diff --git a/data/validation/ball_and_3stick.json b/data/validation/ball_and_3stick.json
new file mode 100644
index 0000000000000000000000000000000000000000..e4121f4383e44dd7a7c15c36598b2a85fba728f2
--- /dev/null
+++ b/data/validation/ball_and_3stick.json
@@ -0,0 +1,158 @@
+[
+ {
+ "nseg": 5,
+ "dt": 0.001,
+ "measurements": {
+ "soma": {
+ "spikes": [
+ 6.943999999998871,
+ 20.48399999999761,
+ 33.862999999979664,
+ 52.52400000006877,
+ 65.9560000001329,
+ 79.3600000001969
+ ],
+ "thresh": 0.0
+ },
+ "clamp": {
+ "spikes": [
+ 7.1399999999987624,
+ 20.448999999997692,
+ 33.722999999978995,
+ 52.61200000006919,
+ 65.85800000013244,
+ 79.18600000019607
+ ],
+ "thresh": 20.0
+ },
+ "dend": {
+ "spikes": [
+ 7.055999999998809,
+ 20.44199999999771,
+ 33.73499999997905,
+ 52.56900000006898,
+ 65.86400000013246,
+ 79.20200000019615
+ ],
+ "thresh": -20.0
+ }
+ }
+ },
+ {
+ "nseg": 11,
+ "dt": 0.001,
+ "measurements": {
+ "soma": {
+ "spikes": [
+ 6.948999999998868,
+ 20.506999999997557,
+ 33.91399999997991,
+ 52.528000000068786,
+ 65.98500000013304,
+ 79.42000000019719
+ ],
+ "thresh": 0.0
+ },
+ "clamp": {
+ "spikes": [
+ 7.147999999998758,
+ 20.478999999997622,
+ 33.77899999997926,
+ 52.62300000006924,
+ 65.8930000001326,
+ 79.24900000019638
+ ],
+ "thresh": 20.0
+ },
+ "dend": {
+ "spikes": [
+ 7.061999999998806,
+ 20.467999999997648,
+ 33.785999999979296,
+ 52.576000000069016,
+ 65.8940000001326,
+ 79.26000000019643
+ ],
+ "thresh": -20.0
+ }
+ }
+ },
+ {
+ "nseg": 51,
+ "dt": 0.001,
+ "measurements": {
+ "soma": {
+ "spikes": [
+ 6.949999999998868,
+ 20.512999999997543,
+ 33.92699999997997,
+ 52.530000000068796,
+ 65.99200000013307,
+ 79.43500000019726
+ ],
+ "thresh": 0.0
+ },
+ "clamp": {
+ "spikes": [
+ 7.150999999998756,
+ 20.486999999997604,
+ 33.793999999979334,
+ 52.626000000069254,
+ 65.90200000013265,
+ 79.26500000019645
+ ],
+ "thresh": 20.0
+ },
+ "dend": {
+ "spikes": [
+ 7.062999999998805,
+ 20.473999999997634,
+ 33.79899999997936,
+ 52.578000000069025,
+ 65.90200000013265,
+ 79.2740000001965
+ ],
+ "thresh": -20.0
+ }
+ }
+ },
+ {
+ "nseg": 101,
+ "dt": 0.001,
+ "measurements": {
+ "soma": {
+ "spikes": [
+ 6.949999999998868,
+ 20.512999999997543,
+ 33.927999999979974,
+ 52.530000000068796,
+ 65.99300000013308,
+ 79.43500000019726
+ ],
+ "thresh": 0.0
+ },
+ "clamp": {
+ "spikes": [
+ 7.150999999998756,
+ 20.486999999997604,
+ 33.793999999979334,
+ 52.626000000069254,
+ 65.90300000013265,
+ 79.26600000019646
+ ],
+ "thresh": 20.0
+ },
+ "dend": {
+ "spikes": [
+ 7.062999999998805,
+ 20.47499999999763,
+ 33.79999999997936,
