diff --git a/arbor/include/arbor/lif_cell.hpp b/arbor/include/arbor/lif_cell.hpp
index cff3eeb55104b4b6da453d661e6a8b467a61c297..64557616f2e03d0fdae119a5c17fe0acda9b2a2e 100644
--- a/arbor/include/arbor/lif_cell.hpp
+++ b/arbor/include/arbor/lif_cell.hpp
@@ -16,11 +16,17 @@ struct ARB_SYMBOL_VISIBLE lif_cell {
double C_m = 20; // Membrane capacitance [pF].
double E_L = 0; // Resting potential [mV].
double V_m = E_L; // Initial value of the Membrane potential [mV].
- double V_reset = E_L; // Reset potential [mV].
double t_ref = 2; // Refractory period [ms].
lif_cell() = delete;
lif_cell(cell_tag_type source, cell_tag_type target): source(std::move(source)), target(std::move(target)) {}
};
+// LIF probe metadata, to be passed to sampler callbacks. Intentionally left blank.
+struct ARB_SYMBOL_VISIBLE lif_probe_metadata {};
+
+// Voltage estimate [mV].
+// Sample value type: `double`
+struct ARB_SYMBOL_VISIBLE lif_probe_voltage {};
+
} // namespace arb
diff --git a/arbor/lif_cell_group.cpp b/arbor/lif_cell_group.cpp
index 0fa71789ec73ee47148e657e05ccc89dc4eda65a..1dffa20d3c89b66b800edd0ff3ae2cc2932b8208 100644
--- a/arbor/lif_cell_group.cpp
+++ b/arbor/lif_cell_group.cpp
@@ -5,6 +5,8 @@
#include "profile/profiler_macro.hpp"
#include "util/rangeutil.hpp"
#include "util/span.hpp"
+#include "util/filter.hpp"
+#include "util/maputil.hpp"
using namespace arb;
@@ -13,8 +15,16 @@ lif_cell_group::lif_cell_group(const std::vector<cell_gid_type>& gids, const rec
gids_(gids)
{
for (auto gid: gids_) {
- if (!rec.get_probes(gid).empty()) {
- throw bad_cell_probe(cell_kind::lif, gid);
+ auto probes = rec.get_probes(gid);
+ for (const auto lid: util::count_along(probes)) {
+ const auto& probe = probes[lid];
+ if (probe.address.type() == typeid(lif_probe_voltage)) {
+ cell_member_type id{gid, static_cast<cell_lid_type>(lid)};
+ probes_[id] = {probe.tag, lif_probe_kind::voltage, {}};
+ }
+ else {
+ throw bad_cell_probe{cell_kind::lif, gid};
+ }
}
}
// Default to no binning of events
@@ -22,6 +32,7 @@ lif_cell_group::lif_cell_group(const std::vector<cell_gid_type>& gids, const rec
cells_.reserve(gids_.size());
last_time_updated_.resize(gids_.size());
+ next_time_updatable_.resize(gids_.size());
for (auto lid: util::make_span(gids_.size())) {
cells_.push_back(util::any_cast<lif_cell>(rec.get_cell_description(gids_[lid])));
@@ -41,11 +52,9 @@ cell_kind lif_cell_group::get_cell_kind() const {
void lif_cell_group::advance(epoch ep, time_type dt, const event_lane_subrange& event_lanes) {
PE(advance:lif);
- if (event_lanes.size() > 0) {
- for (auto lid: util::make_span(gids_.size())) {
- // Advance each cell independently.
- advance_cell(ep.t1, dt, lid, event_lanes[lid]);
- }
+ for (auto lid: util::make_span(gids_.size())) {
+ // Advance each cell independently.
+ advance_cell(ep.t1, dt, lid, event_lanes);
}
PL();
}
@@ -59,10 +68,30 @@ void lif_cell_group::clear_spikes() {
}
// TODO: implement sampler
-void lif_cell_group::add_sampler(sampler_association_handle h, cell_member_predicate probeset_ids,
- schedule sched, sampler_function fn, sampling_policy policy) {}
-void lif_cell_group::remove_sampler(sampler_association_handle h) {}
-void lif_cell_group::remove_all_samplers() {}
+void lif_cell_group::add_sampler(sampler_association_handle h,
+ cell_member_predicate probeset_ids,
+ schedule sched,
+ sampler_function fn,
+ sampling_policy policy) {
+ std::lock_guard<std::mutex> guard(sampler_mex_);
+ std::vector<cell_member_type> probeset =
+ util::assign_from(util::filter(util::keys(probes_), probeset_ids));
+ auto assoc = arb::sampler_association{std::move(sched),
+ std::move(fn),
+ std::move(probeset),
+ policy};
+ auto result = samplers_.insert({h, std::move(assoc)});
+ arb_assert(result.second);
+}
+
+void lif_cell_group::remove_sampler(sampler_association_handle h) {
+ std::lock_guard<std::mutex> guard(sampler_mex_);
+ samplers_.erase(h);
+}
+void lif_cell_group::remove_all_samplers() {
+ std::lock_guard<std::mutex> guard(sampler_mex_);
+ samplers_.clear();
+}
// TODO: implement binner_
void lif_cell_group::set_binning_policy(binning_kind policy, time_type bin_interval) {
@@ -71,52 +100,143 @@ void lif_cell_group::set_binning_policy(binning_kind policy, time_type bin_inter
void lif_cell_group::reset() {
spikes_.clear();
util::fill(last_time_updated_, 0.);
+ util::fill(next_time_updatable_, 0.);
}
// Advances a single cell (lid) with the exact solution (jumps can be arbitrary).
