From 677f96df62bf3796e2689ac321ce9f4972d4fc3d Mon Sep 17 00:00:00 2001
From: Sam Yates <halfflat@gmail.com>
Date: Thu, 8 Aug 2019 18:17:58 +0200
Subject: [PATCH] Fix examples to use new cable cell API. (#832)
Also remove vestigial segment::length_constant() virtual function.
Fixes #831.
---
arbor/include/arbor/segment.hpp | 5 -----
example/dryrun/dryrun.cpp | 9 +++++++--
example/gap_junctions/gap_junctions.cpp | 7 ++++---
example/generators/event_gen.cpp | 6 ++++++
example/ring/ring.cpp | 3 +--
example/single/single.cpp | 27 +++++++++++++++----------
6 files changed, 34 insertions(+), 23 deletions(-)
diff --git a/arbor/include/arbor/segment.hpp b/arbor/include/arbor/segment.hpp
index 38f1849c..ece282fb 100644
--- a/arbor/include/arbor/segment.hpp
+++ b/arbor/include/arbor/segment.hpp
@@ -83,11 +83,6 @@ public:
return false;
}
- // Approximate frequency-dependent length constant lower bound.
- virtual value_type length_constant(value_type freq_Hz) const {
- return 0;
- }
-
util::optional<mechanism_desc&> mechanism(const std::string& name) {
auto it = std::find_if(mechanisms_.begin(), mechanisms_.end(),
[&](mechanism_desc& m) { return m.name()==name; });
diff --git a/example/dryrun/dryrun.cpp b/example/dryrun/dryrun.cpp
index 12728c69..b9e5619e 100644
--- a/example/dryrun/dryrun.cpp
+++ b/example/dryrun/dryrun.cpp
@@ -68,6 +68,12 @@ public:
return cell_kind::cable;
}
+ arb::util::any get_global_properties(arb::cell_kind) const override {
+ arb::cable_cell_global_properties gprop;
+ gprop.default_parameters = arb::neuron_parameter_defaults;
+ return gprop;
+ }
+
// Each cell has one spike detector (at the soma).
cell_size_type num_sources(cell_gid_type gid) const override {
return 1;
@@ -304,10 +310,10 @@ double interp(const std::array<T,2>& r, unsigned i, unsigned n) {
arb::cable_cell branch_cell(arb::cell_gid_type gid, const cell_parameters& params) {
arb::cable_cell cell;
+ cell.default_parameters.axial_resistivity = 100; // [Ω·cm]
// Add soma.
auto soma = cell.add_soma(12.6157/2.0); // For area of 500 μm².
- soma->rL = 100;
soma->add_mechanism("hh");
std::vector<std::vector<unsigned>> levels;
@@ -336,7 +342,6 @@ arb::cable_cell branch_cell(arb::cell_gid_type gid, const cell_parameters& param
auto dend = cell.add_cable(sec, arb::section_kind::dendrite, dend_radius, dend_radius, l);
dend->set_compartments(nc);
dend->add_mechanism("pas");
- dend->rL = 100;
}
}
}
diff --git a/example/gap_junctions/gap_junctions.cpp b/example/gap_junctions/gap_junctions.cpp
index 2e8381f7..4a633a77 100644
--- a/example/gap_junctions/gap_junctions.cpp
+++ b/example/gap_junctions/gap_junctions.cpp
@@ -97,7 +97,8 @@ public:
arb::util::any get_global_properties(cell_kind k) const override {
arb::cable_cell_global_properties a;
- a.temperature_K = 308.15;
+ a.default_parameters = arb::neuron_parameter_defaults;
+ a.default_parameters.temperature_K = 308.15;
return a;
}
@@ -321,6 +322,8 @@ void write_trace_json(const std::vector<arb::trace_data<double>>& trace, unsigne
arb::cable_cell gj_cell(cell_gid_type gid, unsigned ncell, double stim_duration) {
arb::cable_cell cell;
+ cell.default_parameters.axial_resistivity = 100; // [Ω·cm]
+ cell.default_parameters.membrane_capacitance = 0.018; // [F/m²]
arb::mechanism_desc nax("nax");
arb::mechanism_desc kdrmt("kdrmt");
@@ -337,8 +340,6 @@ arb::cable_cell gj_cell(cell_gid_type gid, unsigned ncell, double stim_duration)
};
auto setup_seg = [&](auto seg) {
- seg->rL = 100;
- seg->cm = 0.018;
seg->add_mechanism(nax);
seg->add_mechanism(kdrmt);
seg->add_mechanism(kamt);
diff --git a/example/generators/event_gen.cpp b/example/generators/event_gen.cpp
index 4106e1dc..b7acd24a 100644
--- a/example/generators/event_gen.cpp
+++ b/example/generators/event_gen.cpp
@@ -65,6 +65,12 @@ public:
return cell_kind::cable;
}
+ arb::util::any get_global_properties(arb::cell_kind) const override {
+ arb::cable_cell_global_properties gprop;
+ gprop.default_parameters = arb::neuron_parameter_defaults;
+ return gprop;
+ }
+
// The cell has one target synapse, which receives both inhibitory and exchitatory inputs.
