From 5fdfb02e45cb4128dc5a19babd43b7ba347c1229 Mon Sep 17 00:00:00 2001
From: Nora Abi Akar <nora.abiakar@gmail.com>
Date: Mon, 14 Dec 2020 18:16:07 +0100
Subject: [PATCH] Expose global_properties in Python recipes (#1273)
Extend Ptyhon recipe wrapper to support setting of global cell properties.
* Rename `pyrecipe::get_probes` to `py_recipe::probes`
* Remove `global_properties_shim` : It's easy to make mistakes with the class, as it holds a `mechanism_catalogue` and a `cable_cell_global_properties` which holds a pointer to the catalogue. This would likely have caused issues with the users.
* Expose `py_recipe::global_properties`
---
doc/python/recipe.rst | 13 ++++-
python/cells.cpp | 53 ++++++++++---------
python/cells.hpp | 17 ------
python/example/network_ring.py | 8 ++-
python/example/single_cell_recipe.py | 8 ++-
python/mechanism.cpp | 2 +-
python/recipe.cpp | 28 ++++++++--
python/recipe.hpp | 25 +++++----
python/single_cell_model.cpp | 14 ++---
python/test/unit/test_cable_probes.py | 9 +++-
python/test/unit/test_simulator.py | 10 +++-
.../test/unit_distributed/test_simulator.py | 9 +++-
12 files changed, 121 insertions(+), 75 deletions(-)
delete mode 100644 python/cells.hpp
diff --git a/doc/python/recipe.rst b/doc/python/recipe.rst
index eade1da2..5d74801e 100644
--- a/doc/python/recipe.rst
+++ b/doc/python/recipe.rst
@@ -90,7 +90,7 @@ Recipe
By default returns 0.
- .. function:: get_probes(gid)
+ .. function:: probes(gid)
Returns a list specifying the probe addresses describing probes on the cell ``gid``.
Each address in the list is an opaque object of type :class:`probe` produced by
@@ -100,6 +100,17 @@ Recipe
By default returns an empty list.
+ .. function:: global_properties(kind)
+
+ The global properties of a model.
+
+ This method needs to be implemented for :class:`arbor.cell_kind.cable`, where the
+ properties include ion concentrations and reversal potentials; initial membrane voltage;
+ temperature; axial resistivity; membrane capacitance; cv_policy; and a pointer
+ to the mechanism catalogue.
+
+ By default returns an empty object.
+
Cells
------
diff --git a/python/cells.cpp b/python/cells.cpp
index 9017e445..69b691f1 100644
--- a/python/cells.cpp
+++ b/python/cells.cpp
@@ -26,7 +26,6 @@
#include "arbor/cable_cell_param.hpp"
#include "arbor/cv_policy.hpp"
-#include "cells.hpp"
#include "conversion.hpp"
#include "error.hpp"
#include "pybind11/cast.h"
@@ -129,23 +128,16 @@ struct label_dict_proxy {
}
};
-global_props_shim::global_props_shim():
- cat(arb::global_default_catalogue())
-{
- props.catalogue = &cat;
-}
-
// This isn't pretty. Partly because the information in the global parameters
// is all over the place.
-std::string to_string(const global_props_shim& G) {
+std::string to_string(const arb::cable_cell_global_properties& props) {
std::string s = "{arbor.cable_global_properties";
- const auto& P = G.props;
- const auto& D = P.default_parameters;
+ const auto& D = props.default_parameters;
const auto& I = D.ion_data;
// name, valence, int_con, ext_con, rev_pot, rev_pot_method
s += "\n ions: {";
- for (auto& ion: P.ion_species) {
+ for (auto& ion: props.ion_species) {
if (!I.count(ion.first)) {
s += util::pprintf("\n {name: '{}', valence: {}, int_con: None, ext_con: None, rev_pot: None, rev_pot_method: None}",
ion.first, ion.second);
@@ -437,23 +429,23 @@ void register_cells(pybind11::module& m) {
// arb::cable_cell_global_properties
- pybind11::class_<global_props_shim> gprop(m, "cable_global_properties");
+ pybind11::class_<arb::cable_cell_global_properties> gprop(m, "cable_global_properties");
gprop
.def(pybind11::init<>())
- .def(pybind11::init<const global_props_shim&>())
- .def("check", [](const global_props_shim& shim) {
- arb::check_global_properties(shim.props);},
+ .def(pybind11::init<const arb::cable_cell_global_properties&>())
+ .def("check", [](const arb::cable_cell_global_properties& props) {
+ arb::check_global_properties(props);},
"Test whether all default parameters and ion species properties have been set.")