// Parameter dt is ignored, since we make jumps between two consecutive spikes.
-void lif_cell_group::advance_cell(time_type tfinal, time_type dt, cell_gid_type lid, pse_vector& event_lane) {
- // Current time of last update.
- auto t = last_time_updated_[lid];
+void lif_cell_group::advance_cell(time_type tfinal, time_type dt, cell_gid_type lid, const event_lane_subrange& event_lanes) {
+ const auto gid = gids_[lid];
auto& cell = cells_[lid];
- const auto n_events = event_lane.size();
-
- // Integrate until tfinal using the exact solution of membrane voltage differential equation.
- for (unsigned i=0; i<n_events; ++i ) {
- auto& ev = event_lane[i];
- const auto time = ev.time;
- auto weight = ev.weight;
-
- if (time < t) continue; // skip event if a neuron is in refactory period
- if (time >= tfinal) break; // end of integration interval
-
- // if there are events that happened at the same time as this event, process them as well
- while (i + 1 < n_events && event_lane[i+1].time <= time) {
- weight += event_lane[i+1].weight;
- i++;
+ // time of last update.
+ auto t = last_time_updated_[lid];
+ // spikes to process
+ const auto n_events = static_cast<int>(event_lanes.size() ? event_lanes[lid].size() : 0);
+ int event_idx = 0;
+ // collected sampling data
+ std::unordered_map<sampler_association_handle,
+ std::unordered_map<cell_member_type,
+ std::vector<sample_record>>> sampled;
+ // samples to process
+ std::size_t n_values = 0;
+ std::vector<std::pair<time_type, sampler_association_handle>> samples;
+ {
+ std::lock_guard<std::mutex> guard(sampler_mex_);
+ for (auto& [hdl, assoc]: samplers_) {
+ // Construct sampling times
+ const auto& times = util::make_range(assoc.sched.events(t, tfinal));
+ const auto n_times = times.size();
+ // Count up the samplers touching _our_ gid
+ int delta = 0;
+ for (const auto& pid: assoc.probeset_ids) {
+ if (pid.gid != gid) continue;
+ arb_assert (0 == sampled[hdl].count(pid));
+ sampled[hdl][pid].reserve(n_times);
+ delta += n_times;
+ }
+ if (delta == 0) continue;
+ n_values += delta;
+ // only exact sampling: ignore lax and never look at policy
+ for (auto t: times) samples.emplace_back(t, hdl);
+ }
+ }
+ std::sort(samples.begin(), samples.end());
+ int n_samples = samples.size();
+ int sample_idx = 0;
+ // Now allocate some scratch space for the probed values, if we don't,
+ // re-alloc might move our data
+ std::vector<value_type> sampled_voltages;
+ sampled_voltages.reserve(n_values);
+ // integrate until tfinal using the exact solution of membrane voltage differential equation.
+ for (;;) {
+ const auto event_time = event_idx < n_events ? event_lanes[lid][event_idx].time : tfinal;
+ const auto sample_time = sample_idx < n_samples ? samples[sample_idx].first : tfinal;
+ const auto time = std::min(event_time, sample_time);
+ // bail at end of integration interval
+ if (time >= tfinal) break;
+ // Check what to do, we might need to process events **and/or** perform
+ // sampling.
+ // NB. we put events before samples, if they collide we'll see
+ // the update in sampling.
+
+ bool do_event = time == event_time;
+ bool do_sample = time == sample_time;
+
+ if (do_event) {
+ const auto& event_lane = event_lanes[lid];
+ // process all events at time t
+ auto weight = 0.0;
+ for (; event_idx < n_events && event_lane[event_idx].time <= time; ++event_idx) {
+ weight += event_lane[event_idx].weight;
+ }
+ // skip event if neuron is in refactory period
+ if (time >= t) {
+ // Let the membrane potential decay.
+ cell.V_m *= exp((t - time) / cell.tau_m);
+ // Add jump due to spike(s).
+ cell.V_m += weight / cell.C_m;
+ // Update current time
+ t = time;
+ // If crossing threshold occurred
+ if (cell.V_m >= cell.V_th) {
+ // save spike
+ spikes_.push_back({{gid, 0}, time});
+ // Advance to account for the refractory period.
+ // This means decay will also start at t + t_ref
+ t += cell.t_ref;
+ // Reset the voltage to resting potential.
+ cell.V_m = cell.E_L;
+ }
+ }
}
- // Let the membrane potential decay.
- auto decay = exp(-(time - t) / cell.tau_m);
- cell.V_m *= decay;
- auto update = weight / cell.C_m;
- // Add jump due to spike.
- cell.V_m += update;
- t = time;
- // If crossing threshold occurred
- if (cell.V_m >= cell.V_th) {
- cell_member_type spike_neuron_gid = {gids_[lid], 0};
- spike s = {spike_neuron_gid, t};
- spikes_.push_back(s);
-
- // Advance the last_time_updated to account for the refractory period.
- t += cell.t_ref;
-
- // Reset the voltage to resting potential.
- cell.V_m = cell.E_L;
+ if (do_sample) {
+ // Consume all sample events at this time
+ for (; sample_idx < n_samples && samples[sample_idx].first <= time; ++sample_idx) {
+ const auto& [s_time, hdl] = samples[sample_idx];
+ for (const auto& key: samplers_[hdl].probeset_ids) {
+ const auto& kind = probes_.at(key).kind;
+ // This is the only thing we know how to do: Probing U(t)
+ switch (kind) {
+ case lif_probe_kind::voltage: {
+ // Compute, but do not _set_ V_m
+ auto U = cell.V_m;
+ if (time >= t) U *= exp((t - time) / cell.tau_m);
+ // Store U for later use.
