Skip to content
This repository was archived by the owner on Feb 26, 2025. It is now read-only.

Commit

Permalink
Update gsl-lite submodule to v0.40.0 (#395)
Browse files Browse the repository at this point in the history
  • Loading branch information
@eleftherioszisis
eleftherioszisis authored Mar 28, 2022
1 parent bd2e18e commit 1db89fb
Show file tree
Hide file tree
Showing 6 changed files with 39 additions and 39 deletions.
2 changes: 1 addition & 1 deletion 3rdparty/GSL_LITE
Submodule GSL_LITE updated from 5cbc0e to d6c8af
2 changes: 1 addition & 1 deletion include/morphio/vector_types.h
View file
Original file line number Diff line number Diff line change
Expand Up @@ -6,7 +6,7 @@
#include <string> // std::string
#include <vector>

#include <gsl/gsl>
#include <gsl/gsl-lite.hpp>

namespace morphio {

Expand Down
16 changes: 8 additions & 8 deletions tests/test_helpers.h
View file
Original file line number Diff line number Diff line change
@@ -1,26 +1,26 @@
#include <iostream>

static bool almost_equal(morphio::floatType a, double expected, double epsilon) {
static bool almost_equal(morphio::floatType actual, double expected, double epsilon) {
#ifdef MORPHIO_USE_DOUBLE
bool res = std::abs(a - expected) < epsilon;
bool res = std::abs(actual - expected) < epsilon;
#else
bool res = std::abs(static_cast<double>(a) - expected) < epsilon;
bool res = std::abs(static_cast<double>(actual) - expected) < epsilon;
#endif
if (!res) {
std::cerr << "Failed almost equal: " << a << " != " << expected
std::cerr << "Failed almost equal: " << actual << " != " << expected
<< " (expected) with epsilon of " << epsilon << '\n';
}
return res;
}

static bool array_almost_equal(const std::vector<morphio::floatType>& a,
static bool array_almost_equal(const std::vector<morphio::floatType>& actual,
const std::vector<double>& expected,
double epsilon) {
if (a.size() != expected.size()) {
if (actual.size() != expected.size()) {
return false;
}
for (size_t i = 0; i < a.size(); i++) {
if (!almost_equal(a.at(i), expected.at(i), epsilon)) {
for (size_t i = 0; i < actual.size(); i++) {
if (!almost_equal(actual[i], expected[i], epsilon)) {
return false;
}
}
Expand Down
36 changes: 18 additions & 18 deletions tests/test_immutable_morphology.cpp
View file
Original file line number Diff line number Diff line change
Expand Up @@ -40,9 +40,9 @@ TEST_CASE("fromMut", "[immutableMorphology]") {
}
const auto& expectedMorphs = files.morphs();
for (size_t i = 0; i < expectedMorphs.size(); ++i) {
REQUIRE(expectedMorphs.at(i).somaType() == morphs.at(i).somaType());
REQUIRE(expectedMorphs.at(i).sectionTypes() == morphs.at(i).sectionTypes());
REQUIRE(expectedMorphs.at(i).perimeters() == morphs.at(i).perimeters());
REQUIRE(expectedMorphs[i].somaType() == morphs[i].somaType());
REQUIRE(expectedMorphs[i].sectionTypes() == morphs[i].sectionTypes());
REQUIRE(expectedMorphs[i].perimeters() == morphs[i].perimeters());
}
}

Expand All @@ -61,8 +61,8 @@ TEST_CASE("sections", "[immutableMorphology]") {
{
morphio::Morphology morph0 = morphio::Morphology("data/h5/v1/simple.h5");
morphio::Morphology morph1 = morphio::Morphology("data/h5/v1/simple.h5");
REQUIRE(morph0.rootSections().at(0).hasSameShape(morph1.rootSections().at(0)));
REQUIRE(!morph0.rootSections().at(0).hasSameShape(morph1.rootSections().at(1)));
REQUIRE(morph0.rootSections()[0].hasSameShape(morph1.rootSections()[0]));
REQUIRE(!morph0.rootSections()[0].hasSameShape(morph1.rootSections()[1]));
}
}

