From cfe5f4bf2be8915ea3d1296e30c8e1655b3315d8 Mon Sep 17 00:00:00 2001
From: Sam Yates <halfflat@gmail.com>
Date: Tue, 6 Sep 2016 11:50:05 +0200
Subject: [PATCH] Address PR#92 review comments.
Note: use of non-const reference in `mechanism_catalogue::make`
is an interim solution.
---
src/cell_group.hpp | 6 +--
src/communication/communicator.hpp | 2 +-
src/fvm_multicell.hpp | 49 ++++++++++---------
src/mechanism.hpp | 11 ++---
src/mechanism_catalogue.hpp | 5 +-
src/util/partition.hpp | 2 +
.../test_mpi_gather_all.cpp | 2 +-
7 files changed, 39 insertions(+), 38 deletions(-)
diff --git a/src/cell_group.hpp b/src/cell_group.hpp
index 30bdd99d..86a90593 100644
--- a/src/cell_group.hpp
+++ b/src/cell_group.hpp
@@ -249,13 +249,13 @@ private:
/// use handle partition to get index from id
template <typename Divisions>
- std::size_t handle_partition_lookup(const Divisions& divisions_, cell_member_type id) const {
+ std::size_t handle_partition_lookup(const Divisions& divisions, cell_member_type id) const {
// NB: without any assertion checking, this would just be:
- // return divisions_[id.gid-gid_base_]+id.index;
+ // return divisions[id.gid-gid_base_]+id.index;
EXPECTS(id.gid>=gid_base_);
- auto handle_partition = util::partition_view(divisions_);
+ auto handle_partition = util::partition_view(divisions);
EXPECTS(id.gid-gid_base_<handle_partition.size());
auto ival = handle_partition[id.gid-gid_base_];
diff --git a/src/communication/communicator.hpp b/src/communication/communicator.hpp
index 6d1377f4..764020dc 100644
--- a/src/communication/communicator.hpp
+++ b/src/communication/communicator.hpp
@@ -136,7 +136,7 @@ public:
private:
std::size_t cell_group_index(cell_gid_type cell_gid) const {
EXPECTS(is_local_cell(cell_gid));
- return cell_gid_partition_.find(cell_gid)-cell_gid_partition_.begin();
+ return cell_gid_partition_.index(cell_gid);
}
std::vector<connection_type> connections_;
diff --git a/src/fvm_multicell.hpp b/src/fvm_multicell.hpp
index 1c9c799a..72d22b25 100644
--- a/src/fvm_multicell.hpp
+++ b/src/fvm_multicell.hpp
@@ -214,7 +214,7 @@ private:
// perform area and capacitance calculation on initialization
void compute_cv_area_unnormalized_capacitance(
- std::pair<size_type, size_type> comps, const segment* seg, index_type &parent);
+ std::pair<size_type, size_type> comp_ival, const segment* seg, index_type &parent);
};
////////////////////////////////////////////////////////////////////////////////
@@ -223,24 +223,25 @@ private:
template <typename T, typename I>
void fvm_multicell<T, I>::compute_cv_area_unnormalized_capacitance(
- std::pair<size_type, size_type> comps,
+ std::pair<size_type, size_type> comp_ival,
const segment* seg,
index_type &parent)
{
using util::left;
using util::right;
+ using util::size;
// precondition: group_parent_index[j] holds the correct value for
// j in [base_comp, base_comp+segment.num_compartments()].
