From 41972a06c0d9fb07db4a4789a9897ebdfec4dc80 Mon Sep 17 00:00:00 2001
From: Vasileios Karakasis <karakasis@cscs.ch>
Date: Mon, 18 Apr 2016 11:31:09 +0200
Subject: [PATCH] Reject SWC input if branches are not contiguously numbered.
---
src/algorithms.hpp | 1 +
src/swcio.cpp | 29 ++++++++++++++++++++---------
2 files changed, 21 insertions(+), 9 deletions(-)
diff --git a/src/algorithms.hpp b/src/algorithms.hpp
index d627b755..25210915 100644
--- a/src/algorithms.hpp
+++ b/src/algorithms.hpp
@@ -3,6 +3,7 @@
#include <algorithm>
#include <numeric>
#include <type_traits>
+#include <vector>
/*
* Some simple wrappers around stl algorithms to improve readability of code
diff --git a/src/swcio.cpp b/src/swcio.cpp
index 2c3fe4d2..796972a6 100644
--- a/src/swcio.cpp
+++ b/src/swcio.cpp
@@ -4,6 +4,7 @@
#include <sstream>
#include <unordered_set>
+#include <algorithms.hpp>
#include <swcio.hpp>
namespace nest {
@@ -183,21 +184,21 @@ swc_record_range_clean::swc_record_range_clean(std::istream &is)
bool needsort = false;
swc_record curr_record;
- for (auto c : swc_get_records<swc_io_raw>(is)) {
- if (c.parent() == -1 && ++num_trees > 1) {
+ for (auto r : swc_get_records<swc_io_raw>(is)) {
+ if (r.parent() == -1 && ++num_trees > 1) {
// only a single tree is allowed
break;
}
- auto inserted = ids.insert(c.id());
+ auto inserted = ids.insert(r.id());
if (inserted.second) {
// not a duplicate; insert record
- records_.push_back(c);
- if (!needsort && c.id() < last_id) {
+ records_.push_back(r);
+ if (!needsort && r.id() < last_id) {
needsort = true;
}
- last_id = c.id();
+ last_id = r.id();
}
}
@@ -208,13 +209,23 @@ swc_record_range_clean::swc_record_range_clean(std::istream &is)
// Renumber records if necessary
std::map<swc_record::id_type, swc_record::id_type> idmap;
swc_record::id_type next_id = 0;
- for (auto &c : records_) {
- if (c.id() != next_id) {
- c.renumber(next_id, idmap);
+ for (auto &r : records_) {
+ if (r.id() != next_id) {
+ r.renumber(next_id, idmap);
}
++next_id;
}
+
+ // Reject if branches are not contiguously numbered
+ std::vector<swc_record::id_type> parent_list = { 0 };
+ for (std::size_t i = 1; i < records_.size(); ++i) {
+ parent_list.push_back(records_[i].parent());
+ }
+
+ if (!nest::mc::algorithms::is_contiguously_numbered(parent_list)) {
+ throw swc_parse_error("branches are not contiguously numbered", 0);
+ }
}
} // namespace io
--
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