tests_high_five_base.cpp

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/*
 *  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 <cstdio>
#include <cstdlib>
#include <ctime>
#include <complex>
#include <iostream>
#include <random>
#include <string>
#include <typeinfo>
#include <vector>
#include <memory>
 
#include <stdio.h>
 
#include <highfive/H5DataSet.hpp>
#include <highfive/H5DataSpace.hpp>
#include <highfive/H5File.hpp>
#include <highfive/H5Group.hpp>
#include <highfive/H5Utility.hpp>
 
#define BOOST_TEST_MAIN HighFiveTest
 
#include <boost/mpl/list.hpp>
#include <boost/test/unit_test.hpp>
 
#ifdef H5_USE_BOOST
#include <boost/multi_array.hpp>
#endif
 
using namespace HighFive;
using complex = std::complex<double>;
 
typedef boost::mpl::list<float, double> floating_numerics_test_types;
typedef boost::mpl::list<int, unsigned int, long, unsigned long, unsigned char,
                         char, float, double, long long, unsigned long long,
                         complex>
    numerical_test_types;
typedef boost::mpl::list<int, unsigned int, long, unsigned long, unsigned char,
                         char, float, double, std::string>
    dataset_test_types;
 
template <typename T, typename Func>
void generate2D(T* table, size_t x, size_t y, Func& func) {
    for (size_t i = 0; i < x; i++) {
        for (size_t j = 0; j < y; j++) {
            table[i][j] = func();
        }
    }
}
 
template <typename T, typename Func>
void generate2D(std::vector<std::vector<T>>& vec, size_t x, size_t y,
                Func& func) {
    vec.resize(x);
    for (size_t i = 0; i < x; i++) {
        vec[i].resize(y);
        for (size_t j = 0; j < y; j++) {
            vec[i][j] = func();
        }
    }
}
 
template <typename T>
struct ContentGenerate {
    ContentGenerate() : _init(0), _inc(T(1) + T(1) / T(10)) {}
 
    T operator()() {
        T ret = _init;
        _init += _inc;
        return ret;
    }
 
    T _init, _inc;
};
 
template <>
ContentGenerate<complex>::ContentGenerate()
    : _init(0, 0)
    , _inc(complex(1, 1) + complex(1, 1) / complex(10))
{}
 
template <>
struct ContentGenerate<char> {
    ContentGenerate() : _init('a') {}
 
    char operator()() {
        char ret = _init;
        if (++_init >= ('a' + 26))
            _init = 'a';
        return ret;
    }
 
    char _init;
};
 
template <>
struct ContentGenerate<std::string> {
    ContentGenerate() {}
 
    std::string operator()() {
        ContentGenerate<char> gen;
        std::string random_string;
        std::mt19937_64 rgen;
        rgen.seed(88);
        std::uniform_int_distribution<int> int_dist(0, 1000);
        const size_t size_string = int_dist(rgen);
 
        random_string.resize(size_string);
        std::generate(random_string.begin(), random_string.end(), gen);
        return random_string;
    }
};
 
BOOST_AUTO_TEST_CASE(HighFiveBasic) {
    const std::string FILE_NAME("h5tutr_dset.h5");
    const std::string DATASET_NAME("dset");
 
    // Create a new file using the default property lists.
    File file(FILE_NAME, File::ReadWrite | File::Create | File::Truncate);
 
    BOOST_CHECK_EQUAL(file.getName(), FILE_NAME);
 
    // Create the data space for the dataset.
    std::vector<size_t> dims{4,6};
 
    DataSpace dataspace(dims);
 
    // check if the dataset exist
    bool dataset_exist = file.exist(DATASET_NAME + "_double");
    BOOST_CHECK_EQUAL(dataset_exist, false);
 
    // Create a dataset with double precision floating points
    DataSet dataset_double = file.createDataSet(
        DATASET_NAME + "_double", dataspace, AtomicType<double>());
 
    BOOST_CHECK_EQUAL(file.getObjectName(0), DATASET_NAME + "_double");
 
    {
        // check if it exist again
        dataset_exist = file.exist(DATASET_NAME + "_double");
        BOOST_CHECK_EQUAL(dataset_exist, true);
 
        // and also try to recreate it to the sake of exception testing
        BOOST_CHECK_THROW(
            {
                DataSet fail_duplicated = file.createDataSet(
                    DATASET_NAME + "_double", dataspace, AtomicType<double>());
            },
            DataSetException);
    }
 
    DataSet dataset_size_t =
        file.createDataSet<size_t>(DATASET_NAME + "_size_t", dataspace);
}
 
BOOST_AUTO_TEST_CASE(HighFiveSilence) {
    // Setting up a buffer for stderr so we can detect if the stack trace
    // was disabled
    fflush(stderr);
    char buffer[1024];
    memset(buffer, 0, sizeof(char) * 1024);
    setvbuf(stderr, buffer, _IOLBF, 1023);
 
    try {
        SilenceHDF5 silence;
        File file("nonexistent", File::ReadOnly);
    } catch (const FileException&) {
    }
    BOOST_CHECK_EQUAL(buffer[0], '\0');
 
    // restore the dyn allocated buffer
    // or using stderr will segfault when buffer get out of scope
    fflush(stderr);
    setvbuf(stderr, NULL, _IONBF, 0);
}
 
BOOST_AUTO_TEST_CASE(HighFiveOpenMode) {
    const std::string FILE_NAME("openmodes.h5");
    const std::string DATASET_NAME("dset");
 
    std::remove(FILE_NAME.c_str());
 
    // Attempt open file only ReadWrite should fail (wont create)
    BOOST_CHECK_THROW(
        { File file(FILE_NAME, File::ReadWrite); },
        FileException);
 
    // But with Create flag should be fine
    { File file(FILE_NAME, File::ReadWrite | File::Create); }
 
