From 994e9169a37261b0ac6b58cae20a1a1b99d4886d Mon Sep 17 00:00:00 2001
From: Sam Yates <halfflat@gmail.com>
Date: Thu, 4 Aug 2016 12:32:44 +0200
Subject: [PATCH] Rename catypes.hpp, clarify cell_member_type use.
---
miniapp/miniapp.cpp | 2 +-
miniapp/trace_sampler.hpp | 2 +-
src/CMakeLists.txt | 2 +-
src/cell.hpp | 2 +-
src/cell_group.hpp | 12 +++++++---
src/cell_tree.hpp | 2 +-
src/{catypes.hpp => common_types.hpp} | 25 ++++++++++++++++----
src/{catypes_io.cpp => common_types_io.cpp} | 2 +-
src/communication/mpi_global_policy.hpp | 2 +-
src/compartment.hpp | 2 +-
src/connection.hpp | 2 +-
src/event_queue.hpp | 2 +-
src/model.hpp | 2 +-
src/segment.hpp | 2 +-
tests/unit/test_cell_group.cpp | 2 +-
tests/unit/test_fvm.cpp | 2 +-
tests/unit/test_probe.cpp | 2 +-
tests/validation/validate_ball_and_stick.cpp | 2 +-
tests/validation/validate_soma.cpp | 2 +-
tests/validation/validate_synapses.cpp | 2 +-
20 files changed, 48 insertions(+), 25 deletions(-)
rename src/{catypes.hpp => common_types.hpp} (57%)
rename src/{catypes_io.cpp => common_types_io.cpp} (83%)
diff --git a/miniapp/miniapp.cpp b/miniapp/miniapp.cpp
index 00adf7e5..898e478c 100644
--- a/miniapp/miniapp.cpp
+++ b/miniapp/miniapp.cpp
@@ -6,7 +6,7 @@
#include <json/src/json.hpp>
-#include <catypes.hpp>
+#include <common_types.hpp>
#include <cell.hpp>
#include <cell_group.hpp>
#include <fvm_cell.hpp>
diff --git a/miniapp/trace_sampler.hpp b/miniapp/trace_sampler.hpp
index 96ad269a..1e20bea2 100644
--- a/miniapp/trace_sampler.hpp
+++ b/miniapp/trace_sampler.hpp
@@ -3,7 +3,7 @@
#include <cstdlib>
#include <vector>
-#include <catypes.hpp>
+#include <common_types.hpp>
#include <cell.hpp>
#include <util/optional.hpp>
diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt
index 6b6de968..8e0db887 100644
--- a/src/CMakeLists.txt
+++ b/src/CMakeLists.txt
@@ -2,7 +2,7 @@ set(HEADERS
swcio.hpp
)
set(BASE_SOURCES
- catypes_io.cpp
+ common_types_io.cpp
cell.cpp
parameter_list.cpp
profiling/profiler.cpp
diff --git a/src/cell.hpp b/src/cell.hpp
index effdf925..74654928 100644
--- a/src/cell.hpp
+++ b/src/cell.hpp
@@ -5,7 +5,7 @@
#include <thread>
#include <vector>
-#include "catypes.hpp"
+#include "common_types.hpp"
#include "cell_tree.hpp"
#include "segment.hpp"
#include "stimulus.hpp"
diff --git a/src/cell_group.hpp b/src/cell_group.hpp
index 0143ce83..e70d4b0b 100644
--- a/src/cell_group.hpp
+++ b/src/cell_group.hpp
@@ -4,8 +4,8 @@
#include <functional>
#include <vector>
-#include <catypes.hpp>
#include <cell.hpp>
+#include <common_types.hpp>
#include <event_queue.hpp>
#include <spike.hpp>
#include <spike_source.hpp>
@@ -40,12 +40,18 @@ public:
{
initialize_cells();
- source_id_type source_id={gid_base_,0};
+ // Create spike detectors and associate them with globally unique source ids,
+ // as specified by cell gid and cell-local zero-based index.
