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hdf5_all.cpp
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Sat, Jun 8, 21:43

hdf5_all.cpp
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#include "catch.hpp"
#include "specmicp_common/io/hdf5_timesteps.hpp"
#include "specmicp_common/io/hdf5/file.hpp"
#include "specmicp_common/io/hdf5/group.hpp"
#include "specmicp_common/io/hdf5/dataset.hpp"
#include "specmicp_common/io/hdf5/dataspace.hpp"
#include <iostream>
using namespace specmicp::io;
TEST_CASE("HDF5 wrapper", "[io],[hdf5]")
{
SECTION("File")
{
{
auto file = hdf5::File::open("test_file.h5", hdf5::OpenMode::CreateTruncate);
REQUIRE(file.get_id() >= 0);
REQUIRE(file.get_path() == "/");
}
{
std::cout << "Next error HDF5 is ok :\n -------------------------" << std::endl;
REQUIRE_THROWS(hdf5::File::open("test_file.h5", hdf5::OpenMode::CreateFailIfExist));
std::cout << "---------------------------\n"<< std::endl;
}
{
auto file = hdf5::File::open("test_file.h5", hdf5::OpenMode::OpenReadOnly);
REQUIRE(file.get_id() >= 0);
REQUIRE(file.get_path() == "/");
}
}
SECTION("Group")
{
auto file = hdf5::File::open("test_file.h5", hdf5::OpenMode::OpenReadWrite);
file.create_group("test");
hdf5::Group test_group = file.open_group("test");
REQUIRE(test_group.get_id() >= 0);
REQUIRE(test_group.get_path() == "/test");
CHECK(file.has_link("test"));
}
SECTION("Dataset")
{
auto file = hdf5::File::open("test_file.h5", hdf5::OpenMode::OpenReadWrite);
hdf5::Group test_group = file.open_group("test");
Eigen::VectorXd x(5);
x << 0, 1, 2, 3, 4;
test_group.create_vector_dataset("vector", x);
REQUIRE(test_group.has_link("vector"));
Eigen::VectorXd y = test_group.read_vector_dataset("vector");
REQUIRE(y.rows() == 5);
for (int i=0; i<5; ++i) {
CHECK(y(i) == double(i));
}
// dataspace
hdf5::Dataset dset = test_group.open_dataset("vector");
hdf5::Dataspace dspace = dset.get_dataspace();
REQUIRE(dspace.get_rank() == 1);
hsize_t dims[1];
dspace.get_dimensions(dims);
CHECK(dims[0] == 5);
}
SECTION("String dataset")
{
auto file = hdf5::File::open("test_file.h5", hdf5::OpenMode::OpenReadWrite);
hdf5::Group test_group = file.open_group("test");
std::vector<std::string> to_write {"hello", "world", "!"};
test_group.create_string_dataset("test_string", to_write);
auto to_read = test_group.read_string_dataset("test_string");
CHECK(to_read.size() == to_write.size());
for(std::size_t ind=0; ind< to_read.size(); ++ind)
{
CHECK(to_read[ind] == to_write[ind]);
}
}
SECTION("Attribute")
{
auto file = hdf5::File::open("test_file.h5", hdf5::OpenMode::OpenReadWrite);
hdf5::Group test_group = file.create_group("test_dataspace");
Eigen::VectorXd x(5);
x << 5, 6, 7, 8, 9;
hdf5::Dataset test_dset = test_group.create_vector_dataset("dataset", x);
std::array<double, 3> hop = {0, 1, 2};
test_dset.create_scalar_attribute("test_attribute", hop);
auto res = test_dset.read_scalar_attribute<3>("test_attribute");
for (int i=0; i<3; ++i) {
CHECK(res[i] == double(i));
}
}
}
TEST_CASE("HDF5 timesteps", "[io],[hdf5],[timesteps]")
{
// write some timesteps in a file
auto file = hdf5::File::open("test_file.h5", hdf5::OpenMode::CreateTruncate);
file.create_group("11.1");
file.create_group("22.2");
file.create_group("33.3");
file.create_group("44.4");
SECTION("test") {
CHECK(file.get_number_links() == 4);
auto grp = file.open_group("/");
HDF5Timesteps timesteps(grp);
CHECK(timesteps.size() == 4);
CHECK(timesteps.get_number("22.2") == 22.2);
CHECK(timesteps.get_string(11.1) == "11.1");
CHECK(timesteps.get_string(22.2) == "22.2");
CHECK(timesteps.get_string(33.3) == "33.3");
CHECK(timesteps.get_string(44.4) == "44.4");
CHECK(timesteps.get_string(33.2) == "33.3");
CHECK_THROWS(timesteps.get_string(55.5) == "55.5");
}
}

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