From 75cdf2f22283e7dc8a39b11e81dd26ee62265d4c Mon Sep 17 00:00:00 2001
From: bcumming <bcumming@cscs.ch>
Date: Tue, 24 May 2016 11:06:09 +0200
Subject: [PATCH] refactor unit tests
---
src/cell.cpp | 4 +-
src/cell.hpp | 2 +-
tests/CMakeLists.txt | 3 +-
tests/test_fvm.cpp | 105 +++++++++++++++
tests/test_parameters.cpp | 42 ++++++
tests/test_run.cpp | 265 --------------------------------------
6 files changed, 152 insertions(+), 269 deletions(-)
create mode 100644 tests/test_parameters.cpp
delete mode 100644 tests/test_run.cpp
diff --git a/src/cell.cpp b/src/cell.cpp
index 72bad02a..a6986f06 100644
--- a/src/cell.cpp
+++ b/src/cell.cpp
@@ -155,9 +155,9 @@ std::vector<int> cell::compartment_counts() const
return comp_count;
}
-int cell::num_compartments() const
+size_t cell::num_compartments() const
{
- auto n = 0;
+ auto n = 0u;
for(auto &s : segments_) {
n += s->num_compartments();
}
diff --git a/src/cell.hpp b/src/cell.hpp
index 6e5d95f9..ba5f9b6b 100644
--- a/src/cell.hpp
+++ b/src/cell.hpp
@@ -86,7 +86,7 @@ class cell {
value_type area() const;
/// the total number of compartments over all segments
- int num_compartments() const;
+ size_t num_compartments() const;
std::vector<segment_ptr> const& segments() const;
diff --git a/tests/CMakeLists.txt b/tests/CMakeLists.txt
index 11b88107..cb33af4d 100644
--- a/tests/CMakeLists.txt
+++ b/tests/CMakeLists.txt
@@ -16,10 +16,11 @@ set(TEST_SOURCES
test_algorithms.cpp
test_cell.cpp
test_compartments.cpp
+ test_fvm.cpp
test_matrix.cpp
test_mechanisms.cpp
+ test_parameters.cpp
test_point.cpp
- test_run.cpp
test_segment.cpp
test_stimulus.cpp
test_swcio.cpp
diff --git a/tests/test_fvm.cpp b/tests/test_fvm.cpp
index e69de29b..85a25f35 100644
--- a/tests/test_fvm.cpp
+++ b/tests/test_fvm.cpp
@@ -0,0 +1,105 @@
+#include <fstream>
+
+#include "gtest.h"
+#include "util.hpp"
+
+#include "../src/cell.hpp"
+#include "../src/fvm.hpp"
+
+TEST(fvm, cable)
+{
+ using namespace nest::mc;
+
+ nest::mc::cell cell;
+
+ // setup global state for the mechanisms
+ nest::mc::mechanisms::setup_mechanism_helpers();
+
+ cell.add_soma(6e-4); // 6um in cm
+
+ // 1um radius and 4mm long, all in cm
+ cell.add_cable(0, segmentKind::dendrite, 1e-4, 1e-4, 4e-1);
+ cell.add_cable(0, segmentKind::dendrite, 1e-4, 1e-4, 4e-1);
+
+ //std::cout << cell.segment(1)->area() << " is the area\n";
+ EXPECT_EQ(cell.model().tree.num_segments(), 3u);
+
+ // add passive to all 3 segments in the cell
+ for(auto& seg :cell.segments()) {
+ seg->add_mechanism(pas_parameters());
+ }
+
+ cell.soma()->add_mechanism(hh_parameters());
+ cell.segment(2)->add_mechanism(hh_parameters());
+
+ 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", -54.387);
+
+ cell.segment(1)->set_compartments(4);
+ cell.segment(2)->set_compartments(4);
+
+ using fvm_cell = fvm::fvm_cell<double, int>;
+ fvm_cell fvcell(cell);
+ auto& J = fvcell.jacobian();
+
+ EXPECT_EQ(cell.num_compartments(), 9u);
+
+ // 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, init)
+{
+ using namespace nest::mc;
+
+ nest::mc::cell cell;
+
+ // setup global state for the mechanisms
