diff --git a/data/ball_and_stick.swc b/data/ball_and_stick.swc
index 1737539b1b4d73d202cecab2ecb7e5599d93064e..298398678a91ec8141dd60ce77796dc54155d3f3 100644
--- a/data/ball_and_stick.swc
+++ b/data/ball_and_stick.swc
@@ -3,6 +3,5 @@
# - dendrite with length 200 and radius 0.5
1 1 0.0 0.0 0.0 6.30785 -1
-2 2 6.30785 0.0 0.0 0.5 1
-3 2 206.30785 0.0 0.0 0.5 2
-
+2 3 6.30785 0.0 0.0 0.5 1
+3 3 206.30785 0.0 0.0 0.5 2
diff --git a/src/profiling/profiler.cpp b/src/profiling/profiler.cpp
index 247c8c949958e46c2285d0c9c79341c4699a32bb..b5d2ad0d8d7bd9efe7fd8e55e5f6720ab051b3f1 100644
--- a/src/profiling/profiler.cpp
+++ b/src/profiling/profiler.cpp
@@ -1,3 +1,5 @@
+#include <numeric>
+
#include "profiler.hpp"
#include "util/debug.hpp"
@@ -373,4 +375,3 @@ void profiler_output(double threshold) {}
} // namespace util
} // namespace mc
} // namespace nest
-
diff --git a/src/swcio.cpp b/src/swcio.cpp
index 05cb61170221f3fc715ddef7c8271606c1f359d9..3f38f8e791308819ac2fe3eeecde4c78ab585799 100644
--- a/src/swcio.cpp
+++ b/src/swcio.cpp
@@ -18,7 +18,7 @@ namespace io {
//
// swc_record implementation
//
-void swc_record::renumber(id_type new_id, std::map<id_type, id_type> &idmap)
+void swc_record::renumber(id_type new_id, std::map<id_type, id_type>& idmap)
{
auto old_id = id_;
id_ = new_id;
@@ -59,7 +59,7 @@ void swc_record::check_consistency() const
}
}
-std::istream &operator>>(std::istream &is, swc_record &record)
+std::istream& operator>>(std::istream& is, swc_record& record)
{
swc_parser parser;
parser.parse_record(is, record);
@@ -67,7 +67,7 @@ std::istream &operator>>(std::istream &is, swc_record &record)
}
-std::ostream &operator<<(std::ostream &os, const swc_record &record)
+std::ostream& operator<<(std::ostream& os, const swc_record& record)
{
// output in one-based indexing
os << record.id_+1 << " "
@@ -86,12 +86,28 @@ std::ostream &operator<<(std::ostream &os, const swc_record &record)
// Utility functions
//
-bool starts_with(const std::string &str, const std::string &prefix)
+std::string::size_type find_first_non_whitespace(const std::string& str)
{
- return (str.find(prefix) == 0);
+ return str.find_first_not_of(" \f\n\r\t\v");
}
-void check_parse_status(const std::istream &is, const swc_parser &parser)
+bool starts_with(const std::string& str, const std::string& prefix)
+{
+ // ignore leading whitespace
+ auto pos = find_first_non_whitespace(str);
+ if (pos == std::string::npos) {
+ return false;
+ }
+
+ return str.find(prefix, pos) == pos;
+}
+
+bool is_space(const std::string& str)
+{
+ return find_first_non_whitespace(str) == std::string::npos;
+}
+
+void check_parse_status(const std::istream& is, const swc_parser& parser)
{
if (is.fail()) {
// If we try to read past the eof; fail bit will also be set
@@ -99,8 +115,23 @@ void check_parse_status(const std::istream &is, const swc_parser &parser)
}
}
+nest::mc::segmentKind convert_kind(const swc_record::kind& kind)
+{
+ switch (kind) {
+ case swc_record::kind::soma:
+ return segmentKind::soma;
+ case swc_record::kind::dendrite:
+ return segmentKind::dendrite;
+ case swc_record::kind::axon:
+ return segmentKind::axon;
+ default:
+ throw swc_parse_error("no known conversion for swc record type", 0);
+ }
+}
+
+
template<typename T>
-T parse_value_strict(std::istream &is, const swc_parser &parser)
+T parse_value_strict(std::istream& is, const swc_parser& parser)
{
T val;
check_parse_status(is >> val, parser);
@@ -111,7 +142,7 @@ T parse_value_strict(std::istream &is, const swc_parser &parser)
// specialize parsing for record types
template<>
-swc_record::kind parse_value_strict(std::istream &is, const swc_parser &parser)
+swc_record::kind parse_value_strict(std::istream& is, const swc_parser& parser)