+ sampled_voltages.push_back(U);
+ // Set up reference to sampled value
+ sampled[hdl][key].push_back(sample_record{time, {&sampled_voltages.back()}});
+ break;
+ }
+ default:
+ throw arbor_internal_error{"Invalid LIF probe kind"};
+ }
+ }
+ }
+ }
+ if (!(do_sample || do_event)) {
+ throw arbor_internal_error{"LIF cell group: Must select either sample or spike event; got neither."};
}
+ last_time_updated_[lid] = t;
}
+ arb_assert (sampled_voltages.size() == n_values);
+ // Now we need to call all sampler callbacks with the data we have collected
+ {
+ std::lock_guard<std::mutex> guard(sampler_mex_);
+ for (const auto& [k, vs]: sampled) {
+ const auto& fun = samplers_[k].sampler;
+ for (const auto& [id, us]: vs) {
+ auto meta = get_probe_metadata(id)[0];
+ fun(meta, us.size(), us.data());
+ }
+ }
+ }
+}
- // This is the last time a cell was updated.
- last_time_updated_[lid] = t;
+std::vector<probe_metadata> lif_cell_group::get_probe_metadata(cell_member_type key) const {
+ if (probes_.count(key)) {
+ return {probe_metadata{key, {}, 0, {&probes_.at(key).metadata}}};
+ } else {
+ return {};
+ }
}
diff --git a/arbor/lif_cell_group.hpp b/arbor/lif_cell_group.hpp
index b89e442f863206f13f5b5b1c25e2b293f8044be8..dbebbfa7776bc4a9701fdf77c3ab19a7445a92ee 100644
--- a/arbor/lif_cell_group.hpp
+++ b/arbor/lif_cell_group.hpp
@@ -1,6 +1,7 @@
#pragma once
#include <vector>
+#include <mutex>
#include <arbor/export.hpp>
#include <arbor/common_types.hpp>
@@ -9,6 +10,7 @@
#include <arbor/sampling.hpp>
#include <arbor/spike.hpp>
+#include "sampler_map.hpp"
#include "cell_group.hpp"
#include "label_resolution.hpp"
@@ -37,10 +39,21 @@ public:
virtual void remove_sampler(sampler_association_handle) override;
virtual void remove_all_samplers() override;
+ virtual std::vector<probe_metadata> get_probe_metadata(cell_member_type) const override;
+
private:
+ enum class lif_probe_kind { voltage };
+
+ struct lif_probe_info {
+ probe_tag tag;
+ lif_probe_kind kind;
+ lif_probe_metadata metadata;
+ };
+
+
// Advances a single cell (lid) with the exact solution (jumps can be arbitrary).
// Parameter dt is ignored, since we make jumps between two consecutive spikes.
- void advance_cell(time_type tfinal, time_type dt, cell_gid_type lid, pse_vector& event_lane);
+ void advance_cell(time_type tfinal, time_type dt, cell_gid_type lid, const event_lane_subrange& event_lane);
// List of the gids of the cells in the group.
std::vector<cell_gid_type> gids_;
@@ -53,6 +66,16 @@ private:
// Time when the cell was last updated.
std::vector<time_type> last_time_updated_;
+ // Time when the cell can _next_ be updated;
+ std::vector<time_type> next_time_updatable_;
+
+ // SAFETY: We need to access samplers_ through a mutex since
+ // simulation::add_sampler might be called concurrently.
+ std::mutex sampler_mex_;
+ sampler_association_map samplers_;
+
+ // LIF probe metadata, precalculated to pass to callbacks
+ std::unordered_map<cell_member_type, lif_probe_info> probes_;
};
} // namespace arb
diff --git a/doc/concepts/cable_cell.rst b/doc/concepts/cable_cell.rst
index a619051264b61e50e8ecf49eb786f9f6f81b6d64..3364f20fb435993aac7a4c8eeed1b5d3643fb94f 100644
--- a/doc/concepts/cable_cell.rst
+++ b/doc/concepts/cable_cell.rst
@@ -46,7 +46,6 @@ Once constructed, the cable cell can be queried for specific information about t
labels
mechanisms
decor
- probe_sample
API
---
diff --git a/doc/concepts/index.rst b/doc/concepts/index.rst
index f1cf92b0715ba07eece665febaa1d5534e22e52b..cd0f20c36b2b773de6c1200277c2175c672161eb 100644
--- a/doc/concepts/index.rst
+++ b/doc/concepts/index.rst
@@ -42,3 +42,5 @@ of the model over the locally available computational resources.
In order to visualize the result of detected spikes a spike recorder can be used, and to analyse Arbor's performance a
meter manager is available.
+
+:ref:`probesample` shows how to extract data from simulations.
diff --git a/doc/concepts/lif_cell.rst b/doc/concepts/lif_cell.rst
index c965c967b03998fefb433f3339d429e2a1969100..18fdcd44d21ba757e38a966e5750d98b615848a1 100644
--- a/doc/concepts/lif_cell.rst
+++ b/doc/concepts/lif_cell.rst
@@ -5,19 +5,35 @@ LIF cells
The description of a LIF cell is used to control the leaky integrate-and-fire dynamics:
-* Resting potential.