Expand Down Expand Up @@ -158,7 +158,7 @@ TEST_CASE("properties", "[immutableMorphology]") {
std::string text;
uint32_t major = std::numeric_limits<uint32_t>::max();
uint32_t minor = std::numeric_limits<uint32_t>::max();
std::tie(text, major, minor) = files.morphs().at(0).version();
std::tie(text, major, minor) = files.morphs()[0].version();
REQUIRE(text == "asc");
REQUIRE(major == 1);
REQUIRE(minor == 0);
Expand All @@ -175,12 +175,12 @@ TEST_CASE("iter", "[immutableMorphology]") {
std::vector<size_t> expectedRootSectionId = {0, 1, 4, 2, 3, 5, 6};
count = 0;
for (auto iter = rootSection.breadth_begin(); iter != rootSection.breadth_end(); iter++) {
REQUIRE((*iter).id() == expectedRootSectionId.at(count++));
REQUIRE((*iter).id() == expectedRootSectionId[count++]);
}
std::vector<size_t> expectedMorphSectionId = {0, 7, 1, 4, 8, 9, 2, 3, 5, 6};
count = 0;
for (auto iter = iterMorph.breadth_begin(); iter != iterMorph.breadth_end(); iter++) {
REQUIRE((*iter).id() == expectedMorphSectionId.at(count++));
REQUIRE((*iter).id() == expectedMorphSectionId[count++]);
}

Files files;
Expand All @@ -199,7 +199,7 @@ TEST_CASE("iter", "[immutableMorphology]") {
iter++) {
auto points = (*iter).points();
for (auto point : points) {
REQUIRE(point == expectedPoints.at(count++));
REQUIRE(point == expectedPoints[count++]);
}
}
}
Expand Down Expand Up @@ -229,9 +229,9 @@ TEST_CASE("endoplasmic_reticulum", "[immutableMorphology]") {
morphio::Morphology morph = morphio::Morphology("data/h5/v1/endoplasmic-reticulum.h5");
morphio::EndoplasmicReticulum er = morph.endoplasmicReticulum();
REQUIRE(er.sectionIndices() == std::vector<uint32_t>{1, 4, 5});
REQUIRE(almost_equal(er.volumes().at(0), 10.5500001907, 0.001));
REQUIRE(almost_equal(er.volumes().at(1), 47.1199989319, 0.001));
REQUIRE(almost_equal(er.volumes().at(2), 0.8299999833, 0.001));
REQUIRE(almost_equal(er.volumes()[0], 10.5500001907, 0.001));
REQUIRE(almost_equal(er.volumes()[1], 47.1199989319, 0.001));
REQUIRE(almost_equal(er.volumes()[2], 0.8299999833, 0.001));
REQUIRE(array_almost_equal(er.surfaceAreas(), std::vector<double>{111.24, 87.44, 0.11}, 0.001));
REQUIRE(er.filamentCounts() == std::vector<uint32_t>{12, 42, 8});
}
Expand All @@ -258,11 +258,11 @@ TEST_CASE("glia", "[immutableMorphology]") {
REQUIRE(count_processes == 863);

const auto section = glial.rootSections()[0];
REQUIRE(almost_equal(section.diameters().at(0), 2.03101, 0.001));
REQUIRE(almost_equal(section.diameters().at(1), 1.86179, 0.001));
REQUIRE(almost_equal(section.diameters()[0], 2.03101, 0.001));
REQUIRE(almost_equal(section.diameters()[1], 1.86179, 0.001));

REQUIRE(almost_equal(section.perimeters().at(0), 5.79899, 0.001));
REQUIRE(almost_equal(section.perimeters().at(1), 7.98946, 0.001));
REQUIRE(almost_equal(section.perimeters()[0], 5.79899, 0.001));
REQUIRE(almost_equal(section.perimeters()[1], 7.98946, 0.001));


CHECK_THROWS_AS(morphio::GlialCell("data/simple.swc"), morphio::RawDataError);
Expand All @@ -272,7 +272,7 @@ TEST_CASE("glia", "[immutableMorphology]") {
TEST_CASE("markers", "[immutableMorphology]") {
morphio::Morphology morph = morphio::Morphology("data/pia.asc");
std::vector<morphio::Property::Marker> markers = morph.markers();
REQUIRE(markers.at(0)._label == "pia");
REQUIRE(markers[0]._label == "pia");
}

TEST_CASE("throws", "[immutableMorphology]") {
Expand All @@ -289,7 +289,7 @@ TEST_CASE("annotations", "[immutableMorphology]") {
auto morph = morphio::Morphology(mutMorph);
REQUIRE(morph.annotations().size() == 1);

auto annotation = morph.annotations().at(0);
auto annotation = morph.annotations()[0];
REQUIRE(annotation._sectionId == 1);
REQUIRE(annotation._type == morphio::SINGLE_CHILD);
}
Expand Down
14 changes: 7 additions & 7 deletions tests/test_mitochondria.cpp
View file
Original file line number Diff line number Diff line change
Expand Up @@ -16,7 +16,7 @@ TEST_CASE("mitochondria", "[mitochondria]") {

