diff --git a/src/swcio.cpp b/src/swcio.cpp
index 32724fe8f38685a593c6d82cdbf27448c26a325a..28e189a6f5a19df31c9ee961ffe0fe79be1a7676 100644
--- a/src/swcio.cpp
+++ b/src/swcio.cpp
@@ -174,9 +174,8 @@ cell_record swc_parser::parse_record(std::istringstream &is)
}
-std::vector<cell_record> swc_read_cells(std::istream &is)
+cell_record_range_clean::cell_record_range_clean(std::istream &is)
{
- std::vector<cell_record> cells;
std::unordered_set<cell_record::id_type> ids;
std::size_t num_trees = 0;
@@ -184,40 +183,38 @@ std::vector<cell_record> swc_read_cells(std::istream &is)
bool needsort = false;
cell_record curr_cell;
- while ( !(is >> curr_cell).eof()) {
- if (curr_cell.parent() == -1 && ++num_trees > 1) {
+ for (auto c : swc_get_records<swc_io_raw>(is)) {
+ if (c.parent() == -1 && ++num_trees > 1) {
// only a single tree is allowed
break;
}
- auto inserted = ids.insert(curr_cell.id());
+ auto inserted = ids.insert(c.id());
if (inserted.second) {
// not a duplicate; insert cell
- cells.push_back(curr_cell);
- if (!needsort && curr_cell.id() < last_id) {
+ cells_.push_back(c);
+ if (!needsort && c.id() < last_id) {
needsort = true;
}
- last_id = curr_cell.id();
+ last_id = c.id();
}
}
if (needsort) {
- std::sort(cells.begin(), cells.end());
+ std::sort(cells_.begin(), cells_.end());
}
// Renumber cells if necessary
std::map<cell_record::id_type, cell_record::id_type> idmap;
cell_record::id_type next_id = 0;
- for (auto &c : cells) {
+ for (auto &c : cells_) {
if (c.id() != next_id) {
c.renumber(next_id, idmap);
}
++next_id;
}
-
- return std::move(cells);
}
} // end of nestmc::io
diff --git a/src/swcio.hpp b/src/swcio.hpp
index 5365c8a5b508f6102e06c08d780cd94a64aeae0b..e267c184b4e462b2015fb8c38866e2133d60b8b1 100644
--- a/src/swcio.hpp
+++ b/src/swcio.hpp
@@ -221,16 +221,6 @@ private:
std::istream &operator>>(std::istream &is, cell_record &cell);
-//
-// Reads cells from an input stream until an eof is encountered and returns a
-// cleaned sequence of cell records.
-//
-// For more information check here:
-// https://github.com/eth-cscs/cell_algorithms/wiki/SWC-file-parsing
-//
-std::vector<cell_record> swc_read_cells(std::istream &is);
-
-
class cell_record_stream_iterator :
public std::iterator<std::forward_iterator_tag, cell_record>
{
@@ -355,8 +345,42 @@ private:
std::istream &is_;
};
+//
+// Reads cells from an input stream until an eof is encountered and returns a
+// cleaned sequence of cell records.
+//
+// For more information check here:
+// https://github.com/eth-cscs/cell_algorithms/wiki/SWC-file-parsing
+//
+
class cell_record_range_clean
{
+public:
+ using value_type = cell_record;
+ using reference = value_type &;
+ using const_referene = const value_type &;
+ using iterator = std::vector<cell_record>::iterator;
+ using const_iterator = std::vector<cell_record>::const_iterator;
+
+ cell_record_range_clean(std::istream &is);
+
+ iterator begin()
+ {
+ return cells_.begin();
+ }
+
+ iterator end()
+ {
+ return cells_.end();
+ }
+
+ std::size_t size()
+ {
+ return cells_.size();
+ }
+
+private:
+ std::vector<cell_record> cells_;
};
struct swc_io_raw
@@ -366,11 +390,11 @@ struct swc_io_raw
struct swc_io_clean
{
- using cell_range_type = cell_record_range_raw;
+ using cell_range_type = cell_record_range_clean;
};
template<typename T = swc_io_clean>
- typename T::cell_range_type get_cell_records(std::istream &is)
+ typename T::cell_range_type swc_get_records(std::istream &is)
{
return typename T::cell_range_type(is);
}
diff --git a/tests/test_swcio.cpp b/tests/test_swcio.cpp
index c7b282af14e26a4001216ed3cdf322c0a6bd5d09..7ecd5fc013d98e66428d7a85cb658360e4ca6f2d 100644
--- a/tests/test_swcio.cpp
+++ b/tests/test_swcio.cpp
@@ -186,16 +186,12 @@ TEST(swc_parser, valid_input)
swc_input << c << "\n";
swc_input << "# this is a final comment\n";
- try {
- std::size_t nr_records = 0;
- cell_record cell;
- while ( !(swc_input >> cell).eof()) {
- ASSERT_LT(nr_records, cells_orig.size());
- expect_cell_equals(cells_orig[nr_records], cell);
- ++nr_records;
- }
- } catch (std::exception &e) {
