diff --git a/arbor/CMakeLists.txt b/arbor/CMakeLists.txt
index e54d2d5089268661911881efcee00ec720d49c34..936aa2d9a3a5196cdd0243a908c09ac4381aa2d4 100644
--- a/arbor/CMakeLists.txt
+++ b/arbor/CMakeLists.txt
@@ -21,7 +21,7 @@ set(arbor_sources
io/locked_ostream.cpp
io/serialize_hex.cpp
lif_cell_group.cpp
- mc_cell.cpp
+ cable_cell.cpp
mc_cell_group.cpp
mechcat.cpp
memory/cuda_wrappers.cpp
diff --git a/arbor/mc_cell.cpp b/arbor/cable_cell.cpp
similarity index 61%
rename from arbor/mc_cell.cpp
rename to arbor/cable_cell.cpp
index 5807afd0dafa9f6b26ed783392c90b8f58b42c33..dd831a11743225f78c866ddc1462b732a90ebb7e 100644
--- a/arbor/mc_cell.cpp
+++ b/arbor/cable_cell.cpp
@@ -1,28 +1,28 @@
-#include <arbor/mc_cell.hpp>
-#include <arbor/mc_segment.hpp>
+#include <arbor/cable_cell.hpp>
+#include <arbor/segment.hpp>
#include <arbor/morphology.hpp>
#include "util/rangeutil.hpp"
namespace arb {
-using value_type = mc_cell::value_type;
-using index_type = mc_cell::index_type;
-using size_type = mc_cell::size_type;
+using value_type = cable_cell::value_type;
+using index_type = cable_cell::index_type;
+using size_type = cable_cell::size_type;
-mc_cell::mc_cell() {
+cable_cell::cable_cell() {
// insert a placeholder segment for the soma
segments_.push_back(make_segment<placeholder_segment>());
parents_.push_back(0);
}
-void mc_cell::assert_valid_segment(index_type i) const {
+void cable_cell::assert_valid_segment(index_type i) const {
if (i>=num_segments()) {
- throw mc_cell_error("no such segment");
+ throw cable_cell_error("no such segment");
}
}
-size_type mc_cell::num_segments() const {
+size_type cable_cell::num_segments() const {
return segments_.size();
}
@@ -30,21 +30,21 @@ size_type mc_cell::num_segments() const {
// note: I think that we have to enforce that the soma is the first
// segment that is added
//
-soma_segment* mc_cell::add_soma(value_type radius, point_type center) {
+soma_segment* cable_cell::add_soma(value_type radius, point_type center) {
if (has_soma()) {
- throw mc_cell_error("cell already has soma");
+ throw cable_cell_error("cell already has soma");
}
segments_[0] = make_segment<soma_segment>(radius, center);
return segments_[0]->as_soma();
}
-cable_segment* mc_cell::add_cable(index_type parent, mc_segment_ptr&& cable) {
+cable_segment* cable_cell::add_cable(index_type parent, segment_ptr&& cable) {
if (!cable->as_cable()) {
- throw mc_cell_error("segment is not a cable segment");
+ throw cable_cell_error("segment is not a cable segment");
}
if (parent>num_segments()) {
- throw mc_cell_error("parent index out of range");
+ throw cable_cell_error("parent index out of range");
}
segments_.push_back(std::move(cable));
@@ -53,35 +53,35 @@ cable_segment* mc_cell::add_cable(index_type parent, mc_segment_ptr&& cable) {
return segments_.back()->as_cable();
}
-mc_segment* mc_cell::segment(index_type index) {
+segment* cable_cell::segment(index_type index) {
assert_valid_segment(index);
return segments_[index].get();
}
-mc_segment const* mc_cell::segment(index_type index) const {
+segment const* cable_cell::segment(index_type index) const {
assert_valid_segment(index);
return segments_[index].get();
}
-bool mc_cell::has_soma() const {
+bool cable_cell::has_soma() const {
return !segment(0)->is_placeholder();
}
-soma_segment* mc_cell::soma() {
+soma_segment* cable_cell::soma() {
return has_soma()? segment(0)->as_soma(): nullptr;
}
-const soma_segment* mc_cell::soma() const {
+const soma_segment* cable_cell::soma() const {
return has_soma()? segment(0)->as_soma(): nullptr;
}
-cable_segment* mc_cell::cable(index_type index) {
+cable_segment* cable_cell::cable(index_type index) {
assert_valid_segment(index);
auto cable = segment(index)->as_cable();
- return cable? cable: throw mc_cell_error("segment is not a cable segment");
+ return cable? cable: throw cable_cell_error("segment is not a cable segment");
}
-std::vector<size_type> mc_cell::compartment_counts() const {
+std::vector<size_type> cable_cell::compartment_counts() const {
std::vector<size_type> comp_count;
comp_count.reserve(num_segments());
for (const auto& s: segments()) {
@@ -90,26 +90,26 @@ std::vector<size_type> mc_cell::compartment_counts() const {
return comp_count;
}
-size_type mc_cell::num_compartments() const {
+size_type cable_cell::num_compartments() const {
return util::sum_by(segments_,
- [](const mc_segment_ptr& s) { return s->num_compartments(); });
+ [](const segment_ptr& s) { return s->num_compartments(); });
}
-void mc_cell::add_stimulus(segment_location loc, i_clamp stim) {
+void cable_cell::add_stimulus(segment_location loc, i_clamp stim) {
(void)segment(loc.segment); // assert loc.segment in range
stimuli_.push_back({loc, std::move(stim)});
}
-void mc_cell::add_detector(segment_location loc, double threshold) {
+void cable_cell::add_detector(segment_location loc, double threshold) {
spike_detectors_.push_back({loc, threshold});
}
// Construct cell from flat morphology specification.
-mc_cell make_mc_cell(const morphology& morph, bool compartments_from_discretization) {
- using point3d = mc_cell::point_type;
- mc_cell newcell;
+cable_cell make_cable_cell(const morphology& morph, bool compartments_from_discretization) {
+ using point3d = cable_cell::point_type;
+ cable_cell newcell;
if (!morph) {
return newcell;
@@ -127,7 +127,7 @@ mc_cell make_mc_cell(const morphology& morph, bool compartments_from_discretizat
kind = section_kind::dendrite;
break;
case section_kind::soma:
- throw mc_cell_error("no support for complex somata");
+ throw cable_cell_error("no support for complex somata");
break;
default: ;
}
diff --git a/arbor/cell_group_factory.cpp b/arbor/cell_group_factory.cpp
index e3dc6a749d9a26dbfaf8db855e81e0ccdbb81c9d..68f3f9a294f15d3a1b1df92afd88d8e2a576a2a2 100644
--- a/arbor/cell_group_factory.cpp
+++ b/arbor/cell_group_factory.cpp
@@ -25,7 +25,7 @@ cell_group_factory cell_kind_implementation(
using gid_vector = std::vector<cell_gid_type>;
switch (ck) {
- case cell_kind::cable1d_neuron:
+ case cell_kind::cable:
return [bk, ctx](const gid_vector& gids, const recipe& rec) {
return make_cell_group<mc_cell_group>(gids, rec, make_fvm_lowered_cell(bk, ctx));
};
@@ -37,7 +37,7 @@ cell_group_factory cell_kind_implementation(
return make_cell_group<spike_source_cell_group>(gids, rec);
};
- case cell_kind::lif_neuron:
+ case cell_kind::lif:
if (bk!=backend_kind::multicore) break;
return [](const gid_vector& gids, const recipe& rec) {
diff --git a/arbor/common_types_io.cpp b/arbor/common_types_io.cpp
index c5b904784f700af08d78c8805a04728cf096001d..c08d0b66f614ca0ce5ca1d314fd95717dc4e11ac 100644
--- a/arbor/common_types_io.cpp
+++ b/arbor/common_types_io.cpp
@@ -13,10 +13,10 @@ std::ostream& operator<<(std::ostream& o, arb::cell_kind k) {
switch (k) {
case arb::cell_kind::spike_source:
return o << "spike_source";
- case arb::cell_kind::cable1d_neuron:
- return o << "cable1d_neuron";
- case arb::cell_kind::lif_neuron:
- return o << "lif_neuron";
+ case arb::cell_kind::cable:
+ return o << "cable";
+ case arb::cell_kind::lif:
+ return o << "lif";
case arb::cell_kind::benchmark:
return o << "benchmark_cell";
}
diff --git a/arbor/fvm_layout.cpp b/arbor/fvm_layout.cpp
index 7e43669cd0336c7bdb5e50cba64be1ce0fd114a5..1612734baf6d208745bada5e1a0488dcc7149c49 100644
--- a/arbor/fvm_layout.cpp
+++ b/arbor/fvm_layout.cpp
@@ -4,7 +4,7 @@
#include <vector>
#include <arbor/arbexcept.hpp>
-#include <arbor/mc_cell.hpp>
+#include <arbor/cable_cell.hpp>
#include "algorithms.hpp"
#include "fvm_compartment.hpp"
@@ -39,7 +39,7 @@ namespace {
std::vector<tree::int_type> parent_index;
std::vector<tree::int_type> segment_index;
- explicit compartment_model(const mc_cell& cell) {
+ explicit compartment_model(const cable_cell& cell) {
tree = arb::tree(cell.parents());
auto counts = cell.compartment_counts();
parent_index = make_parent_index(tree, counts);
@@ -118,7 +118,7 @@ namespace {
// = 1/R · hVâ‚Vâ‚‚/(h₂²Vâ‚+h₲Vâ‚‚)
//
-fvm_discretization fvm_discretize(const std::vector<mc_cell>& cells) {
+fvm_discretization fvm_discretize(const std::vector<cable_cell>& cells) {
using value_type = fvm_value_type;
using index_type = fvm_index_type;
@@ -127,11 +127,11 @@ fvm_discretization fvm_discretize(const std::vector<mc_cell>& cells) {
fvm_discretization D;
util::make_partition(D.cell_segment_bounds,
- transform_view(cells, [](const mc_cell& c) { return c.num_segments(); }));
+ transform_view(cells, [](const cable_cell& c) { return c.num_segments(); }));
std::vector<index_type> cell_comp_bounds;
auto cell_comp_part = make_partition(cell_comp_bounds,
- transform_view(cells, [](const mc_cell& c) { return c.num_compartments(); }));
+ transform_view(cells, [](const cable_cell& c) { return c.num_compartments(); }));
D.ncell = cells.size();
D.ncomp = cell_comp_part.bounds().second;
@@ -160,7 +160,7 @@ fvm_discretization fvm_discretize(const std::vector<mc_cell>& cells) {
seg_comp_bounds.clear();
auto seg_comp_part = make_partition(
seg_comp_bounds,
- transform_view(c.segments(), [](const mc_segment_ptr& s) { return s->num_compartments(); }),
+ transform_view(c.segments(), [](const segment_ptr& s) { return s->num_compartments(); }),
cell_comp_base);
const auto nseg = seg_comp_part.size();
@@ -257,7 +257,7 @@ fvm_discretization fvm_discretize(const std::vector<mc_cell>& cells) {
// IIb. Density mechanism CVs, parameter values; ion channel default concentration contributions.
// IIc. Point mechanism CVs, parameter values, and targets.
-fvm_mechanism_data fvm_build_mechanism_data(const mechanism_catalogue& catalogue, const std::vector<mc_cell>& cells, const fvm_discretization& D, bool coalesce_syanpses) {
+fvm_mechanism_data fvm_build_mechanism_data(const mechanism_catalogue& catalogue, const std::vector<cable_cell>& cells, const fvm_discretization& D, bool coalesce_syanpses) {
using util::assign;
using util::sort_by;
using util::optional;
diff --git a/arbor/fvm_layout.hpp b/arbor/fvm_layout.hpp
index abf7389e2dc1fb3c33f00406ae9ab29fa4dadd35..459fb5136e46ec2540355c6b8c9ab56a7198d16b 100644
--- a/arbor/fvm_layout.hpp
+++ b/arbor/fvm_layout.hpp
@@ -1,7 +1,7 @@
#pragma once
#include <arbor/fvm_types.hpp>
-#include <arbor/mc_cell.hpp>
+#include <arbor/cable_cell.hpp>
#include <arbor/mechanism.hpp>
#include <arbor/mechinfo.hpp>
#include <arbor/mechcat.hpp>
@@ -87,7 +87,7 @@ struct fvm_discretization {
}
};
-fvm_discretization fvm_discretize(const std::vector<mc_cell>& cells);
+fvm_discretization fvm_discretize(const std::vector<cable_cell>& cells);
// Post-discretization data for point and density mechanism instantiation.