    // But if its there and exclusive is given, should fail
    BOOST_CHECK_THROW(
        { File file(FILE_NAME, File::ReadWrite | File::Excl); },
        FileException);
    // ReadWrite and Excl flags are fine together (posix)
    std::remove(FILE_NAME.c_str());
    { File file(FILE_NAME, File::ReadWrite | File::Excl); }
    // All three are fine as well (as long as the file does not exist)
    std::remove(FILE_NAME.c_str());
    { File file(FILE_NAME, File::ReadWrite | File::Create | File::Excl); }
 
    // Just a few combinations are incompatible, detected by hdf5lib
    BOOST_CHECK_THROW(
        { File file(FILE_NAME, File::Truncate | File::Excl); },
        FileException);
 
    std::remove(FILE_NAME.c_str());
    BOOST_CHECK_THROW(
        { File file(FILE_NAME, File::Truncate | File::Excl); },
        FileException);
 
    // But in most cases we will truncate and that should always work
    { File file(FILE_NAME, File::Truncate); }
    std::remove(FILE_NAME.c_str());
    { File file(FILE_NAME, File::Truncate); }
 
    // Last but not least, defaults should be ok
    { File file(FILE_NAME); }     // ReadOnly
    { File file(FILE_NAME, 0); }  // force empty-flags, does open without flags
}
 
 
BOOST_AUTO_TEST_CASE(HighFiveGroupAndDataSet) {
    const std::string FILE_NAME("h5_group_test.h5");
    const std::string DATASET_NAME("dset");
    const std::string CHUNKED_DATASET_NAME("chunked_dset");
    const std::string CHUNKED_DATASET_SMALL_NAME("chunked_dset_small");
    const std::string GROUP_NAME1("/group1");
    const std::string GROUP_NAME2("group2");
    const std::string GROUP_NESTED_NAME("group_nested");
 
    {
        // Create a new file using the default property lists.
        File file(FILE_NAME, File::ReadWrite | File::Create | File::Truncate);
 
        // absolute group
        file.createGroup(GROUP_NAME1);
        // nested group absolute
        file.createGroup(GROUP_NAME1 + "/" + GROUP_NESTED_NAME);
        // relative group
        Group g1 = file.createGroup(GROUP_NAME2);
        // relative group
        Group nested = g1.createGroup(GROUP_NESTED_NAME);
 
        // Create the data space for the dataset.
        std::vector<size_t> dims{4, 6};
 
        DataSpace dataspace(dims);
 
        DataSet dataset_absolute = file.createDataSet(
            GROUP_NAME1 + "/" + GROUP_NESTED_NAME + "/" + DATASET_NAME,
            dataspace, AtomicType<double>());
 
        DataSet dataset_relative =
            nested.createDataSet(DATASET_NAME, dataspace, AtomicType<double>());
 
        DataSetCreateProps goodChunking;
        goodChunking.add(Chunking(std::vector<hsize_t>{2, 2}));
        DataSetAccessProps cacheConfig;
        cacheConfig.add(Caching(13, 1024, 0.5));
 
        // will fail because exceeds dimensions
        DataSetCreateProps badChunking0;
        badChunking0.add(Chunking(std::vector<hsize_t>{10, 10}));
 
        DataSetCreateProps badChunking1;
        badChunking1.add(Chunking(std::vector<hsize_t>{1, 1, 1}));
 
 
        BOOST_CHECK_THROW(file.createDataSet(CHUNKED_DATASET_NAME, dataspace,
                                             AtomicType<double>(),
                                             badChunking0),
                          DataSetException);
 
        BOOST_CHECK_THROW(file.createDataSet(CHUNKED_DATASET_NAME, dataspace,
                                             AtomicType<double>(),
                                             badChunking1),
                          DataSetException);
 
        // here we use the other signature
        DataSet dataset_chunked = file.createDataSet<float>(
            CHUNKED_DATASET_NAME, dataspace, goodChunking, cacheConfig);
 
        // Here we resize to smaller than the chunking size
        DataSet dataset_chunked_small = file.createDataSet<float>(
            CHUNKED_DATASET_SMALL_NAME, dataspace, goodChunking);
 
        dataset_chunked_small.resize({1, 1});
    }
    // read it back
    {
        File file(FILE_NAME, File::ReadOnly);
        Group g1 = file.getGroup(GROUP_NAME1);
        Group g2 = file.getGroup(GROUP_NAME2);
        Group nested_group2 = g2.getGroup(GROUP_NESTED_NAME);
 
        DataSet dataset_absolute = file.getDataSet(
            GROUP_NAME1 + "/" + GROUP_NESTED_NAME + "/" + DATASET_NAME);
        BOOST_CHECK_EQUAL(4, dataset_absolute.getSpace().getDimensions()[0]);
 
        DataSet dataset_relative = nested_group2.getDataSet(DATASET_NAME);
        BOOST_CHECK_EQUAL(4, dataset_relative.getSpace().getDimensions()[0]);
 
        DataSetAccessProps accessProps;
        accessProps.add(Caching(13, 1024, 0.5));
        DataSet dataset_chunked = file.getDataSet(CHUNKED_DATASET_NAME,
                                                  accessProps);
        BOOST_CHECK_EQUAL(4, dataset_chunked.getSpace().getDimensions()[0]);
 
        DataSet dataset_chunked_small =
            file.getDataSet(CHUNKED_DATASET_SMALL_NAME);
        BOOST_CHECK_EQUAL(1,
                          dataset_chunked_small.getSpace().getDimensions()[0]);
    }
}
 
BOOST_AUTO_TEST_CASE(HighFiveExtensibleDataSet) {
    const std::string FILE_NAME("create_extensible_dataset_example.h5");
    const std::string DATASET_NAME("dset");
    constexpr double t1[3][1] = {{2.0}, {2.0}, {4.0}};
    constexpr double t2[1][3] = {{4.0, 8.0, 6.0}};
 
    {
        // Create a new file using the default property lists.
        File file(FILE_NAME, File::ReadWrite | File::Create | File::Truncate);
 
        // Create a dataspace with initial shape and max shape
        DataSpace dataspace = DataSpace({4, 5}, {17, DataSpace::UNLIMITED});
 