+ 52.578000000069025,
+ 65.90200000013265,
+ 79.2750000001965
+ ],
+ "thresh": -20.0
+ }
+ }
+ }
+]
\ No newline at end of file
diff --git a/data/validation/ball_and_stick.json b/data/validation/ball_and_stick.json
new file mode 100644
index 0000000000000000000000000000000000000000..5b459a3a287e012def1539866531efa458f66cc0
--- /dev/null
+++ b/data/validation/ball_and_stick.json
@@ -0,0 +1,158 @@
+[
+ {
+ "nseg": 5,
+ "dt": 0.001,
+ "measurements": {
+ "soma": {
+ "spikes": [
+ 6.980999999998851,
+ 20.98699999999644,
+ 34.792999999984104,
+ 48.61100000005008,
+ 62.43100000011607,
+ 76.25100000018206
+ ],
+ "thresh": 0.0
+ },
+ "clamp": {
+ "spikes": [
+ 7.2499999999987015,
+ 21.193999999995956,
+ 34.97599999998498,
+ 48.78900000005093,
+ 62.60700000011691,
+ 76.4270000001829
+ ],
+ "thresh": 10.0
+ },
+ "dend": {
+ "spikes": [
+ 7.169999999998746,
+ 21.177999999995993,
+ 34.97799999998499,
+ 48.79400000005096,
+ 62.614000000116945,
+ 76.43400000018293
+ ],
+ "thresh": -10.0
+ }
+ }
+ },
+ {
+ "nseg": 11,
+ "dt": 0.001,
+ "measurements": {
+ "soma": {
+ "spikes": [
+ 6.998999999998841,
+ 21.078999999996224,
+ 34.983999999985016,
+ 48.9080000000515,
+ 62.835000000118,
+ 76.7630000001845
+ ],
+ "thresh": 0.0
+ },
+ "clamp": {
+ "spikes": [
+ 7.277999999998686,
+ 21.29999999999571,
+ 35.17999999998595,
+ 49.09800000005241,
+ 63.0240000001189,
+ 76.9510000001854
+ ],
+ "thresh": 10.0
+ },
+ "dend": {
+ "spikes": [
+ 7.181999999998739,
+ 21.2609999999958,
+ 35.15899999998585,
+ 49.08100000005233,
+ 63.00700000011882,
+ 76.93400000018532
+ ],
+ "thresh": -10.0
+ }
+ }
+ },
+ {
+ "nseg": 51,
+ "dt": 0.001,
+ "measurements": {
+ "soma": {
+ "spikes": [
+ 7.003999999998838,
+ 21.10199999999617,
+ 35.03299999998525,
+ 48.98500000005187,
+ 62.9400000001185,
+ 76.89500000018514
+ ],
+ "thresh": 0.0
+ },
+ "clamp": {
+ "spikes": [
+ 7.284999999998682,
+ 21.32599999999565,
+ 35.232999999986205,
+ 49.17800000005279,
+ 63.13200000011942,
+ 77.08700000018605
+ ],
+ "thresh": 10.0
+ },
+ "dend": {
+ "spikes": [
+ 7.185999999998737,
+ 21.28199999999575,
+ 35.20499999998607,
+ 49.15500000005268,
+ 63.10900000011931,
+ 77.06400000018594
+ ],
+ "thresh": -10.0
+ }
+ }
+ },
+ {
+ "nseg": 101,
+ "dt": 0.001,
+ "measurements": {
+ "soma": {
+ "spikes": [
+ 7.003999999998838,
+ 21.102999999996168,
+ 35.03499999998526,
+ 48.98800000005188,
+ 62.94400000011852,
+ 76.90000000018516
+ ],
+ "thresh": 0.0
+ },
+ "clamp": {
+ "spikes": [
+ 7.284999999998682,
+ 21.326999999995646,
+ 35.234999999986215,
+ 49.181000000052805,
+ 63.13500000011943,
+ 77.09100000018607
+ ],
