From 42acdda8eef04f8ef60e40da0a0f8f2241fe6820 Mon Sep 17 00:00:00 2001
From: Nora Abi Akar <nora.abiakar@gmail.com>
Date: Tue, 29 Sep 2020 20:55:38 +0200
Subject: [PATCH] fix examples (#1164)
* Update `dryrun` to generate some spikes again, add a voltage printer.
* Fix `ring.py` recipe.
* Fix labels in `single_cell_builder.py` and `single_cell_swc.py`.
---
example/dryrun/dryrun.cpp | 38 +++++++++++++++++++++++++--
python/example/ring.py | 16 +++++------
python/example/single_cell_builder.py | 2 +-
python/example/single_cell_swc.py | 16 +++++------
python/recipe.cpp | 6 ++---
5 files changed, 53 insertions(+), 25 deletions(-)
diff --git a/example/dryrun/dryrun.cpp b/example/dryrun/dryrun.cpp
index 0ef5193d..54757996 100644
--- a/example/dryrun/dryrun.cpp
+++ b/example/dryrun/dryrun.cpp
@@ -18,6 +18,7 @@
#include <arbor/morph/primitives.hpp>
#include <arbor/profile/meter_manager.hpp>
#include <arbor/profile/profiler.hpp>
+#include <arbor/simple_sampler.hpp>
#include <arbor/simulation.hpp>
#include <arbor/symmetric_recipe.hpp>
#include <arbor/recipe.hpp>
@@ -44,6 +45,7 @@ struct run_params {
cell_parameters cell;
};
+void write_trace_json(const arb::trace_data<double>& trace);
run_params read_options(int argc, char** argv);
using arb::cell_gid_type;
@@ -115,7 +117,7 @@ public:
std::vector<arb::event_generator> event_generators(cell_gid_type gid) const override {
std::vector<arb::event_generator> gens;
if (gid%20 == 0) {
- gens.push_back(arb::explicit_generator(arb::pse_vector{{{gid, 0}, 0.1, 1.0}}));
+ gens.push_back(arb::explicit_generator(arb::pse_vector{{{gid, 0}, 1.0, event_weight_}}));
}
return gens;
}
@@ -130,7 +132,7 @@ private:
cell_size_type num_tiles_;
cell_parameters cell_params_;
double min_delay_;
- float event_weight_ = 0.01;
+ float event_weight_ = 0.05;
};
int main(int argc, char** argv) {
@@ -186,6 +188,15 @@ int main(int argc, char** argv) {
// Construct the model.
arb::simulation sim(recipe, decomp, ctx);
+ // The id of the only probe on the cell: the cell_member type points to (cell 0, probe 0)
+ auto probe_id = cell_member_type{0, 0};
+ // The schedule for sampling is 10 samples every 1 ms.
+ auto sched = arb::regular_schedule(1);
+ // This is where the voltage samples will be stored as (time, value) pairs
+ arb::trace_vector<double> voltage;
+ // Now attach the sampler at probe_id, with sampling schedule sched, writing to voltage
+ sim.add_sampler(arb::one_probe(probe_id), sched, arb::make_simple_sampler(voltage));
+
// Set up recording of spikes to a vector on the root process.
std::vector<arb::spike> recorded_spikes;
if (root) {
@@ -221,6 +232,8 @@ int main(int argc, char** argv) {
fid.write(linebuf, n);
}
}
+ // Write the samples to a json file.
+ write_trace_json(voltage.at(0));
}
auto profile = arb::profile::profiler_summary();
@@ -237,6 +250,27 @@ int main(int argc, char** argv) {
return 0;
}
+void write_trace_json(const arb::trace_data<double>& trace) {
+ std::string path = "./voltages.json";
+
+ nlohmann::json json;
+ json["name"] = "ring demo";
+ json["units"] = "mV";
+ json["cell"] = "0.0";
+ json["probe"] = "0";
+
+ auto& jt = json["data"]["time"];
+ auto& jy = json["data"]["voltage"];
+
+ for (const auto& sample: trace) {
+ jt.push_back(sample.t);
+ jy.push_back(sample.v);
+ }
+
+ std::ofstream file(path);
+ file << std::setw(1) << json << "\n";
+}
+
run_params read_options(int argc, char** argv) {
using sup::param_from_json;
diff --git a/python/example/ring.py b/python/example/ring.py
index 8ddaaf54..17d01f10 100644
--- a/python/example/ring.py
+++ b/python/example/ring.py
@@ -33,12 +33,12 @@ def make_cable_cell(gid):
cell = b.build()
# Put hh dynamics on soma, and passive properties on the dendrites.
- cell.paint('soma', 'hh')
- cell.paint('dend', 'pas')
+ cell.paint('"soma"', 'hh')
+ cell.paint('"dend"', 'pas')
# Attach a single synapse.
- cell.place('synapse_site', 'expsyn')
+ cell.place('"synapse_site"', 'expsyn')
# Attach a spike detector with threshold of -10 mV.
- cell.place('root', arbor.spike_detector(-10))
+ cell.place('"root"', arbor.spike_detector(-10))
return cell
@@ -84,13 +84,9 @@ class ring_recipe (arbor.recipe):
return [arbor.event_generator(arbor.cell_member(0,0), 0.1, sched)]
return []
- # Define one probe (for measuring voltage at the soma) on each cell.
