From df3bc45d5aff6021a49821c425c25faf887e4eb0 Mon Sep 17 00:00:00 2001
From: Sam Yates <yates@cscs.ch>
Date: Fri, 1 Mar 2019 18:11:58 +0100
Subject: [PATCH] Add single cell example. (#703)
Adds a small self contained example demonstrating the use of SWC and morphology specifications, to fill a void that will be left when the miniapp is removed.
* Adds `single-cell` example, together with short README and example SWC file.
* Removes redundant constructors for context objects.
* Corrects and simplifies some of the context comments.
* Add a method to `mc_segment` for calculating (approximately) a lower bound on the length constant of that segment for a given frequency, for use with a NEURON 'd-lambda' style discretization rule.
---
arbor/execution_context.cpp | 8 -
arbor/execution_context.hpp | 3 +-
arbor/include/arbor/context.hpp | 39 +-
arbor/include/arbor/mc_segment.hpp | 25 +
example/CMakeLists.txt | 1 +
example/single/CMakeLists.txt | 3 +
example/single/README.md | 36 +
example/single/example.swc | 1062 ++++++++++++++++++++++++++++
example/single/single.cpp | 166 +++++
9 files changed, 1311 insertions(+), 32 deletions(-)
create mode 100644 example/single/CMakeLists.txt
create mode 100644 example/single/README.md
create mode 100644 example/single/example.swc
create mode 100644 example/single/single.cpp
diff --git a/arbor/execution_context.cpp b/arbor/execution_context.cpp
index 989ef13f..2ef429f2 100644
--- a/arbor/execution_context.cpp
+++ b/arbor/execution_context.cpp
@@ -14,10 +14,6 @@
namespace arb {
-execution_context::execution_context():
- execution_context(proc_allocation())
-{}
-
execution_context::execution_context(const proc_allocation& resources):
distributed(make_local_context()),
thread_pool(std::make_shared<threading::task_system>(resources.num_threads)),
@@ -25,10 +21,6 @@ execution_context::execution_context(const proc_allocation& resources):
: std::make_shared<gpu_context>())
{}
-context make_context() {
- return context(new execution_context(), [](execution_context* p){delete p;});
-}
-
context make_context(const proc_allocation& p) {
return context(new execution_context(p), [](execution_context* p){delete p;});
}
diff --git a/arbor/execution_context.hpp b/arbor/execution_context.hpp
index ee1e8415..79935f75 100644
--- a/arbor/execution_context.hpp
+++ b/arbor/execution_context.hpp
@@ -24,8 +24,7 @@ struct execution_context {
task_system_handle thread_pool;
gpu_context_handle gpu;
- execution_context();
- execution_context(const proc_allocation& resources);
+ execution_context(const proc_allocation& resources = proc_allocation{});
// Use a template for constructing with a specific distributed context.
// Specialised implementations are implemented in execution_context.cpp.
diff --git a/arbor/include/arbor/context.hpp b/arbor/include/arbor/context.hpp
index d28b8659..b1210c3f 100644
--- a/arbor/include/arbor/context.hpp
+++ b/arbor/include/arbor/context.hpp
@@ -4,7 +4,7 @@
namespace arb {
-/// Requested dry-run parameters
+// Requested dry-run parameters.
struct dry_run_info {
unsigned num_ranks;
unsigned num_cells_per_rank;
@@ -13,17 +13,18 @@ struct dry_run_info {
num_cells_per_rank(cells_per_rank) {}
};
-/// A subset of local computation resources to use in a computation.
+// A description of local computation resources to use in a computation.
+// By default, a proc_allocation will comprise one thread and no GPU.
+
struct proc_allocation {
unsigned num_threads;
- // The gpu id corresponds to the `int device` parameter used by CUDA API calls
- // to identify gpu devices.
- // Set to -1 to indicate that no GPU device is to be used.
- // see CUDA documenation for cudaSetDevice and cudaDeviceGetAttribute
+ // The gpu id corresponds to the `int device` parameter used by
+ // CUDA API calls to identify gpu devices.
+ // A gpud id of -1 indicates no GPU device is to be used.