+ "thresh": 10.0
+ },
+ "dend": {
+ "spikes": [
+ 7.185999999998737,
+ 21.28299999999575,
+ 35.20699999998608,
+ 49.15700000005269,
+ 63.11300000011933,
+ 77.06900000018597
+ ],
+ "thresh": -10.0
+ }
+ }
+ }
+]
\ No newline at end of file
diff --git a/data/validation/simple_exp2_synapse.json b/data/validation/simple_exp2_synapse.json
new file mode 100644
index 0000000000000000000000000000000000000000..137d9e6f86916e945b9f8c87d02369912fa03df0
--- /dev/null
+++ b/data/validation/simple_exp2_synapse.json
@@ -0,0 +1,90 @@
+[
+ {
+ "nseg": 5,
+ "dt": 0.0125,
+ "measurements": {
+ "soma": {
+ "spikes": [
+ 11.23749999999963,
+ 21.72500000000066,
+ 41.2625000000051
+ ],
+ "thresh": 20.0
+ },
+ "dend": {
+ "spikes": [
+ 11.087499999999638,
+ 21.487500000000605,
+ 41.11250000000506
+ ],
+ "thresh": -10.0
+ }
+ }
+ },
+ {
+ "nseg": 11,
+ "dt": 0.0125,
+ "measurements": {
+ "soma": {
+ "spikes": [
+ 11.23749999999963,
+ 21.73750000000066,
+ 41.2750000000051
+ ],
+ "thresh": 20.0
+ },
+ "dend": {
+ "spikes": [
+ 11.087499999999638,
+ 21.487500000000605,
+ 41.11250000000506
+ ],
+ "thresh": -10.0
+ }
+ }
+ },
+ {
+ "nseg": 51,
+ "dt": 0.0125,
+ "measurements": {
+ "soma": {
+ "spikes": [
+ 11.23749999999963,
+ 21.73750000000066,
+ 41.2750000000051
+ ],
+ "thresh": 20.0
+ },
+ "dend": {
+ "spikes": [
+ 11.087499999999638,
+ 21.487500000000605,
+ 41.11250000000506
+ ],
+ "thresh": -10.0
+ }
+ }
+ },
+ {
+ "nseg": 101,
+ "dt": 0.0125,
+ "measurements": {
+ "soma": {
+ "spikes": [
+ 11.23749999999963,
+ 21.73750000000066,
+ 41.2750000000051
+ ],
+ "thresh": 20.0
+ },
+ "dend": {
+ "spikes": [
+ 11.087499999999638,
+ 21.487500000000605,
+ 41.11250000000506
+ ],
+ "thresh": -10.0
+ }
+ }
+ }
+]
\ No newline at end of file
diff --git a/data/validation/simple_exp_synapse.json b/data/validation/simple_exp_synapse.json
new file mode 100644
index 0000000000000000000000000000000000000000..675f8accd5753b720efe80020f3665df9ba47318
--- /dev/null
+++ b/data/validation/simple_exp_synapse.json
@@ -0,0 +1,90 @@
+[
+ {
+ "nseg": 5,
+ "dt": 0.0125,
+ "measurements": {
+ "soma": {
+ "spikes": [
+ 11.087499999999638,
+ 21.525000000000613,
+ 41.11250000000506
+ ],
+ "thresh": 20.0
+ },
+ "dend": {
+ "spikes": [
+ 11.087499999999638,
+ 21.51250000000061,
+ 41.10000000000506
+ ],
+ "thresh": -10.0
+ }
+ }
+ },
+ {
+ "nseg": 11,
+ "dt": 0.0125,
+ "measurements": {
+ "soma": {
+ "spikes": [
+ 11.099999999999637,
+ 21.537500000000616,
+ 41.125000000005066
+ ],
+ "thresh": 20.0
+ },
+ "dend": {
+ "spikes": [
+ 11.087499999999638,
+ 21.525000000000613,
+ 41.11250000000506
+ ],