        // Use chunking
        DataSetCreateProps props;
        props.add(Chunking(std::vector<hsize_t>{2, 2}));
 
        // Create the dataset
        DataSet dataset = file.createDataSet(DATASET_NAME, dataspace,
                                             AtomicType<double>(), props);
 
        // Write into the initial part of the dataset
        dataset.select({0, 0}, {3, 1}).write(t1);
 
        // Resize the dataset to a larger size
        dataset.resize({4, 6});
 
        BOOST_CHECK_EQUAL(4, dataset.getSpace().getDimensions()[0]);
        BOOST_CHECK_EQUAL(6, dataset.getSpace().getDimensions()[1]);
 
        // Write into the new part of the dataset
        dataset.select({3, 3}, {1, 3}).write(t2);
 
        // Try resize out of bounds
        BOOST_CHECK_THROW(dataset.resize({18, 1}), DataSetException);
        // Try resize invalid dimensions
        BOOST_CHECK_THROW(dataset.resize({1, 2, 3}), DataSetException);
    }
 
    // read it back
    {
        File file(FILE_NAME, File::ReadOnly);
 
        DataSet dataset_absolute = file.getDataSet("/" + DATASET_NAME);
        const auto dims = dataset_absolute.getSpace().getDimensions();
        double values[4][6];
        dataset_absolute.read(values);
        BOOST_CHECK_EQUAL(4, dims[0]);
        BOOST_CHECK_EQUAL(6, dims[1]);
 
        BOOST_CHECK_EQUAL(t1[0][0], values[0][0]);
        BOOST_CHECK_EQUAL(t1[1][0], values[1][0]);
        BOOST_CHECK_EQUAL(t1[2][0], values[2][0]);
 
        BOOST_CHECK_EQUAL(t2[0][0], values[3][3]);
        BOOST_CHECK_EQUAL(t2[0][1], values[3][4]);
        BOOST_CHECK_EQUAL(t2[0][2], values[3][5]);
    }
}
 
BOOST_AUTO_TEST_CASE(HighFiveRefCountMove) {
    const std::string FILE_NAME("h5_ref_count_test.h5");
    const std::string DATASET_NAME("dset");
    const std::string GROUP_NAME1("/group1");
    const std::string GROUP_NAME2("/group2");
 
    // Create a new file using the default property lists.
    File file(FILE_NAME, File::ReadWrite | File::Create | File::Truncate);
 
    std::unique_ptr<DataSet> d1_ptr;
    std::unique_ptr<Group> g_ptr;
 
    {
        // create group
        Group g1 = file.createGroup(GROUP_NAME1);
 
        // override object
        g1 = file.createGroup(GROUP_NAME2);
 
        // Create the data space for the dataset.
        std::vector<size_t> dims = {10, 10};
 
        DataSpace dataspace(dims);
 
        DataSet d1 = file.createDataSet(GROUP_NAME1 + DATASET_NAME, dataspace,
                                        AtomicType<double>());
 
        double values[10][10] = {{0}};
        values[5][0] = 1;
        d1.write(values);
 
        // force move
        d1_ptr.reset(new DataSet(std::move(d1)));
 
        // force copy
        g_ptr.reset(new Group(g1));
    }
    // read it back
    {
        DataSet d2(std::move(*d1_ptr));
        d1_ptr.reset();
 
        double values[10][10];
        memset(values, 255, 10 * 10);
 
        d2.read(values);
 
        for (std::size_t i = 0; i < 10; ++i) {
            for (std::size_t j = 0; j < 10; ++j) {
                double v = values[i][j];
 
                if (i == 5 && j == 0) {
                    BOOST_CHECK_EQUAL(v, 1);
                } else {
                    BOOST_CHECK_EQUAL(v, 0);
                }
            }
        }
 
        // force copy
        Group g2 = *g_ptr;
 
        // add a subgroup
        g2.createGroup("blabla");
    }
}
 
BOOST_AUTO_TEST_CASE(HighFiveSimpleListing) {
    const std::string FILE_NAME("h5_list_test.h5");
    const std::string GROUP_NAME_CORE("group_name");
    const std::string GROUP_NESTED_NAME("/group_nested");
 
    // Create a new file using the default property lists.
    File file(FILE_NAME, File::ReadWrite | File::Create | File::Truncate);
 
    {
        // absolute group
        for (int i = 0; i < 2; ++i) {
            std::ostringstream ss;
            ss << "/" << GROUP_NAME_CORE << "_" << i;
            file.createGroup(ss.str());
        }
 
        size_t n_elem = file.getNumberObjects();
        BOOST_CHECK_EQUAL(2, n_elem);
 
        std::vector<std::string> elems = file.listObjectNames();
        BOOST_CHECK_EQUAL(2, elems.size());
        std::vector<std::string> reference_elems;
        for (int i = 0; i < 2; ++i) {
            std::ostringstream ss;
            ss << GROUP_NAME_CORE << "_" << i;
            reference_elems.push_back(ss.str());
        }
 
        BOOST_CHECK_EQUAL_COLLECTIONS(elems.begin(), elems.end(),
                                      reference_elems.begin(),
                                      reference_elems.end());
    }
 
    {
        file.createGroup(GROUP_NESTED_NAME);
        Group g_nest = file.getGroup(GROUP_NESTED_NAME);
 
        for (int i = 0; i < 50; ++i) {
            std::ostringstream ss;
            ss << GROUP_NAME_CORE << "_" << i;
            g_nest.createGroup(ss.str());
        }
 
        size_t n_elem = g_nest.getNumberObjects();
        BOOST_CHECK_EQUAL(50, n_elem);
 
        std::vector<std::string> elems = g_nest.listObjectNames();
        BOOST_CHECK_EQUAL(50, elems.size());
        std::vector<std::string> reference_elems;
 
        for (int i = 0; i < 50; ++i) {
            std::ostringstream ss;
            ss << GROUP_NAME_CORE << "_" << i;
            reference_elems.push_back(ss.str());
        }
        // there is no guarantee on the order of the hdf5 index, let's sort it
        // to put them in order
        std::sort(elems.begin(), elems.end());
        std::sort(reference_elems.begin(), reference_elems.end());
 
