From 7ae3f39fdfe970cff70ee74f472cd08bd9f3cfa8 Mon Sep 17 00:00:00 2001
From: Ben Cumming <bcumming@cscs.ch>
Date: Fri, 19 Mar 2021 09:46:00 +0100
Subject: [PATCH] Fix bug attaching branches to the soma in ASCII file
descriptions (#1440)
Fix bug attaching branches to the soma in ASCII file descriptions.
Branches in an ASCII description attached to the soma were incorrectly creating a segment
from the center of the soma to the first point in the branch.
---
arborio/neurolucida.cpp | 21 ++++--
test/unit/CMakeLists.txt | 2 +-
test/unit/test_asc.cpp | 137 ++++++++++++++++++++++++++++-----------
3 files changed, 115 insertions(+), 45 deletions(-)
diff --git a/arborio/neurolucida.cpp b/arborio/neurolucida.cpp
index cd231c3e..705082d5 100644
--- a/arborio/neurolucida.cpp
+++ b/arborio/neurolucida.cpp
@@ -643,12 +643,22 @@ asc_morphology parse_asc_string(const char* input) {
tails.pop_back();
auto parent = head.parent_id;
+ auto& branch = *head.child;
auto prox_sample = head.sample;
- auto& b = *head.child;
- for (auto& dist_sample: b.samples) {
- parent = stree.append(parent, prox_sample, dist_sample, tag);
- prox_sample = dist_sample;
+ if (!branch.samples.empty()) { // Skip empty branches, which are permitted
+ auto it = branch.samples.begin();
+ // Don't connect the first sample to the distal end of the parent
+ // branch if the parent is the soma center.
+ if (parent==arb::mnpos) {
+ prox_sample = *it;
+ ++it;
+ }
+ do {
+ parent = stree.append(parent, prox_sample, *it, tag);
+ prox_sample = *it;
+ ++it;
+ } while (it!=branch.samples.end());
}
// Push child branches to stack in reverse order.
@@ -656,7 +666,8 @@ asc_morphology parse_asc_string(const char* input) {
// order they were described in the file, so that segments in the
// segment tree were added in the same order they are described
// in the file, to give deterministic branch numbering.
- for (auto it=b.children.rbegin(); it!=b.children.rend(); ++it) {
+ const auto& kids = branch.children;
+ for (auto it=kids.rbegin(); it!=kids.rend(); ++it) {
tails.push_back({&(*it), parent, prox_sample});
}
}
diff --git a/test/unit/CMakeLists.txt b/test/unit/CMakeLists.txt
index a6d0f519..7333b9ae 100644
--- a/test/unit/CMakeLists.txt
+++ b/test/unit/CMakeLists.txt
@@ -216,7 +216,7 @@ if(${CMAKE_POSITION_INDEPENDENT_CODE})
MECHS dummy
ARBOR "${PROJECT_SOURCE_DIR}"
STANDALONE ON
- VERBOSE ON)
+ VERBOSE OFF)
target_compile_definitions(unit PRIVATE USE_DYNAMIC_CATALOGUES)
add_dependencies(unit dummy-catalogue)
endif()
diff --git a/test/unit/test_asc.cpp b/test/unit/test_asc.cpp
index 05807fa7..e1ecd098 100644
--- a/test/unit/test_asc.cpp
+++ b/test/unit/test_asc.cpp
@@ -135,10 +135,8 @@ TEST(asc, sub_tree_meta) {
}
}
-TEST(asc, branching) {
- {
- // Soma composed of 2 branches, and stick and fork dendrite composed of 3 branches.
- const char* input =
+// Soma composed of 2 branches, and stick and fork dendrite composed of 3 branches.
+const char *asc_ball_and_y_dendrite =
"((CellBody)\
(0 0 0 2)\
)\
@@ -151,20 +149,9 @@ TEST(asc, branching) {
(6 5 0 1)\
)\
)";
- auto result = arborio::parse_asc_string(input);
- const auto& m = result.morphology;
- EXPECT_EQ(m.num_branches(), 5u);
- EXPECT_EQ(m.branch_children(0).size(), 0u);
- EXPECT_EQ(m.branch_children(1).size(), 0u);
- EXPECT_EQ(m.branch_children(2).size(), 2u);
- EXPECT_EQ(m.branch_children(2)[0], 3u);
- EXPECT_EQ(m.branch_children(2)[1], 4u);
- EXPECT_EQ(m.branch_children(3).size(), 0u);
- EXPECT_EQ(m.branch_children(4).size(), 0u);
- }
- {
- // Soma composed of 2 branches, and a dendrite with a bit more interesting branching.
