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Unverified Commit 085c4299 authored by Sam Yates's avatar Sam Yates Committed by GitHub
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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
parent 43f4ec85
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arbor/morph/embed_pwlin.cpp
+ 10
− 3
View file @ 085c4299
......@@ -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.
......
test/unit/test_morph_embedding.cpp
+ 81
− 39
View file @ 085c4299
......@@ -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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