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Commit d04de96a authored by Vasileios Karakasis's avatar Vasileios Karakasis
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Algorithm for checking contiguous numbering in cell branches. 

+ converted swc_record::kind to an ``enum class``
parent 11b9bfd3
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src/algorithms.hpp
+ 26
− 0
View file @ d04de96a
......@@ -99,6 +99,32 @@ namespace algorithms{
return true;
}
template<typename C>
bool is_contiguously_numbered(const C &parent_list)
{
static_assert(
std::is_integral<typename C::value_type>::value,
"integral type required"
);
std::vector<bool> is_leaf(parent_list.size(), false);
auto ret = true;
for (std::size_t i = 1; i < parent_list.size(); ++i) {
if (is_leaf[parent_list[i]]) {
ret = false;
break;
}
if (parent_list[i] != i-1) {
// we have a branch and i-1 is a leaf node
is_leaf[i-1] = true;
}
}
return ret;
}
} // namespace algorithms
} // namespace mc
} // namespace nest
src/swcio.cpp
+ 5
− 4
View file @ d04de96a
......@@ -32,7 +32,8 @@ void swc_record::check_consistency() const
{
// Check record type as well; enum's do not offer complete type safety,
// since you can cast anything that fits to its underlying type
if (type_ < 0 || type_ > custom) {
if (static_cast<int>(type_) < 0 ||
static_cast<int>(type_) > static_cast<int>(kind::custom)) {
throw std::invalid_argument("unknown record type");
}
......@@ -65,7 +66,7 @@ std::ostream &operator<<(std::ostream &os, const swc_record &record)
{
// output in one-based indexing
os << record.id_+1 << " "
<< record.type_ << " "
<< static_cast<int>(record.type_) << " "
<< std::setprecision(7) << record.x_ << " "
<< std::setprecision(7) << record.y_ << " "
<< std::setprecision(7) << record.z_ << " "
......@@ -177,9 +178,9 @@ swc_record_range_clean::swc_record_range_clean(std::istream &is)
{
std::unordered_set<swc_record::id_type> ids;
std::size_t num_trees = 0;
std::size_t num_trees = 0;
swc_record::id_type last_id = -1;
bool needsort = false;
bool needsort = false;
swc_record curr_record;
for (auto c : swc_get_records<swc_io_raw>(is)) {
......
src/swcio.hpp
+ 5
− 9
View file @ d04de96a
......@@ -15,11 +15,8 @@ class swc_record
public:
using id_type = int;
// FIXME: enum's are not completely type-safe, since they can accept
// anything that can be casted to their underlying type.
//
// More on SWC files: http://research.mssm.edu/cnic/swc.html
enum kind {
enum class kind {
undefined = 0,
soma,
axon,
......@@ -31,9 +28,9 @@ public:
};
// swc records assume zero-based indexing; root's parent remains -1
swc_record(kind type, int id,
float x, float y, float z, float r,
int parent_id)
swc_record(swc_record::kind type, int id,
float x, float y, float z, float r,
int parent_id)
: type_(type)
, id_(id)
, x_(x)
......@@ -46,7 +43,7 @@ public:
}
swc_record()
: type_(swc_record::undefined)
: type_(swc_record::kind::undefined)
, id_(0)
, x_(0)
, y_(0)
......@@ -409,4 +406,3 @@ template<typename T = swc_io_clean>
} // namespace io
} // namespace mc