+ "thresh": -10.0
+ }
+ }
+ },
+ {
+ "nseg": 51,
+ "dt": 0.0125,
+ "measurements": {
+ "soma": {
+ "spikes": [
+ 11.099999999999637,
+ 21.537500000000616,
+ 41.125000000005066
+ ],
+ "thresh": 20.0
+ },
+ "dend": {
+ "spikes": [
+ 11.087499999999638,
+ 21.525000000000613,
+ 41.11250000000506
+ ],
+ "thresh": -10.0
+ }
+ }
+ },
+ {
+ "nseg": 101,
+ "dt": 0.0125,
+ "measurements": {
+ "soma": {
+ "spikes": [
+ 11.099999999999637,
+ 21.537500000000616,
+ 41.125000000005066
+ ],
+ "thresh": 20.0
+ },
+ "dend": {
+ "spikes": [
+ 11.087499999999638,
+ 21.525000000000613,
+ 41.11250000000506
+ ],
+ "thresh": -10.0
+ }
+ }
+ }
+]
\ No newline at end of file
diff --git a/data/validation/soma.json b/data/validation/soma.json
new file mode 100644
index 0000000000000000000000000000000000000000..b0de340ce5891e8cc95fdfb5cc92d956751f37da
--- /dev/null
+++ b/data/validation/soma.json
@@ -0,0 +1,62 @@
+[
+ {
+ "dt": 0.05,
+ "spikes": [
+ 12.04999999999985,
+ 27.57499999999897,
+ 42.85000000000118,
+ 58.10000000000465,
+ 73.37500000000811,
+ 88.62500000001158,
+ 103.90000000001505
+ ]
+ },
+ {
+ "dt": 0.02,
+ "spikes": [
+ 12.04999999999985,
+ 27.57499999999897,
+ 42.85000000000118,
+ 58.10000000000465,
+ 73.37500000000811,
+ 88.62500000001158,
+ 103.90000000001505
+ ]
+ },
+ {
+ "dt": 0.01,
+ "spikes": [
+ 12.037499999999584,
+ 27.525000000001977,
+ 42.76250000000544,
+ 57.9875000000089,
+ 73.21250000000188,
+ 88.43749999998803,
+ 103.66249999997419
+ ]
+ },
+ {
+ "dt": 0.001,
+ "spikes": [
+ 12.026000000003206,
+ 27.476999999981313,
+ 42.68400000002178,
+ 57.881000000094346,
+ 73.0770000001669,
+ 88.27300000023946,
+ 103.46900000031202
+ ]
+ },
+ {
+ "dt": 0.0001,
+ "spikes": [
+ 12.024499999978646,
+ 27.473100000350247,
+ 42.67780000085499,
+ 57.87230000135939,
+ 73.06600000186377,
+ 88.25970000236815,
+ 103.45330000287252
+ ]
+ }
+]
\ No newline at end of file
diff --git a/nrn/ball_and_3stick.py b/nrn/ball_and_3stick.py
index 15ece3d3da151daf7bdb90f1af1d6cd368352489..4333072216b56d203708430243e28ef008cdfa68 100644
--- a/nrn/ball_and_3stick.py
+++ b/nrn/ball_and_3stick.py
@@ -4,11 +4,21 @@ from matplotlib import pyplot
import numpy as np
import json
import argparse
+import sys
from neuron import gui, h
parser = argparse.ArgumentParser(description='generate spike train ball and stick model with hh channels at soma and pas channels in dendrite')
parser.add_argument('--plot', action='store_true', dest='plot')
-args = parser.parse_args()
+
+# hack to make things work with nrniv ... -python:
+# throw away args before -python foo.py if -python present.
