diff --git a/arbor/include/arbor/swcio.hpp b/arbor/include/arbor/swcio.hpp
index efcd17fa0a97e3591bbf0389cd84e068002b7872..db5b672f2cfdf39f576699ba39f734d4b9db9944 100644
--- a/arbor/include/arbor/swcio.hpp
+++ b/arbor/include/arbor/swcio.hpp
@@ -33,11 +33,6 @@ struct swc_duplicate_record_id: swc_error {
explicit swc_duplicate_record_id(int record_id);
};
-// Irregular record ordering.
-struct swc_irregular_id: swc_error {
- explicit swc_irregular_id(int record_id);
-};
-
// Smells like a spherical soma.
struct swc_spherical_soma: swc_error {
explicit swc_spherical_soma(int record_id);
@@ -88,25 +83,22 @@ struct swc_data {
// in comments (stripping initial '#' and subsequent whitespace).
// Stops at EOF or after reading the first line that does not parse as SWC.
//
-// Note that 'one-point soma' SWC files are explicitly not supported.
-//
// In `relaxed` mode, it will check that:
// * There are no duplicate record ids.
// * All record ids are positive.
// * There are no records whose parent id is not less than the record id.
// * Only one record has parent id -1; all other parent ids correspond to records.
-// * There are at least two records.
//
-// In `strict` mode, it will additionally check:
-// * Record ids are numbered contiguously from 1.
-// * The data cannot be interpreted as a 'spherical soma' SWC file.
-// Specifically, the root record shares its tag with at least one other
-// record with has the root as parent.
+// In `strict` mode, it will additionally check that the data cannot be interpreted
+// as a 'spherical soma' SWC file:
+// * The root record must share its tag with at least one other record
+// which has the root as parent. This implies that there must be at least
+// two SWC records.
//
// Throws a corresponding exception of type derived from `swc_error` if any of the
// conditions above are encountered.
//
-// SWC records are stored in id order.
+// SWC records are returned in id order.
enum class swc_mode { relaxed, strict };
@@ -118,6 +110,14 @@ swc_data parse_swc(const std::string& text, swc_mode mode = swc_mode::strict);
swc_data parse_swc(std::vector<swc_record>, swc_mode = swc_mode::strict);
// Convert a valid, ordered sequence of SWC records to a morphological segment tree.
+//
+// Note that 'one-point soma' SWC files are explicitly not supported; the swc_data
+// is expected to abide by the restrictions of `strict` mode parsing as described
+// above.
+//
+// The generated segment tree will be contiguous. There will be one segment for
+// each SWC record after the first: this record defines the tag and distal point
+// of the segment, while the proximal point is taken from the parent record.
segment_tree as_segment_tree(const std::vector<swc_record>&);
diff --git a/arbor/swcio.cpp b/arbor/swcio.cpp
index 1703f1a7e902acaaa00ce668a98ee74aacda0c1c..c17b375ecf14e226f81083a5308be2fc5ee75558 100644
--- a/arbor/swcio.cpp
+++ b/arbor/swcio.cpp