// set cable properties
.def("set_property",
- [](global_props_shim& G,
+ [](arb::cable_cell_global_properties& props,
optional<double> Vm, optional<double> cm,
optional<double> rL, optional<double> tempK)
{
- if (Vm) G.props.default_parameters.init_membrane_potential = Vm;
- if (cm) G.props.default_parameters.membrane_capacitance=cm;
- if (rL) G.props.default_parameters.axial_resistivity=rL;
- if (tempK) G.props.default_parameters.temperature_K=tempK;
+ if (Vm) props.default_parameters.init_membrane_potential = Vm;
+ if (cm) props.default_parameters.membrane_capacitance=cm;
+ if (rL) props.default_parameters.axial_resistivity=rL;
+ if (tempK) props.default_parameters.temperature_K=tempK;
},
pybind11::arg_v("Vm", pybind11::none(), "initial membrane voltage [mV]."),
pybind11::arg_v("cm", pybind11::none(), "membrane capacitance [F/m²]."),
@@ -462,16 +454,16 @@ void register_cells(pybind11::module& m) {
"Set global default values for cable and cell properties.")
// add/modify ion species
.def("set_ion",
- [](global_props_shim& G, const char* ion,
+ [](arb::cable_cell_global_properties& props, const char* ion,
optional<double> int_con, optional<double> ext_con,
optional<double> rev_pot, pybind11::object method)
{
- auto& data = G.props.default_parameters.ion_data[ion];
+ 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 (rev_pot) data.init_reversal_potential = *rev_pot;
if (auto m = maybe_method(method)) {
- G.props.default_parameters.reversal_potential_method[ion] = *m;
+ props.default_parameters.reversal_potential_method[ion] = *m;
}
},
pybind11::arg_v("ion", "name of the ion species."),
@@ -484,9 +476,18 @@ void register_cells(pybind11::module& m) {
"specific regions using the paint interface, while the method for calculating\n"
"reversal potential is global for all compartments in the cell, and can't be\n"
"overriden locally.")
- .def_readwrite("catalogue", &global_props_shim::cat, "The mechanism catalogue.")
- .def("__str__", [](const global_props_shim& p){return to_string(p);});
-
+ .def("register", [](arb::cable_cell_global_properties& props, const arb::mechanism_catalogue& cat) {
+ props.catalogue = &cat;
+ },
+ "Register the pointer to the mechanism catalogue in the global properties")
+ .def("__str__", [](const arb::cable_cell_global_properties& p){return to_string(p);});
+
+ m.def("neuron_cable_propetries", []() {
+ arb::cable_cell_global_properties prop;
+ prop.default_parameters = arb::neuron_parameter_defaults;
+ return prop;
+ },
+ "default NEURON cable_global_properties");
pybind11::class_<arb::decor> decor(m, "decor",
"Description of the decorations to be applied to a cable cell, that is the painted,\n"
diff --git a/python/cells.hpp b/python/cells.hpp
deleted file mode 100644
index 8560f16a..00000000
--- a/python/cells.hpp
+++ /dev/null
@@ -1,17 +0,0 @@
-#pragma once
-
-#include <pybind11/pybind11.h>
-
-#include <arbor/cable_cell_param.hpp>
-#include <arbor/mechcat.hpp>
-#include <arbor/util/unique_any.hpp>
-
-namespace pyarb {
-
-struct global_props_shim {
- arb::mechanism_catalogue cat;
- arb::cable_cell_global_properties props;
- global_props_shim();
-};
-
-}
diff --git a/python/example/network_ring.py b/python/example/network_ring.py
index b080ab02..1fb552ad 100755
--- a/python/example/network_ring.py
+++ b/python/example/network_ring.py
@@ -62,6 +62,9 @@ class ring_recipe (arbor.recipe):
# all memory in the C++ class is initialized correctly.
arbor.recipe.__init__(self)
self.ncells = n
+ self.props = arbor.neuron_cable_propetries()
+ self.cat = arbor.default_catalogue()
+ self.props.register(self.cat)