@@ -140,6 +140,6 @@ struct fvm_mechanism_data {
std::size_t ntarget = 0;
};
-fvm_mechanism_data fvm_build_mechanism_data(const mechanism_catalogue& catalogue, const std::vector<mc_cell>& cells, const fvm_discretization& D, bool coalesce = true);
+fvm_mechanism_data fvm_build_mechanism_data(const mechanism_catalogue& catalogue, const std::vector<cable_cell>& cells, const fvm_discretization& D, bool coalesce = true);
} // namespace arb
diff --git a/arbor/fvm_lowered_cell_impl.hpp b/arbor/fvm_lowered_cell_impl.hpp
index 15d95a44944f7224c80ce4769b3bf17754236a98..b1cb1ff9c3932d32c96ea6395c472e7d1c704d1f 100644
--- a/arbor/fvm_lowered_cell_impl.hpp
+++ b/arbor/fvm_lowered_cell_impl.hpp
@@ -64,7 +64,7 @@ public:
std::vector<sample_event> staged_samples) override;
std::vector<fvm_gap_junction> fvm_gap_junctions(
- const std::vector<mc_cell>& cells,
+ const std::vector<cable_cell>& cells,
const std::vector<cell_gid_type>& gids,
const recipe& rec,
const fvm_discretization& D);
@@ -333,28 +333,28 @@ void fvm_lowered_cell_impl<B>::initialize(
set_gpu();
- std::vector<mc_cell> cells;
+ std::vector<cable_cell> cells;
const std::size_t ncell = gids.size();
cells.reserve(ncell);
for (auto gid: gids) {
try {
- cells.push_back(any_cast<mc_cell>(rec.get_cell_description(gid)));
+ cells.push_back(any_cast<cable_cell>(rec.get_cell_description(gid)));
}
catch (util::bad_any_cast&) {
throw bad_cell_description(rec.get_cell_kind(gid), gid);
}
}
- mc_cell_global_properties global_props;
+ cable_cell_global_properties global_props;
try {
- util::any rec_props = rec.get_global_properties(cell_kind::cable1d_neuron);
+ util::any rec_props = rec.get_global_properties(cell_kind::cable);
if (rec_props.has_value()) {
- global_props = any_cast<mc_cell_global_properties>(rec_props);
+ global_props = any_cast<cable_cell_global_properties>(rec_props);
}
}
catch (util::bad_any_cast&) {
- throw bad_global_property(cell_kind::cable1d_neuron);
+ throw bad_global_property(cell_kind::cable);
}
const mechanism_catalogue* catalogue = global_props.catalogue;
@@ -509,7 +509,7 @@ void fvm_lowered_cell_impl<B>::initialize(
// Get vector of gap_junctions
template <typename B>
std::vector<fvm_gap_junction> fvm_lowered_cell_impl<B>::fvm_gap_junctions(
- const std::vector<mc_cell>& cells,
+ const std::vector<cable_cell>& cells,
const std::vector<cell_gid_type>& gids,
const recipe& rec, const fvm_discretization& D) {
@@ -533,7 +533,7 @@ std::vector<fvm_gap_junction> fvm_lowered_cell_impl<B>::fvm_gap_junctions(
auto gj_list = rec.gap_junctions_on(gid);
for (auto g: gj_list) {
if (gid != g.local.gid && gid != g.peer.gid) {
- throw arb::bad_cell_description(cell_kind::cable1d_neuron, gid);
+ throw arb::bad_cell_description(cell_kind::cable, gid);
}
cell_gid_type cv0, cv1;
try {
@@ -541,7 +541,7 @@ std::vector<fvm_gap_junction> fvm_lowered_cell_impl<B>::fvm_gap_junctions(
cv1 = gid_to_cvs[g.peer.gid].at(g.peer.index);
}
catch (std::out_of_range&) {
- throw arb::bad_cell_description(cell_kind::cable1d_neuron, gid);
+ throw arb::bad_cell_description(cell_kind::cable, gid);
}
if (gid != g.local.gid) {
std::swap(cv0, cv1);
@@ -585,7 +585,7 @@ fvm_size_type fvm_lowered_cell_impl<B>::fvm_intdom(
cell_gid_type peer =
gj.local.gid==g? gj.peer.gid:
gj.peer.gid==g? gj.local.gid:
- throw bad_cell_description(cell_kind::cable1d_neuron, g);
+ throw bad_cell_description(cell_kind::cable, g);
if (!gid_to_loc.count(peer)) {
throw gj_unsupported_domain_decomposition(g, peer);
diff --git a/arbor/include/arbor/mc_cell.hpp b/arbor/include/arbor/cable_cell.hpp
similarity index 87%
rename from arbor/include/arbor/mc_cell.hpp
rename to arbor/include/arbor/cable_cell.hpp
index 82aa8cb58e806e1111619ef256b6c2543363f42c..dd865de8cb4b0c90ac570c1079b2570f6c0024f8 100644
--- a/arbor/include/arbor/mc_cell.hpp
+++ b/arbor/include/arbor/cable_cell.hpp
@@ -10,15 +10,15 @@
#include <arbor/ion.hpp>
#include <arbor/mechcat.hpp>
#include <arbor/morphology.hpp>
-#include <arbor/mc_segment.hpp>
+#include <arbor/segment.hpp>
namespace arb {
// Specialize arbor exception for errors in cell building.
-struct mc_cell_error: arbor_exception {
- mc_cell_error(const std::string& what):
- arbor_exception("mc_cell: "+what)
+struct cable_cell_error: arbor_exception {
+ cable_cell_error(const std::string& what):
+ arbor_exception("cable_cell: "+what)
{}
};
@@ -66,7 +66,7 @@ struct cell_probe_address {
// Global parameter type for cell descriptions.
-struct mc_cell_global_properties {
+struct cable_cell_global_properties {
const mechanism_catalogue* catalogue = &global_default_catalogue();
// If >0, check membrane voltage magnitude is less than limit
@@ -94,7 +94,7 @@ struct mc_cell_global_properties {
};
/// high-level abstract representation of a cell and its segments
-class mc_cell {
+class cable_cell {
public:
using index_type = cell_lid_type;
using size_type = cell_local_size_type;
@@ -119,10 +119,10 @@ public:
};
/// Default constructor
- mc_cell();
+ cable_cell();
/// Copy constructor
- mc_cell(const mc_cell& other):
+ cable_cell(const cable_cell& other):
parents_(other.parents_),
stimuli_(other.stimuli_),
synapses_(other.synapses_),
@@ -137,11 +137,11 @@ public:
}
/// Move constructor
- mc_cell(mc_cell&& other) = default;
+ cable_cell(cable_cell&& other) = default;
/// Return the kind of cell, used for grouping into cell_groups
cell_kind get_cell_kind() const {
- return cell_kind::cable1d_neuron;
+ return cell_kind::cable;
}
/// add a soma to the cell
@@ -151,7 +151,7 @@ public:
/// add a cable
/// parent is the index of the parent segment for the cable section
/// cable is the segment that will be moved into the cell
- cable_segment* add_cable(index_type parent, mc_segment_ptr&& cable);
+ cable_segment* add_cable(index_type parent, segment_ptr&& cable);
/// add a cable by constructing it in place
/// parent is the index of the parent segment for the cable section
@@ -164,8 +164,8 @@ public:
bool has_soma() const;
- class mc_segment* segment(index_type index);
- const class mc_segment* segment(index_type index) const;
+ class segment* segment(index_type index);
+ const class segment* segment(index_type index) const;
/// access pointer to the soma
/// returns nullptr if the cell has no soma
@@ -173,14 +173,14 @@ public:
const soma_segment* soma() const;
/// access pointer to a cable segment
- /// will throw an mc_cell_error exception if
+ /// will throw an cable_cell_error exception if
/// the cable index is not valid
cable_segment* cable(index_type index);
/// the total number of compartments over all segments
size_type num_compartments() const;
- std::vector<mc_segment_ptr> const& segments() const {
+ std::vector<segment_ptr> const& segments() const {
return segments_;
}
@@ -244,7 +244,7 @@ public:
// - volume and area properties of each segment
// - number of compartments in each segment
// (note: just used for testing: move to test code?)
- friend bool cell_basic_equality(const mc_cell&, const mc_cell&);
+ friend bool cell_basic_equality(const cable_cell&, const cable_cell&);
// Public view of parent indices vector.
const std::vector<index_type>& parents() const {
@@ -258,7 +258,7 @@ private:
std::vector<index_type> parents_;
// the segments
- std::vector<mc_segment_ptr> segments_;
+ std::vector<segment_ptr> segments_;
// the stimuli
std::vector<stimulus_instance> stimuli_;
@@ -275,11 +275,11 @@ private:
// create a cable by forwarding cable construction parameters provided by the user
template <typename... Args>
-cable_segment* mc_cell::add_cable(mc_cell::index_type parent, Args&&... args)
+cable_segment* cable_cell::add_cable(cable_cell::index_type parent, Args&&... args)
{
// check for a valid parent id
if (parent>=num_segments()) {
- throw mc_cell_error("parent index of cell segment is out of range");
+ throw cable_cell_error("parent index of cell segment is out of range");
}
segments_.push_back(make_segment<cable_segment>(std::forward<Args>(args)...));
parents_.push_back(parent);
@@ -291,6 +291,6 @@ cable_segment* mc_cell::add_cable(mc_cell::index_type parent, Args&&... args)
// If compartments_from_discretization is true, set number of compartments in
// each segment to be the number of piecewise linear sections in the corresponding
// section of the morphologu.
-mc_cell make_mc_cell(const morphology&, bool compartments_from_discretization=false);
+cable_cell make_cable_cell(const morphology&, bool compartments_from_discretization=false);
} // namespace arb
diff --git a/arbor/include/arbor/common_types.hpp b/arbor/include/arbor/common_types.hpp
index 418ba7865b5e18ce8cafabfcd0d506fb7b78ceee..3741f120119c3ad596af592cf6e1a23ea743db22 100644
--- a/arbor/include/arbor/common_types.hpp
+++ b/arbor/include/arbor/common_types.hpp
@@ -75,8 +75,8 @@ enum class backend_kind {
// group equal kinds in the same cell group.
enum class cell_kind {
- cable1d_neuron, // Our own special mc neuron.
- lif_neuron, // Leaky-integrate and fire neuron.
+ cable, // Our own special mc neuron.
+ lif, // Leaky-integrate and fire neuron.
spike_source, // Cell that generates spikes at a user-supplied sequence of time points.
benchmark, // Proxy cell used for benchmarking.
};
diff --git a/arbor/include/arbor/mc_segment.hpp b/arbor/include/arbor/segment.hpp
similarity index 91%
rename from arbor/include/arbor/mc_segment.hpp
rename to arbor/include/arbor/segment.hpp
index ded52d54857d6a57f7ab98dc0eddabc7c4a00492..1f408850f1b0757a6e30fa49d22c8343cf0f48b2 100644
--- a/arbor/include/arbor/mc_segment.hpp
+++ b/arbor/include/arbor/segment.hpp
@@ -77,14 +77,14 @@ class soma_segment;
class cable_segment;
// abstract base class for a cell segment
-class mc_segment {
+class segment {
public:
using value_type = double;
using size_type = cell_local_size_type;
using point_type = point<value_type>;
// (Yet more motivation for a separate morphology description class!)
- virtual std::unique_ptr<mc_segment> clone() const = 0;
+ virtual std::unique_ptr<segment> clone() const = 0;
section_kind kind() const {
return kind_;
@@ -108,7 +108,7 @@ public:
virtual size_type num_compartments() const = 0;
virtual void set_compartments(size_type) = 0;
- virtual ~mc_segment() = default;
+ virtual ~segment() = default;
virtual cable_segment* as_cable()
{
@@ -169,17 +169,17 @@ public:
value_type cm = 0.01; // capacitance [F/m^2] : 10 nF/mm^2 = 0.01 F/m^2
protected:
- mc_segment(section_kind kind): kind_(kind) {}
+ segment(section_kind kind): kind_(kind) {}
section_kind kind_;
std::vector<mechanism_desc> mechanisms_;
};
-class placeholder_segment : public mc_segment {
+class placeholder_segment : public segment {
public:
- placeholder_segment(): mc_segment(section_kind::none) {}
+ placeholder_segment(): segment(section_kind::none) {}
- std::unique_ptr<mc_segment> clone() const override {
+ std::unique_ptr<segment> clone() const override {
// use default copy constructor
return std::make_unique<placeholder_segment>(*this);
}
@@ -197,14 +197,14 @@ public:
virtual void set_compartments(size_type) override {}
};
-class soma_segment : public mc_segment {
+class soma_segment : public segment {
public:
soma_segment() = delete;
explicit soma_segment(value_type r, point_type c = point_type{}):
- mc_segment(section_kind::soma), radius_{r}, center_(c) {}
+ segment(section_kind::soma), radius_{r}, center_(c) {}
- std::unique_ptr<mc_segment> clone() const override {
+ std::unique_ptr<segment> clone() const override {
// use default copy constructor
return std::make_unique<soma_segment>(*this);
}
@@ -244,9 +244,9 @@ private :
point_type center_;
};
-class cable_segment : public mc_segment {
+class cable_segment : public segment {
public:
- using base = mc_segment;
+ using base = segment;
using base::kind_;
using base::value_type;
using base::point_type;
@@ -256,7 +256,7 @@ public:
// constructors for a cable with no location information
cable_segment(section_kind k, std::vector<value_type> r, std::vector<value_type> lens):
- mc_segment(k), radii_(std::move(r)), lengths_(std::move(lens))
+ segment(k), radii_(std::move(r)), lengths_(std::move(lens))
{
arb_assert(kind_==section_kind::dendrite || kind_==section_kind::axon);
}
@@ -268,7 +268,7 @@ public:
// constructor that lets the user describe the cable as a
// seriew of radii and locations
cable_segment(section_kind k, std::vector<value_type> r, std::vector<point_type> p):
- mc_segment(k), radii_(std::move(r)), locations_(std::move(p))
+ segment(k), radii_(std::move(r)), locations_(std::move(p))
{
arb_assert(kind_==section_kind::dendrite || kind_==section_kind::axon);
update_lengths();
@@ -287,7 +287,7 @@ public:
cable_segment(k, {r1, r2}, {p1, p2})
{}
- std::unique_ptr<mc_segment> clone() const override {
+ std::unique_ptr<segment> clone() const override {
// use default copy constructor
return std::make_unique<cable_segment>(*this);
}
@@ -404,14 +404,14 @@ private:
std::vector<point_type> locations_;
};
-using mc_segment_ptr = std::unique_ptr<mc_segment>;
+using segment_ptr = std::unique_ptr<segment>;
/// Helper for constructing segments in a segment_ptr unique pointer wrapper.