        BOOST_CHECK_EQUAL_COLLECTIONS(elems.begin(), elems.end(),
                                      reference_elems.begin(),
                                      reference_elems.end());
    }
}
 
BOOST_AUTO_TEST_CASE(DataTypeEqualSimple) {
    using namespace HighFive;
 
    AtomicType<double> d_var;
    AtomicType<size_t> size_var;
    AtomicType<double> d_var_test;
    AtomicType<size_t> size_var_cpy(size_var);
    AtomicType<int> int_var;
    AtomicType<unsigned int> uint_var;
 
    // check different type matching
    BOOST_CHECK(d_var == d_var_test);
    BOOST_CHECK(d_var != size_var);
 
    // check type copy matching
    BOOST_CHECK(size_var_cpy == size_var);
 
    // check sign change not matching
    BOOST_CHECK(int_var != uint_var);
}
 
BOOST_AUTO_TEST_CASE(DataTypeEqualTakeBack) {
    using namespace HighFive;
 
    const std::string FILE_NAME("h5tutr_dset.h5");
    const std::string DATASET_NAME("dset");
 
    // Create a new file using the default property lists.
    File file(FILE_NAME, File::ReadWrite | File::Create | File::Truncate);
 
    // Create the data space for the dataset.
    std::vector<size_t> dims{10, 1};
 
    DataSpace dataspace(dims);
 
    // Create a dataset with double precision floating points
    DataSet dataset =
        file.createDataSet<size_t>(DATASET_NAME + "_double", dataspace);
 
    AtomicType<size_t> s;
    AtomicType<double> d;
 
    BOOST_CHECK(s == dataset.getDataType());
    BOOST_CHECK(d != dataset.getDataType());
}
 
BOOST_AUTO_TEST_CASE(DataSpaceTest) {
    using namespace HighFive;
 
    const std::string FILE_NAME("h5tutr_space.h5");
    const std::string DATASET_NAME("dset");
 
    // Create a new file using the default property lists.
    File file(FILE_NAME, File::ReadWrite | File::Create | File::Truncate);
 
    // Create the data space for the dataset.
    DataSpace dataspace{std::vector<size_t>{10, 1}};
 
    // Create a dataset with size_t type
    DataSet dataset = file.createDataSet<size_t>(DATASET_NAME, dataspace);
 
    DataSpace space = dataset.getSpace();
    DataSpace space2 = dataset.getSpace();
 
    // verify space id are different
    BOOST_CHECK_NE(space.getId(), space2.getId());
 
    // verify space id are consistent
    BOOST_CHECK_EQUAL(space.getDimensions().size(), 2);
    BOOST_CHECK_EQUAL(space.getDimensions()[0], 10);
    BOOST_CHECK_EQUAL(space.getDimensions()[1], 1);
}
 
BOOST_AUTO_TEST_CASE(DataSpaceVectorTest) {
    using namespace HighFive;
 
    // Create 1D shortcut dataspace
    DataSpace space(7);
 
    BOOST_CHECK_EQUAL(space.getDimensions().size(), 1);
    BOOST_CHECK_EQUAL(space.getDimensions()[0], 7);
 
    // Initializer list (explicit)
    DataSpace space3({8, 9, 10});
    auto space3_res = space3.getDimensions();
    std::vector<size_t> space3_ans{8, 9, 10};
 
    BOOST_CHECK_EQUAL_COLLECTIONS(space3_res.begin(), space3_res.end(),
                                  space3_ans.begin(), space3_ans.end());
 
    // Verify 2D works (note that without the {}, this matches the iterator constructor)
    DataSpace space2(std::vector<size_t>{3, 4});
 
    auto space2_res = space2.getDimensions();
    std::vector<size_t> space2_ans{3, 4};
 
    BOOST_CHECK_EQUAL_COLLECTIONS(space2_res.begin(), space2_res.end(),
                                  space2_ans.begin(), space2_ans.end());
 
}
 
BOOST_AUTO_TEST_CASE(DataSpaceVariadicTest) {
    using namespace HighFive;
 
    // Create 1D shortcut dataspace
    DataSpace space1 {7};
 
    auto space1_res = space1.getDimensions();
    std::vector<size_t> space1_ans{7};
 
    BOOST_CHECK_EQUAL_COLLECTIONS(space1_res.begin(), space1_res.end(),
                                  space1_ans.begin(), space1_ans.end());
 
 
    // Initializer list (explicit)
    DataSpace space3{8, 9, 10};
 
    auto space3_res = space3.getDimensions();
    std::vector<size_t> space3_ans{8, 9, 10};
 
    BOOST_CHECK_EQUAL_COLLECTIONS(space3_res.begin(), space3_res.end(),
                                  space3_ans.begin(), space3_ans.end());
 
    // Verify 2D works using explicit syntax
    DataSpace space2{3, 4};
 
    auto space2_res = space2.getDimensions();
    std::vector<size_t> space2_ans{3, 4};
 
    BOOST_CHECK_EQUAL_COLLECTIONS(space2_res.begin(), space2_res.end(),
                                  space2_ans.begin(), space2_ans.end());
 
    // Verify 2D works using old syntax (this used to match the iterator!)
    DataSpace space2b(3, 4);
 
    auto space2b_res = space2b.getDimensions();
    std::vector<size_t> space2b_ans{3, 4};
 
    BOOST_CHECK_EQUAL_COLLECTIONS(space2b_res.begin(), space2b_res.end(),
                                  space2b_ans.begin(), space2b_ans.end());
}
 
BOOST_AUTO_TEST_CASE(ChunkingConstructorsTest) {
    Chunking first(1,2,3);
 
    auto first_res = first.getDimensions();
    std::vector<hsize_t> first_ans{1,2,3};
 
    BOOST_CHECK_EQUAL_COLLECTIONS(first_res.begin(), first_res.end(),
                                  first_ans.begin(), first_ans.end());
 