+
+if '-python' in sys.argv:
+ argv = sys.argv[sys.argv.index('-python')+2:]
+else:
+ argv = sys.argv
+
+args = parser.parse_args(argv)
soma = h.Section(name='soma')
dend = [
diff --git a/nrn/ball_and_stick.py b/nrn/ball_and_stick.py
index 24562337a4baffd7a1ae3a1e7885cb07e06987ec..10932d1adcda27e60e5c8781f491a665b6d8cd8c 100644
--- a/nrn/ball_and_stick.py
+++ b/nrn/ball_and_stick.py
@@ -4,11 +4,21 @@ from matplotlib import pyplot
import numpy as np
import json
import argparse
+import sys
from neuron import gui, h
parser = argparse.ArgumentParser(description='generate spike train ball and stick model with hh channels at soma and pas channels in dendrite')
parser.add_argument('--plot', action='store_true', dest='plot')
-args = parser.parse_args()
+
+# hack to make things work with nrniv ... -python:
+# throw away args before -python foo.py if -python present.
+
+if '-python' in sys.argv:
+ argv = sys.argv[sys.argv.index('-python')+2:]
+else:
+ argv = sys.argv
+
+args = parser.parse_args(argv)
soma = h.Section(name='soma')
dend = h.Section(name='dend')
diff --git a/nrn/generate_validation.sh b/nrn/generate_validation.sh
index c42b1d5ce66512b8dc5ff46bf13e85f4707bd8ef..532a7cd738d53a1a0f8342d07f09c016b5e24857 100755
--- a/nrn/generate_validation.sh
+++ b/nrn/generate_validation.sh
@@ -1,4 +1,5 @@
python2.7 ./soma.py
python2.7 ./ball_and_stick.py
python2.7 ./ball_and_3stick.py
-python2.7 ./simple_synapse.py
+python2.7 ./simple_synapse.py --synapse exp2
+python2.7 ./simple_synapse.py --synapse exp
diff --git a/nrn/soma.py b/nrn/soma.py
index 3af4f50f3e6e1ae7761591ab68fd32a1187f9c87..9decb2c1700a6fd113530019835dad3e807c2b9b 100644
--- a/nrn/soma.py
+++ b/nrn/soma.py
@@ -4,11 +4,21 @@ from matplotlib import pyplot
import numpy as np
import json
import argparse
+import sys
from neuron import gui, h
parser = argparse.ArgumentParser(description='generate spike train info for a soma with hh channels')
parser.add_argument('--plot', action='store_true', dest='plot')
-args = parser.parse_args()
+
+# hack to make things work with nrniv ... -python:
+# throw away args before -python foo.py if -python present.
+
+if '-python' in sys.argv:
+ argv = sys.argv[sys.argv.index('-python')+2:]
+else:
+ argv = sys.argv
+
+args = parser.parse_args(argv)
if args.plot :
print '-- plotting turned on'
diff --git a/src/cell_group.hpp b/src/cell_group.hpp
index a6ee8b8fedb39250870db4b613716c417aaa27b3..ff146bd1110eb873d5d83c35969b981a48579b5f 100644
--- a/src/cell_group.hpp
+++ b/src/cell_group.hpp
@@ -130,7 +130,7 @@ public:
}
template <typename R>
- void enqueue_events(R events) {
+ void enqueue_events(const R& events) {
for (auto e : events) {
e.target -= first_target_gid_;
events_.push(e);
diff --git a/tests/test_util.hpp b/tests/test_util.hpp
index cfa89896af8039e6188d8fbc460f412d3407a1b3..0f9935d8c517758a4aa1308921b382ea56b596fc 100644
--- a/tests/test_util.hpp
+++ b/tests/test_util.hpp
