Ejemplo n.º 1
0
/*-------------------------------------------------------------------------
 * Function:    leave
 *
 * Purpose:     Close the H5 Tools library and exit
 *
 * Return:      Does not return
 *
 * Programmer:  Vailin Choi; August 2010
 *
 * Modifications:
 *
 *-------------------------------------------------------------------------
 */
static void
leave(int ret)
{
    h5tools_close();

    exit(ret);
}
Ejemplo n.º 2
0
Archivo: h5jam.c Proyecto: ElaraFX/hdf5
/*-------------------------------------------------------------------------
 * Function:    leave
 *
 * Purpose:     Shutdown and call exit()
 *
 * Return:      Does not return
 *
 *-------------------------------------------------------------------------
 */
static void
leave(int ret)
{
    if (ub_file)
        HDfree (ub_file);
    if (input_file)
        HDfree (input_file);
    if (output_file)
        HDfree (output_file);

    h5tools_close();

    HDexit(ret);
}
Ejemplo n.º 3
0
/*-------------------------------------------------------------------------
 * Function:    leave
 *
 * Purpose:     Shutdown MPI and/or HDF5 and call exit()
 *
 * Return:      Does not return
 *
 * Programmer: Quincey Koziol, 2/13/2007
 *
 *-------------------------------------------------------------------------
 */
static void
leave(int ret)
{
    size_t curr_group;

    if (params.fname)
        HDfree (params.fname);
    if (params.ngroups) {
        for(curr_group = 0; curr_group < params.ngroups; curr_group++)
            HDfree (params.groups[curr_group]);
        HDfree (params.groups);
    }
    h5tools_close();
    HDexit(ret);
} /* end leave() */
Ejemplo n.º 4
0
/*-------------------------------------------------------------------------
 * Function:    leave
 *
 * Purpose:     Shutdown MPI & HDF5 and call exit()
 *
 * Return:      Does not return
 *
 * Programmer:  Quincey Koziol
 *              Saturday, 31. January 2004
 *
 * Modifications:
 *
 *-------------------------------------------------------------------------
 */
static void
leave(int ret)
{
    if (fname_src)
        HDfree(fname_src);
    if (fname_dst)
        HDfree(fname_dst);
    if (oname_dst)
        HDfree(oname_dst);
    if (oname_src)
        HDfree(oname_src);
    if (str_flag)
        HDfree(str_flag);

    h5tools_close();
    HDexit(ret);
}
Ejemplo n.º 5
0
/*-------------------------------------------------------------------------
 * Function:    main
 *
 * Purpose:     HDF5 user block unjammer
 *
 * Return:      Success:    0
 *              Failure:    1
 *
 * Programmer:
 *
 * Modifications:
 *
 *-------------------------------------------------------------------------
 */
int
main(int argc, const char *argv[])
{
    void               *edata;
    H5E_auto2_t         func;
    hid_t               ifile = -1;
    hid_t               plist = -1;
    off_t               fsize;
    hsize_t             usize;
    htri_t              testval;
    herr_t              status;
    int                 res;
    h5_stat_t           sbuf;

    h5tools_setprogname(PROGRAMNAME);
    h5tools_setstatus(EXIT_SUCCESS);

    /* Disable error reporting  */
    H5Eget_auto2(H5E_DEFAULT, &func, &edata);
    H5Eset_auto2(H5E_DEFAULT, NULL, NULL);

    /* Initialize h5tools lib  */
    h5tools_init();

    if(EXIT_FAILURE == parse_command_line(argc, argv))
        goto done;

    if (input_file == NULL) {
        /* no user block  */
        error_msg("missing arguemnt for HDF5 file input.\n");
        help_ref_msg(stderr);
        h5tools_setstatus(EXIT_FAILURE);
        goto done;
    }
  
    testval = H5Fis_hdf5(input_file);

    if (testval <= 0) {
        error_msg("Input HDF5 file \"%s\" is not HDF\n", input_file);
        help_ref_msg (stderr);
        h5tools_setstatus(EXIT_FAILURE);
        goto done;
    }

    ifile = H5Fopen(input_file, H5F_ACC_RDONLY , H5P_DEFAULT);

