Syn
+ POINT_PROCESS exp2syn
RANGE tau1, tau2, e
NONSPECIFIC_CURRENT i
}
@@ -11,8 +11,8 @@ UNITS {
}
PARAMETER {
- tau1=.1 (ms) : <1e-9,1e9>
- tau2 = 10 (ms) : <1e-9,1e9>
+ tau1 = .5 (ms) : <1e-9,1e9>
+ tau2 = 2 (ms) : <1e-9,1e9>
e=0 (mV)
}
diff --git a/mechanisms/mod/expsyn.mod b/mechanisms/mod/expsyn.mod
index db1f6d6ed61a8b563141ea2516658b8f87a35637..16d10c5cf856cd87e50252dca2163d844588e2b9 100644
--- a/mechanisms/mod/expsyn.mod
+++ b/mechanisms/mod/expsyn.mod
@@ -1,5 +1,5 @@
NEURON {
- POINT_PROCESS ExpSyn
+ POINT_PROCESS expsyn
RANGE tau, e
NONSPECIFIC_CURRENT i
}
diff --git a/miniapp/miniapp.cpp b/miniapp/miniapp.cpp
index dfff77fa544cb68be9f0454dec8380c99aa530f8..ea5207dc732c69a42b3e66f1aa525a08cf69abca 100644
--- a/miniapp/miniapp.cpp
+++ b/miniapp/miniapp.cpp
@@ -425,8 +425,9 @@ mc::cell make_cell(int compartments_per_segment, int num_synapses) {
auto distribution = std::uniform_real_distribution<float>(0.f, 1.0f);
// distribute the synapses at random locations the terminal dendrites in a
// round robin manner
+ nest::mc::parameter_list syn_default("expsyn");
for (auto i=0; i<num_synapses; ++i) {
- cell.add_synapse({2+(i%2), distribution(gen)});
+ cell.add_synapse({2+(i%2), distribution(gen)}, syn_default);
}
// add probes:
diff --git a/src/cell.cpp b/src/cell.cpp
index 3a2d5672a12bb74e2e484765e16b93e870b2bd4b..01d681a7e080c8c0444fe0299820181d5154028e 100644
--- a/src/cell.cpp
+++ b/src/cell.cpp
@@ -201,16 +201,6 @@ std::vector<int> const& cell::segment_parents() const
return parents_;
}
-void cell::add_synapse(segment_location loc)
-{
- synapses_.push_back(loc);
-}
-
-const std::vector<segment_location>& cell::synapses() const
-{
- return synapses_;
-}
-
// Rough and ready comparison of two cells.
// We don't use an operator== because equality of two cells is open to
// interpretation. For example, it is possible to have two viable representations
diff --git a/src/cell.hpp b/src/cell.hpp
index 744c9970e26af7f439f9cee7cfb2f88c96014624..1cb9b9f65dedbdcc4476c2b447eed1d1dea243ca 100644
--- a/src/cell.hpp
+++ b/src/cell.hpp
@@ -52,6 +52,11 @@ public:
using index_type = int;
using value_type = double;
using point_type = point<value_type>;
+
+ struct synapse_instance {
+ segment_location location;
+ parameter_list mechanism;
+ };
struct probe_instance {
segment_location location;
probeKind kind;
@@ -138,9 +143,13 @@ public:
//////////////////
// synapses
//////////////////
- void add_synapse(segment_location loc);
-
- const std::vector<segment_location>& synapses() const;
+ void add_synapse(segment_location loc, parameter_list p)
+ {
+ synapses_.push_back(synapse_instance{loc, std::move(p)});
+ }
+ const std::vector<synapse_instance>& synapses() const {
+ return synapses_;
+ }
//////////////////
// spike detectors
@@ -180,7 +189,7 @@ private:
std::vector<stimulus_instance> stimulii_;
// the synapses
- std::vector<segment_location> synapses_;
+ std::vector<synapse_instance> synapses_;
// the sensors
std::vector<detector_instance> spike_detectors_;
diff --git a/src/fvm_cell.hpp b/src/fvm_cell.hpp
index 25c0ae9a0c67dd42e7bcf680a9b32a0c6070290b..05bce5bd02b57c8d8fe9a9c3e90962eeee8188b3 100644
--- a/src/fvm_cell.hpp
