diff --git a/arbor/cable_cell.cpp b/arbor/cable_cell.cpp
index 90dcd74438148e6adf4d9cd262af4ea004303a21..55bdb9392f483743c30256274e8d4fd7f61b7246 100644
--- a/arbor/cable_cell.cpp
+++ b/arbor/cable_cell.cpp
@@ -17,20 +17,117 @@ using value_type = cable_cell::value_type;
using index_type = cable_cell::index_type;
using size_type = cable_cell::size_type;
-cable_cell::cable_cell() {
- // insert a placeholder segment for the soma
- segments_.push_back(make_segment<placeholder_segment>());
- parents_.push_back(0);
-}
+struct cable_cell_impl {
+ using value_type = cable_cell::value_type;
+ using index_type = cable_cell::index_type;
+ using size_type = cable_cell::size_type;
+
+ using stimulus_instance = cable_cell::stimulus_instance;
+ using synapse_instance = cable_cell::synapse_instance;
+ using gap_junction_instance = cable_cell::gap_junction_instance;
+ using detector_instance = cable_cell::detector_instance;
+
+ using region_map = cable_cell::region_map;
+ using locset_map = cable_cell::locset_map;
+
+ cable_cell_impl() {
+ segments.push_back(make_segment<placeholder_segment>());
+ parents.push_back(0);
+ }
-void cable_cell::assert_valid_segment(index_type i) const {
- if (i>=num_segments()) {
- throw cable_cell_error("no such segment");
+ cable_cell_impl(const cable_cell_impl& other) {
+ parents = other.parents;
+ stimuli = other.stimuli;
+ synapses = other.synapses;
+ gap_junction_sites = other.gap_junction_sites;
+ spike_detectors = other.spike_detectors;
+ regions = other.regions;
+ morph = other.morph;
+ locations = other.locations;
+
+ // unique_ptr's cannot be copy constructed, do a manual assignment
+ segments.reserve(other.segments.size());
+ for (const auto& s: other.segments) {
+ segments.push_back(s->clone());
+ }
}
+
+ cable_cell_impl(cable_cell_impl&& other) = default;
+
+ // storage for connections
+ std::vector<index_type> parents;
+
+ // the segments
+ std::vector<segment_ptr> segments;
+
+ // the stimuli
+ std::vector<stimulus_instance> stimuli;
+
+ // the synapses
+ std::vector<synapse_instance> synapses;
+
+ // the gap_junctions
+ std::vector<gap_junction_instance> gap_junction_sites;
+
+ // the sensors
+ std::vector<detector_instance> spike_detectors;
+
+ // Named regions
+ region_map regions;
+
+ // Named location sets
+ locset_map locations;
+
+ // Underlying embedded morphology
+ em_morphology morph;
+
+ template <typename Desc, typename T>
+ lid_range place(const mlocation_list& locs, const Desc& desc, std::vector<T>& list) {
+ const auto first = list.size();
+
+ list.reserve(first+locs.size());
+ for (auto loc: locs) {
+ list.push_back({loc, desc});
+ }
+
+ return lid_range(first, list.size());
+ }
+
+ lid_range place_gj(const mlocation_list& locs) {
+ const auto first = gap_junction_sites.size();
+
+ gap_junction_sites.insert(gap_junction_sites.end(), locs.begin(), locs.end());
+
+ return lid_range(first, gap_junction_sites.size());
+ }
+
+ void assert_valid_segment(index_type i) const {
+ if (i>=segments.size()) {
+ throw cable_cell_error("no such segment");
+ }
+ }
+
+ bool valid_location(const mlocation& loc) const {
+ return test_invariants(loc) && loc.branch<segments.size();
+ }
+};
+
+using impl_ptr = std::unique_ptr<cable_cell_impl, void (*)(cable_cell_impl*)>;
+impl_ptr make_impl(cable_cell_impl* c) {
+ return impl_ptr(c, [](cable_cell_impl* p){delete p;});
}
+cable_cell::cable_cell():
+ impl_(make_impl(new cable_cell_impl()))
+{}
+
+cable_cell::cable_cell(const cable_cell& other):
+ default_parameters(other.default_parameters),
+ impl_(make_impl(new cable_cell_impl(*other.impl_)))
+{}
+
size_type cable_cell::num_segments() const {
- return segments_.size();
+ return impl_->segments.size();
}
//
@@ -41,8 +138,8 @@ soma_segment* cable_cell::add_soma(value_type radius, point_type center) {
if (has_soma()) {
throw cable_cell_error("cell already has soma");
}
- segments_[0] = make_segment<soma_segment>(radius, center);
- return segments_[0]->as_soma();
+ impl_->segments[0] = make_segment<soma_segment>(radius, center);
+ return impl_->segments[0]->as_soma();
}
cable_segment* cable_cell::add_cable(index_type parent, segment_ptr&& cable) {
@@ -54,41 +151,210 @@ cable_segment* cable_cell::add_cable(index_type parent, segment_ptr&& cable) {
throw cable_cell_error("parent index out of range");
}
- segments_.push_back(std::move(cable));
- parents_.push_back(parent);
+ impl_->segments.push_back(std::move(cable));
+ impl_->parents.push_back(parent);
- return segments_.back()->as_cable();
+ return impl_->segments.back()->as_cable();
}
segment* cable_cell::segment(index_type index) {
- assert_valid_segment(index);
- return segments_[index].get();
+ impl_->assert_valid_segment(index);
+ return impl_->segments[index].get();
}
+
segment const* cable_cell::parent(index_type index) const {
- assert_valid_segment(index);
- return segments_[parents_[index]].get();
+ impl_->assert_valid_segment(index);
+ return impl_->segments[impl_->parents[index]].get();
}
segment const* cable_cell::segment(index_type index) const {
- assert_valid_segment(index);
- return segments_[index].get();
+ impl_->assert_valid_segment(index);
+ return impl_->segments[index].get();
+}
+
+const std::vector<segment_ptr>& cable_cell::segments() const {
+ return impl_->segments;
+}
+
+const std::vector<index_type>& cable_cell::parents() const {
+ return impl_->parents;
+}
+
+value_type cable_cell::segment_length_constant(value_type frequency, index_type segidx,
+ const cable_cell_parameter_set& global_defaults) const
+{
+ return 0.5/segment_mean_attenuation(frequency, segidx, global_defaults);
}
bool cable_cell::has_soma() const {
return !segment(0)->is_placeholder();
}
-void cable_cell::paint(const std::string& target, const std::string& description) {
- auto it = regions_.find(target);
+const std::vector<cable_cell::gap_junction_instance>& cable_cell::gap_junction_sites() const {
+ return impl_->gap_junction_sites;
+}
+
+const std::vector<cable_cell::synapse_instance>& cable_cell::synapses() const {
+ return impl_->synapses;
+}
+
+const std::vector<cable_cell::detector_instance>& cable_cell::detectors() const {
+ return impl_->spike_detectors;
+}
+
+const std::vector<cable_cell::stimulus_instance>& cable_cell::stimuli() const {
+ return impl_->stimuli;
+}
+
+void cable_cell::set_regions(cable_cell::region_map r) {
+ impl_->regions = std::move(r);
+}
+
+void cable_cell::set_locsets(cable_cell::locset_map l) {
+ impl_->locations = std::move(l);
+}
+
+//
+// Painters.
+//
+// Implementation of user API for painting density channel and electrical properties on cells.
+//
+
+void cable_cell::paint(const std::string& target, mechanism_desc desc) {
+ auto it = impl_->regions.find(target);
// Nothing to do if there are no regions that match.
- if (it==regions_.end()) return;
+ if (it==impl_->regions.end()) return;
+
+ for (auto c: it->second) {
+ if (c.prox_pos!=0 || c.dist_pos!=1) {
+ throw cable_cell_error(util::pprintf(
+ "cable_cell does not support regions with partial branches: \"{}\": {}",
+ target, c));
+ }
+ segment(c.branch)->add_mechanism(std::move(desc));
+ }
+}
+
+//
+// Placers.
+//
+// Implementation of user API for placing discrete items on cell morphology,
+// such as synapses, spike detectors and stimuli.
+//
+
+//
+// Synapses
+//
+
+lid_range cable_cell::place(const std::string& target, const mechanism_desc& desc) {
+ const auto first = impl_->synapses.size();
+
+ const auto it = impl_->locations.find(target);
+ if (it==impl_->locations.end()) return lid_range(first, first);
+
+ return impl_->place(it->second, desc, impl_->synapses);
+}
+
+/*
+lid_range cable_cell::place(const locset& ls, const mechanism_desc& desc) {
+ const auto locs = thingify(ls, impl_->morph);
+ return impl_->place(locs, desc, impl_->synapses);
+}
+*/
+
+lid_range cable_cell::place(const mlocation& loc, const mechanism_desc& desc) {
+ if (!impl_->valid_location(loc)) {
+ throw cable_cell_error(util::pprintf(
+ "Attempt to add synapse at invalid location: \"{}\"", loc));
+ }
+ return impl_->place({loc}, desc, impl_->synapses);
+}
+
+//
+// Stimuli
+//
+
+lid_range cable_cell::place(const std::string& target, const i_clamp& desc) {
+ const auto first = impl_->stimuli.size();
+
+ const auto it = impl_->locations.find(target);
+ if (it==impl_->locations.end()) return lid_range(first, first);
+
+ return impl_->place(it->second, desc, impl_->stimuli);
+}
+
+/*
+lid_range cable_cell::place(const locset& ls, const i_clamp& desc) {
+ const auto locs = thingify(ls, impl_->morph);
+ return impl_->place(locs, desc, impl_->stimuli);
+}
+*/
+
+lid_range cable_cell::place(const mlocation& loc, const i_clamp& desc) {
+ if (!impl_->valid_location(loc)) {
+ throw cable_cell_error(util::pprintf(
+ "Attempt to add stimulus at invalid location: {}", loc));
+ }
+ return impl_->place({loc}, desc, impl_->stimuli);
+}
- for (auto i: it->second) {
- segment(i)->add_mechanism(description);
+//
+// Gap junctions.
+//
+
+lid_range cable_cell::place(const std::string& target, gap_junction_site) {
+ const auto first = impl_->stimuli.size();
+
+ const auto it = impl_->locations.find(target);
+ if (it==impl_->locations.end()) return lid_range(first, first);
+
+ return impl_->place_gj(it->second);
+}
+
+/*
+lid_range cable_cell::place(const locset& ls, gap_junction_site) {
+ const auto locs = thingify(ls, impl_->morph);
+ return impl_->place_gj(locs);
+}
+*/
+
+lid_range cable_cell::place(const mlocation& loc, gap_junction_site) {
+ if (!impl_->valid_location(loc)) {
+ throw cable_cell_error(util::pprintf(
+ "Attempt to add gap junction site at invalid location: {}", loc));
}
+ return impl_->place_gj({loc});
+}
+
+//
+// Spike detectors.
