From 0a31d40c1855c469318da6f0451fd30aa67d3865 Mon Sep 17 00:00:00 2001
From: "w.klijn" <w.klijn@fz-juelich.de>
Date: Fri, 1 Jul 2016 12:46:04 +0200
Subject: [PATCH] Add save_getline with windows EOL support
Issue 34 parse errors when opening a file created in windows.
Solution is a method that reads the lines in a windows and linux save manner.
Includes a unit/regression tests toggling between red and green after the fix is applied.
---
src/swcio.cpp | 37 ++++++++++++++++++++++++++++++++++++-
src/swcio.hpp | 3 +++
tests/test_swcio.cpp | 34 ++++++++++++++++++++++++++++++++++
3 files changed, 73 insertions(+), 1 deletion(-)
diff --git a/src/swcio.cpp b/src/swcio.cpp
index 203f69eb..588d969d 100644
--- a/src/swcio.cpp
+++ b/src/swcio.cpp
@@ -123,11 +123,46 @@ swc_record::kind parse_value_strict(std::istream &is, const swc_parser &parser)
// swc_parser implementation
//
+std::istream& swc_parser::safe_getline(std::istream& is, std::string& t)
+{
+ // Based on http://stackoverflow.com/questions/6089231/getting-std-ifstream-to-handle-lf-cr-and-crlf
+ t.clear();
+
+ // The characters in the stream are read one-by-one using a std::streambuf.
+ // That is faster than reading them one-by-one using the std::istream.
+ // Code that uses streambuf this way must be guarded by a sentry object.
+ // The sentry object performs various tasks,
+ // such as thread synchronization and updating the stream state.
+
+ std::istream::sentry se(is, true);
+ std::streambuf* sb = is.rdbuf();
+
+ for (;;) {
+ int c = sb->sbumpc();
+ switch (c) {
+ case '\n':
+ return is;
+ case '\r':
+ if (sb->sgetc() == '\n')
+ sb->sbumpc();
+ return is;
+ case EOF:
+ // Also handle the case when the last line has no line ending
+ if (t.empty())
+ is.setstate(std::ios::eofbit);
+ return is;
+ default:
+ t += (char)c;
+ }
+ }
+}
+
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_);
+ safe_getline(is, linebuff_);
+
++lineno_;
if (!linebuff_.empty() && !starts_with(linebuff_, comment_prefix_))
break;
diff --git a/src/swcio.hpp b/src/swcio.hpp
index 70f979cd..09c89f81 100644
--- a/src/swcio.hpp
+++ b/src/swcio.hpp
@@ -211,6 +211,9 @@ public:
std::istream &parse_record(std::istream &is, swc_record &record);
+ // Getline version supporting both windows and linux line endings
+ std::istream &safe_getline(std::istream& is, std::string& t);
+
private:
// Read the record from a string stream; will be treated like a single line
swc_record parse_record(std::istringstream &is);
diff --git a/tests/test_swcio.cpp b/tests/test_swcio.cpp
index 5ba0b991..fed88fb3 100644
--- a/tests/test_swcio.cpp
+++ b/tests/test_swcio.cpp
@@ -521,3 +521,37 @@ 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)
+{
+ std::string datadir{ DATADIR };
+ auto fname = datadir + "/ball_and_stick.swc";
+ std::ifstream fid(fname);
+
+ // 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";
+ 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";
+
+ // read the file into a cell object
+ auto cell = nest::mc::io::swc_read_cell(fid);
+
+ // 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));
+}
--
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