@@ -33,10 +33,6 @@ swc_duplicate_record_id::swc_duplicate_record_id(int record_id):
swc_error("duplicate SWC sample id", record_id)
{}
-swc_irregular_id::swc_irregular_id(int record_id):
- swc_error("SWC record id not numbered consecutively from 1", record_id)
-{}
-
swc_spherical_soma::swc_spherical_soma(int record_id):
swc_error("SWC with spherical somata are not supported", record_id)
{}
@@ -94,10 +90,6 @@ static std::vector<swc_record> sort_and_validate_swc(std::vector<swc_record> rec
throw swc_record_precedes_parent(r.id);
}
- if (mode==swc_mode::strict && r.id != (int)i+1) {
- throw swc_irregular_id(r.id);
- }
-
if (!seen.insert(r.id).second) {
throw swc_duplicate_record_id(r.id);
}
diff --git a/test/unit/test_swcio.cpp b/test/unit/test_swcio.cpp
index ab890246d7474d7080245d34ba9f40f07152f18b..debcb072109ed22912b6bd68b3ed9b0d497bed93 100644
--- a/test/unit/test_swcio.cpp
+++ b/test/unit/test_swcio.cpp
@@ -4,6 +4,8 @@
#include <sstream>
#include <arbor/cable_cell.hpp>
+#include <arbor/morph/primitives.hpp>
+#include <arbor/morph/segment_tree.hpp>
#include <arbor/swcio.hpp>
#include "../gtest.h"
@@ -110,16 +112,29 @@ TEST(swc_parser, bad_relaxed) {
EXPECT_THROW(parse_swc(bad5, swc_mode::relaxed), swc_no_such_parent);
}
+}
+TEST(swc_parser, bad_strict) {
{
std::string bad6 =
- "1 1 0.1 0.2 0.3 0.4 -1\n";
+ "1 7 0.1 0.2 0.3 0.4 -1\n"; // just one record
EXPECT_THROW(parse_swc(bad6, swc_mode::relaxed), swc_spherical_soma);
}
+ {
+ std::string bad3 =
+ "1 4 0.1 0.2 0.3 0.4 -1\n" // solitary tag
+ "2 6 0.1 0.2 0.3 0.4 1\n"
+ "3 6 0.1 0.2 0.3 0.4 2\n"
+ "4 6 0.1 0.2 0.3 0.4 1\n";
+
+ EXPECT_THROW(parse_swc(bad3, swc_mode::strict), swc_spherical_soma);
+ EXPECT_NO_THROW(parse_swc(bad3, swc_mode::relaxed));
+ }
}
-TEST(swc_parser, bad_strict) {
+TEST(swc_parser, valid_relaxed) {
+ // Non-contiguous is okay.
{
std::string bad1 =
"1 1 0.1 0.2 0.3 0.4 -1\n"
@@ -127,10 +142,10 @@ TEST(swc_parser, bad_strict) {
"3 1 0.1 0.2 0.3 0.4 2\n"
"5 1 0.1 0.2 0.3 0.4 3\n"; // non-contiguous
- EXPECT_THROW(parse_swc(bad1, swc_mode::strict), swc_irregular_id);
EXPECT_NO_THROW(parse_swc(bad1, swc_mode::relaxed));
}
+ // As is out of order.
{
std::string bad2 =
"1 1 0.1 0.2 0.3 0.4 -1\n"
@@ -138,23 +153,9 @@ TEST(swc_parser, bad_strict) {
"2 1 0.1 0.2 0.3 0.4 1\n"
"4 1 0.1 0.2 0.3 0.4 3\n";
- EXPECT_THROW(parse_swc(bad2, swc_mode::strict), swc_irregular_id);
EXPECT_NO_THROW(parse_swc(bad2, swc_mode::relaxed));
}
- {
- std::string bad3 =
- "1 1 0.1 0.2 0.3 0.4 -1\n" // solitary tag
- "2 0 0.1 0.2 0.3 0.4 1\n"
- "3 0 0.1 0.2 0.3 0.4 2\n"
- "4 0 0.1 0.2 0.3 0.4 1\n";
-
- EXPECT_THROW(parse_swc(bad3, swc_mode::strict), swc_spherical_soma);
- EXPECT_NO_THROW(parse_swc(bad3, swc_mode::relaxed));
- }
-}
-
-TEST(swc_parser, valid_relaxed) {
}
TEST(swc_parser, valid_strict) {
@@ -169,12 +170,13 @@ TEST(swc_parser, valid_strict) {
}
{
+ // Non-contiguous, out of order records are fine.