{
swc_record::id_type val;
check_parse_status(is >> val, parser);
@@ -124,17 +155,15 @@ swc_record::kind parse_value_strict(std::istream &is, const swc_parser &parser)
// swc_parser implementation
//
-std::istream &swc_parser::parse_record(std::istream &is, swc_record &record)
+std::istream& swc_parser::parse_record(std::istream& is, swc_record& record)
{
while (!is.eof() && !is.bad()) {
// consume empty and comment lines first
std::getline(is, linebuff_);
++lineno_;
- if (!linebuff_.empty() &&
- !starts_with(linebuff_, comment_prefix_) &&
- !starts_with(linebuff_, "\r"))
- {
+ if (!is_space(linebuff_) &&
+ !starts_with(linebuff_, comment_prefix_)) {
break;
}
}
@@ -145,7 +174,7 @@ std::istream &swc_parser::parse_record(std::istream &is, swc_record &record)
}
if (is.eof() &&
- (linebuff_.empty() || starts_with(linebuff_, comment_prefix_))) {
+ (is_space(linebuff_) || starts_with(linebuff_, comment_prefix_))) {
// last line is either empty or a comment; don't parse anything
return is;
}
@@ -157,7 +186,7 @@ std::istream &swc_parser::parse_record(std::istream &is, swc_record &record)
std::istringstream line(linebuff_);
try {
record = parse_record(line);
- } catch (std::invalid_argument &e) {
+ } catch (std::invalid_argument& e) {
// Rethrow as a parse error
throw swc_parse_error(e.what(), lineno_);
}
@@ -165,7 +194,7 @@ std::istream &swc_parser::parse_record(std::istream &is, swc_record &record)
return is;
}
-swc_record swc_parser::parse_record(std::istringstream &is)
+swc_record swc_parser::parse_record(std::istringstream& is)
{
auto id = parse_value_strict<int>(is, *this);
auto type = parse_value_strict<swc_record::kind>(is, *this);
@@ -184,7 +213,7 @@ swc_record swc_parser::parse_record(std::istringstream &is)
}
-swc_record_range_clean::swc_record_range_clean(std::istream &is)
+swc_record_range_clean::swc_record_range_clean(std::istream& is)
{
std::unordered_set<swc_record::id_type> ids;
@@ -218,7 +247,7 @@ 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 &r : records_) {
+ for (auto& r : records_) {
if (r.id() != next_id) {
r.renumber(next_id, idmap);
}
@@ -237,14 +266,14 @@ swc_record_range_clean::swc_record_range_clean(std::istream &is)
}
}
-cell swc_read_cell(std::istream &is)
+cell swc_read_cell(std::istream& is)
{
using namespace nest::mc;
cell newcell;
std::vector<swc_record::id_type> parent_index;
std::vector<swc_record> swc_records;
- for (const auto &r : swc_get_records<swc_io_clean>(is)) {
+ for (const auto& r : swc_get_records<swc_io_clean>(is)) {
swc_records.push_back(r);
parent_index.push_back(r.parent());
}
@@ -290,7 +319,7 @@ cell swc_read_cell(std::istream &is)
// add the new cable
newcell.add_cable(new_parent_index[i],
- nest::mc::segmentKind::dendrite, radii, points);
+ convert_kind(b_start->type()), radii, points);
}
return newcell;
diff --git a/src/swcio.hpp b/src/swcio.hpp
index 4b6457123e062c65a2091853bc3e581e3c1eb8e7..6530cba35190049d58be20dcebdcf9d81570053e 100644
--- a/src/swcio.hpp
+++ b/src/swcio.hpp
@@ -13,8 +13,7 @@ namespace nest {
namespace mc {
namespace io {
-class swc_record
-{
+class swc_record {
public:
using id_type = int;
using coord_type = double;
@@ -56,10 +55,10 @@ public:
, parent_id_(-1)
{ }
- swc_record(const swc_record &other) = default;
- swc_record &operator=(const swc_record &other) = default;
+ swc_record(const swc_record& other) = default;
+ swc_record& operator=(const swc_record& other) = default;
- bool strict_equals(const swc_record &other) const
+ bool strict_equals(const swc_record& other) const
{
return id_ == other.id_ &&
x_ == other.x_ &&
@@ -70,43 +69,43 @@ public:
}
// Equality and comparison operators
- friend bool operator==(const swc_record &lhs,
- const swc_record &rhs)
