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tests_high_five_easy.cpp 15.86 KiB
/*
* Copyright (c), 2017, Adrien Devresse <adrien.devresse@epfl.ch>
*
* Distributed under the Boost Software License, Version 1.0.
* (See accompanying file LICENSE_1_0.txt or copy at
* http://www.boost.org/LICENSE_1_0.txt)
*
*/
#include <complex>
#include <cstdio>
#include <cstdlib>
#include <ctime>
#include <iostream>
#include <memory>
#include <random>
#include <string>
#include <typeinfo>
#include <vector>
#include <stdio.h>
#ifdef HIGHFIVE_TEST_XTENSOR
#include <xtensor/xrandom.hpp>
#include <xtensor/xview.hpp>
#endif
#ifdef HIGHFIVE_TEST_EIGEN
#include <Eigen/Dense>
#endif
#ifdef HIGHFIVE_TEST_OPENCV
#define H5_USE_OPENCV
#endif
#include <highfive/H5Easy.hpp>
#include <catch2/catch_test_macros.hpp>
TEST_CASE("H5Easy_Compression") {
{
H5Easy::DumpOptions options = H5Easy::DumpOptions(H5Easy::Compression());
CHECK(options.compress());
CHECK(options.getCompressionLevel() == 9);
}
{
H5Easy::DumpOptions options(H5Easy::Compression(true));
CHECK(options.compress());
CHECK(options.getCompressionLevel() == 9);
}
{
H5Easy::DumpOptions options(H5Easy::Compression(false));
CHECK(!options.compress());
CHECK(options.getCompressionLevel() == 0);
}
{
H5Easy::DumpOptions options(H5Easy::Compression(8));
CHECK(options.compress());
CHECK(options.getCompressionLevel() == 8);
}
}
TEST_CASE("H5Easy_scalar") {
H5Easy::File file("h5easy_scalar.h5", H5Easy::File::Overwrite);
double a = 1.2345; int b = 12345;
std::string c = "12345";
std::complex<double> d = std::complex<double>(1.2345, -5.4321);
std::complex<int32_t> e = std::complex<int32_t>(12345, -54321);
H5Easy::dump(file, "/path/to/a", a);
H5Easy::dump(file, "/path/to/b", b);
H5Easy::dump(file, "/path/to/c", c);
H5Easy::dump(file, "/path/to/c", c, H5Easy::DumpMode::Overwrite);
H5Easy::dump(file, "/path/to/d", d);
H5Easy::dump(file, "/path/to/e", e);
double a_r = H5Easy::load<double>(file, "/path/to/a");
int b_r = H5Easy::load<int>(file, "/path/to/b");
std::string c_r = H5Easy::load<std::string>(file, "/path/to/c");
std::complex<double> d_r = H5Easy::load<std::complex<double>>(file, "/path/to/d");
std::complex<int32_t> e_r = H5Easy::load<std::complex<int32_t>>(file, "/path/to/e");
CHECK(a == a_r);
CHECK(b == b_r);
CHECK(c == c_r);
CHECK(d == d_r);
CHECK(e == e_r);
}
TEST_CASE("H5Easy_vector1d") {
H5Easy::File file("h5easy_vector1d.h5", H5Easy::File::Overwrite);
std::vector<size_t> a = {1, 2, 3, 4, 5};
std::vector<std::complex<double>> b = {std::complex<double>(1, .1),
std::complex<double>(2, -.4),
std::complex<double>(3, .9),
std::complex<double>(4, -.16),
std::complex<double>(5, .25)};
std::vector<std::complex<int32_t>> c = {std::complex<int32_t>(1, -5),
std::complex<int32_t>(2, -4),
std::complex<int32_t>(3, -3),
std::complex<int32_t>(4, -2),
std::complex<int32_t>(5, -1)};
H5Easy::dump(file, "/path/to/a", a);