    Chunking second{1,2,3};
 
    auto second_res = second.getDimensions();
    std::vector<hsize_t> second_ans{1,2,3};
 
    BOOST_CHECK_EQUAL_COLLECTIONS(second_res.begin(), second_res.end(),
                                  second_ans.begin(), second_ans.end());
 
    Chunking third({1,2,3});
 
    auto third_res = third.getDimensions();
    std::vector<hsize_t> third_ans{1,2,3};
 
    BOOST_CHECK_EQUAL_COLLECTIONS(third_res.begin(), third_res.end(),
                                  third_ans.begin(), third_ans.end());
}
 
template <typename T>
void readWrite2DArrayTest() {
    std::ostringstream filename;
    filename << "h5_rw_2d_array_" << typeid(T).name() << "_test.h5";
    const std::string DATASET_NAME("dset");
    const size_t x_size = 100;
    const size_t y_size = 10;
 
    // Create a new file using the default property lists.
    File file(filename.str(), File::ReadWrite | File::Create | File::Truncate);
 
    // Create the data space for the dataset.
    std::vector<size_t> dims{x_size, y_size};
 
    DataSpace dataspace(dims);
 
    // Create a dataset with arbitrary type
    DataSet dataset = file.createDataSet<T>(DATASET_NAME, dataspace);
 
    T array[x_size][y_size];
 
    ContentGenerate<T> generator;
    generate2D(array, x_size, y_size, generator);
 
    dataset.write(array);
 
    T result[x_size][y_size];
 
    dataset.read(result);
 
    for (size_t i = 0; i < x_size; ++i) {
        for (size_t j = 0; j < y_size; ++j) {
            BOOST_CHECK_EQUAL(result[i][j], array[i][j]);
        }
    }
}
 
BOOST_AUTO_TEST_CASE_TEMPLATE(ReadWrite2DArray, T, numerical_test_types) {
    readWrite2DArrayTest<T>();
}
 
BOOST_AUTO_TEST_CASE(HighFiveReadWriteShortcut) {
    using namespace HighFive;
 
    std::ostringstream filename;
    filename << "h5_rw_vec_shortcut_test.h5";
 
    const size_t x_size = 800;
    const std::string DATASET_NAME("dset");
    std::vector<int> vec;
    vec.resize(x_size);
    for(size_t i=0; i < x_size; i++)
        vec[i] = i * 2;
    std::string at_contents("Contents of string");
    int my_int = 3;
    std::vector<std::vector<int>> my_nested = {{1,2},{3,4}};
 
    // Create a new file using the default property lists.
    File file(filename.str(), File::ReadWrite | File::Create | File::Truncate);
 
    // Create a dataset with int points
    DataSet dataset = file.createDataSet(DATASET_NAME, vec);
    dataset.createAttribute("str", at_contents);
 
    DataSet ds_int = file.createDataSet("/TmpInt", my_int);
    DataSet ds_nested = file.createDataSet("/TmpNest", my_nested);
 
    std::vector<int> result;
    dataset.read(result);
    BOOST_CHECK_EQUAL_COLLECTIONS(vec.begin(), vec.end(),
                                  result.begin(), result.end());
 
    std::string read_in;
    dataset.getAttribute("str").read(read_in);
    BOOST_CHECK_EQUAL(read_in, at_contents);
 
    int out_int = 0;
    ds_int.read(out_int);
    BOOST_CHECK_EQUAL(my_int, out_int);
 
    decltype(my_nested) out_nested;
    ds_nested.read(out_nested);
 
    for (size_t i = 0; i < 2; ++i) {
        for (size_t j = 0; j < 2; ++j) {
            BOOST_CHECK_EQUAL(my_nested[i][j], out_nested[i][j]);
        }
    }
}
 
template <typename T>
void readWriteVectorTest() {
    using namespace HighFive;
 
    std::ostringstream filename;
    filename << "h5_rw_vec_" << typeid(T).name() << "_test.h5";
 
    const size_t x_size = 800;
    const std::string DATASET_NAME("dset");
    typename std::vector<T> vec;
    vec.resize(x_size);
    ContentGenerate<T> generator;
    std::generate(vec.begin(), vec.end(), generator);
 
    // Create a new file using the default property lists.
    File file(filename.str(), File::ReadWrite | File::Create | File::Truncate);
 
    // Create a dataset with type T points
    DataSet dataset = file.createDataSet<T>(DATASET_NAME, DataSpace::From(vec));
 
    dataset.write(vec);
 
    typename std::vector<T> result;
 
    dataset.read(result);
 
    BOOST_CHECK_EQUAL(vec.size(), x_size);
    BOOST_CHECK_EQUAL(result.size(), x_size);
 
    BOOST_CHECK_EQUAL_COLLECTIONS(result.begin(), result.end(),
                                  vec.begin(), vec.end());
}
BOOST_AUTO_TEST_CASE_TEMPLATE(readWriteVector, T, numerical_test_types) {
    readWriteVectorTest<T>();
}
 
template <typename T>
void readWriteArrayTest() {
    using namespace HighFive;
 
    std::ostringstream filename;
    filename << "h5_rw_arr_" << typeid(T).name() << "_test.h5";
 
    const size_t x_size = 800;
    const std::string DATASET_NAME("dset");
    typename std::array<T, x_size> vec;
    ContentGenerate<T> generator;
    std::generate(vec.begin(), vec.end(), generator);
 
    // Create a new file using the default property lists.
    File file(filename.str(), File::ReadWrite | File::Create | File::Truncate);
 
    // Create a dataset with type T points
    DataSet dataset = file.createDataSet<T>(DATASET_NAME, DataSpace::From(vec));
 
    dataset.write(vec);
 
    typename std::array<T, x_size> result;
 
    dataset.read(result);
 