cell_size_type num_targets(cell_gid_type gid) const override {
arb_assert(gid==0); // There is only one cell in the model
diff --git a/example/ring/ring.cpp b/example/ring/ring.cpp
index 150baf13..4bbcefd6 100644
--- a/example/ring/ring.cpp
+++ b/example/ring/ring.cpp
@@ -301,10 +301,10 @@ double interp(const std::array<T,2>& r, unsigned i, unsigned n) {
arb::cable_cell branch_cell(arb::cell_gid_type gid, const cell_parameters& params) {
arb::cable_cell cell;
+ cell.default_parameters.axial_resistivity = 100; // [Ω·cm]
// Add soma.
auto soma = cell.add_soma(12.6157/2.0); // For area of 500 μm².
- soma->rL = 100;
soma->add_mechanism("hh");
std::vector<std::vector<unsigned>> levels;
@@ -333,7 +333,6 @@ arb::cable_cell branch_cell(arb::cell_gid_type gid, const cell_parameters& param
auto dend = cell.add_cable(sec, arb::section_kind::dendrite, dend_radius, dend_radius, l);
dend->set_compartments(nc);
dend->add_mechanism("pas");
- dend->rL = 100;
}
}
}
diff --git a/example/single/single.cpp b/example/single/single.cpp
index d1c82bdb..3855f9de 100644
--- a/example/single/single.cpp
+++ b/example/single/single.cpp
@@ -26,7 +26,9 @@ arb::morphology default_morphology();
arb::morphology read_swc(const std::string& path);
struct single_recipe: public arb::recipe {
- explicit single_recipe(arb::morphology m): morpho(m) {}
+ explicit single_recipe(arb::morphology m): morpho(m) {
+ gprop.default_parameters = arb::neuron_parameter_defaults;
+ }
arb::cell_size_type num_cells() const override { return 1; }
arb::cell_size_type num_probes(arb::cell_gid_type) const override { return 1; }
@@ -46,24 +48,26 @@ struct single_recipe: public arb::recipe {
return arb::cell_kind::cable;
}
+ arb::util::any get_global_properties(arb::cell_kind) const override {
+ return gprop;
+ }
+
arb::util::unique_any get_cell_description(arb::cell_gid_type) const override {
arb::cable_cell c = make_cable_cell(morpho);
// Add HH mechanism to soma, passive channels to dendrites.
// Discretize dendrites according to the NEURON d-lambda rule.
- for (auto& segment: c.segments()) {
- if (segment->is_soma()) {
- segment->add_mechanism("hh");
- }
- else {
- segment->add_mechanism("pas");
+ c.soma()->add_mechanism("hh");
+ auto& segments = c.segments();
+ for (std::size_t i = 1; i<segments.size(); ++i) {
+ double dx = c.segment_length_constant(100., i, gprop.default_parameters)*0.3;
- double dx = segment->length_constant(100.)*0.3;
- unsigned n = std::ceil(segment->as_cable()->length()/dx);
- segment->set_compartments(n);
+ arb::cable_segment* seg = c.cable(i);
+ seg->add_mechanism("pas");
- }
+ unsigned n = std::ceil(seg->length()/dx);
+ seg->set_compartments(n);
}
// Add synapse to last segment.
@@ -76,6 +80,7 @@ struct single_recipe: public arb::recipe {
}
arb::morphology morpho;
+ arb::cable_cell_global_properties gprop;
};
int main(int argc, char** argv) {
--
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