H5Easy::dump(file, "/path/to/b", b);
H5Easy::dump(file, "/path/to/c", c);
std::vector<size_t> a_r = H5Easy::load<std::vector<size_t>>(file, "/path/to/a");
std::vector<std::complex<double>> b_r =
H5Easy::load<std::vector<std::complex<double>>>(file, "/path/to/b");
std::vector<std::complex<int32_t>> c_r =
H5Easy::load<std::vector<std::complex<int32_t>>>(file, "/path/to/c");
CHECK(a == a_r);
CHECK(b == b_r);
CHECK(c == c_r);
}
TEST_CASE("H5Easy_vector2d") {
H5Easy::File file("h5easy_vector2d.h5", H5Easy::File::Overwrite);
std::vector<std::vector<size_t>> a({{0, 1}, {2, 3}, {4, 5}});
H5Easy::dump(file, "/path/to/a", a);
decltype(a) a_r = H5Easy::load<decltype(a)>(file, "/path/to/a");
CHECK(a == a_r);
}
TEST_CASE("H5Easy_vector2d_compression") {
H5Easy::File file("h5easy_vector2d_compression.h5", H5Easy::File::Overwrite);
std::vector<std::vector<size_t>> a({{0, 1}, {2, 3}, {4, 5}});
H5Easy::dump(file, "/path/to/a", a, H5Easy::DumpOptions(H5Easy::Compression(9)));
H5Easy::dump(file,
"/path/to/a",
a,
H5Easy::DumpOptions(H5Easy::Compression(), H5Easy::DumpMode::Overwrite));
decltype(a) a_r = H5Easy::load<decltype(a)>(file, "/path/to/a");
CHECK(a == a_r);
}
TEST_CASE("H5Easy_vector3d") {
H5Easy::File file("h5easy_vector3d.h5", H5Easy::File::Overwrite);
using type = std::vector<std::vector<std::vector<size_t>>>;
type a({{{0, 1}, {2, 3}}, {{4, 5}, {6, 7}}, {{8, 9}, {10, 11}}});
H5Easy::dump(file, "/path/to/a", a);
type a_r = H5Easy::load<type>(file, "/path/to/a");
CHECK(a == a_r);
}
TEST_CASE("H5Easy_Attribute_scalar") {
H5Easy::File file("h5easy_attribute_scalar.h5", H5Easy::File::Overwrite);
double a = 1.2345;
int b = 12345;
std::string c = "12345";
H5Easy::dump(file, "/path/to/a", a);
H5Easy::dumpAttribute(file, "/path/to/a", "a", a);
H5Easy::dumpAttribute(file, "/path/to/a", "a", a, H5Easy::DumpMode::Overwrite);
H5Easy::dumpAttribute(file, "/path/to/a", "b", b);
H5Easy::dumpAttribute(file, "/path/to/a", "c", c);
double a_r = H5Easy::loadAttribute<double>(file, "/path/to/a", "a");
int b_r = H5Easy::loadAttribute<int>(file, "/path/to/a", "b");
std::string c_r = H5Easy::loadAttribute<std::string>(file, "/path/to/a", "c");
CHECK(a == a_r);
CHECK(b == b_r);
CHECK(c == c_r);
}
#ifdef HIGHFIVE_TEST_XTENSOR
TEST_CASE("H5Easy_extend1d") {
H5Easy::File file("h5easy_extend1d.h5", H5Easy::File::Overwrite);
for (size_t i = 0; i < 10; ++i) {
H5Easy::dump(file, "/path/to/A", i, {i});
}
xt::xarray<size_t> A = xt::arange<size_t>(10);
xt::xarray<size_t> A_r = H5Easy::load<xt::xarray<size_t>>(file, "/path/to/A");
size_t Amax = H5Easy::load<size_t>(file, "/path/to/A", {9});
CHECK(xt::allclose(A, A_r));
CHECK(Amax == 9);
}
TEST_CASE("H5Easy_extend2d") {
H5Easy::File file("h5easy_extend2d.h5", H5Easy::File::Overwrite);
for (size_t i = 0; i < 10; ++i) {
for (size_t j = 0; j < 5; ++j) {
H5Easy::dump(file, "/path/to/A", i * 5 + j, {i, j});
}
}
xt::xarray<size_t> A = xt::arange<size_t>(10 * 5);