-* Reset potential.
-* Initial value of membrane potential.
-* Membrane potential decaying constant.
-* Membrane capacitance.
-* Firing threshold.
-* Refractory period.
-
-The morphology of a LIF cell is automatically modelled as a single :term:`compartment <control volume>`;
-each cell has one built-in **source** and one built-in **target** which need to be given labels when the
-cell is created. The labels are used to form connections to and from the cell.
-LIF cells do not support adding additional **sources** or **targets** to the description. They do not support
-**gap junctions**. They do not support adding density or point mechanisms.
+* Resting potential :math:`E_\mathrm{L}`
+* Membrane potential decaying constant :math:`\tau_\mathrm{m}`
+* Membrane capacitance :math:`C_\mathrm{m}`
+* Firing threshold :math:`U_\mathrm{threshold}`
+* Refractory period :math:`t_\mathrm{ref}`
+
+The morphology of a LIF cell is automatically modelled as a single
+:term:`compartment <control volume>`; each cell has one built-in **source** and
+one built-in **target** which need to be given labels when the cell is created.
+The labels are used to form connections to and from the cell. LIF cells do not
+support adding additional **sources** or **targets** to the description. They do
+not support **gap junctions**. They do not support adding density or point
+mechanisms.
+
+The LIF cell's time dynamics are this:
+
+0. :math:`U_\mathrm{m}(0) = E_\mathrm{L}`
+1. If the cell is in its refractory state :math:`U_\mathrm{m}(t) = E_\mathrm{L}`
+2. Otherwise :math:`U'_\mathrm{m}(t) = \sum\limits_\mathrm{spike} w_\mathrm{spike} \cdot\delta(t - t_\mathrm{spike}) -\frac{1}{\tau_\mathrm{m}}U_\mathrm{m}(t)`
+3. If :math:`U_\mathrm{m}(t_0) \geq U_\mathrm{threshold}`: emit spike and enter refractory period until :math:`t = t_0 + t_\mathrm{ref}`
+
+LIF cells can be probed to obtain their current membrane potential, see :ref:`probesample`.
+
+.. figure:: ../images/lif.svg
+ :width: 400
+ :align: center
+
+ Plot of the potential over time for a LIF cell.
+
API
---
diff --git a/doc/concepts/probe_sample.rst b/doc/concepts/probe_sample.rst
index 0e3b0fcf94eb9c5f923a876459638b842a5ae298..9b553eb6833ea294de65a4d81eeb111b5d1ece3f 100644
--- a/doc/concepts/probe_sample.rst
+++ b/doc/concepts/probe_sample.rst
@@ -1,7 +1,12 @@
.. _probesample:
-Cable cell probing and sampling
-===============================
+Probing and Sampling
+====================
+
+Both cable cells and LIF cells can be probed, see here for more details on cells
+:ref:`modelcells`. The LIF cell, however, has a much smaller set of observable
+quantities and only offers scalar probes. Thus, the following discussion is
+tailored to the cable cell.
Definitions
***********
@@ -64,7 +69,6 @@ Spiking
Threshold detectors have a dual use: they can be used to record spike times, but are also used in propagating signals
between cells. See also :term:`threshold detector` and :ref:`cablecell-threshold-detectors`.
-
API
---
diff --git a/doc/cpp/probe_sample.rst b/doc/cpp/probe_sample.rst
index cb7b08cfbbc5a2dbf666c2e340e850416b987c89..c9eb0c231eb8aadc3cce12ed60e9f11b80cd94df 100644
--- a/doc/cpp/probe_sample.rst
+++ b/doc/cpp/probe_sample.rst
@@ -660,3 +660,19 @@ call the *sampler* callback once for probe in *probe set*, with *n* sample value
In addition to the ``lax`` sampling policy, ``mc_cell_group`` supports the ``exact``
policy. Integration steps will be shortened such that any sample times associated
with an ``exact`` policy can be satisfied precisely.
+
+LIF cell probing and sampling
+===============================
+
+Membrane voltage
+----------------
+
+.. code::
+
+ struct lif_probe_voltage {};
+
+Queries cell membrane potential.
+
+* Sample value: ``double``. Membrane potential (mV).
