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test_fvm_multi.cpp 7.96 KiB
#include <fstream>
#include "gtest.h"
#include <common_types.hpp>
#include <cell.hpp>
#include <fvm_multicell.hpp>
#include <util/rangeutil.hpp>
#include "../test_util.hpp"
#include "../test_common_cells.hpp"
TEST(fvm_multi, cable)
{
using namespace nest::mc;
nest::mc::cell cell=make_cell_ball_and_3sticks();
using fvm_cell = fvm::fvm_multicell<double, cell_lid_type>;
std::vector<fvm_cell::target_handle> targets;
std::vector<fvm_cell::detector_handle> detectors;
std::vector<fvm_cell::probe_handle> probes;
fvm_cell fvcell;
fvcell.initialize(util::singleton_view(cell), detectors, targets, probes);
auto& J = fvcell.jacobian();
// 1 (soma) + 3 (dendritic segments) × 4 compartments
EXPECT_EQ(cell.num_compartments(), 13u);
// assert that the matrix has one row for each compartment
EXPECT_EQ(J.size(), cell.num_compartments());
fvcell.setup_matrix(0.02);
// assert that the number of cv areas is the same as the matrix size
// i.e. both should equal the number of compartments
EXPECT_EQ(fvcell.cv_areas().size(), J.size());
}
TEST(fvm_multi, init)
{
using namespace nest::mc;
nest::mc::cell cell = make_cell_ball_and_stick();
const auto m = cell.model();
EXPECT_EQ(m.tree.num_segments(), 2u);
auto& soma_hh = cell.soma()->mechanism("hh");
soma_hh.set("gnabar", 0.12);
soma_hh.set("gkbar", 0.036);
soma_hh.set("gl", 0.0003);
soma_hh.set("el", -54.3);
// check that parameter values were set correctly
EXPECT_EQ(cell.soma()->mechanism("hh").get("gnabar").value, 0.12);
EXPECT_EQ(cell.soma()->mechanism("hh").get("gkbar").value, 0.036);
EXPECT_EQ(cell.soma()->mechanism("hh").get("gl").value, 0.0003);
EXPECT_EQ(cell.soma()->mechanism("hh").get("el").value, -54.3);
cell.segment(1)->set_compartments(10);
using fvm_cell = fvm::fvm_multicell<double, cell_lid_type>;
std::vector<fvm_cell::target_handle> targets;
std::vector<fvm_cell::detector_handle> detectors;
std::vector<fvm_cell::probe_handle> probes;
fvm_cell fvcell;
fvcell.initialize(util::singleton_view(cell), detectors, targets, probes);
auto& J = fvcell.jacobian();
EXPECT_EQ(J.size(), 11u);
fvcell.setup_matrix(0.01);
}
TEST(fvm_multi, multi_init)
{
using namespace nest::mc;
nest::mc::cell cells[] = {
make_cell_ball_and_stick(),
make_cell_ball_and_3sticks()
};
EXPECT_EQ(cells[0].num_segments(), 2u);
EXPECT_EQ(cells[0].segment(1)->num_compartments(), 4u);
EXPECT_EQ(cells[1].num_segments(), 4u);
EXPECT_EQ(cells[1].segment(1)->num_compartments(), 4u);
EXPECT_EQ(cells[1].segment(2)->num_compartments(), 4u);
EXPECT_EQ(cells[1].segment(3)->num_compartments(), 4u);
cells[0].add_synapse({1, 0.4}, parameter_list("expsyn"));
cells[0].add_synapse({1, 0.4}, parameter_list("expsyn"));
cells[1].add_synapse({2, 0.4}, parameter_list("exp2syn"));
cells[1].add_synapse({3, 0.4}, parameter_list("expsyn"));
cells[1].add_detector({0, 0}, 3.3);
using fvm_cell = fvm::fvm_multicell<double, cell_lid_type>;
std::vector<fvm_cell::target_handle> targets(4);
std::vector<fvm_cell::detector_handle> detectors(1);
std::vector<fvm_cell::probe_handle> probes;
fvm_cell fvcell;
fvcell.initialize(cells, detectors, targets, probes);
auto& J = fvcell.jacobian();
EXPECT_EQ(J.size(), 5u+13u);
// check indices in instantiated mechanisms
for (const auto& mech: fvcell.mechanisms()) {
if (mech->name()=="hh") {
// HH on somas of two cells, with group compartment indices
// 0 and 5.
ASSERT_EQ(mech->node_index().size(), 2u);
EXPECT_EQ(mech->node_index()[0], 0u);
EXPECT_EQ(mech->node_index()[1], 5u);
}
if (mech->name()=="expsyn") {
// Three expsyn synapses, two in second compartment
// of dendrite segment of first cell, one in second compartment
// of last segment of second cell.