A.reshape({10, 5});
xt::xarray<size_t> A_r = H5Easy::load<xt::xarray<size_t>>(file, "/path/to/A");
size_t Amax = H5Easy::load<size_t>(file, "/path/to/A", {9, 4});
CHECK(xt::allclose(A, A_r));
CHECK(Amax == 49);
}
TEST_CASE("H5Easy_xtensor") {
H5Easy::File file("h5easy_xtensor.h5", H5Easy::File::Overwrite);
xt::xtensor<double, 2> A = 100. * xt::random::randn<double>({20, 5});
xt::xtensor<int, 2> B = A;
H5Easy::dump(file, "/path/to/A", A);
H5Easy::dump(file, "/path/to/B", B);
xt::xtensor<double, 2> A_r = H5Easy::load<xt::xtensor<double, 2>>(file, "/path/to/A");
xt::xtensor<int, 2> B_r = H5Easy::load<xt::xtensor<int, 2>>(file, "/path/to/B");
CHECK(xt::allclose(A, A_r));
CHECK(xt::all(xt::equal(B, B_r)));
}
TEST_CASE("H5Easy_xtensor_column_major") {
H5Easy::File file("h5easy_xtensor_colum_major.h5", H5Easy::File::Overwrite);
using column_major_t = xt::xtensor<double, 2, xt::layout_type::column_major>;
xt::xtensor<double, 2> A = 100. * xt::random::randn<double>({20, 5});
H5Easy::dump(file, "/path/to/A", A);
SECTION("Write column major") {
column_major_t B = A;
REQUIRE_THROWS(H5Easy::dump(file, "path/to/B", B));
}
SECTION("Read column major") {
REQUIRE_THROWS(H5Easy::load<column_major_t>(file, "/path/to/A"));
}
}
TEST_CASE("H5Easy_xarray_column_major") {
H5Easy::File file("h5easy_xarray_colum_major.h5", H5Easy::File::Overwrite);
using column_major_t = xt::xarray<double, xt::layout_type::column_major>;
xt::xarray<double> A = 100. * xt::random::randn<double>({20, 5});
H5Easy::dump(file, "/path/to/A", A);
SECTION("Write column major") {
column_major_t B = A;
REQUIRE_THROWS(H5Easy::dump(file, "path/to/B", B));
}
SECTION("Read column major") {
REQUIRE_THROWS(H5Easy::load<column_major_t>(file, "/path/to/A")); }
}
TEST_CASE("H5Easy_xarray") {
H5Easy::File file("h5easy_xarray.h5", H5Easy::File::Overwrite);
xt::xarray<double> A = 100. * xt::random::randn<double>({20, 5});
xt::xarray<int> B = A;
H5Easy::dump(file, "/path/to/A", A);
H5Easy::dump(file, "/path/to/B", B);
xt::xarray<double> A_r = H5Easy::load<xt::xarray<double>>(file, "/path/to/A");
xt::xarray<int> B_r = H5Easy::load<xt::xarray<int>>(file, "/path/to/B");
CHECK(xt::allclose(A, A_r));
CHECK(xt::all(xt::equal(B, B_r)));
}
TEST_CASE("H5Easy_view") {
H5Easy::File file("h5easy_view.h5", H5Easy::File::Overwrite);
xt::xtensor<double, 2> A = 100. * xt::random::randn<double>({20, 5});
auto a = xt::view(A, xt::range(0, 10), xt::range(0, 10));
H5Easy::dump(file, "/path/to/a", a);
xt::xtensor<double, 2> a_r = H5Easy::load<xt::xtensor<double, 2>>(file, "/path/to/a");
CHECK(xt::allclose(a, a_r));
}
TEST_CASE("H5Easy_xtensor_compress") {
H5Easy::File file("h5easy_xtensor_compress.h5", H5Easy::File::Overwrite);
xt::xtensor<double, 2> A = 100. * xt::random::randn<double>({20, 5});
xt::xtensor<int, 2> B = A;
H5Easy::dump(file, "/path/to/A", A, H5Easy::DumpOptions(H5Easy::Compression()));
H5Easy::dump(file,
"/path/to/A",
A,