+//
+lid_range cable_cell::place(const std::string& target, const threshold_detector& desc) {
+ const auto first = impl_->stimuli.size();
+
+ const auto it = impl_->locations.find(target);
+ if (it==impl_->locations.end()) return lid_range(first, first);
+
+ return impl_->place(it->second, desc.threshold, impl_->spike_detectors);
}
+/*
+lid_range cable_cell::place(const locset& ls, const threshold_detector& desc) {
+ const auto locs = thingify(ls, impl_->morph);
+ return impl_->place(locs, desc.threshold, impl_->spike_detectors);
+}
+*/
+
+lid_range cable_cell::place(const mlocation& loc, const threshold_detector& desc) {
+ if (!impl_->valid_location(loc)) {
+ throw cable_cell_error(util::pprintf(
+ "Attempt to add spike detector at invalid location: {}", loc));
+ }
+ return impl_->place({loc}, desc.threshold, impl_->spike_detectors);
+}
+
+
soma_segment* cable_cell::soma() {
return has_soma()? segment(0)->as_soma(): nullptr;
}
@@ -98,13 +364,13 @@ const soma_segment* cable_cell::soma() const {
}
cable_segment* cable_cell::cable(index_type index) {
- assert_valid_segment(index);
+ impl_->assert_valid_segment(index);
auto cable = segment(index)->as_cable();
return cable? cable: throw cable_cell_error("segment is not a cable segment");
}
const cable_segment* cable_cell::cable(index_type index) const {
- assert_valid_segment(index);
+ impl_->assert_valid_segment(index);
auto cable = segment(index)->as_cable();
return cable? cable: throw cable_cell_error("segment is not a cable segment");
}
@@ -118,18 +384,17 @@ std::vector<size_type> cable_cell::compartment_counts() const {
return comp_count;
}
-size_type cable_cell::num_compartments() const {
- return util::sum_by(segments_,
- [](const segment_ptr& s) { return s->num_compartments(); });
+const em_morphology* cable_cell::morphology() const {
+ return &(impl_->morph);
}
-void cable_cell::add_stimulus(mlocation loc, i_clamp stim) {
- (void)segment(loc.branch); // assert loc.segment in range
- stimuli_.push_back({loc, std::move(stim)});
+void cable_cell::set_morphology(em_morphology m) {
+ impl_->morph = std::move(m);
}
-void cable_cell::add_detector(mlocation loc, double threshold) {
- spike_detectors_.push_back({loc, threshold});
+size_type cable_cell::num_compartments() const {
+ return util::sum_by(impl_->segments,
+ [](const segment_ptr& s) { return s->num_compartments(); });
}
// Approximating wildly by ignoring O(x) effects entirely, the attenuation b
@@ -145,8 +410,10 @@ value_type cable_cell::segment_mean_attenuation(
value_type frequency, index_type segidx,
const cable_cell_parameter_set& global_defaults) const
{
- value_type R = default_parameters.axial_resistivity.value_or(global_defaults.axial_resistivity.value());
- value_type C = default_parameters.membrane_capacitance.value_or(global_defaults.membrane_capacitance.value());
+ value_type R = default_parameters.axial_resistivity.value_or(
+ global_defaults.axial_resistivity.value());
+ value_type C = default_parameters.membrane_capacitance.value_or(
+ global_defaults.membrane_capacitance.value());
value_type length_factor = 0; // [1/õm]
@@ -186,10 +453,10 @@ cable_cell make_cable_cell(const morphology& m,
bool compartments_from_discretization)
{
using point3d = cable_cell::point_type;
- cable_cell newcell;
+ cable_cell cell;
if (!m.num_branches()) {
- return newcell;
+ return cell;
}
// Add the soma.
@@ -197,7 +464,7 @@ cable_cell make_cable_cell(const morphology& m,
// If there is no spherical root/soma use a zero-radius soma.
double srad = m.spherical_root()? loc.radius: 0.;
- newcell.add_soma(srad, point3d(loc.x, loc.y, loc.z));
+ cell.add_soma(srad, point3d(loc.x, loc.y, loc.z));
auto& samples = m.samples();
for (auto i: util::make_span(1, m.num_branches())) {
@@ -232,7 +499,7 @@ cable_cell make_cable_cell(const morphology& m,
if (!m.spherical_root()) {
pid = pid==mnpos? 0: pid+1;
}
- auto cable = newcell.add_cable(pid, kind, radii, points);
+ auto cable = cell.add_cable(pid, make_segment<cable_segment>(kind, radii, points));
if (compartments_from_discretization) {
cable->as_cable()->set_compartments(radii.size()-1);
}
@@ -242,23 +509,21 @@ cable_cell make_cable_cell(const morphology& m,
// Ignores the pointsets, for now.
auto em = em_morphology(m); // for converting labels to "segments"
- std::unordered_map<std::string, std::vector<msize_t>> regions;
+ std::unordered_map<std::string, mcable_list> regions;
for (auto r: dictionary.regions()) {
- mcable_list L = thingify(r.second, em);
- std::vector<msize_t> bids;
- for (auto c: L) {
- if (c.prox_pos!=0 || c.dist_pos!=1) {
- throw cable_cell_error(util::pprintf(
- "cable_cell does not support regions with partial branches: \"{}\": {}",
- r.first, c));
- }
- bids.push_back(c.branch);
- }
- regions[r.first] = bids;
+ regions[r.first] = thingify(r.second, em);
}
- newcell.set_regions(std::move(regions));
+ cell.set_regions(std::move(regions));
+
+ std::unordered_map<std::string, mlocation_list> locsets;
+ for (auto l: dictionary.locsets()) {
+ locsets[l.first] = thingify(l.second, em);
+ }
+ cell.set_locsets(std::move(locsets));
+
+ cell.set_morphology(std::move(em));
- return newcell;
+ return cell;
}
} // namespace arb
diff --git a/arbor/include/arbor/cable_cell.hpp b/arbor/include/arbor/cable_cell.hpp
index 2303aaff7f63e70277b005b0c38e7fd1f9c307ea..2e35ded6c276c9a441c756b71b1134cc26d3b034 100644
--- a/arbor/include/arbor/cable_cell.hpp
+++ b/arbor/include/arbor/cable_cell.hpp
@@ -1,5 +1,6 @@
#pragma once
+
#include <unordered_map>
#include <string>
#include <vector>
@@ -16,22 +17,17 @@
namespace arb {
-// Current clamp description for stimulus specification.
-
-struct i_clamp {
- using value_type = double;
-
- value_type delay = 0; // [ms]
- value_type duration = 0; // [ms]
- value_type amplitude = 0; // [nA]
-
- i_clamp(value_type delay, value_type duration, value_type amplitude):
- delay(delay), duration(duration), amplitude(amplitude)
- {}
+// Pair of indexes that describe range of local indices.
+// Returned by cable_cell::place() calls, so that the caller can
+// refer to targets, detectors, etc on the cell.
+struct lid_range {
+ cell_lid_type begin;
+ cell_lid_type end;
+ lid_range(cell_lid_type b, cell_lid_type e):
+ begin(b), end(e) {}
};
// Probe type for cell descriptions.
-
struct cell_probe_address {
enum probe_kind {
membrane_voltage, membrane_current
@@ -41,7 +37,10 @@ struct cell_probe_address {
probe_kind kind;
};
-/// high-level abstract representation of a cell and its segments
+// Forward declare the implementation, for PIMPL.
+struct cable_cell_impl;
+
+// High-level abstract representation of a cell and its segments
class cable_cell {
public:
using index_type = cell_lid_type;
@@ -49,9 +48,10 @@ public:
using value_type = double;
using point_type = point<value_type>;
- using gap_junction_instance = mlocation;
+ using region_map = std::unordered_map<std::string, mcable_list>;
+ using locset_map = std::unordered_map<std::string, mlocation_list>;
- using region_map = std::unordered_map<std::string, std::vector<msize_t>>;
+ using gap_junction_instance = mlocation;
struct synapse_instance {
mlocation location;
@@ -74,30 +74,11 @@ public:
cable_cell();
/// Copy constructor
- cable_cell(const cable_cell& other):
- default_parameters(other.default_parameters),
- parents_(other.parents_),
- stimuli_(other.stimuli_),
- synapses_(other.synapses_),
- gap_junction_sites_(other.gap_junction_sites_),
- spike_detectors_(other.spike_detectors_),
- regions_(other.regions_)
- {
- // unique_ptr's cannot be copy constructed, do a manual assignment
- segments_.reserve(other.segments_.size());
- for (const auto& s: other.segments_) {
- segments_.push_back(s->clone());
- }
- }
+ cable_cell(const cable_cell& other);
/// Move constructor
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::cable;
- }
-
/// add a soma to the cell
/// radius must be specified
soma_segment* add_soma(value_type radius, point_type center=point_type());
@@ -107,102 +88,85 @@ public:
/// cable is the segment that will be moved into the cell
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
- /// args are the arguments to be used to consruct the new cable
- template <typename... Args>
- cable_segment* add_cable(index_type parent, Args&&... args);
-
- /// the number of segments in the cell
- size_type num_segments() const;
-
bool has_soma() const;
class segment* segment(index_type index);
const class segment* parent(index_type index) const;
const class segment* segment(index_type index) const;
- /// access pointer to the soma
- /// returns nullptr if the cell has no soma
+ // access pointer to the soma
+ // returns nullptr if the cell has no soma
+ // LEGACY
soma_segment* soma();
const soma_segment* soma() const;
- /// access pointer to a cable segment
- /// will throw an cable_cell_error exception if
- /// the cable index is not valid
+ // access pointer to a cable segment
+ // will throw an cable_cell_error exception if
+ // the cable index is not valid
+ // LEGACY
cable_segment* cable(index_type index);
const cable_segment* cable(index_type index) const;
- /// the total number of compartments over all segments
- size_type num_compartments() const;
+ const std::vector<segment_ptr>& segments() const;
- std::vector<segment_ptr> const& segments() const {
- return segments_;
- }
+ // the number of segments in the cell
+ size_type num_segments() const;
- /// return a vector with the compartment count for each segment in the cell
+ // return a vector with the compartment count for each segment in the cell
+ // LEGACY
std::vector<size_type> compartment_counts() const;
- //////////////////
- // stimuli
- //////////////////
- void add_stimulus(mlocation loc, i_clamp stim);
-
- std::vector<stimulus_instance>&
- stimuli() {
- return stimuli_;
- }
-
- const std::vector<stimulus_instance>&
- stimuli() const {
- return stimuli_;
- }
-
- //////////////////
- // painters
- //////////////////
- void paint(const std::string& target, const std::string& description);
-
- //////////////////
- // synapses
- //////////////////
- void add_synapse(mlocation loc, mechanism_desc p)
- {
- synapses_.push_back(synapse_instance{loc, std::move(p)});
- }
- const std::vector<synapse_instance>& synapses() const {
- return synapses_;
- }
-
- //////////////////
- // gap-junction
- //////////////////
- void add_gap_junction(mlocation location)
- {
- gap_junction_sites_.push_back(location);
- }
- const std::vector<gap_junction_instance>& gap_junction_sites() const {
- return gap_junction_sites_;
- }
-
- //////////////////
+ // The total number of compartments in the discretised cell.
+ // LEGACY
+ size_type num_compartments() const;
+
+ //
+ // Painters and placers.
+ //
+ // Used to describe regions and locations where density channels, stimuli,
+ // synapses, gap juncitons and detectors are located.
+ //
+
+ // Density channels.
+ void paint(const std::string& target, mechanism_desc);
+
+ // Synapses.