- def num_probes(self, gid):
- return 1
-
- def get_probe(self, id):
+ def get_probes(self, gid):
loc = arbor.location(0, 0) # at the soma
- return arbor.cable_probe('voltage', id, loc)
+ return [arbor.cable_probe('voltage', loc)]
context = arbor.context(threads=12, gpu_id=None)
print(context)
diff --git a/python/example/single_cell_builder.py b/python/example/single_cell_builder.py
index 58e7054c..98ce339b 100644
--- a/python/example/single_cell_builder.py
+++ b/python/example/single_cell_builder.py
@@ -64,7 +64,7 @@ cell.place('"stim_site"', arbor.iclamp( 10, 2, 0.8))
cell.place('"stim_site"', arbor.iclamp( 50, 2, 0.8))
cell.place('"stim_site"', arbor.iclamp( 80, 2, 0.8))
# Add a spike detector with threshold of -10 mV.
-cell.place('root', arbor.spike_detector(-10))
+cell.place('"root"', arbor.spike_detector(-10))
# Make single cell model.
m = arbor.single_cell_model(cell)
diff --git a/python/example/single_cell_swc.py b/python/example/single_cell_swc.py
index 957dc8bf..f50768bb 100644
--- a/python/example/single_cell_swc.py
+++ b/python/example/single_cell_swc.py
@@ -14,9 +14,7 @@ from arbor import location as loc
import matplotlib.pyplot as plt
# Load a cell morphology from an swc file.
-# The model has 31 branches, including soma, dendrites and axon.
-#tree = arbor.load_swc('../../test/unit/swc/example.swc')
-tree = arbor.load_swc('example.swc')
+tree = arbor.load_swc('../../test/unit/swc/pyramidal.swc')
# Define the regions and locsets in the model.
defs = {'soma': '(tag 1)', # soma has tag 1 in swc files.
@@ -30,7 +28,7 @@ labels = arbor.label_dict(defs)
# Combine morphology with region and locset definitions to make a cable cell.
cell = arbor.cable_cell(tree, labels)
-print(cell.locations('axon_end'))
+print(cell.locations('"axon_end"'))
# Set initial membrane potential to -55 mV
cell.set_properties(Vm=-55)
@@ -44,8 +42,8 @@ cell.paint('"dend"', 'pas')
# Increase resistivity on dendrites.
cell.paint('"dend"', rL=500)
# Attach stimuli that inject 0.8 nA currents for 1 ms, starting at 3 and 8 ms.
-cell.place('"stim_site"', arbor.iclamp(3, 1, current=0.5))
-cell.place('"stim_site"', arbor.iclamp(8, 1, current=1))
+cell.place('"stim_site"', arbor.iclamp(3, 1, current=2))
+cell.place('"stim_site"', arbor.iclamp(8, 1, current=4))
# Detect spikes at the soma with a voltage threshold of -10 mV.
cell.place('"root"', arbor.spike_detector(-10))
@@ -56,10 +54,10 @@ cell.compartments_on_segments()
m = arbor.single_cell_model(cell)
# Attach voltage probes that sample at 50 kHz.
-m.probe('voltage', where='root', frequency=50000)
+m.probe('voltage', where='"root"', frequency=50000)
m.probe('voltage', where=loc(2,1), frequency=50000)
-m.probe('voltage', where='stim_site', frequency=50000)
-m.probe('voltage', where='axon_end', frequency=50000)
+m.probe('voltage', where='"stim_site"', frequency=50000)
+m.probe('voltage', where='"axon_end"', frequency=50000)
# Simulate the cell for 15 ms.
tfinal=15
diff --git a/python/recipe.cpp b/python/recipe.cpp
index 45c5cfa3..922f47e5 100644
--- a/python/recipe.cpp
+++ b/python/recipe.cpp
@@ -29,7 +29,7 @@ arb::util::unique_any py_recipe_shim::get_cell_description(arb::cell_gid_type gi
"Python error already thrown");
}
-arb::probe_info cable_loc_probe(std::string kind, arb::cell_member_type id, arb::mlocation loc) {
+arb::probe_info cable_loc_probe(std::string kind, arb::mlocation loc) {
if (kind == "voltage") {
return arb::cable_probe_membrane_voltage{loc};
}
@@ -170,9 +170,9 @@ void register_recipe(pybind11::module& m) {
// Probes
m.def("cable_probe", &cable_loc_probe,
- "Description of a probe at a location on a cable cell with id available for monitoring data of kind "\
+ "Description of a probe at a location available for monitoring data of kind "\
"where kind is one of 'voltage' or 'ionic current density'.",
- "kind"_a, "id"_a, "location"_a);
+ "kind"_a, "location"_a);
pybind11::class_<arb::probe_info> probe(m, "probe");
probe
--
GitLab