+
+ cell_gid_type source_gid = gid_base_;
+ cell_lid_type source_lid = 0u;
+
for (auto& d : c.detectors()) {
+ cell_member_type source_id{source_gid, source_lid++};
+
spike_sources_.push_back({
source_id, spike_detector_type(cell_, d.location, d.threshold, 0.f)
});
- ++source_id.index;
}
}
diff --git a/src/cell_tree.hpp b/src/cell_tree.hpp
index 3bbcb3ef..ce06d69a 100644
--- a/src/cell_tree.hpp
+++ b/src/cell_tree.hpp
@@ -11,7 +11,7 @@
#include <vector/include/Vector.hpp>
-#include "catypes.hpp"
+#include "common_types.hpp"
#include "tree.hpp"
#include "util.hpp"
diff --git a/src/catypes.hpp b/src/common_types.hpp
similarity index 57%
rename from src/catypes.hpp
rename to src/common_types.hpp
index e2e9799b..da81ed5d 100644
--- a/src/catypes.hpp
+++ b/src/common_types.hpp
@@ -13,18 +13,35 @@
namespace nest {
namespace mc {
-// for identifying cells globally
+// For identifying cells globally.
+
using cell_gid_type = std::uint32_t;
-// for sizes of collections of cells
+// For sizes of collections of cells.
+
using cell_size_type = typename std::make_unsigned<cell_gid_type>::type;
-// for indexes into cell-local data
+// For indexes into cell-local data.
+//
+// Local indices for items within a particular cell-local collection should be
+// zero-based and numbered contiguously.
+
using cell_lid_type = std::uint32_t;
-// for counts of cell-local data
+// For counts of cell-local data.
+
using cell_local_size_type = typename std::make_unsigned<cell_lid_type>::type;
+// For global identification of an item of cell local data.
+//
+// Items of cell_member_type must:
+//
+// * be associated with a unique cell, identified by the member `gid`
+// (see: cell_gid_type);
+//
+// * identify an item within a cell-local collection by the member `index`
+// (see: cell_lid_type).
+
struct cell_member_type {
cell_gid_type gid;
cell_lid_type index;
diff --git a/src/catypes_io.cpp b/src/common_types_io.cpp
similarity index 83%
rename from src/catypes_io.cpp
rename to src/common_types_io.cpp
index 4c9d185f..ad6ca540 100644
--- a/src/catypes_io.cpp
+++ b/src/common_types_io.cpp
@@ -1,6 +1,6 @@
#include <iostream>
-#include <catypes.hpp>
+#include <common_types.hpp>
std::ostream& operator<<(std::ostream& O, nest::mc::cell_member_type m) {
return O << m.gid << ':' << m.index;
diff --git a/src/communication/mpi_global_policy.hpp b/src/communication/mpi_global_policy.hpp
index 54ded32c..0e9ec333 100644
--- a/src/communication/mpi_global_policy.hpp
+++ b/src/communication/mpi_global_policy.hpp
@@ -9,7 +9,7 @@
#include <vector>
#include <algorithms.hpp>
-#include <catypes.hpp>
+#include <common_types.hpp>
#include <communication/mpi.hpp>
#include <spike.hpp>
diff --git a/src/compartment.hpp b/src/compartment.hpp
index c69f622f..da6bbcf5 100644
--- a/src/compartment.hpp
+++ b/src/compartment.hpp
@@ -3,7 +3,7 @@
#include <iterator>
#include <utility>
-#include "catypes.hpp"
+#include "common_types.hpp"
namespace nest {
namespace mc {
diff --git a/src/connection.hpp b/src/connection.hpp
index 3ef99a9c..b9e40fb5 100644
--- a/src/connection.hpp
+++ b/src/connection.hpp
@@ -2,7 +2,7 @@
#include <cstdint>