+ lid_range place(const std::string& target, const mechanism_desc&);
+ lid_range place(const mlocation&, const mechanism_desc&); // LEGACY
+ //lid_range place(const locset&, const mechanism_desc&);
+
+ // Stimuli.
+ lid_range place(const std::string& target, const i_clamp&);
+ lid_range place(const mlocation&, const i_clamp&); // LEGACY
+ //lid_range place(const locset&, const i_clamp&);
+
+ // Gap junctions.
+ lid_range place(const std::string&, gap_junction_site);
+ lid_range place(const mlocation& loc, gap_junction_site); // LEGACY
+ //lid_range place(const locset&, gap_junction_site);
+
// spike detectors
- //////////////////
- void add_detector(mlocation loc, double threshold);
+ lid_range place(const std::string&, const threshold_detector&);
+ lid_range place(const mlocation&, const threshold_detector&); // LEGACY
+ //lid_range place(const locset&, const threshold_detector&);
+
+ //
+ // access to placed items
+ //
- std::vector<detector_instance>&
- detectors() {
- return spike_detectors_;
- }
+ const std::vector<synapse_instance>& synapses() const;
+ const std::vector<gap_junction_instance>& gap_junction_sites() const;
+ const std::vector<detector_instance>& detectors() const;
+ const std::vector<stimulus_instance>& stimuli() const;
- const std::vector<detector_instance>&
- detectors() const {
- return spike_detectors_;
- }
+ // These setters are temporary, for "side-loading" in make_cable_cell.
+ // In the regions, locset and morphology descriptions will be passed directly
+ // to the cable_cell constructor.
+ void set_regions(region_map r);
+ void set_locsets(locset_map l);
+ void set_morphology(em_morphology m);
- void set_regions(region_map r) {
- regions_ = std::move(r);
- }
+ const em_morphology* morphology() const;
// Checks that two cells have the same
// - number and type of segments
@@ -212,9 +176,7 @@ public:
friend bool cell_basic_equality(const cable_cell&, const cable_cell&);
// Public view of parent indices vector.
- const std::vector<index_type>& parents() const {
- return parents_;
- }
+ const std::vector<index_type>& parents() const;
// Approximate per-segment mean attenuation b(f) at given frequency f,
// ignoring membrane resistance [1/µm].
@@ -225,50 +187,13 @@ public:
// Hines and Carnevale (2001), "NEURON: A Tool for Neuroscientists",
// Neuroscientist 7, pp. 123-135.
value_type segment_length_constant(value_type frequency, index_type segidx,
- const cable_cell_parameter_set& global_defaults) const
- {
- return 0.5/segment_mean_attenuation(frequency, segidx, global_defaults);
- }
+ const cable_cell_parameter_set& global_defaults) const;
private:
- void assert_valid_segment(index_type) const;
-
- // storage for connections
- std::vector<index_type> parents_;
-
- // the segments
- std::vector<segment_ptr> segments_;
-
- // the stimuli
- std::vector<stimulus_instance> stimuli_;
- // the synapses
- std::vector<synapse_instance> synapses_;
-
- // the gap_junctions
- std::vector<gap_junction_instance> gap_junction_sites_;
-
- // the sensors
- std::vector<detector_instance> spike_detectors_;
-
- // Named regions, oh my.
- region_map regions_;
+ std::unique_ptr<cable_cell_impl, void (*)(cable_cell_impl*)> impl_;
};
-// create a cable by forwarding cable construction parameters provided by the user
-template <typename... 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 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);
-
- return segments_.back()->as_cable();
-}
-
// Create a cable cell from a morphology specification.
// If compartments_from_discretization is true, set number of compartments
// in each segment to be the number of piecewise linear sections in the
diff --git a/arbor/include/arbor/cable_cell_param.hpp b/arbor/include/arbor/cable_cell_param.hpp
index 2c147c0ce25667eb91ee1b0ee12e285e4cbfc754..8ef752abae28868b00d2feecb11ebd065d61e77e 100644
--- a/arbor/include/arbor/cable_cell_param.hpp
+++ b/arbor/include/arbor/cable_cell_param.hpp
@@ -16,6 +16,30 @@ struct cable_cell_error: arbor_exception {
arbor_exception("cable_cell: "+what) {}
};
+// Current clamp description for stimulus specification.
+struct i_clamp {
+ using value_type = double;
+
+ value_type delay = 0; // [ms]
+ value_type duration = 0; // [ms]
+ value_type amplitude = 0; // [nA]
+
+ i_clamp() = default;
+
+ i_clamp(value_type delay, value_type duration, value_type amplitude):
+ delay(delay), duration(duration), amplitude(amplitude)
+ {}
+};
+
+// Threshold detector description.
+struct threshold_detector {
+ double threshold;
+};
+
+// Tag type for dispatching cable_cell::place() calls that add gap junction sites.
+struct gap_junction_site {};
+
+
// Mechanism description, viz. mechanism name and
// (non-global) parameter settings. Used to assign
// density and point mechanisms to segments and
diff --git a/arbor/include/arbor/morph/locset.hpp b/arbor/include/arbor/morph/locset.hpp
index 00c7e97386025aa9dbbeea782bb0ed178e01733a..63e0e6923e1fc4ecf772cb6c7de0c53f43e1eb81 100644
--- a/arbor/include/arbor/morph/locset.hpp
+++ b/arbor/include/arbor/morph/locset.hpp
@@ -17,10 +17,10 @@ namespace arb {
// interface for concretising locsets.
class em_morphology;
+class locset;
+
class locset {
public:
- locset() = delete;
-
template <typename Impl,
typename X=std::enable_if_t<!std::is_same<std::decay_t<Impl>, locset>::value>>
explicit locset(Impl&& impl):
@@ -40,6 +40,12 @@ public:
return *this;
}
+ // The default constructor creates an empty "nil" set.
+ locset();
+
+ // Construct an explicit location set with a single location.
+ locset(mlocation other);
+
template <typename Impl,
typename X=std::enable_if_t<!std::is_same<std::decay_t<Impl>, locset>::value>>
locset& operator=(Impl&& other) {
diff --git a/arbor/include/arbor/morph/morphology.hpp b/arbor/include/arbor/morph/morphology.hpp
index 0c9ed9b0e6726ee811fa3579c8fefc198f0f7329..16d41ec763479797434a39f533e6b29ec8afcc68 100644
--- a/arbor/include/arbor/morph/morphology.hpp
+++ b/arbor/include/arbor/morph/morphology.hpp
@@ -21,6 +21,7 @@ class morphology {
public:
morphology(sample_tree m, bool use_spherical_root);
morphology(sample_tree m);
+ morphology();
// Whether the root of the morphology is spherical.
bool spherical_root() const;
diff --git a/arbor/include/arbor/morph/region.hpp b/arbor/include/arbor/morph/region.hpp
index d3d7f735d553202da1070300be948a57619bed47..1cb884b025bde88fdb3440e4f0bd14a1e9dcb8a9 100644
--- a/arbor/include/arbor/morph/region.hpp
+++ b/arbor/include/arbor/morph/region.hpp
@@ -19,8 +19,6 @@ class em_morphology;
class region {
public:
- region() = delete;
-
template <typename Impl,
typename X=std::enable_if_t<!std::is_same<std::decay_t<Impl>, region>::value>>
explicit region(Impl&& impl):
@@ -32,6 +30,9 @@ public:
region(region&& other) = default;
+ // The default constructor creates an empty "nil" region.
+ region();
+
region(const region& other):
impl_(other.impl_->clone()) {}
@@ -110,6 +111,9 @@ private:
namespace reg {
+// An empty region.
+region nil();
+
// An explicit cable section.
region cable(mcable);
diff --git a/arbor/morph/em_morphology.cpp b/arbor/morph/em_morphology.cpp
index ba6d275131217ae32a7b175c25e893ee0fb23e31..f00865e3c59259730e020fff7370d715451b0b5e 100644
--- a/arbor/morph/em_morphology.cpp
+++ b/arbor/morph/em_morphology.cpp
@@ -25,6 +25,8 @@ em_morphology::em_morphology(const morphology& m):
const auto ns = morph_.num_samples();
const auto nb = morph_.num_branches();
+ if (!ns) return;
+
// Cache distance of each sample from the root.
dist2root_.resize(ns);
dist2root_[0] = 0.;
@@ -52,7 +54,7 @@ em_morphology::em_morphology(const morphology& m):
for (auto i: idx) {
sample_locs_[i] = {msize_t(b), (dist2root_[i]-start)/len};
}
- // For ensure that all non-spherical branches have their last sample
+ // Ensure that all non-spherical branches have their last sample
if (idx.size()>1u) {
sample_locs_[idx.back()] = mlocation{msize_t(b), 1};
}
@@ -72,6 +74,10 @@ em_morphology::em_morphology(const morphology& m):
}
}
+em_morphology::em_morphology():
+ em_morphology(morphology())
+{}
+
const morphology& em_morphology::morph() const {
return morph_;
}
diff --git a/arbor/morph/em_morphology.hpp b/arbor/morph/em_morphology.hpp
index 94aa5b0fe783551928d3506d5cdc5910d2ea0d5b..1e47dd59b5dd4c32ec33fd1e5bfc7f11ba315063 100644
--- a/arbor/morph/em_morphology.hpp
+++ b/arbor/morph/em_morphology.hpp
@@ -19,6 +19,7 @@ class em_morphology {
std::vector<double> branch_lengths_;
public:
+ em_morphology();
em_morphology(const morphology& m);
const morphology& morph() const;
diff --git a/arbor/morph/label_dict.cpp b/arbor/morph/label_dict.cpp
index a6bf10c8a546f83bd0fed9866eb00a0fff0d85e2..e72c40067ebf50e5618fe65d25ca03e1b7f61a03 100644
--- a/arbor/morph/label_dict.cpp
+++ b/arbor/morph/label_dict.cpp
@@ -24,16 +24,7 @@ void label_dict::set(const std::string& name, arb::locset ls) {
throw morphology_error(util::pprintf(
"Attempt to add a locset \"{}\" to a label dictionary that already contains a region with the same name.", name));
}
- // First remove an entry with the same name if it exists.
- // Has to be this way, because insert_or_assign() is C++17, and we
- // can't use operator[] because locset is not default constructable.
- auto it = locsets_.find(name);
- if (it!=locsets_.end()) {
- it->second = std::move(ls);
- }
- else {
- locsets_.emplace(name, std::move(ls));
- }
+ locsets_[name] = std::move(ls);
}
void label_dict::set(const std::string& name, arb::region reg) {
@@ -41,16 +32,7 @@ void label_dict::set(const std::string& name, arb::region reg) {
throw morphology_error(util::pprintf(
"Attempt to add a region \"{}\" to a label dictionary that already contains a locset with the same name.", name));
}
- // First remove an entry with the same name if it exists.
- // Has to be this way, because insert_or_assign() is C++17, and we
- // can't use operator[] because region is not default constructable.
