Merge pull request #37 from halfflat/feature/probe_unit_tests

Unit tests for probe functionality

src/fvm_cell.hpp

@@ -133,6 +133,9 @@ public:
     /// returns voltage at a segment location
     value_type voltage(segment_location loc) const;
 
+    /// returns current at a segment location
+    value_type current(segment_location loc) const;
+
     value_type time() const { return t_; }
 
     value_type probe(uint32_t i) const {
@@ -484,6 +487,12 @@ T fvm_cell<T, I>::voltage(segment_location loc) const
     return voltage_[compartment_index(loc)];
 }
 
+template <typename T, typename I>
+T fvm_cell<T, I>::current(segment_location loc) const
+{
+    return current_[compartment_index(loc)];
+}
+
 template <typename T, typename I>
 void fvm_cell<T, I>::initialize()
 {

tests/CMakeLists.txt

@@ -24,6 +24,7 @@ set(TEST_SOURCES
     test_optional.cpp
     test_parameters.cpp
     test_point.cpp
+    test_probe.cpp
     test_segment.cpp
     test_spikes.cpp
     test_stimulus.cpp

tests/test_probe.cpp

+#include "gtest.h"
+
+#include "cell.hpp"
+#include "fvm_cell.hpp"
+
+TEST(probe, instantiation)
+{
+    using namespace nest::mc;
+
+    cell c1;
+
+    segment_location loc1{0, 0};
+    segment_location loc2{1, 0.6};
+
+    auto p1 = c1.add_probe(loc1, probeKind::membrane_voltage);
+    auto p2 = c1.add_probe(loc2, probeKind::membrane_current);
+
+    // expect locally provided probe ids to be numbered sequentially from zero.
+    
+    EXPECT_EQ(0, p1);
+    EXPECT_EQ(1, p2);
+
+    // expect the probes() return to be a collection with these two probes.
+
+    auto probes = c1.probes();
+    EXPECT_EQ(2u, probes.size());
+
+    EXPECT_EQ(loc1, probes[0].location);
+    EXPECT_EQ(probeKind::membrane_voltage, probes[0].kind);
+
+    EXPECT_EQ(loc2, probes[1].location);
+    EXPECT_EQ(probeKind::membrane_current, probes[1].kind);
+}
+
+TEST(probe, fvm_cell)
+{
+    using namespace nest::mc;
+
+    cell bs;
+
+    // ball-and-stick model morphology
+
+    bs.add_soma(12.6157/2.0);
+    bs.add_cable(0, segmentKind::dendrite, 0.5, 0.5, 200);
+    bs.soma()->set_compartments(5);
+
+    segment_location loc0{0, 0};
+    segment_location loc1{1, 1};
+    segment_location loc2{1, 0.5};
+
+    auto pv0 = bs.add_probe(loc0, probeKind::membrane_voltage);
+    auto pv1 = bs.add_probe(loc1, probeKind::membrane_voltage);
+    auto pi2 = bs.add_probe(loc2, probeKind::membrane_current);
+    
+    i_clamp stim(0, 100, 0.3);
+    bs.add_stimulus({1, 1}, stim);
+
+    fvm::fvm_cell<double, int> lcell(bs);
+    lcell.setup_matrix(0.01);
+    lcell.initialize();
+
+    EXPECT_EQ(3u, lcell.num_probes());
+
+    // expect probe values and direct queries of voltage and current
+    // to be equal in fvm cell
+
+    EXPECT_EQ(lcell.voltage(loc0), lcell.probe(pv0));
+    EXPECT_EQ(lcell.voltage(loc1), lcell.probe(pv1));
+    EXPECT_EQ(lcell.current(loc2), lcell.probe(pi2));
+
+    lcell.advance(0.05);
+
+    EXPECT_EQ(lcell.voltage(loc0), lcell.probe(pv0));
+    EXPECT_EQ(lcell.voltage(loc1), lcell.probe(pv1));
+    EXPECT_EQ(lcell.current(loc2), lcell.probe(pi2));
+}
+
+