/// Forwards the supplied arguments to construct a segment of type SegmentType.
/// e.g. auto my_cable = make_segment<cable>(section_kind::dendrite, ... );
template <typename SegmentType, typename... Args>
-mc_segment_ptr make_segment(Args&&... args) {
- return mc_segment_ptr(new SegmentType(std::forward<Args>(args)...));
+segment_ptr make_segment(Args&&... args) {
+ return segment_ptr(new SegmentType(std::forward<Args>(args)...));
}
} // namespace arb
diff --git a/arbor/lif_cell_group.cpp b/arbor/lif_cell_group.cpp
index 7622dab2ab8ed04724f7ee3868b7ac00a3f465c8..c87c6692a07006eb7289cb99bc28c124a47f054c 100644
--- a/arbor/lif_cell_group.cpp
+++ b/arbor/lif_cell_group.cpp
@@ -21,7 +21,7 @@ lif_cell_group::lif_cell_group(const std::vector<cell_gid_type>& gids, const rec
}
cell_kind lif_cell_group::get_cell_kind() const {
- return cell_kind::lif_neuron;
+ return cell_kind::lif;
}
void lif_cell_group::advance(epoch ep, time_type dt, const event_lane_subrange& event_lanes) {
diff --git a/arbor/mc_cell_group.hpp b/arbor/mc_cell_group.hpp
index f22d3b22ea14a59b748a9c8bee61cda3d397dfb8..70f255dc98e9244150aecbf7714e59c6e75e3fe0 100644
--- a/arbor/mc_cell_group.hpp
+++ b/arbor/mc_cell_group.hpp
@@ -33,7 +33,7 @@ public:
mc_cell_group(const std::vector<cell_gid_type>& gids, const recipe& rec, fvm_lowered_cell_ptr lowered);
cell_kind get_cell_kind() const override {
- return cell_kind::cable1d_neuron;
+ return cell_kind::cable;
}
void reset() override;
diff --git a/arbor/partition_load_balance.cpp b/arbor/partition_load_balance.cpp
index c393f51cce863d9d3f7afc2dfb28efc8e8d7c7a7..cc09a8618ab2829b4f5c3c29ce99610d9891bb3b 100644
--- a/arbor/partition_load_balance.cpp
+++ b/arbor/partition_load_balance.cpp
@@ -91,7 +91,7 @@ domain_decomposition partition_load_balance(
auto conns = rec.gap_junctions_on(element);
for (auto c: conns) {
if (element != c.local.gid && element != c.peer.gid) {
- throw bad_cell_description(cell_kind::cable1d_neuron, element);
+ throw bad_cell_description(cell_kind::cable, element);
}
cell_member_type other = c.local.gid == element ? c.peer : c.local;
diff --git a/example/brunel/brunel_miniapp.cpp b/example/brunel/brunel_miniapp.cpp
index 320bdcb53c05be51d7a42bc40beafda1b917d7ab..131f273010d72d658493abb012dd926d471250ef 100644
--- a/example/brunel/brunel_miniapp.cpp
+++ b/example/brunel/brunel_miniapp.cpp
@@ -89,7 +89,7 @@ public:
}
cell_kind get_cell_kind(cell_gid_type gid) const override {
- return cell_kind::lif_neuron;
+ return cell_kind::lif;
}
std::vector<cell_connection> connections_on(cell_gid_type gid) const override {
@@ -255,7 +255,7 @@ int main(int argc, char** argv) {
brunel_recipe recipe(nexc, ninh, next, in_degree_prop, w, d, rel_inh_strength, poiss_lambda, seed);
partition_hint_map hints;
- hints[cell_kind::lif_neuron].cpu_group_size = group_size;
+ hints[cell_kind::lif].cpu_group_size = group_size;
auto decomp = partition_load_balance(recipe, context, hints);
simulation sim(recipe, decomp, context);
diff --git a/example/dryrun/dryrun.cpp b/example/dryrun/dryrun.cpp
index 92203545756391163c1dc8295724381235c24a06..12728c69617e455ca331d9bf922ac873d5f97697 100644
--- a/example/dryrun/dryrun.cpp
+++ b/example/dryrun/dryrun.cpp
@@ -13,7 +13,7 @@
#include <arbor/common_types.hpp>
#include <arbor/context.hpp>
#include <arbor/load_balance.hpp>
-#include <arbor/mc_cell.hpp>
+#include <arbor/cable_cell.hpp>
#include <arbor/profile/meter_manager.hpp>
#include <arbor/profile/profiler.hpp>
#include <arbor/simple_sampler.hpp>
@@ -41,7 +41,7 @@ using arb::time_type;
using arb::cell_probe_address;
// Generate a cell.
-arb::mc_cell branch_cell(arb::cell_gid_type gid, const cell_parameters& params);
+arb::cable_cell branch_cell(arb::cell_gid_type gid, const cell_parameters& params);
class tile_desc: public arb::tile {
public:
@@ -65,7 +65,7 @@ public:
}
cell_kind get_cell_kind(cell_gid_type gid) const override {
- return cell_kind::cable1d_neuron;
+ return cell_kind::cable;
}
// Each cell has one spike detector (at the soma).
@@ -143,7 +143,7 @@ struct cell_stats {
size_type nsegs_tmp = 0;
size_type ncomp_tmp = 0;
for (size_type i=b; i<e; ++i) {
- auto c = arb::util::any_cast<arb::mc_cell>(r.get_cell_description(i));
+ auto c = arb::util::any_cast<arb::cable_cell>(r.get_cell_description(i));
nsegs_tmp += c.num_segments();
ncomp_tmp += c.num_compartments();
}
@@ -155,7 +155,7 @@ struct cell_stats {
nranks = 1;
ncells = r.num_cells();
for (size_type i = 0; i < ncells; ++i) {
- auto c = arb::util::any_cast<arb::mc_cell>(r.get_cell_description(i));
+ auto c = arb::util::any_cast<arb::cable_cell>(r.get_cell_description(i));
nsegs += c.num_segments();
ncomp += c.num_compartments();
}
@@ -166,7 +166,7 @@ struct cell_stats {
ncells = r.num_cells(); //total number of cells across all ranks
for (size_type i = 0; i < params.num_cells_per_rank; ++i) {
- auto c = arb::util::any_cast<arb::mc_cell>(r.get_cell_description(i));
+ auto c = arb::util::any_cast<arb::cable_cell>(r.get_cell_description(i));
nsegs += c.num_segments();
ncomp += c.num_compartments();
}
@@ -302,8 +302,8 @@ double interp(const std::array<T,2>& r, unsigned i, unsigned n) {
return r[0] + p*(r1-r0);
}
-arb::mc_cell branch_cell(arb::cell_gid_type gid, const cell_parameters& params) {
- arb::mc_cell cell;
+arb::cable_cell branch_cell(arb::cell_gid_type gid, const cell_parameters& params) {
+ arb::cable_cell cell;
// Add soma.
auto soma = cell.add_soma(12.6157/2.0); // For area of 500 μm².
diff --git a/example/dryrun/parameters.hpp b/example/dryrun/parameters.hpp
index 316ac3ce9746f6902ea7e1e33a71eddaa0cac65c..e355fcf8793e88ad9e2fc1a33300839fd3c9554b 100644
--- a/example/dryrun/parameters.hpp
+++ b/example/dryrun/parameters.hpp
@@ -5,7 +5,7 @@
#include <fstream>
#include <random>
-#include <arbor/mc_cell.hpp>
+#include <arbor/cable_cell.hpp>
#include <sup/json_params.hpp>
diff --git a/example/dryrun/readme.md b/example/dryrun/readme.md
index 1fd9037cb665fa19a7ca5c13d20d3038f78ba827..c0ee998cb90480bc93360aa00c38b0cde2e6f33a 100644
--- a/example/dryrun/readme.md
+++ b/example/dryrun/readme.md
@@ -4,7 +4,7 @@ A miniapp that demonstrates how to use dry-run mode on a simple network
duplicated across `num_ranks`.
It uses the `arb::tile` to build a network of `num_cells_per_rank` cells of type
-`arb::mc_cell`. The network is translated over `num_ranks` domains using
+`arb::cable_cell`. The network is translated over `num_ranks` domains using
`arb::symmetric_recipe`.
Example:
diff --git a/example/gap_junctions/gap_junctions.cpp b/example/gap_junctions/gap_junctions.cpp
index e37bb671a4f5fab8df2d1bafc339114505cafc36..2e8381f7542f900b9271cb6891a765af41f63184 100644
--- a/example/gap_junctions/gap_junctions.cpp
+++ b/example/gap_junctions/gap_junctions.cpp
@@ -13,7 +13,7 @@
#include <arbor/common_types.hpp>
#include <arbor/context.hpp>
#include <arbor/load_balance.hpp>
-#include <arbor/mc_cell.hpp>
+#include <arbor/cable_cell.hpp>
#include <arbor/profile/meter_manager.hpp>
#include <arbor/profile/profiler.hpp>
#include <arbor/simple_sampler.hpp>
@@ -46,7 +46,7 @@ using arb::cell_probe_address;
void write_trace_json(const std::vector<arb::trace_data<double>>& trace, unsigned rank);
// Generate a cell.
-arb::mc_cell gj_cell(cell_gid_type gid, unsigned ncells, double stim_duration);
+arb::cable_cell gj_cell(cell_gid_type gid, unsigned ncells, double stim_duration);
class gj_recipe: public arb::recipe {
public:
@@ -61,7 +61,7 @@ public:
}
cell_kind get_cell_kind(cell_gid_type gid) const override {
- return cell_kind::cable1d_neuron;
+ return cell_kind::cable;
}
// Each cell has one spike detector (at the soma).
@@ -96,7 +96,7 @@ public:
}
arb::util::any get_global_properties(cell_kind k) const override {
- arb::mc_cell_global_properties a;
+ arb::cable_cell_global_properties a;
a.temperature_K = 308.15;
return a;
}
@@ -146,7 +146,7 @@ struct cell_stats {
size_type nsegs_tmp = 0;
size_type ncomp_tmp = 0;
for (size_type i=b; i<e; ++i) {
- auto c = arb::util::any_cast<arb::mc_cell>(r.get_cell_description(i));
+ auto c = arb::util::any_cast<arb::cable_cell>(r.get_cell_description(i));
nsegs_tmp += c.num_segments();
ncomp_tmp += c.num_compartments();
}
@@ -155,7 +155,7 @@ struct cell_stats {
#else
ncells = r.num_cells();
for (size_type i=0; i<ncells; ++i) {
- auto c = arb::util::any_cast<arb::mc_cell>(r.get_cell_description(i));
+ auto c = arb::util::any_cast<arb::cable_cell>(r.get_cell_description(i));
nsegs += c.num_segments();
ncomp += c.num_compartments();
}
@@ -319,8 +319,8 @@ void write_trace_json(const std::vector<arb::trace_data<double>>& trace, unsigne
}
}
-arb::mc_cell gj_cell(cell_gid_type gid, unsigned ncell, double stim_duration) {
- arb::mc_cell cell;
+arb::cable_cell gj_cell(cell_gid_type gid, unsigned ncell, double stim_duration) {
+ arb::cable_cell cell;
arb::mechanism_desc nax("nax");
arb::mechanism_desc kdrmt("kdrmt");
diff --git a/example/gap_junctions/parameters.hpp b/example/gap_junctions/parameters.hpp
index f7dc5f05e539cdc22117ee4c8cc8a493d5b6136f..f68ddfd26df2975b12c595479cd98df19e425afe 100644
--- a/example/gap_junctions/parameters.hpp
+++ b/example/gap_junctions/parameters.hpp
@@ -5,7 +5,7 @@
#include <fstream>
#include <random>
-#include <arbor/mc_cell.hpp>
+#include <arbor/cable_cell.hpp>
#include <sup/json_params.hpp>
diff --git a/example/generators/event_gen.cpp b/example/generators/event_gen.cpp
index 7ea031c489a00e3e922502eab4a71e41a2d40f53..4106e1dc2a10fb19e3aa5848769c9db7a28d7fe0 100644
--- a/example/generators/event_gen.cpp
+++ b/example/generators/event_gen.cpp
@@ -17,7 +17,7 @@
#include <arbor/domain_decomposition.hpp>
#include <arbor/event_generator.hpp>
#include <arbor/load_balance.hpp>
-#include <arbor/mc_cell.hpp>
+#include <arbor/cable_cell.hpp>
#include <arbor/simple_sampler.hpp>
#include <arbor/recipe.hpp>
#include <arbor/simulation.hpp>
@@ -47,7 +47,7 @@ public:
// capacitance: 0.01 F/m² [default]
// synapses: 1 * expsyn
arb::util::unique_any get_cell_description(cell_gid_type gid) const override {
- arb::mc_cell c;
+ arb::cable_cell c;
c.add_soma(18.8/2.0); // convert 18.8 μm diameter to radius
c.soma()->add_mechanism("pas");
@@ -62,7 +62,7 @@ public:
cell_kind get_cell_kind(cell_gid_type gid) const override {
arb_assert(gid==0); // There is only one cell in the model
- return cell_kind::cable1d_neuron;
+ return cell_kind::cable;
}
// The cell has one target synapse, which receives both inhibitory and exchitatory inputs.
diff --git a/example/generators/readme.md b/example/generators/readme.md
index f3f5c87016b2480611c92f2b490c397fc8f60bce..0f2e71f220d83f1d4ffbfbe6996b230b794d9b6d 100644
--- a/example/generators/readme.md
+++ b/example/generators/readme.md
@@ -46,7 +46,7 @@ which returns an empty list of connections for a cell.