- auto it = regions_.find(name);
- if (it!=regions_.end()) {
- it->second = std::move(reg);
- }
- else {
- regions_.emplace(name, std::move(reg));
- }
+ regions_[name] = std::move(reg);
}
util::optional<const region&> label_dict::region(const std::string& name) const {
diff --git a/arbor/morph/locset.cpp b/arbor/morph/locset.cpp
index f1215c4eaf2fa301988eff86736e373b7d8cda09..55c0752ccf366594db1c6fb211e91a4d85fe72f9 100644
--- a/arbor/morph/locset.cpp
+++ b/arbor/morph/locset.cpp
@@ -244,4 +244,12 @@ locset sum(locset lhs, locset rhs) {
return locset(ls::lsum(std::move(lhs), std::move(rhs)));
}
+locset::locset() {
+ *this = ls::nil();
+}
+
+locset::locset(mlocation other) {
+ *this = ls::location(other);
+}
+
} // namespace arb
diff --git a/arbor/morph/morphology.cpp b/arbor/morph/morphology.cpp
index 35a73def3deffcf56ec3c0b45146cabde9f6c6d4..ee78c8532ef3a2121aeed365ee0fe1b9cfb53999 100644
--- a/arbor/morph/morphology.cpp
+++ b/arbor/morph/morphology.cpp
@@ -182,6 +182,10 @@ morphology::morphology(sample_tree m):
impl_(std::make_shared<const morphology_impl>(std::move(m)))
{}
+morphology::morphology():
+ morphology(sample_tree())
+{}
+
// The parent branch of branch b.
msize_t morphology::branch_parent(msize_t b) const {
return impl_->branch_parents_[b];
diff --git a/arbor/morph/region.cpp b/arbor/morph/region.cpp
index 90d999b7fe0a5fcbf4a78aff428987e23c187d61..b456c42e19da81d06fa8d615be573d7e65dede88 100644
--- a/arbor/morph/region.cpp
+++ b/arbor/morph/region.cpp
@@ -98,6 +98,23 @@ mcable_list remove_cover(mcable_list cables, const em_morphology& m) {
return merge(cables);
}
+//
+// Null/empty region
+//
+struct nil_ {};
+
+region nil() {
+ return region{nil_{}};
+}
+
+mcable_list thingify_(const nil_& x, const em_morphology& m) {
+ return {};
+}
+
+std::ostream& operator<<(std::ostream& o, const nil_& x) {
+ return o << "nil";
+}
+
//
// Explicit cable section
//
@@ -300,4 +317,8 @@ region join(region l, region r) {
return region{reg::reg_or(std::move(l), std::move(r))};
}
+region::region() {
+ *this = reg::nil();
+}
+
} // namespace arb
diff --git a/example/dryrun/dryrun.cpp b/example/dryrun/dryrun.cpp
index e54bc1a70faeb29bc30a3e001e2dbeb1f18678d3..ff300d93951699d26a4557598d91ffccafde49cb 100644
--- a/example/dryrun/dryrun.cpp
+++ b/example/dryrun/dryrun.cpp
@@ -364,7 +364,7 @@ arb::cable_cell branch_cell(arb::cell_gid_type gid, const cell_parameters& param
for (unsigned j=0; j<2; ++j) {
if (dis(gen)<bp) {
sec_ids.push_back(nsec++);
- auto dend = cell.add_cable(sec, arb::section_kind::dendrite, dend_radius, dend_radius, l);
+ auto dend = cell.add_cable(sec, arb::make_segment<arb::cable_segment>(arb::section_kind::dendrite, dend_radius, dend_radius, l));
dend->set_compartments(nc);
dend->add_mechanism("pas");
}
@@ -377,10 +377,10 @@ arb::cable_cell branch_cell(arb::cell_gid_type gid, const cell_parameters& param
}
// Add spike threshold detector at the soma.
- cell.add_detector({0,0}, 10);
+ cell.place(arb::mlocation{0,0}, arb::threshold_detector{10});
// Add a synapse to the mid point of the first dendrite.
- cell.add_synapse({1, 0.5}, "expsyn");
+ cell.place(arb::mlocation{1, 0.5}, "expsyn");
return cell;
}
diff --git a/example/gap_junctions/gap_junctions.cpp b/example/gap_junctions/gap_junctions.cpp
index 8212beec6b8d181de0cf96d089b6dd59c96d007a..4e3aa846f75176670c1060b23abab22c5812b617 100644
--- a/example/gap_junctions/gap_junctions.cpp
+++ b/example/gap_junctions/gap_junctions.cpp
@@ -363,23 +363,23 @@ arb::cable_cell gj_cell(cell_gid_type gid, unsigned ncell, double stim_duration)
set_reg_params();
setup_seg(soma);
- auto dend = cell.add_cable(0, arb::section_kind::dendrite, 3.0/2.0, 3.0/2.0, 300); //cable 1
+ auto dend = cell.add_cable(0, arb::make_segment<arb::cable_segment>(arb::section_kind::dendrite, 3.0/2.0, 3.0/2.0, 300)); //cable 1
dend->set_compartments(1);
set_reg_params();
setup_seg(dend);
- cell.add_detector({0,0}, 10);
+ cell.place(arb::mlocation{0,0}, arb::threshold_detector{10});
- cell.add_gap_junction({0, 1});
- cell.add_gap_junction({1, 1});
+ cell.place(arb::mlocation{0, 1}, arb::gap_junction_site{});
+ cell.place(arb::mlocation{1, 1}, arb::gap_junction_site{});
if (!gid) {
arb::i_clamp stim(0, stim_duration, 0.4);
- cell.add_stimulus({0, 0.5}, stim);
+ cell.place(arb::mlocation{0, 0.5}, stim);
}
// Add a synapse to the mid point of the first dendrite.
- cell.add_synapse({1, 0.5}, "expsyn");
+ cell.place(arb::mlocation{1, 0.5}, "expsyn");
return cell;
}
diff --git a/example/generators/generators.cpp b/example/generators/generators.cpp
index 9c18c5deba2430698db2ee81c934ce1de2335b62..9d48f0c6bb1f999a2785eb564219c3720b44b13a 100644
--- a/example/generators/generators.cpp
+++ b/example/generators/generators.cpp
@@ -55,7 +55,7 @@ public:
// Add one synapse at the soma.
// This synapse will be the target for all events, from both
// event_generators.
- c.add_synapse({0, 0.5}, "expsyn");
+ c.place(arb::mlocation{0, 0.5}, "expsyn");
return std::move(c);
}
diff --git a/example/ring/ring.cpp b/example/ring/ring.cpp
index 4cc95891bbe7a41e0c24933a031c1368b7173376..ac7d344f304f569a6a7dbba52a08c200db0b748d 100644
--- a/example/ring/ring.cpp
+++ b/example/ring/ring.cpp
@@ -367,7 +367,7 @@ arb::cable_cell branch_cell(arb::cell_gid_type gid, const cell_parameters& param
for (unsigned j=0; j<2; ++j) {
if (dis(gen)<bp) {
sec_ids.push_back(nsec++);
- auto dend = cell.add_cable(sec, arb::section_kind::dendrite, dend_radius, dend_radius, l);
+ auto dend = cell.add_cable(sec, arb::make_segment<arb::cable_segment>(arb::section_kind::dendrite, dend_radius, dend_radius, l));
dend->set_compartments(nc);
dend->add_mechanism("pas");
}
@@ -380,14 +380,14 @@ arb::cable_cell branch_cell(arb::cell_gid_type gid, const cell_parameters& param
}
// Add spike threshold detector at the soma.
- cell.add_detector({0,0}, 10);
+ cell.place(arb::mlocation{0,0}, arb::threshold_detector{10});
// Add a synapse to the mid point of the first dendrite.
- cell.add_synapse({1, 0.5}, "expsyn");
+ cell.place(arb::mlocation{1, 0.5}, "expsyn");
// Add additional synapses that will not be connected to anything.
for (unsigned i=1u; i<params.synapses; ++i) {
- cell.add_synapse({1, 0.5}, "expsyn");
+ cell.place(arb::mlocation{1, 0.5}, "expsyn");
}
return cell;
diff --git a/example/single/single.cpp b/example/single/single.cpp
index 6673ef09460ca8352d774391c5b0d42b0531e58c..501969f5de77ca9aafbe9fc7853cfd0945e248a5 100644
--- a/example/single/single.cpp
+++ b/example/single/single.cpp
@@ -77,7 +77,7 @@ struct single_recipe: public arb::recipe {
arb::cell_lid_type last_segment = c.num_segments()-1;
arb::mlocation end_last_segment = { last_segment, 1. };
- c.add_synapse(end_last_segment, "exp2syn");
+ c.place(end_last_segment, "exp2syn");
return c;
}
diff --git a/modcc/solvers.cpp b/modcc/solvers.cpp
index 1c8ca27e7bf3d0a1cea7bd1766ae00fe92aa1155..c3b42d574c72382f8d2e276960f59d7094b025e1 100644
--- a/modcc/solvers.cpp
+++ b/modcc/solvers.cpp
@@ -390,7 +390,8 @@ void SparseSolverVisitor::finalize() {
// State variable updates given by rhs/diagonal for reduced matrix.
Location loc;
- for (unsigned i = 0; i<A_.nrow(); ++i) {
+ auto nrow = A_.nrow();
+ for (unsigned i = 0; i<nrow; ++i) {
const symge::sym_row& row = A_[i];
unsigned rhs_col = A_.augcol();
unsigned lhs_col = -1;
@@ -401,7 +402,7 @@ void SparseSolverVisitor::finalize() {
}
}
- if (lhs_col==-1) {
+ if (lhs_col==unsigned(-1)) {
throw std::logic_error("zero row in sparse solver matrix");
}
@@ -480,7 +481,8 @@ void LinearSolverVisitor::finalize() {
// State variable updates given by rhs/diagonal for reduced matrix.
Location loc;
- for (unsigned i = 0; i < A_.nrow(); ++i) {
+ auto nrow = A_.nrow();
+ for (unsigned i = 0; i < nrow; ++i) {
const symge::sym_row& row = A_[i];
unsigned rhs = A_.augcol();
unsigned lhs = -1;
@@ -491,7 +493,7 @@ void LinearSolverVisitor::finalize() {
}
}
- if (lhs==-1) {
+ if (lhs==unsigned(-1)) {
throw std::logic_error("zero row in linear solver matrix");
}
diff --git a/python/cells.cpp b/python/cells.cpp
index ed332548bada6508f605b220fb15fc3bdeb5e1d0..21a93db2d8df0b9f6f7c7fc0c38d002e1df48d0f 100644
--- a/python/cells.cpp
+++ b/python/cells.cpp
@@ -115,7 +115,7 @@ arb::cable_cell make_cable_cell(arb::cell_gid_type gid, const cell_parameters& p
for (unsigned j=0; j<2; ++j) {
if (dis(gen)<bp) {
sec_ids.push_back(nsec++);
- auto dend = cell.add_cable(sec, arb::section_kind::dendrite, dend_radius, dend_radius, l);
+ auto dend = cell.add_cable(sec, arb::make_segment<arb::cable_segment>(arb::section_kind::dendrite, dend_radius, dend_radius, l));
dend->set_compartments(nc);
dend->add_mechanism("pas");
}
@@ -128,14 +128,14 @@ arb::cable_cell make_cable_cell(arb::cell_gid_type gid, const cell_parameters& p
}
// Add spike threshold detector at the soma.
- cell.add_detector({0,0}, 10);
+ cell.place(arb::mlocation{0,0}, arb::threshold_detector{10});
// Add a synapse to the mid point of the first dendrite.