+++ b/src/fvm_cell.hpp
@@ -20,8 +20,6 @@
#include <profiling/profiler.hpp>
#include <vector/include/Vector.hpp>
-#include <mechanisms/expsyn.hpp>
-
namespace nest {
namespace mc {
@@ -185,10 +183,12 @@ private:
/// the potential in mV in each CV
vector_type voltage_;
+#if 0
/// synapses
using synapse_type =
mechanisms::ExpSyn::mechanism_ExpSyn<value_type, size_type>;
- std::size_t synapse_index_;
+#endif
+ std::size_t synapse_index_; // synapses at the end of mechanisms_, from here
/// the set of mechanisms present in the cell
std::vector<mechanism_type> mechanisms_;
@@ -342,6 +342,52 @@ fvm_cell<T, I>::fvm_cell(nest::mc::cell const& cell)
);
}
+ synapse_index_ = mechanisms_.size();
+
+ std::multimap<std::string, int> syn_map;
+ for (const auto& syn: cell.synapses()) {
+ syn_map.insert({syn.mechanism.name(), find_compartment_index(syn.location, graph)});
+ }
+
+ auto syn_i = syn_map.begin();
+ while (syn_i!=syn_map.end()) {
+ const auto& mech_name = syn_i->first;
+ auto& helper = nest::mc::mechanisms::get_mechanism_helper(mech_name);
+
+ auto span = syn_map.equal_range(mech_name);
+ auto num_comp = std::distance(span.first, span.second);
+
+ index_type compartment_index(num_comp);
+ for (auto p = compartment_index.data(); syn_i!=span.second; ++p, ++syn_i) {
+ *p = syn_i->second;
+ }
+
+ auto mech = helper->new_mechanism(voltage_, current_, compartment_index);
+ mech->set_areas(cv_areas_);
+ mechanisms_.push_back(std::move(mech));
+ }
+
+#if 0
+ // add the synapses
+ std::vector<size_type> synapse_indexes;
+ synapse_indexes.reserve(cell.synapses().size());
+ for(auto loc : cell.synapses()) {
+ synapse_indexes.push_back(
+ find_compartment_index(loc, graph)
+ );
+ }
+
+ mechanisms_.push_back(
+ mechanisms::make_mechanism<synapse_type>(
+ voltage_, current_, index_view(synapse_indexes)
+ )
+ );
+ synapse_index_ = mechanisms_.size()-1;
+ // don't forget to give point processes access to cv_areas_
+ mechanisms_[synapse_index_]->set_areas(cv_areas_);
+#endif
+
+
/////////////////////////////////////////////
// build the ion species
/////////////////////////////////////////////
@@ -398,24 +444,6 @@ fvm_cell<T, I>::fvm_cell(nest::mc::cell const& cell)
stimulii_.push_back( {idx, stim.clamp} );
}
- // add the synapses
- std::vector<size_type> synapse_indexes;
- synapse_indexes.reserve(cell.synapses().size());
- for(auto loc : cell.synapses()) {
- synapse_indexes.push_back(
- find_compartment_index(loc, graph)
- );
- }
-
- mechanisms_.push_back(
- mechanisms::make_mechanism<synapse_type>(
- voltage_, current_, index_view(synapse_indexes)
- )
- );
- synapse_index_ = mechanisms_.size()-1;
- // don't forget to give point processes access to cv_areas_
- mechanisms_[synapse_index_]->set_areas(cv_areas_);
-
// record probe locations by index into corresponding state vector
for (auto probe : cell.probes()) {
uint32_t comp = find_compartment_index(probe.location, graph);
diff --git a/src/mechanism_interface.cpp b/src/mechanism_interface.cpp
index f44d1f561d3efcc51b262b5bb32e0a95084bbcb5..680e8739d11ee0dad16890bb1088a1a7d4b774b5 100644
--- a/src/mechanism_interface.cpp
+++ b/src/mechanism_interface.cpp
@@ -6,6 +6,8 @@
#include <mechanisms/hh.hpp>