- ADD_FAILURE() << "unexpected exception thrown\n";
+
+ std::size_t nr_records = 0;
+ for (auto cell : swc_get_records<swc_io_raw>(swc_input)) {
+ ASSERT_LT(nr_records, cells_orig.size());
+ expect_cell_equals(cells_orig[nr_records], cell);
+ ++nr_records;
}
}
}
@@ -213,8 +209,7 @@ TEST(swc_parser, from_allen_db)
// load the cell records into a std::vector
std::vector<io::cell_record> nodes;
- io::cell_record node;
- while( !(fid >> node).eof()) {
+ for (auto node : io::swc_get_records<io::swc_io_raw>(fid)) {
nodes.push_back(std::move(node));
}
@@ -234,8 +229,7 @@ TEST(swc_parser, input_cleaning)
is << "2 1 14.566132 34.873772 7.857000 0.717830 1\n";
is << "2 1 14.566132 34.873772 7.857000 0.717830 1\n";
- auto cells = swc_read_cells(is);
- EXPECT_EQ(2u, cells.size());
+ EXPECT_EQ(2u, swc_get_records(is).size());
}
{
@@ -246,7 +240,7 @@ TEST(swc_parser, input_cleaning)
is << "3 1 14.566132 34.873772 7.857000 0.717830 -1\n";
is << "4 1 14.566132 34.873772 7.857000 0.717830 1\n";
- auto cells = swc_read_cells(is);
+ auto cells = swc_get_records(is);
EXPECT_EQ(2u, cells.size());
}
@@ -259,14 +253,15 @@ TEST(swc_parser, input_cleaning)
is << "1 1 14.566132 34.873772 7.857000 0.717830 -1\n";
std::array<cell_record::id_type, 4> expected_id_list = {{ 0, 1, 2, 3 }};
- auto cells = swc_read_cells(is);
- ASSERT_EQ(4u, cells.size());
auto expected_id = expected_id_list.cbegin();
- for (const auto &c : cells) {
+ for (auto c : swc_get_records(is)) {
EXPECT_EQ(*expected_id, c.id());
++expected_id;
}
+
+ // Check that we have read through the whole input
+ EXPECT_EQ(expected_id_list.end(), expected_id);
}
{
@@ -279,21 +274,23 @@ TEST(swc_parser, input_cleaning)
is << "51 1 14.566132 34.873772 7.857000 0.717830 1\n";
is << "61 1 14.566132 34.873772 7.857000 0.717830 51\n";
- auto cells = swc_read_cells(is);
std::array<cell_record::id_type, 6> expected_id_list =
{{ 0, 1, 2, 3, 4, 5 }};
std::array<cell_record::id_type, 6> expected_parent_list =
{{ -1, 0, 1, 1, 0, 4 }};
- ASSERT_EQ(6u, cells.size());
auto expected_id = expected_id_list.cbegin();
auto expected_parent = expected_parent_list.cbegin();
- for (const auto &c : cells) {
+ for (auto c : swc_get_records(is)) {
EXPECT_EQ(*expected_id, c.id());
EXPECT_EQ(*expected_parent, c.parent());
++expected_id;
++expected_parent;
}
+
+ // Check that we have read through the whole input
+ EXPECT_EQ(expected_id_list.end(), expected_id);
+ EXPECT_EQ(expected_parent_list.end(), expected_parent);
}
}
@@ -310,7 +307,7 @@ TEST(cell_record_ranges, raw)
is << "4 1 14.566132 34.873772 7.857000 0.717830 1\n";
std::vector<cell_record> cells;
- for (auto c : get_cell_records<swc_io_raw>(is)) {
+ for (auto c : swc_get_records<swc_io_raw>(is)) {
cells.push_back(c);
}
@@ -318,8 +315,8 @@ TEST(cell_record_ranges, raw)
bool entered = false;
auto citer = cells.begin();
- for (auto c : get_cell_records<swc_io_raw>(is)) {
- EXPECT_TRUE(c.strict_equals(*citer++));
+ for (auto c : swc_get_records<swc_io_raw>(is)) {
+ expect_cell_equals(c, *citer++);
entered = true;
}
@@ -331,7 +328,7 @@ TEST(cell_record_ranges, raw)
std::stringstream is;
is << "1 1 14.566132 34.873772 7.857000 0.717830 -1\n";
- auto ibegin = get_cell_records<swc_io_raw>(is).begin();
+ auto ibegin = swc_get_records<swc_io_raw>(is).begin();
EXPECT_NO_THROW(++ibegin);
EXPECT_THROW(*ibegin, std::out_of_range);
@@ -343,8 +340,8 @@ TEST(cell_record_ranges, raw)
std::stringstream is;
is << "1 1 14.566132 34.873772 7.857000 0.717830 -1\n";
- auto iter = get_cell_records<swc_io_raw>(is).begin();
- auto iend = get_cell_records<swc_io_raw>(is).end();
+ auto iter = swc_get_records<swc_io_raw>(is).begin();
+ auto iend = swc_get_records<swc_io_raw>(is).end();
cell_record c;
EXPECT_NO_THROW(c = *iter++);
@@ -365,11 +362,11 @@ TEST(cell_record_ranges, raw)
std::vector<cell_record> cells;
try {
- for (auto c : get_cell_records<swc_io_raw>(is)) {
+ for (auto c : swc_get_records<swc_io_raw>(is)) {
cells.push_back(c);
}
- FAIL() << "expected an exception";
+ ADD_FAILURE() << "expected an exception\n";
} catch (const swc_parse_error &e) {
EXPECT_EQ(3u, e.lineno());
}