- cell.add_synapse({1, 0.5}, "expsyn");
+ cell.place(arb::mlocation{1, 0.5}, "expsyn");
// Add additional synapses.
for (unsigned i=1u; i<params.synapses; ++i) {
- cell.add_synapse({1, 0.5}, "expsyn");
+ cell.place(arb::mlocation{1, 0.5}, "expsyn");
}
return cell;
diff --git a/test/common_cells.hpp b/test/common_cells.hpp
index 0694bf6daf874a97904bde52815fb77b5dd52eab..dd40bc91d0add02c8f101651d685d1bc6ab8a316 100644
--- a/test/common_cells.hpp
+++ b/test/common_cells.hpp
@@ -27,7 +27,7 @@ inline cable_cell make_cell_soma_only(bool with_stim = true) {
soma->add_mechanism("hh");
if (with_stim) {
- c.add_stimulus({0,0.5}, {10., 100., 0.1});
+ c.place(mlocation{0,0.5}, i_clamp{10., 100., 0.1});
}
return c;
@@ -60,7 +60,7 @@ inline cable_cell make_cell_ball_and_stick(bool with_stim = true) {
auto soma = c.add_soma(12.6157/2.0);
soma->add_mechanism("hh");
- c.add_cable(0, section_kind::dendrite, 1.0/2, 1.0/2, 200.0);
+ c.add_cable(0, make_segment<cable_segment>(section_kind::dendrite, 1.0/2, 1.0/2, 200.0));
for (auto& seg: c.segments()) {
if (seg->is_dendrite()) {
@@ -70,7 +70,7 @@ inline cable_cell make_cell_ball_and_stick(bool with_stim = true) {
}
if (with_stim) {
- c.add_stimulus({1,1}, {5., 80., 0.3});
+ c.place(mlocation{1,1}, i_clamp{5., 80., 0.3});
}
return c;
}
@@ -104,7 +104,7 @@ inline cable_cell make_cell_ball_and_taper(bool with_stim = true) {
auto soma = c.add_soma(12.6157/2.0);
soma->add_mechanism("hh");
- c.add_cable(0, section_kind::dendrite, 1.0/2, 0.4/2, 200.0);
+ c.add_cable(0, make_segment<cable_segment>(section_kind::dendrite, 1.0/2, 0.4/2, 200.0));
for (auto& seg: c.segments()) {
if (seg->is_dendrite()) {
@@ -114,7 +114,7 @@ inline cable_cell make_cell_ball_and_taper(bool with_stim = true) {
}
if (with_stim) {
- c.add_stimulus({1,1}, {5., 80., 0.3});
+ c.place(mlocation{1,1}, i_clamp{5., 80., 0.3});
}
return c;
}
@@ -172,7 +172,7 @@ inline cable_cell make_cell_ball_and_squiggle(bool with_stim = true) {
}
if (with_stim) {
- c.add_stimulus({1,1}, {5., 80., 0.3});
+ c.place(mlocation{1,1}, i_clamp{5., 80., 0.3});
}
return c;
}
@@ -207,9 +207,9 @@ inline cable_cell make_cell_ball_and_3stick(bool with_stim = true) {
auto soma = c.add_soma(12.6157/2.0);
soma->add_mechanism("hh");
- c.add_cable(0, section_kind::dendrite, 0.5, 0.5, 100);
- c.add_cable(1, section_kind::dendrite, 0.5, 0.5, 100);
- c.add_cable(1, section_kind::dendrite, 0.5, 0.5, 100);
+ c.add_cable(0, make_segment<cable_segment>(section_kind::dendrite, 0.5, 0.5, 100));
+ c.add_cable(1, make_segment<cable_segment>(section_kind::dendrite, 0.5, 0.5, 100));
+ c.add_cable(1, make_segment<cable_segment>(section_kind::dendrite, 0.5, 0.5, 100));
for (auto& seg: c.segments()) {
if (seg->is_dendrite()) {
@@ -219,8 +219,8 @@ inline cable_cell make_cell_ball_and_3stick(bool with_stim = true) {
}
if (with_stim) {
- c.add_stimulus({2,1}, {5., 80., 0.45});
- c.add_stimulus({3,1}, {40., 10.,-0.2});
+ c.place(mlocation{2,1}, i_clamp{5., 80., 0.45});
+ c.place(mlocation{3,1}, i_clamp{40., 10.,-0.2});
}
return c;
}
@@ -253,7 +253,7 @@ inline cable_cell make_cell_simple_cable(bool with_stim = true) {
c.default_parameters.membrane_capacitance = 0.01;
c.add_soma(0);
- c.add_cable(0, section_kind::dendrite, 0.5, 0.5, 1000);
+ c.add_cable(0, make_segment<cable_segment>(section_kind::dendrite, 0.5, 0.5, 1000));
double gbar = 0.000025;
double I = 0.1;
@@ -272,7 +272,7 @@ inline cable_cell make_cell_simple_cable(bool with_stim = true) {
if (with_stim) {
// stimulus in the middle of our zero-volume 'soma'
// corresponds to proximal end of cable.
- c.add_stimulus({0,0.5}, {0., INFINITY, I});
+ c.place(mlocation{0,0.5}, i_clamp{0., INFINITY, I});
}
return c;
}
diff --git a/test/unit/test_cable_cell.cpp b/test/unit/test_cable_cell.cpp
index f297a50d5c4035ce8d9981604e5297827cf1ffb0..49d16a9e74b4e82d79f4a7f4b7350d0e8423db96 100644
--- a/test/unit/test_cable_cell.cpp
+++ b/test/unit/test_cable_cell.cpp
@@ -2,6 +2,7 @@
#include <arbor/cable_cell.hpp>
#include <arbor/math.hpp>
+#include <arbor/morph/locset.hpp>
#include "tree.hpp"
@@ -37,9 +38,6 @@ TEST(cable_cell, soma) {
auto s = c.soma();
EXPECT_EQ(s->radius(), soma_radius);
EXPECT_EQ(s->center().is_set(), true);
-
- // add expression template library for points
- //EXPECT_EQ(s->center(), point<double>(0,0,1));
}
}
@@ -78,7 +76,7 @@ TEST(cable_cell, add_segment) {
c.add_cable(
0,
- section_kind::dendrite, cable_radius, cable_radius, cable_length
+ make_segment<cable_segment>(section_kind::dendrite, cable_radius, cable_radius, cable_length)
);
EXPECT_EQ(c.num_segments(), 2u);
@@ -95,9 +93,9 @@ TEST(cable_cell, add_segment) {
c.add_cable(
0,
- section_kind::dendrite,
- std::vector<double>{cable_radius, cable_radius, cable_radius, cable_radius},
- std::vector<double>{cable_length, cable_length, cable_length}
+ make_segment<cable_segment>(section_kind::dendrite,
+ std::vector<double>{cable_radius, cable_radius, cable_radius, cable_radius},
+ std::vector<double>{cable_length, cable_length, cable_length})
);
EXPECT_EQ(c.num_segments(), 2u);
@@ -196,14 +194,13 @@ TEST(cable_cell, clone) {
cable_cell c;
c.add_soma(2.1);
- c.add_cable(0, section_kind::dendrite, 0.3, 0.2, 10);
+ c.add_cable(0, make_segment<cable_segment>(section_kind::dendrite, 0.3, 0.2, 10));
c.segment(1)->set_compartments(3);
- c.add_cable(1, section_kind::dendrite, 0.2, 0.15, 20);
+ c.add_cable(1, make_segment<cable_segment>(section_kind::dendrite, 0.2, 0.15, 20));
c.segment(2)->set_compartments(5);
- c.add_synapse({1, 0.3}, "expsyn");
-
- c.add_detector({0, 0.5}, 10.0);
+ c.place(mlocation{1, 0.3}, "expsyn");
+ c.place(mlocation{0, 0.5}, threshold_detector{10.0});
// make clone
@@ -230,20 +227,10 @@ TEST(cable_cell, clone) {
// check clone is independent
- c.add_cable(2, section_kind::dendrite, 0.15, 0.1, 20);
+ c.add_cable(2, make_segment<cable_segment>(section_kind::dendrite, 0.15, 0.1, 20));
EXPECT_NE(c.num_segments(), d.num_segments());
- d.detectors()[0].threshold = 13.0;
- ASSERT_EQ(1u, c.detectors().size());
- ASSERT_EQ(1u, d.detectors().size());
- EXPECT_NE(c.detectors()[0].threshold, d.detectors()[0].threshold);
-
c.segment(1)->set_compartments(7);
EXPECT_NE(c.segment(1)->num_compartments(), d.segment(1)->num_compartments());
EXPECT_EQ(c.segment(2)->num_compartments(), d.segment(2)->num_compartments());
}
-
-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 9acd94e09dbe8888f6b17a40295b2d291f33f9fd..30524dec9ff0aac23ea52dc61f86c753227b50ae 100644
--- a/test/unit/test_domain_decomposition.cpp
+++ b/test/unit/test_domain_decomposition.cpp
@@ -66,7 +66,7 @@ namespace {
arb::util::unique_any get_cell_description(cell_gid_type) const override {
cable_cell c;
c.add_soma(20);
- c.add_gap_junction({0,1});
+ c.place(mlocation{0,1}, gap_junction_site{});
return {std::move(c)};
}
diff --git a/test/unit/test_event_delivery.cpp b/test/unit/test_event_delivery.cpp
index cafba40f1982fde675cccc26d0cce059b6a7e320..a4d4b632c7edca338f6719c31a6c2181aa3c9713 100644
--- a/test/unit/test_event_delivery.cpp
+++ b/test/unit/test_event_delivery.cpp
@@ -29,9 +29,9 @@ struct test_recipe: public n_cable_cell_recipe {
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);
- c.add_gap_junction({0, 0.5});
+ c.place(mlocation{0, 0.5}, "expsyn");
+ c.place(mlocation{0, 0.5}, threshold_detector{-64});
+ c.place(mlocation{0, 0.5}, gap_junction_site{});
return c;
}
diff --git a/test/unit/test_fvm_layout.cpp b/test/unit/test_fvm_layout.cpp
index 3bd981cd580c884e1dd9fcbaef2af08f4785fce1..6ad308015644738ab31c73b50fdd30897cc85dc5 100644
--- a/test/unit/test_fvm_layout.cpp
+++ b/test/unit/test_fvm_layout.cpp
@@ -10,6 +10,7 @@
#include "util/maputil.hpp"
#include "util/rangeutil.hpp"
#include "util/span.hpp"
+#include "io/sepval.hpp"
#include "common.hpp"
#include "unit_test_catalogue.hpp"
@@ -99,17 +100,17 @@ namespace {
s = c2.add_soma(14./2);
s->add_mechanism("hh");
- s = c2.add_cable(0, section_kind::dendrite, 1.0/2, 1.0/2, 200);
+ s = c2.add_cable(0, make_segment<cable_segment>(section_kind::dendrite, 1.0/2, 1.0/2, 200));
s->parameters.membrane_capacitance = 0.017;
- s = c2.add_cable(1, section_kind::dendrite, 0.8/2, 0.8/2, 300);
+ s = c2.add_cable(1, make_segment<cable_segment>(section_kind::dendrite, 0.8/2, 0.8/2, 300));
s->parameters.membrane_capacitance = 0.013;
- s = c2.add_cable(1, section_kind::dendrite, 0.7/2, 0.7/2, 180);
+ s = c2.add_cable(1, make_segment<cable_segment>(section_kind::dendrite, 0.7/2, 0.7/2, 180));
s->parameters.membrane_capacitance = 0.018;
- c2.add_stimulus({2,1}, {5., 80., 0.45});
- c2.add_stimulus({3,1}, {40., 10.,-0.2});
+ c2.place(mlocation{2,1}, i_clamp{5., 80., 0.45});
+ c2.place(mlocation{3,1}, i_clamp{40., 10.,-0.2});
for (auto& seg: c2.segments()) {
if (seg->is_dendrite()) {
@@ -289,10 +290,10 @@ TEST(fvm_layout, mech_index) {
check_two_cell_system(cells);
// Add four synapses of two varieties across the cells.