+ nest::mc::mechanisms::setup_mechanism_helpers();
+
+ cell.add_soma(12.6157/2.0);
+ //auto& props = cell.soma()->properties;
+
+ cell.add_cable(0, segmentKind::dendrite, 0.5, 0.5, 200);
+
+ const auto m = cell.model();
+ EXPECT_EQ(m.tree.num_segments(), 2u);
+
+ // in this context (i.e. attached to a segment on a high-level cell)
+ // a mechanism is essentially a set of parameters
+ // - the only "state" is that used to define parameters
+ cell.soma()->add_mechanism(hh_parameters());
+
+ 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_cell<double, int>;
+ fvm_cell fvcell(cell);
+ auto& J = fvcell.jacobian();
+ EXPECT_EQ(J.size(), 11u);
+
+ fvcell.setup_matrix(0.01);
+}
+
diff --git a/tests/test_parameters.cpp b/tests/test_parameters.cpp
new file mode 100644
index 00000000..0dce58b0
--- /dev/null
+++ b/tests/test_parameters.cpp
@@ -0,0 +1,42 @@
+
+#include <fstream>
+
+#include "gtest.h"
+#include "util.hpp"
+
+#include <parameter_list.hpp>
+
+// test out the parameter infrastructure
+TEST(parameters, setting)
+{
+ nest::mc::parameter_list list("test");
+ EXPECT_EQ(list.name(), "test");
+ EXPECT_EQ(list.num_parameters(), 0);
+
+ nest::mc::parameter p("a", 0.12, {0, 10});
+
+ // add_parameter() returns a bool that indicates whether
+ // it was able to successfull add the parameter
+ EXPECT_TRUE(list.add_parameter(std::move(p)));
+ EXPECT_EQ(list.num_parameters(), 1);
+
+ // test in place construction of a parameter
+ EXPECT_TRUE(list.add_parameter({"b", -3.0}));
+ EXPECT_EQ(list.num_parameters(), 2);
+
+ // check that adding a parameter that already exists returns false
+ // and does not increase the number of parameters
+ EXPECT_FALSE(list.add_parameter({"b", -3.0}));
+ EXPECT_EQ(list.num_parameters(), 2);
+
+ auto &parms = list.parameters();
+ EXPECT_EQ(parms[0].name, "a");
+ EXPECT_EQ(parms[0].value, 0.12);
+ EXPECT_EQ(parms[0].range.min, 0);
+ EXPECT_EQ(parms[0].range.max, 10);
+
+ EXPECT_EQ(parms[1].name, "b");
+ EXPECT_EQ(parms[1].value, -3);
+ EXPECT_FALSE(parms[1].range.has_lower_bound());
+ EXPECT_FALSE(parms[1].range.has_upper_bound());
+}
diff --git a/tests/test_run.cpp b/tests/test_run.cpp
deleted file mode 100644
index aa4d9bba..00000000
--- a/tests/test_run.cpp
+++ /dev/null
@@ -1,265 +0,0 @@
-#include <fstream>
-
-#include "gtest.h"
-#include "util.hpp"
-
-#include "../src/cell.hpp"
-#include "../src/fvm.hpp"
-
-// based on hh/Neuron/steps_A.py
-TEST(run, single_compartment)
-{
- using namespace nest::mc;
-
- std::vector<std::vector<double>> results(2);
-
- nest::mc::cell cell;
-
- // setup global state for the mechanisms
- nest::mc::mechanisms::setup_mechanism_helpers();
-
- // Soma with diameter 18.8um and HH channel
- auto soma = cell.add_soma(18.8/2.0);
- soma->mechanism("membrane").set("r_L", 123); // no effect for single compartment cell
- soma->add_mechanism(hh_parameters());
-
- // add stimulus to the soma
- //cell.add_stimulus({0,0}, {5., 3., 0.1});
- cell.add_stimulus({0,0.5}, {10., 100., 0.1});
-
- // make the lowered finite volume cell
- fvm::fvm_cell<double, int> model(cell);
-
- // set initial conditions
- using memory::all;
