From 3e19099c6fdaa920b6ac877e477aaf3f73e25078 Mon Sep 17 00:00:00 2001
From: Sam Yates <halfflat@gmail.com>
Date: Fri, 1 Jul 2016 17:06:28 +0200
Subject: [PATCH] Unit tests for probe functionality
* Also exposes current values from fvm_cell by segment location.
---
src/fvm_cell.hpp | 9 +++++
tests/CMakeLists.txt | 1 +
tests/test_probe.cpp | 78 ++++++++++++++++++++++++++++++++++++++++++++
3 files changed, 88 insertions(+)
create mode 100644 tests/test_probe.cpp
diff --git a/src/fvm_cell.hpp b/src/fvm_cell.hpp
index 90e7f7be..932c0a48 100644
--- a/src/fvm_cell.hpp
+++ b/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()
{
diff --git a/tests/CMakeLists.txt b/tests/CMakeLists.txt
index ebebb306..9061fb8d 100644
--- a/tests/CMakeLists.txt
+++ b/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
diff --git a/tests/test_probe.cpp b/tests/test_probe.cpp
new file mode 100644
index 00000000..52ac4e7f
--- /dev/null
+++ b/tests/test_probe.cpp
@@ -0,0 +1,78 @@
+#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));
+}
+
+
--
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