diff --git a/src/swcio.cpp b/src/swcio.cpp
index e87eaa1846458f9d00d9b97e7c8c3de4bfc54a2a..32724fe8f38685a593c6d82cdbf27448c26a325a 100644
--- a/src/swcio.cpp
+++ b/src/swcio.cpp
@@ -13,7 +13,7 @@ namespace io
//
// cell_record implementation
-//
+//
void cell_record::renumber(id_type new_id, std::map<id_type, id_type> &idmap)
{
auto old_id = id_;
@@ -79,26 +79,26 @@ std::ostream &operator<<(std::ostream &os, const cell_record &cell)
//
// Utility functions
-//
+//
bool starts_with(const std::string &str, const std::string &prefix)
{
return (str.find(prefix) == 0);
}
-void check_parse_status(const std::istream &is)
+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
- throw swc_parse_error("could not parse value");
+ throw swc_parse_error("could not parse value", parser.lineno());
}
}
template<typename T>
-T parse_value_strict(std::istream &is)
+T parse_value_strict(std::istream &is, const swc_parser &parser)
{
T val;
- check_parse_status(is >> val);
+ check_parse_status(is >> val, parser);
// everything's fine
return val;
@@ -106,10 +106,10 @@ T parse_value_strict(std::istream &is)
// specialize parsing for cell types
template<>
-cell_record::kind parse_value_strict(std::istream &is)
+cell_record::kind parse_value_strict(std::istream &is, const swc_parser &parser)
{
cell_record::id_type val;
- check_parse_status(is >> val);
+ check_parse_status(is >> val, parser);
// Let cell_record's constructor check for the type validity
return static_cast<cell_record::kind>(val);
@@ -117,13 +117,14 @@ cell_record::kind parse_value_strict(std::istream &is)
//
// swc_parser implementation
-//
+//
std::istream &swc_parser::parse_record(std::istream &is, cell_record &cell)
{
while (!is.eof() && !is.bad()) {
// consume empty and comment lines first
std::getline(is, linebuff_);
+ ++lineno_;
if (!linebuff_.empty() && !starts_with(linebuff_, comment_prefix_))
break;
}
@@ -140,23 +141,29 @@ std::istream &swc_parser::parse_record(std::istream &is, cell_record &cell)
}
if (is.fail()) {
- throw swc_parse_error("too long line detected");
+ throw swc_parse_error("too long line detected", lineno_);
}
std::istringstream line(linebuff_);
- cell = parse_record(line);
+ try {
+ cell = parse_record(line);
+ } catch (std::invalid_argument &e) {
+ // Rethrow as a parse error
+ throw swc_parse_error(e.what(), lineno_);
+ }
+
return is;
}
cell_record swc_parser::parse_record(std::istringstream &is)
{
- auto id = parse_value_strict<int>(is);
- auto type = parse_value_strict<cell_record::kind>(is);
- auto x = parse_value_strict<float>(is);
- auto y = parse_value_strict<float>(is);
- auto z = parse_value_strict<float>(is);
- auto r = parse_value_strict<float>(is);
- auto parent_id = parse_value_strict<cell_record::id_type>(is);
+ auto id = parse_value_strict<int>(is, *this);
+ auto type = parse_value_strict<cell_record::kind>(is, *this);
+ auto x = parse_value_strict<float>(is, *this);
+ auto y = parse_value_strict<float>(is, *this);
+ auto z = parse_value_strict<float>(is, *this);
+ auto r = parse_value_strict<float>(is, *this);
+ auto parent_id = parse_value_strict<cell_record::id_type>(is, *this);
// Convert to zero-based, leaving parent_id as-is if -1
if (parent_id != -1) {
diff --git a/src/swcio.hpp b/src/swcio.hpp
index 0348eb4f149303362c736d885afae8d1d77c2eb5..5365c8a5b508f6102e06c08d780cd94a64aeae0b 100644
--- a/src/swcio.hpp
+++ b/src/swcio.hpp
@@ -166,13 +166,23 @@ private:
class swc_parse_error : public std::runtime_error
{
public:
- explicit swc_parse_error(const char *msg)
+ 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)
+ explicit swc_parse_error(const std::string &msg, std::size_t lineno)
: std::runtime_error(msg)
+ , lineno_(lineno)
{ }
+
+ std::size_t lineno() const
+ {
+ return lineno_;
+ }
+
+private:
+ std::size_t lineno_;
};
class swc_parser
@@ -182,13 +192,20 @@ public:
std::string comment_prefix)
: delim_(delim)
, comment_prefix_(comment_prefix)
+ , lineno_(0)
{ }
swc_parser()
: delim_(" ")
, comment_prefix_("#")
+ , lineno_(0)
{ }
+ std::size_t lineno() const
+ {
+ return lineno_;
+ }
+
std::istream &parse_record(std::istream &is, cell_record &cell);
private:
@@ -198,6 +215,7 @@ private:
std::string delim_;
std::string comment_prefix_;
std::string linebuff_;
+ std::size_t lineno_;
};
diff --git a/tests/test_swcio.cpp b/tests/test_swcio.cpp
index 5912a1e5086bfe6a25120bf2dcfe72ccd6e9f1ba..16e6de8c4eb0d7a9b7c7de6264ba66a4f7f7a192 100644
--- a/tests/test_swcio.cpp
+++ b/tests/test_swcio.cpp
@@ -129,7 +129,7 @@ TEST(swc_parser, invalid_input)
std::istringstream is(
"1 10 14.566132 34.873772 7.857000 0.717830 -1\n");
cell_record cell;
- EXPECT_THROW(is >> cell, std::invalid_argument);
+ EXPECT_THROW(is >> cell, swc_parse_error);
}
}
@@ -340,12 +340,12 @@ TEST(cell_record_ranges, raw)
}
{
+ // Check iterator increments
std::stringstream is;
is << "1 1 14.566132 34.873772 7.857000 0.717830 -1\n";
- // Check postfix operator++
auto iter = get_cell_records<swc_io_raw>(is).begin();
- auto iend = get_cell_records<swc_io_raw>(is).end();
+ auto iend = get_cell_records<swc_io_raw>(is).end();
cell_record c;
EXPECT_NO_THROW(c = *iter++);
@@ -355,4 +355,24 @@ TEST(cell_record_ranges, raw)
// Try to read past eof
EXPECT_THROW(*iter, std::out_of_range);
}
+
+ {
+ // Check parse error context
+ std::stringstream is;
+ is << "1 1 14.566132 34.873772 7.857000 0.717830 -1\n";
+ is << "2 1 14.566132 34.873772 7.857000 0.717830 1\n";
+ is << "3 10 14.566132 34.873772 7.857000 0.717830 1\n";
+ is << "4 1 14.566132 34.873772 7.857000 0.717830 1\n";
+
+ std::vector<cell_record> cells;
+ try {
+ for (auto c : get_cell_records<swc_io_raw>(is)) {
+ cells.push_back(c);
+ }
+
+ FAIL() << "expected an exception";
+ } catch (const swc_parse_error &e) {
+ EXPECT_EQ(3u, e.lineno());
+ }
+ }
}