#include <mechanisms/pas.hpp>
+#include <mechanisms/expsyn.hpp>
+#include <mechanisms/exp2syn.hpp>
namespace nest {
@@ -24,6 +26,16 @@ void setup_mechanism_helpers() {
make_mechanism_helper<
mechanisms::hh::helper<value_type, index_type>
>();
+
+ mechanism_helpers["expsyn"] =
+ make_mechanism_helper<
+ mechanisms::expsyn::helper<value_type, index_type>
+ >();
+
+ mechanism_helpers["exp2syn"] =
+ make_mechanism_helper<
+ mechanisms::exp2syn::helper<value_type, index_type>
+ >();
}
mechanism_helper_ptr<value_type, index_type>&
diff --git a/tests/unit/test_mechanisms.cpp b/tests/unit/test_mechanisms.cpp
index aef84890275263ca7ef9570c1017864736a6f331..2e31f1139d25cb3e36bc1ff0b32a3ec8a4316a4b 100644
--- a/tests/unit/test_mechanisms.cpp
+++ b/tests/unit/test_mechanisms.cpp
@@ -6,7 +6,7 @@
TEST(mechanisms, helpers) {
nest::mc::mechanisms::setup_mechanism_helpers();
- EXPECT_EQ(nest::mc::mechanisms::mechanism_helpers.size(), 2u);
+ EXPECT_EQ(nest::mc::mechanisms::mechanism_helpers.size(), 4u);
// verify that the hh and pas channels are available
EXPECT_EQ(nest::mc::mechanisms::get_mechanism_helper("hh")->name(), "hh");
diff --git a/tests/unit/test_synapses.cpp b/tests/unit/test_synapses.cpp
index ff79c1e6488a2534a03303aa30f05403bd4acdf9..9ad68c2444ef17d6f2b2355e3c388f76ca9220e6 100644
--- a/tests/unit/test_synapses.cpp
+++ b/tests/unit/test_synapses.cpp
@@ -3,6 +3,8 @@
#include <cell.hpp>
#include <fvm_cell.hpp>
+#include <mechanisms/expsyn.hpp>
+#include <mechanisms/exp2syn.hpp>
// compares results with those generated by nrn/ball_and_stick.py
TEST(synapses, add_to_cell)
@@ -18,29 +20,37 @@ TEST(synapses, add_to_cell)
auto soma = cell.add_soma(12.6157/2.0);
soma->add_mechanism(hh_parameters());
- cell.add_synapse({0, 0.1});
- cell.add_synapse({1, 0.2});
- cell.add_synapse({0, 0.3});
+ parameter_list exp_default("expsyn");
+ parameter_list exp2_default("exp2syn");
+
+ cell.add_synapse({0, 0.1}, exp_default);
+ cell.add_synapse({1, 0.2}, exp2_default);
+ cell.add_synapse({0, 0.3}, exp_default);
EXPECT_EQ(3u, cell.synapses().size());
- EXPECT_EQ(cell.synapses()[0].segment, 0);
- EXPECT_EQ(cell.synapses()[0].position, 0.1);
- EXPECT_EQ(cell.synapses()[1].segment, 1);
- EXPECT_EQ(cell.synapses()[1].position, 0.2);
- EXPECT_EQ(cell.synapses()[2].segment, 0);
- EXPECT_EQ(cell.synapses()[2].position, 0.3);
+ const auto& syns = cell.synapses();
+
+ EXPECT_EQ(syns[0].location.segment, 0);
+ EXPECT_EQ(syns[0].location.position, 0.1);
+ EXPECT_EQ(syns[0].mechanism.name(), "expsyn");
+
+ EXPECT_EQ(syns[1].location.segment, 1);
+ EXPECT_EQ(syns[1].location.position, 0.2);
+ EXPECT_EQ(syns[1].mechanism.name(), "exp2syn");
+
+ EXPECT_EQ(syns[2].location.segment, 0);
+ EXPECT_EQ(syns[2].location.position, 0.3);
+ EXPECT_EQ(syns[2].mechanism.name(), "expsyn");
}
// compares results with those generated by nrn/ball_and_stick.py
-TEST(synapses, basic_state)
+TEST(synapses, expsyn_basic_state)
{
using namespace nest::mc;
- // setup global state for the mechanisms
- nest::mc::mechanisms::setup_mechanism_helpers();
-
- using synapse_type = mechanisms::ExpSyn::mechanism_ExpSyn<double, int>;
+ using synapse_type = mechanisms::expsyn::mechanism_expsyn<double, int>;
