diff --git a/arborio/cableio.cpp b/arborio/cableio.cpp
index 5fde6ff6986d9927cb528d9feac2e0bad42382d4..469fe96d4036708351ff5013e738237fa4d59e2d 100644
--- a/arborio/cableio.cpp
+++ b/arborio/cableio.cpp
@@ -8,6 +8,7 @@
#include <arborio/label_parse.hpp>
#include <arborio/cableio.hpp>
+#include <arborio/cv_policy_parse.hpp>
#include "parse_helpers.hpp"
#include "parse_s_expr.hpp"
@@ -88,7 +89,7 @@ s_expr mksexp(const msegment& seg) {
s_expr mksexp(const cv_policy& c) {
std::stringstream s;
s << c;
- return parse_s_expr(s.str());
+ return slist("cv-policy"_symbol, parse_s_expr(s.str()));
}
s_expr mksexp(const decor& d) {
auto round_trip = [](auto& x) {
@@ -217,6 +218,9 @@ arb::i_clamp make_i_clamp_pulse(pulse_tuple p, double freq, double phase) {
arb::gap_junction_site make_gap_junction_site() {
return arb::gap_junction_site{};
}
+arb::cv_policy make_cv_policy(const cv_policy& p) {
+ return p;
+}
arb::ion_reversal_potential_method make_ion_reversal_potential_method(const std::string& ion, const arb::mechanism_desc& mech) {
return ion_reversal_potential_method{ion, mech};
}
@@ -536,17 +540,19 @@ parse_hopefully<std::any> eval(const s_expr& e, const eval_map& map, const eval_
}
}
- // If it's not in the provided map, maybe it's a label expression
- // the corresponding parser is provided by the arbor lib
+ // If it's not in the provided map, it could be a label expression
if (auto l = parse_label_expression(e)) {
if (match<region>(l->type())) return eval_cast<region>(l.value());
if (match<locset>(l->type())) return eval_cast<locset>(l.value());
}
+ // Or it could be a cv-policy expression
+ if (auto p = parse_cv_policy_expression(e)) return p.value();
+
// Unable to find a match: try to return a helpful error message.
const auto nc = std::distance(matches.first, matches.second);
std::string msg = "No matches for found for "+name+" with "+std::to_string(args->size())+" arguments.\n"
- "There are "+std::to_string(nc)+" potential candiates"+(nc?":":".");
+ "There are "+std::to_string(nc)+" potential candidates"+(nc?":":".");
int count = 0;
for (auto i=matches.first; i!=matches.second; ++i) {
msg += "\n Candidate "+std::to_string(++count)+": "+i->second.message;
@@ -558,34 +564,36 @@ parse_hopefully<std::any> eval(const s_expr& e, const eval_map& map, const eval_
eval_map named_evals{
{"membrane-potential", make_call<double>(make_init_membrane_potential,
- "'membrane-potential' with 1 argument (val:real)")},
+ "'membrane-potential' with 1 argument (val:real)")},
{"temperature-kelvin", make_call<double>(make_temperature_K,
- "'temperature-kelvin' with 1 argument (val:real)")},
+ "'temperature-kelvin' with 1 argument (val:real)")},
{"axial-resistivity", make_call<double>(make_axial_resistivity,
- "'axial-resistivity' with 1 argument (val:real)")},
+ "'axial-resistivity' with 1 argument (val:real)")},
{"membrane-capacitance", make_call<double>(make_membrane_capacitance,
- "'membrane-capacitance' with 1 argument (val:real)")},
+ "'membrane-capacitance' with 1 argument (val:real)")},
{"ion-internal-concentration", make_call<std::string, double>(make_init_int_concentration,
- "'ion_internal_concentration' with 2 arguments (ion:string val:real)")},
+ "'ion_internal_concentration' with 2 arguments (ion:string val:real)")},
{"ion-external-concentration", make_call<std::string, double>(make_init_ext_concentration,
- "'ion_external_concentration' with 2 arguments (ion:string val:real)")},
+ "'ion_external_concentration' with 2 arguments (ion:string val:real)")},
{"ion-reversal-potential", make_call<std::string, double>(make_init_reversal_potential,
- "'ion_reversal_potential' with 2 arguments (ion:string val:real)")},
+ "'ion_reversal_potential' with 2 arguments (ion:string val:real)")},
{"envelope", make_arg_vec_call<envelope_tuple>(make_envelope,
- "`envelope` with one or more pairs of start time and amplitude (start:real amplitude:real)")},
+ "'envelope' with one or more pairs of start time and amplitude (start:real amplitude:real)")},
{"envelope-pulse", make_call<double, double, double>(make_envelope_pulse,
- "'envelope-pulse' with 3 arguments (delay:real duration:real amplitude:real)")},
+ "'envelope-pulse' with 3 arguments (delay:real duration:real amplitude:real)")},