+
+* Metadata: none
diff --git a/doc/images/lif.svg b/doc/images/lif.svg
new file mode 100644
index 0000000000000000000000000000000000000000..b4c31ddb8ffbe5ba1c45bc325adfe110a6d90ea9
--- /dev/null
+++ b/doc/images/lif.svg
@@ -0,0 +1,1297 @@
+<?xml version="1.0" encoding="utf-8" standalone="no"?>
+<!DOCTYPE svg PUBLIC "-//W3C//DTD SVG 1.1//EN"
+ "http://www.w3.org/Graphics/SVG/1.1/DTD/svg11.dtd">
+<!-- Created with matplotlib (https://matplotlib.org/) -->
+<svg height="288pt" version="1.1" viewBox="0 0 432 288" width="432pt" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink">
+ <metadata>
+ <rdf:RDF xmlns:cc="http://creativecommons.org/ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+ <cc:Work>
+ <dc:type rdf:resource="http://purl.org/dc/dcmitype/StillImage"/>
+ <dc:date>2022-10-27T16:15:02.520502</dc:date>
+ <dc:format>image/svg+xml</dc:format>
+ <dc:creator>
+ <cc:Agent>
+ <dc:title>Matplotlib v3.3.4, https://matplotlib.org/</dc:title>
+ </cc:Agent>
+ </dc:creator>
+ </cc:Work>
+ </rdf:RDF>
+ </metadata>
+ <defs>
+ <style type="text/css">*{stroke-linecap:butt;stroke-linejoin:round;}</style>
+ </defs>
+ <g id="figure_1">
+ <g id="patch_1">
+ <path d="M 0 288
+L 432 288
+L 432 0
+L 0 0
+z
+" style="fill:none;"/>
+ </g>
+ <g id="axes_1">
+ <g id="patch_2">
+ <path d="M 54 252
+L 388.8 252
+L 388.8 34.56
+L 54 34.56
+z
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+ </g>
+ <g id="PathCollection_1">
+ <defs>
+ <path d="M 0 3
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+ <g clip-path="url(#pe30e7958f1)">
+ <use style="stroke:#000000;stroke-width:1.5;" x="109.8" xlink:href="#m13e9bbe748" y="88.92"/>
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diff --git a/doc/index.rst b/doc/index.rst
index af35bfc62fc4babf421df1090235a2ac5b1579c1..a13eafa3e1e2608d4c27ca73ac51f1258f92ff6c 100644
--- a/doc/index.rst
+++ b/doc/index.rst
@@ -129,6 +129,7 @@ A full list of our software attributions can be found `here <https://github.com/
concepts/lif_cell
concepts/spike_source_cell
concepts/benchmark_cell
+ concepts/probe_sample
.. toctree::
:caption: Modelling:
diff --git a/doc/python/lif_cell.rst b/doc/python/lif_cell.rst
index d8623077df2f5084877d5a44a9825318f5ee4c5d..e79f1b1cfeb381b2e18901bbb5b7eab7c3bc1365 100644
--- a/doc/python/lif_cell.rst
+++ b/doc/python/lif_cell.rst
@@ -48,7 +48,3 @@ LIF cells
.. attribute:: t_ref
Refractory period [ms].
-
- .. attribute:: V_reset
-
- Reset potential [mV].
\ No newline at end of file
diff --git a/doc/python/probe_sample.rst b/doc/python/probe_sample.rst
index da12e17a5245b9738c3624c2e4971a39145c5ddd..634237fbb96230db480c7d52ea850ca870d64403 100644
--- a/doc/python/probe_sample.rst
+++ b/doc/python/probe_sample.rst
@@ -298,3 +298,12 @@ Ionic external concentration
Kind: :term:`vector probe`.
+LIF Cell probing
+================
+
+Membrane voltage
+ .. py:function:: lif_probe_voltage()
+
+ Current cell membrane potential (mV).
+
+ Metadata: none
diff --git a/example/brunel/brunel.cpp b/example/brunel/brunel.cpp
index e1e19b3b8399cd6a50297ce4e05d9b2085fd8f80..1807b11d38af6956e404f88040bcba81600617db 100644
--- a/example/brunel/brunel.cpp
+++ b/example/brunel/brunel.cpp
@@ -136,7 +136,6 @@ public:
cell.C_m = 20;
cell.E_L = 0;
cell.V_m = 0;
- cell.V_reset = 0;
cell.t_ref = 2;
return cell;
}
diff --git a/python/CMakeLists.txt b/python/CMakeLists.txt
index 678bfe0693f48b2d2b07a404a94093cc4fced5f3..69e0f8bd1c6895cbee200eb930fd6adb1b93c883 100644
--- a/python/CMakeLists.txt
+++ b/python/CMakeLists.txt
@@ -23,7 +23,7 @@ endif()
set(pyarb_source
cable_cell_io.cpp
- cable_probes.cpp
+ probes.cpp
cells.cpp
config.cpp
context.cpp
diff --git a/python/cells.cpp b/python/cells.cpp
index 7d9159e52345dc6043a37983f8070cf60a50ee65..01ca7384ac2846e6822b67854d291af2c323a72f 100644
--- a/python/cells.cpp
+++ b/python/cells.cpp
@@ -130,8 +130,8 @@ std::optional<arb::mechanism_desc> maybe_method(pybind11::object method) {
std::string lif_str(const arb::lif_cell& c){
return util::pprintf(
- "<arbor.lif_cell: tau_m {}, V_th {}, C_m {}, E_L {}, V_m {}, t_ref {}, V_reset {}>",
- c.tau_m, c.V_th, c.C_m, c.E_L, c.V_m, c.t_ref, c.V_reset);
+ "<arbor.lif_cell: tau_m {}, V_th {}, C_m {}, E_L {}, V_m {}, t_ref {}>",
+ c.tau_m, c.V_th, c.C_m, c.E_L, c.V_m, c.t_ref);
}
@@ -230,8 +230,6 @@ void register_cells(pybind11::module& m) {
"Initial value of the Membrane potential [mV].")
.def_readwrite("t_ref", &arb::lif_cell::t_ref,
"Refractory period [ms].")
- .def_readwrite("V_reset", &arb::lif_cell::V_reset,
- "Reset potential [mV].")
.def_readwrite("source", &arb::lif_cell::source,
"Label of the single build-in source on the cell.")