ASSERT_EQ(mech->node_index().size(), 3u);
EXPECT_EQ(mech->node_index()[0], 2u);
EXPECT_EQ(mech->node_index()[1], 2u);
EXPECT_EQ(mech->node_index()[2], 15u);
}
if (mech->name()=="exp2syn") {
// One exp2syn synapse, in second compartment
// of penultimate segment of second cell.
ASSERT_EQ(mech->node_index().size(), 1u);
EXPECT_EQ(mech->node_index()[0], 11u);
}
}
fvcell.setup_matrix(0.01);
}
// test that stimuli are added correctly
TEST(fvm_multi, stimulus)
{
using namespace nest::mc;
using util::singleton_view;
// the default ball and stick has one stimulus at the terminal end of the dendrite
auto cell = make_cell_ball_and_stick();
// ... so add a second at the soma to make things more interesting
cell.add_stimulus({0,0.5}, {1., 2., 0.1});
// now we have two stims :
//
// |stim0 |stim1
// -----------------------
// delay | 5 | 1
// duration | 80 | 2
// amplitude | 0.3 | 0.1
// compmnt | 4 | 0
using fvm_cell = fvm::fvm_multicell<double, cell_lid_type>;
std::vector<fvm_cell::target_handle> targets;
std::vector<fvm_cell::detector_handle> detectors;
std::vector<fvm_cell::probe_handle> probes;
fvm_cell fvcell;
fvcell.initialize(singleton_view(cell), detectors, targets, probes);
auto& stim = fvcell.stimuli();
EXPECT_EQ(stim.size(), 2u);
EXPECT_EQ(stim[0].first, 4u);
EXPECT_EQ(stim[1].first, 0u);
EXPECT_EQ(stim[0].second.delay(), 5.);
EXPECT_EQ(stim[1].second.delay(), 1.);
EXPECT_EQ(stim[0].second.duration(), 80.);
EXPECT_EQ(stim[1].second.duration(), 2.);
EXPECT_EQ(stim[0].second.amplitude(), 0.3);
EXPECT_EQ(stim[1].second.amplitude(), 0.1);
}
// test that mechanism indexes are computed correctly
TEST(fvm_multi, mechanism_indexes)
{
using namespace nest::mc;
// create a cell with 4 sements:
// a soma with a branching dendrite
// - hh on soma and first branch of dendrite (segs 0 and 2)
// - pas on main dendrite and second branch (segs 1 and 3)
//
// /
// pas
// /
// hh---pas--.
// \.
// hh
// \.
cell c;
auto soma = c.add_soma(12.6157/2.0);
soma->add_mechanism(hh_parameters());
// add dendrite of length 200 um and diameter 1 um with passive channel c.add_cable(0, segmentKind::dendrite, 0.5, 0.5, 100);
c.add_cable(1, segmentKind::dendrite, 0.5, 0.5, 100);
c.add_cable(1, segmentKind::dendrite, 0.5, 0.5, 100);
auto& segs = c.segments();
segs[1]->add_mechanism(pas_parameters());
segs[2]->add_mechanism(hh_parameters());
segs[3]->add_mechanism(pas_parameters());
for (auto& seg: segs) {
if (seg->is_dendrite()) {
seg->mechanism("membrane").set("r_L", 100);
seg->set_compartments(4);
}
}
// generate the lowered fvm cell
using fvm_cell = fvm::fvm_multicell<double, cell_lid_type>;
std::vector<fvm_cell::target_handle> targets;
std::vector<fvm_cell::detector_handle> detectors;
std::vector<fvm_cell::probe_handle> probes;
fvm_cell fvcell;
fvcell.initialize(util::singleton_view(c), detectors, targets, probes);
// make vectors with the expected CV indexes for each mechanism
std::vector<unsigned> hh_index = {0u, 4u, 5u, 6u, 7u, 8u};
std::vector<unsigned> pas_index = {0u, 1u, 2u, 3u, 4u, 9u, 10u, 11u, 12u};
// iterate over mechanisms and test whether they were assigned to the correct CVs
// TODO : this fails because we do not handle CVs at branching points (including soma) correctly
for(auto& mech : fvcell.mechanisms()) {
auto const& n = mech->node_index();
std::vector<unsigned> ni(n.begin(), n.end());
if(mech->name()=="hh") {
EXPECT_EQ(ni, hh_index);
}
else if(mech->name()=="pas") {
EXPECT_EQ(ni, pas_index);
}
}
}