    BOOST_CHECK_EQUAL_COLLECTIONS(result.begin(), result.end(),
                                  vec.begin(), vec.end());
 
    typename std::array<T, 1> tooSmall;
    BOOST_CHECK_THROW(dataset.read(tooSmall), DataSpaceException);
}
BOOST_AUTO_TEST_CASE_TEMPLATE(readWriteArray, T, numerical_test_types) {
    readWriteArrayTest<T>();
}
 
template <typename T>
void readWriteAttributeVectorTest() {
    using namespace HighFive;
 
    std::ostringstream filename;
    filename << "h5_rw_attribute_vec_" << typeid(T).name() << "_test.h5";
 
    std::srand((unsigned int)std::time(0));
    const size_t x_size = 25;
    const std::string DATASET_NAME("dset");
    typename std::vector<T> vec;
 
    // Create a new file using the default property lists.
    File file(filename.str(), File::ReadWrite | File::Create | File::Truncate);
 
    vec.resize(x_size);
    ContentGenerate<T> generator;
    std::generate(vec.begin(), vec.end(), generator);
 
    {
        // Create a dummy group to annotate with an attribute
        Group g = file.createGroup("dummy_group");
 
        // check that no attributes are there
        std::size_t n = g.getNumberAttributes();
        BOOST_CHECK_EQUAL(n, 0);
 
        std::vector<std::string> all_attribute_names = g.listAttributeNames();
        BOOST_CHECK_EQUAL(all_attribute_names.size(), 0);
 
        bool has_attribute = g.hasAttribute("my_attribute");
        BOOST_CHECK_EQUAL(has_attribute, false);
 
        Attribute a1 =
            g.createAttribute<T>("my_attribute", DataSpace::From(vec));
        a1.write(vec);
 
        // check now that we effectively have an attribute listable
        std::size_t n2 = g.getNumberAttributes();
        BOOST_CHECK_EQUAL(n2, 1);
 
        has_attribute = g.hasAttribute("my_attribute");
        BOOST_CHECK_EQUAL(has_attribute, true);
 
        all_attribute_names = g.listAttributeNames();
        BOOST_CHECK_EQUAL(all_attribute_names.size(), 1);
        BOOST_CHECK_EQUAL(all_attribute_names[0], std::string("my_attribute"));
 
        // Create the same attribute on a newly created dataset
        DataSet s =
            g.createDataSet("dummy_dataset", DataSpace(1), AtomicType<int>());
 
        Attribute a2 =
            s.createAttribute<T>("my_attribute_copy", DataSpace::From(vec));
        a2.write(vec);
    }
 
    typename std::vector<T> result1, result2;
 
    {
        Attribute a1_read =
            file.getGroup("dummy_group").getAttribute("my_attribute");
        a1_read.read(result1);
 
        BOOST_CHECK_EQUAL(vec.size(), x_size);
        BOOST_CHECK_EQUAL(result1.size(), x_size);
 
        for (size_t i = 0; i < x_size; ++i)
            BOOST_CHECK_EQUAL(result1[i], vec[i]);
 
        Attribute a2_read = file.getDataSet("/dummy_group/dummy_dataset")
                                .getAttribute("my_attribute_copy");
        a2_read.read(result2);
 
        BOOST_CHECK_EQUAL(vec.size(), x_size);
        BOOST_CHECK_EQUAL(result2.size(), x_size);
 
        for (size_t i = 0; i < x_size; ++i)
            BOOST_CHECK_EQUAL(result2[i], vec[i]);
    }
}
 
BOOST_AUTO_TEST_CASE_TEMPLATE(ReadWriteAttributeVector, T, dataset_test_types) {
    readWriteAttributeVectorTest<T>();
}
 
template <typename T>
void readWriteVector2DTest() {
    using namespace HighFive;
 
    std::ostringstream filename;
    filename << "h5_rw_vec_2d_" << typeid(T).name() << "_test.h5";
 
    const size_t x_size = 10;
    const size_t y_size = 10;
    const std::string DATASET_NAME("dset");
    typename std::vector<std::vector<T>> vec;
 
    // Create a new file using the default property lists.
    File file(filename.str(), File::ReadWrite | File::Create | File::Truncate);
 
    vec.resize(x_size);
    ContentGenerate<T> generator;
 
    generate2D(vec, x_size, y_size, generator);
 
    // Create a dataset with type T points
    DataSet dataset = file.createDataSet<T>(DATASET_NAME, DataSpace::From(vec));
 
    dataset.write(vec);
 
    typename std::vector<std::vector<T>> result;
 
    dataset.read(result);
 
    BOOST_CHECK_EQUAL(vec.size(), x_size);
    BOOST_CHECK_EQUAL(result.size(), x_size);
 
    BOOST_CHECK_EQUAL(vec[0].size(), y_size);
    BOOST_CHECK_EQUAL(result[0].size(), y_size);
 
    for (size_t i = 0; i < x_size; ++i) {
        for (size_t j = 0; i < y_size; ++i) {
            BOOST_CHECK_EQUAL(result[i][j], vec[i][j]);
        }
    }
}
 
BOOST_AUTO_TEST_CASE_TEMPLATE(readWriteVector2D, T, numerical_test_types) {
    readWriteVector2DTest<T>();
}
 
BOOST_AUTO_TEST_CASE(datasetOffset) {
    std::string filename = "datasetOffset.h5";
    std::string dsetname = "dset";
    const size_t size_dataset = 20;
 
    File file(filename, File::ReadWrite | File::Create | File::Truncate);
    std::vector<int> data(size_dataset);
    DataSet ds = file.createDataSet<int>(dsetname, DataSpace::From(data));
    ds.write(data);
    DataSet ds_read = file.getDataSet(dsetname);
    BOOST_CHECK(ds_read.getOffset() > 0);
}
 
#ifdef H5_USE_BOOST
 
template <typename T>
void MultiArray3DTest() {
    typedef typename boost::multi_array<T, 3> MultiArray;
 
    std::ostringstream filename;
    filename << "h5_rw_multiarray_" << typeid(T).name() << "_test.h5";
 
    const size_t size_x = 10, size_y = 10, size_z = 10;
    const std::string DATASET_NAME("dset");
    MultiArray array(boost::extents[size_x][size_y][size_z]);
 