    if (ifile < 0) {
        error_msg("Can't open input HDF5 file \"%s\"\n", input_file);
        h5tools_setstatus(EXIT_FAILURE);
        goto done;
    }

    plist = H5Fget_create_plist(ifile);
    if (plist < 0) {
        error_msg("Can't get file creation plist for file \"%s\"\n", input_file);
        h5tools_setstatus(EXIT_FAILURE);
        goto done;
    }

    status = H5Pget_userblock(plist, & usize);
    if (status < 0) {
        error_msg("Can't get user block for file \"%s\"\n", input_file);
        h5tools_setstatus(EXIT_FAILURE);
        goto done;
    }

    status = H5Pclose(plist);
    HDassert(status >= 0);
    status = H5Fclose(ifile);
    HDassert(status >= 0);

    if (usize == 0) {
  /* no user block to remove: message? */
        error_msg("\"%s\" has no user block: no change to file\n", input_file);
        h5tools_setstatus(EXIT_SUCCESS);
        goto done;
    }

    res = HDfstat(HDfileno(rawinstream), &sbuf);
    if(res < 0) {
        error_msg("Can't stat file \"%s\"\n", input_file);
        h5tools_setstatus(EXIT_FAILURE);
        goto done;
    }

    fsize = sbuf.st_size;

    if (do_delete && (ub_file != NULL)) {
        error_msg("??\"%s\"\n", ub_file);
        h5tools_setstatus(EXIT_FAILURE);
        goto done;
    }

    if (output_file == NULL) {
            error_msg("unable to open output HDF5 file \"%s\"\n", input_file);
            h5tools_setstatus(EXIT_FAILURE);
            goto done;
    } 

    /* copy from 0 to 'usize - 1' into ufid  */
    if (!do_delete) {
        if(copy_to_file(rawinstream, rawoutstream, 0, (ssize_t) usize) < 0) {
            error_msg("unable to copy user block to output file \"%s\"\n", ub_file);
            h5tools_setstatus(EXIT_FAILURE);
            goto done;
        }
    }

    /* copy from usize to end of file into h5fid,
     * starting at end of user block if present */
   if(copy_to_file(rawinstream, rawdatastream, (ssize_t) usize, (ssize_t)(fsize - (ssize_t)usize)) < 0) {
        error_msg("unable to copy hdf5 data to output file \"%s\"\n", output_file);
        h5tools_setstatus(EXIT_FAILURE);
        goto done;
    }
 
done:
    if(input_file)
        HDfree(input_file);
		
    if(output_file)
        HDfree(output_file);
		
    if(ub_file) {
        HDfree(ub_file);
    }
	   
    h5tools_close();

    return h5tools_getstatus();
}
Ejemplo n.º 6
0
/*-------------------------------------------------------------------------
 * Function: main
 *
 * Purpose: Create group(s) in an HDF5 file
 *
 * Programmer: Quincey Koziol, 2/13/2007
 *
 *-------------------------------------------------------------------------
 */
int
main(int argc, const char *argv[])
{
    hid_t fid;                  /* HDF5 file ID */
    hid_t fapl_id;              /* File access property list ID */
    hid_t lcpl_id;              /* Link creation property list ID */
    size_t curr_group;          /* Current group to create */

    h5tools_setprogname(PROGRAMNAME);
    h5tools_setstatus(EXIT_SUCCESS);

    /* Disable the HDF5 library's error reporting */
    H5Eset_auto2(H5E_DEFAULT, NULL, NULL);

    /* Initialize h5tools lib */
    h5tools_init();

    /* Parse command line */
    HDmemset(&params, 0, sizeof(params));
    if(parse_command_line(argc, argv, &params) < 0) {
        error_msg("unable to parse command line arguments\n");
        leave(EXIT_FAILURE);
    } /* end if */

    /* Create file access property list */
    if((fapl_id = H5Pcreate(H5P_FILE_ACCESS)) < 0) {
        error_msg("Could not create file access property list\n");
        leave(EXIT_FAILURE);
    } /* end if */

