diff --git a/arbor/cable_cell.cpp b/arbor/cable_cell.cpp
index 2d643732fd54e0f1c6bcf72a723627dcea4f4504..ca7cc23b15e14bd734271f00a283076925a9abc9 100644
--- a/arbor/cable_cell.cpp
+++ b/arbor/cable_cell.cpp
@@ -88,8 +88,16 @@ struct cable_cell_impl {
return region_map.get<mechanism_desc>()[desc.name()];
}
- mcable_map<initial_ion_data>& get_region_map(const initial_ion_data& init) {
- return region_map.get<initial_ion_data>()[init.ion];
+ mcable_map<init_int_concentration>& get_region_map(const init_int_concentration& init) {
+ return region_map.get<init_int_concentration>()[init.ion];
+ }
+
+ mcable_map<init_ext_concentration>& get_region_map(const init_ext_concentration& init) {
+ return region_map.get<init_ext_concentration>()[init.ion];
+ }
+
+ mcable_map<init_reversal_potential>& get_region_map(const init_reversal_potential& init) {
+ return region_map.get<init_reversal_potential>()[init.ion];
}
template <typename Property>
@@ -168,7 +176,8 @@ void cable_cell::paint(const region& target, proptype prop) {\
}
ARB_PP_FOREACH(FWD_PAINT,\
mechanism_desc, init_membrane_potential, axial_resistivity,\
- temperature_K, membrane_capacitance, initial_ion_data)
+ temperature_K, membrane_capacitance, init_int_concentration,
+ init_ext_concentration, init_reversal_potential)
// Forward place methods to implementation class.
diff --git a/arbor/cable_cell_param.cpp b/arbor/cable_cell_param.cpp
index b20a93a1b9067e3d0ef36106603380d8ff05f9a3..a83d5d31db8dbfbc7dad24de8fd21089de4a4777 100644
--- a/arbor/cable_cell_param.cpp
+++ b/arbor/cable_cell_param.cpp
@@ -38,13 +38,13 @@ void check_global_properties(const cable_cell_global_properties& G) {
for (const auto& kv: param.ion_data) {
auto& ion = kv.first;
const cable_cell_ion_data& data = kv.second;
- if (std::isnan(data.init_int_concentration)) {
+ if (!data.init_int_concentration) {
throw cable_cell_error("missing init_int_concentration for ion "+ion);
}
- if (std::isnan(data.init_ext_concentration)) {
+ if (!data.init_ext_concentration) {
throw cable_cell_error("missing init_ext_concentration for ion "+ion);
}
- if (std::isnan(data.init_reversal_potential) && !param.reversal_potential_method.count(ion)) {
+ if (!data.init_reversal_potential && !param.reversal_potential_method.count(ion)) {
throw cable_cell_error("missing init_reversal_potential or reversal_potential_method for ion "+ion);
}
}
diff --git a/arbor/fvm_layout.cpp b/arbor/fvm_layout.cpp
index e370372a7cf4ce90337ac60f6fcb01b985a6c465..451002a97c27341fe7279c6ab3fd8d81031ec0bf 100644
--- a/arbor/fvm_layout.cpp
+++ b/arbor/fvm_layout.cpp
@@ -1096,7 +1096,9 @@ fvm_mechanism_data fvm_build_mechanism_data(const cable_cell_global_properties&
// Ions:
- auto initial_ion_data_map = cell.region_assignments().get<initial_ion_data>();
+ auto initial_iconc_map = cell.region_assignments().get<init_int_concentration>();
+ auto initial_econc_map = cell.region_assignments().get<init_ext_concentration>();
+ auto initial_rvpot_map = cell.region_assignments().get<init_reversal_potential>();
for (const auto& ion_cvs: ion_support) {
const std::string& ion = ion_cvs.first;
@@ -1111,12 +1113,20 @@ fvm_mechanism_data fvm_build_mechanism_data(const cable_cell_global_properties&
config.reset_econc.resize(n_cv);
config.init_revpot.resize(n_cv);
- cable_cell_ion_data ion_data = *(value_by_key(dflt.ion_data, ion) | value_by_key(global_dflt.ion_data, ion));
- double dflt_iconc = ion_data.init_int_concentration;
- double dflt_econc = ion_data.init_ext_concentration;
- double dflt_rvpot = ion_data.init_reversal_potential;
+ auto global_ion_data = value_by_key(global_dflt.ion_data, ion).value();
+ auto dflt_iconc = global_ion_data.init_int_concentration.value();
+ auto dflt_econc = global_ion_data.init_ext_concentration.value();
+ auto dflt_rvpot = global_ion_data.init_reversal_potential.value();
- const mcable_map<initial_ion_data>& ion_on_cable = initial_ion_data_map[ion];
+ if (auto ion_data = value_by_key(dflt.ion_data, ion)) {
+ dflt_iconc = ion_data.value().init_int_concentration.value_or(dflt_iconc);
+ dflt_econc = ion_data.value().init_ext_concentration.value_or(dflt_econc);