@@ -55,28 +55,6 @@ void write_vis_file(const std::string& fname, std::vector<std::vector<double>> v
}
}
-[[gnu::unused]] static
-nlohmann::json
-load_spike_data(const std::string& input_name)
-{
- nlohmann::json cell_data;
- std::ifstream fid(input_name);
- if(!fid.is_open()) {
- std::cerr << "error : unable to open file " << input_name
- << " : run the validation generation script first\n";
- return {};
- }
-
- try {
- fid >> cell_data;
- }
- catch (...) {
- std::cerr << "error : incorrectly formatted json file " << input_name << "\n";
- return {};
- }
- return cell_data;
-}
-
template <typename T>
std::vector<T> find_spikes(std::vector<T> const& v, T threshold, T dt)
{
diff --git a/tests/validation/CMakeLists.txt b/tests/validation/CMakeLists.txt
index 31477528d45b62aef700fbbdff3e3ea686a66ee4..c6c72fa04efab7394190288ba3face603d141faf 100644
--- a/tests/validation/CMakeLists.txt
+++ b/tests/validation/CMakeLists.txt
@@ -1,23 +1,11 @@
-set(HEADERS
- ${PROJECT_SOURCE_DIR}/src/cell.hpp
- ${PROJECT_SOURCE_DIR}/src/cell_tree.hpp
- ${PROJECT_SOURCE_DIR}/src/math.hpp
- ${PROJECT_SOURCE_DIR}/src/point.hpp
- ${PROJECT_SOURCE_DIR}/src/segment.hpp
- ${PROJECT_SOURCE_DIR}/src/swcio.hpp
- ${PROJECT_SOURCE_DIR}/src/tree.hpp
-)
-
-set(TEST_SOURCES
- # unit test driver
- test.cpp
-)
-
set(VALIDATION_SOURCES
# unit tests
validate_ball_and_stick.cpp
validate_soma.cpp
- #validate_synapses.cpp
+ validate_synapses.cpp
+
+ # support code
+ validation_data.cpp
# unit test driver
validate.cpp
diff --git a/tests/validation/test.cpp b/tests/validation/test.cpp
deleted file mode 100644
index f2eab0931a0b4b2a5b17ed12ba6c2f3d1d09d27c..0000000000000000000000000000000000000000
--- a/tests/validation/test.cpp
+++ /dev/null
@@ -1,11 +0,0 @@
-#include <iostream>
-#include <fstream>
-#include <numeric>
-#include <vector>
-
-#include "gtest.h"
-
-int main(int argc, char **argv) {
- ::testing::InitGoogleTest(&argc, argv);
- return RUN_ALL_TESTS();
-}
diff --git a/tests/validation/validate.cpp b/tests/validation/validate.cpp
index d814fca1512dd79b22763a4f9a769f2984ca5269..1e71cde23cd107b7a784b19a5f90feb61042b437 100644
--- a/tests/validation/validate.cpp
+++ b/tests/validation/validate.cpp
@@ -1,7 +1,30 @@
+#include <iostream>
+#include <fstream>
+#include <numeric>
+#include <vector>
+
#include "gtest.h"
+#include "validation_data.hpp"
+
+int usage(const char* argv0) {
+ std::cerr << "usage: " << argv0 << " [-p|--path validation_data_directory]\n";
+ return 1;
+}
int main(int argc, char **argv) {
::testing::InitGoogleTest(&argc, argv);
+
+ if (argv[1] && (!strcmp(argv[1], "-p") || !strcmp(argv[1], "--path"))) {
+ if (argv[2]) {
+ testing::g_validation_data.set_path(argv[2]);
+ }
+ else {
+ return usage(argv[0]);
+ }
+ }
+ else if (argv[1]) {
+ return usage(argv[0]);
+ }
+
return RUN_ALL_TESTS();
}
-
diff --git a/tests/validation/validate_ball_and_stick.cpp b/tests/validation/validate_ball_and_stick.cpp