Above you can see the definition of `recipe::num_cells()`, which is trivial for this model, which has only once cell.
The `recipe::get_cell_description(gid)` and `recipe::get_cell_kind(gid)` methods are defined to return a single
-compartment cell with one synapse, and a `arb::cell_kind::cable1d_neuron` respectively:
+compartment cell with one synapse, and a `arb::cell_kind::cable` respectively:
```C++
// Return an arb::cell that describes a single compartment cell with
@@ -66,7 +66,7 @@ compartment cell with one synapse, and a `arb::cell_kind::cable1d_neuron` respec
}
cell_kind get_cell_kind(cell_gid_type gid) const override {
- return cell_kind::cable1d_neuron;
+ return cell_kind::cable;
}
// There is one synapse, i.e. target, on the cell.
diff --git a/example/ring/parameters.hpp b/example/ring/parameters.hpp
index 74eb177db794bd5d041e7f9158637d1df3f66ab7..6343cb3c1e9fd73bb7174f5391a6a975952dd68a 100644
--- a/example/ring/parameters.hpp
+++ b/example/ring/parameters.hpp
@@ -5,7 +5,7 @@
#include <fstream>
#include <random>
-#include <arbor/mc_cell.hpp>
+#include <arbor/cable_cell.hpp>
#include <sup/json_params.hpp>
diff --git a/example/ring/ring.cpp b/example/ring/ring.cpp
index 09d6e78b9666a3faeee8e8da4f67827e6c0c9cbd..150baf134983926c956bbcb1b76723c699bcbc13 100644
--- a/example/ring/ring.cpp
+++ b/example/ring/ring.cpp
@@ -13,7 +13,7 @@
#include <arbor/common_types.hpp>
#include <arbor/context.hpp>
#include <arbor/load_balance.hpp>
-#include <arbor/mc_cell.hpp>
+#include <arbor/cable_cell.hpp>
#include <arbor/profile/meter_manager.hpp>
#include <arbor/profile/profiler.hpp>
#include <arbor/simple_sampler.hpp>
@@ -46,7 +46,7 @@ using arb::cell_probe_address;
void write_trace_json(const arb::trace_data<double>& trace);
// Generate a cell.
-arb::mc_cell branch_cell(arb::cell_gid_type gid, const cell_parameters& params);
+arb::cable_cell branch_cell(arb::cell_gid_type gid, const cell_parameters& params);
class ring_recipe: public arb::recipe {
public:
@@ -65,7 +65,7 @@ public:
}
cell_kind get_cell_kind(cell_gid_type gid) const override {
- return cell_kind::cable1d_neuron;
+ return cell_kind::cable;
}
// Each cell has one spike detector (at the soma).
@@ -133,7 +133,7 @@ struct cell_stats {
size_type nsegs_tmp = 0;
size_type ncomp_tmp = 0;
for (size_type i=b; i<e; ++i) {
- auto c = arb::util::any_cast<arb::mc_cell>(r.get_cell_description(i));
+ auto c = arb::util::any_cast<arb::cable_cell>(r.get_cell_description(i));
nsegs_tmp += c.num_segments();
ncomp_tmp += c.num_compartments();
}
@@ -142,7 +142,7 @@ struct cell_stats {
#else
ncells = r.num_cells();
for (size_type i=0; i<ncells; ++i) {
- auto c = arb::util::any_cast<arb::mc_cell>(r.get_cell_description(i));
+ auto c = arb::util::any_cast<arb::cable_cell>(r.get_cell_description(i));
nsegs += c.num_segments();
ncomp += c.num_compartments();
}
@@ -299,8 +299,8 @@ double interp(const std::array<T,2>& r, unsigned i, unsigned n) {
return r[0] + p*(r1-r0);
}
-arb::mc_cell branch_cell(arb::cell_gid_type gid, const cell_parameters& params) {
- arb::mc_cell cell;
+arb::cable_cell branch_cell(arb::cell_gid_type gid, const cell_parameters& params) {
+ arb::cable_cell cell;
// Add soma.
auto soma = cell.add_soma(12.6157/2.0); // For area of 500 μm².
diff --git a/example/single/single.cpp b/example/single/single.cpp
index 9237f33503c456c3a91d1d7008d4f487d955e0f2..d1c82bdbba46e5781a642abc1133953360e5119b 100644
--- a/example/single/single.cpp
+++ b/example/single/single.cpp
@@ -6,7 +6,7 @@
#include <vector>
#include <arbor/load_balance.hpp>
-#include <arbor/mc_cell.hpp>
+#include <arbor/cable_cell.hpp>
#include <arbor/morphology.hpp>
#include <arbor/swcio.hpp>
#include <arbor/simulation.hpp>
@@ -43,11 +43,11 @@ struct single_recipe: public arb::recipe {
}
arb::cell_kind get_cell_kind(arb::cell_gid_type) const override {
- return arb::cell_kind::cable1d_neuron;
+ return arb::cell_kind::cable;
}
arb::util::unique_any get_cell_description(arb::cell_gid_type) const override {
- arb::mc_cell c = make_mc_cell(morpho);
+ 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.
diff --git a/test/common_cells.hpp b/test/common_cells.hpp
index 134395caf17a2c391f40b83c20688acea49ecfd0..ae15233e463645caec0ae67c0f74af6919dad4c4 100644
--- a/test/common_cells.hpp
+++ b/test/common_cells.hpp
@@ -1,7 +1,7 @@
#include <cmath>
-#include <arbor/mc_cell.hpp>
-#include <arbor/mc_segment.hpp>
+#include <arbor/cable_cell.hpp>
+#include <arbor/segment.hpp>
#include <arbor/mechinfo.hpp>
#include <arbor/recipe.hpp>
@@ -20,8 +20,8 @@ namespace arb {
* soma centre, t=[10 ms, 110 ms), 0.1 nA
*/
-inline mc_cell make_cell_soma_only(bool with_stim = true) {
- mc_cell c;
+inline cable_cell make_cell_soma_only(bool with_stim = true) {
+ cable_cell c;
auto soma = c.add_soma(18.8/2.0);
soma->add_mechanism("hh");
@@ -54,8 +54,8 @@ inline mc_cell make_cell_soma_only(bool with_stim = true) {
* end of dendrite, t=[5 ms, 85 ms), 0.3 nA
*/
-inline mc_cell make_cell_ball_and_stick(bool with_stim = true) {
- mc_cell c;
+inline cable_cell make_cell_ball_and_stick(bool with_stim = true) {
+ cable_cell c;
auto soma = c.add_soma(12.6157/2.0);
soma->add_mechanism("hh");
@@ -98,8 +98,8 @@ inline mc_cell make_cell_ball_and_stick(bool with_stim = true) {
* end of dendrite, t=[5 ms, 85 ms), 0.3 nA
*/
-inline mc_cell make_cell_ball_and_taper(bool with_stim = true) {
- mc_cell c;
+inline cable_cell make_cell_ball_and_taper(bool with_stim = true) {
+ cable_cell c;
auto soma = c.add_soma(12.6157/2.0);
soma->add_mechanism("hh");
@@ -140,14 +140,14 @@ inline mc_cell make_cell_ball_and_taper(bool with_stim = true) {
* end of dendrite, t=[5 ms, 85 ms), 0.3 nA
*/
-inline mc_cell make_cell_ball_and_squiggle(bool with_stim = true) {
- mc_cell c;
+inline cable_cell make_cell_ball_and_squiggle(bool with_stim = true) {
+ cable_cell c;
auto soma = c.add_soma(12.6157/2.0);
soma->add_mechanism("hh");
- std::vector<mc_cell::value_type> radii;
- std::vector<mc_cell::point_type> points;
+ std::vector<cable_cell::value_type> radii;
+ std::vector<cable_cell::point_type> points;
double length = 100.0;
int npoints = 200;
@@ -201,8 +201,8 @@ inline mc_cell make_cell_ball_and_squiggle(bool with_stim = true) {
* end of second terminal branch, t=[40 ms, 50 ms), -0.2 nA
*/
-inline mc_cell make_cell_ball_and_3stick(bool with_stim = true) {
- mc_cell c;
+inline cable_cell make_cell_ball_and_3stick(bool with_stim = true) {
+ cable_cell c;
auto soma = c.add_soma(12.6157/2.0);
soma->add_mechanism("hh");
@@ -246,8 +246,8 @@ inline mc_cell make_cell_ball_and_3stick(bool with_stim = true) {
* work-around for some existing fvm modelling issues.
*/
-inline mc_cell make_cell_simple_cable(bool with_stim = true) {
- mc_cell c;
+inline cable_cell make_cell_simple_cable(bool with_stim = true) {
+ cable_cell c;
c.add_soma(0);
c.add_cable(0, section_kind::dendrite, 0.5, 0.5, 1000);
diff --git a/test/simple_recipes.hpp b/test/simple_recipes.hpp
index bcf528540890a947cb2888057d0628914dad4e5c..6dded63c62e2b721f48bad2547294cb28af764b1 100644
--- a/test/simple_recipes.hpp
+++ b/test/simple_recipes.hpp
@@ -6,7 +6,7 @@
#include <vector>
#include <arbor/event_generator.hpp>
-#include <arbor/mc_cell.hpp>
+#include <arbor/cable_cell.hpp>
#include <arbor/recipe.hpp>
namespace arb {
@@ -39,7 +39,7 @@ public:
util::any get_global_properties(cell_kind k) const override {
switch (k) {
- case cell_kind::cable1d_neuron:
+ case cell_kind::cable:
return cell_gprop_;
default:
return util::any{};
@@ -52,7 +52,7 @@ public:
protected:
std::unordered_map<cell_gid_type, std::vector<probe_info>> probes_;
- mc_cell_global_properties cell_gprop_;
+ cable_cell_global_properties cell_gprop_;
mechanism_catalogue catalogue_;
};
@@ -84,7 +84,7 @@ protected:
Description desc_;
};
-// Recipe for a set of `cable1d_neuron` neurons without connections,
+// Recipe for a set of `cable` neurons without connections,
// and probes which can be added by `add_probe()` (similar to above).
//
// Cell descriptions passed to the constructor are cloned.