.def_readwrite("target", &arb::lif_cell::target,
diff --git a/python/example/brunel.py b/python/example/brunel.py
index a147e7378402a30567abe8891541652318cb9309..ba8258e2c807f989dd7960ff8b651a3c3ea7c152 100755
--- a/python/example/brunel.py
+++ b/python/example/brunel.py
@@ -105,7 +105,6 @@ class brunel_recipe(arbor.recipe):
cell.C_m = 20
cell.E_L = 0
cell.V_m = 0
- cell.V_reset = 0
cell.t_ref = 2
return cell
diff --git a/python/cable_probes.cpp b/python/probes.cpp
similarity index 88%
rename from python/cable_probes.cpp
rename to python/probes.cpp
index a309578ad772965a3fbc65b82a91ec380a24089a..a589166bdcc3c10dd2188017d5ede7317111655c 100644
--- a/python/cable_probes.cpp
+++ b/python/probes.cpp
@@ -8,6 +8,7 @@
#include <arborio/label_parse.hpp>
#include <arbor/cable_cell.hpp>
+#include <arbor/lif_cell.hpp>
#include <arbor/morph/locset.hpp>
#include <arbor/recipe.hpp>
#include <arbor/sampling.hpp>
@@ -26,7 +27,7 @@ namespace pyarb {
// to cable_cell scalar- and vector-valued probes.
template <typename Meta>
-struct recorder_cable_base: sample_recorder {
+struct recorder_base: sample_recorder {
// Return stride-column array: first column is time, remainder correspond to sample.
py::object samples() const override {
@@ -49,14 +50,14 @@ protected:
std::vector<double> sample_raw_;
std::ptrdiff_t stride_;
- recorder_cable_base(const Meta* meta_ptr, std::ptrdiff_t width):
+ recorder_base(const Meta* meta_ptr, std::ptrdiff_t width):
meta_(*meta_ptr), stride_(1+width)
{}
};
template <typename Meta>
-struct recorder_cable_scalar: recorder_cable_base<Meta> {
- using recorder_cable_base<Meta>::sample_raw_;
+struct recorder_cable_scalar: recorder_base<Meta> {
+ using recorder_base<Meta>::sample_raw_;
void record(any_ptr, std::size_t n_sample, const arb::sample_record* records) override {
for (std::size_t i = 0; i<n_sample; ++i) {
@@ -71,12 +72,32 @@ struct recorder_cable_scalar: recorder_cable_base<Meta> {
}
protected:
- recorder_cable_scalar(const Meta* meta_ptr): recorder_cable_base<Meta>(meta_ptr, 1) {}
+ recorder_cable_scalar(const Meta* meta_ptr): recorder_base<Meta>(meta_ptr, 1) {}
};
+struct recorder_lif: recorder_base<arb::lif_probe_metadata> {
+ using recorder_base<arb::lif_probe_metadata>::sample_raw_;
+
+ void record(any_ptr, std::size_t n_sample, const arb::sample_record* records) override {
+ for (std::size_t i = 0; i<n_sample; ++i) {
+ if (auto* v_ptr = any_cast<double*>(records[i].data)) {
+ sample_raw_.push_back(records[i].time);
+ sample_raw_.push_back(*v_ptr);
+ }
+ else {
+ std::string ty = records[i].data.type().name();
+ throw arb::arbor_internal_error("LIF recorder: unexpected sample type " + ty);
+ }
+ }
+ }
+
+ recorder_lif(const arb::lif_probe_metadata* meta_ptr): recorder_base<arb::lif_probe_metadata>(meta_ptr, 1) {}
+};
+
+
template <typename Meta>
-struct recorder_cable_vector: recorder_cable_base<Meta> {
- using recorder_cable_base<Meta>::sample_raw_;
+struct recorder_cable_vector: recorder_base<Meta> {
+ using recorder_base<Meta>::sample_raw_;
void record(any_ptr, std::size_t n_sample, const arb::sample_record* records) override {
for (std::size_t i = 0; i<n_sample; ++i) {
@@ -92,7 +113,7 @@ struct recorder_cable_vector: recorder_cable_base<Meta> {
protected:
recorder_cable_vector(const Meta* meta_ptr, std::ptrdiff_t width):
- recorder_cable_base<Meta>(meta_ptr, width) {}
+ recorder_base<Meta>(meta_ptr, width) {}
};
// Specific recorder classes:
@@ -132,6 +153,8 @@ void register_probe_meta_maps(pyarb_global_ptr g) {
});
}
+
+
// Wrapper functions around cable_cell probe types that return arb::probe_info values:
// (Probe tag value is implicitly left at zero.)
@@ -211,6 +234,12 @@ arb::probe_info cable_probe_ion_ext_concentration_cell(const char* ion) {
return arb::cable_probe_ion_ext_concentration_cell{ion};
}
+// LIF cell probes
+arb::probe_info lif_probe_voltage() {
+ return arb::lif_probe_voltage{};
+}
+
+
// Add wrappers to module, recorder factories to global data.