auto num_syn = 4;
+
synapse_type::index_type indexes(num_syn);
synapse_type::vector_type voltage(num_syn, -65.0);
synapse_type::vector_type current(num_syn, 1.0);
@@ -81,3 +91,54 @@ TEST(synapses, basic_state)
EXPECT_EQ(ptr->g[1], 3.14);
EXPECT_EQ(ptr->g[3], 1.04);
}
+
+TEST(synapses, exp2syn_basic_state)
+{
+ using namespace nest::mc;
+
+ using synapse_type = mechanisms::exp2syn::mechanism_exp2syn<double, int>;
+ auto num_syn = 4;
+
+ synapse_type::index_type indexes(num_syn);
+ synapse_type::vector_type voltage(num_syn, -65.0);
+ synapse_type::vector_type current(num_syn, 1.0);
+ auto mech = mechanisms::make_mechanism<synapse_type>( voltage, current, indexes );
+
+ auto ptr = dynamic_cast<synapse_type*>(mech.get());
+
+ // parameters initialized to default values
+ for(auto e : ptr->e) {
+ EXPECT_EQ(e, 0.);
+ }
+ for(auto tau1: ptr->tau1) {
+ EXPECT_EQ(tau1, 0.5);
+ }
+ for(auto tau2: ptr->tau2) {
+ EXPECT_EQ(tau2, 2.0);
+ }
+
+ // should be initialized to NaN
+ for(auto factor: ptr->factor) {
+ EXPECT_NE(factor, factor);
+ }
+
+ // initialize state then check factor has sane (positive) value
+ // and A and B are zero
+ ptr->nrn_init();
+ for(auto factor: ptr->factor) {
+ EXPECT_GT(factor, 0.);
+ }
+ for(auto A: ptr->A) {
+ EXPECT_EQ(A, 0.);
+ }
+ for(auto B: ptr->B) {
+ EXPECT_EQ(B, 0.);
+ }
+
+ // call net_receive on two of the synapses
+ ptr->net_receive(1, 3.14);
+ ptr->net_receive(3, 1.04);
+
+ EXPECT_NEAR(ptr->A[1], ptr->factor[1]*3.14, 1e-6);
+ EXPECT_NEAR(ptr->B[3], ptr->factor[3]*1.04, 1e-6);
+}
diff --git a/tests/validation/validate_synapses.cpp b/tests/validation/validate_synapses.cpp
index 694887ce1cab4e27a322d48789200d5e07493608..42ace29c3393bb177b878ab3e8c6eb6de42d8676 100644
--- a/tests/validation/validate_synapses.cpp
+++ b/tests/validation/validate_synapses.cpp
@@ -46,7 +46,7 @@ struct result {
};
// compares results with those generated by nrn/simple_synapse.py
-TEST(simple_synapse, neuron_baseline)
+void run_neuron_baseline(const char* syn_type, const char* data_file)
{
using namespace nest::mc;
using namespace nlohmann;
@@ -67,10 +67,11 @@ TEST(simple_synapse, neuron_baseline)
dendrite->mechanism("membrane").set("r_L", 100);
soma->mechanism("membrane").set("r_L", 100);
- // add stimulus
- cell.add_synapse({1, 0.5});
+ // add synapse
+ parameter_list syn_default(syn_type);
+ cell.add_synapse({1, 0.5}, syn_default);
- // add porbes
+ // add probes
auto probe_soma = cell.add_probe({0,0}, probeKind::membrane_voltage);
auto probe_dend = cell.add_probe({1,0.5}, probeKind::membrane_voltage);
@@ -82,7 +83,7 @@ TEST(simple_synapse, neuron_baseline)
};
// load data from file
- auto cell_data = testing::g_validation_data.load("simple_exp_synapse.json");
+ auto cell_data = testing::g_validation_data.load(data_file);
EXPECT_TRUE(cell_data.size()>0);
if(cell_data.size()==0) return;
@@ -164,3 +165,12 @@ TEST(simple_synapse, neuron_baseline)
}
}
+TEST(simple_synapse, expsyn_neuron_baseline) {
+ SCOPED_TRACE("expsyn");
+ run_neuron_baseline("expsyn","simple_exp_synapse.json");
+}
+
+TEST(simple_synapse, exp2syn_neuron_baseline) {
+ SCOPED_TRACE("exp2syn");
+ run_neuron_baseline("exp2syn","simple_exp2_synapse.json");
+}