# The num_cells method that returns the total number of cells in the model
# must be implemented.
@@ -97,9 +100,12 @@ class ring_recipe (arbor.recipe):
return [arbor.event_generator(arbor.cell_member(0,0), 0.1, sched)]
return []
- def get_probes(self, gid):
+ def probes(self, gid):
return [arbor.cable_probe_membrane_voltage('(location 0 0)')]
+ def global_properties(self, kind):
+ return self.props
+
context = arbor.context(threads=12, gpu_id=None)
print(context)
diff --git a/python/example/single_cell_recipe.py b/python/example/single_cell_recipe.py
index a9b72880..76af62c5 100644
--- a/python/example/single_cell_recipe.py
+++ b/python/example/single_cell_recipe.py
@@ -12,6 +12,9 @@ class single_recipe (arbor.recipe):
arbor.recipe.__init__(self)
self.the_cell = cell
self.the_probes = probes
+ self.the_props = arbor.neuron_cable_propetries()
+ self.the_cat = arbor.default_catalogue()
+ self.the_props.register(self.the_cat)
def num_cells(self):
return 1
@@ -25,9 +28,12 @@ class single_recipe (arbor.recipe):
def cell_description(self, gid):
return self.the_cell
- def get_probes(self, gid):
+ def probes(self, gid):
return self.the_probes
+ def global_properties(self, kind):
+ return self.the_props
+
# (2) Create a cell.
# Morphology
diff --git a/python/mechanism.cpp b/python/mechanism.cpp
index e0fc9846..70e2c528 100644
--- a/python/mechanism.cpp
+++ b/python/mechanism.cpp
@@ -103,7 +103,7 @@ void register_mechanisms(pybind11::module& m) {
[](const arb::mechanism_info& inf) {
return util::pprintf("(arbor.mechanism_info)"); });
- pybind11::class_<arb::mechanism_catalogue> cat(m, "mechanism_catalogue");
+ pybind11::class_<arb::mechanism_catalogue> cat(m, "catalogue");
cat
.def(pybind11::init<const arb::mechanism_catalogue&>())
.def("has", &arb::mechanism_catalogue::has,
diff --git a/python/recipe.cpp b/python/recipe.cpp
index d543fe6d..21b9a7ec 100644
--- a/python/recipe.cpp
+++ b/python/recipe.cpp
@@ -14,7 +14,6 @@
#include <arbor/morph/primitives.hpp>
#include <arbor/recipe.hpp>
-#include "cells.hpp"
#include "conversion.hpp"
#include "error.hpp"
#include "event_generator.hpp"
@@ -64,6 +63,26 @@ static arb::util::unique_any convert_cell(pybind11::object o) {
"Python error already thrown");
}
+// Convert global properties inside a Python object to a
+// std::any, as required by the recipe interface.
+// This helper is only to called while holding the GIL, see above.
+static std::any convert_gprop(pybind11::object o) {
+ if (o.is(pybind11::none())) {
+ return {};
+ }
+ return pybind11::cast<arb::cable_cell_global_properties>(o);
+}
+
+// The py::recipe::global_properties returns a pybind11::object, that is
+// unwrapped and copied into an std::any.
+std::any py_recipe_shim::get_global_properties(arb::cell_kind kind) const {
+ return try_catch_pyexception([&](){
+ pybind11::gil_scoped_acquire guard;
+ return convert_gprop(impl_->global_properties(kind));
+ },
+ "Python error already thrown");
+}
+
// This helper is only to called while holding the GIL, see above.
static std::vector<arb::event_generator> convert_gen(std::vector<pybind11::object> pygens, arb::cell_gid_type gid) {
using namespace std::string_literals;
@@ -95,7 +114,7 @@ std::vector<arb::event_generator> py_recipe_shim::event_generators(arb::cell_gid
pybind11::gil_scoped_acquire guard;
return convert_gen(impl_->event_generators(gid), gid);
},
- "Python error already thrown");
+ "Python error already thrown");
}
std::string con_to_string(const arb::cell_connection& c) {
@@ -186,9 +205,12 @@ void register_recipe(pybind11::module& m) {
.def("gap_junctions_on", &py_recipe::gap_junctions_on,
"gid"_a,
"A list of the gap junctions connected to gid, [] by default.")