    ContentGenerate<T> generator;
    std::generate(array.data(), array.data() + array.num_elements(), generator);
 
    // Create a new file using the default property lists.
    File file(filename.str(), File::ReadWrite | File::Create | File::Truncate);
 
    DataSet dataset =
        file.createDataSet<T>(DATASET_NAME, DataSpace::From(array));
 
    dataset.write(array);
 
    // read it back
    MultiArray result;
 
    dataset.read(result);
 
    for (size_t i = 0; i < size_x; ++i) {
        for (size_t j = 0; j < size_y; ++j) {
            for (size_t k = 0; k < size_z; ++k) {
                BOOST_CHECK_EQUAL(array[i][j][k], result[i][j][k]);
            }
        }
    }
}
 
BOOST_AUTO_TEST_CASE_TEMPLATE(MultiArray3D, T, numerical_test_types) {
    MultiArray3DTest<T>();
}
 
template <typename T>
void ublas_matrix_Test() {
    typedef typename boost::numeric::ublas::matrix<T> Matrix;
 
    std::ostringstream filename;
    filename << "h5_rw_multiarray_" << typeid(T).name() << "_test.h5";
 
    const size_t size_x = 10, size_y = 10;
    const std::string DATASET_NAME("dset");
 
    Matrix mat(size_x, size_y);
 
    ContentGenerate<T> generator;
    for (std::size_t i = 0; i < mat.size1(); ++i) {
        for (std::size_t j = 0; j < mat.size2(); ++j) {
            mat(i, j) = generator();
        }
    }
 
    // Create a new file using the default property lists.
    File file(filename.str(), File::ReadWrite | File::Create | File::Truncate);
 
    DataSet dataset = file.createDataSet<T>(DATASET_NAME, DataSpace::From(mat));
 
    dataset.write(mat);
 
    // read it back
    Matrix result;
 
    dataset.read(result);
 
    for (size_t i = 0; i < size_x; ++i) {
        for (size_t j = 0; j < size_y; ++j) {
            BOOST_CHECK_EQUAL(mat(i, j), result(i, j));
        }
    }
}
 
BOOST_AUTO_TEST_CASE_TEMPLATE(ublas_matrix, T, numerical_test_types) {
    ublas_matrix_Test<T>();
}
 
#endif
 
template <typename T>
void selectionArraySimpleTest() {
    typedef typename std::vector<T> Vector;
 
    std::ostringstream filename;
    filename << "h5_rw_select_test_" << typeid(T).name() << "_test.h5";
 
    const size_t size_x = 10;
    const size_t offset_x = 2, count_x = 5;
 
    const std::string DATASET_NAME("dset");
 
    Vector values(size_x);
 
    ContentGenerate<T> generator;
    std::generate(values.begin(), values.end(), generator);
 
    // Create a new file using the default property lists.
    File file(filename.str(), File::ReadWrite | File::Create | File::Truncate);
 
    DataSet dataset =
        file.createDataSet<T>(DATASET_NAME, DataSpace::From(values));
 
    dataset.write(values);
 
    file.flush();
 
    // select slice
    {
        // read it back
        Vector result;
        std::vector<size_t> offset{offset_x};
        std::vector<size_t> size{count_x};
 
        Selection slice = dataset.select(offset, size);
 
        BOOST_CHECK_EQUAL(slice.getSpace().getDimensions()[0], size_x);
        BOOST_CHECK_EQUAL(slice.getMemSpace().getDimensions()[0], count_x);
 
        slice.read(result);
 
        BOOST_CHECK_EQUAL(result.size(), 5);
 
        for (size_t i = 0; i < count_x; ++i) {
            BOOST_CHECK_EQUAL(values[i + offset_x], result[i]);
        }
    }
 
    // select cherry pick
    {
        // read it back
        Vector result;
        std::vector<size_t> ids{1,3,4,7};
 
        Selection slice = dataset.select(ElementSet(ids));
 
        BOOST_CHECK_EQUAL(slice.getSpace().getDimensions()[0], size_x);
        BOOST_CHECK_EQUAL(slice.getMemSpace().getDimensions()[0], ids.size());
 
        slice.read(result);
 
        BOOST_CHECK_EQUAL(result.size(), ids.size());
 
        for (size_t i = 0; i < ids.size(); ++i) {
            const std::size_t id = ids[i];
            BOOST_CHECK_EQUAL(values[id], result[i]);
        }
    }
}
 
BOOST_AUTO_TEST_CASE_TEMPLATE(selectionArraySimple, T, dataset_test_types) {
    selectionArraySimpleTest<T>();
}
 
template <typename T>
void columnSelectionTest() {
    std::ostringstream filename;
    filename << "h5_rw_select_column_test_" << typeid(T).name() << "_test.h5";
 
    const size_t x_size = 10;
    const size_t y_size = 7;
 
    const std::string DATASET_NAME("dset");
 
    T values[x_size][y_size];
 
    ContentGenerate<T> generator;
    generate2D(values, x_size, y_size, generator);
 
    // Create a new file using the default property lists.
    File file(filename.str(), File::ReadWrite | File::Create | File::Truncate);
 
    // Create the data space for the dataset.
    std::vector<size_t> dims{x_size, y_size};
 
    DataSpace dataspace(dims);
    // Create a dataset with arbitrary type
    DataSet dataset = file.createDataSet<T>(DATASET_NAME, dataspace);
 
    dataset.write(values);
 
    file.flush();
 
    std::vector<size_t> columns{1, 3, 5};
 
    Selection slice = dataset.select(columns);
    T result[x_size][3];
    slice.read(result);
 
    BOOST_CHECK_EQUAL(slice.getSpace().getDimensions()[0], x_size);
    BOOST_CHECK_EQUAL(slice.getMemSpace().getDimensions()[0], x_size);
 
    for (size_t i = 0; i < 3; ++i)
        for (size_t j = 0; j < x_size; ++j)
            BOOST_CHECK_EQUAL(result[j][i], values[j][columns[i]]);
}
 