- auto ncomp = comps.second-comps.first;
+ auto ncomp = comp_ival.second-comp_ival.first;
if (auto soma = seg->as_soma()) {
// confirm assumption that there is one compartment in soma
if (ncomp!=1) {
throw std::logic_error("soma allocated more than one compartment");
}
- auto i = comps.first;
+ auto i = comp_ival.first;
auto area = math::area_sphere(soma->radius());
cv_areas_[i] += area;
@@ -266,10 +267,10 @@ void fvm_multicell<T, I>::compute_cv_area_unnormalized_capacitance(
auto r_L = cable->mechanism("membrane").get("r_L").value;
const auto& compartments = cable->compartments();
- EXPECTS(util::size(compartments)==ncomp);
+ EXPECTS(size(compartments)==ncomp);
- for (auto i: util::make_span(comps)) {
- const auto& c = compartments[i-comps.first];
+ for (auto i: util::make_span(comp_ival)) {
+ const auto& c = compartments[i-comp_ival.first];
auto j = parent[i];
auto radius_center = math::mean(c.radius);
@@ -308,11 +309,11 @@ void fvm_multicell<T, I>::initialize(
size_type detectors_count = 0u;
size_type targets_count = 0u;
size_type probes_count = 0u;
- size_type detectors_size = util::size(detector_handles);
- size_type targets_size = util::size(target_handles);
- size_type probes_size = util::size(probe_handles);
+ size_type detectors_size = size(detector_handles);
+ size_type targets_size = size(target_handles);
+ size_type probes_size = size(probe_handles);
- auto ncell = util::size(cells);
+ auto ncell = size(cells);
auto cell_num_compartments =
transform_view(cells, [](const cell& c) { return c.num_compartments(); });
@@ -325,7 +326,7 @@ void fvm_multicell<T, I>::initialize(
face_alpha_ = vector_type{ncomp, T{0}};
cv_capacitance_ = vector_type{ncomp, T{0}};
current_ = vector_type{ncomp, T{0}};
- voltage_ = vector_type{ncomp, T{0}};
+ voltage_ = vector_type{ncomp, T{resting_potential_}};
// create maps for mechanism initialization.
std::map<std::string, std::vector<std::pair<size_type, size_type>>> mech_map;
@@ -342,12 +343,12 @@ void fvm_multicell<T, I>::initialize(
for (size_type i = 0; i<ncell; ++i) {
const auto& c = cells[i];
- auto comps = cell_comp_part[i];
+ auto comp_ival = cell_comp_part[i];
auto graph = c.model();
- for (auto k: make_span(comps)) {
- group_parent_index[k] = graph.parent_index[k-comps.first]+comps.first;
+ for (auto k: make_span(comp_ival)) {
+ group_parent_index[k] = graph.parent_index[k-comp_ival.first]+comp_ival.first;
}
auto seg_num_compartments =
@@ -355,17 +356,17 @@ void fvm_multicell<T, I>::initialize(
auto nseg = seg_num_compartments.size();
std::vector<cell_lid_type> seg_comp_bounds;
- auto seg_comp_part = make_partition(seg_comp_bounds, seg_num_compartments, comps.first);
+ auto seg_comp_part = make_partition(seg_comp_bounds, seg_num_compartments, comp_ival.first);
for (size_type j = 0; j<nseg; ++j) {
const auto& seg = c.segment(j);
- const auto& seg_comps = seg_comp_part[j];
+ const auto& seg_comp_ival = seg_comp_part[j];
- compute_cv_area_unnormalized_capacitance(seg_comps, seg, group_parent_index);
+ compute_cv_area_unnormalized_capacitance(seg_comp_ival, seg, group_parent_index);
for (const auto& mech: seg->mechanisms()) {
if (mech.name()!="membrane") {
- mech_map[mech.name()].push_back(seg_comps);
+ mech_map[mech.name()].push_back(seg_comp_ival);
}
}
}
@@ -386,7 +387,7 @@ void fvm_multicell<T, I>::initialize(
auto& map_entry = syn_mech_map[syn_mech_index];
- size_type syn_comp = comps.first+find_compartment_index(syn.location, graph);
+ size_type syn_comp = comp_ival.first+find_compartment_index(syn.location, graph);
size_type syn_index = map_entry.size();
map_entry.push_back(syn_comp);
@@ -395,13 +396,13 @@ void fvm_multicell<T, I>::initialize(
}