index 803550641694fb1226bf90c42877634aa9a4fd34..0e41bd021534af6020482659f082eca0867fb63a 100644
--- a/tests/validation/validate_ball_and_stick.cpp
+++ b/tests/validation/validate_ball_and_stick.cpp
@@ -1,12 +1,13 @@
#include <fstream>
#include <json/src/json.hpp>
-#include "gtest.h"
-#include "../test_util.hpp"
-
#include <cell.hpp>
#include <fvm_cell.hpp>
+#include "gtest.h"
+#include "../test_util.hpp"
+#include "validation_data.hpp"
+
// compares results with those generated by nrn/ball_and_stick.py
TEST(ball_and_stick, neuron_baseline)
{
@@ -32,7 +33,7 @@ TEST(ball_and_stick, neuron_baseline)
cell.add_stimulus({1,1}, {5., 80., 0.3});
// load data from file
- auto cell_data = testing::load_spike_data("../nrn/ball_and_stick.json");
+ auto cell_data = testing::g_validation_data.load("ball_and_stick.json");
EXPECT_TRUE(cell_data.size()>0);
if(cell_data.size()==0) return;
@@ -187,7 +188,7 @@ TEST(ball_and_3stick, neuron_baseline)
cell.add_stimulus({3,1}, {40., 10.,-0.2});
// load data from file
- auto cell_data = testing::load_spike_data("../nrn/ball_and_3stick.json");
+ auto cell_data = testing::g_validation_data.load("ball_and_3stick.json");
EXPECT_TRUE(cell_data.size()>0);
if(cell_data.size()==0) return;
diff --git a/tests/validation/validate_soma.cpp b/tests/validation/validate_soma.cpp
index dac3ca0fd7604a307b46ed25441334d5641b1ca7..9c3c9fdfa56b14b9aa948c762023355541866d9a 100644
--- a/tests/validation/validate_soma.cpp
+++ b/tests/validation/validate_soma.cpp
@@ -1,12 +1,13 @@
#include <fstream>
#include <json/src/json.hpp>
-#include "gtest.h"
-#include "../test_util.hpp"
-
#include <cell.hpp>
#include <fvm_cell.hpp>
+#include "gtest.h"
+#include "../test_util.hpp"
+#include "validation_data.hpp"
+
// compares results with those generated by nrn/soma.py
// single compartment model with HH channels
TEST(soma, neuron_baseline)
@@ -31,7 +32,7 @@ TEST(soma, neuron_baseline)
fvm::fvm_cell<double, int> model(cell);
// load data from file
- auto cell_data = testing::load_spike_data("../nrn/soma.json");
+ auto cell_data = testing::g_validation_data.load("soma.json");
EXPECT_TRUE(cell_data.size()>0);
if(cell_data.size()==0) return;
diff --git a/tests/validation/validate_synapses.cpp b/tests/validation/validate_synapses.cpp
index 3b53b3c1ab48f8d2fc234550c9d27a6ac4644910..694887ce1cab4e27a322d48789200d5e07493608 100644
--- a/tests/validation/validate_synapses.cpp
+++ b/tests/validation/validate_synapses.cpp
@@ -1,13 +1,16 @@
#include <fstream>
+#include <iterator>
-#include "gtest.h"
-#include "../test_util.hpp"
+#include <json/src/json.hpp>
#include <cell.hpp>
+#include <cell_group.hpp>
#include <fvm_cell.hpp>
+#include <mechanism_interface.hpp>
-#include <json/src/json.hpp>
-
+#include "gtest.h"
+#include "../test_util.hpp"
+#include "validation_data.hpp"
// For storing the results of a simulation along with the information required
// to compare two simulations for accuracy.