-#include <catypes.hpp>
+#include <common_types.hpp>
#include <event_queue.hpp>
#include <spike.hpp>
diff --git a/src/event_queue.hpp b/src/event_queue.hpp
index b78cc0ca..31f6a5a1 100644
--- a/src/event_queue.hpp
+++ b/src/event_queue.hpp
@@ -4,7 +4,7 @@
#include <ostream>
#include <queue>
-#include "catypes.hpp"
+#include "common_types.hpp"
#include "util/optional.hpp"
namespace nest {
diff --git a/src/model.hpp b/src/model.hpp
index e819ff8b..3b773823 100644
--- a/src/model.hpp
+++ b/src/model.hpp
@@ -1,7 +1,7 @@
#include <cstdlib>
#include <vector>
-#include <catypes.hpp>
+#include <common_types.hpp>
#include <cell.hpp>
#include <cell_group.hpp>
#include <communication/communicator.hpp>
diff --git a/src/segment.hpp b/src/segment.hpp
index a7600da9..248306a6 100644
--- a/src/segment.hpp
+++ b/src/segment.hpp
@@ -4,7 +4,7 @@
#include <vector>
#include "algorithms.hpp"
-#include "catypes.hpp"
+#include "common_types.hpp"
#include "compartment.hpp"
#include "math.hpp"
#include "parameter_list.hpp"
diff --git a/tests/unit/test_cell_group.cpp b/tests/unit/test_cell_group.cpp
index 1f74cac9..3aed2220 100644
--- a/tests/unit/test_cell_group.cpp
+++ b/tests/unit/test_cell_group.cpp
@@ -1,6 +1,6 @@
#include "gtest.h"
-#include <catypes.hpp>
+#include <common_types.hpp>
#include <fvm_cell.hpp>
#include <cell_group.hpp>
diff --git a/tests/unit/test_fvm.cpp b/tests/unit/test_fvm.cpp
index ea8cd7da..c0ed438f 100644
--- a/tests/unit/test_fvm.cpp
+++ b/tests/unit/test_fvm.cpp
@@ -2,7 +2,7 @@
#include "gtest.h"
-#include <catypes.hpp>
+#include <common_types.hpp>
#include <cell.hpp>
#include <fvm_cell.hpp>
diff --git a/tests/unit/test_probe.cpp b/tests/unit/test_probe.cpp
index 888e710e..5af744d2 100644
--- a/tests/unit/test_probe.cpp
+++ b/tests/unit/test_probe.cpp
@@ -1,6 +1,6 @@
#include "gtest.h"
-#include "catypes.hpp"
+#include "common_types.hpp"
#include "cell.hpp"
#include "fvm_cell.hpp"
diff --git a/tests/validation/validate_ball_and_stick.cpp b/tests/validation/validate_ball_and_stick.cpp
index a819173e..62d06b4d 100644
--- a/tests/validation/validate_ball_and_stick.cpp
+++ b/tests/validation/validate_ball_and_stick.cpp
@@ -1,7 +1,7 @@
#include <fstream>
#include <json/src/json.hpp>
-#include <catypes.hpp>
+#include <common_types.hpp>
#include <cell.hpp>
#include <fvm_cell.hpp>
diff --git a/tests/validation/validate_soma.cpp b/tests/validation/validate_soma.cpp
index 20396701..24a0c1c5 100644
--- a/tests/validation/validate_soma.cpp
+++ b/tests/validation/validate_soma.cpp
@@ -1,7 +1,7 @@
#include <fstream>
#include <json/src/json.hpp>
-#include <catypes.hpp>
+#include <common_types.hpp>
#include <cell.hpp>
#include <fvm_cell.hpp>
diff --git a/tests/validation/validate_synapses.cpp b/tests/validation/validate_synapses.cpp
index 9bc67172..876b24eb 100644
--- a/tests/validation/validate_synapses.cpp
+++ b/tests/validation/validate_synapses.cpp
@@ -3,7 +3,7 @@
#include <json/src/json.hpp>
-#include <catypes.hpp>
+#include <common_types.hpp>
#include <cell.hpp>
#include <cell_group.hpp>
#include <fvm_cell.hpp>
--
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