diff --git a/arborio/neurolucida.cpp b/arborio/neurolucida.cpp
index 4bccd0dbb16f1c40e3472b89a9899fa00b99b6dc..f4b547d08bf5a4ca0457339dec18c29afc972689 100644
--- a/arborio/neurolucida.cpp
+++ b/arborio/neurolucida.cpp
@@ -591,39 +591,39 @@ asc_morphology parse_asc_string(const char* input) {
arb::segment_tree stree;
- // Form a soma composed of two cylinders, extended along the positive and negative
- // z axis from the center of the soma.
+ // Form a soma composed of two cylinders, extended along the negative then positive
+ // y axis from the center of the soma.
//
- // -------- soma_b
+ // -------- soma_2
// | |
- // | |
- // -------- soma_c
- // | |
- // | |
- // -------- soma_e
+ // | | y
+ // -------- soma_0 | z
+ // | | | /
+ // | | |/
+ // -------- soma_1 o--- x
//
- arb::mpoint soma_c, soma_b, soma_e;
+ arb::mpoint soma_0, soma_1, soma_2;
if (soma_count==1u) {
const auto& st = sub_trees[soma_contours.front()];
const auto& samples = st.root.samples;
if (samples.size()==1u) {
// The soma is described as a sphere with a single sample.
- soma_c = samples.front();
+ soma_0 = samples.front();
}
else {
// The soma is described by a contour.
const auto ns = samples.size();
- soma_c.x = std::accumulate(samples.begin(), samples.end(), 0., [](double a, auto& s) {return a+s.x;}) / ns;
- soma_c.y = std::accumulate(samples.begin(), samples.end(), 0., [](double a, auto& s) {return a+s.y;}) / ns;
- soma_c.z = std::accumulate(samples.begin(), samples.end(), 0., [](double a, auto& s) {return a+s.z;}) / ns;
- soma_c.radius = std::accumulate(samples.begin(), samples.end(), 0.,
- [&soma_c](double a, auto& c) {return a+arb::distance(c, soma_c);}) / ns;
+ soma_0.x = std::accumulate(samples.begin(), samples.end(), 0., [](double a, auto& s) {return a+s.x;}) / ns;
+ soma_0.y = std::accumulate(samples.begin(), samples.end(), 0., [](double a, auto& s) {return a+s.y;}) / ns;
+ soma_0.z = std::accumulate(samples.begin(), samples.end(), 0., [](double a, auto& s) {return a+s.z;}) / ns;
+ soma_0.radius = std::accumulate(samples.begin(), samples.end(), 0.,
+ [&soma_0](double a, auto& c) {return a+arb::distance(c, soma_0);}) / ns;
}
- soma_b = {soma_c.x, soma_c.y, soma_c.z-soma_c.radius, soma_c.radius};
- soma_e = {soma_c.x, soma_c.y, soma_c.z+soma_c.radius, soma_c.radius};
- stree.append(arb::mnpos, soma_c, soma_b, 1);
- stree.append(arb::mnpos, soma_c, soma_e, 1);
+ soma_1 = {soma_0.x, soma_0.y-soma_0.radius, soma_0.z, soma_0.radius};
+ soma_2 = {soma_0.x, soma_0.y+soma_0.radius, soma_0.z, soma_0.radius};
+ stree.append(arb::mnpos, soma_0, soma_1, 1);
+ stree.append(arb::mnpos, soma_0, soma_2, 1);
}
// Append the dend, axon and apical dendrites.
@@ -633,7 +633,7 @@ asc_morphology parse_asc_string(const char* input) {
// Skip soma contours.
if (tag==1) continue;
- // For now attach everything to the center of the soma at soma_c.
+ // For now attach everything to the center of the soma at soma_0.
// Later we could try to attach to whichever end of the soma is closest.
// Also need to push parent id
struct binf {
@@ -642,7 +642,7 @@ asc_morphology parse_asc_string(const char* input) {
arb::mpoint sample;
};
- std::vector<binf> tails = {{&st.root, arb::mnpos, soma_c}};
+ std::vector<binf> tails = {{&st.root, arb::mnpos, soma_0}};
while (!tails.empty()) {
auto head = tails.back();
diff --git a/doc/fileformat/asc.rst b/doc/fileformat/asc.rst
index cc1c5ccdd35a3f255e360ae942a041f1b2dc68e8..70d648f1d9475e40259f3404729f63f1897f60e8 100644
--- a/doc/fileformat/asc.rst
+++ b/doc/fileformat/asc.rst
@@ -36,18 +36,18 @@ and locsets from the meta data.
