hdf5-and-contiguous-array.c

#include <stdio.h>
#include <stdlib.h>
#include <hdf5.h>

double **
Plain_init(int x, int y) {
    double **plain = malloc(sizeof(double*)*x);
    double *space = malloc(sizeof(double)*x*y);
    for (int i = 0; i < x; i++) {
        plain[i] = space + i * y;
    }
    return plain;
}

herr_t
Plain_read(double** plain, hid_t dataset) {
    return H5Dread(
        dataset, H5T_NATIVE_DOUBLE,
        H5S_ALL, H5S_ALL, H5P_DEFAULT,
        &(plain[0][0])
    );
}

herr_t
Plain_write(double** plain, hid_t dataset) {
    H5Dwrite(
        dataset, H5T_NATIVE_DOUBLE,
        H5S_ALL, H5S_ALL, H5P_DEFAULT,
        &(plain[0][0])
    );
}

double ***
Cube_init(int x, int y, int z) {
    double ***cube = malloc(sizeof(double**)*x);
    double **slice = malloc(sizeof(double*)*x*y);
    double *space = malloc(sizeof(double)*x*y*z);
    for (int i = 0; i < x; i++) {
        cube[i] = slice + i * y;
    }
    for (int i = 0; i < x; i++) {
        for (int j = 0; j < y; j++) {
            cube[i][j] = space + i * y * z + j * z;
        }
    }
    return cube;
}

herr_t
Cube_read(double ***cube, hid_t dataset) {
    return H5Dread(
        dataset, H5T_NATIVE_DOUBLE,
        H5S_ALL, H5S_ALL, H5P_DEFAULT,
        &(cube[0][0][0])
    );
}

herr_t
Cube_write(double ***cube, hid_t dataset) {
    return H5Dwrite(
        dataset, H5T_NATIVE_DOUBLE,
        H5S_ALL, H5S_ALL, H5P_DEFAULT,
        &(cube[0][0][0])
    );
}

int main() {
    hid_t   file_id;
    herr_t  status;

    file_id = H5Fcreate("test.hdf5", H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT);

    H5Gcreate2(file_id, "/foo", H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
    H5Gcreate2(file_id, "/bar", H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);

    hsize_t dims[2] = { 3, 3 };
    hid_t dataspace_id = H5Screate_simple(2, dims, NULL);

    hid_t dataset_id = H5Dcreate(file_id, "dataset", H5T_NATIVE_DOUBLE, dataspace_id,
                                    H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);

    double **init = Plain_init(3, 3);
    Plain_read(init, dataset_id);
    for (int i = 0; i < 3; i++) {
        for (int j = 0; j < 3; j++) {
            printf("%f\n", init[i][j]);
        }
    }

    double **plain = Plain_init(3, 3);
    for (int i = 0; i < 3; i++) {
        for (int j = 0; j < 3; j++) {
            plain[i][j] = (double)i + (double)j;
        }
    }
    Plain_write(plain, dataset_id);

    status = H5Dclose(dataset_id);
    printf("close dataset %i\n", status);
    status = H5Sclose(dataspace_id);
    printf("close dataspace %i\n", status);
    status = H5Fclose(file_id);
    printf("close file %i\n", status);

    return 0;
}