@@ -98,13 +98,13 @@ public:
}
}
- explicit cable1d_recipe(const mc_cell& c) {
+ explicit cable1d_recipe(const cable_cell& c) {
cells_.reserve(1);
cells_.emplace_back(c);
}
cell_size_type num_cells() const override { return cells_.size(); }
- cell_kind get_cell_kind(cell_gid_type) const override { return cell_kind::cable1d_neuron; }
+ cell_kind get_cell_kind(cell_gid_type) const override { return cell_kind::cable; }
cell_size_type num_sources(cell_gid_type i) const override {
return cells_.at(i).detectors().size();
@@ -115,11 +115,11 @@ public:
}
util::unique_any get_cell_description(cell_gid_type i) const override {
- return util::make_unique_any<mc_cell>(cells_[i]);
+ return util::make_unique_any<cable_cell>(cells_[i]);
}
protected:
- std::vector<mc_cell> cells_;
+ std::vector<cable_cell> cells_;
};
} // namespace arb
diff --git a/test/ubench/mech_vec.cpp b/test/ubench/mech_vec.cpp
index 2d910a31b0a97184c09f4261a5a309011844b9a2..1691002a72c7a9c4d9c15603100c2d02249e879a 100644
--- a/test/ubench/mech_vec.cpp
+++ b/test/ubench/mech_vec.cpp
@@ -4,7 +4,7 @@
#include <fstream>
-#include <arbor/mc_cell.hpp>
+#include <arbor/cable_cell.hpp>
#include "backends/multicore/fvm.hpp"
#include "benchmark/benchmark.h"
@@ -40,7 +40,7 @@ public:
}
virtual util::unique_any get_cell_description(cell_gid_type gid) const override {
- mc_cell c;
+ cable_cell c;
auto soma = c.add_soma(12.6157/2.0);
soma->add_mechanism("pas");
@@ -64,7 +64,7 @@ public:
}
virtual cell_kind get_cell_kind(cell_gid_type) const override {
- return cell_kind::cable1d_neuron;
+ return cell_kind::cable;
}
};
@@ -79,7 +79,7 @@ public:
}
virtual util::unique_any get_cell_description(cell_gid_type gid) const override {
- mc_cell c;
+ cable_cell c;
auto soma = c.add_soma(12.6157/2.0);
soma->add_mechanism("pas");
@@ -96,7 +96,7 @@ public:
}
virtual cell_kind get_cell_kind(cell_gid_type) const override {
- return cell_kind::cable1d_neuron;
+ return cell_kind::cable;
}
};
@@ -111,7 +111,7 @@ public:
}
virtual util::unique_any get_cell_description(cell_gid_type gid) const override {
- mc_cell c;
+ cable_cell c;
auto soma = c.add_soma(12.6157/2.0);
soma->add_mechanism("pas");
@@ -130,7 +130,7 @@ public:
}
virtual cell_kind get_cell_kind(cell_gid_type) const override {
- return cell_kind::cable1d_neuron;
+ return cell_kind::cable;
}
};
@@ -145,7 +145,7 @@ public:
}
virtual util::unique_any get_cell_description(cell_gid_type gid) const override {
- mc_cell c;
+ cable_cell c;
auto soma = c.add_soma(12.6157/2.0);
soma->add_mechanism("hh");
@@ -162,7 +162,7 @@ public:
}
virtual cell_kind get_cell_kind(cell_gid_type) const override {
- return cell_kind::cable1d_neuron;
+ return cell_kind::cable;
}
};
@@ -177,7 +177,7 @@ public:
}
virtual util::unique_any get_cell_description(cell_gid_type gid) const override {
- mc_cell c;
+ cable_cell c;
auto soma = c.add_soma(12.6157/2.0);
soma->add_mechanism("pas");
@@ -196,7 +196,7 @@ public:
}
virtual cell_kind get_cell_kind(cell_gid_type) const override {
- return cell_kind::cable1d_neuron;
+ return cell_kind::cable;
}
};
diff --git a/test/unit-distributed/test_communicator.cpp b/test/unit-distributed/test_communicator.cpp
index 4eda7ccbba3a0378561f66801e9d9a532788528e..bfa3eef27f524165f5568fdbf80bd10445230021 100644
--- a/test/unit-distributed/test_communicator.cpp
+++ b/test/unit-distributed/test_communicator.cpp
@@ -198,7 +198,7 @@ namespace {
}
cell_kind get_cell_kind(cell_gid_type gid) const override {
- return gid%2? cell_kind::cable1d_neuron: cell_kind::spike_source;
+ return gid%2? cell_kind::cable: cell_kind::spike_source;
}
cell_size_type num_sources(cell_gid_type) const override { return 1; }
@@ -261,7 +261,7 @@ namespace {
return {};
}
cell_kind get_cell_kind(cell_gid_type gid) const override {
- return gid%2? cell_kind::cable1d_neuron: cell_kind::spike_source;
+ return gid%2? cell_kind::cable: cell_kind::spike_source;
}
cell_size_type num_sources(cell_gid_type) const override { return 1; }
diff --git a/test/unit-distributed/test_domain_decomposition.cpp b/test/unit-distributed/test_domain_decomposition.cpp
index 27e69004ddd0520720e008eb6b2e85c51fb3a471..e4a903d630d87f8580cd3128bdfbc099373dee1e 100644
--- a/test/unit-distributed/test_domain_decomposition.cpp
+++ b/test/unit-distributed/test_domain_decomposition.cpp
@@ -27,7 +27,7 @@ namespace {
// Dummy recipes types for testing.
struct dummy_cell {};
- using homo_recipe = homogeneous_recipe<cell_kind::cable1d_neuron, dummy_cell>;
+ using homo_recipe = homogeneous_recipe<cell_kind::cable, dummy_cell>;
// Heterogenous cell population of cable and rss cells.
// Interleaved so that cells with even gid are cable cells, and even gid are
@@ -48,7 +48,7 @@ namespace {
cell_kind get_cell_kind(cell_gid_type gid) const override {
return gid%2?
cell_kind::spike_source:
- cell_kind::cable1d_neuron;
+ cell_kind::cable;
}
cell_size_type num_sources(cell_gid_type) const override { return 0; }
@@ -81,7 +81,7 @@ namespace {
}
cell_kind get_cell_kind(cell_gid_type gid) const override {
- return cell_kind::cable1d_neuron;
+ return cell_kind::cable;
}
std::vector<gap_junction_connection> gap_junctions_on(cell_gid_type gid) const override {
unsigned shift = (gid/size_)*size_;
@@ -122,7 +122,7 @@ namespace {
}
cell_kind get_cell_kind(cell_gid_type gid) const override {
- return cell_kind::cable1d_neuron;
+ return cell_kind::cable;
}
std::vector<gap_junction_connection> gap_junctions_on(cell_gid_type gid) const override {
unsigned group = gid/groups_;
@@ -175,7 +175,7 @@ TEST(domain_decomposition, homogeneous_population_mc) {
EXPECT_EQ(I, (unsigned)D.gid_domain(gid));
}
- // Each cell group contains 1 cell of kind cable1d_neuron
+ // Each cell group contains 1 cell of kind cable
// Each group should also be tagged for cpu execution
for (auto i: gids) {
auto local_group = i-b;
@@ -183,7 +183,7 @@ TEST(domain_decomposition, homogeneous_population_mc) {
EXPECT_EQ(grp.gids.size(), 1u);
EXPECT_EQ(grp.gids.front(), unsigned(i));
EXPECT_EQ(grp.backend, backend_kind::multicore);
- EXPECT_EQ(grp.kind, cell_kind::cable1d_neuron);
+ EXPECT_EQ(grp.kind, cell_kind::cable);
}
}
@@ -226,7 +226,7 @@ TEST(domain_decomposition, homogeneous_population_gpu) {
EXPECT_EQ(I, (unsigned)D.gid_domain(gid));
}
- // Each cell group contains 1 cell of kind cable1d_neuron
+ // Each cell group contains 1 cell of kind cable
// Each group should also be tagged for cpu execution
auto grp = D.groups[0u];
@@ -234,7 +234,7 @@ TEST(domain_decomposition, homogeneous_population_gpu) {
EXPECT_EQ(grp.gids.front(), b);
EXPECT_EQ(grp.gids.back(), e-1);
EXPECT_EQ(grp.backend, backend_kind::gpu);
- EXPECT_EQ(grp.kind, cell_kind::cable1d_neuron);
+ EXPECT_EQ(grp.kind, cell_kind::cable);
}
#endif
@@ -272,7 +272,7 @@ TEST(domain_decomposition, heterogeneous_population) {
EXPECT_EQ(I, (unsigned)D.gid_domain(gid));
}
- // Each cell group contains 1 cell of kind cable1d_neuron
+ // Each cell group contains 1 cell of kind cable
// Each group should also be tagged for cpu execution
auto grps = util::make_span(0, n_local_grps);
std::map<cell_kind, std::set<cell_gid_type>> kind_lists;
@@ -283,7 +283,7 @@ TEST(domain_decomposition, heterogeneous_population) {
EXPECT_EQ(grp.backend, backend_kind::multicore);
}
- for (auto k: {cell_kind::cable1d_neuron, cell_kind::spike_source}) {
+ for (auto k: {cell_kind::cable, cell_kind::spike_source}) {
const auto& gids = kind_lists[k];
EXPECT_EQ(gids.size(), n_local/2);
for (auto gid: gids) {
@@ -329,8 +329,8 @@ TEST(domain_decomposition, symmetric_groups)
// Test different group_hints
partition_hint_map hints;
- hints[cell_kind::cable1d_neuron].cpu_group_size = R.num_cells();
- hints[cell_kind::cable1d_neuron].prefer_gpu = false;
+ hints[cell_kind::cable].cpu_group_size = R.num_cells();
+ hints[cell_kind::cable].prefer_gpu = false;
const auto D1 = partition_load_balance(R, ctx, hints);
EXPECT_EQ(1u, D1.groups.size());
@@ -345,8 +345,8 @@ TEST(domain_decomposition, symmetric_groups)
EXPECT_EQ(i/cells_per_rank, (unsigned)D1.gid_domain(i));
}
- hints[cell_kind::cable1d_neuron].cpu_group_size = cells_per_rank/2;
- hints[cell_kind::cable1d_neuron].prefer_gpu = false;
+ hints[cell_kind::cable].cpu_group_size = cells_per_rank/2;
+ hints[cell_kind::cable].prefer_gpu = false;
const auto D2 = partition_load_balance(R, ctx, hints);
EXPECT_EQ(2u, D2.groups.size());
diff --git a/test/unit/CMakeLists.txt b/test/unit/CMakeLists.txt
index 977372b9f2d3f734d4ac7ff0157e4db82dd1c80d..696683f1f61400f18d9f0bcbaaca5b54003d7f56 100644
--- a/test/unit/CMakeLists.txt
+++ b/test/unit/CMakeLists.txt
@@ -77,7 +77,7 @@ set(unit_sources
test_mask_stream.cpp
test_math.cpp
test_matrix.cpp
- test_mc_cell.cpp
+ test_cable_cell.cpp
test_mechanisms.cpp
test_mech_temperature.cpp
test_mechcat.cpp
diff --git a/test/unit/test_mc_cell.cpp b/test/unit/test_cable_cell.cpp
similarity index 93%
rename from test/unit/test_mc_cell.cpp
rename to test/unit/test_cable_cell.cpp
index 683f133e43fb599d2cb6fc092ccee4994343f3ee..f297a50d5c4035ce8d9981604e5297827cf1ffb0 100644
--- a/test/unit/test_mc_cell.cpp
+++ b/test/unit/test_cable_cell.cpp
@@ -1,6 +1,6 @@
#include "../gtest.h"
-#include <arbor/mc_cell.hpp>
+#include <arbor/cable_cell.hpp>
#include <arbor/math.hpp>
#include "tree.hpp"
@@ -8,11 +8,11 @@
using namespace arb;
using ::arb::math::pi;
-TEST(mc_cell, soma) {
+TEST(cable_cell, soma) {
// test that insertion of a soma works
// define with no centre point
{
- mc_cell c;
+ cable_cell c;
auto soma_radius = 2.1;
EXPECT_EQ(c.has_soma(), false);
@@ -27,7 +27,7 @@ TEST(mc_cell, soma) {
// test that insertion of a soma works
// define with centre point @ (0,0,1)
{
- mc_cell c;
+ cable_cell c;
auto soma_radius = 3.2;
EXPECT_EQ(c.has_soma(), false);
@@ -43,10 +43,10 @@ TEST(mc_cell, soma) {
}
}
-TEST(mc_cell, add_segment) {
+TEST(cable_cell, add_segment) {
// add a pre-defined segment
{
- mc_cell c;
+ cable_cell c;
auto soma_radius = 2.1;
auto cable_radius = 0.1;
@@ -67,7 +67,7 @@ TEST(mc_cell, add_segment) {
// add segment on the fly
{
- mc_cell c;
+ cable_cell c;
auto soma_radius = 2.1;
auto cable_radius = 0.1;
@@ -84,7 +84,7 @@ TEST(mc_cell, add_segment) {
EXPECT_EQ(c.num_segments(), 2u);
}
{
- mc_cell c;
+ cable_cell c;
auto soma_radius = 2.1;
auto cable_radius = 0.1;
@@ -104,7 +104,7 @@ TEST(mc_cell, add_segment) {
}
}
-TEST(mc_cell, multiple_cables) {
+TEST(cable_cell, multiple_cables) {
// generate a cylindrical cable segment of length 1/pi and radius 1
// volume = 1
// area = 2
@@ -114,7 +114,7 @@ TEST(mc_cell, multiple_cables) {
// add a pre-defined segment
{
- mc_cell c;
+ cable_cell c;
auto soma_radius = std::pow(3./(4.*pi<double>), 1./3.);
@@ -158,8 +158,8 @@ TEST(mc_cell, multiple_cables) {
}
}
-TEST(mc_cell, unbranched_chain) {
- mc_cell c;
+TEST(cable_cell, unbranched_chain) {
+ cable_cell c;
auto soma_radius = std::pow(3./(4.*pi<double>), 1./3.);
@@ -191,10 +191,10 @@ TEST(mc_cell, unbranched_chain) {
EXPECT_EQ(con.num_children(2), 0u);
}
-TEST(mc_cell, clone) {
+TEST(cable_cell, clone) {
// make simple cell with multiple segments
- mc_cell c;
+ cable_cell c;
c.add_soma(2.1);
c.add_cable(0, section_kind::dendrite, 0.3, 0.2, 10);
c.segment(1)->set_compartments(3);
@@ -207,7 +207,7 @@ TEST(mc_cell, clone) {
// make clone
- mc_cell d(c);
+ cable_cell d(c);
// check equality
@@ -243,7 +243,7 @@ TEST(mc_cell, clone) {
EXPECT_EQ(c.segment(2)->num_compartments(), d.segment(2)->num_compartments());
}
-TEST(mc_cell, get_kind) {
- mc_cell c;
- EXPECT_EQ(cell_kind::cable1d_neuron, c.get_cell_kind());
+TEST(cable_cell, get_kind) {
+ cable_cell c;
+ EXPECT_EQ(cell_kind::cable, c.get_cell_kind());
}
diff --git a/test/unit/test_domain_decomposition.cpp b/test/unit/test_domain_decomposition.cpp
index d19313b1a9cf7f84a924500593824e7f9868c26a..9acd94e09dbe8888f6b17a40295b2d291f33f9fd 100644
--- a/test/unit/test_domain_decomposition.cpp
+++ b/test/unit/test_domain_decomposition.cpp
@@ -28,7 +28,7 @@ namespace {
// Dummy recipes types for testing.
struct dummy_cell {};
- using homo_recipe = homogeneous_recipe<cell_kind::cable1d_neuron, dummy_cell>;
+ using homo_recipe = homogeneous_recipe<cell_kind::cable, dummy_cell>;
// Heterogenous cell population of cable and spike source cells.