    /* Check for creating groups with new format version */
    if(params.latest) {
        /* Set the "use the latest version of the format" bounds */
        if(H5Pset_libver_bounds(fapl_id, H5F_LIBVER_LATEST, H5F_LIBVER_LATEST) < 0) {
            error_msg("Could not set property for using latest version of the format\n");
            leave(EXIT_FAILURE);
        } /* end if */

        /* Display some output if requested */
        if(params.verbose)
            printf("%s: Creating groups with latest version of the format\n", h5tools_getprogname());
    } /* end if */

    /* Attempt to open an existing HDF5 file first */
    fid = h5tools_fopen(params.fname, H5F_ACC_RDWR, fapl_id, NULL, NULL, 0);

    /* If we couldn't open an existing file, try creating file */
    /* (use "EXCL" instead of "TRUNC", so we don't blow away existing non-HDF5 file) */
    if(fid < 0)
        fid = H5Fcreate(params.fname, H5F_ACC_EXCL, H5P_DEFAULT, fapl_id);

    /* Test for error in opening file */
    if(fid < 0) {
        error_msg("Could not open output file '%s'\n", params.fname);
        leave(EXIT_FAILURE);
    } /* end if */

    /* Create link creation property list */
    if((lcpl_id = H5Pcreate(H5P_LINK_CREATE)) < 0) {
        error_msg("Could not create link creation property list\n");
        leave(EXIT_FAILURE);
    } /* end if */

    /* Check for creating intermediate groups */
    if(params.parents) {
        /* Set the intermediate group creation property */
        if(H5Pset_create_intermediate_group(lcpl_id, TRUE) < 0) {
            error_msg("Could not set property for creating parent groups\n");
            leave(EXIT_FAILURE);
        } /* end if */

        /* Display some output if requested */
        if(params.verbose)
            printf("%s: Creating parent groups\n", h5tools_getprogname());
    } /* end if */

    /* Loop over creating requested groups */
    for(curr_group = 0; curr_group < params.ngroups; curr_group++) {
        hid_t gid;              /* Group ID */

        /* Attempt to create a group */
        if((gid = H5Gcreate2(fid, params.groups[curr_group], lcpl_id, H5P_DEFAULT, H5P_DEFAULT)) < 0) {
            error_msg("Could not create group '%s'\n", params.groups[curr_group]);
            leave(EXIT_FAILURE);
        } /* end if */

        /* Close the group */
        if(H5Gclose(gid) < 0) {
            error_msg("Could not close group '%s'??\n", params.groups[curr_group]);
            leave(EXIT_FAILURE);
        } /* end if */

        /* Display some output if requested */
        if(params.verbose)
            printf("%s: created group '%s'\n", h5tools_getprogname(), params.groups[curr_group]);
    } /* end for */

    /* Close link creation property list */
    if(H5Pclose(lcpl_id) < 0) {
        error_msg("Could not close link creation property list\n");
        leave(EXIT_FAILURE);
    } /* end if */

    /* Close file */
    if(H5Fclose(fid) < 0) {
        error_msg("Could not close output file '%s'??\n", params.fname);
        leave(EXIT_FAILURE);
    } /* end if */

    /* Close file access property list */
    if(H5Pclose(fapl_id) < 0) {
        error_msg("Could not close file access property list\n");
        leave(EXIT_FAILURE);
    } /* end if */

    /* Shut down h5tools lib */
    h5tools_close();

    leave(EXIT_SUCCESS);
} /* end main() */
Ejemplo n.º 7
0
int
main (int argc, const char *argv[])
{
    hid_t        fid_src=-1;
    hid_t        fid_dst=-1;
    char         *fname_src=NULL;
    char         *fname_dst=NULL;
    char         *oname_src=NULL;
    char         *oname_dst=NULL;
    unsigned     flag=0;
    unsigned     verbose=0;
    unsigned     parents=0;
    hid_t        ocpl_id = (-1);          /* Object copy property list */
    hid_t        lcpl_id = (-1);          /* Link creation property list */
    char         str_flag[20];
    int          opt;
    int          li_ret;
    h5tool_link_info_t linkinfo;
    int          i, len;
    char         *str_ptr=NULL;

    h5tools_setprogname(PROGRAMNAME);
    h5tools_setstatus(EXIT_SUCCESS);
    /* initialize h5tools lib */
    h5tools_init();

