From 085c42999de9542096b8a2ae6d44522ceca91e57 Mon Sep 17 00:00:00 2001
From: Sam Yates <halfflat@gmail.com>
Date: Fri, 19 Mar 2021 09:16:18 +0100
Subject: [PATCH] Amend segment cables for zero length branches. (#1443)
Amend segment cables for zero length branches.
Ensure cables corresponding to segments cover even zero length branches, by setting the segment cables to (b, 0, 0) for all but the last segment in a zero-length branch b, and setting that last segment cable to (b, 0, 1).
Fixes #1442
---
arbor/morph/embed_pwlin.cpp | 13 +++-
test/unit/test_morph_embedding.cpp | 120 +++++++++++++++++++----------
2 files changed, 91 insertions(+), 42 deletions(-)
diff --git a/arbor/morph/embed_pwlin.cpp b/arbor/morph/embed_pwlin.cpp
index f419b436..03acfaa7 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 ba702667..00345b08 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
--
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