BOOST_AUTO_TEST_CASE_TEMPLATE(columnSelection, T, numerical_test_types) {
    columnSelectionTest<T>();
}
 
template <typename T>
void attribute_scalar_rw() {
    std::ostringstream filename;
    filename << "h5_rw_attribute_scalar_rw" << typeid(T).name() << "_test.h5";
 
    File h5file(filename.str(),
                File::ReadWrite | File::Create | File::Truncate);
 
    ContentGenerate<T> generator;
 
    const T attribute_value(generator());
 
    Group g = h5file.createGroup("metadata");
 
    bool family_exist = g.hasAttribute("family");
    BOOST_CHECK_EQUAL(family_exist, false);
 
    // write a scalar attribute
    {
        T out(attribute_value);
        Attribute att = g.createAttribute<T>("family", DataSpace::From(out));
        att.write(out);
    }
 
    h5file.flush();
 
    // test if attribute exist
    family_exist = g.hasAttribute("family");
    BOOST_CHECK_EQUAL(family_exist, true);
 
    // read back a scalar attribute
    {
        T res;
        Attribute att = g.getAttribute("family");
        att.read(res);
        BOOST_CHECK_EQUAL(res, attribute_value);
    }
}
 
BOOST_AUTO_TEST_CASE_TEMPLATE(attribute_scalar_rw_all, T, dataset_test_types) {
    attribute_scalar_rw<T>();
}
 
// regression test https://github.com/BlueBrain/HighFive/issues/98
BOOST_AUTO_TEST_CASE(HighFiveOutofDimension) {
    std::string filename("h5_rw_reg_zero_dim_test.h5");
 
    const std::string DATASET_NAME("dset");
 
    {
        // Create a new file using the default property lists.
        File file(filename, File::ReadWrite | File::Create | File::Truncate);
 
        DataSpace d_null(DataSpace::DataspaceType::datascape_null);
 
        DataSet d1 = file.createDataSet<double>(DATASET_NAME, d_null);
 
        file.flush();
 
        DataSpace recovered_d1 = d1.getSpace();
 
        auto ndim = recovered_d1.getNumberDimensions();
        BOOST_CHECK_EQUAL(ndim, 0);
 
        auto dims = recovered_d1.getDimensions();
        BOOST_CHECK_EQUAL(dims.size(), 0);
    }
}
 
template <typename T>
void readWriteShuffleDeflateTest() {
    std::ostringstream filename;
    filename << "h5_rw_deflate_" << typeid(T).name() << "_test.h5";
    const std::string DATASET_NAME("dset");
    const size_t x_size = 128;
    const size_t y_size = 32;
    const size_t x_chunk = 16;
    const size_t y_chunk = 16;
 
    const int deflate_level = 9;
 
    T array[x_size][y_size];
 
    // write a compressed file
    {
        File file(filename.str(), File::ReadWrite | File::Create | File::Truncate);
 
        // Create the data space for the dataset.
        std::vector<size_t> dims{x_size, y_size};
 
        DataSpace dataspace(dims);
 
        // Use chunking
        DataSetCreateProps props;
        props.add(Chunking(std::vector<hsize_t>{x_chunk, y_chunk}));
 
        // Enable shuffle
        props.add(Shuffle());
 
        // Enable deflate
        props.add(Deflate(deflate_level));
 
        // Create a dataset with arbitrary type
        DataSet dataset = file.createDataSet<T>(DATASET_NAME, dataspace, props);
 
        ContentGenerate<T> generator;
        generate2D(array, x_size, y_size, generator);
 
        dataset.write(array);
 
        file.flush();
    }
 
    // read it back
    {
        File file_read(filename.str(), File::ReadOnly);
        DataSet dataset_read = file_read.getDataSet("/" + DATASET_NAME);
 
        T result[x_size][y_size];
 
        dataset_read.read(result);
 
        for (size_t i = 0; i < x_size; ++i) {
            for (size_t j = 0; i < y_size; ++i) {
                BOOST_CHECK_EQUAL(result[i][j], array[i][j]);
            }
        }
    }
}
 
BOOST_AUTO_TEST_CASE_TEMPLATE(ReadWriteShuffleDeflate, T, numerical_test_types) {
    readWriteShuffleDeflateTest<T>();
}
 
// Broadcasting is supported
BOOST_AUTO_TEST_CASE(ReadInBroadcastDims) {
 
    const std::string FILE_NAME("h5_missmatch1_dset.h5");
    const std::string DATASET_NAME("dset");
 
    // Create a new file using the default property lists.
    File file(FILE_NAME, File::ReadWrite | File::Create | File::Truncate);
 
    // Create the data space for the dataset.
    std::vector<size_t> dims_a{1,3};
    std::vector<size_t> dims_b{3,1};
 
    // 1D input / output vectors
    std::vector<double> some_data{5.0, 6.0, 7.0};
    std::vector<double> data_a;
    std::vector<double> data_b;
 
    DataSpace dataspace_a(dims_a);
    DataSpace dataspace_b(dims_b);
 
    // Create a dataset with double precision floating points
    DataSet dataset_a = file.createDataSet(DATASET_NAME + "_a", dataspace_a,
                                           AtomicType<double>());
    DataSet dataset_b = file.createDataSet(DATASET_NAME + "_b", dataspace_b,
                                           AtomicType<double>());
 
    dataset_a.write(some_data);
    dataset_b.write(some_data);
 
    DataSet out_a = file.getDataSet(DATASET_NAME + "_a");
    DataSet out_b = file.getDataSet(DATASET_NAME + "_b");
 
    out_a.read(data_a);
    out_b.read(data_b);
 
    BOOST_CHECK_EQUAL_COLLECTIONS(
            data_a.begin(), data_a.end(),
            some_data.begin(), some_data.end());
 
    BOOST_CHECK_EQUAL_COLLECTIONS(
            data_b.begin(), data_b.end(),
            some_data.begin(), some_data.end());
}