+ // See CUDA documenation for cudaSetDevice and cudaDeviceGetAttribute.
int gpu_id;
- // By default use one thread and no GPU.
proc_allocation(): proc_allocation(1, -1) {}
proc_allocation(unsigned threads, int gpu):
@@ -36,30 +37,24 @@ struct proc_allocation {
}
};
-// arb::execution_context is a container defined in the implementation for state
-// related to execution resources, specifically thread pools, gpus and MPI
-// communicators.
+// arb::execution_context encapsulates the execution resources used in
+// a simulation, namely the task system thread pools, GPU handle, and
+// MPI communicator if applicable.
// Forward declare execution_context.
struct execution_context;
-// arb::context is an opaque handle for this container presented in the
-// public API.
-// It doesn't make sense to copy contexts, so we use a std::unique_ptr to
-// implement the handle with lifetime management.
+// arb::context is an opaque handle for the execution context for use
+// in the public API, implemented as a unique pointer.
//
-// Because execution_context is an incomplete type, a destructor prototype must
-// be provided.
+// As execution_context is an incomplete type, an explicit deleter must be
+// provided.
using context = std::unique_ptr<execution_context, void (*)(execution_context*)>;
-
// Helpers for creating contexts. These are implemented in the back end.
-// Non-distributed context that uses all detected threads and one GPU if available.
-context make_context();
-
-// Non-distributed context that uses resources described by resources
-context make_context(const proc_allocation& resources);
+// Non-distributed context using the requested resources.
+context make_context(const proc_allocation& resources = proc_allocation{});
// Distributed context that uses MPI communicator comm, and local resources
// described by resources. Or dry run context that uses dry_run_info.
diff --git a/arbor/include/arbor/mc_segment.hpp b/arbor/include/arbor/mc_segment.hpp
index 7a0a7c28..ded52d54 100644
--- a/arbor/include/arbor/mc_segment.hpp
+++ b/arbor/include/arbor/mc_segment.hpp
@@ -11,6 +11,7 @@
#include <arbor/assert.hpp>
#include <arbor/common_types.hpp>
+#include <arbor/math.hpp>
#include <arbor/morphology.hpp>
#include <arbor/mechinfo.hpp>
#include <arbor/point.hpp>
@@ -134,6 +135,11 @@ public:
return false;
}
+ // Approximate frequency-dependent length constant lower bound.
+ virtual value_type length_constant(value_type freq_Hz) const {
+ return 0;
+ }
+
util::optional<mechanism_desc&> mechanism(const std::string& name) {
auto it = std::find_if(mechanisms_.begin(), mechanisms_.end(),
[&](mechanism_desc& m) { return m.name()==name; });
@@ -291,6 +297,25 @@ public:
return std::accumulate(lengths_.begin(), lengths_.end(), value_type{});
}
+ value_type length_constant(value_type freq_Hz) const override {
+ // Following Hine and Carnevale (2001), "NEURON: A Tool for Neuroscientists",
+ // Neuroscientist 7, pp. 123-135.
+ //
+ // λ(f) = approx. sqrt(diameter/(pi*f*rL*cm))/2.
+ //
+ // Pick smallest non-zero diameter in the segment.
+
+ value_type r_min = 0;
+ for (auto r: radii_) {
+ if (r>0 && (r_min==0 || r<r_min)) r_min = r;
+ }
+ value_type d_min = r_min*2e-6; // [m]
+ value_type rc = rL*0.01*cm; // [s/m]
+ value_type lambda = std::sqrt(d_min/(math::pi<double>*freq_Hz*rc))/2.; // [m]
+
+ return lambda*1e6; // [µm]
+ }
+
bool has_locations() const
{
return locations_.size() > 0;
diff --git a/example/CMakeLists.txt b/example/CMakeLists.txt
index 990a5671..d1e68b39 100644
--- a/example/CMakeLists.txt
+++ b/example/CMakeLists.txt
@@ -9,3 +9,4 @@ add_subdirectory(brunel)
add_subdirectory(bench)
add_subdirectory(ring)
add_subdirectory(gap_junctions)
+add_subdirectory(single)
diff --git a/example/single/CMakeLists.txt b/example/single/CMakeLists.txt
new file mode 100644
index 00000000..6b2afe48
--- /dev/null
+++ b/example/single/CMakeLists.txt
@@ -0,0 +1,3 @@
+add_executable(single-cell EXCLUDE_FROM_ALL single.cpp)
+add_dependencies(examples single-cell)
+target_link_libraries(single-cell PRIVATE arbor arborenv arbor-sup)
diff --git a/example/single/README.md b/example/single/README.md
new file mode 100644
index 00000000..64f34801
--- /dev/null
+++ b/example/single/README.md
@@ -0,0 +1,36 @@
+# 'single' example.