+ friend bool operator==(const swc_record& lhs,
+ const swc_record& rhs)
{
return lhs.id_ == rhs.id_;
}
- friend bool operator<(const swc_record &lhs,
- const swc_record &rhs)
+ friend bool operator<(const swc_record& lhs,
+ const swc_record& rhs)
{
return lhs.id_ < rhs.id_;
}
- friend bool operator<=(const swc_record &lhs,
- const swc_record &rhs)
+ friend bool operator<=(const swc_record& lhs,
+ const swc_record& rhs)
{
return (lhs < rhs) || (lhs == rhs);
}
- friend bool operator!=(const swc_record &lhs,
- const swc_record &rhs)
+ friend bool operator!=(const swc_record& lhs,
+ const swc_record& rhs)
{
return !(lhs == rhs);
}
- friend bool operator>(const swc_record &lhs,
- const swc_record &rhs)
+ friend bool operator>(const swc_record& lhs,
+ const swc_record& rhs)
{
return !(lhs < rhs) && (lhs != rhs);
}
- friend bool operator>=(const swc_record &lhs,
- const swc_record &rhs)
+ friend bool operator>=(const swc_record& lhs,
+ const swc_record& rhs)
{
return !(lhs < rhs);
}
- friend std::ostream &operator<<(std::ostream &os, const swc_record &record);
+ friend std::ostream& operator<<(std::ostream& os, const swc_record& record);
kind type() const
{
@@ -153,7 +152,7 @@ public:
return nest::mc::point<coord_type>(x_, y_, z_);
}
- void renumber(id_type new_id, std::map<id_type, id_type> &idmap);
+ void renumber(id_type new_id, std::map<id_type, id_type>& idmap);
private:
void check_consistency() const;
@@ -169,12 +168,12 @@ private:
class swc_parse_error : public std::runtime_error
{
public:
- explicit swc_parse_error(const char *msg, std::size_t lineno)
+ explicit swc_parse_error(const char* msg, std::size_t lineno)
: std::runtime_error(msg)
, lineno_(lineno)
{ }
- explicit swc_parse_error(const std::string &msg, std::size_t lineno)
+ explicit swc_parse_error(const std::string& msg, std::size_t lineno)
: std::runtime_error(msg)
, lineno_(lineno)
{ }
@@ -188,11 +187,9 @@ private:
std::size_t lineno_;
};
-class swc_parser
-{
+class swc_parser {
public:
- swc_parser(const std::string &delim,
- std::string comment_prefix)
+ swc_parser(const std::string& delim, std::string comment_prefix)
: delim_(delim)
, comment_prefix_(comment_prefix)
, lineno_(0)
@@ -209,12 +206,11 @@ public:
return lineno_;
}
- std::istream &parse_record(std::istream &is, swc_record &record);
+ std::istream& parse_record(std::istream& is, swc_record& record);
private:
-
// Read the record from a string stream; will be treated like a single line
- swc_record parse_record(std::istringstream &is);
+ swc_record parse_record(std::istringstream& is);
std::string delim_;
std::string comment_prefix_;
@@ -223,15 +219,14 @@ private:
};
-std::istream &operator>>(std::istream &is, swc_record &record);
+std::istream& operator>>(std::istream& is, swc_record& record);
class swc_record_stream_iterator :
- public std::iterator<std::forward_iterator_tag, swc_record>
-{
+ public std::iterator<std::forward_iterator_tag, swc_record> {
public:
struct eof_tag { };
- swc_record_stream_iterator(std::istream &is)
+ swc_record_stream_iterator(std::istream& is)
: is_(is)
, eof_(false)
{
@@ -240,19 +235,19 @@ public:
read_next_record();
}
- swc_record_stream_iterator(std::istream &is, eof_tag)
+ swc_record_stream_iterator(std::istream& is, eof_tag)
: is_(is)
, eof_(true)
{ }
- swc_record_stream_iterator(const swc_record_stream_iterator &other)
+ swc_record_stream_iterator(const swc_record_stream_iterator& other)
: is_(other.is_)
, parser_(other.parser_)
, curr_record_(other.curr_record_)
, eof_(other.eof_)
{ }
- swc_record_stream_iterator &operator++()
+ swc_record_stream_iterator& operator++()
{
if (eof_) {
throw std::out_of_range("attempt to read past eof");
@@ -278,7 +273,7 @@ public:
