diff --git a/arbor/morph/embed_pwlin.cpp b/arbor/morph/embed_pwlin.cpp
index f419b436fe9510cf42f2e577a6cb39e87c4023f4..03acfaa74d3c6ff8f427e004424870d3f6749b9f 100644
--- a/arbor/morph/embed_pwlin.cpp
+++ b/arbor/morph/embed_pwlin.cpp
@@ -249,11 +249,18 @@ embed_pwlin::embed_pwlin(const arb::morphology& m) {
if (branch_length!=0) {
for (auto& d: seg_pos) {
d /= branch_length;
+ all_segment_ends_.push_back({bid, d});
}
}
-
- for (auto d: seg_pos) {
- all_segment_ends_.push_back({bid, d});
+ else {
+ // In zero length branch, set all segment ends to be 0,
+ // except for last, which is 1. This ensures that the
+ // union of the cables corresponding to a branch cover
+ // the branch.
+ seg_pos.back() = 1;
+ for (auto d: seg_pos) {
+ all_segment_ends_.push_back({bid, d});
+ }
}
// Second pass over segments to store associated cables.
diff --git a/test/unit/test_morph_embedding.cpp b/test/unit/test_morph_embedding.cpp
index ba702667f7fae1c371ae9efd793feedfe3d0b89c..00345b08aad138ebf0bb9de64fd4bc4adba84aa4 100644
--- a/test/unit/test_morph_embedding.cpp
+++ b/test/unit/test_morph_embedding.cpp
@@ -55,6 +55,46 @@ TEST(embedding, segments_and_branch_length) {
EXPECT_EQ(10., em.branch_length(0));
}
+ // Zero-length branch?
+ // Four samples - point indices:
+ //
+ // 0
+ // 1 2
+ // 3
+ //
+ // Point 0, 2, and 3 colocated.
+ // Expect all but most distal segment on zero length branch
+ // to have cable (bid, 0, 0), and the most distal to have (bid, 0, 1).
+ {
+ pvec parents = {mnpos, 0, 0, 2};
+
+ svec points = {
+ { 0, 0, 3, 2},
+ { 10, 0, 3, 2},
+ { 0, 0, 3, 2},
+ { 0, 0, 3, 2},
+ };
+ morphology m(segments_from_points(points, parents));
+
+ ASSERT_EQ(2u, m.num_branches());
+
+ embedding em(m);
+ const auto& locs = em.segment_ends();
+ ASSERT_EQ(5u, locs.size());
+ EXPECT_TRUE(mlocation_eq(locs[0], (loc{0,0})));
+ EXPECT_TRUE(mlocation_eq(locs[1], (loc{0,1})));
+ EXPECT_TRUE(mlocation_eq(locs[2], (loc{1,0})));
+ EXPECT_TRUE(mlocation_eq(locs[3], (loc{1,0})));
+ EXPECT_TRUE(mlocation_eq(locs[4], (loc{1,1})));
+
+ EXPECT_TRUE(cable_eq(mcable{0, 0, 1}, em.segment(0)));
+ EXPECT_TRUE(cable_eq(mcable{1, 0, 0}, em.segment(1)));
+ EXPECT_TRUE(cable_eq(mcable{1, 0, 1}, em.segment(2)));
+
+ EXPECT_EQ(10, em.branch_length(0));
+ EXPECT_EQ(0, em.branch_length(1));
+ }
+
// Eight samples - point indices:
//
// 0
@@ -62,49 +102,51 @@ TEST(embedding, segments_and_branch_length) {
// 2 4
// 5 6
// 7
- pvec parents = {mnpos, 0, 1, 0, 3, 4, 4, 6};
+ {
+ pvec parents = {mnpos, 0, 1, 0, 3, 4, 4, 6};
- svec points = {
- { 0, 0, 0, 2},
- { 10, 0, 0, 2},
- {100, 0, 0, 2},
- { 0, 10, 0, 2},
- { 0,100, 0, 2},
- {100,100, 0, 2},
- { 0,130, 0, 2},
- { 0,300, 0, 2},
- };
- morphology m(segments_from_points(points, parents));
