path: root/src/util/hdf5_merge.c

 /*@@
   @file      hdf5_merge.c
   @date      Thu 10 Jan 2002
   @author    Thomas Radke
   @desc
              This utility program takes a list of Cactus HDF5 datafiles,
              merges them at the group hierarchy level and dumps the resulting
              tree to a new HDF5 file.
   @enddesc
   @version   $Id$
 @@*/

#include "cctk.h"

#include <hdf5.h>
#include <stdio.h> 
#include <stdlib.h>
#include <string.h>
#include "CactusPUGHIO/IOHDF5Util/src/ioHDF5UtilGH.h"

/* the rcs ID and its dummy function to use it */
static const char *rcsid = "$Header$";
CCTK_FILEVERSION(CactusPUGHIO_IOHDF5_util_hdf5_merge_c)


/*****************************************************************************/
/*                           macro definitions                               */
/*****************************************************************************/
/* uncomment the following to get some debugging output */
/* #define IOHDF5_DEBUG  1 */

/* macro to do an HDF5 call, check its return code, and print a warning
   in case of an error */
#define CHECK_ERROR(hdf5_call)                                                \
          do                                                                  \
          {                                                                   \
            int _error_code = hdf5_call;                                      \
                                                                              \
                                                                              \
            if (_error_code < 0)                                              \
            {                                                                 \
              fprintf (stderr, "WARNING: line %d: HDF5 call '%s' returned "   \
                               "error code %d\n",                             \
                                __LINE__, #hdf5_call, _error_code);           \
              nerrors++;                                                      \
            }                                                                 \
          } while (0)


/*****************************************************************************/
/*                           global variables                                */
/*****************************************************************************/
/* NOTE: although it isn't good programming practice
         we make these variables global for convenience
         since they are accessed from recursively or
         indirectly called routines which only get passed
         a single user-supplied argument */
static char *pathname = NULL;      /* pathname of the current object */
static unsigned int nerrors = 0;   /* global error counter */

/*****************************************************************************/
/*                           local function prototypes                       */
/*****************************************************************************/
static herr_t CopyObject (hid_t copy_from, const char *objectname, void *arg);
static herr_t CopyAttribute (hid_t src, const char *attr_name, void *arg);


 /*@@
   @routine    main
   @date       Sat 24 Feb 2001
   @author     Thomas Radke
   @desc
               Main routine of the HDF5 file merger
   @enddesc

   @calls      CopyObject

   @var        argc
   @vdesc      number of command line arguments
   @vtype      int
   @vio        in
   @endvar
   @var        argv
   @vdesc      command line arguments
   @vtype      char *[]
   @vio        in
   @endvar

   @returntype int
   @returndesc
               0 for success, negative return values indicate an error
   @endreturndesc
@@*/
int main (int argc, char *argv[])
{
  int i;
  hid_t *infiles, outfile;


  /* give some help if called with incorrect number of parameters */
  if (argc < 3)
  {
    fprintf (stderr, "Usage: %s <infile1> [<infile2> ...] <outfile>\n",argv[0]);
    fprintf (stderr, "   eg, %s alp.time*.h5 alp.h5"
                     "\n\n", argv[0]);
    return (0);
  }

  H5E_BEGIN_TRY
  {
    /* open the input files */
    infiles = (hid_t *) malloc ((argc - 2) * sizeof (hid_t));
    for (i = 0; i < argc - 2; i++)
    {
      infiles[i] = H5Fopen (argv[i + 1], H5F_ACC_RDONLY, H5P_DEFAULT);
      if (infiles[i] < 0)
      {
        fprintf (stderr, "ERROR: Cannot open HDF5 input file '%s' !\n\n",
                 argv[i + 1]);
        return (-1);
      }
    }

    /* try to open an existing outfile file in append mode,
       if this fails create it as a new file */
    outfile = H5Fopen (argv[argc-1], H5F_ACC_RDWR, H5P_DEFAULT);
    if (outfile < 0)
    {
      outfile = H5Fcreate (argv[argc-1], H5F_ACC_TRUNC, H5P_DEFAULT,
                           H5P_DEFAULT);
    }
    if (outfile < 0)
    {
      fprintf (stderr, "ERROR: Cannot open HDF5 output file '%s' !\n\n",
               argv[argc - 1]);
      return (-1);
    }
  } H5E_END_TRY

  printf ("\n  -------------------------\n"
            "  Cactus 4 HDF5 File Merger\n"
            "  -------------------------\n");

  /* do the copying by iterating over all objects */
  for (i = 0; i < argc - 2; i++)
  {
    printf ("\n  Merging objects from input file '%s' into output file '%s'\n",
            argv[i + 1], argv[argc-1]);
    pathname = "";
    CHECK_ERROR (H5Giterate (infiles[i], "/", NULL, CopyObject, &outfile));
  }

  /* finally, close all open files */
  for (i = 0; i < argc - 2; i++)
  {
    CHECK_ERROR (H5Fclose (infiles[i]));
  }
  CHECK_ERROR (H5Fclose (outfile));
  free (infiles);

  /* report status */
  if (nerrors == 0)
  {
    printf ("\n\n   *** All input files successfully merged. ***\n\n");
  }
  else
  {
    fprintf (stderr, "\n\n   *** WARNING: %d errors occured during "
                     "file merging. ***\n\n", nerrors);
  }

  return (0);
}


/*****************************************************************************/
/*                           local routines                                  */
/*****************************************************************************/
 /*@@
   @routine    CopyObject
   @date       Sat 24 Feb 2001
   @author     Thomas Radke
   @desc
               Iterator recursively called by H5Giterate() for every object
               in the input file
               It copies the current object to the output file if it didn't
               already exist there.
   @enddesc