- model.voltage()(all) = -65.;
- model.initialize(); // have to do this _after_ initial conditions are set
-
- // run the simulation
- auto dt = 0.0005; // ms
- auto tfinal = 120.; // ms
- int nt = tfinal/dt;
- results[0].push_back(0.);
- results[1].push_back(model.voltage()[0]);
- for(auto i=0; i<nt; ++i) {
- model.advance(dt);
- // save voltage at soma
- results[0].push_back((i+1)*dt);
- results[1].push_back(model.voltage()[0]);
- }
-
- testing::write_vis_file("v.dat", results);
-}
-
-TEST(run, ball_and_stick)
-{
- using namespace nest::mc;
-
- std::vector<std::vector<double>> results(3);
-
- nest::mc::cell cell;
-
- // setup global state for the mechanisms
- nest::mc::mechanisms::setup_mechanism_helpers();
-
- // Soma with diameter 12.6157 um and HH channel
- auto soma = cell.add_soma(12.6157/2.0);
- soma->add_mechanism(hh_parameters());
-
- // add dendrite of length 200 um and diameter 1 um with passive channel
- auto dendrite = cell.add_cable(0, segmentKind::dendrite, 0.5, 0.5, 200);
- dendrite->set_compartments(10);
- dendrite->add_mechanism(pas_parameters());
-
- dendrite->mechanism("membrane").set("r_L", 100); // no effect for single compartment cell
-
- // add stimulus
- //cell.add_stimulus({0,0}, {5., 1., 0.1}); // soma
- cell.add_stimulus({1,1}, {5., 1., 0.5});
-
- // make the lowered finite volume cell
- fvm::fvm_cell<double, int> model(cell);
-
- std::cout << "CV areas " << model.cv_areas() << "\n";
-
- // set initial conditions
- using memory::all;
- model.voltage()(all) = -65.;
- model.initialize(); // have to do this _after_ initial conditions are set
-
- // run the simulation
- auto pos = model.size()-1;
- auto dt = 0.001; // ms
- auto tfinal = 25.; // ms
- int nt = tfinal/dt;
- results[0].push_back(0.);
- results[1].push_back(model.voltage()[0]);
- results[2].push_back(model.voltage()[pos]);
- for(auto i=0; i<nt; ++i) {
- model.advance(dt);
- results[0].push_back((i+1)*dt);
- results[1].push_back(model.voltage()[0]);
- results[2].push_back(model.voltage()[pos]);
- }
-
- testing::write_vis_file("v.dat", results);
-}
-
-TEST(run, cable)
-{
- using namespace nest::mc;
-
- nest::mc::cell cell;
-
- // setup global state for the mechanisms
- nest::mc::mechanisms::setup_mechanism_helpers();
-
- cell.add_soma(6e-4); // 6um in cm
-
- // 1um radius and 4mm long, all in cm
- cell.add_cable(0, segmentKind::dendrite, 1e-4, 1e-4, 4e-1);
- cell.add_cable(0, segmentKind::dendrite, 1e-4, 1e-4, 4e-1);
-
- //std::cout << cell.segment(1)->area() << " is the area\n";
- EXPECT_EQ(cell.model().tree.num_segments(), 3u);
-
- // add passive to all 3 segments in the cell
- for(auto& seg :cell.segments()) {
- seg->add_mechanism(pas_parameters());
- }
-
- cell.soma()->add_mechanism(hh_parameters());
- cell.segment(2)->add_mechanism(hh_parameters());
-
- 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", -54.387);
-
- cell.segment(1)->set_compartments(4);
- cell.segment(2)->set_compartments(4);
-
- using fvm_cell = fvm::fvm_cell<double, int>;
- fvm_cell fvcell(cell);
- auto& J = fvcell.jacobian();
- EXPECT_EQ(J.size(), 9u);
-
- fvcell.setup_matrix(0.02);
