From a408c1edad651a174071a87958cad3cc99fee1a1 Mon Sep 17 00:00:00 2001
From: Thorsten Hater <24411438+thorstenhater@users.noreply.github.com>
Date: Wed, 18 May 2022 13:24:40 +0200
Subject: [PATCH] Add introspection for global properties. (#1890)
Add accessors for the following items in `global_properties`
- ion_species (name -> valence) RO
- ion_data (name -> initial values) RO
- ion_rev_pot (name -> rev pot mech) RO
- Vm, rL, TK, Cm: RW
Fixes: #1802
---
python/cells.cpp | 27 +++++++++++++++++++++++++--
1 file changed, 25 insertions(+), 2 deletions(-)
diff --git a/python/cells.cpp b/python/cells.cpp
index 175ce812..f103764a 100644
--- a/python/cells.cpp
+++ b/python/cells.cpp
@@ -497,6 +497,11 @@ void register_cells(pybind11::module& m) {
return util::pprintf("(threshold_detector {})", d.threshold);});
// arb::cable_cell_global_properties
+ pybind11::class_<arb::cable_cell_ion_data> ion_data(m, "ion_data");
+ ion_data
+ .def_readonly("internal_concentration", &arb::cable_cell_ion_data::init_int_concentration, "Internal concentration.")
+ .def_readonly("external_concentration", &arb::cable_cell_ion_data::init_ext_concentration, "External concentration.")
+ .def_readonly("reversal_concentration", &arb::cable_cell_ion_data::init_reversal_potential, "Reversal potential.");
pybind11::class_<arb::cable_cell_global_properties> gprop(m, "cable_global_properties");
gprop
@@ -506,6 +511,24 @@ void register_cells(pybind11::module& m) {
arb::check_global_properties(props);},
"Test whether all default parameters and ion species properties have been set.")
// set cable properties
+ .def_property("membrane_potential",
+ [](const arb::cable_cell_global_properties& props) { return props.default_parameters.init_membrane_potential; },
+ [](arb::cable_cell_global_properties& props, double u) { props.default_parameters.init_membrane_potential = u; })
+ .def_property("membrane_capacitance",
+ [](const arb::cable_cell_global_properties& props) { return props.default_parameters.membrane_capacitance; },
+ [](arb::cable_cell_global_properties& props, double u) { props.default_parameters.membrane_capacitance = u; })
+ .def_property("temperature",
+ [](const arb::cable_cell_global_properties& props) { return props.default_parameters.temperature_K; },
+ [](arb::cable_cell_global_properties& props, double u) { props.default_parameters.temperature_K = u; })
+ .def_property("axial_resisitivity",
+ [](const arb::cable_cell_global_properties& props) { return props.default_parameters.axial_resistivity; },
+ [](arb::cable_cell_global_properties& props, double u) { props.default_parameters.axial_resistivity = u; })
+ .def_property_readonly("ion_data",
+ [](const arb::cable_cell_global_properties& props) { return props.default_parameters.ion_data; })
+ .def_property_readonly("ion_valence",
+ [](const arb::cable_cell_global_properties& props) { return props.ion_species; })
+ .def_property_readonly("ion_reversal_potential",
+ [](const arb::cable_cell_global_properties& props) { return props.default_parameters.reversal_potential_method; })
.def("set_property",
[](arb::cable_cell_global_properties& props,
optional<double> Vm, optional<double> cm,
@@ -534,8 +557,8 @@ void register_cells(pybind11::module& m) {
if (valence) props.ion_species[ion] = *valence;
auto& data = props.default_parameters.ion_data[ion];
- if (int_con) data.init_int_concentration = *int_con;
- if (ext_con) data.init_ext_concentration = *ext_con;
+ if (int_con) data.init_int_concentration = *int_con;
+ if (ext_con) data.init_ext_concentration = *ext_con;
if (rev_pot) data.init_reversal_potential = *rev_pot;
if (auto m = maybe_method(method)) {
--
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