    /* init linkinfo struct */
    HDmemset(&linkinfo, 0, sizeof(h5tool_link_info_t));

    /* Check for no command line parameters */
    if(argc == 1) 
    {
        usage();
        leave(EXIT_FAILURE);
    } /* end if */

    /* parse command line options */
    while ((opt = get_option(argc, argv, s_opts, l_opts)) != EOF)
    {
        switch ((char)opt)
        {
        case 'd':
            oname_dst = HDstrdup(opt_arg);
            break;

        case 'f':
            /* validate flag */
            if (parse_flag(opt_arg,&flag)<0)
            {
                usage();
                leave(EXIT_FAILURE);
            }
            HDstrcpy(str_flag,opt_arg);
            break;

        case 'h':
            usage();
            leave(EXIT_SUCCESS);
            break;

        case 'i':
            fname_src = HDstrdup(opt_arg);
            break;

        case 'o':
            fname_dst = HDstrdup(opt_arg);
            break;

        case 'p':
            parents = 1;
            break;

        case 's':
            oname_src = HDstrdup(opt_arg);
            break;

        case 'V':
            print_version(h5tools_getprogname());
            leave(EXIT_SUCCESS);
            break;

        case 'v':
            verbose = 1;
            break;

        default:
            usage();
            leave(EXIT_FAILURE);
        }
    } /* end of while */

/*-------------------------------------------------------------------------
 * check for missing file/object names
 *-------------------------------------------------------------------------*/

    if (fname_src==NULL)
    {
        error_msg("Input file name missing\n");
        usage();
        leave(EXIT_FAILURE);
    }

    if (fname_dst==NULL)
    {
        error_msg("Output file name missing\n");
        usage();
        leave(EXIT_FAILURE);
    }

    if (oname_src==NULL)
    {
        error_msg("Source object name missing\n");
        usage();
        leave(EXIT_FAILURE);
    }

    if (oname_dst==NULL)
    {
        error_msg("Destination object name missing\n");
        usage();
        leave(EXIT_FAILURE);
    }

   /*-------------------------------------------------------------------------
    * open output file
    *-------------------------------------------------------------------------*/

    /* Attempt to open an existing HDF5 file first. Need to open the dst file
       before the src file just in case that the dst and src are the same file
     */
    fid_dst = h5tools_fopen(fname_dst, H5F_ACC_RDWR, H5P_DEFAULT, NULL, NULL, 0);

   /*-------------------------------------------------------------------------
    * open input file
    *-------------------------------------------------------------------------*/

    fid_src = h5tools_fopen(fname_src, H5F_ACC_RDONLY, H5P_DEFAULT, NULL, NULL, 0);

   /*-------------------------------------------------------------------------
    * test for error in opening input file
    *-------------------------------------------------------------------------*/
    if (fid_src==-1)
    {
        error_msg("Could not open input file <%s>...Exiting\n", fname_src);
        if (fname_src)
            HDfree(fname_src);
        leave(EXIT_FAILURE);
    }


   /*-------------------------------------------------------------------------
    * create an output file when failed to open it
    *-------------------------------------------------------------------------*/

    /* If we couldn't open an existing file, try creating file */
    /* (use "EXCL" instead of "TRUNC", so we don't blow away existing non-HDF5 file) */
    if(fid_dst < 0)
        fid_dst = H5Fcreate(fname_dst, H5F_ACC_EXCL, H5P_DEFAULT, H5P_DEFAULT);

   /*-------------------------------------------------------------------------
    * test for error in opening output file
    *-------------------------------------------------------------------------*/
    if (fid_dst==-1)
    {
        error_msg("Could not open output file <%s>...Exiting\n", fname_dst);
        if (fname_src)
            HDfree(fname_src);
        if (fname_dst)
            HDfree(fname_dst);
        leave(EXIT_FAILURE);
    }

   /*-------------------------------------------------------------------------
    * print some info
    *-------------------------------------------------------------------------*/

    if (verbose)
    {
        printf("Copying file <%s> and object <%s> to file <%s> and object <%s>\n",
        fname_src, oname_src, fname_dst, oname_dst);
        if (flag)
            printf("Using %s flag\n", str_flag);
    }