- const char* input =
+
+// Soma composed of 2 branches, and a dendrite with a bit more interesting branching.
+const char *asc_ball_and_fancy_dendrite=
"((CellBody)\
(0 0 0 2)\
)\
@@ -182,25 +169,10 @@ TEST(asc, branching) {
(6 5 0 1)\
)\
)";
- auto result = arborio::parse_asc_string(input);
- const auto& m = result.morphology;
- EXPECT_EQ(m.num_branches(), 7u);
- EXPECT_EQ(m.branch_children(0).size(), 0u);
- EXPECT_EQ(m.branch_children(1).size(), 0u);
- EXPECT_EQ(m.branch_children(2).size(), 2u);
- EXPECT_EQ(m.branch_children(2)[0], 3u);
- EXPECT_EQ(m.branch_children(2)[1], 6u);
- EXPECT_EQ(m.branch_children(3).size(), 2u);
- EXPECT_EQ(m.branch_children(3)[0], 4u);
- EXPECT_EQ(m.branch_children(3)[1], 5u);
- EXPECT_EQ(m.branch_children(4).size(), 0u);
- EXPECT_EQ(m.branch_children(5).size(), 0u);
- EXPECT_EQ(m.branch_children(6).size(), 0u);
- }
- {
- // Soma composed of 2 branches, and stick and fork dendrite and axon
- // composed of 3 branches each.
- const char* input =
+
+// Soma composed of 2 branches, and stick and fork dendrite and axon
+// composed of 3 branches each.
+const char* asc_ball_and_y_dendrite_and_y_axon =
"((CellBody)\
(0 0 0 2)\
)\
@@ -222,7 +194,38 @@ TEST(asc, branching) {
(6 -5 0 1)\
)\
)";
- auto result = arborio::parse_asc_string(input);
+
+TEST(asc, branching) {
+ {
+ auto result = arborio::parse_asc_string(asc_ball_and_y_dendrite);
+ const auto& m = result.morphology;
+ EXPECT_EQ(m.num_branches(), 5u);
+ EXPECT_EQ(m.branch_children(0).size(), 0u);
+ EXPECT_EQ(m.branch_children(1).size(), 0u);
+ EXPECT_EQ(m.branch_children(2).size(), 2u);
+ EXPECT_EQ(m.branch_children(2)[0], 3u);
+ EXPECT_EQ(m.branch_children(2)[1], 4u);
+ EXPECT_EQ(m.branch_children(3).size(), 0u);
+ EXPECT_EQ(m.branch_children(4).size(), 0u);
+ }
+ {
+ auto result = arborio::parse_asc_string(asc_ball_and_fancy_dendrite);
+ const auto& m = result.morphology;
+ EXPECT_EQ(m.num_branches(), 7u);
+ EXPECT_EQ(m.branch_children(0).size(), 0u);
+ EXPECT_EQ(m.branch_children(1).size(), 0u);
+ EXPECT_EQ(m.branch_children(2).size(), 2u);
+ EXPECT_EQ(m.branch_children(2)[0], 3u);
+ EXPECT_EQ(m.branch_children(2)[1], 6u);
+ EXPECT_EQ(m.branch_children(3).size(), 2u);
+ EXPECT_EQ(m.branch_children(3)[0], 4u);
+ EXPECT_EQ(m.branch_children(3)[1], 5u);
+ EXPECT_EQ(m.branch_children(4).size(), 0u);
+ EXPECT_EQ(m.branch_children(5).size(), 0u);
+ EXPECT_EQ(m.branch_children(6).size(), 0u);
+ }
+ {
+ auto result = arborio::parse_asc_string(asc_ball_and_y_dendrite_and_y_axon);
const auto& m = result.morphology;
EXPECT_EQ(m.num_branches(), 8u);
EXPECT_EQ(m.branch_children(0).size(), 0u);
@@ -238,6 +241,62 @@ TEST(asc, branching) {
EXPECT_EQ(m.branch_children(6).size(), 0u);
EXPECT_EQ(m.branch_children(7).size(), 0u);
}
-
}
+// Test that
+// * first segment in branches connected to the soma has as its
+// proximal sample the first sample in the branch
+// * all other non-soma branches have the distal end of the parent
+// branch as their proximal sample.