std::string valid2 =
"# Some people put\n"
"# <xml /> in here!\n"
"1 1 0.1 0.2 0.3 0.4 -1\n"
"2 1 0.3 0.4 0.5 0.3 1\n"
- "3 2 0.2 0.6 0.8 0.2 2\n"
+ "5 2 0.2 0.6 0.8 0.2 2\n"
"4 0 0.2 0.8 0.6 0.3 2";
swc_data data = parse_swc(valid2, swc_mode::strict);
@@ -182,8 +184,8 @@ TEST(swc_parser, valid_strict) {
ASSERT_EQ(4u, data.records.size());
EXPECT_EQ(swc_record(1, 1, 0.1, 0.2, 0.3, 0.4, -1), data.records[0]);
EXPECT_EQ(swc_record(2, 1, 0.3, 0.4, 0.5, 0.3, 1), data.records[1]);
- EXPECT_EQ(swc_record(3, 2, 0.2, 0.6, 0.8, 0.2, 2), data.records[2]);
- EXPECT_EQ(swc_record(4, 0, 0.2, 0.8, 0.6, 0.3, 2), data.records[3]);
+ EXPECT_EQ(swc_record(4, 0, 0.2, 0.8, 0.6, 0.3, 2), data.records[2]);
+ EXPECT_EQ(swc_record(5, 2, 0.2, 0.6, 0.8, 0.2, 2), data.records[3]);
// Trailing garbage is ignored in data records.
std::string valid3 =
@@ -199,6 +201,63 @@ TEST(swc_parser, valid_strict) {
}
}
+TEST(swc_parser, segment_tree) {
+ {
+ // Missing parent record will throw.
+ std::vector<swc_record> swc{
+ {1, 1, 0., 0., 0., 1., -1},
+ {5, 3, 1., 1., 1., 1., 2}
+ };
+ EXPECT_THROW(as_segment_tree(swc), bad_swc_data);
+ }
+ {
+ // A single SWC record will throw.
+ std::vector<swc_record> swc{
+ {1, 1, 0., 0., 0., 1., -1}
+ };
+ EXPECT_THROW(as_segment_tree(swc), bad_swc_data);
+ }
+ {
+ // Otherwise, ensure segment ends and tags correspond.
+ mpoint p0{0.1, 0.2, 0.3, 0.4};
+ mpoint p1{0.3, 0.4, 0.5, 0.3};
+ mpoint p2{0.2, 0.8, 0.6, 0.3};
+ mpoint p3{0.2, 0.6, 0.8, 0.2};
+ mpoint p4{0.4, 0.5, 0.5, 0.1};
+
+ std::vector<swc_record> swc{
+ {1, 1, p0.x, p0.y, p0.z, p0.radius, -1},
+ {2, 1, p1.x, p1.y, p1.z, p1.radius, 1},
+ {4, 3, p2.x, p2.y, p2.z, p2.radius, 2},
+ {5, 2, p3.x, p3.y, p3.z, p3.radius, 2},
+ {7, 3, p4.x, p4.y, p4.z, p4.radius, 4}
+ };
+
+ segment_tree tree = as_segment_tree(swc);
+ ASSERT_EQ(4u, tree.segments().size());
+
+ EXPECT_EQ(mnpos, tree.parents()[0]);
+ EXPECT_EQ(1, tree.segments()[0].tag);
+ EXPECT_EQ(p0, tree.segments()[0].prox);
+ EXPECT_EQ(p1, tree.segments()[0].dist);
+
+ EXPECT_EQ(0u, tree.parents()[1]);
+ EXPECT_EQ(3, tree.segments()[1].tag);
+ EXPECT_EQ(p1, tree.segments()[1].prox);
+ EXPECT_EQ(p2, tree.segments()[1].dist);
+
+ EXPECT_EQ(0u, tree.parents()[2]);
+ EXPECT_EQ(2, tree.segments()[2].tag);
+ EXPECT_EQ(p1, tree.segments()[2].prox);
+ EXPECT_EQ(p3, tree.segments()[2].dist);
+
+ EXPECT_EQ(1u, tree.parents()[3]);
+ EXPECT_EQ(3, tree.segments()[3].tag);
+ EXPECT_EQ(p2, tree.segments()[3].prox);
+ EXPECT_EQ(p4, tree.segments()[3].dist);
+ }
+}
+
// hipcc bug in reading DATADIR
#ifndef ARB_HIP
TEST(swc_parser, from_neuromorpho)