return curr_record_;
}
- bool operator==(const swc_record_stream_iterator &other) const
+ bool operator==(const swc_record_stream_iterator& other) const
{
if (eof_ && other.eof_) {
return true;
@@ -287,13 +282,13 @@ public:
}
}
- bool operator!=(const swc_record_stream_iterator &other) const
+ bool operator!=(const swc_record_stream_iterator& other) const
{
return !(*this == other);
}
- friend std::ostream &operator<<(std::ostream &os,
- const swc_record_stream_iterator &iter)
+ friend std::ostream& operator<<(std::ostream& os,
+ const swc_record_stream_iterator& iter)
{
os << "{ is_.tellg(): " << iter.is_.tellg() << ", "
<< "curr_record_: " << iter.curr_record_ << ", "
@@ -311,7 +306,7 @@ private:
}
}
- std::istream &is_;
+ std::istream& is_;
swc_parser parser_;
swc_record curr_record_;
@@ -321,16 +316,15 @@ private:
};
-class swc_record_range_raw
-{
+class swc_record_range_raw {
public:
using value_type = swc_record;
- using reference = value_type &;
- using const_reference = const value_type &;
+ using reference = value_type&;
+ using const_reference = const value_type&;
using iterator = swc_record_stream_iterator;
using const_iterator = const swc_record_stream_iterator;
- swc_record_range_raw(std::istream &is)
+ swc_record_range_raw(std::istream& is)
: is_(is)
{ }
@@ -351,7 +345,7 @@ public:
}
private:
- std::istream &is_;
+ std::istream& is_;
};
//
@@ -362,16 +356,15 @@ private:
// https://github.com/eth-cscs/cell_algorithms/wiki/SWC-file-parsing
//
-class swc_record_range_clean
-{
+class swc_record_range_clean {
public:
using value_type = swc_record;
- using reference = value_type &;
- using const_referene = const value_type &;
+ using reference = value_type&;
+ using const_referene = const value_type&;
using iterator = std::vector<swc_record>::iterator;
using const_iterator = std::vector<swc_record>::const_iterator;
- swc_record_range_clean(std::istream &is);
+ swc_record_range_clean(std::istream& is);
iterator begin()
{
@@ -408,12 +401,12 @@ struct swc_io_clean
};
template<typename T = swc_io_clean>
-typename T::record_range_type swc_get_records(std::istream &is)
+typename T::record_range_type swc_get_records(std::istream& is)
{
return typename T::record_range_type(is);
}
-cell swc_read_cell(std::istream &is);
+cell swc_read_cell(std::istream& is);
} // namespace io
} // namespace mc
diff --git a/tests/test_swcio.cpp b/tests/test_swcio.cpp
index 0ebe9c84b06ff7c22db289ebcb79c21eb50239d4..32eaff75b967ccf9c5f8b7ef7f06c8b3d8b10f3e 100644
--- a/tests/test_swcio.cpp
+++ b/tests/test_swcio.cpp
@@ -13,12 +13,12 @@
// Path to data directory can be overriden at compile time.
#if !defined(DATADIR)
-#define DATADIR "../data"
+# define DATADIR "../data"
#endif
// SWC tests
-void expect_record_equals(const nest::mc::io::swc_record &expected,
- const nest::mc::io::swc_record &actual)
+void expect_record_equals(const nest::mc::io::swc_record& expected,
+ const nest::mc::io::swc_record& actual)
{
EXPECT_EQ(expected.id(), actual.id());
EXPECT_EQ(expected.type(), actual.type());
@@ -159,7 +159,7 @@ TEST(swc_parser, invalid_input)
}
FAIL() << "expected swc_parse_error, none was thrown\n";
- } catch (const swc_parse_error &e) {
+ } catch (const swc_parse_error& e) {
SUCCEED();
}
}
@@ -187,6 +187,58 @@ TEST(swc_parser, valid_input)
expect_record_equals(record_orig, record);
}
+ {
+ // check comment not starting at first character
+ swc_record record, record_orig;
+ std::istringstream is(" #comment");
+ EXPECT_NO_THROW(is >> record);
+ expect_record_equals(record_orig, record);
+ }
+
+ {
+ // check whitespace lines
+ swc_record record;
+ std::stringstream is;
+ is << "#comment\n";
+ is << " \t\n";
+ is << "1 1 14.566132 34.873772 7.857000 0.717830 -1\n";