   @calls      CopyAttribute

   @var        from
   @vdesc      identifier for the group the current object belongs to
   @vtype      hid_t
   @vio        in
   @endvar
   @var        objectname
   @vdesc      name of the current object
   @vtype      const char *
   @vio        in
   @endvar
   @var        _to
   @vdesc      user-supplied argument indicating the output object identifier
   @vtype      hid_t
   @vio        in
   @endvar

   @returntype int
   @returndesc
               0 - continue the iteration for following group objects
               1 - short-curcuit, no further iteration of this group
   @endreturndesc
@@*/
static herr_t CopyObject (hid_t from,
                          const char *objectname,
                          void *_to)
{
  int i;
  hid_t to, datatype, dataspace;
  H5G_stat_t objectinfo;
  char *current_pathname;
  size_t objectsize;
  void *data;


  /* get the output object identifier */
  to = *(hid_t *) _to;

  /* check whether an object by that name already exists */
  H5E_BEGIN_TRY
  {
    i = H5Gget_objinfo (to, objectname, 0, &objectinfo) >= 0;
  } H5E_END_TRY
  if (i)
  {
    printf ("   object '%s/%s' will not be copied (already exists)\n",
            pathname, objectname);
    return (0);
  }

  /* build the full pathname for the current to object to process */
  current_pathname = pathname;
  pathname = (char *) malloc (strlen (current_pathname) +
                              strlen (objectname) + 2);
  sprintf (pathname, "%s/%s", current_pathname, objectname);

  /* check the type of the current object */
  CHECK_ERROR (H5Gget_objinfo (from, objectname, 0, &objectinfo));
  if (objectinfo.type == H5G_GROUP)
  {
    printf ("   copying group '%s'\n", pathname);

    CHECK_ERROR (from = H5Gopen (from, objectname));
    CHECK_ERROR (to = H5Gcreate (to, objectname, 0));
    /* iterate over all objects in the (first) input file */
    CHECK_ERROR (H5Giterate (from, ".", NULL, CopyObject, &to));
    CHECK_ERROR (H5Aiterate (from, NULL, CopyAttribute, &to));
    CHECK_ERROR (H5Gclose (to));
    CHECK_ERROR (H5Gclose (from));
  }
  else if (objectinfo.type == H5G_DATASET)
  {
    printf ("   copying dataset '%s'\n", pathname);

    CHECK_ERROR (from = H5Dopen (from, objectname));
    CHECK_ERROR (datatype = H5Dget_type (from));
    CHECK_ERROR (dataspace = H5Dget_space (from));
    CHECK_ERROR (to = H5Dcreate (to, objectname, datatype, dataspace,
                                 H5P_DEFAULT));
    objectsize = H5Dget_storage_size (from);
    if (objectsize > 0)
    {
      data = malloc (objectsize);
      CHECK_ERROR (H5Dread (from, datatype, H5S_ALL, H5S_ALL, H5P_DEFAULT,
                            data));
      CHECK_ERROR (H5Dwrite (to, datatype, H5S_ALL, H5S_ALL, H5P_DEFAULT,data));
      free (data);
    }
    CHECK_ERROR (H5Aiterate (from, NULL, CopyAttribute, &to));
    CHECK_ERROR (H5Dclose (to));
    CHECK_ERROR (H5Dclose (from));
    CHECK_ERROR (H5Sclose (dataspace));
    CHECK_ERROR (H5Tclose (datatype));
  }
  else
  {
    fprintf (stderr, "WARNING: Found object '%s' which is not neither a "
                     "group nor a dataset ! Object will not be copied.\n",
                     pathname);
    nerrors++;
  }

  /* reset the pathname */
  free (pathname);
  pathname = current_pathname;

  return (0);
}


 /*@@
   @routine    CopyAttribute
   @date       Sat 24 Feb 2001
   @author     Thomas Radke
   @desc
               Iterator recursively called by H5Aiterate() for every attribute
               of an object (dataset or group)
   @enddesc

   @var        from
   @vdesc      identifier for the group or dataset to read the attribute from
   @vtype      hid_t
   @vio        in
   @endvar
   @var        attrname
   @vdesc      name of the current attribute
   @vtype      const char *
   @vio        in
   @endvar
   @var        _to
   @vdesc      user-supplied argument indicating the group or dataset
               to copy the attribute to
   @vtype      hid_t
   @vio        in
   @endvar

   @returntype int
   @returndesc
               0 - continue the iteration for following attributes
   @endreturndesc
@@*/
static herr_t CopyAttribute (hid_t from,
                             const char *attrname,
                             void *_to)
{
  hid_t attr, datatype, dataspace, to;
  size_t attrsize;
  void *value;


  /* get the target group/dataset identifier */
  to = *(hid_t *) _to;

  /* open the attribute given by its name, get type, dataspace, and value
     and just copy it */
  CHECK_ERROR (attr = H5Aopen_name (from, attrname));
  CHECK_ERROR (datatype = H5Aget_type (attr));
  CHECK_ERROR (dataspace = H5Aget_space (attr));
  attrsize = H5Tget_size (datatype);
  if (H5Sis_simple (dataspace) > 0)
  {
    attrsize *= H5Sget_simple_extent_npoints (dataspace);
  }
  if (attrsize > 0)
  {
    value = malloc (attrsize);
    CHECK_ERROR (H5Aread (attr, datatype, value));
    CHECK_ERROR (H5Aclose (attr));
    CHECK_ERROR (attr = H5Acreate (to, attrname, datatype, dataspace,
                                   H5P_DEFAULT));
    CHECK_ERROR (H5Awrite (attr, datatype, value));
    free (value);
  }
  CHECK_ERROR (H5Aclose (attr));
  CHECK_ERROR (H5Sclose (dataspace));
  CHECK_ERROR (H5Tclose (datatype));

  return (0);
}