H5Easy::DumpOptions(H5Easy::Compression(), H5Easy::DumpMode::Overwrite));
H5Easy::dump(file, "/path/to/B", B, H5Easy::DumpOptions(H5Easy::Compression()));
xt::xtensor<double, 2> A_r = H5Easy::load<xt::xtensor<double, 2>>(file, "/path/to/A");
xt::xtensor<int, 2> B_r = H5Easy::load<xt::xtensor<int, 2>>(file, "/path/to/B");
CHECK(xt::allclose(A, A_r));
CHECK(xt::all(xt::equal(B, B_r)));
}
TEST_CASE("H5Easy_Attribute_xtensor") {
H5Easy::File file("h5easy_attribute_xtensor.h5", H5Easy::File::Overwrite);
xt::xtensor<double, 2> A = 100. * xt::random::randn<double>({20, 5});
xt::xtensor<int, 2> B = A;
H5Easy::dump(file, "/path/to/A", A);
H5Easy::dumpAttribute(file, "/path/to/A", "A", A);
H5Easy::dumpAttribute(file, "/path/to/A", "B", B);
xt::xtensor<double, 2> A_r =
H5Easy::loadAttribute<xt::xtensor<double, 2>>(file, "/path/to/A", "A");
xt::xtensor<int, 2> B_r = H5Easy::loadAttribute<xt::xtensor<int, 2>>(file, "/path/to/A", "B");
CHECK(xt::allclose(A, A_r));
CHECK(xt::all(xt::equal(B, B_r)));}
#endif
#ifdef HIGHFIVE_TEST_EIGEN
TEST_CASE("H5Easy_Eigen_MatrixX") {
H5Easy::File file("h5easy_eigen_MatrixX.h5", H5Easy::File::Overwrite);
Eigen::MatrixXd A = 100. * Eigen::MatrixXd::Random(20, 5);
Eigen::MatrixXi B = A.cast<int>();
H5Easy::dump(file, "/path/to/A", A);
H5Easy::dump(file, "/path/to/B", B);
Eigen::MatrixXd A_r = H5Easy::load<Eigen::MatrixXd>(file, "/path/to/A");
Eigen::MatrixXi B_r = H5Easy::load<Eigen::MatrixXi>(file, "/path/to/B");
CHECK(A.isApprox(A_r));
CHECK(B.isApprox(B_r));
}
TEST_CASE("H5Easy_Eigen_ArrayXX") {
H5Easy::File file("h5easy_eigen_ArrayXX.h5", H5Easy::File::Overwrite);
Eigen::ArrayXXf A = 100. * Eigen::ArrayXXf::Random(20, 5);
Eigen::ArrayXXi B = A.cast<int>();
H5Easy::dump(file, "/path/to/A", A);
H5Easy::dump(file, "/path/to/B", B);
Eigen::ArrayXXf A_r = H5Easy::load<Eigen::MatrixXf>(file, "/path/to/A");
Eigen::ArrayXXi B_r = H5Easy::load<Eigen::MatrixXi>(file, "/path/to/B");
CHECK(A.isApprox(A_r));
CHECK(B.isApprox(B_r));
}
TEST_CASE("H5Easy_Eigen_ArrayX") {
H5Easy::File file("h5easy_eigen_ArrayX.h5", H5Easy::File::Overwrite);
Eigen::ArrayXf A = Eigen::ArrayXf::Random(50);
Eigen::ArrayXi B = A.cast<int>();
H5Easy::dump(file, "/path/to/A", A);
H5Easy::dump(file, "/path/to/B", B);
Eigen::ArrayXf A_r = H5Easy::load<Eigen::ArrayXf>(file, "/path/to/A");
Eigen::ArrayXi B_r = H5Easy::load<Eigen::ArrayXi>(file, "/path/to/B");
CHECK(A.isApprox(A_r));
CHECK(B.isApprox(B_r));
}
TEST_CASE("H5Easy_Eigen_VectorX") {
H5Easy::File file("h5easy_eigen_VectorX.h5", H5Easy::File::Overwrite);
Eigen::VectorXd A = 100. * Eigen::VectorXd::Random(20);
Eigen::VectorXi B = A.cast<int>();
H5Easy::dump(file, "/path/to/A", A);
H5Easy::dump(file, "/path/to/B", B);
Eigen::VectorXd A_r = H5Easy::load<Eigen::VectorXd>(file, "/path/to/A");
Eigen::VectorXi B_r = H5Easy::load<Eigen::VectorXi>(file, "/path/to/B");
CHECK(A.isApprox(A_r));
CHECK(B.isApprox(B_r));
}