- .def("get_probes", &py_recipe::get_probes,
+ .def("probes", &py_recipe::probes,
"gid"_a,
"The probes to allow monitoring.")
+ .def("global_properties", &py_recipe::global_properties,
+ "kind"_a,
+ "The default properties applied to all cells of type 'kind' in the model.")
// TODO: py_recipe::global_properties
.def("__str__", [](const py_recipe&){return "<arbor.recipe>";})
.def("__repr__", [](const py_recipe&){return "<arbor.recipe>";});
diff --git a/python/recipe.hpp b/python/recipe.hpp
index a6196d0f..b00a608c 100644
--- a/python/recipe.hpp
+++ b/python/recipe.hpp
@@ -51,9 +51,12 @@ public:
virtual std::vector<arb::gap_junction_connection> gap_junctions_on(arb::cell_gid_type) const {
return {};
}
- virtual std::vector<arb::probe_info> get_probes(arb::cell_gid_type gid) const {
+ virtual std::vector<arb::probe_info> probes(arb::cell_gid_type gid) const {
return {};
}
+ virtual pybind11::object global_properties(arb::cell_kind kind) const {
+ return pybind11::none();
+ };
//TODO: virtual pybind11::object global_properties(arb::cell_kind kind) const {return pybind11::none();};
};
@@ -95,8 +98,12 @@ public:
PYBIND11_OVERLOAD(std::vector<arb::gap_junction_connection>, py_recipe, gap_junctions_on, gid);
}
- std::vector<arb::probe_info> get_probes(arb::cell_gid_type gid) const override {
- PYBIND11_OVERLOAD(std::vector<arb::probe_info>, py_recipe, get_probes, gid);
+ std::vector<arb::probe_info> probes(arb::cell_gid_type gid) const override {
+ PYBIND11_OVERLOAD(std::vector<arb::probe_info>, py_recipe, probes, gid);
+ }
+
+ pybind11::object global_properties(arb::cell_kind kind) const override {
+ PYBIND11_OVERLOAD(pybind11::object, py_recipe, global_properties, kind);
}
};
@@ -152,18 +159,10 @@ public:
}
std::vector<arb::probe_info> get_probes(arb::cell_gid_type gid) const override {
- return try_catch_pyexception([&](){ return impl_->get_probes(gid); }, msg);
+ return try_catch_pyexception([&](){ return impl_->probes(gid); }, msg);
}
- // TODO: make thread safe
- std::any get_global_properties(arb::cell_kind kind) const override {
- if (kind==arb::cell_kind::cable) {
- arb::cable_cell_global_properties gprop;
- gprop.default_parameters = arb::neuron_parameter_defaults;
- return gprop;
- }
- return std::any{};
- }
+ std::any get_global_properties(arb::cell_kind kind) const override;
};
} // namespace pyarb
diff --git a/python/single_cell_model.cpp b/python/single_cell_model.cpp
index 43029969..fae9d364 100644
--- a/python/single_cell_model.cpp
+++ b/python/single_cell_model.cpp
@@ -13,7 +13,6 @@
#include <arbor/simulation.hpp>
#include <arbor/util/any_cast.hpp>
-#include "cells.hpp"
#include "error.hpp"
#include "strprintf.hpp"
@@ -149,15 +148,14 @@ class single_cell_model {
std::vector<trace> traces_;
public:
- // Make gprop public to make it possible to expose it as a field in Python:
- // model.properties.catalogue = my_custom_cat
- //arb::cable_cell_global_properties gprop;
- global_props_shim gprop;
+ arb::cable_cell_global_properties gprop;
+ arb::mechanism_catalogue cat;
single_cell_model(arb::cable_cell c):
cell_(std::move(c)), ctx_(arb::make_context())
{
- gprop.props.default_parameters = arb::neuron_parameter_defaults;
+ gprop.default_parameters = arb::neuron_parameter_defaults;
+ cat = arb::global_default_catalogue();
}
// example use:
@@ -180,7 +178,8 @@ public:
}
void run(double tfinal, double dt) {
- single_cell_recipe rec(cell_, probes_, gprop.props);
+ gprop.catalogue = &cat;
+ single_cell_recipe rec(cell_, probes_, gprop);
auto domdec = arb::partition_load_balance(rec, ctx_);
@@ -270,6 +269,7 @@ void register_single_cell(pybind11::module& m) {
return m.traces();},
"Holds sample traces after a call to run().")