+
+Example of simulating a single neuron with morphology described by an SWC file.
+
+A cell is constructed from a supplied morphology with H–H channels
+on the soma and passive channels on the dendrites. A simple exponential
+synapse is added at the end of the last dendrite in the morphology,
+and is triggered at time t = 1 ms.
+
+The simulation outputs a trace of the soma membrane voltage in a simple CSV
+format.
+
+## Features
+
+The example demonstrates the use of:
+
+* Generating a morphology from an SWC file.
+* Using a morphology to construct a cable cell.
+* Injecting an artificial spike event into the simulation.
+* Adding a voltage probe to a cell and running a sampler on the simulation.
+
+## Running the example
+
+By default, `single-cell` will simulate a 'ball-and-stick' neuron for 20 ms,
+with a maxium dt of 0.025 ms and samples taken every 0.1 ms. The default
+synaptic weight is 0.01 µS.
+
+### Command line options
+
+| Option | Effect |
+|-----------------------|--------|
+| -m, --morphology FILE | Load the morphology from FILE in SWC format |
+| -d, --dt TIME | Set the maximum integration time step [ms] |
+| -t, --t-end TIME | Set the simulation duration [ms] |
+| -w, --weight WEIGHT | Set the synaptic weight [µS] |
+
diff --git a/example/single/example.swc b/example/single/example.swc
new file mode 100644
index 00000000..84addf08
--- /dev/null
+++ b/example/single/example.swc
@@ -0,0 +1,1062 @@
+#example swc file from the Allen DB
+#name C:/neuron tracing and reconstruction/vaa3d/vaa3d_bin_msvc_64bit_v2921_a/vaa3d_bin_msvc_64bit_v2921_a/Sst-IRES-Cre;Ai14(IVSCC)-173191.06.01.01.DS.swc_resampled.swc_sorted.swc_pruned.swc_pruned.swc
+#comment
+##n,type,x,y,z,radius,parent
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diff --git a/example/single/single.cpp b/example/single/single.cpp
new file mode 100644
index 00000000..9237f335
--- /dev/null
+++ b/example/single/single.cpp
@@ -0,0 +1,166 @@
+#include <fstream>
+#include <iomanip>
+#include <iostream>
+#include <stdexcept>
+#include <string>
+#include <vector>
+
+#include <arbor/load_balance.hpp>
+#include <arbor/mc_cell.hpp>
+#include <arbor/morphology.hpp>
+#include <arbor/swcio.hpp>
+#include <arbor/simulation.hpp>
+#include <arbor/simple_sampler.hpp>
+
+#include <sup/tinyopt.hpp>
+
+struct options {
+ std::string swc_file;
+ double t_end = 20;
+ double dt = 0.025;
+ float syn_weight = 0.01;
+};
+
+options parse_options(int argc, char** argv);
+arb::morphology default_morphology();
+arb::morphology read_swc(const std::string& path);
+
+struct single_recipe: public arb::recipe {
+ explicit single_recipe(arb::morphology m): morpho(m) {}
+
+ arb::cell_size_type num_cells() const override { return 1; }
+ arb::cell_size_type num_probes(arb::cell_gid_type) const override { return 1; }
+ arb::cell_size_type num_targets(arb::cell_gid_type) const override { return 1; }
+
+ arb::probe_info get_probe(arb::cell_member_type probe_id) const override {
+ arb::segment_location mid_soma = {0, 0.5};
+ arb::cell_probe_address probe = {mid_soma, arb::cell_probe_address::membrane_voltage};
+
+ // Probe info consists of: the probe id, a tag value to distinguish this probe
+ // from others for any attached sampler (unused), and the cell probe address.
