From eef88d1e06af6f4f7c91cbee3bdd2e5653c52489 Mon Sep 17 00:00:00 2001
From: Sam Yates <sam@quux.dropbear.id.au>
Date: Wed, 25 Mar 2020 20:33:01 +0100
Subject: [PATCH] Add canonical repn for mextent cables. (#989)
Provide canonical function for mextent that returns a reduced
mcable_list representation which excludes redundant zero-length
cables.
---
arbor/include/arbor/morph/morphology.hpp | 3 ++
arbor/morph/morphology.cpp | 21 ++++++++++
test/unit/test_morphology.cpp | 53 ++++++++++++++++++++++++
3 files changed, 77 insertions(+)
diff --git a/arbor/include/arbor/morph/morphology.hpp b/arbor/include/arbor/morph/morphology.hpp
index 4285e3ae..aa9ad61b 100644
--- a/arbor/include/arbor/morph/morphology.hpp
+++ b/arbor/include/arbor/morph/morphology.hpp
@@ -128,5 +128,8 @@ private:
mcable_list cables_;
};
+// Reduced representation of an extent, excluding zero-length cables
+// that are covered by more proximal or non-zero-length cables.
+mcable_list canonical(const morphology& m, const mextent& a);
} // namespace arb
diff --git a/arbor/morph/morphology.cpp b/arbor/morph/morphology.cpp
index ead854d2..ad93e472 100644
--- a/arbor/morph/morphology.cpp
+++ b/arbor/morph/morphology.cpp
@@ -481,5 +481,26 @@ mextent join(const mextent& a, const mextent& b) {
return m;
}
+mcable_list canonical(const morphology& m, const mextent& a) {
+ // For zero-length cables representing isolated points, keep
+ // only the most proximal. All other zero-length cables should be
+ // elided.
+
+ mcable_list result;
+ std::unordered_set<msize_t> remove_set;
+
+ for (auto& c: a.cables()) {
+ if (c.prox_pos==0 && c.dist_pos>0) {
+ remove_set.insert(m.branch_parent(c.branch));
+ }
+ }
+ for (auto& c: a.cables()) {
+ if (c.prox_pos==1 && remove_set.count(c.branch)) continue;
+ if (c.dist_pos==0 && m.branch_parent(c.branch)!=mnpos) continue;
+ result.push_back(c);
+ }
+ return result;
+}
+
} // namespace arb
diff --git a/test/unit/test_morphology.cpp b/test/unit/test_morphology.cpp
index 5bf31027..fd3bece9 100644
--- a/test/unit/test_morphology.cpp
+++ b/test/unit/test_morphology.cpp
@@ -734,3 +734,56 @@ TEST(mextent, intersects) {
EXPECT_TRUE(x3.intersects(mlocation{3, 0.}));
EXPECT_FALSE(x3.intersects(mlocation{3, 1.}));
}
+
+TEST(mextent, canonical) {
+ using namespace arb;
+ using testing::cablelist_eq;
+
+ using pvec = std::vector<msize_t>;
+ using svec = std::vector<msample>;
+ using cl = mcable_list;
+
+ // Eight samples
+ // no-sphere
+ // sample branch
+ // 0 0
+ // 1 3 0 1
+ // 2 4 0 1
+ // 5 6 2 3
+ // 7 3
+ pvec parents = {mnpos, 0, 1, 0, 3, 4, 4, 6};
+ svec samples = {
+ {{ 0, 0, 0, 2}, 3},
+ {{ 10, 0, 0, 2}, 3},
+ {{100, 0, 0, 2}, 3},
+ {{ 0, 10, 0, 2}, 3},
+ {{ 0,100, 0, 2}, 3},
+ {{100,100, 0, 2}, 3},
+ {{ 0,200, 0, 2}, 3},
+ {{ 0,300, 0, 2}, 3},
+ };
+
+ morphology m(sample_tree(samples, parents));
+
+ mextent x1(m, cl{{0, 0.3, 0.7}, {1, 0.5, 0.7}, {3, 0.4, 1}});
+ EXPECT_TRUE(cablelist_eq(canonical(m, x1), x1.cables()));
+
+ mcable_list cl2{{1, 0.5, 1}, {2, 0, 0.5}}; // a reduced representation
+ mextent x2(m, cl2);
+ EXPECT_FALSE(cablelist_eq(cl2, x2.cables()));
+ EXPECT_TRUE(cablelist_eq(cl2, canonical(m, x2)));
+
+ mcable_list cl3{{3, 0, 0}}; // extent is cover of fork point
+ mextent x3(m, cl3);
+ EXPECT_TRUE(cablelist_eq(cl{{1, 1, 1}}, canonical(m, x3)));
+
+ mcable_list cl4{{1, 1, 1}, {3, 0, 0.5}}; // canonical repn excludes zero-length cable
+ mextent x4(m, cl4);
+ EXPECT_TRUE(cablelist_eq(cl{{3, 0, 0.5}}, canonical(m, x4)));
+
+ // Heads of top-level branches should be preserved.
+ mcable_list cl5{{1, 0, 0}};
+ mextent x5(m, cl5);
+ EXPECT_TRUE(cablelist_eq(cl{{0, 0, 0}, {1, 0, 0}}, x5.cables()));
+ EXPECT_TRUE(cablelist_eq(x5.cables(), canonical(m, x5)));
+}
--
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