// Interleaved so that cells with even gid are cable cells, and odd gid are
@@ -48,7 +48,7 @@ namespace {
cell_kind get_cell_kind(cell_gid_type gid) const override {
return gid%2?
cell_kind::spike_source:
- cell_kind::cable1d_neuron;
+ cell_kind::cable;
}
private:
@@ -64,14 +64,14 @@ namespace {
}
arb::util::unique_any get_cell_description(cell_gid_type) const override {
- mc_cell c;
+ cable_cell c;
c.add_soma(20);
c.add_gap_junction({0,1});
return {std::move(c)};
}
cell_kind get_cell_kind(cell_gid_type gid) const override {
- return cell_kind::cable1d_neuron;
+ return cell_kind::cable;
}
std::vector<gap_junction_connection> gap_junctions_on(cell_gid_type gid) const override {
switch (gid) {
@@ -135,7 +135,7 @@ TEST(domain_decomposition, homogenous_population)
EXPECT_EQ(0, D.gid_domain(gid));
}
- // Each cell group contains 1 cell of kind cable1d_neuron
+ // Each cell group contains 1 cell of kind cable
// Each group should also be tagged for cpu execution
auto grp = D.groups[0u];
@@ -143,7 +143,7 @@ TEST(domain_decomposition, homogenous_population)
EXPECT_EQ(grp.gids.front(), 0u);
EXPECT_EQ(grp.gids.back(), num_cells-1);
EXPECT_EQ(grp.backend, backend_kind::gpu);
- EXPECT_EQ(grp.kind, cell_kind::cable1d_neuron);
+ EXPECT_EQ(grp.kind, cell_kind::cable);
}
{
resources.gpu_id = -1; // disable GPU if available
@@ -166,14 +166,14 @@ TEST(domain_decomposition, homogenous_population)
EXPECT_EQ(0, D.gid_domain(gid));
}
- // Each cell group contains 1 cell of kind cable1d_neuron
+ // Each cell group contains 1 cell of kind cable
// Each group should also be tagged for cpu execution
for (auto i: gids) {
auto& grp = D.groups[i];
EXPECT_EQ(grp.gids.size(), 1u);
EXPECT_EQ(grp.gids.front(), unsigned(i));
EXPECT_EQ(grp.backend, backend_kind::multicore);
- EXPECT_EQ(grp.kind, cell_kind::cable1d_neuron);
+ EXPECT_EQ(grp.kind, cell_kind::cable);
}
}
}
@@ -205,7 +205,7 @@ TEST(domain_decomposition, heterogenous_population)
for (auto i: grps) {
auto& grp = D.groups[i];
auto k = grp.kind;
- if (k==cell_kind::cable1d_neuron) {
+ if (k==cell_kind::cable) {
EXPECT_EQ(grp.backend, backend_kind::gpu);
EXPECT_EQ(grp.gids.size(), num_cells/2);
for (auto gid: grp.gids) {
@@ -244,7 +244,7 @@ TEST(domain_decomposition, heterogenous_population)
EXPECT_EQ(0, D.gid_domain(gid));
}
- // Each cell group contains 1 cell of kind cable1d_neuron
+ // Each cell group contains 1 cell of kind cable
// Each group should also be tagged for cpu execution
auto grps = make_span(num_cells);
std::map<cell_kind, std::set<cell_gid_type>> kind_lists;
@@ -256,7 +256,7 @@ TEST(domain_decomposition, heterogenous_population)
EXPECT_EQ(grp.backend, backend_kind::multicore);
}
- for (auto k: {cell_kind::cable1d_neuron, cell_kind::spike_source}) {
+ for (auto k: {cell_kind::cable, cell_kind::spike_source}) {
const auto& gids = kind_lists[k];
EXPECT_EQ(gids.size(), num_cells/2);
for (auto gid: gids) {
@@ -276,8 +276,8 @@ TEST(domain_decomposition, hints) {
auto ctx = make_context();
partition_hint_map hints;
- hints[cell_kind::cable1d_neuron].cpu_group_size = 3;
- hints[cell_kind::cable1d_neuron].prefer_gpu = false;
+ hints[cell_kind::cable].cpu_group_size = 3;
+ hints[cell_kind::cable].prefer_gpu = false;
hints[cell_kind::spike_source].cpu_group_size = 4;
domain_decomposition D = partition_load_balance(
@@ -294,9 +294,9 @@ TEST(domain_decomposition, hints) {
std::vector<std::vector<cell_gid_type>> c1d_groups, ss_groups;
for (auto& g: D.groups) {
- EXPECT_TRUE(g.kind==cell_kind::cable1d_neuron || g.kind==cell_kind::spike_source);
+ EXPECT_TRUE(g.kind==cell_kind::cable || g.kind==cell_kind::spike_source);
- if (g.kind==cell_kind::cable1d_neuron) {
+ if (g.kind==cell_kind::cable) {
c1d_groups.push_back(g.gids);
}
else if (g.kind==cell_kind::spike_source) {
@@ -328,8 +328,8 @@ TEST(domain_decomposition, compulsory_groups)
// Test different group_hints
partition_hint_map hints;
- hints[cell_kind::cable1d_neuron].cpu_group_size = 3;
- hints[cell_kind::cable1d_neuron].prefer_gpu = false;
+ hints[cell_kind::cable].cpu_group_size = 3;
+ hints[cell_kind::cable].prefer_gpu = false;
const auto D1 = partition_load_balance(R, ctx, hints);
EXPECT_EQ(5u, D1.groups.size());
@@ -341,8 +341,8 @@ TEST(domain_decomposition, compulsory_groups)
EXPECT_EQ(expected_groups1[i], D1.groups[i].gids);
}
- hints[cell_kind::cable1d_neuron].cpu_group_size = 20;
- hints[cell_kind::cable1d_neuron].prefer_gpu = false;
+ hints[cell_kind::cable].cpu_group_size = 20;
+ hints[cell_kind::cable].prefer_gpu = false;
const auto D2 = partition_load_balance(R, ctx, hints);
EXPECT_EQ(1u, D2.groups.size());
diff --git a/test/unit/test_event_delivery.cpp b/test/unit/test_event_delivery.cpp
index 905d8cb428a6ea48b8b5c5bf66ceb6c43f4f01f1..cafba40f1982fde675cccc26d0cce059b6a7e320 100644
--- a/test/unit/test_event_delivery.cpp
+++ b/test/unit/test_event_delivery.cpp
@@ -9,7 +9,7 @@
#include <arbor/common_types.hpp>
#include <arbor/domain_decomposition.hpp>
#include <arbor/simulation.hpp>
-#include <arbor/mc_cell.hpp>
+#include <arbor/cable_cell.hpp>
#include <arbor/spike.hpp>
#include <arbor/spike_event.hpp>
@@ -21,13 +21,13 @@
using namespace arb;
-using n_mc_cell_recipe = homogeneous_recipe<cell_kind::cable1d_neuron, mc_cell>;
+using n_cable_cell_recipe = homogeneous_recipe<cell_kind::cable, cable_cell>;
-struct test_recipe: public n_mc_cell_recipe {
- explicit test_recipe(int n): n_mc_cell_recipe(n, test_cell()) {}
+struct test_recipe: public n_cable_cell_recipe {
+ explicit test_recipe(int n): n_cable_cell_recipe(n, test_cell()) {}
- static mc_cell test_cell() {
- mc_cell c;
+ static cable_cell test_cell() {
+ cable_cell c;
c.add_soma(10.)->add_mechanism("pas");
c.add_synapse({0, 0.5}, "expsyn");
c.add_detector({0, 0.5}, -64);
@@ -53,7 +53,7 @@ std::vector<cell_gid_type> run_test_sim(const recipe& R, const group_gids_type&
D.num_global_cells = n;
for (const auto& gidvec: group_gids) {
- group_description group{cell_kind::cable1d_neuron, gidvec, backend_kind::multicore};
+ group_description group{cell_kind::cable, gidvec, backend_kind::multicore};
D.groups.push_back(group);
}
diff --git a/test/unit/test_fvm_layout.cpp b/test/unit/test_fvm_layout.cpp
index a3d6039e13325652953985c0292932abbbe04948..0b9496a0ced1a3a4b7aa86cffb0cb20a58877830 100644
--- a/test/unit/test_fvm_layout.cpp
+++ b/test/unit/test_fvm_layout.cpp
@@ -4,7 +4,7 @@
#include <arbor/util/optional.hpp>
#include <arbor/mechcat.hpp>
#include <arbor/math.hpp>
-#include <arbor/mc_cell.hpp>
+#include <arbor/cable_cell.hpp>
#include "fvm_layout.hpp"
#include "util/maputil.hpp"
@@ -22,7 +22,7 @@ using util::count_along;
using util::value_by_key;
namespace {
- double area(const mc_segment* s) {
+ double area(const segment* s) {
if (auto soma = s->as_soma()) {
return math::area_sphere(soma->radius());
}
@@ -39,7 +39,7 @@ namespace {
}
}
- double volume(const mc_segment* s) {
+ double volume(const segment* s) {
if (auto soma = s->as_soma()) {
return math::volume_sphere(soma->radius());
}
@@ -56,8 +56,8 @@ namespace {
}
}
- std::vector<mc_cell> two_cell_system() {
- std::vector<mc_cell> cells;
+ std::vector<cable_cell> two_cell_system() {
+ std::vector<cable_cell> cells;
// Cell 0: simple ball and stick (see common_cells.hpp)
cells.push_back(make_cell_ball_and_stick());
@@ -90,8 +90,8 @@ namespace {
//
// All dendrite segments with 4 compartments.
- mc_cell c2;
- mc_segment* s;
+ cable_cell c2;
+ segment* s;
s = c2.add_soma(14./2);
s->add_mechanism("hh");
@@ -119,7 +119,7 @@ namespace {
return cells;
}
- void check_two_cell_system(std::vector<mc_cell>& cells) {
+ void check_two_cell_system(std::vector<cable_cell>& cells) {
ASSERT_EQ(2u, cells[0].num_segments());
ASSERT_EQ(cells[0].segment(1)->num_compartments(), 4u);
ASSERT_EQ(cells[1].num_segments(), 4u);
@@ -130,7 +130,7 @@ namespace {
} // namespace
TEST(fvm_layout, topology) {
- std::vector<mc_cell> cells = two_cell_system();
+ std::vector<cable_cell> cells = two_cell_system();
check_two_cell_system(cells);
fvm_discretization D = fvm_discretize(cells);
@@ -210,7 +210,7 @@ TEST(fvm_layout, topology) {
}
TEST(fvm_layout, area) {
- std::vector<mc_cell> cells = two_cell_system();
+ std::vector<cable_cell> cells = two_cell_system();
check_two_cell_system(cells);
fvm_discretization D = fvm_discretize(cells);
@@ -283,7 +283,7 @@ TEST(fvm_layout, area) {
}
TEST(fvm_layout, mech_index) {
- std::vector<mc_cell> cells = two_cell_system();
+ std::vector<cable_cell> cells = two_cell_system();
check_two_cell_system(cells);
// Add four synapses of two varieties across the cells.