- cells[0].add_synapse({1, 0.4}, "expsyn");
- cells[0].add_synapse({1, 0.4}, "expsyn");
- cells[1].add_synapse({2, 0.4}, "exp2syn");
- cells[1].add_synapse({3, 0.4}, "expsyn");
+ cells[0].place(mlocation{1, 0.4}, "expsyn");
+ cells[0].place(mlocation{1, 0.4}, "expsyn");
+ cells[1].place(mlocation{2, 0.4}, "exp2syn");
+ cells[1].place(mlocation{3, 0.4}, "expsyn");
cable_cell_global_properties gprop;
gprop.default_parameters = neuron_parameter_defaults;
@@ -337,9 +338,49 @@ TEST(fvm_layout, mech_index) {
EXPECT_EQ(ivec({0,6}), M.ions.at("k"s).cv);
}
+struct exp_instance {
+ int cv;
+ int multiplicity;
+ std::vector<unsigned> targets;
+ double e;
+ double tau;
+
+ template <typename Seq>
+ exp_instance(int cv, const Seq& tgts, double e, double tau):
+ cv(cv), multiplicity(util::size(tgts)), e(e), tau(tau)
+ {
+ targets.reserve(util::size(tgts));
+ for (auto t: tgts) targets.push_back(t);
+ util::sort(targets);
+ }
+
+ bool matches(const exp_instance& I) const {
+ return I.cv==cv && I.e==e && I.tau==tau && I.targets==targets;
+ }
+
+ bool is_in(const arb::fvm_mechanism_config& C) const {
+ std::vector<unsigned> _;
+ auto part = util::make_partition(_, C.multiplicity);
+ auto& evals = *value_by_key(C.param_values, "e");
+ // Handle both expsyn and exp2syn by looking for "tau1" if "tau"
+ // parameter is not found.
+ auto& tauvals = value_by_key(C.param_values, "tau")?
+ *value_by_key(C.param_values, "tau"):
+ *value_by_key(C.param_values, "tau1");
+
+ for (auto i: make_span(C.multiplicity.size())) {
+ exp_instance other(C.cv[i],
+ util::subrange_view(C.target, part[i]),
+ evals[i],
+ tauvals[i]);
+ if (matches(other)) return true;
+ }
+ return false;
+ }
+};
+
TEST(fvm_layout, coalescing_synapses) {
using ivec = std::vector<fvm_index_type>;
- using fvec = std::vector<fvm_value_type>;
auto syn_desc = [&](const char* name, double val0, double val1) {
mechanism_desc m(name);
@@ -363,14 +404,16 @@ TEST(fvm_layout, coalescing_synapses) {
gprop_coalesce.default_parameters = neuron_parameter_defaults;
gprop_coalesce.coalesce_synapses = true;
+ using L=std::initializer_list<unsigned>;
+
{
cable_cell cell = make_cell_ball_and_stick();
// Add synapses of two varieties.
- cell.add_synapse({1, 0.3}, "expsyn");
- cell.add_synapse({1, 0.5}, "expsyn");
- cell.add_synapse({1, 0.7}, "expsyn");
- cell.add_synapse({1, 0.9}, "expsyn");
+ cell.place(mlocation{1, 0.3}, "expsyn");
+ cell.place(mlocation{1, 0.5}, "expsyn");
+ cell.place(mlocation{1, 0.7}, "expsyn");
+ cell.place(mlocation{1, 0.9}, "expsyn");
fvm_discretization D = fvm_discretize({cell}, neuron_parameter_defaults);
fvm_mechanism_data M = fvm_build_mechanism_data(gprop_coalesce, {cell}, D);
@@ -383,10 +426,10 @@ TEST(fvm_layout, coalescing_synapses) {
cable_cell cell = make_cell_ball_and_stick();
// Add synapses of two varieties.
- cell.add_synapse({1, 0.3}, "expsyn");
- cell.add_synapse({1, 0.5}, "exp2syn");
- cell.add_synapse({1, 0.7}, "expsyn");
- cell.add_synapse({1, 0.9}, "exp2syn");
+ cell.place(mlocation{1, 0.3}, "expsyn");
+ cell.place(mlocation{1, 0.5}, "exp2syn");
+ cell.place(mlocation{1, 0.7}, "expsyn");
+ cell.place(mlocation{1, 0.9}, "exp2syn");
fvm_discretization D = fvm_discretize({cell}, neuron_parameter_defaults);
fvm_mechanism_data M = fvm_build_mechanism_data(gprop_coalesce, {cell}, D);
@@ -402,10 +445,10 @@ TEST(fvm_layout, coalescing_synapses) {
{
cable_cell cell = make_cell_ball_and_stick();
- cell.add_synapse({1, 0.3}, "expsyn");
- cell.add_synapse({1, 0.5}, "expsyn");
- cell.add_synapse({1, 0.7}, "expsyn");
- cell.add_synapse({1, 0.9}, "expsyn");
+ cell.place(mlocation{1, 0.3}, "expsyn");
+ cell.place(mlocation{1, 0.5}, "expsyn");
+ cell.place(mlocation{1, 0.7}, "expsyn");
+ cell.place(mlocation{1, 0.9}, "expsyn");
fvm_discretization D = fvm_discretize({cell}, neuron_parameter_defaults);
fvm_mechanism_data M = fvm_build_mechanism_data(gprop_no_coalesce, {cell}, D);
@@ -418,10 +461,10 @@ TEST(fvm_layout, coalescing_synapses) {
cable_cell cell = make_cell_ball_and_stick();
// Add synapses of two varieties.
- cell.add_synapse({1, 0.3}, "expsyn");
- cell.add_synapse({1, 0.5}, "exp2syn");
- cell.add_synapse({1, 0.7}, "expsyn");
- cell.add_synapse({1, 0.9}, "exp2syn");
+ cell.place(mlocation{1, 0.3}, "expsyn");
+ cell.place(mlocation{1, 0.5}, "exp2syn");
+ cell.place(mlocation{1, 0.7}, "expsyn");
+ cell.place(mlocation{1, 0.9}, "exp2syn");
fvm_discretization D = fvm_discretize({cell}, neuron_parameter_defaults);
fvm_mechanism_data M = fvm_build_mechanism_data(gprop_no_coalesce, {cell}, D);
@@ -438,10 +481,10 @@ TEST(fvm_layout, coalescing_synapses) {
cable_cell cell = make_cell_ball_and_stick();
// Add synapses of two varieties.
- cell.add_synapse({1, 0.3}, "expsyn");
- cell.add_synapse({1, 0.3}, "expsyn");
- cell.add_synapse({1, 0.7}, "expsyn");
- cell.add_synapse({1, 0.7}, "expsyn");
+ cell.place(mlocation{1, 0.3}, "expsyn");
+ cell.place(mlocation{1, 0.3}, "expsyn");
+ cell.place(mlocation{1, 0.7}, "expsyn");
+ cell.place(mlocation{1, 0.7}, "expsyn");
fvm_discretization D = fvm_discretize({cell}, neuron_parameter_defaults);
fvm_mechanism_data M = fvm_build_mechanism_data(gprop_coalesce, {cell}, D);
@@ -454,74 +497,80 @@ TEST(fvm_layout, coalescing_synapses) {
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));
- cell.add_synapse({1, 0.3}, syn_desc("expsyn", 0, 0.2));
- cell.add_synapse({1, 0.3}, syn_desc("expsyn", 0.1, 0.2));
- cell.add_synapse({1, 0.7}, syn_desc("expsyn", 0.1, 0.2));
+ cell.place(mlocation{1, 0.3}, syn_desc("expsyn", 0, 0.2));
+ cell.place(mlocation{1, 0.3}, syn_desc("expsyn", 0, 0.2));
+ cell.place(mlocation{1, 0.3}, syn_desc("expsyn", 0.1, 0.2));
+ cell.place(mlocation{1, 0.7}, syn_desc("expsyn", 0.1, 0.2));
fvm_discretization D = fvm_discretize({cell}, neuron_parameter_defaults);
fvm_mechanism_data M = fvm_build_mechanism_data(gprop_coalesce, {cell}, D);
- auto &expsyn_config = M.mechanisms.at("expsyn");
- EXPECT_EQ(ivec({2, 2, 4}), expsyn_config.cv);
- EXPECT_EQ(ivec({2, 1, 1}), expsyn_config.multiplicity);
- EXPECT_EQ(fvec({0, 0.1, 0.1}), expsyn_config.param_values[0].second);
- EXPECT_EQ(fvec({0.2, 0.2, 0.2}), expsyn_config.param_values[1].second);
+ std::vector<exp_instance> instances{
+ exp_instance(2, L{0, 1}, 0., 0.2),
+ exp_instance(2, L{2}, 0.1, 0.2),
+ exp_instance(4, L{3}, 0.1, 0.2),
+ };
+ auto& config = M.mechanisms.at("expsyn");
+ for (auto& instance: instances) {
+ EXPECT_TRUE(instance.is_in(config));
+ }
}
{
cable_cell cell = make_cell_ball_and_stick();
// Add synapses of two varieties.
- cell.add_synapse({1, 0.7}, syn_desc("expsyn", 0, 3));
- cell.add_synapse({1, 0.7}, syn_desc("expsyn", 1, 3));
- cell.add_synapse({1, 0.7}, syn_desc("expsyn", 0, 3));
- cell.add_synapse({1, 0.7}, syn_desc("expsyn", 1, 3));
- cell.add_synapse({1, 0.3}, syn_desc("expsyn", 0, 2));
- cell.add_synapse({1, 0.3}, syn_desc("expsyn", 1, 2));
- cell.add_synapse({1, 0.3}, syn_desc("expsyn", 0, 2));
- cell.add_synapse({1, 0.3}, syn_desc("expsyn", 1, 2));
+ cell.place(mlocation{1, 0.7}, syn_desc("expsyn", 0, 3));
+ cell.place(mlocation{1, 0.7}, syn_desc("expsyn", 1, 3));
+ cell.place(mlocation{1, 0.7}, syn_desc("expsyn", 0, 3));
+ cell.place(mlocation{1, 0.7}, syn_desc("expsyn", 1, 3));
+ cell.place(mlocation{1, 0.3}, syn_desc("expsyn", 0, 2));
+ cell.place(mlocation{1, 0.3}, syn_desc("expsyn", 1, 2));
+ cell.place(mlocation{1, 0.3}, syn_desc("expsyn", 0, 2));
+ cell.place(mlocation{1, 0.3}, syn_desc("expsyn", 1, 2));
fvm_discretization D = fvm_discretize({cell}, neuron_parameter_defaults);
fvm_mechanism_data M = fvm_build_mechanism_data(gprop_coalesce, {cell}, D);
- auto &expsyn_config = M.mechanisms.at("expsyn");
- EXPECT_EQ(ivec({2, 2, 4, 4}), expsyn_config.cv);
- EXPECT_EQ(ivec({4, 6, 5, 7, 0, 2, 1, 3}), expsyn_config.target);
- EXPECT_EQ(ivec({2, 2, 2, 2}), expsyn_config.multiplicity);
- EXPECT_EQ(fvec({0, 1, 0, 1}), expsyn_config.param_values[0].second);
- EXPECT_EQ(fvec({2, 2, 3, 3}), expsyn_config.param_values[1].second);
+ std::vector<exp_instance> instances{
+ exp_instance(2, L{4, 6}, 0.0, 2.0),
+ exp_instance(2, L{5, 7}, 1.0, 2.0),
+ exp_instance(4, L{0, 2}, 0.0, 3.0),
+ exp_instance(4, L{1, 3}, 1.0, 3.0),
+ };
+ auto& config = M.mechanisms.at("expsyn");
+ for (auto& instance: instances) {
+ EXPECT_TRUE(instance.is_in(config));
+ }
}
{
cable_cell cell = make_cell_ball_and_stick();
// Add synapses of two varieties.
