From dbb2340692fd420b5736e46d421fb4ce5839952a Mon Sep 17 00:00:00 2001
From: Vasileios Karakasis <karakasis@cscs.ch>
Date: Tue, 5 Jul 2016 16:13:16 +0200
Subject: [PATCH] Fixed has_contiguous_segments implementation.
The previous implementation was failing when nodes were numbered in
breadth-first order. Also gave a more descriptive name to the
algorithm.
---
src/algorithms.hpp | 45 +++++++++++++++++----------------------
src/swcio.cpp | 2 +-
tests/test_algorithms.cpp | 27 +++++++++++++++++------
3 files changed, 40 insertions(+), 34 deletions(-)
diff --git a/src/algorithms.hpp b/src/algorithms.hpp
index a1f6bad6..1d55535f 100644
--- a/src/algorithms.hpp
+++ b/src/algorithms.hpp
@@ -121,49 +121,42 @@ bool is_positive(C const& c)
}
template<typename C>
-bool has_contiguous_segments(const C &parent_index)
+std::vector<typename C::value_type> child_count(const C& parent_index)
{
static_assert(
std::is_integral<typename C::value_type>::value,
"integral type required"
);
- if (!is_minimal_degree(parent_index)) {
- return false;
- }
-
- int n = parent_index.size();
- std::vector<bool> is_leaf(n, false);
-
- for(auto i=1; i<n; ++i) {
- auto p = parent_index[i];
- if(is_leaf[p]) {
- return false;
- }
-
- if(p != i-1) {
- // we have a branch and i-1 is a leaf node
- is_leaf[i-1] = true;
- }
+ std::vector<typename C::value_type> count(parent_index.size(), 0);
+ for (auto i = 1u; i < parent_index.size(); ++i) {
+ ++count[parent_index[i]];
}
- return true;
+ return count;
}
template<typename C>
-std::vector<typename C::value_type> child_count(const C &parent_index)
+bool has_contiguous_compartments(const C& parent_index)
{
static_assert(
std::is_integral<typename C::value_type>::value,
"integral type required"
);
- std::vector<typename C::value_type> count(parent_index.size(), 0);
- for (std::size_t i = 1; i < parent_index.size(); ++i) {
- ++count[parent_index[i]];
+ if (!is_minimal_degree(parent_index)) {
+ return false;
}
- return count;
+ auto num_child = child_count(parent_index);
+ for (auto i = 1u; i < parent_index.size(); ++i) {
+ auto p = parent_index[i];
+ if (num_child[p] == 1 && p != i-1) {
+ return false;
+ }
+ }
+
+ return true;
}
template<typename C>
@@ -174,7 +167,7 @@ std::vector<typename C::value_type> branches(const C& parent_index)
"integral type required"
);
- EXPECTS(has_contiguous_segments(parent_index));
+ EXPECTS(has_contiguous_compartments(parent_index));
std::vector<typename C::value_type> branch_index;
if (parent_index.empty()) {
@@ -250,7 +243,7 @@ std::vector<typename C::value_type> make_parent_index(
}
EXPECTS(parent_index.size() == branch_index.back());
- EXPECTS(has_contiguous_segments(parent_index));
+ EXPECTS(has_contiguous_compartments(parent_index));
EXPECTS(is_strictly_monotonic_increasing(branch_index));
// expand the branch index
diff --git a/src/swcio.cpp b/src/swcio.cpp
index 3f38f8e7..db8001be 100644
--- a/src/swcio.cpp
+++ b/src/swcio.cpp
@@ -261,7 +261,7 @@ swc_record_range_clean::swc_record_range_clean(std::istream& is)
parent_list.push_back(records_[i].parent());
}
- if (!nest::mc::algorithms::has_contiguous_segments(parent_list)) {
+ if (!nest::mc::algorithms::has_contiguous_compartments(parent_list)) {
throw swc_parse_error("branches are not contiguously numbered", 0);
}
}
diff --git a/tests/test_algorithms.cpp b/tests/test_algorithms.cpp
index d1ffdf11..1a363be6 100644
--- a/tests/test_algorithms.cpp
+++ b/tests/test_algorithms.cpp
@@ -172,7 +172,7 @@ TEST(algorithms, is_positive)
);
}
-TEST(algorithms, has_contiguous_segments)
+TEST(algorithms, has_contiguous_compartments)
{
//
// 0
@@ -186,7 +186,7 @@ TEST(algorithms, has_contiguous_segments)
// 5 6
//
EXPECT_FALSE(
- nest::mc::algorithms::has_contiguous_segments(
+ nest::mc::algorithms::has_contiguous_compartments(
std::vector<int>{0, 0, 1, 2, 2, 3, 4, 2}
)
);
@@ -203,7 +203,7 @@ TEST(algorithms, has_contiguous_segments)
// 4 7
//
EXPECT_FALSE(
- nest::mc::algorithms::has_contiguous_segments(
+ nest::mc::algorithms::has_contiguous_compartments(
std::vector<int>{0, 0, 1, 2, 3, 2, 2, 5}
)
);
@@ -220,7 +220,7 @@ TEST(algorithms, has_contiguous_segments)
// 4 6
//
EXPECT_TRUE(
- nest::mc::algorithms::has_contiguous_segments(
+ nest::mc::algorithms::has_contiguous_compartments(
std::vector<int>{0, 0, 1, 2, 3, 2, 5, 2}
)
);
@@ -237,21 +237,34 @@ TEST(algorithms, has_contiguous_segments)
// 4 6
//
EXPECT_TRUE(
- nest::mc::algorithms::has_contiguous_segments(
+ nest::mc::algorithms::has_contiguous_compartments(
std::vector<int>{0, 0, 1, 2, 3, 2, 5, 1}
)
);
+ //
+ // 0
+ // / \
+ // 1 2
+ // / \
+ // 3 4
+ //
+ EXPECT_TRUE(
+ nest::mc::algorithms::has_contiguous_compartments(
+ std::vector<int>{0, 0, 0, 1, 1}
+ )
+ );
+
// Soma-only list
EXPECT_TRUE(
- nest::mc::algorithms::has_contiguous_segments(
+ nest::mc::algorithms::has_contiguous_compartments(
std::vector<int>{0}
)
);
// Empty list
EXPECT_TRUE(
- nest::mc::algorithms::has_contiguous_segments(
+ nest::mc::algorithms::has_contiguous_compartments(
std::vector<int>{}
)
);
--
GitLab