@@ -51,7 +54,7 @@ TEST(simple_synapse, neuron_baseline)
nest::mc::cell cell;
// setup global state for the mechanisms
- nest::mc::mechanisms::setup_mechanism_helpers();
+ mechanisms::setup_mechanism_helpers();
// Soma with diameter 12.6157 um and HH channel
auto soma = cell.add_soma(12.6157/2.0);
@@ -67,8 +70,19 @@ TEST(simple_synapse, neuron_baseline)
// add stimulus
cell.add_synapse({1, 0.5});
+ // add porbes
+ auto probe_soma = cell.add_probe({0,0}, probeKind::membrane_voltage);
+ auto probe_dend = cell.add_probe({1,0.5}, probeKind::membrane_voltage);
+
+ // injected spike events
+ postsynaptic_spike_event synthetic_events[] = {
+ {0u, 10.0, 0.04},
+ {0u, 20.0, 0.04},
+ {0u, 40.0, 0.04}
+ };
+
// load data from file
- auto cell_data = testing::load_spike_data("../nrn/simple_synapse.json");
+ auto cell_data = testing::g_validation_data.load("simple_exp_synapse.json");
EXPECT_TRUE(cell_data.size()>0);
if(cell_data.size()==0) return;
@@ -91,34 +105,26 @@ TEST(simple_synapse, neuron_baseline)
std::vector<std::vector<double>> v(2);
// make the lowered finite volume cell
- fvm::fvm_cell<double, int> model(cell);
- auto graph = cell.model();
-
- // set initial conditions
- using memory::all;
- model.voltage()(all) = -65.;
- model.initialize(); // have to do this _after_ initial conditions are set
+ cell_group<fvm::fvm_cell<double, int>> group(cell);
+ group.set_source_gids(0);
+ group.set_target_gids(0);
// add the 3 spike events to the queue
- model.queue().push({0u, 10.0, 0.04});
- model.queue().push({0u, 20.0, 0.04});
- model.queue().push({0u, 40.0, 0.04});
+ group.enqueue_events(synthetic_events);
// run the simulation
- auto soma_comp = nest::mc::find_compartment_index({0,0}, graph);
- auto dend_comp = nest::mc::find_compartment_index({1,0.5}, graph);
- v[0].push_back(model.voltage()[soma_comp]);
- v[1].push_back(model.voltage()[dend_comp]);
+ v[0].push_back(group.cell().probe(probe_soma));
+ v[1].push_back(group.cell().probe(probe_dend));
double t = 0.;
while(t < tfinal) {
t += dt;
- model.advance_to(t, dt);
- // save voltage at soma
- v[0].push_back(model.voltage()[soma_comp]);
- v[1].push_back(model.voltage()[dend_comp]);
+ group.advance(t, dt);
+ // save voltage at soma and dendrite
+ v[0].push_back(group.cell().probe(probe_soma));
+ v[1].push_back(group.cell().probe(probe_dend));
}
- results.push_back( {num_compartments, dt, v, measurements} );
+ results.push_back({num_compartments, dt, v, measurements});
}
// print results
diff --git a/tests/validation/validation_data.cpp b/tests/validation/validation_data.cpp
new file mode 100644
index 0000000000000000000000000000000000000000..306adbaf38c02171f56a042f62662702d4faa3be
--- /dev/null
+++ b/tests/validation/validation_data.cpp
@@ -0,0 +1,21 @@
+#include "validation_data.hpp"
+
+#include <fstream>
+
+namespace testing {
+
+nlohmann::json data_loader::load(const std::string& name) const {
+ std::string data_path=path_+'/'+name;
+ std::ifstream fid(data_path);
+ if (!fid) {
+ throw std::runtime_error("unable to load validation data: "+data_path);
+ }
+
+ nlohmann::json data;
+ fid >> data;
+ return data;
+}
+
+data_loader g_validation_data;
+
+} // namespace testing
diff --git a/tests/validation/validation_data.hpp b/tests/validation/validation_data.hpp
new file mode 100644
index 0000000000000000000000000000000000000000..4abf6cca3aee6a6edd9ea7c0b8629cf62793b241
--- /dev/null
+++ b/tests/validation/validation_data.hpp
@@ -0,0 +1,25 @@
+#pragma once
+
+#include <json/src/json.hpp>
+
+#ifndef DATADIR
+#define DATADIR "../data"
+#endif
+
+namespace testing {
+
+struct data_loader {
+ // set where to find the validation JSON files
+ void set_path(const std::string& path) { path_=path; }
+
+ // load JSON file from path plus name, throw exception
+ // if cannot be found or loaded.
+ nlohmann::json load(const std::string& name) const;
+
+private:
+ std::string path_=DATADIR "/validation";
+};
+
+extern data_loader g_validation_data;
+
+} // namespace testing