+ dflt_rvpot = ion_data.value().init_reversal_potential.value_or(dflt_rvpot);
+ }
+
+ const mcable_map<init_int_concentration>& iconc_on_cable = initial_iconc_map[ion];
+ const mcable_map<init_ext_concentration>& econc_on_cable = initial_econc_map[ion];
+ const mcable_map<init_reversal_potential>& rvpot_on_cable = initial_rvpot_map[ion];
auto pw_times = [](const pw_elements<double>& a, const pw_elements<double>& b) {
return zip(a, b, [](double left, double right, pw_element<double> a, pw_element<double> b) { return a.second*b.second; });
@@ -1127,9 +1137,9 @@ fvm_mechanism_data fvm_build_mechanism_data(const cable_cell_global_properties&
if (D.cv_area[cv]==0) continue;
for (mcable c: D.geometry.cables(cv)) {
- auto iconc = pw_over_cable(ion_on_cable, c, dflt_iconc, [](auto x) { return x.initial.init_int_concentration; });
- auto econc = pw_over_cable(ion_on_cable, c, dflt_econc, [](auto x) { return x.initial.init_ext_concentration; });
- auto rvpot = pw_over_cable(ion_on_cable, c, dflt_rvpot, [](auto x) { return x.initial.init_reversal_potential; });
+ auto iconc = pw_over_cable(iconc_on_cable, c, dflt_iconc);
+ auto econc = pw_over_cable(econc_on_cable, c, dflt_econc);
+ auto rvpot = pw_over_cable(rvpot_on_cable, c, dflt_rvpot);
config.reset_iconc[i] += embedding.integrate_area(c.branch, iconc);
config.reset_econc[i] += embedding.integrate_area(c.branch, econc);
diff --git a/arbor/include/arbor/cable_cell.hpp b/arbor/include/arbor/cable_cell.hpp
index 574750a60a20f14feae01411793b20e904b9a912..70b42e0e8bf16c526267e3d18de0d3ddfb184b10 100644
--- a/arbor/include/arbor/cable_cell.hpp
+++ b/arbor/include/arbor/cable_cell.hpp
@@ -191,7 +191,8 @@ struct cable_cell_impl;
template <typename T>
using region_assignment =
std::conditional_t<
- std::is_same<T, mechanism_desc>::value || std::is_same<T, initial_ion_data>::value,
+ std::is_same<T, mechanism_desc>::value || std::is_same<T, init_int_concentration>::value ||
+ std::is_same<T, init_ext_concentration>::value || std::is_same<T, init_reversal_potential>::value,
std::unordered_map<std::string, mcable_map<T>>,
mcable_map<T>>;
@@ -215,7 +216,8 @@ using location_assignment =
using cable_cell_region_map = static_typed_map<region_assignment,
mechanism_desc, init_membrane_potential, axial_resistivity,
- temperature_K, membrane_capacitance, initial_ion_data>;
+ temperature_K, membrane_capacitance, init_int_concentration,
+ init_ext_concentration, init_reversal_potential>;
using cable_cell_location_map = static_typed_map<location_assignment,
mechanism_desc, i_clamp, gap_junction_site, threshold_detector>;
@@ -275,6 +277,18 @@ public:
default_parameters.ion_data[prop.ion] = prop.initial;
}
+ void set_default(init_int_concentration prop) {
+ default_parameters.ion_data[prop.ion].init_int_concentration = prop.value;
+ }
+
+ void set_default(init_ext_concentration prop) {
+ default_parameters.ion_data[prop.ion].init_ext_concentration = prop.value;
+ }
+
+ void set_default(init_reversal_potential prop) {
+ default_parameters.ion_data[prop.ion].init_reversal_potential = prop.value;
+ }
+
void set_default(ion_reversal_potential_method prop) {
default_parameters.reversal_potential_method[prop.ion] = prop.method;
}
@@ -292,7 +306,9 @@ public:
void paint(const region&, axial_resistivity);
void paint(const region&, temperature_K);
void paint(const region&, membrane_capacitance);
- void paint(const region&, initial_ion_data);
+ void paint(const region&, init_int_concentration);
+ void paint(const region&, init_ext_concentration);
+ void paint(const region&, init_reversal_potential);
// Synapses.
lid_range place(const locset&, mechanism_desc);
diff --git a/arbor/include/arbor/cable_cell_param.hpp b/arbor/include/arbor/cable_cell_param.hpp
index 804ab131cfe3a2820ca28ddef47394f388955c3f..6f733ad2a41cec0738ef8a65e215dbdbb0a72e00 100644
--- a/arbor/include/arbor/cable_cell_param.hpp
+++ b/arbor/include/arbor/cable_cell_param.hpp
@@ -21,13 +21,14 @@ struct cable_cell_error: arbor_exception {
// Ion inital concentration and reversal potential
// parameters, as used in cable_cell_parameter_set,
-// and set locally via painting initial_ion_data
-// (see below).