// normalize capacitance across cell
- for (auto k: make_span(comps)) {
+ for (auto k: make_span(comp_ival)) {
cv_capacitance_[k] /= cv_areas_[k];
}
// add the stimuli
for (const auto& stim: c.stimuli()) {
- auto idx = comps.first+find_compartment_index(stim.location, graph);
+ auto idx = comp_ival.first+find_compartment_index(stim.location, graph);
stimuli_.push_back({idx, stim.clamp});
}
@@ -409,7 +410,7 @@ void fvm_multicell<T, I>::initialize(
for (const auto& detector: c.detectors()) {
EXPECTS(detectors_count < detectors_size);
- auto comp = comps.first+find_compartment_index(detector.location, graph);
+ auto comp = comp_ival.first+find_compartment_index(detector.location, graph);
*detector_hi++ = comp;
++detectors_count;
}
@@ -418,7 +419,7 @@ void fvm_multicell<T, I>::initialize(
for (const auto& probe: c.probes()) {
EXPECTS(probes_count < probes_size);
- auto comp = comps.first+find_compartment_index(probe.location, graph);
+ auto comp = comp_ival.first+find_compartment_index(probe.location, graph);
switch (probe.kind) {
case probeKind::membrane_voltage:
*probe_hi++ = {&fvm_multicell::voltage_, comp};
diff --git a/src/mechanism.hpp b/src/mechanism.hpp
index c9c801fd..ce978660 100644
--- a/src/mechanism.hpp
+++ b/src/mechanism.hpp
@@ -1,7 +1,9 @@
#pragma once
+#include <algorithm>
#include <memory>
#include <string>
+#include <util/meta.hpp>
#include "indexed_view.hpp"
#include "ion.hpp"
@@ -16,9 +18,7 @@ enum class mechanismKind {point, density};
template <typename T, typename I>
class mechanism {
-
public:
-
using value_type = T;
using size_type = I;
@@ -31,11 +31,8 @@ public:
using ion_type = ion<value_type, size_type>;
- mechanism(view_type vec_v, view_type vec_i, index_view node_index)
- : vec_v_(vec_v)
- , vec_i_(vec_i)
- , node_index_(node_index)
- , vec_area_(nullptr, 0)
+ mechanism(view_type vec_v, view_type vec_i, index_view node_index):
+ vec_v_(vec_v), vec_i_(vec_i), node_index_(node_index), vec_area_(nullptr, 0)
{}
std::size_t size() const
diff --git a/src/mechanism_catalogue.hpp b/src/mechanism_catalogue.hpp
index aecea5ce..7fb2927c 100644
--- a/src/mechanism_catalogue.hpp
+++ b/src/mechanism_catalogue.hpp
@@ -24,14 +24,15 @@ struct catalogue {
const std::string& name,
view_type vec_v,
view_type vec_i,
- Indices node_indices)
+ Indices& node_indices)
{
auto entry = mech_map.find(name);
if (entry==mech_map.end()) {
throw std::out_of_range("no such mechanism");
}
- return entry->second(vec_v, vec_i, index_view{node_indices});
+ auto node_view = index_view{node_indices};
+ return entry->second(vec_v, vec_i, node_view);
}
static bool has(const std::string& name) {
diff --git a/src/util/partition.hpp b/src/util/partition.hpp
index 376b769e..425d41f1 100644
--- a/src/util/partition.hpp
+++ b/src/util/partition.hpp
@@ -36,6 +36,8 @@ public:
using base::back;
using base::empty;
+ // `npos` is returned by the `index()` method if the search fails;
+ // analogous to `std::string::npos`.
static constexpr size_type npos = static_cast<size_type>(-1);
partition_range() = default;
diff --git a/tests/global_communication/test_mpi_gather_all.cpp b/tests/global_communication/test_mpi_gather_all.cpp
index ed99089f..50fbf405 100644
--- a/tests/global_communication/test_mpi_gather_all.cpp
+++ b/tests/global_communication/test_mpi_gather_all.cpp
@@ -17,7 +17,7 @@ struct big_thing {
big_thing(int i): value_(i) {}
bool operator==(const big_thing& other) const {
- return value_==other.value_ && !memcmp(salt_, other.salt_, sizeof(salt_));
+ return value_==other.value_ && !std::memcmp(salt_, other.salt_, sizeof(salt_));
}
bool operator!=(const big_thing& other) const {
--
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