.def_readwrite("properties", &single_cell_model::gprop, "Global properties.")
+ .def_readwrite("catalogue", &single_cell_model::cat, "Mechanism catalogue.")
.def("__repr__", [](const single_cell_model&){return "<arbor.single_cell_model>";})
.def("__str__", [](const single_cell_model&){return "<arbor.single_cell_model>";});
}
diff --git a/python/test/unit/test_cable_probes.py b/python/test/unit/test_cable_probes.py
index 791b2397..27524179 100644
--- a/python/test/unit/test_cable_probes.py
+++ b/python/test/unit/test_cable_probes.py
@@ -33,6 +33,10 @@ class cc_recipe(A.recipe):
self.cell = A.cable_cell(st, A.label_dict(), dec)
+ self.cat = A.default_catalogue()
+ self.props = A.neuron_cable_propetries()
+ self.props.register(self.cat)
+
def num_cells(self):
return 1
@@ -45,7 +49,10 @@ class cc_recipe(A.recipe):
def cell_kind(self, gid):
return A.cell_kind.cable
- def get_probes(self, gid):
+ def global_properties(self, kind):
+ return self.props
+
+ def probes(self, gid):
# Use keyword arguments to check that the wrappers have actually declared keyword arguments correctly.
# Place single-location probes at (location 0 0.01*j) where j is the index of the probe address in
# the returned list.
diff --git a/python/test/unit/test_simulator.py b/python/test/unit/test_simulator.py
index 9dc26acd..d25c371d 100644
--- a/python/test/unit/test_simulator.py
+++ b/python/test/unit/test_simulator.py
@@ -29,6 +29,9 @@ class cc2_recipe(A.recipe):
st.append(i, (1, 3, 0, 5), 1)
st.append(i, (1, -4, 0, 3), 1)
self.the_morphology = A.morphology(st)
+ self.the_cat = A.default_catalogue()
+ self.the_props = A.neuron_cable_propetries()
+ self.the_props.register(self.the_cat)
def num_cells(self):
return 2
@@ -48,7 +51,10 @@ class cc2_recipe(A.recipe):
def event_generators(self, gid):
return []
- def get_probes(self, gid):
+ def global_properties(self, kind):
+ return self.the_props
+
+ def probes(self, gid):
# Cell 0 has three voltage probes:
# 0, 0: end of branch 1
# 0, 1: end of branch 2
@@ -105,7 +111,7 @@ class lif2_recipe(A.recipe):
weight = 400
return [A.event_generator((gid,0), weight, A.regular_schedule(sched_dt)) for gid in range(0, self.num_cells())]
- def get_probes(self, gid):
+ def probes(self, gid):
return []
def cell_description(self, gid):
diff --git a/python/test/unit_distributed/test_simulator.py b/python/test/unit_distributed/test_simulator.py
index ee0da551..8ca179a2 100644
--- a/python/test/unit_distributed/test_simulator.py
+++ b/python/test/unit_distributed/test_simulator.py
@@ -25,7 +25,9 @@ class lifN_recipe(A.recipe):
def __init__(self, n_cell):
A.recipe.__init__(self)
self.n_cell = n_cell
-
+ self.cat = A.default_catalogue()
+ self.props = A.neuron_cable_propetries()
+ self.props.register(self.cat)
def num_cells(self):
return self.n_cell
@@ -46,9 +48,12 @@ class lifN_recipe(A.recipe):
weight = 400
return [A.event_generator((gid,0), weight, A.regular_schedule(sched_dt)) for gid in range(0, self.num_cells())]
- def get_probes(self, gid):
+ def probes(self, gid):
return []
+ def global_properties(self,kind):
+ return self.props
+
def cell_description(self, gid):
c = A.lif_cell()
if gid%2==0:
--
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