void register_cable_probes(pybind11::module& m, pyarb_global_ptr global_ptr) {
@@ -219,6 +248,9 @@ void register_cable_probes(pybind11::module& m, pyarb_global_ptr global_ptr) {
// Probe metadata wrappers:
+ py::class_<arb::lif_probe_metadata> lif_probe_metadata(m, "lif_probe_metadata",
+ "Probe metadata associated with a LIF cell probe.");
+
py::class_<arb::cable_probe_point_info> cable_probe_point_info(m, "cable_probe_point_info",
"Probe metadata associated with a cable cell probe for point process state.");
@@ -236,6 +268,9 @@ void register_cable_probes(pybind11::module& m, pyarb_global_ptr global_ptr) {
// Probe address constructors:
+ m.def("lif_probe_voltage", &lif_probe_voltage,
+ "Probe specification for LIF cell membrane voltage.");
+
m.def("cable_probe_membrane_voltage", &cable_probe_membrane_voltage,
"Probe specification for cable cell membrane voltage interpolated at points in a location set.",
"where"_a);
@@ -314,6 +349,7 @@ void register_cable_probes(pybind11::module& m, pyarb_global_ptr global_ptr) {
register_probe_meta_maps<arb::cable_probe_point_info, recorder_cable_scalar_point_info>(global_ptr);
register_probe_meta_maps<arb::mcable_list, recorder_cable_vector_mcable>(global_ptr);
register_probe_meta_maps<std::vector<arb::cable_probe_point_info>, recorder_cable_vector_point_info>(global_ptr);
+ register_probe_meta_maps<arb::lif_probe_metadata, recorder_lif>(global_ptr);
}
} // namespace pyarb
diff --git a/python/pyarb.hpp b/python/pyarb.hpp
index 954195a4396ed3ccc7af40ea9843dfdec2fb3f53..1b4241c113e10fcbf1904c611d532fa95ca696b0 100644
--- a/python/pyarb.hpp
+++ b/python/pyarb.hpp
@@ -57,7 +57,8 @@ struct recorder_factory_map {
return map_.at(meta.type())(meta);
}
catch (std::out_of_range&) {
- throw arb::arbor_internal_error("unrecognized probe metadata type");
+ std::string ty = meta.type().name();
+ throw arb::arbor_internal_error("unrecognized probe metadata type " + ty);
}
}
};
diff --git a/python/test/unit/test_cable_probes.py b/python/test/unit/test_probes.py
similarity index 78%
rename from python/test/unit/test_cable_probes.py
rename to python/test/unit/test_probes.py
index daa0ffd29c474eea45a67c0262abf0befd91b514..ff045a64cb5b4f00a88d87400359955ced3f3aef 100644
--- a/python/test/unit/test_cable_probes.py
+++ b/python/test/unit/test_probes.py
@@ -2,6 +2,7 @@
import unittest
import arbor as A
+import numpy as np
"""
tests for cable probe wrappers
@@ -166,3 +167,63 @@ class TestCableProbes(unittest.TestCase):
m = sim.probe_metadata((0, 16))
self.assertEqual(1, len(m))
self.assertEqual(all_cv_cables, m[0])
+
+
+class lif_recipe(A.recipe):
+ def __init__(self):
+ A.recipe.__init__(self)
+
+ def num_cells(self):
+ return 1
+
+ def cell_kind(self, gid):
+ return A.cell_kind.lif
+
+ def global_properties(self, kind):
+ return None
+
+ def probes(self, gid):
+ return [
+ # probe id (0, 0)
+ A.lif_probe_voltage(),
+ ]
+
+ def cell_description(self, gid):
+ cell = A.lif_cell("src", "tgt")
+ cell.E_L = -42
+ cell.V_m = -23
+ cell.t_ref = 0.2
+ return cell
+
+
+class TestLifProbes(unittest.TestCase):
+ def test_probe_addr_metadata(self):
+ rec = lif_recipe()
+ sim = A.simulation(rec)
+
+ m = sim.probe_metadata((0, 0))
+ self.assertEqual(1, len(m))
+ self.assertTrue(all(isinstance(i, A.lif_probe_metadata) for i in m))
+
+ def test_probe_result(self):
+ rec = lif_recipe()
+ sim = A.simulation(rec)
+ hdl = sim.sample((0, 0), A.regular_schedule(0.1))
+ sim.run(1.0, 0.05)
+ smp = sim.samples(hdl)
+ exp = np.array(
+ [
+ [0.0, -23.0],
+ [0.1, -22.77114618],
+ [0.2, -22.54456949],
+ [0.3, -22.32024727],
+ [0.4, -22.0981571],
+ [0.5, -21.87827676],
+ [0.6, -21.66058427],
+ [0.7, -21.44505786],
+ [0.8, -21.23167597],
+ [0.9, -21.02041726],
+ ]
+ )
+ for d, _ in smp:
+ np.testing.assert_allclose(d, exp)
diff --git a/test/unit/test_lif_cell_group.cpp b/test/unit/test_lif_cell_group.cpp
index 6916f01a999ad3d385393b72cc4ddc84ca7aeda0..60d8d8c9eee2caff969e33e6e28a0aa2c1570dbe 100644
--- a/test/unit/test_lif_cell_group.cpp
+++ b/test/unit/test_lif_cell_group.cpp
@@ -1,5 +1,7 @@
#include <gtest/gtest.h>
+#include "common.hpp"
+
#include <arbor/arbexcept.hpp>
#include <arbor/cable_cell.hpp>
#include <arbor/domain_decomposition.hpp>
@@ -114,7 +116,7 @@ public:
probe_recipe() {}
cell_size_type num_cells() const override {
- return 1;
+ return 2;
}
cell_kind get_cell_kind(cell_gid_type gid) const override {
return cell_kind::lif;
@@ -123,17 +125,29 @@ public:
return {};
}
util::unique_any get_cell_description(cell_gid_type gid) const override {
- return lif_cell("src", "tgt");
+ auto cell = lif_cell("src", "tgt");
+ if (gid == 0) {
+ cell.E_L = -42;
+ cell.V_m = -23;
+ cell.t_ref = 0.2;
+ }
+ return cell;
}
- std::vector<probe_info> get_probes(cell_gid_type gid) const override{
- return {arb::cable_probe_membrane_voltage{mlocation{0, 0}}};
+ std::vector<probe_info> get_probes(cell_gid_type gid) const override {
+ if (gid == 0) {
+ return {arb::lif_probe_voltage{}, arb::lif_probe_voltage{}};
+ } else {
+ return {arb::lif_probe_voltage{}};
+ }
}
+ std::vector<event_generator> event_generators(cell_gid_type) const override { return {regular_generator({"tgt"}, 100.0, 0.25, 0.05)}; }
};
+
TEST(lif_cell_group, throw) {
probe_recipe rec;
auto context = make_context();
auto decomp = partition_load_balance(rec, context);
- EXPECT_THROW(simulation(rec, context, decomp), bad_cell_probe);
+ EXPECT_NO_THROW(simulation(rec, context, decomp));
}
TEST(lif_cell_group, recipe)
@@ -188,12 +202,9 @@ TEST(lif_cell_group, ring)
// Total simulation time.
