diff --git a/external/vector b/external/vector
index 193df3683a3eaa2bf203bbcfa935d7e7019b1719..8284611f05b0fbe21a1f84630e2726015cb1d96d 160000
--- a/external/vector
+++ b/external/vector
@@ -1 +1 @@
-Subproject commit 193df3683a3eaa2bf203bbcfa935d7e7019b1719
+Subproject commit 8284611f05b0fbe21a1f84630e2726015cb1d96d
diff --git a/src/cell_tree.hpp b/src/cell_tree.hpp
index 1e04fc2c3bcc4e0fe887c7048997afd272fa4bff..4d9f70b1a934ab3b5bdb840d6bb0bd1b8419dfec 100644
--- a/src/cell_tree.hpp
+++ b/src/cell_tree.hpp
@@ -32,7 +32,7 @@ class cell_tree {
public :
// use a signed 16-bit integer for storage of indexes, which is reasonable given
// that typical cells have at most 1000-2000 segments
- using int_type = int16_t;
+ using int_type = int;
using index_type = memory::HostVector<int_type>;
using view_type = index_type::view_type;
using const_view_type = index_type::const_view_type;
@@ -298,4 +298,3 @@ private :
} // namespace mc
} // namespace nest
-
diff --git a/src/tree.hpp b/src/tree.hpp
index 3d76a9dc1e8171f62026320a98f71078e91f1dc5..98ff9aa43656f9d68b879297a6ffd5399348b6f0 100644
--- a/src/tree.hpp
+++ b/src/tree.hpp
@@ -17,7 +17,7 @@ class tree {
public :
- using int_type = int16_t;
+ using int_type = int;
using index_type = memory::HostVector<int_type>;
using view_type = index_type::view_type;
@@ -62,92 +62,22 @@ class tree {
);
}
- // n = number of compartment in cell
- auto n = parent_index.size();
+ auto new_parent_index = algorithms::make_parent_index(
+ parent_index, algorithms::branches(parent_index));
- // On completion of this loop child_count[i] is the number of children
- // of compartment i compensate count for compartment 0, which has itself
- // as its own parent
- index_type child_count(n, 0);
- child_count[0] = -1;
- for(auto i : parent_index) {
- ++child_count[i];
- }
+ init(new_parent_index.size());
+ parents_(memory::all) = new_parent_index;
+ parents_[0] = -1;
- // Find the number of branches by summing the number of children of all
- // compartments with more than 1 child.
- auto nbranches = 1 + child_count[0]; // children of the root node are counted differently
- for(auto i : range(1,n)) {
- if(child_count[i]>1) {
- nbranches += child_count[i];
- }
- }
+ child_index_(memory::all) =
+ algorithms::make_index(algorithms::child_count(parents_));
- // allocate memory for storing the tree
- init(nbranches);
-
- // index of the branch for each compartment
- std::vector<I> branch_index(n);
-
- // Mark the parent of the root node as -1.
- // This simplifies the implementation of some algorithms on the tree
- parents_[0]=-1;
-
- // bcount records how many branches have been created in the loop
- auto bcount=0;
-
- for(auto i : range(1,n)) {
- // the branch index of the parent of compartment i
- auto parent_node = parent_index[i];
- // index of the parent of compartment i
- auto parent_branch = branch_index[parent_node];
-
- // if this compartments's parent
- // - has more than one child
- // - or is the root branch
- // this is the first compartment in a branch, so mark it as such
- if(child_count[parent_node]>1 || parent_node==0) {
- bcount++;
- branch_index[i] = bcount;
- parents_[bcount] = parent_branch;
- }
- // not the first compartment in a branch,
- // so inherit the parent's branch number
- else {
- branch_index[i] = parent_branch;
- }
- }
-
- child_index_(memory::all) = 0;
- // the root node has to be handled separately: all of its children must
- // be counted
- child_index_[1] = child_count[0];
- for(auto i : range(1, n)) {
- if(child_count[i]>1) {
- child_index_[branch_index[i]+1] = child_count[i];
- }
- }
- std::partial_sum(child_index_.begin(), child_index_.end(), child_index_.begin());
-
- // Fill in the list of children of each branch.
- // Requires some additional book keeping to keep track of how many
- // children have already been filled in for each branch.
- for(auto i : range(1, nbranches)) {
- // parents_[i] is the parent of branch i, for which i must be added
- // as a child, and child_index_[p] is the index into which the next
- // child of p is to be stored
+ std::vector<int> pos(parents_.size(), 0);
+ for (auto i = 1u; i < parents_.size(); ++i) {
auto p = parents_[i];
- children_[child_index_[p]] = i;
- ++child_index_[p];
- }
-
- // The child index has already been calculated as a side-effect of the
- // loop above, but is shifted one value to the left, so perform a
- // rotation to the right.
- for(auto i=nbranches-1; i>=00; --i) {
- child_index_[i+1] = child_index_[i];
+ children_[child_index_[p] + pos[p]] = i;
+ ++pos[p];
}
- child_index_[0] = 0;
}
size_t num_children() const {
diff --git a/tests/test_tree.cpp b/tests/test_tree.cpp
index 1e06b3a90fdf92f96e43e2c93036d37788c3efa6..ca9c6d73b1d9e4bde0bb90fc9061ff34f69f0503 100644
--- a/tests/test_tree.cpp
+++ b/tests/test_tree.cpp
@@ -142,20 +142,27 @@ TEST(cell_tree, from_parent_index) {
{
//
// 0
- // / \.
- // 1 2
+ // /|\.
+ // 1 4 5
// / \.
- // 3 4
- std::vector<int> parent_index = {0,0,0,1,1};
+ // 2 3
+ std::vector<int> parent_index = {0,0,1,1,0,0};
cell_tree tree(parent_index);
- EXPECT_EQ(tree.num_segments(), 5u);
+ EXPECT_EQ(tree.num_segments(), 6u);
- EXPECT_EQ(tree.num_children(0), 2u);
+ EXPECT_EQ(tree.num_children(0), 3u);
EXPECT_EQ(tree.num_children(1), 2u);
EXPECT_EQ(tree.num_children(2), 0u);
EXPECT_EQ(tree.num_children(3), 0u);
EXPECT_EQ(tree.num_children(4), 0u);
+
+ // Check children
+ EXPECT_EQ(1, tree.children(0)[0]);
+ EXPECT_EQ(4, tree.children(0)[1]);
+ EXPECT_EQ(5, tree.children(0)[2]);
+ EXPECT_EQ(2, tree.children(1)[0]);
+ EXPECT_EQ(3, tree.children(1)[1]);
}
{
// 0