+// and set locally via painting init_int_concentration,
+// init_ext_concentration and init_reversal_potential
+// separately (see below).
struct cable_cell_ion_data {
- double init_int_concentration = NAN;
- double init_ext_concentration = NAN;
- double init_reversal_potential = NAN;
+ util::optional<double> init_int_concentration;
+ util::optional<double> init_ext_concentration;
+ util::optional<double> init_reversal_potential;
};
// Current clamp description for stimulus specification.
@@ -72,6 +73,21 @@ struct membrane_capacitance {
double value = NAN; // [F/m²]
};
+struct init_int_concentration {
+ std::string ion;
+ double value = NAN;
+};
+
+struct init_ext_concentration {
+ std::string ion;
+ double value = NAN;
+};
+
+struct init_reversal_potential {
+ std::string ion;
+ double value = NAN;
+};
+
// Mechanism description, viz. mechanism name and
// (non-global) parameter settings. Used to assign
// density and point mechanisms to segments and
diff --git a/arbor/morph/region.cpp b/arbor/morph/region.cpp
index 68ff60d380413f2ee087b28d0276fa6c4e2fb488..e78a59b4c8da8ce974a5e0323876d1927bf7c3b8 100644
--- a/arbor/morph/region.cpp
+++ b/arbor/morph/region.cpp
@@ -547,7 +547,7 @@ mextent thingify_(const named_& n, const mprovider& p) {
}
std::ostream& operator<<(std::ostream& o, const named_& x) {
- return o << "(region \"" << x.name << "\")";
+ return o << "(region " << x.name << ")";
}
// Adds all cover points to a region.
diff --git a/python/cells.cpp b/python/cells.cpp
index 30d72bf3a78ef7178d12b8c148782be40655f07f..cc867f6a5a368f0ec7efe9ebebea88843b9503e3 100644
--- a/python/cells.cpp
+++ b/python/cells.cpp
@@ -165,7 +165,6 @@ global_props_shim::global_props_shim():
std::string to_string(const global_props_shim& G) {
std::string s = "{arbor.cable_global_properties";
- auto nan_is_none = [](double x) {return x==x? std::to_string(x): "None";};
const auto& P = G.props;
const auto& D = P.default_parameters;
const auto& I = D.ion_data;
@@ -182,9 +181,9 @@ std::string to_string(const global_props_shim& G) {
"'"+D.reversal_potential_method.at(ion.first).name()+"'": "None";
s += util::pprintf("\n {name: '{}', valence: {}, int_con: {}, ext_con: {}, rev_pot: {}, rev_pot_method: {}}",
ion.first, ion.second,
- nan_is_none(props.init_int_concentration),
- nan_is_none(props.init_ext_concentration),
- nan_is_none(props.init_reversal_potential),
+ props.init_int_concentration,
+ props.init_ext_concentration,
+ props.init_reversal_potential,
method);
}
}
@@ -554,12 +553,20 @@ void register_cells(pybind11::module& m) {
" rL: axial resistivity [Ω·cm].\n"
" tempK: temperature [Kelvin].")
+
+
// Paint ion species initial conditions on a region.
.def("paint",
- [](arb::cable_cell& c, const char* region, const arb::initial_ion_data& d) {
- c.paint(region, d);
+ [](arb::cable_cell& c, const char* region, const char* name,
+ optional<double> int_con, optional<double> ext_con, optional<double> rev_pot) {
+ if (int_con) c.paint(region, arb::init_int_concentration{name, *int_con});
+ if (ext_con) c.paint(region, arb::init_int_concentration{name, *ext_con});
+ if (rev_pot) c.paint(region, arb::init_int_concentration{name, *rev_pot});
},
- "region"_a, "ion_data"_a,
+ "region"_a, "ion_name"_a,
+ pybind11::arg_v("int_con", pybind11::none(), "Intial internal concentration [mM]"),
+ pybind11::arg_v("ext_con", pybind11::none(), "Intial external concentration [mM]"),
+ pybind11::arg_v("rev_pot", pybind11::none(), "Intial reversal potential [mV]"),
"Set ion species properties conditions on a region.")
// Place synapses
.def("place",
diff --git a/test/unit/test_fvm_layout.cpp b/test/unit/test_fvm_layout.cpp
index 0f55d42991f9c80279df36fb895fbce4e5cd4a4c..8403a30d4f829926c5d04812db44a930240bace4 100644
--- a/test/unit/test_fvm_layout.cpp
+++ b/test/unit/test_fvm_layout.cpp
@@ -769,8 +769,8 @@ TEST(fvm_layout, ion_weights) {
gprop.catalogue = &testcat;
gprop.default_parameters = neuron_parameter_defaults;
- fvm_value_type cai = gprop.default_parameters.ion_data["ca"].init_int_concentration;
- fvm_value_type cao = gprop.default_parameters.ion_data["ca"].init_ext_concentration;
+ fvm_value_type cai = gprop.default_parameters.ion_data["ca"].init_int_concentration.value();
+ fvm_value_type cao = gprop.default_parameters.ion_data["ca"].init_ext_concentration.value();
for (auto& v: expected_init_iconc) {
for (auto& iconc: v) {