+
+ return {probe_id, 0, probe};
+ }
+
+ arb::cell_kind get_cell_kind(arb::cell_gid_type) const override {
+ return arb::cell_kind::cable1d_neuron;
+ }
+
+ arb::util::unique_any get_cell_description(arb::cell_gid_type) const override {
+ arb::mc_cell c = make_mc_cell(morpho);
+
+ // Add HH mechanism to soma, passive channels to dendrites.
+ // Discretize dendrites according to the NEURON d-lambda rule.
+
+ for (auto& segment: c.segments()) {
+ if (segment->is_soma()) {
+ segment->add_mechanism("hh");
+ }
+ else {
+ segment->add_mechanism("pas");
+
+ double dx = segment->length_constant(100.)*0.3;
+ unsigned n = std::ceil(segment->as_cable()->length()/dx);
+ segment->set_compartments(n);
+
+ }
+ }
+
+ // Add synapse to last segment.
+
+ arb::cell_lid_type last_segment = morpho.components()-1;
+ arb::segment_location end_last_segment = { last_segment, 1. };
+ c.add_synapse(end_last_segment, "exp2syn");
+
+ return c;
+ }
+
+ arb::morphology morpho;
+};
+
+int main(int argc, char** argv) {
+ try {
+ options opt = parse_options(argc, argv);
+ single_recipe R(opt.swc_file.empty()? default_morphology(): read_swc(opt.swc_file));
+
+ auto context = arb::make_context();
+ arb::simulation sim(R, arb::partition_load_balance(R, context), context);
+
+ // Attach a sampler to the probe described in the recipe, sampling every 0.1 ms.
+
+ arb::trace_data<double> trace;
+ sim.add_sampler(arb::all_probes, arb::regular_schedule(0.1), arb::make_simple_sampler(trace));
+
+ // Trigger the single synapse (target is gid 0, index 0) at t = 1 ms with
+ // the given weight.
+
+ arb::spike_event spike = {{0, 0}, 1., opt.syn_weight};
+ sim.inject_events({spike});
+
+ sim.run(opt.t_end, opt.dt);
+
+ std::cout << std::fixed << std::setprecision(4);
+ for (auto entry: trace) {
+ std::cout << entry.t << ", " << entry.v << "\n";
+ }
+ }
+ catch (std::exception& e) {
+ std::cerr << "caught exception: " << e.what() << "\n";
+ return 2;
+ }
+}
+
+options parse_options(int argc, char** argv) {
+ using namespace to;
+ options opt;
+
+ char** arg = argv+1;
+ while (*arg) {
+ if (auto dt = parse_opt<double>(arg, 'd', "dt")) {
+ opt.dt = dt.value();
+ }
+ else if (auto t_end = parse_opt<double>(arg, 't', "t-end")) {
+ opt.t_end = t_end.value();
+ }
+ else if (auto weight = parse_opt<float>(arg, 'w', "weight")) {
+ opt.syn_weight = weight.value();
+ }
+ else if (auto swc = parse_opt<std::string>(arg, 'm', "morphology")) {
+ opt.swc_file = swc.value();
+ }
+ else {
+ usage(argv[0], "[-m|--morphology SWCFILE] [-d|--dt TIME] [-t|--t-end TIME] [-w|--weight WEIGHT]");
+ std::exit(1);
+ }
+ }
+ return opt;
+}
+
+// If no SWC file is given, the default morphology consists
+// of a soma of radius 6.3 µm and a single unbranched dendrite
+// of length 200 µm and radius decreasing linearly from 0.5 µm
+// to 0.2 µm.
+
+arb::morphology default_morphology() {
+ arb::morphology m;
+
+ // Points in a morphology are expressed as (x, y, z, r),
+ // with r being the radius. Units are µm.
+
+ m.soma = {0., 0., 0., 6.3};
+
+ std::vector<arb::section_point> dendrite = {
+ {6.3, 0., 0., 0.5},
+ {206.3, 0., 0., 0.2}
+ };
+ m.add_section(dendrite, 0);
+
+ return m;
+}
+
+arb::morphology read_swc(const std::string& path) {
+ std::ifstream f(path);
+ if (!f) throw std::runtime_error("unable to open SWC file: "+path);
+
+ return arb::swc_as_morphology(arb::parse_swc_file(f));
+}
--
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