How to know what is in a H5 file

gouyon · May 16, 2024, 11:55am

Hello

I use the H5 library in a C program to read H5 files. But I need to know what is in my file (groups, datasets…)
I check over internet and found theses functions:

/* Open an existing file. */
    file_id = H5Fopen(FILE, H5F_ACC_RDWR, H5P_DEFAULT);

    hid_t gid = H5Groot(file_id);
    char name[256];
    int num_objects;
    while (H5Gnext(gid, &name, &num_objects) != H5G_ERROR_END) {
        printf("%s\n", name);
        
    }

But for my compiler (visual studio 2019) H5Groot,H5Gnext and H5G_ERROR_END are not defined.
I tried to found the definition in the different source file of the H5fd library with no success
I also check the H5FD library documentation (https://docs.hdfgroup.org/hdf5/v1_14/v1_14_4/index.html) but it seems theses functions are not described
So if any one has already successfully used these functions please let me know how you did.

brtnfld · May 16, 2024, 4:54pm

Those H5G APIs are not valid; maybe some AI model hallucination?

If you are just interested in seeing the contents of the hdf5 file, you can use HDF5 tools h5ls and h5dump, or use the hdfview, https://www.hdfgroup.org/downloads/hdfview/

If you are interested in getting that information from inside your code, take a look at the examples:

github.com

HDFGroup/hdf5/blob/develop/HDF5Examples/C/H5G/h5ex_g_iterate.c

/************************************************************

  This example shows how to iterate over group members using
  H5Literate.

 ************************************************************/

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

#define FILE "h5ex_g_iterate.h5"

/*
 * Operator function to be called by H5Literate.
 */
herr_t op_func(hid_t loc_id, const char *name, const H5L_info_t *info, void *operator_data);

int
main(void)
{

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github.com

HDFGroup/hdf5/blob/develop/HDF5Examples/C/H5G/h5ex_g_traverse.c

/************************************************************

  This example shows a way to recursively traverse the file
  using H5Literate.  The method shown here guarantees that
  the recursion will not enter an infinite loop, but does
  not prevent objects from being visited more than once.
  The program prints the directory structure of the file
  specified in FILE.  The default file used by this example
  implements the structure described in the User's Guide,
  chapter 4, figure 26.

 ************************************************************/

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

#define FILE "h5ex_g_traverse.h5"

/*
 * Define operator data structure type for H5Literate callback.

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github.com

HDFGroup/hdf5/blob/develop/HDF5Examples/C/H5G/h5ex_g_visit.c

/************************************************************

  This example shows how to recursively traverse a file
  using H5Ovisit and H5Lvisit.  The program prints all of
  the objects in the file specified in FILE, then prints all
  of the links in that file.  The default file used by this
  example implements the structure described in the User's
  Guide, chapter 4, figure 26.

 ************************************************************/

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

#define FILE "h5ex_g_visit.h5"

/*
 * Operator function to be called by H5Ovisit.
 */
herr_t op_func(hid_t loc_id, const char *name, const H5O_info_t *info, void *operator_data);

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gouyon · May 22, 2024, 11:37am

Yes I was interested in getting informations inside my code.
I tried your solution and it’s work

Attention! https://support.hdfgroup.org is the NEW home for documentation from The HDF Group. (Details)

How to know what is in a H5 file