Merge pull request #63 from halfflat/feature/model+recipe

Feature/model+recipe

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>

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>
 

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

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"

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>
@@ -40,9 +40,15 @@ 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()) {
-            ++source_id.index;
+            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)
             });

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"
 

src/catypes.hpp → 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;

src/catypes_io.cpp → src/common_types_io.cpp

 #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;

src/communication/communicator.hpp

@@ -5,12 +5,12 @@
 #include <vector>
 #include <random>
 
-#include <spike.hpp>
-#include <threading/threading.hpp>
 #include <algorithms.hpp>
+#include <connection.hpp>
 #include <event_queue.hpp>
-
-#include "connection.hpp"
+#include <spike.hpp>
+#include <threading/threading.hpp>
+#include <util/debug.hpp>
 
 namespace nest {
 namespace mc {

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>
 

src/compartment.hpp

@@ -3,7 +3,7 @@
 #include <iterator>
 #include <utility>
 
-#include "catypes.hpp"
+#include "common_types.hpp"
 
 namespace nest {
 namespace mc {

src/connection.hpp

@@ -2,7 +2,7 @@
 
 #include <cstdint>
 
-#include <catypes.hpp>
+#include <common_types.hpp>
 #include <event_queue.hpp>
 #include <spike.hpp>
 

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 {

src/model.hpp

 #include <cstdlib>
 #include <vector>
 
-#include <catypes.hpp>
+#include <common_types.hpp>
 #include <cell.hpp>
 #include <cell_group.hpp>
 #include <communication/communicator.hpp>

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"

tests/unit/test_cell_group.cpp

 #include "gtest.h"
 
-#include <catypes.hpp>
+#include <common_types.hpp>
 #include <fvm_cell.hpp>
 #include <cell_group.hpp>
 
@@ -20,10 +20,8 @@ nest::mc::cell make_cell() {
 
     dendrite->mechanism("membrane").set("r_L", 100);
 
-    // add stimulus
-    cell.add_stimulus({1,1}, {5., 80., 0.3});
-
-    cell.add_detector({0,0}, 0);
+    cell.add_detector({0, 0}, 0);
+    cell.add_stimulus({1, 1}, {5., 80., 0.3});
 
     return cell;
 }
@@ -41,3 +39,36 @@ TEST(cell_group, test)
     EXPECT_EQ(group.spikes().size(), 4u);
 }
 
+TEST(cell_group, sources)
+{
+    using namespace nest::mc;
+
+    // TODO: extend to multi-cell cell groups when the time comes
+
+    using cell_group_type = cell_group<fvm::fvm_cell<double, cell_local_size_type>>;
+
+    auto cell = make_cell();
+    EXPECT_EQ(cell.detectors().size(), 1u);
+    // add another detector on the cell to make things more interesting
+    cell.add_detector({1, 0.3}, 2.3);
+
+    cell_gid_type first_gid = 37u;
+    auto group = cell_group_type{first_gid, cell};
+
+    // expect group sources to be lexicographically sorted by source id
+    // with gids in cell group's range and indices starting from zero
+
+    const auto& sources = group.spike_sources();
+    for (unsigned i = 0; i<sources.size(); ++i) {
+        auto id = sources[i].source_id;
+        if (i==0) {
+            EXPECT_EQ(id.gid, first_gid);
+            EXPECT_EQ(id.index, 0u);
+        }
+        else {
+            auto prev = sources[i-1].source_id;
+            EXPECT_GT(id, prev);
+            EXPECT_EQ(id.index, id.gid==prev.gid? prev.index+1: 0u);
+        }
+    }
+}

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>
 

tests/unit/test_lexcmp.cpp

@@ -62,8 +62,8 @@ class lexcmp_test_refmemfn {
 public:
     explicit lexcmp_test_refmemfn(int foo): foo_(foo) {}
 
-    const int &foo() const { return foo_; }
-    int &foo() { return foo_; }
+    const int& foo() const { return foo_; }
+    int& foo() { return foo_; }
 
 private:
     int foo_;

tests/unit/test_probe.cpp

 #include "gtest.h"
 
-#include "catypes.hpp"
+#include "common_types.hpp"
 #include "cell.hpp"
 #include "fvm_cell.hpp"
 

tests/validation/validate_ball_and_stick.cpp

 #include <fstream>
 #include <json/src/json.hpp>
 
-#include <catypes.hpp>
+#include <common_types.hpp>
 #include <cell.hpp>
 #include <fvm_cell.hpp>