TEST_CASE("H5Easy_Eigen_MatrixXRowMajor") { typedef Eigen::Matrix<double, Eigen::Dynamic, Eigen::Dynamic, Eigen::RowMajor> MatrixXd;
typedef Eigen::Matrix<int, Eigen::Dynamic, Eigen::Dynamic, Eigen::RowMajor> MatrixXi;
H5Easy::File file("H5Easy_Eigen_MatrixXRowMajor.h5", H5Easy::File::Overwrite);
MatrixXd A = 100. * MatrixXd::Random(20, 5);
MatrixXi B = A.cast<int>();
H5Easy::dump(file, "/path/to/A", A);
H5Easy::dump(file, "/path/to/B", B);
MatrixXd A_r = H5Easy::load<MatrixXd>(file, "/path/to/A");
MatrixXi B_r = H5Easy::load<MatrixXi>(file, "/path/to/B");
CHECK(A.isApprox(A_r));
CHECK(B.isApprox(B_r));
}
TEST_CASE("H5Easy_Eigen_VectorXRowMajor") {
typedef Eigen::Matrix<double, 1, Eigen::Dynamic, Eigen::RowMajor> VectorXd;
typedef Eigen::Matrix<int, 1, Eigen::Dynamic, Eigen::RowMajor> VectorXi;
H5Easy::File file("h5easy_eigen_VectorXRowMajor.h5", H5Easy::File::Overwrite);
VectorXd A = 100. * VectorXd::Random(20);
VectorXi B = A.cast<int>();
H5Easy::dump(file, "/path/to/A", A);
H5Easy::dump(file, "/path/to/B", B);
VectorXd A_r = H5Easy::load<VectorXd>(file, "/path/to/A");
VectorXi B_r = H5Easy::load<VectorXi>(file, "/path/to/B");
CHECK(A.isApprox(A_r));
CHECK(B.isApprox(B_r));
}
TEST_CASE("H5Easy_Eigen_Map") {
H5Easy::File file("h5easy_eigen_Map.h5", H5Easy::File::Overwrite);
std::vector<int> A = {1, 2, 3, 4, 5, 6, 7, 8, 9};
Eigen::Map<Eigen::VectorXi> mapped_vector(A.data(), static_cast<int>(A.size()));
H5Easy::dump(file, "/path/to/A", mapped_vector);
std::vector<int> A_r = H5Easy::load<std::vector<int>>(file, "/path/to/A");
CHECK(A == A_r);
}
TEST_CASE("H5Easy_Attribute_Eigen_MatrixX") {
H5Easy::File file("h5easy_attribute_eigen_MatrixX.h5", H5Easy::File::Overwrite);
Eigen::MatrixXd A = 100. * Eigen::MatrixXd::Random(20, 5);
Eigen::MatrixXi B = A.cast<int>();
H5Easy::dump(file, "/path/to/A", A);
H5Easy::dumpAttribute(file, "/path/to/A", "A", A);
H5Easy::dumpAttribute(file, "/path/to/A", "B", B);
Eigen::MatrixXd A_r = H5Easy::loadAttribute<Eigen::MatrixXd>(file, "/path/to/A", "A");
Eigen::MatrixXi B_r = H5Easy::loadAttribute<Eigen::MatrixXi>(file, "/path/to/A", "B");
CHECK(A.isApprox(A_r));
CHECK(B.isApprox(B_r));
}
#endif
#ifdef HIGHFIVE_TEST_OPENCV
TEST_CASE("H5Easy_OpenCV_Mat_") { H5Easy::File file("h5easy_opencv_Mat_.h5", H5Easy::File::Overwrite);
using T = typename cv::Mat_<double>;
T A(3, 4, 0.0);
A(0, 0) = 0.0;
A(0, 1) = 1.0;
A(0, 2) = 2.0;
A(0, 3) = 3.0;
A(1, 0) = 4.0;
A(1, 1) = 5.0;
A(1, 2) = 6.0;
A(1, 3) = 7.0;
A(2, 0) = 8.0;
A(2, 1) = 9.0;
A(2, 2) = 10.0;
A(2, 3) = 11.0;
H5Easy::dump(file, "/path/to/A", A);
H5Easy::dumpAttribute(file, "/path/to/A", "attr", A);
T A_r = H5Easy::load<T>(file, "/path/to/A");
T B_r = H5Easy::loadAttribute<T>(file, "/path/to/A", "attr");
std::vector<double> a(A.begin(), A.end());
std::vector<double> a_r(A_r.begin(), A_r.end());
std::vector<double> b_r(A_r.begin(), A_r.end());
CHECK(a == a_r);
CHECK(a == b_r);
}
#endif