{"current-clamp", make_call<std::vector<arb::i_clamp::envelope_point>, double, double>(make_i_clamp,
- "`current-clamp` with 3 arguments (env:envelope freq:real phase:real)")},
+ "'current-clamp' with 3 arguments (env:envelope freq:real phase:real)")},
{"current-clamp", make_call<pulse_tuple, double, double>(make_i_clamp_pulse,
- "`current-clamp` with 3 arguments (env:envelope_pulse freq:real phase:real)")},
+ "'current-clamp' with 3 arguments (env:envelope_pulse freq:real phase:real)")},
{"threshold-detector", make_call<double>(make_threshold_detector,
- "'threshold-detector' with 1 argument (threshold:real)")},
+ "'threshold-detector' with 1 argument (threshold:real)")},
{"gap-junction-site", make_call<>(make_gap_junction_site,
- "'gap-junction-site' with 0 arguments")},
+ "'gap-junction-site' with 0 arguments")},
{"ion-reversal-potential-method", make_call<std::string, arb::mechanism_desc>(
- make_ion_reversal_potential_method,
- "'ion-reversal-potential-method' with 2 arguments (ion:string mech:mechanism)")},
+ make_ion_reversal_potential_method,
+ "'ion-reversal-potential-method' with 2 arguments (ion:string mech:mechanism)")},
+ {"cv-policy", make_call<cv_policy>(make_cv_policy,
+ "'cv-policy' with 1 argument (p:policy)")},
{"mechanism", make_mech_call("'mechanism' with a name argument, and 0 or more parameter settings"
"(name:string (param:string val:real))")},
{"place", make_call<locset, gap_junction_site, std::string>(make_place, "'place' with 3 arguments (ls:locset gj:gap-junction-site name:string)")},
@@ -610,28 +618,29 @@ eval_map named_evals{
{"default", make_call<init_ext_concentration>(make_default, "'default' with 1 argument (v:ion-external-concentration)")},
{"default", make_call<init_reversal_potential>(make_default, "'default' with 1 argument (v:ion-reversal-potential)")},
{"default", make_call<ion_reversal_potential_method>(make_default, "'default' with 1 argument (v:ion-reversal-potential-method)")},
+ {"default", make_call<cv_policy>(make_default, "'default' with 1 argument (v:cv-policy)")},
{"locset-def", make_call<std::string, locset>(make_locset_pair,
- "'locset-def' with 2 arguments (name:string ls:locset)")},
+ "'locset-def' with 2 arguments (name:string ls:locset)")},
{"region-def", make_call<std::string, region>(make_region_pair,
- "'region-def' with 2 arguments (name:string reg:region)")},
+ "'region-def' with 2 arguments (name:string reg:region)")},
{"point", make_call<double, double, double, double>(make_point,
- "'point' with 4 arguments (x:real y:real z:real radius:real)")},
+ "'point' with 4 arguments (x:real y:real z:real radius:real)")},
{"segment", make_call<int, mpoint, mpoint, int>(make_segment,
- "'segment' with 4 arguments (parent:int prox:point dist:point tag:int)")},
+ "'segment' with 4 arguments (parent:int prox:point dist:point tag:int)")},
{"branch", make_branch_call(
- "'branch' with 2 integers and 1 or more segment arguments (id:int parent:int s0:segment s1:segment ..)")},
+ "'branch' with 2 integers and 1 or more segment arguments (id:int parent:int s0:segment s1:segment ..)")},
{"decor", make_arg_vec_call<place_tuple, paint_pair, defaultable>(make_decor,
- "'decor' with 1 or more `paint`, `place` or `default` arguments")},
+ "'decor' with 1 or more `paint`, `place` or `default` arguments")},
{"label-dict", make_arg_vec_call<locset_pair, region_pair>(make_label_dict,
- "'label-dict' with 1 or more `locset-def` or `region-def` arguments")},
+ "'label-dict' with 1 or more `locset-def` or `region-def` arguments")},
{"morphology", make_arg_vec_call<branch_tuple>(make_morphology,
- "'morphology' 1 or more `branch` arguments")},
+ "'morphology' 1 or more `branch` arguments")},
{"cable-cell", make_unordered_call<morphology, label_dict, decor>(make_cable_cell,
- "'cable-cell' with 3 arguments: `morphology`, `label-dict`, and `decor` in any order")},
+ "'cable-cell' with 3 arguments: `morphology`, `label-dict`, and `decor` in any order")},
{"version", make_call<std::string>(make_version, "'version' with one argment (val:std::string)")},
{"meta-data", make_call<version_tuple>(make_meta_data, "'meta-data' with one argument (v:version)")},
diff --git a/arborio/cv_policy_parse.cpp b/arborio/cv_policy_parse.cpp