+
+ EXPECT_NO_THROW(is >> record);
+ swc_record record_expected(
+ swc_record::kind::soma,
+ 0, 14.566132, 34.873772, 7.857000, 0.717830, -1);
+
+ expect_record_equals(record_expected, record);
+ }
+
+ {
+ // check windows eol
+ swc_record record;
+ std::stringstream is;
+ is << "#comment\r\n";
+ is << "\r\n";
+ is << "1 1 14.566132 34.873772 7.857000 0.717830 -1\r\n";
+
+ EXPECT_NO_THROW(is >> record);
+ swc_record record_expected(
+ swc_record::kind::soma,
+ 0, 14.566132, 34.873772, 7.857000, 0.717830, -1);
+
+ expect_record_equals(record_expected, record);
+ }
+
+ {
+ // check old-style mac eol; these eol are treated as simple whitespace
+ // characters, so in the following case no parse error shall be thrown
+ // and no record shall be read
+ swc_record record, record_expected;
+ std::stringstream is;
+ is << "#comment\r";
+ is << "1 1 14.566132 34.873772 7.857000 0.717830 -1\r";
+
+ EXPECT_NO_THROW(is >> record);
+ expect_record_equals(record_expected, record);
+ }
{
// check last line case (no newline at the end)
@@ -233,9 +285,9 @@ TEST(swc_parser, from_allen_db)
using namespace nest::mc;
std::string datadir{DATADIR};
- auto fname = datadir+"/example.swc";
+ auto fname = datadir + "/example.swc";
std::ifstream fid(fname);
- if(!fid.is_open()) {
+ if (!fid.is_open()) {
std::cerr << "unable to open file " << fname << "... skipping test\n";
return;
}
@@ -400,7 +452,7 @@ TEST(swc_record_ranges, raw)
}
ADD_FAILURE() << "expected an exception\n";
- } catch (const swc_parse_error &e) {
+ } catch (const swc_parse_error& e) {
EXPECT_EQ(3u, e.lineno());
}
}
@@ -432,11 +484,11 @@ TEST(swc_io, cell_construction)
std::stringstream is;
is << "1 1 0 0 0 2.1 -1\n";
- is << "2 2 0.1 1.2 1.2 1.3 1\n";
- is << "3 2 1.0 2.0 2.2 1.1 2\n";
- is << "4 2 1.5 3.3 1.3 2.2 3\n";
- is << "5 2 2.5 5.3 2.5 0.7 3\n";
- is << "6 2 3.5 2.3 3.7 3.4 5\n";
+ is << "2 3 0.1 1.2 1.2 1.3 1\n";
+ is << "3 3 1.0 2.0 2.2 1.1 2\n";
+ is << "4 3 1.5 3.3 1.3 2.2 3\n";
+ is << "5 3 2.5 5.3 2.5 0.7 3\n";
+ is << "6 3 3.5 2.3 3.7 3.4 5\n";
using point_type = point<double>;
std::vector<point_type> points = {
@@ -500,9 +552,9 @@ TEST(swc_io, cell_construction)
TEST(swc_parser, from_file_ball_and_stick)
{
std::string datadir{DATADIR};
- auto fname = datadir+"/ball_and_stick.swc";
+ auto fname = datadir + "/ball_and_stick.swc";
std::ifstream fid(fname);
- if(!fid.is_open()) {
+ if (!fid.is_open()) {
std::cerr << "unable to open file " << fname << "... skipping test\n";
return;
}
@@ -521,35 +573,3 @@ TEST(swc_parser, from_file_ball_and_stick)
EXPECT_TRUE(nest::mc::cell_basic_equality(local_cell, cell));
}
-
-// check that windows EOL are supported in linux.
-// This test is based on the ball_and_stick.swc with windows endings inserted
-// manually in a file stream, regression test for issue_34
-TEST(swc_parser, windows_eol)
-{
-
- // Check valid usage
- std::stringstream is;
- is << "# ball and stick model with\r\n";
- is << "# - soma with radius 12.6157 2\r\n";
- is << "# - dendrite with length 200 and radius 0.5\r\n";
- is << "\r\n"; // parser stubles over empty line with \r\n
- is << "1 1 0.0 0.0 0.0 6.30785 -1\r\n";
- is << "2 2 6.30785 0.0 0.0 0.5 1\r\n";
- is << "3 2 206.30785 0.0 0.0 0.5 2\r\n";
- is << "\n";
-
- // read the file into a cell object
- auto cell = nest::mc::io::swc_read_cell(is);
-
- // verify that the correct number of nodes was read
- EXPECT_EQ(cell.num_segments(), 2);
- EXPECT_EQ(cell.num_compartments(), 2u);
-
- // make an equivalent cell via C++ interface
- nest::mc::cell local_cell;
- local_cell.add_soma(6.30785);
- local_cell.add_cable(0, nest::mc::segmentKind::dendrite, 0.5, 0.5, 200);
-
- EXPECT_TRUE(nest::mc::cell_basic_equality(local_cell, cell));
-}