diff --git a/arborio/swcio.cpp b/arborio/swcio.cpp
index 9bf47ea08959918af4f6e2994faa5bfd822877c0..89c5ea3141f5f4b2b96145c9661f1bdfada29366 100644
--- a/arborio/swcio.cpp
+++ b/arborio/swcio.cpp
@@ -183,7 +183,7 @@ swc_data parse_swc(std::istream& in) {
}
swc_record r;
- while (in && in >> r) {
+ while (in && (in.peek() != '\n') && in >> r) {
records.push_back(r);
}
diff --git a/doc/concepts/morphology.rst b/doc/concepts/morphology.rst
index accf25681151cf0ec641ac377a644c76372a9020..ed4b1393f309bba0c11bcbbe8407cccba714fb23 100644
--- a/doc/concepts/morphology.rst
+++ b/doc/concepts/morphology.rst
@@ -494,10 +494,11 @@ SWC
Arbor supports reading morphologies described using the
`SWC <http://www.neuronland.org/NLMorphologyConverter/MorphologyFormats/SWC/Spec.html>`_ file format.
-SWC files describe the morphology as a list of samples with an id, an `x,y,z` location is space, a radius, a tag
-and a parent id. Arbor parses these samples, performs some checks, then generates a
-:ref:`segment tree <morph-segment_tree>` describing the morphology according to one of three possible
-interpretations.
+SWC files may contain comments, which are stored as metadata. A blank line anywhere in the file is
+interpreted as end of data. The description of the morphology is encoded as a list of samples with an id,
+an `x,y,z` location in space, a radius, a tag and a parent id. Arbor parses these samples, performs some checks,
+then generates a :ref:`segment tree <morph-segment_tree>` describing the morphology according to one of three
+possible interpretations.
The SWC file format specifications are not very detailed, which has lead different simulators to interpret
SWC files in different ways, especially when it comes to the soma. Arbor has its own an interpretation that
diff --git a/python/morphology.cpp b/python/morphology.cpp
index dba6f59494896250562d37ef034a5258b10c7bd6..c7de23acb0c61ffb48102721c7f78bbd1bbaef12 100644
--- a/python/morphology.cpp
+++ b/python/morphology.cpp
@@ -14,6 +14,12 @@
namespace pyarb {
+void check_trailing(std::istream& in, std::string fname) {
+ if (!(in >> std::ws).eof()) {
+ throw pyarb_error(util::pprintf("Trailing data found at end of file '{}'", fname));
+ }
+}
+
void register_morphology(pybind11::module& m) {
using namespace pybind11::literals;
@@ -142,7 +148,9 @@ void register_morphology(pybind11::module& m) {
throw pyarb_error(util::pprintf("can't open file '{}'", fname));
}
try {
- return arborio::load_swc_arbor(arborio::parse_swc(fid));
+ auto data = arborio::parse_swc(fid);
+ check_trailing(fid, fname);
+ return arborio::load_swc_arbor(data);
}
catch (arborio::swc_error& e) {
// Try to produce helpful error messages for SWC parsing errors.
@@ -166,7 +174,10 @@ void register_morphology(pybind11::module& m) {
throw pyarb_error(util::pprintf("can't open file '{}'", fname));
}
try {
- return arborio::load_swc_allen(arborio::parse_swc(fid), no_gaps);
+ auto data = arborio::parse_swc(fid);
+ check_trailing(fid, fname);
+ return arborio::load_swc_allen(data, no_gaps);
+
}
catch (arborio::swc_error& e) {
// Try to produce helpful error messages for SWC parsing errors.
@@ -199,7 +210,9 @@ void register_morphology(pybind11::module& m) {
throw pyarb_error(util::pprintf("can't open file '{}'", fname));
}
try {
- return arborio::load_swc_neuron(arborio::parse_swc(fid));
+ auto data = arborio::parse_swc(fid);
+ check_trailing(fid, fname);
+ return arborio::load_swc_neuron(data);
}
catch (arborio::swc_error& e) {
// Try to produce helpful error messages for SWC parsing errors.
diff --git a/test/unit/swc/ball_and_stick.swc b/test/unit/swc/ball_and_stick.swc
index 298398678a91ec8141dd60ce77796dc54155d3f3..2faf51388e4885fb6785986d5dce70ca18219d26 100644
--- a/test/unit/swc/ball_and_stick.swc
+++ b/test/unit/swc/ball_and_stick.swc
@@ -1,7 +1,6 @@
# ball and stick model with
# - soma with radius 12.6157/2
# - dendrite with length 200 and radius 0.5
-
1 1 0.0 0.0 0.0 6.30785 -1
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/test/unit/test_swcio.cpp b/test/unit/test_swcio.cpp
index d836bc0d3c8e97bdbec282ede206c0ed3a765476..06c6397ba8252137747512792b5434f4f2a3ad04 100644
--- a/test/unit/test_swcio.cpp
+++ b/test/unit/test_swcio.cpp
@@ -182,6 +182,75 @@ TEST(swc_parser, valid_parse) {
swc_data data2 = parse_swc(valid4);
EXPECT_EQ(data.records(), data2.records());
}
+}
+
+TEST(swc_parser, stream_validity) {
+ {
+ std::string valid =
+ "# metadata\n"
+ "1 1 0.1 0.2 0.3 0.4 -1\n"
+ "2 1 0.1 0.2 0.3 0.4 1\n";
+
+ std::istringstream is(valid);
+
+ auto data = parse_swc(is);
+ ASSERT_EQ(2u, data.records().size());
+ EXPECT_TRUE(data.metadata() == "metadata\n");
+ EXPECT_TRUE(is.eof());
+ }
+ {
+ std::string valid =
+ "# metadata\n"
+ "\n"
+ "1 1 0.1 0.2 0.3 0.4 -1\n"
+ "2 1 0.1 0.2 0.3 0.4 1\n";
+
+ std::istringstream is(valid);
+
+ auto data = parse_swc(is);
+ ASSERT_EQ(0u, data.records().size());
+ EXPECT_TRUE(data.metadata() == "metadata\n");
+ EXPECT_TRUE(is.good());
+
+ is >> std::ws;
+ data = parse_swc(is);
+ ASSERT_EQ(2u, data.records().size());
+ EXPECT_TRUE(data.metadata().empty());
+ EXPECT_TRUE(is.eof());
+ }
+ {
+ std::string invalid =
+ "# metadata\n"
+ "1 1 0.1 0.2 0.3 \n"
+ "2 1 0.1 0.2 0.3 0.4 1\n";
+
+ std::istringstream is(invalid);
+
+ auto data = parse_swc(is);
+ ASSERT_EQ(0u, data.records().size());
+ EXPECT_TRUE(data.metadata() == "metadata\n");
+ EXPECT_FALSE(is.good());
+ }
+ {
+ std::string invalid =
+ "# metadata\n"
+ "1 1 0.1 0.2 0.3 \n"
+ "2 1 0.1 0.2 0.3 0.4 1\n";
+
+ std::istringstream is(invalid);
+
+ auto data = parse_swc(is);
+ EXPECT_TRUE(data.metadata() == "metadata\n");
+ ASSERT_EQ(0u, data.records().size());
+ EXPECT_TRUE(data.metadata() == "metadata\n");
+ EXPECT_FALSE(is.good());
+
+ is >> std::ws;
+ data = parse_swc(is);
+ ASSERT_EQ(0u, data.records().size());
+ EXPECT_TRUE(data.metadata().empty());
+ EXPECT_FALSE(is.good());
+ }
}