index c013efe751499b4c34b3b0f1dba052cdb6ad8656..16ad8160861eae2b714f860e5a415052398c07d0 100644
--- a/arborio/cv_policy_parse.cpp
+++ b/arborio/cv_policy_parse.cpp
@@ -188,8 +188,8 @@ parse_hopefully<std::any> eval(const s_expr& e) {
}
}
-parse_cv_policy_hopefully parse_cv_policy_expression(const std::string& s) {
- if (auto e = eval(parse_s_expr(s))) {
+parse_cv_policy_hopefully parse_cv_policy_expression(const arb::s_expr& s) {
+ if (auto e = eval(s)) {
if (e->type() == typeid(cv_policy)) {
return {std::move(std::any_cast<cv_policy&>(*e))};
}
@@ -200,5 +200,7 @@ parse_cv_policy_hopefully parse_cv_policy_expression(const std::string& s) {
return util::unexpected(cv_policy_parse_error(std::string() + e.error().what()));
}
}
-
+parse_cv_policy_hopefully parse_cv_policy_expression(const std::string& s) {
+ return parse_cv_policy_expression(parse_s_expr(s));
+}
} // namespace arb
diff --git a/arborio/include/arborio/cv_policy_parse.hpp b/arborio/include/arborio/cv_policy_parse.hpp
index 8a899d468312426b02cfaf1558cf7da4735933cf..6069740a9f509097356682ac5cd478642b1368d8 100644
--- a/arborio/include/arborio/cv_policy_parse.hpp
+++ b/arborio/include/arborio/cv_policy_parse.hpp
@@ -18,6 +18,7 @@ struct cv_policy_parse_error: arb::arbor_exception {
using parse_cv_policy_hopefully = arb::util::expected<arb::cv_policy, cv_policy_parse_error>;
parse_cv_policy_hopefully parse_cv_policy_expression(const std::string& s);
+parse_cv_policy_hopefully parse_cv_policy_expression(const arb::s_expr& s);
namespace literals {
@@ -29,4 +30,4 @@ arb::cv_policy operator "" _cvp(const char* s, std::size_t) {
} // namespace literals
-} // namespace arb
+} // namespace arborio
diff --git a/test/unit/test_s_expr.cpp b/test/unit/test_s_expr.cpp
index 477fc8e94aaf19f6b6d25230ea517c79bbc51cac..fcae3e4ee2c29aca6872ebde02f6122da1d6e47f 100644
--- a/test/unit/test_s_expr.cpp
+++ b/test/unit/test_s_expr.cpp
@@ -6,8 +6,8 @@
#include <arbor/morph/region.hpp>
#include <arbor/morph/locset.hpp>
#include <arbor/cv_policy.hpp>
-
#include <arbor/s_expr.hpp>
+#include <arbor/util/any_visitor.hpp>
#include <arborio/cv_policy_parse.hpp>
#include <arborio/cableio.hpp>
@@ -514,8 +514,11 @@ std::ostream& operator<<(std::ostream& o, const place_tuple& p) {
return o << " \"" << std::get<2>(p) << "\")";
}
std::ostream& operator<<(std::ostream& o, const defaultable& p) {
+ auto default_visitor = arb::util::overload(
+ [&](const cv_policy& p) { o << "(cv-policy " << p << ")"; },
+ [&](const auto& p){ o << p; });
o << "(default ";
- std::visit([&](auto&& x) {o << x;}, p);
+ std::visit(default_visitor, p);
return o << ")";
}
std::ostream& operator<<(std::ostream& o, const locset_pair& p) {
@@ -531,6 +534,11 @@ std::string to_string(const T& obj) {
s << obj;
return s.str();
}
+std::string to_string(const cv_policy& p) {
+ std::stringstream s;
+ s << "(cv-policy " << p << ')';
+ return s.str();
+}
std::string to_string(const arborio::cable_cell_component& c) {
std::stringstream s;
arborio::write_component(s, c);
@@ -598,7 +606,9 @@ TEST(decor_literals, round_tripping) {
"(mechanism \"pas\" (\"g\" 0.02))",
};
auto default_literals = {
- "(ion-reversal-potential-method \"ca\" (mechanism \"nernst/ca\"))"};
+ "(ion-reversal-potential-method \"ca\" (mechanism \"nernst/ca\"))",
+ "(cv-policy (single (segment 0)))"
+ };
auto place_literals = {
"(current-clamp (envelope (10 0.5) (110 0.5) (110 0)) 10 0.25)",
"(threshold-detector -10)",
@@ -658,7 +668,8 @@ TEST(decor_expressions, round_tripping) {
"(default (ion-internal-concentration \"ca\" 75.1))",
"(default (ion-external-concentration \"h\" -50.1))",
"(default (ion-reversal-potential \"na\" 30))",
- "(default (ion-reversal-potential-method \"ca\" (mechanism \"nernst/ca\")))"
+ "(default (ion-reversal-potential-method \"ca\" (mechanism \"nernst/ca\")))",
+ "(default (cv-policy (max-extent 2 (region \"soma\") 2)))"
};
auto decorate_place_literals = {
"(place (location 3 0.2) (current-clamp (envelope (10 0.5) (110 0.5) (110 0)) 0.5 0.25) \"clamp\")",
@@ -724,6 +735,11 @@ TEST(decor, round_tripping) {
" (default \n"
" (ion-reversal-potential-method \"na\" \n"
" (mechanism \"nernst\")))\n"
+ " (default \n"
+ " (cv-policy \n"
+ " (fixed-per-branch 10 \n"
+ " (all)\n"
+ " 1)))\n"
" (paint \n"
" (region \"dend\")\n"
" (mechanism \"pas\"))\n"