} // namespace nest
tests/test_algorithms.cpp
+ 86
− 0
View file @ d04de96a
......@@ -169,3 +169,89 @@ TEST(algorithms, is_positive)
)
);
}
TEST(algorithms, is_contiguously_numbered)
{
//
// 0
// |
// 1
// |
// 2
// /|\
// 3 7 4
// / \
// 5 6
//
EXPECT_FALSE(
nest::mc::algorithms::is_contiguously_numbered(
std::vector<int>{0, 0, 1, 2, 2, 3, 4, 2}
)
);
//
// 0
// |
// 1
// |
// 2
// /|\
// 3 6 5
// / \
// 4 7
//
EXPECT_FALSE(
nest::mc::algorithms::is_contiguously_numbered(
std::vector<int>{0, 0, 1, 2, 3, 2, 2, 5}
)
);
//
// 0
// |
// 1
// |
// 2
// /|\
// 3 7 5
// / \
// 4 6
//
EXPECT_TRUE(
nest::mc::algorithms::is_contiguously_numbered(
std::vector<int>{0, 0, 1, 2, 3, 2, 5, 2}
)
);
//
// 0
// |
// 1
// / \
// 2 7
// / \
// 3 5
// / \
// 4 6
//
EXPECT_TRUE(
nest::mc::algorithms::is_contiguously_numbered(
std::vector<int>{0, 0, 1, 2, 3, 2, 5, 1}
)
);
// Soma-only list
EXPECT_TRUE(
nest::mc::algorithms::is_contiguously_numbered(
std::vector<int>{0}
)
);
// Empty list
EXPECT_TRUE(
nest::mc::algorithms::is_contiguously_numbered(
std::vector<int>{}
)
);
}
tests/test_swcio.cpp
+ 43
− 18
View file @ d04de96a
......@@ -36,43 +36,43 @@ TEST(swc_record, construction)
{
// invalid id
EXPECT_THROW(swc_record record(
swc_record::custom, -3, 1., 1., 1., 1., 5),
swc_record::kind::custom, -3, 1., 1., 1., 1., 5),
std::invalid_argument);
}
{
// invalid parent id
EXPECT_THROW(swc_record record(
swc_record::custom, 0, 1., 1., 1., 1., -5),
swc_record::kind::custom, 0, 1., 1., 1., 1., -5),
std::invalid_argument);
}
{
// invalid radius
EXPECT_THROW(swc_record record(
swc_record::custom, 0, 1., 1., 1., -1., -1),
swc_record::kind::custom, 0, 1., 1., 1., -1., -1),
std::invalid_argument);
}
{
// parent_id > id
EXPECT_THROW(swc_record record(
swc_record::custom, 0, 1., 1., 1., 1., 2),
swc_record::kind::custom, 0, 1., 1., 1., 1., 2),
std::invalid_argument);
}
{
// parent_id == id
EXPECT_THROW(swc_record record(
swc_record::custom, 0, 1., 1., 1., 1., 0),
swc_record::kind::custom, 0, 1., 1., 1., 1., 0),
std::invalid_argument);
}
{
// check standard construction by value
swc_record record(swc_record::custom, 0, 1., 1., 1., 1., -1);
swc_record record(swc_record::kind::custom, 0, 1., 1., 1., 1., -1);
EXPECT_EQ(record.id(), 0);
EXPECT_EQ(record.type(), swc_record::custom);
EXPECT_EQ(record.type(), swc_record::kind::custom);
EXPECT_EQ(record.x(), 1.);
EXPECT_EQ(record.y(), 1.);
EXPECT_EQ(record.z(), 1.);
......@@ -83,7 +83,7 @@ TEST(swc_record, construction)
{
// check copy constructor
swc_record record_orig(swc_record::custom, 0, 1., 1., 1., 1., -1);
swc_record record_orig(swc_record::kind::custom, 0, 1., 1., 1., 1., -1);
swc_record record(record_orig);
expect_record_equals(record_orig, record);
}
......@@ -95,9 +95,9 @@ TEST(swc_record, comparison)
{
// check comparison operators
swc_record record0(swc_record::custom, 0, 1., 1., 1., 1., -1);
swc_record record1(swc_record::custom, 0, 2., 3., 4., 5., -1);
swc_record record2(swc_record::custom, 1, 2., 3., 4., 5., -1);
swc_record record0(swc_record::kind::custom, 0, 1., 1., 1., 1., -1);
