From 37dd7de28972a74979259b64f51898e716ae4c60 Mon Sep 17 00:00:00 2001
From: Nora Abi Akar <nora.abiakar@gmail.com>
Date: Fri, 27 Aug 2021 14:25:15 +0200
Subject: [PATCH] Check that mechanisms have the right kind (#1633)
- Expose `arb_mechanism_kind` to `mechanism_info`.
- While building mechanism data in `fvm_build_mechanism_data`, check that synapses, painted region dynamics and reversal potential methods have the expected `arb_mechanism_kind`.
- Add unit test.
---
arbor/fvm_layout.cpp | 19 +++++++++++++++----
arbor/include/arbor/mechanism_abi.h | 9 +++++++++
arbor/include/arbor/mechinfo.hpp | 3 +++
arbor/mechinfo.cpp | 1 +
doc/python/mechanisms.rst | 10 ++++++++++
python/mechanism.cpp | 6 ++++++
test/unit/test_fvm_layout.cpp | 25 +++++++++++++++++++++++++
7 files changed, 69 insertions(+), 4 deletions(-)
diff --git a/arbor/fvm_layout.cpp b/arbor/fvm_layout.cpp
index 3261726f..d2ee99ce 100644
--- a/arbor/fvm_layout.cpp
+++ b/arbor/fvm_layout.cpp
@@ -858,14 +858,17 @@ fvm_mechanism_data fvm_build_mechanism_data(const cable_cell_global_properties&
const std::string& name = entry.first;
mechanism_info info = catalogue[name];
- std::vector<double> param_dflt;
fvm_mechanism_config config;
- config.kind = arb_mechanism_kind_density;
+ if (info.kind != arb_mechanism_kind_density) {
+ throw cable_cell_error("expected density mechanism, got " +name +" which has " +arb_mechsnism_kind_str(info.kind));
+ }
+ config.kind = info.kind;
std::vector<std::string> param_names;
assign(param_names, util::keys(info.parameters));
sort(param_names);
+ std::vector<double> param_dflt;
std::size_t n_param = param_names.size();
param_dflt.reserve(n_param);
config.param_values.reserve(n_param);
@@ -963,6 +966,10 @@ fvm_mechanism_data fvm_build_mechanism_data(const cable_cell_global_properties&
const std::string& name = entry.first;
mechanism_info info = catalogue[name];
+ if (info.kind != arb_mechanism_kind_point) {
+ throw cable_cell_error("expected point mechanism, got " +name +" which has " +arb_mechsnism_kind_str(info.kind));
+ }
+
post_events |= info.post_events;
std::size_t n_param = info.parameters.size();
std::size_t n_inst = entry.second.size();
@@ -1044,7 +1051,7 @@ fvm_mechanism_data fvm_build_mechanism_data(const cable_cell_global_properties&
bool coalesce = catalogue[name].linear && gprop.coalesce_synapses;
fvm_mechanism_config config;
- config.kind = arb_mechanism_kind_point;
+ config.kind = info.kind;
for (auto& kv: info.parameters) {
config.param_values.emplace_back(kv.first, std::vector<value_type>{});
if (!coalesce) {
@@ -1210,6 +1217,10 @@ fvm_mechanism_data fvm_build_mechanism_data(const cable_cell_global_properties&
{
const mechanism_desc& revpot = *maybe_revpot;
mechanism_info info = catalogue[revpot.name()];
+ if (info.kind != arb_mechanism_kind_reversal_potential) {
+ throw cable_cell_error("expected reversal potential mechanism for ion " +ion +", got "+ revpot.name() +" which has " +arb_mechsnism_kind_str(info.kind));
+ }
+
verify_mechanism(info, revpot);
revpot_specified.insert(ion);
@@ -1248,7 +1259,7 @@ fvm_mechanism_data fvm_build_mechanism_data(const cable_cell_global_properties&
}
else {
fvm_mechanism_config config;
- config.kind = arb_mechanism_kind_reversal_potential;
+ config.kind = info.kind;
config.cv = M.ions[ion].cv;
config.norm_area.assign(config.cv.size(), 1.);
diff --git a/arbor/include/arbor/mechanism_abi.h b/arbor/include/arbor/mechanism_abi.h
index ce85067f..83770e2e 100644
--- a/arbor/include/arbor/mechanism_abi.h
+++ b/arbor/include/arbor/mechanism_abi.h
@@ -27,6 +27,15 @@ typedef uint32_t arb_backend_kind;
#define arb_backend_kind_cpu 1
#define arb_backend_kind_gpu 2
+inline const char* arb_mechsnism_kind_str(const arb_mechanism_kind& mech) {
+ switch (mech) {
+ case arb_mechanism_kind_density: return "density mechanism kind";
+ case arb_mechanism_kind_point: return "point mechanism kind";
+ case arb_mechanism_kind_reversal_potential: return "reversal potential mechanism kind";
+ default: return "unknown mechanism kind";
+ }
+}
+
// Ion state variables; view into shared_state
typedef struct arb_ion_state {
arb_value_type* current_density;
diff --git a/arbor/include/arbor/mechinfo.hpp b/arbor/include/arbor/mechinfo.hpp
index 3e4ff24b..904fa90d 100644
--- a/arbor/include/arbor/mechinfo.hpp
+++ b/arbor/include/arbor/mechinfo.hpp
@@ -58,6 +58,9 @@ struct mechanism_info {
mechanism_info(const arb_mechanism_type&);
mechanism_info() = default;
+ // Mechanism kind
+ arb_mechanism_kind kind;
+
// Global fields have one value common to an instance of a mechanism, are
// constant in time and set at instantiation.