Soma / CellBody
""""""""""""""""
-The soma, or CellBody, is described in one of three different methods (that we are aware of) in
-an ASCII file.
+The soma, or CellBody, is described in one of three different methods in an ASCII file:
1. As a CellBody statement containing a single location and radius, which models **a sphere**.
2. As a CellBody statement containing an unbranched sequence of locations that define **a single contour**.
3. As multiple CellBody statements, each defining a contour, that describe the soma as **a stack of contours**.
-Arbor supports description methods 1 and 2, and support for method 3 can be added on request
-(open an issue).
+Arbor supports description methods 1 and 2 following the `neuromporpho policies <http://neuromorpho.org/SomaFormat.html>`_.
+Currently multiple contours in method 3 are not supported, and if you need support make
+the request with an `issue <https://github.com/arbor-sim/arbor/issues>`_.
In each case, the soma is modeled as a cylinder with diameter equal to it's length, centred
-at the centre of the soma, and oriented along the z axis.
+at the centre of the soma, and oriented along the y axis.
For a **spherical** soma, the centre and diameter are that of the sphere. For
a **contour**, the centre is the centroid of the locations that define the contour,
diff --git a/test/unit/test_asc.cpp b/test/unit/test_asc.cpp
index e1ecd098fcda15be0c7249186f5a0332e6b61ee7..daf0eb5f609abe3c250d5fef94af3d2ff4662a45 100644
--- a/test/unit/test_asc.cpp
+++ b/test/unit/test_asc.cpp
@@ -62,12 +62,12 @@ TEST(asc, only_cell_body) {
auto& segs1 = m.morphology.branch_segments(0);
EXPECT_EQ(segs1.size(), 1u);
EXPECT_EQ(segs1[0].prox, (arb::mpoint{0., 0., 1., 2.}));
- EXPECT_EQ(segs1[0].dist, (arb::mpoint{0., 0., -1., 2.}));
+ EXPECT_EQ(segs1[0].dist, (arb::mpoint{0.,-2., 1., 2.}));
auto& segs2 = m.morphology.branch_segments(1);
EXPECT_EQ(segs2.size(), 1u);
EXPECT_EQ(segs2[0].prox, (arb::mpoint{0., 0., 1., 2.}));
- EXPECT_EQ(segs2[0].dist, (arb::mpoint{0., 0., 3., 2.}));
+ EXPECT_EQ(segs2[0].dist, (arb::mpoint{0., 2., 1., 2.}));
}
@@ -81,12 +81,12 @@ TEST(asc, only_cell_body) {
auto& segs1 = m.morphology.branch_segments(0);
EXPECT_EQ(segs1.size(), 1u);
EXPECT_EQ(segs1[0].prox, (arb::mpoint{0., 0., 1., 2.}));
- EXPECT_EQ(segs1[0].dist, (arb::mpoint{0., 0., -1., 2.}));
+ EXPECT_EQ(segs1[0].dist, (arb::mpoint{0.,-2., 1., 2.}));
auto& segs2 = m.morphology.branch_segments(1);
EXPECT_EQ(segs2.size(), 1u);
EXPECT_EQ(segs2[0].prox, (arb::mpoint{0., 0., 1., 2.}));
- EXPECT_EQ(segs2[0].dist, (arb::mpoint{0., 0., 3., 2.}));
+ EXPECT_EQ(segs2[0].dist, (arb::mpoint{0., 2., 1., 2.}));
}
{ // Cell with two CellBodys: unsupported feature ATM.
@@ -257,9 +257,9 @@ TEST(asc, soma_connection) {
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(0)[0].dist, (arb::mpoint{0,-2, 0, 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}));
+ EXPECT_EQ(m.branch_segments(1)[0].dist, (arb::mpoint{0, 2, 0, 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}));
@@ -271,9 +271,9 @@ TEST(asc, soma_connection) {
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(0)[0].dist, (arb::mpoint{0,-2, 0, 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}));
+ EXPECT_EQ(m.branch_segments(1)[0].dist, (arb::mpoint{0, 2, 0, 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}));
@@ -287,9 +287,9 @@ TEST(asc, soma_connection) {
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(0)[0].dist, (arb::mpoint{0,-2, 0, 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}));
+ EXPECT_EQ(m.branch_segments(1)[0].dist, (arb::mpoint{0, 2, 0, 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}));