- EXPECT_EQ(fvcell.cv_areas().size(), J.size());
-
- // inspect ion channels
- /*
- std::cout << "ion na index : " << fvcell.ion_na().node_index() << "\n";
- std::cout << "ion ca index : " << fvcell.ion_ca().node_index() << "\n";
- std::cout << "ion k index : " << fvcell.ion_k().node_index() << "\n";
-
- std::cout << "ion na E : " << fvcell.ion_na().reversal_potential() << "\n";
- std::cout << "ion ca E : " << fvcell.ion_ca().reversal_potential() << "\n";
- std::cout << "ion k E : " << fvcell.ion_k().reversal_potential() << "\n";
- */
-
- //auto& cable_parms = cell.segment(1)->mechanism("membrane");
- //std::cout << soma_hh << std::endl;
- //std::cout << cable_parms << std::endl;
-
- //std::cout << "l " << J.l() << "\n";
- //std::cout << "d " << J.d() << "\n";
- //std::cout << "u " << J.u() << "\n";
- //std::cout << "p " << J.p() << "\n";
-
- J.rhs()(memory::all) = 1.;
- J.rhs()[0] = 10.;
-
- J.solve();
-}
-
-TEST(run, init)
-{
- using namespace nest::mc;
-
- nest::mc::cell cell;
-
- // setup global state for the mechanisms
- nest::mc::mechanisms::setup_mechanism_helpers();
-
- cell.add_soma(12.6157/2.0);
- //auto& props = cell.soma()->properties;
-
- cell.add_cable(0, segmentKind::dendrite, 0.5, 0.5, 200);
-
- const auto m = cell.model();
- EXPECT_EQ(m.tree.num_segments(), 2u);
-
- // in this context (i.e. attached to a segment on a high-level cell)
- // a mechanism is essentially a set of parameters
- // - the only "state" is that used to define parameters
- cell.soma()->add_mechanism(hh_parameters());
-
- 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_cell<double, int>;
- fvm_cell fvcell(cell);
- auto& J = fvcell.jacobian();
- EXPECT_EQ(J.size(), 11u);
-
- fvcell.setup_matrix(0.01);
- //std::cout << "areas " << fvcell.cv_areas() << "\n";
-
- J.rhs()(memory::all) = 1.;
- J.rhs()[0] = 10.;
-
- J.solve();
-
- //std::cout << "x" << J.rhs() << "\n";
-}
-
-// test out the parameter infrastructure
-TEST(run, parameters)
-{
- nest::mc::parameter_list list("test");
- EXPECT_EQ(list.name(), "test");
- EXPECT_EQ(list.num_parameters(), 0);
-
- nest::mc::parameter p("a", 0.12, {0, 10});
-
- // add_parameter() returns a bool that indicates whether
- // it was able to successfull add the parameter
- EXPECT_EQ(list.add_parameter(std::move(p)), true);
- EXPECT_EQ(list.num_parameters(), 1);
-
- // test in place construction of a parameter
- EXPECT_EQ(list.add_parameter({"b", -3.0}), true);
- EXPECT_EQ(list.num_parameters(), 2);
-
- // check that adding a parameter that already exists returns false
- // and does not increase the number of parameters
- EXPECT_EQ(list.add_parameter({"b", -3.0}), false);
- EXPECT_EQ(list.num_parameters(), 2);
-
- auto &parms = list.parameters();
- EXPECT_EQ(parms[0].name, "a");
- EXPECT_EQ(parms[0].value, 0.12);
- EXPECT_EQ(parms[0].range.min, 0);
- EXPECT_EQ(parms[0].range.max, 10);
-
- EXPECT_EQ(parms[1].name, "b");
- EXPECT_EQ(parms[1].value, -3);
- EXPECT_EQ(parms[1].range.has_lower_bound(), false);
- EXPECT_EQ(parms[1].range.has_upper_bound(), false);
-}
-
--
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