swc_record record1(swc_record::kind::custom, 0, 2., 3., 4., 5., -1);
swc_record record2(swc_record::kind::custom, 1, 2., 3., 4., 5., -1);
EXPECT_EQ(record0, record1);
EXPECT_LT(record0, record2);
EXPECT_GT(record2, record1);
......@@ -131,6 +131,31 @@ TEST(swc_parser, invalid_input)
swc_record record;
EXPECT_THROW(is >> record, swc_parse_error);
}
{
// Non-contiguous numbering in branches is considered invalid
// 1
// / \
// 2 3
// /
// 4
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 1 14.566132 34.873772 7.857000 0.717830 1\n";
is << "4 1 14.566132 34.873772 7.857000 0.717830 2\n";
std::vector<swc_record> records;
try {
for (auto c : swc_get_records<swc_io_clean>(is)) {
records.push_back(std::move(c));
}
FAIL() << "expected swc_parse_error, none was thrown\n";
} catch (const swc_parse_error &e) {
SUCCEED();
}
}
}
......@@ -162,7 +187,7 @@ TEST(swc_parser, valid_input)
swc_record record;
EXPECT_NO_THROW(is >> record);
EXPECT_EQ(0, record.id()); // zero-based indexing
EXPECT_EQ(swc_record::soma, record.type());
EXPECT_EQ(swc_record::kind::soma, record.type());
EXPECT_FLOAT_EQ(14.566132, record.x());
EXPECT_FLOAT_EQ(34.873772, record.y());
EXPECT_FLOAT_EQ( 7.857000, record.z());
......@@ -173,9 +198,9 @@ TEST(swc_parser, valid_input)
{
// check valid input with a series of records
std::vector<swc_record> records_orig = {
swc_record(swc_record::soma, 0,
swc_record(swc_record::kind::soma, 0,
14.566132, 34.873772, 7.857000, 0.717830, -1),
swc_record(swc_record::dendrite, 1,
swc_record(swc_record::kind::dendrite, 1,
14.566132+1, 34.873772+1, 7.857000+1, 0.717830+1, -1)
};
......@@ -229,7 +254,7 @@ TEST(swc_parser, input_cleaning)
is << "2 1 14.566132 34.873772 7.857000 0.717830 1\n";
is << "2 1 14.566132 34.873772 7.857000 0.717830 1\n";
EXPECT_EQ(2u, swc_get_records(is).size());
EXPECT_EQ(2u, swc_get_records<swc_io_clean>(is).size());
}
{
......@@ -240,7 +265,7 @@ TEST(swc_parser, input_cleaning)
is << "3 1 14.566132 34.873772 7.857000 0.717830 -1\n";
is << "4 1 14.566132 34.873772 7.857000 0.717830 1\n";
auto records = swc_get_records(is);
auto records = swc_get_records<swc_io_clean>(is);
EXPECT_EQ(2u, records.size());
}
......@@ -255,7 +280,7 @@ TEST(swc_parser, input_cleaning)
std::array<swc_record::id_type, 4> expected_id_list = {{ 0, 1, 2, 3 }};
auto expected_id = expected_id_list.cbegin();
for (auto c : swc_get_records(is)) {
for (auto c : swc_get_records<swc_io_clean>(is)) {
EXPECT_EQ(*expected_id, c.id());
++expected_id;
}
......@@ -281,7 +306,7 @@ TEST(swc_parser, input_cleaning)
auto expected_id = expected_id_list.cbegin();
auto expected_parent = expected_parent_list.cbegin();
for (auto c : swc_get_records(is)) {
for (auto c : swc_get_records<swc_io_clean>(is)) {
EXPECT_EQ(*expected_id, c.id());
EXPECT_EQ(*expected_parent, c.parent());
++expected_id;
......
vector @ c2fc6318
Compare 7fc001ef...c2fc6318
Subproject commit 7fc001ef98c01383d384541de08b861328c29405
Subproject commit c2fc6318f6d65ae9d7aad60309f3b53d590a00ec
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