+ svec points = {
+ { 0, 0, 0, 2},
+ { 10, 0, 0, 2},
+ {100, 0, 0, 2},
+ { 0, 10, 0, 2},
+ { 0,100, 0, 2},
+ {100,100, 0, 2},
+ { 0,130, 0, 2},
+ { 0,300, 0, 2},
+ };
+ morphology m(segments_from_points(points, parents));
- ASSERT_EQ(4u, m.num_branches());
+ ASSERT_EQ(4u, m.num_branches());
- embedding em(m);
+ embedding em(m);
- const auto& locs = em.segment_ends();
- EXPECT_TRUE(mlocation_eq(locs[0], (loc{0,0})));
- EXPECT_TRUE(mlocation_eq(locs[1], (loc{0,0.1})));
- EXPECT_TRUE(mlocation_eq(locs[2], (loc{0,1})));
- EXPECT_TRUE(mlocation_eq(locs[3], (loc{1,0})));
- EXPECT_TRUE(mlocation_eq(locs[4], (loc{1,0.1})));
- EXPECT_TRUE(mlocation_eq(locs[5], (loc{1,1})));
- EXPECT_TRUE(mlocation_eq(locs[6], (loc{2,0})));
- EXPECT_TRUE(mlocation_eq(locs[7], (loc{2,1})));
- EXPECT_TRUE(mlocation_eq(locs[8], (loc{3,0})));
- EXPECT_TRUE(mlocation_eq(locs[9], (loc{3,0.15})));
- EXPECT_TRUE(mlocation_eq(locs[10], (loc{3,1})));
-
- EXPECT_TRUE(cable_eq(mcable{0, 0. , 0.1 }, em.segment(0)));
- EXPECT_TRUE(cable_eq(mcable{0, 0.1 , 1. }, em.segment(1)));
- EXPECT_TRUE(cable_eq(mcable{1, 0. , 0.1 }, em.segment(2)));
- EXPECT_TRUE(cable_eq(mcable{1, 0.1 , 1. }, em.segment(3)));
- EXPECT_TRUE(cable_eq(mcable{2, 0. , 1. }, em.segment(4)));
- EXPECT_TRUE(cable_eq(mcable{3, 0. , 0.15}, em.segment(5)));
- EXPECT_TRUE(cable_eq(mcable{3, 0.15, 1. }, em.segment(6)));
-
- EXPECT_EQ(100., em.branch_length(0));
- EXPECT_EQ(100., em.branch_length(1));
- EXPECT_EQ(100., em.branch_length(2));
- EXPECT_EQ(200., em.branch_length(3));
+ const auto& locs = em.segment_ends();
+ EXPECT_TRUE(mlocation_eq(locs[0], (loc{0,0})));
+ EXPECT_TRUE(mlocation_eq(locs[1], (loc{0,0.1})));
+ EXPECT_TRUE(mlocation_eq(locs[2], (loc{0,1})));
+ EXPECT_TRUE(mlocation_eq(locs[3], (loc{1,0})));
+ EXPECT_TRUE(mlocation_eq(locs[4], (loc{1,0.1})));
+ EXPECT_TRUE(mlocation_eq(locs[5], (loc{1,1})));
+ EXPECT_TRUE(mlocation_eq(locs[6], (loc{2,0})));
+ EXPECT_TRUE(mlocation_eq(locs[7], (loc{2,1})));
+ EXPECT_TRUE(mlocation_eq(locs[8], (loc{3,0})));
+ EXPECT_TRUE(mlocation_eq(locs[9], (loc{3,0.15})));
+ EXPECT_TRUE(mlocation_eq(locs[10], (loc{3,1})));
+
+ EXPECT_TRUE(cable_eq(mcable{0, 0. , 0.1 }, em.segment(0)));
+ EXPECT_TRUE(cable_eq(mcable{0, 0.1 , 1. }, em.segment(1)));
+ EXPECT_TRUE(cable_eq(mcable{1, 0. , 0.1 }, em.segment(2)));
+ EXPECT_TRUE(cable_eq(mcable{1, 0.1 , 1. }, em.segment(3)));
+ EXPECT_TRUE(cable_eq(mcable{2, 0. , 1. }, em.segment(4)));
+ EXPECT_TRUE(cable_eq(mcable{3, 0. , 0.15}, em.segment(5)));
+ EXPECT_TRUE(cable_eq(mcable{3, 0.15, 1. }, em.segment(6)));
+
+ EXPECT_EQ(100., em.branch_length(0));
+ EXPECT_EQ(100., em.branch_length(1));
+ EXPECT_EQ(100., em.branch_length(2));
+ EXPECT_EQ(200., em.branch_length(3));
+ }
}
// TODO: integrator tests