@@ -351,7 +351,7 @@ TEST(fvm_layout, coalescing_synapses) {
};
{
- mc_cell cell = make_cell_ball_and_stick();
+ cable_cell cell = make_cell_ball_and_stick();
// Add synapses of two varieties.
cell.add_synapse({1, 0.3}, "expsyn");
@@ -367,7 +367,7 @@ TEST(fvm_layout, coalescing_synapses) {
EXPECT_EQ(ivec({1, 1, 1, 1}), expsyn_config.multiplicity);
}
{
- mc_cell cell = make_cell_ball_and_stick();
+ cable_cell cell = make_cell_ball_and_stick();
// Add synapses of two varieties.
cell.add_synapse({1, 0.3}, "expsyn");
@@ -387,7 +387,7 @@ TEST(fvm_layout, coalescing_synapses) {
EXPECT_EQ(ivec({1, 1}), exp2syn_config.multiplicity);
}
{
- mc_cell cell = make_cell_ball_and_stick();
+ cable_cell cell = make_cell_ball_and_stick();
// Add synapses of two varieties.
cell.add_synapse({1, 0.3}, "expsyn");
@@ -403,7 +403,7 @@ TEST(fvm_layout, coalescing_synapses) {
EXPECT_EQ(ivec({2, 2}), expsyn_config.multiplicity);
}
{
- mc_cell cell = make_cell_ball_and_stick();
+ cable_cell cell = make_cell_ball_and_stick();
// Add synapses of two varieties.
cell.add_synapse({1, 0.3}, syn_desc("expsyn", 0, 0.2));
@@ -421,7 +421,7 @@ TEST(fvm_layout, coalescing_synapses) {
EXPECT_EQ(fvec({0.2, 0.2, 0.2}), expsyn_config.param_values[1].second);
}
{
- mc_cell cell = make_cell_ball_and_stick();
+ cable_cell cell = make_cell_ball_and_stick();
// Add synapses of two varieties.
cell.add_synapse({1, 0.7}, syn_desc("expsyn", 0, 3));
@@ -444,7 +444,7 @@ TEST(fvm_layout, coalescing_synapses) {
EXPECT_EQ(fvec({2, 2, 3, 3}), expsyn_config.param_values[1].second);
}
{
- mc_cell cell = make_cell_ball_and_stick();
+ cable_cell cell = make_cell_ball_and_stick();
// Add synapses of two varieties.
cell.add_synapse({1, 0.3}, syn_desc("expsyn", 1, 2));
@@ -478,7 +478,7 @@ TEST(fvm_layout, coalescing_synapses) {
}
TEST(fvm_layout, synapse_targets) {
- std::vector<mc_cell> cells = two_cell_system();
+ std::vector<cable_cell> cells = two_cell_system();
// Add synapses with different parameter values so that we can
// ensure: 1) CVs for each synapse mechanism are sorted while
@@ -587,8 +587,8 @@ TEST(fvm_layout, density_norm_area) {
//
// Use divided compartment view on segments to compute area contributions.
- std::vector<mc_cell> cells(1);
- mc_cell& c = cells[0];
+ std::vector<cable_cell> cells(1);
+ cable_cell& c = cells[0];
auto soma = c.add_soma(12.6157/2.0);
c.add_cable(0, section_kind::dendrite, 0.5, 0.5, 100);
@@ -606,7 +606,7 @@ TEST(fvm_layout, density_norm_area) {
double seg3_gl = .0004;
for (int i = 0; i<4; ++i) {
- mc_segment& seg = *segs[i];
+ segment& seg = *segs[i];
seg.set_compartments(3);
mechanism_desc hh("hh");
@@ -717,7 +717,7 @@ TEST(fvm_layout, ion_weights) {
// the same as a 100µm dendrite, which makes it easier to describe the
// expected weights.
- auto construct_cell = [](mc_cell& c) {
+ auto construct_cell = [](cable_cell& c) {
c.add_soma(5);
c.add_cable(0, section_kind::dendrite, 0.5, 0.5, 100);
@@ -744,8 +744,8 @@ TEST(fvm_layout, ion_weights) {
};
for (auto run: count_along(mech_segs)) {
- std::vector<mc_cell> cells(1);
- mc_cell& c = cells[0];
+ std::vector<cable_cell> cells(1);
+ cable_cell& c = cells[0];
construct_cell(c);
for (auto i: mech_segs[run]) {
diff --git a/test/unit/test_fvm_lowered.cpp b/test/unit/test_fvm_lowered.cpp
index 8e2c2f25bd01e43c274061a9d52f82c5cc75a240..cdc09371322f6e018aa5f9127c364ea1a3b10ce8 100644
--- a/test/unit/test_fvm_lowered.cpp
+++ b/test/unit/test_fvm_lowered.cpp
@@ -8,8 +8,8 @@
#include <arbor/fvm_types.hpp>
#include <arbor/load_balance.hpp>
#include <arbor/math.hpp>
-#include <arbor/mc_cell.hpp>
-#include <arbor/mc_segment.hpp>
+#include <arbor/cable_cell.hpp>
+#include <arbor/segment.hpp>
#include <arbor/recipe.hpp>
#include <arbor/sampling.hpp>
#include <arbor/simulation.hpp>
@@ -87,14 +87,14 @@ public:
}
arb::util::unique_any get_cell_description(cell_gid_type gid) const override {
- mc_cell c;
+ cable_cell c;
c.add_soma(20);
c.add_gap_junction({0, 1});
return {std::move(c)};
}
cell_kind get_cell_kind(cell_gid_type gid) const override {
- return cell_kind::cable1d_neuron;
+ return cell_kind::cable;
}
std::vector<gap_junction_connection> gap_junctions_on(cell_gid_type gid) const override {
switch (gid) {
@@ -133,13 +133,13 @@ public:
}
arb::util::unique_any get_cell_description(cell_gid_type) const override {
- mc_cell c;
+ cable_cell c;
c.add_soma(20);
return {std::move(c)};
}
cell_kind get_cell_kind(cell_gid_type gid) const override {
- return cell_kind::cable1d_neuron;
+ return cell_kind::cable;
}
private:
@@ -155,14 +155,14 @@ public:
}
arb::util::unique_any get_cell_description(cell_gid_type) const override {
- mc_cell c;
+ cable_cell c;
c.add_soma(20);
c.add_gap_junction({0,1});
return {std::move(c)};
}
cell_kind get_cell_kind(cell_gid_type gid) const override {
- return cell_kind::cable1d_neuron;
+ return cell_kind::cable;
}
std::vector<gap_junction_connection> gap_junctions_on(cell_gid_type gid) const override {
switch (gid) {
@@ -208,7 +208,7 @@ TEST(fvm_lowered, matrix_init)
auto ispos = [](auto v) { return v>0; };
auto isneg = [](auto v) { return v<0; };
- mc_cell cell = make_cell_ball_and_stick();
+ cable_cell cell = make_cell_ball_and_stick();
ASSERT_EQ(2u, cell.num_segments());
cell.segment(1)->set_compartments(10);
@@ -243,7 +243,7 @@ TEST(fvm_lowered, target_handles) {
execution_context context;
- mc_cell cells[] = {
+ cable_cell cells[] = {
make_cell_ball_and_stick(),
make_cell_ball_and_3stick()
};
@@ -305,7 +305,7 @@ TEST(fvm_lowered, stimulus) {
execution_context context;
- std::vector<mc_cell> cells;
+ std::vector<cable_cell> cells;
cells.push_back(make_cell_ball_and_stick(false));
cells[0].add_stimulus({1,1}, {5., 80., 0.3});
@@ -381,9 +381,9 @@ TEST(fvm_lowered, derived_mechs) {
//
// 3. Cell with both test_kin1 and custom_kin1.
- std::vector<mc_cell> cells(3);
+ std::vector<cable_cell> cells(3);
for (int i = 0; i<3; ++i) {
- mc_cell& c = cells[i];
+ cable_cell& c = cells[i];
c.add_soma(6.0);
c.add_cable(0, section_kind::dendrite, 0.5, 0.5, 100);
@@ -508,7 +508,7 @@ TEST(fvm_lowered, weighted_write_ion) {
execution_context context;
- mc_cell c;
+ cable_cell c;
c.add_soma(5);
c.add_cable(0, section_kind::dendrite, 0.5, 0.5, 100);
@@ -581,7 +581,7 @@ TEST(fvm_lowered, gj_coords_simple) {
gap_recipe() {}
cell_size_type num_cells() const override { return n_; }
- cell_kind get_cell_kind(cell_gid_type) const override { return cell_kind::cable1d_neuron; }
+ cell_kind get_cell_kind(cell_gid_type) const override { return cell_kind::cable; }
util::unique_any get_cell_description(cell_gid_type gid) const override {
return {};
}
@@ -599,8 +599,8 @@ TEST(fvm_lowered, gj_coords_simple) {
fvm_cell fvcell(context);
gap_recipe rec;
- std::vector<mc_cell> cells;
- mc_cell c, d;
+ std::vector<cable_cell> cells;
+ cable_cell c, d;
c.add_soma(2.1);
c.add_cable(0, section_kind::dendrite, 0.3, 0.2, 10);
c.segment(1)->set_compartments(5);
@@ -637,7 +637,7 @@ TEST(fvm_lowered, gj_coords_complex) {
gap_recipe() {}
cell_size_type num_cells() const override { return n_; }
- cell_kind get_cell_kind(cell_gid_type) const override { return cell_kind::cable1d_neuron; }
+ cell_kind get_cell_kind(cell_gid_type) const override { return cell_kind::cable; }
util::unique_any get_cell_description(cell_gid_type gid) const override {
return {};
}
@@ -673,8 +673,8 @@ TEST(fvm_lowered, gj_coords_complex) {
fvm_cell fvcell(context);
gap_recipe rec;
- mc_cell c0, c1, c2;
- std::vector<mc_cell> cells;
+ cable_cell c0, c1, c2;
+ std::vector<cable_cell> cells;
// Make 3 cells
c0.add_soma(2.1);
@@ -760,7 +760,7 @@ TEST(fvm_lowered, cell_group_gj) {
gap_recipe() {}
cell_size_type num_cells() const override { return n_; }
- cell_kind get_cell_kind(cell_gid_type) const override { return cell_kind::cable1d_neuron; }
+ cell_kind get_cell_kind(cell_gid_type) const override { return cell_kind::cable; }
util::unique_any get_cell_description(cell_gid_type gid) const override {
return {};
}
@@ -783,12 +783,12 @@ TEST(fvm_lowered, cell_group_gj) {
fvm_cell fvcell(context);
gap_recipe rec;
- std::vector<mc_cell> cell_group0;
- std::vector<mc_cell> cell_group1;
+ std::vector<cable_cell> cell_group0;
+ std::vector<cable_cell> cell_group1;
// Make 20 cells
for (unsigned i = 0; i < 20; i++) {
- mc_cell c;
+ cable_cell c;
c.add_soma(2.1);
if (i % 2 == 0) {
c.add_gap_junction({0, 1});
diff --git a/test/unit/test_lif_cell_group.cpp b/test/unit/test_lif_cell_group.cpp
index 7f0e8d839fbb3f93d47ad3155c1949e8635e4684..2247ef483158a4bff3954d5c30809f9723ddecdf 100644
--- a/test/unit/test_lif_cell_group.cpp
+++ b/test/unit/test_lif_cell_group.cpp
@@ -28,7 +28,7 @@ public:
if (gid == 0) {
return cell_kind::spike_source;
}
- return cell_kind::lif_neuron;
+ return cell_kind::lif;
}
std::vector<cell_connection> connections_on(cell_gid_type gid) const override {
@@ -99,7 +99,7 @@ public:
}
cell_kind get_cell_kind(cell_gid_type gid) const override {
- return cell_kind::lif_neuron;
+ return cell_kind::lif;
}
std::vector<cell_connection> connections_on(cell_gid_type gid) const override {
diff --git a/test/unit/test_mc_cell_group.cpp b/test/unit/test_mc_cell_group.cpp
index 11e333007d9d4153174a63c90a45ae273ec3db51..ed9cc54345e8ed05a7878877152ebd0268894c36 100644
--- a/test/unit/test_mc_cell_group.cpp
+++ b/test/unit/test_mc_cell_group.cpp
@@ -20,7 +20,7 @@ namespace {
return make_fvm_lowered_cell(backend_kind::multicore, context);
}
- mc_cell make_cell() {
+ cable_cell make_cell() {
auto c = make_cell_ball_and_stick();
c.add_detector({0, 0}, 0);
@@ -38,7 +38,7 @@ ACCESS_BIND(
TEST(mc_cell_group, get_kind) {
mc_cell_group group{{0}, cable1d_recipe(make_cell()), lowered_cell()};
- EXPECT_EQ(cell_kind::cable1d_neuron, group.get_cell_kind());
+ EXPECT_EQ(cell_kind::cable, group.get_cell_kind());
}
TEST(mc_cell_group, test) {
@@ -53,7 +53,7 @@ TEST(mc_cell_group, test) {
TEST(mc_cell_group, sources) {
// Make twenty cells, with an extra detector on gids 0, 3 and 17
// to make things more interesting.