time_type simulation_time = 100;
- auto context = make_context();
auto recipe = ring_recipe(num_lif_cells, weight, delay);
- auto decomp = partition_load_balance(recipe, context);
-
// Creates a simulation with a ring recipe of lif neurons
- simulation sim(recipe, context, decomp);
+ simulation sim(recipe);
std::vector<spike> spike_buffer;
@@ -221,3 +232,115 @@ TEST(lif_cell_group, ring)
}
}
+struct Um_type {
+ constexpr static double delta = 1e-6;
+
+ double t;
+ double u;
+
+ friend std::ostream& operator<<(std::ostream& os, const Um_type& um) {
+ os << "{ " << um.t << ", " << um.u << " }";
+ return os;
+ }
+
+ friend bool operator==(const Um_type& lhs, const Um_type& rhs) {
+ return (std::abs(lhs.t - rhs.t) <= delta)
+ && (std::abs(lhs.u - rhs.u) <= delta);
+ }
+};
+
+TEST(lif_cell_group, probe) {
+ auto ums = std::unordered_map<cell_member_type, std::vector<Um_type>>{};
+ auto fun = [&ums](probe_metadata pm,
+ std::size_t n,
+ const sample_record* samples) {
+ for (int ix = 0; ix < n; ++ix) {
+ const auto& [t, v] = samples[ix];
+ double u = *util::any_cast<double*>(v);
+ ums[pm.id].push_back({t, u});
+ }
+ };
+ auto rec = probe_recipe{};
+ auto sim = simulation(rec);
+
+ sim.add_sampler(all_probes, regular_schedule(0.025), fun);
+
+ std::vector<double> spikes;
+
+ sim.set_global_spike_callback(
+ [&spikes](const std::vector<spike>& spk) { for (const auto& s: spk) spikes.push_back(s.time); }
+ );
+
+ sim.run(1.5, 0.005);
+ std::vector<Um_type> exp = {{0, -23},
+ {0.025, -22.9425718},
+ {0.05, -22.885287},
+ {0.075, -22.8281453},
+ {0.1, -22.7711462},
+ {0.125, -22.7142894},
+ {0.15, -22.6575746},
+ {0.175, -22.6010014},
+ {0.2, -22.5445695},
+ {0.225, -22.4882785},
+ {0.25, -17.432128},
+ {0.275, -17.3886021},
+ {0.3, -12.3451849},
+ {0.325, -12.3143605},
+ {0.35, -7.28361301},
+ {0.375, -7.26542672},
+ {0.4, -2.24728584},
+ {0.425, -2.24167464},
+ {0.45, 2.76392255},
+ {0.475, 2.75702137},
+ {0.5, 7.75013743},
+ {0.525, 7.73078628},
+ {0.55, -42},
+ {0.575, -42},
+ {0.6, -42},
+ {0.625, -42},
+ {0.65, -42},
+ {0.675, -42},
+ {0.7, -42},
+ {0.725, -42},
+ {0.75, -37},
+ {0.775, -36.9076155},
+ {0.8, -31.8154617},
+ {0.825, -31.7360224},
+ {0.85, -26.6567815},
+ {0.875, -26.5902227},
+ {0.9, -21.5238302},
+ {0.925, -21.4700878},
+ {0.95, -16.4164796},
+ {0.975, -16.3754897},
+ {1, -11.3346021},
+ {1.025, -11.306301},
+ {1.05, -6.27807055},
+ {1.075, -6.26239498},
+ {1.1, -1.24675854},
+ {1.125, -1.24364554},
+ {1.15, 3.75945969},
+ {1.175, 3.75007278},
+ {1.2, 8.74070931},
+ {1.225, 8.71888483},
+ {1.25, -42},
+ {1.275, -42},
+ {1.3, -42},
+ {1.325, -42},
+ {1.35, -42},
+ {1.375, -42},
+ {1.4, -42},
+ {1.425, -42},
+ {1.45, -37},
+ {1.475, -36.9076155},};
+
+ ASSERT_TRUE(testing::seq_eq(ums[{0, 0}], exp));
+ ASSERT_TRUE(testing::seq_eq(ums[{0, 1}], exp));
+ // gid == 1 is different, but of same size
+ EXPECT_EQ((ums[{1, 0}].size()), exp.size());
+ ASSERT_FALSE(testing::seq_eq(ums[{1, 0}], exp));
+ // now check the spikes
+ std::sort(spikes.begin(), spikes.end());
+ EXPECT_EQ(spikes.size(), 3);
+ std::vector<double> sexp{0.35, 0.55, 1.25};
+ ASSERT_TRUE(testing::seq_almost_eq<double>(spikes, sexp));
+}