- cell.add_synapse({1, 0.3}, syn_desc("expsyn", 1, 2));
- cell.add_synapse({1, 0.3}, syn_desc_2("exp2syn", 4, 1));
- cell.add_synapse({1, 0.3}, syn_desc("expsyn", 1, 2));
- cell.add_synapse({1, 0.3}, syn_desc("expsyn", 5, 1));
- cell.add_synapse({1, 0.3}, syn_desc_2("exp2syn", 1, 3));
- cell.add_synapse({1, 0.3}, syn_desc("expsyn", 1, 2));
- cell.add_synapse({1, 0.7}, syn_desc_2("exp2syn", 2, 2));
- cell.add_synapse({1, 0.7}, syn_desc_2("exp2syn", 2, 1));
- cell.add_synapse({1, 0.7}, syn_desc_2("exp2syn", 2, 1));
- cell.add_synapse({1, 0.7}, syn_desc_2("exp2syn", 2, 2));
+ cell.place(mlocation{1, 0.3}, syn_desc("expsyn", 1, 2));
+ cell.place(mlocation{1, 0.3}, syn_desc_2("exp2syn", 4, 1));
+ cell.place(mlocation{1, 0.3}, syn_desc("expsyn", 1, 2));
+ cell.place(mlocation{1, 0.3}, syn_desc("expsyn", 5, 1));
+ cell.place(mlocation{1, 0.3}, syn_desc_2("exp2syn", 1, 3));
+ cell.place(mlocation{1, 0.3}, syn_desc("expsyn", 1, 2));
+ cell.place(mlocation{1, 0.7}, syn_desc_2("exp2syn", 2, 2));
+ cell.place(mlocation{1, 0.7}, syn_desc_2("exp2syn", 2, 1));
+ cell.place(mlocation{1, 0.7}, syn_desc_2("exp2syn", 2, 1));
+ cell.place(mlocation{1, 0.7}, syn_desc_2("exp2syn", 2, 2));
fvm_discretization D = fvm_discretize({cell}, neuron_parameter_defaults);
fvm_mechanism_data M = fvm_build_mechanism_data(gprop_coalesce, {cell}, D);
- auto &expsyn_config = M.mechanisms.at("expsyn");
- EXPECT_EQ(ivec({2, 2}), expsyn_config.cv);
- EXPECT_EQ(ivec({0, 2, 5, 3}), expsyn_config.target);
- EXPECT_EQ(ivec({3, 1}), expsyn_config.multiplicity);
- EXPECT_EQ(fvec({1, 5}), expsyn_config.param_values[0].second);
- EXPECT_EQ(fvec({2, 1}), expsyn_config.param_values[1].second);
+ for (auto &instance: {exp_instance(2, L{0,2,5}, 1, 2),
+ exp_instance(2, L{3}, 5, 1)}) {
+ EXPECT_TRUE(instance.is_in(M.mechanisms.at("expsyn")));
+ }
- auto &exp2syn_config = M.mechanisms.at("exp2syn");
- EXPECT_EQ(ivec({2, 2, 4, 4}), exp2syn_config.cv);
- EXPECT_EQ(ivec({4, 1, 7, 8, 6, 9}), exp2syn_config.target);
- EXPECT_EQ(ivec({1, 1, 2, 2}), exp2syn_config.multiplicity);
- EXPECT_EQ(fvec({1, 4, 2, 2}), exp2syn_config.param_values[0].second);
- EXPECT_EQ(fvec({3, 1, 1, 2}), exp2syn_config.param_values[1].second);
+ for (auto &instance: {exp_instance(2, L{4}, 1, 3),
+ exp_instance(2, L{1}, 4, 1),
+ exp_instance(4, L{7,8}, 2, 1),
+ exp_instance(4, L{6,9}, 2, 2)}) {
+ EXPECT_TRUE(instance.is_in(M.mechanisms.at("exp2syn")));
+ }
}
}
@@ -543,14 +592,14 @@ TEST(fvm_layout, synapse_targets) {
return mechanism_desc(name).set("e", syn_e.at(idx));
};
- cells[0].add_synapse({1, 0.9}, syn_desc("expsyn", 0));
- cells[0].add_synapse({0, 0.5}, syn_desc("expsyn", 1));
- cells[0].add_synapse({1, 0.4}, syn_desc("expsyn", 2));
+ cells[0].place(mlocation{1, 0.9}, syn_desc("expsyn", 0));
+ cells[0].place(mlocation{0, 0.5}, syn_desc("expsyn", 1));
+ cells[0].place(mlocation{1, 0.4}, syn_desc("expsyn", 2));
- cells[1].add_synapse({2, 0.4}, syn_desc("exp2syn", 3));
- cells[1].add_synapse({1, 0.4}, syn_desc("exp2syn", 4));
- cells[1].add_synapse({3, 0.4}, syn_desc("expsyn", 5));
- cells[1].add_synapse({3, 0.7}, syn_desc("exp2syn", 6));
+ cells[1].place(mlocation{2, 0.4}, syn_desc("exp2syn", 3));
+ cells[1].place(mlocation{1, 0.4}, syn_desc("exp2syn", 4));
+ cells[1].place(mlocation{3, 0.4}, syn_desc("expsyn", 5));
+ cells[1].place(mlocation{3, 0.7}, syn_desc("exp2syn", 6));
cable_cell_global_properties gprop;
gprop.default_parameters = neuron_parameter_defaults;
@@ -639,9 +688,9 @@ TEST(fvm_layout, density_norm_area) {
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);
- c.add_cable(1, section_kind::dendrite, 0.5, 0.1, 200);
- c.add_cable(1, section_kind::dendrite, 0.4, 0.4, 150);
+ c.add_cable(0, make_segment<cable_segment>(section_kind::dendrite, 0.5, 0.5, 100));
+ c.add_cable(1, make_segment<cable_segment>(section_kind::dendrite, 0.5, 0.1, 200));
+ c.add_cable(1, make_segment<cable_segment>(section_kind::dendrite, 0.4, 0.4, 150));
auto& segs = c.segments();
@@ -803,9 +852,9 @@ TEST(fvm_layout, ion_weights) {
auto construct_cell = [](cable_cell& c) {
c.add_soma(5);
- c.add_cable(0, section_kind::dendrite, 0.5, 0.5, 100);
- c.add_cable(1, section_kind::dendrite, 0.5, 0.5, 200);
- c.add_cable(1, section_kind::dendrite, 0.5, 0.5, 100);
+ c.add_cable(0, make_segment<cable_segment>(section_kind::dendrite, 0.5, 0.5, 100));
+ c.add_cable(1, make_segment<cable_segment>(section_kind::dendrite, 0.5, 0.5, 200));
+ c.add_cable(1, make_segment<cable_segment>(section_kind::dendrite, 0.5, 0.5, 100));
for (auto& s: c.segments()) s->set_compartments(1);
};
@@ -875,9 +924,9 @@ TEST(fvm_layout, revpot) {
auto construct_cell = [](cable_cell& c) {
c.add_soma(5);
- c.add_cable(0, section_kind::dendrite, 0.5, 0.5, 100);
- c.add_cable(1, section_kind::dendrite, 0.5, 0.5, 200);
- c.add_cable(1, section_kind::dendrite, 0.5, 0.5, 100);
+ c.add_cable(0, make_segment<cable_segment>(section_kind::dendrite, 0.5, 0.5, 100));
+ c.add_cable(1, make_segment<cable_segment>(section_kind::dendrite, 0.5, 0.5, 200));
+ c.add_cable(1, make_segment<cable_segment>(section_kind::dendrite, 0.5, 0.5, 100));
for (auto& s: c.segments()) s->set_compartments(1);
diff --git a/test/unit/test_fvm_lowered.cpp b/test/unit/test_fvm_lowered.cpp
index 42726b6b15511743a58fdec44518521cc4f23fc9..a82132f497579e916fee647bd3a7fab7c84b6798 100644
--- a/test/unit/test_fvm_lowered.cpp
+++ b/test/unit/test_fvm_lowered.cpp
@@ -94,7 +94,7 @@ public:
arb::util::unique_any get_cell_description(cell_gid_type gid) const override {
cable_cell c;
c.add_soma(20);
- c.add_gap_junction({0, 1});
+ c.place(mlocation{0, 1}, gap_junction_site{});
return {std::move(c)};
}
@@ -162,7 +162,7 @@ public:
arb::util::unique_any get_cell_description(cell_gid_type) const override {
cable_cell c;
c.add_soma(20);
- c.add_gap_junction({0,1});
+ c.place(mlocation{0,1}, gap_junction_site{});
return {std::move(c)};
}
@@ -257,12 +257,12 @@ TEST(fvm_lowered, target_handles) {
EXPECT_EQ(cells[1].num_segments(), 4u);
// (in increasing target order)
- cells[0].add_synapse({1, 0.4}, "expsyn");
- cells[0].add_synapse({0, 0.5}, "expsyn");
- cells[1].add_synapse({2, 0.2}, "exp2syn");
- cells[1].add_synapse({2, 0.8}, "expsyn");
+ cells[0].place(mlocation{1, 0.4}, "expsyn");
+ cells[0].place(mlocation{0, 0.5}, "expsyn");
+ cells[1].place(mlocation{2, 0.2}, "exp2syn");
+ cells[1].place(mlocation{2, 0.8}, "expsyn");
- cells[1].add_detector({0, 0}, 3.3);
+ cells[1].place(mlocation{0, 0}, threshold_detector{3.3});
std::vector<target_handle> targets;
std::vector<fvm_index_type> cell_to_intdom;
@@ -321,8 +321,8 @@ TEST(fvm_lowered, stimulus) {
std::vector<cable_cell> cells;
cells.push_back(make_cell_ball_and_stick(false));
- cells[0].add_stimulus({1,1}, {5., 80., 0.3});
- cells[0].add_stimulus({0,0.5}, {1., 2., 0.1});
+ cells[0].place(mlocation{1,1}, i_clamp{5., 80., 0.3});
+ cells[0].place(mlocation{0,0.5}, i_clamp{1., 2., 0.1});
const fvm_size_type soma_cv = 0u;
const fvm_size_type tip_cv = 5u;
@@ -401,7 +401,7 @@ TEST(fvm_lowered, derived_mechs) {
for (int i = 0; i<3; ++i) {
cable_cell& c = cells[i];
c.add_soma(6.0);
- c.add_cable(0, section_kind::dendrite, 0.5, 0.5, 100);
+ c.add_cable(0, make_segment<cable_segment>(section_kind::dendrite, 0.5, 0.5, 100));
c.segment(1)->set_compartments(4);
for (auto& seg: c.segments()) {
@@ -612,7 +612,7 @@ TEST(fvm_lowered, point_ionic_current) {
double soma_area_m2 = 4*math::pi<double>*r*r*1e-12; // [m²]
// Event weight is translated by point_ica_current into a current contribution in nA.