- std::vector<mc_cell> cells;
+ std::vector<cable_cell> cells;
for (int i=0; i<20; ++i) {
cells.push_back(make_cell());
diff --git a/test/unit/test_mc_cell_group_gpu.cpp b/test/unit/test_mc_cell_group_gpu.cpp
index 7628dce147c61966aa77bab1cdbb24cbc62f6d65..b859b9a5532274da03ddd952a1012e999ff6b2e9 100644
--- a/test/unit/test_mc_cell_group_gpu.cpp
+++ b/test/unit/test_mc_cell_group_gpu.cpp
@@ -18,7 +18,7 @@ namespace {
return make_fvm_lowered_cell(backend_kind::gpu, context);
}
- mc_cell make_cell() {
+ cable_cell make_cell() {
auto c = make_cell_ball_and_stick();
c.add_detector({0, 0}, 0);
diff --git a/test/unit/test_mechinfo.cpp b/test/unit/test_mechinfo.cpp
index e5f63588dfb9260b925be7c1646a09645ccaa2e4..d7d20c8dbf1db84369201bfb3c78c538b76fe744 100644
--- a/test/unit/test_mechinfo.cpp
+++ b/test/unit/test_mechinfo.cpp
@@ -2,7 +2,7 @@
#include <string>
#include <vector>
-#include <arbor/mc_cell.hpp>
+#include <arbor/cable_cell.hpp>
#include "../gtest.h"
diff --git a/test/unit/test_probe.cpp b/test/unit/test_probe.cpp
index 6f449cb165346ef53925407ede2508047746e531..989a6cc822cfd3617959e3adc7821c838c168f7b 100644
--- a/test/unit/test_probe.cpp
+++ b/test/unit/test_probe.cpp
@@ -1,7 +1,7 @@
#include "../gtest.h"
#include <arbor/common_types.hpp>
-#include <arbor/mc_cell.hpp>
+#include <arbor/cable_cell.hpp>
#include "backends/event.hpp"
#include "backends/multicore/fvm.hpp"
@@ -21,7 +21,7 @@ ACCESS_BIND(std::unique_ptr<shared_state> fvm_cell::*, fvm_state_ptr, &fvm_cell:
TEST(probe, fvm_lowered_cell) {
execution_context context;
- mc_cell bs = make_cell_ball_and_stick(false);
+ cable_cell bs = make_cell_ball_and_stick(false);
i_clamp stim(0, 100, 0.3);
bs.add_stimulus({1, 1}, stim);
diff --git a/test/unit/test_segment.cpp b/test/unit/test_segment.cpp
index 128f629bb83e8ce3395e5d98c53947539f621fa1..509f889c3ac381a0f7ef5ced0fa984ca294b86c9 100644
--- a/test/unit/test_segment.cpp
+++ b/test/unit/test_segment.cpp
@@ -3,11 +3,11 @@
#include "../gtest.h"
#include <arbor/math.hpp>
-#include <arbor/mc_segment.hpp>
+#include <arbor/segment.hpp>
using namespace arb;
-TEST(mc_segment, kinfs) {
+TEST(segment, kinfs) {
using ::arb::math::pi;
{
diff --git a/test/unit/test_swcio.cpp b/test/unit/test_swcio.cpp
index 172439e6707f82322240f73ec77c11b660bace7b..3a22d257cc3fdc29f310fc7d31f98e140d9ea7eb 100644
--- a/test/unit/test_swcio.cpp
+++ b/test/unit/test_swcio.cpp
@@ -7,7 +7,7 @@
#include <type_traits>
#include <vector>
-#include <arbor/mc_cell.hpp>
+#include <arbor/cable_cell.hpp>
#include <arbor/morphology.hpp>
#include <arbor/swcio.hpp>
@@ -457,7 +457,7 @@ TEST(swc_io, cell_construction) {
// swc -> morphology
auto morph = swc_as_morphology(parse_swc_file(is));
- mc_cell cell = make_mc_cell(morph, true);
+ cable_cell cell = make_cable_cell(morph, true);
EXPECT_TRUE(cell.has_soma());
EXPECT_EQ(4u, cell.num_segments());
diff --git a/test/unit/test_synapses.cpp b/test/unit/test_synapses.cpp
index c433099fa67d0d2c25084bc1e4658ff5ed5642e6..7b46ad4a9d34143eac848562a471244db26824da 100644
--- a/test/unit/test_synapses.cpp
+++ b/test/unit/test_synapses.cpp
@@ -7,7 +7,7 @@
#include <arbor/constants.hpp>
#include <arbor/mechcat.hpp>
#include <arbor/util/optional.hpp>
-#include <arbor/mc_cell.hpp>
+#include <arbor/cable_cell.hpp>
#include "backends/multicore/fvm.hpp"
#include "backends/multicore/mechanism.hpp"
@@ -32,7 +32,7 @@ ACCESS_BIND(value_type* multicore::mechanism::*, vec_i_ptr, &multicore::mechanis
TEST(synapses, add_to_cell) {
using namespace arb;
- mc_cell cell;
+ cable_cell cell;
// Soma with diameter 12.6157 um and HH channel
auto soma = cell.add_soma(12.6157/2.0);
diff --git a/test/unit/test_threading_exceptions.cpp b/test/unit/test_threading_exceptions.cpp
index 14569bf2824709fcbb6c78033a738a25618d21fe..c83896406c05b6acf76a07684b7e01ce11a70143 100644
--- a/test/unit/test_threading_exceptions.cpp
+++ b/test/unit/test_threading_exceptions.cpp
@@ -7,7 +7,7 @@
#include <arbor/recipe.hpp>
#include <arbor/simulation.hpp>
#include <arbor/context.hpp>
-#include <arbor/mc_cell.hpp>
+#include <arbor/cable_cell.hpp>
#include <arbor/version.hpp>
#include "threading/threading.hpp"
diff --git a/test/validation/convergence_test.hpp b/test/validation/convergence_test.hpp
index e0ee8496241f48343db001a90d41c92275d3fef1..189615bbc551637e1a362e9f0fdb803ee3e52967 100644
--- a/test/validation/convergence_test.hpp
+++ b/test/validation/convergence_test.hpp
@@ -159,7 +159,7 @@ public:
* Extract time points to exclude from current stimulus end-points.
*/
-inline std::vector<float> stimulus_ends(const mc_cell& c) {
+inline std::vector<float> stimulus_ends(const cable_cell& c) {
std::vector<float> ts;
for (const auto& stimulus: c.stimuli()) {
diff --git a/test/validation/validate_ball_and_stick.cpp b/test/validation/validate_ball_and_stick.cpp
index 22f12314af8ae0ca1167494e841a290498b87019..a7843adcb7983ae82790557fb30f070be2a64495 100644
--- a/test/validation/validate_ball_and_stick.cpp
+++ b/test/validation/validate_ball_and_stick.cpp
@@ -7,7 +7,7 @@
#include <arbor/domain_decomposition.hpp>
#include <arbor/context.hpp>
#include <arbor/load_balance.hpp>
-#include <arbor/mc_cell.hpp>
+#include <arbor/cable_cell.hpp>
#include <arbor/recipe.hpp>
#include <arbor/simple_sampler.hpp>
#include <arbor/simulation.hpp>
@@ -35,7 +35,7 @@ void run_ncomp_convergence_test(
const char* model_name,
const sup::path& ref_data_path,
context& context,
- const mc_cell& c,
+ const cable_cell& c,
ProbePointSeq& probe_points,
float t_end=100.f)
{
@@ -89,7 +89,7 @@ void run_ncomp_convergence_test(
void validate_ball_and_stick(context& ctx) {
using namespace arb;
- mc_cell c = make_cell_ball_and_stick();
+ cable_cell c = make_cell_ball_and_stick();
probe_point points[] = {
{"soma.mid", {0u, 0.5}},
{"dend.mid", {1u, 0.5}},
@@ -107,7 +107,7 @@ void validate_ball_and_stick(context& ctx) {
void validate_ball_and_taper(context& ctx) {
using namespace arb;
- mc_cell c = make_cell_ball_and_taper();
+ cable_cell c = make_cell_ball_and_taper();
probe_point points[] = {
{"soma.mid", {0u, 0.5}},
{"taper.mid", {1u, 0.5}},
@@ -125,7 +125,7 @@ void validate_ball_and_taper(context& ctx) {
void validate_ball_and_3stick(context& ctx) {
using namespace arb;
- mc_cell c = make_cell_ball_and_3stick();
+ cable_cell c = make_cell_ball_and_3stick();
probe_point points[] = {
{"soma.mid", {0u, 0.5}},
{"dend1.mid", {1u, 0.5}},
@@ -147,7 +147,7 @@ void validate_ball_and_3stick(context& ctx) {
void validate_rallpack1(context& ctx) {
using namespace arb;
- mc_cell c = make_cell_simple_cable();
+ cable_cell c = make_cell_simple_cable();
probe_point points[] = {
{"cable.x0.0", {1u, 0.0}},
{"cable.x0.3", {1u, 0.3}},
@@ -166,7 +166,7 @@ void validate_rallpack1(context& ctx) {
void validate_ball_and_squiggle(context& ctx) {
using namespace arb;
- mc_cell c = make_cell_ball_and_squiggle();
+ cable_cell c = make_cell_ball_and_squiggle();
probe_point points[] = {
{"soma.mid", {0u, 0.5}},
{"dend.mid", {1u, 0.5}},
diff --git a/test/validation/validate_kinetic.cpp b/test/validation/validate_kinetic.cpp
index 9bf35611a6159e8d1ac9c8fdc53ffe2dcb622816..57ddd135174af948de68699bccdfa0ff36808e60 100644
--- a/test/validation/validate_kinetic.cpp
+++ b/test/validation/validate_kinetic.cpp
@@ -8,7 +8,7 @@
#include <arbor/common_types.hpp>
#include <arbor/domain_decomposition.hpp>
#include <arbor/load_balance.hpp>
-#include <arbor/mc_cell.hpp>
+#include <arbor/cable_cell.hpp>
#include <arbor/recipe.hpp>
#include <arbor/simple_sampler.hpp>
#include <arbor/simulation.hpp>
@@ -23,7 +23,7 @@
void run_kinetic_dt(
const arb::context& context,
- arb::mc_cell& c,
+ arb::cable_cell& c,
arb::cell_probe_address probe,
float t_end,
nlohmann::json meta,
@@ -71,7 +71,7 @@ void validate_kinetic_kin1(const arb::context& ctx) {
using namespace arb;
// 20 µm diameter soma with single mechanism, current probe
- mc_cell c;
+ cable_cell c;
auto soma = c.add_soma(10);
soma->add_mechanism("test_kin1");
cell_probe_address probe{{0, 0.5}, cell_probe_address::membrane_current};
@@ -89,7 +89,7 @@ void validate_kinetic_kinlva(const arb::context& ctx) {
using namespace arb;
// 20 µm diameter soma with single mechanism, current probe
- mc_cell c;
+ cable_cell c;
auto soma = c.add_soma(10);
c.add_stimulus({0,0.5}, {20., 130., -0.025});
soma->add_mechanism("test_kinlva");
diff --git a/test/validation/validate_soma.cpp b/test/validation/validate_soma.cpp
index 5e5fdd6e91db9079c9753944c10f410e5110991b..6d5c9c6db7e4697b1b8b3cbb03fcb96d1baf6409 100644
--- a/test/validation/validate_soma.cpp
+++ b/test/validation/validate_soma.cpp
@@ -4,7 +4,7 @@
#include <arbor/context.hpp>
#include <arbor/domain_decomposition.hpp>
#include <arbor/load_balance.hpp>
-#include <arbor/mc_cell.hpp>
+#include <arbor/cable_cell.hpp>
#include <arbor/recipe.hpp>
#include <arbor/simple_sampler.hpp>
#include <arbor/simulation.hpp>
@@ -24,7 +24,7 @@ using namespace arb;
void validate_soma(const context& context) {
float sample_dt = g_trace_io.sample_dt();
- mc_cell c = make_cell_soma_only();
+ cable_cell c = make_cell_soma_only();
cable1d_recipe rec{c};
rec.add_probe(0, 0, cell_probe_address{{0, 0.5}, cell_probe_address::membrane_voltage});
diff --git a/test/validation/validate_synapses.cpp b/test/validation/validate_synapses.cpp
index a72d285a65b543dfa7096e241a53d28600b62ea2..1fd4de8c9020bfeb96b391c26e74881036d2ef60 100644
--- a/test/validation/validate_synapses.cpp
+++ b/test/validation/validate_synapses.cpp
@@ -3,7 +3,7 @@
#include <arbor/context.hpp>
#include <arbor/domain_decomposition.hpp>
#include <arbor/load_balance.hpp>
-#include <arbor/mc_cell.hpp>
+#include <arbor/cable_cell.hpp>
#include <arbor/recipe.hpp>
#include <arbor/simple_sampler.hpp>
#include <arbor/simulation.hpp>
@@ -38,7 +38,7 @@ void run_synapse_test(
{"backend_kind", arb::has_gpu(context)? "gpu": "multicore"}
};
- mc_cell c = make_cell_ball_and_stick(false); // no stimuli
+ cable_cell c = make_cell_ball_and_stick(false); // no stimuli
mechanism_desc syn_default(syn_type);
c.add_synapse({1, 0.5}, syn_default);