REQUIRE(mito.rootSections().size() == 2);

auto rootSection = mito.rootSections().at(0);
auto rootSection = mito.rootSections()[0];
REQUIRE(rootSection.id() == 0);

auto diameters = rootSection.diameters();
Expand All @@ -27,8 +27,8 @@ TEST_CASE("mitochondria", "[mitochondria]") {
auto res = std::vector<morphio::floatType>(relativePathLength.begin(),
relativePathLength.end());

REQUIRE(almost_equal(res.at(0), 0.5, 0.001));
REQUIRE(almost_equal(res.at(1), 0.6000000238, 0.001));
REQUIRE(almost_equal(res[0], 0.5, 0.001));
REQUIRE(almost_equal(res[1], 0.6000000238, 0.001));

auto neuriteSectionIds = rootSection.neuriteSectionIds();
REQUIRE(array_almost_equal(std::vector<morphio::floatType>(neuriteSectionIds.begin(),
Expand All @@ -37,7 +37,7 @@ TEST_CASE("mitochondria", "[mitochondria]") {
0.01));
REQUIRE(rootSection.children().size() == 1);

auto child = rootSection.children().at(0);
auto child = rootSection.children()[0];
REQUIRE(child.parent().id() == rootSection.id());

diameters = child.diameters();
Expand All @@ -56,7 +56,7 @@ TEST_CASE("mitochondria", "[mitochondria]") {
neuriteSectionIds.end()),
std::vector<double>{3.0, 4.0, 4.0, 5.0},
0.01));
rootSection = mito.rootSections().at(1);
rootSection = mito.rootSections()[1];
diameters = rootSection.diameters();
REQUIRE(array_almost_equal(std::vector<morphio::floatType>(diameters.begin(), diameters.end()),
std::vector<double>{5.0, 6.0, 7.0, 8.0},
Expand Down Expand Up @@ -91,7 +91,7 @@ TEST_CASE("mitochondria.sections", "[mitochondria]") {
TEST_CASE("mitochondria.iteration", "[mitochondria]") {
const auto mito = morphio::Morphology("data/h5/v1/mitochondria.h5").mitochondria();

const auto rootSection = mito.rootSections().at(0);
const auto rootSection = mito.rootSections()[0];

std::vector<std::size_t> res;
std::transform(rootSection.depth_begin(),
Expand All @@ -118,5 +118,5 @@ TEST_CASE("mitochondria.iteration", "[mitochondria]") {
TEST_CASE("mitochondria.hasSameShape", "[mitochondria]") {
morphio::Morphology morph0 = morphio::Morphology("data/h5/v1/mitochondria.h5");
morphio::Morphology morph1 = morphio::Morphology("data/h5/v1/mitochondria.h5");
REQUIRE(morph0.rootSections().at(0).hasSameShape(morph1.rootSections().at(0)));
REQUIRE(morph0.rootSections()[0].hasSameShape(morph1.rootSections()[0]));
}
8 changes: 4 additions & 4 deletions tests/test_mutable_morphology.cpp
View file
Original file line number Diff line number Diff line change
Expand Up @@ -34,15 +34,15 @@ TEST_CASE("hasSameShape", "[mutableMorphology]") {
std::string path = "data/simple.asc";
auto morph0 = morphio::mut::Morphology(path);
auto morph1 = morphio::mut::Morphology(path);
REQUIRE(morph0.rootSections().at(0)->hasSameShape(*morph1.rootSections().at(0)));
REQUIRE(!morph0.rootSections().at(0)->hasSameShape(*morph1.rootSections().at(1)));
REQUIRE(morph0.rootSections()[0]->hasSameShape(*morph1.rootSections()[0]));
REQUIRE(!morph0.rootSections()[0]->hasSameShape(*morph1.rootSections()[1]));
}
{
std::string path = "data/h5/v1/mitochondria.h5";
auto morph0 = morphio::mut::Morphology(path);
auto morph1 = morphio::mut::Morphology(path);
REQUIRE(morph0.mitochondria().rootSections().at(0)->hasSameShape(
*morph1.mitochondria().rootSections().at(0)));
REQUIRE(morph0.mitochondria().rootSections()[0]->hasSameShape(
*morph1.mitochondria().rootSections()[0]));
}
}

Expand Down

0 comments on commit 1db89fb

Please sign in to comment.