- c.add_synapse({0u, 0.5}, "point_ica_current");
+ c.place(mlocation{0u, 0.5}, "point_ica_current");
cable1d_recipe rec(c);
rec.catalogue() = make_unit_test_catalogue();
@@ -676,9 +676,9 @@ TEST(fvm_lowered, weighted_write_ion) {
cable_cell c;
c.add_soma(5);
- c.add_cable(0, section_kind::dendrite, 0.5, 0.5, 100);
- c.add_cable(1, section_kind::dendrite, 0.5, 0.5, 200);
- c.add_cable(1, section_kind::dendrite, 0.5, 0.5, 100);
+ c.add_cable(0, make_segment<cable_segment>(section_kind::dendrite, 0.5, 0.5, 100));
+ c.add_cable(1, make_segment<cable_segment>(section_kind::dendrite, 0.5, 0.5, 200));
+ c.add_cable(1, make_segment<cable_segment>(section_kind::dendrite, 0.5, 0.5, 100));
for (auto& s: c.segments()) s->set_compartments(1);
@@ -770,15 +770,15 @@ TEST(fvm_lowered, gj_coords_simple) {
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.add_cable(0, make_segment<cable_segment>(section_kind::dendrite, 0.3, 0.2, 10));
c.segment(1)->set_compartments(5);
- c.add_gap_junction({1, 0.8});
+ c.place(mlocation{1, 0.8}, gap_junction_site{});
cells.push_back(std::move(c));
d.add_soma(2.4);
- d.add_cable(0, section_kind::dendrite, 0.3, 0.2, 10);
+ d.add_cable(0, make_segment<cable_segment>(section_kind::dendrite, 0.3, 0.2, 10));
d.segment(1)->set_compartments(2);
- d.add_gap_junction({1, 1});
+ d.place(mlocation{1, 1}, gap_junction_site{});
cells.push_back(std::move(d));
fvm_discretization D = fvm_discretize(cells, neuron_parameter_defaults);
@@ -846,41 +846,41 @@ TEST(fvm_lowered, gj_coords_complex) {
// Make 3 cells
c0.add_soma(2.1);
- c0.add_cable(0, section_kind::dendrite, 0.3, 0.2, 8);
+ c0.add_cable(0, make_segment<cable_segment>(section_kind::dendrite, 0.3, 0.2, 8));
c0.segment(1)->set_compartments(4);
c1.add_soma(1.4);
- c1.add_cable(0, section_kind::dendrite, 0.3, 0.5, 12);
+ c1.add_cable(0, make_segment<cable_segment>(section_kind::dendrite, 0.3, 0.5, 12));
c1.segment(1)->set_compartments(6);
- c1.add_cable(1, section_kind::dendrite, 0.3, 0.2, 9);
+ c1.add_cable(1, make_segment<cable_segment>(section_kind::dendrite, 0.3, 0.2, 9));
c1.segment(2)->set_compartments(3);
- c1.add_cable(1, section_kind::dendrite, 0.2, 0.2, 15);
+ c1.add_cable(1, make_segment<cable_segment>(section_kind::dendrite, 0.2, 0.2, 15));
c1.segment(3)->set_compartments(5);
c2.add_soma(2.9);
- c2.add_cable(0, section_kind::dendrite, 0.3, 0.5, 4);
+ c2.add_cable(0, make_segment<cable_segment>(section_kind::dendrite, 0.3, 0.5, 4));
c2.segment(1)->set_compartments(2);
- c2.add_cable(1, section_kind::dendrite, 0.4, 0.2, 6);
+ c2.add_cable(1, make_segment<cable_segment>(section_kind::dendrite, 0.4, 0.2, 6));
c2.segment(2)->set_compartments(2);
- c2.add_cable(1, section_kind::dendrite, 0.1, 0.2, 8);
+ c2.add_cable(1, make_segment<cable_segment>(section_kind::dendrite, 0.1, 0.2, 8));
c2.segment(3)->set_compartments(2);
- c2.add_cable(2, section_kind::dendrite, 0.2, 0.2, 4);
+ c2.add_cable(2, make_segment<cable_segment>(section_kind::dendrite, 0.2, 0.2, 4));
c2.segment(4)->set_compartments(2);
- c2.add_cable(2, section_kind::dendrite, 0.2, 0.2, 4);
+ c2.add_cable(2, make_segment<cable_segment>(section_kind::dendrite, 0.2, 0.2, 4));
c2.segment(5)->set_compartments(2);
// Add 5 gap junctions
- c0.add_gap_junction({1, 1});
- c0.add_gap_junction({1, 0.5});
+ c0.place(mlocation{1, 1}, gap_junction_site{});
+ c0.place(mlocation{1, 0.5}, gap_junction_site{});
- c1.add_gap_junction({2, 1});
- c1.add_gap_junction({1, 1});
- c1.add_gap_junction({1, 0.45});
- c1.add_gap_junction({1, 0.1});
+ c1.place(mlocation{2, 1}, gap_junction_site{});
+ c1.place(mlocation{1, 1}, gap_junction_site{});
+ c1.place(mlocation{1, 0.45}, gap_junction_site{});
+ c1.place(mlocation{1, 0.1}, gap_junction_site{});
- c2.add_gap_junction({1, 0.5});
- c2.add_gap_junction({4, 1});
- c2.add_gap_junction({2, 1});
+ c2.place(mlocation{1, 0.5}, gap_junction_site{});
+ c2.place(mlocation{4, 1}, gap_junction_site{});
+ c2.place(mlocation{2, 1}, gap_junction_site{});
cells.push_back(std::move(c0));
cells.push_back(std::move(c1));
@@ -958,7 +958,7 @@ TEST(fvm_lowered, cell_group_gj) {
cable_cell c;
c.add_soma(2.1);
if (i % 2 == 0) {
- c.add_gap_junction({0, 1});
+ c.place(mlocation{0, 1}, gap_junction_site{});
}
if (i < 10) {
cell_group0.push_back(std::move(c));
diff --git a/test/unit/test_mc_cell_group.cpp b/test/unit/test_mc_cell_group.cpp
index 5a453dd6d6056979e14c311e97222f05c26ca330..25415273f1d19c78a1fc0ec5710ff3eeb94f0c87 100644
--- a/test/unit/test_mc_cell_group.cpp
+++ b/test/unit/test_mc_cell_group.cpp
@@ -23,7 +23,7 @@ namespace {
cable_cell make_cell() {
auto c = make_cell_ball_and_stick();
- c.add_detector({0, 0}, 0);
+ c.place(mlocation{0, 0}, threshold_detector{0});
c.segment(1)->set_compartments(101);
return c;
@@ -63,7 +63,7 @@ TEST(mc_cell_group, sources) {
for (int i=0; i<20; ++i) {
cells.push_back(make_cell());
if (i==0 || i==3 || i==17) {
- cells.back().add_detector({1, 0.3}, 2.3);
+ cells.back().place(mlocation{1, 0.3}, threshold_detector{2.3});
}
EXPECT_EQ(1u + (i==0 || i==3 || i==17), cells.back().detectors().size());
diff --git a/test/unit/test_mc_cell_group_gpu.cpp b/test/unit/test_mc_cell_group_gpu.cpp
index 58524dce64d37c09177d667897a043376ac9a62b..05b3d68193969ea63461e956fc3be763948b26cc 100644
--- a/test/unit/test_mc_cell_group_gpu.cpp
+++ b/test/unit/test_mc_cell_group_gpu.cpp
@@ -21,7 +21,7 @@ namespace {
cable_cell make_cell() {
auto c = make_cell_ball_and_stick();
- c.add_detector({0, 0}, 0);
+ c.place(mlocation{0, 0}, threshold_detector{0});
c.segment(1)->set_compartments(101);
return c;
diff --git a/test/unit/test_probe.cpp b/test/unit/test_probe.cpp
index 5afba4f3e89a1f040eaf2e6764a4d58b49192464..7ac92d3c395a403d72ae9ef15f76535b148ac4ad 100644
--- a/test/unit/test_probe.cpp
+++ b/test/unit/test_probe.cpp
@@ -24,7 +24,7 @@ TEST(probe, fvm_lowered_cell) {
cable_cell bs = make_cell_ball_and_stick(false);
i_clamp stim(0, 100, 0.3);
- bs.add_stimulus({1, 1}, stim);
+ bs.place(mlocation{1, 1}, stim);
cable1d_recipe rec(bs);
diff --git a/test/unit/test_synapses.cpp b/test/unit/test_synapses.cpp
index b7983f1ebadbb90924da1a461c3c1b52b2a68ee6..03695d9345eebe3cbc8cf267d0ee50810d6a7d0d 100644
--- a/test/unit/test_synapses.cpp
+++ b/test/unit/test_synapses.cpp
@@ -38,9 +38,9 @@ TEST(synapses, add_to_cell) {
auto soma = cell.add_soma(12.6157/2.0);
soma->add_mechanism("hh");
- cell.add_synapse({0, 0.1}, "expsyn");
- cell.add_synapse({1, 0.2}, "exp2syn");
- cell.add_synapse({0, 0.3}, "expsyn");
+ cell.place(mlocation{0, 0.1}, "expsyn");
+ cell.place(mlocation{0, 0.2}, "exp2syn");
+ cell.place(mlocation{0, 0.3}, "expsyn");
EXPECT_EQ(3u, cell.synapses().size());
const auto& syns = cell.synapses();
@@ -49,13 +49,16 @@ TEST(synapses, add_to_cell) {
EXPECT_EQ(syns[0].location.pos, 0.1);
EXPECT_EQ(syns[0].mechanism.name(), "expsyn");
- EXPECT_EQ(syns[1].location.branch, 1u);
+ EXPECT_EQ(syns[1].location.branch, 0u);
EXPECT_EQ(syns[1].location.pos, 0.2);
EXPECT_EQ(syns[1].mechanism.name(), "exp2syn");
EXPECT_EQ(syns[2].location.branch, 0u);
EXPECT_EQ(syns[2].location.pos, 0.3);
EXPECT_EQ(syns[2].mechanism.name(), "expsyn");
+
+ // adding a synapse to an invalid branch location should throw.
+ EXPECT_THROW(cell.place(mlocation{1, 0.3}, "expsyn"), arb::cable_cell_error);
}
template <typename Seq>