std::unordered_map<std::string, mechanism_field_spec> globals;
diff --git a/arbor/mechinfo.cpp b/arbor/mechinfo.cpp
index abfe6c97..341568a7 100644
--- a/arbor/mechinfo.cpp
+++ b/arbor/mechinfo.cpp
@@ -4,6 +4,7 @@
namespace arb {
mechanism_info::mechanism_info(const arb_mechanism_type& m) {
+ kind = m.kind;
post_events = m.has_post_events;
linear = m.is_linear;
fingerprint = m.fingerprint;
diff --git a/doc/python/mechanisms.rst b/doc/python/mechanisms.rst
index 54c6a32e..cb19925f 100644
--- a/doc/python/mechanisms.rst
+++ b/doc/python/mechanisms.rst
@@ -138,6 +138,11 @@ mechanism that is to be painted or placed on the cable cell.
print(mech.parameters['tau'].default)
# 2.0
+ .. py:attribute:: kind
+ :type: string
+
+ String representation of the kind of the mechanism: density, point or reversal potential.
+
.. py:attribute:: globals
:type: dict[str, mechanism_field]
@@ -163,6 +168,11 @@ mechanism that is to be painted or placed on the cable cell.
True if a synapse mechanism has linear current contributions so that multiple instances on the same :term:`control volume` can be coalesced.
+ .. py:attribute:: post_events
+ :type: bool
+
+ True if a synapse mechanism has a `POST_EVENT` procedure defined.
+
.. py:class:: ion_dependency
diff --git a/python/mechanism.cpp b/python/mechanism.cpp
index 2a27eccb..16f9f25e 100644
--- a/python/mechanism.cpp
+++ b/python/mechanism.cpp
@@ -96,6 +96,12 @@ void register_mechanisms(pybind11::module& m) {
"Ion dependencies.")
.def_readonly("linear", &arb::mechanism_info::linear,
"True if a synapse mechanism has linear current contributions so that multiple instances on the same compartment can be coalesced.")
+ .def_readonly("post_events", &arb::mechanism_info::post_events,
+ "True if a synapse mechanism has a `POST_EVENT` procedure defined.")
+ .def_property_readonly("kind",
+ [](const arb::mechanism_info& info) {
+ return arb_mechsnism_kind_str(info.kind);
+ }, "String representation of the kind of the mechanism.")
.def("__repr__",
[](const arb::mechanism_info& inf) {
return util::pprintf("(arbor.mechanism_info)"); })
diff --git a/test/unit/test_fvm_layout.cpp b/test/unit/test_fvm_layout.cpp
index 6d4e3a5a..981b291a 100644
--- a/test/unit/test_fvm_layout.cpp
+++ b/test/unit/test_fvm_layout.cpp
@@ -129,6 +129,31 @@ namespace {
}
} // namespace
+template<typename P>
+void check_compatible_mechanism_failure(cable_cell_global_properties gprop, P painter) {
+ auto system = two_cell_system();
+
+ painter(system);
+
+ auto cells = system.cells();
+ check_two_cell_system(cells);
+ fvm_cv_discretization D = fvm_cv_discretize(cells, gprop.default_parameters);
+
+ EXPECT_THROW(fvm_build_mechanism_data(gprop, cells, D), arb::cable_cell_error);
+}
+
+TEST(fvm_layout, compatible_mechanisms) {
+ cable_cell_global_properties gprop;
+ gprop.default_parameters = neuron_parameter_defaults;
+
+ check_compatible_mechanism_failure(gprop, [](auto& sys) {sys.descriptions[0].decorations.place(sys.builders[0].location({1, 0.4}), "hh", "syn0"); });
+ check_compatible_mechanism_failure(gprop, [](auto& sys) {sys.descriptions[1].decorations.paint(sys.builders[1].cable(mcable{0}), "expsyn"); });
+ check_compatible_mechanism_failure(gprop, [](auto& sys) {sys.descriptions[0].decorations.set_default(ion_reversal_potential_method{"na", "expsyn"}); });
+
+ gprop.default_parameters.reversal_potential_method["na"] = "pas";
+ check_compatible_mechanism_failure(gprop, [](auto& sys) {});
+}
+
TEST(fvm_layout, mech_index) {
auto system = two_cell_system();
auto& descriptions = system.descriptions;
--
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