   /*-------------------------------------------------------------------------
    * create property lists for copy
    *-------------------------------------------------------------------------*/

    /* create property to pass copy options */
    if ( (ocpl_id = H5Pcreate(H5P_OBJECT_COPY)) < 0)
        goto error;

    /* set options for object copy */
    if (flag)
    {
        if ( H5Pset_copy_object(ocpl_id, flag) < 0)
            goto error;
    }

    /* Create link creation property list */
    if((lcpl_id = H5Pcreate(H5P_LINK_CREATE)) < 0) {
        error_msg("Could not create link creation property list\n");
        goto error;
    } /* end if */

    /* Check for creating intermediate groups */
    if(parents) {
        /* Set the intermediate group creation property */
        if(H5Pset_create_intermediate_group(lcpl_id, 1) < 0) {
            error_msg("Could not set property for creating parent groups\n");
            goto error;
        } /* end if */

        /* Display some output if requested */
        if(verbose)
            printf("%s: Creating parent groups\n", h5tools_getprogname());
    } /* end if */
    else /* error, if parent groups doesn't already exist in destination file */
    {
        len = HDstrlen(oname_dst);        
        /* check if all the parents groups exist. skip root group */
        for (i = 1; i < len; i++)
        {
            if ('/'==oname_dst[i])
            {
                str_ptr = (char*)HDcalloc((size_t)i+1, sizeof(char));
                HDstrncpy (str_ptr, oname_dst, (size_t)i);
                str_ptr[i]='\0';
                if (H5Lexists(fid_dst, str_ptr, H5P_DEFAULT) <= 0)
                {
                    error_msg("group <%s> doesn't exist. Use -p to create parent groups.\n", str_ptr);
                    HDfree(str_ptr);
                    goto error;
                }
                HDfree(str_ptr);
            }
        }
    }

   /*-------------------------------------------------------------------------
    * do the copy
    *-------------------------------------------------------------------------*/
 
    if(verbose)
        linkinfo.opt.msg_mode = 1;
 
    li_ret = H5tools_get_symlink_info(fid_src, oname_src, &linkinfo, 1);
    if (li_ret == 0) /* dangling link */
    {
        if(H5Lcopy(fid_src, oname_src, 
                   fid_dst, oname_dst,
                   H5P_DEFAULT, H5P_DEFAULT) < 0)
            goto error;
    }
    else /* valid link */
    {
        if (H5Ocopy(fid_src,          /* Source file or group identifier */
                  oname_src,        /* Name of the source object to be copied */
                  fid_dst,          /* Destination file or group identifier  */
                  oname_dst,        /* Name of the destination object  */
                  ocpl_id,          /* Object copy property list */
                  lcpl_id)<0)       /* Link creation property list */
            goto error;
    }

    /* free link info path */
    if (linkinfo.trg_path)
        HDfree(linkinfo.trg_path);

    /* close propertis */
    if(H5Pclose(ocpl_id)<0)
        goto error;
    if(H5Pclose(lcpl_id)<0)
        goto error;

    /* close files */
    if (H5Fclose(fid_src)<0)
        goto error;
    if (H5Fclose(fid_dst)<0)
        goto error;

    if (fname_src)
        HDfree(fname_src);
    if (fname_dst)
        HDfree(fname_dst);
    if (oname_dst)
        HDfree(oname_dst);
    if (oname_src)
        HDfree(oname_src);

    h5tools_close();

    return EXIT_SUCCESS;

error:
    printf("Error in copy...Exiting\n");

    /* free link info path */
    if (linkinfo.trg_path)
        HDfree(linkinfo.trg_path);

 H5E_BEGIN_TRY {
    H5Pclose(ocpl_id);
    H5Pclose(lcpl_id);
    H5Fclose(fid_src);
    H5Fclose(fid_dst);
 } H5E_END_TRY;
    if (fname_src)
        HDfree(fname_src);
    if (fname_dst)
        HDfree(fname_dst);
    if (oname_dst)
        HDfree(oname_dst);
    if (oname_src)
        HDfree(oname_src);

    h5tools_close();

    return EXIT_FAILURE;
}