+// * the soma is composed of two branches, attached to the soma center,
+// and extending along the z axis
+TEST(asc, soma_connection) {
+ {
+ auto result = arborio::parse_asc_string(asc_ball_and_y_dendrite);
+ const auto& m = result.morphology;
+ EXPECT_EQ(m.num_branches(), 5u);
+ // Test soma
+ EXPECT_EQ(m.branch_segments(0)[0].prox, (arb::mpoint{0, 0, 0, 2}));
+ EXPECT_EQ(m.branch_segments(0)[0].dist, (arb::mpoint{0, 0,-2, 2}));
+ EXPECT_EQ(m.branch_segments(1)[0].prox, (arb::mpoint{0, 0, 0, 2}));
+ EXPECT_EQ(m.branch_segments(1)[0].dist, (arb::mpoint{0, 0, 2, 2}));
+ // Test dendrite proximal ends
+ EXPECT_EQ(m.branch_segments(2)[0].prox, (arb::mpoint{0, 2, 0, 1}));
+ EXPECT_EQ(m.branch_segments(3)[0].prox, (arb::mpoint{0, 5, 0, 1}));
+ EXPECT_EQ(m.branch_segments(4)[0].prox, (arb::mpoint{0, 5, 0, 1}));
+ }
+ {
+ auto result = arborio::parse_asc_string(asc_ball_and_fancy_dendrite);
+ const auto& m = result.morphology;
+ EXPECT_EQ(m.num_branches(), 7u);
+ // Test soma
+ EXPECT_EQ(m.branch_segments(0)[0].prox, (arb::mpoint{0, 0, 0, 2}));
+ EXPECT_EQ(m.branch_segments(0)[0].dist, (arb::mpoint{0, 0,-2, 2}));
+ EXPECT_EQ(m.branch_segments(1)[0].prox, (arb::mpoint{0, 0, 0, 2}));
+ EXPECT_EQ(m.branch_segments(1)[0].dist, (arb::mpoint{0, 0, 2, 2}));
+ // Test dendrite proximal ends
+ EXPECT_EQ(m.branch_segments(2)[0].prox, (arb::mpoint{ 0, 2, 0, 1}));
+ EXPECT_EQ(m.branch_segments(3)[0].prox, (arb::mpoint{ 0, 5, 0, 1}));
+ EXPECT_EQ(m.branch_segments(4)[0].prox, (arb::mpoint{-5, 5, 0, 1}));
+ EXPECT_EQ(m.branch_segments(5)[0].prox, (arb::mpoint{-5, 5, 0, 1}));
+ EXPECT_EQ(m.branch_segments(6)[0].prox, (arb::mpoint{ 0, 5, 0, 1}));
+ }
+ {
+ auto result = arborio::parse_asc_string(asc_ball_and_y_dendrite_and_y_axon);
+ const auto& m = result.morphology;
+ EXPECT_EQ(m.num_branches(), 8u);
+ // Test soma
+ EXPECT_EQ(m.branch_segments(0)[0].prox, (arb::mpoint{0, 0, 0, 2}));
+ EXPECT_EQ(m.branch_segments(0)[0].dist, (arb::mpoint{0, 0,-2, 2}));
+ EXPECT_EQ(m.branch_segments(1)[0].prox, (arb::mpoint{0, 0, 0, 2}));
+ EXPECT_EQ(m.branch_segments(1)[0].dist, (arb::mpoint{0, 0, 2, 2}));
+ // Test dendrite proximal ends
+ EXPECT_EQ(m.branch_segments(2)[0].prox, (arb::mpoint{0, 2, 0, 1}));
+ EXPECT_EQ(m.branch_segments(3)[0].prox, (arb::mpoint{0, 5, 0, 1}));
+ EXPECT_EQ(m.branch_segments(4)[0].prox, (arb::mpoint{0, 5, 0, 1}));
+ // Test axon proximal ends
+ EXPECT_EQ(m.branch_segments(5)[0].prox, (arb::mpoint{0,-2, 0, 1}));
+ EXPECT_EQ(m.branch_segments(6)[0].prox, (arb::mpoint{0,-5, 0, 1}));
+ EXPECT_EQ(m.branch_segments(7)[0].prox, (arb::mpoint{0,-5, 0, 1}));
+ }
+}
--
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