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https://github.com/HDFGroup/hdf5.git
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26e1b18a57
bug fix Description: h5repack was not dealing with family files Solution: use the toolslib function h5tools_open to open the file instead of H5Fopen in h5repack Platforms tested: linux solaris AIX Misc. update:
739 lines
20 KiB
C
739 lines
20 KiB
C
/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
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* Copyright by the Board of Trustees of the University of Illinois. *
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* All rights reserved. *
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* *
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* This file is part of HDF5. The full HDF5 copyright notice, including *
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* terms governing use, modification, and redistribution, is contained in *
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* the files COPYING and Copyright.html. COPYING can be found at the root *
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* of the source code distribution tree; Copyright.html can be found at the *
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* root level of an installed copy of the electronic HDF5 document set and *
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* is linked from the top-level documents page. It can also be found at *
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* http://hdf.ncsa.uiuc.edu/HDF5/doc/Copyright.html. If you do not have *
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* access to either file, you may request a copy from hdfhelp@ncsa.uiuc.edu. *
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* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
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#include <stdlib.h>
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#include <string.h>
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#include <stdio.h>
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#include "H5private.h"
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#include "h5repack.h"
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#if 0
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#define PRINT_DEBUG
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#endif
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/*-------------------------------------------------------------------------
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* Function: print_obj
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*
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* Purpose: print name and filters of an object
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*
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*-------------------------------------------------------------------------
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*/
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static void print_obj(hid_t dcpl_id, char *name)
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{
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char str[255];
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#if defined (PRINT_DEBUG )
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char temp[255];
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#endif
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int nfilters; /* number of filters */
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unsigned filt_flags; /* filter flags */
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H5Z_filter_t filtn; /* filter identification number */
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unsigned cd_values[20]; /* filter client data values */
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size_t cd_nelmts; /* filter client number of values */
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char f_name[256]; /* filter name */
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int i;
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strcpy(str,"\0");
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/* get information about input filters */
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if ((nfilters = H5Pget_nfilters(dcpl_id))<0)
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return;
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for ( i=0; i<nfilters; i++)
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{
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cd_nelmts = NELMTS(cd_values);
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#ifdef H5_WANT_H5_V1_6_COMPAT
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filtn = H5Pget_filter(dcpl_id,
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(unsigned)i,
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&filt_flags,
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&cd_nelmts,
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cd_values,
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sizeof(f_name),
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f_name);
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#else
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filtn = H5Pget_filter(dcpl_id,
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(unsigned)i,
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&filt_flags,
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&cd_nelmts,
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cd_values,
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sizeof(f_name),
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f_name,
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NULL);
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#endif /* H5_WANT_H5_V1_6_COMPAT */
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switch (filtn)
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{
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default:
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break;
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case H5Z_FILTER_DEFLATE:
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strcat(str,"GZIP ");
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#if defined (PRINT_DEBUG)
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{
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unsigned level=cd_values[0];
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sprintf(temp,"(%d)",level);
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strcat(str,temp);
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}
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#endif
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break;
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case H5Z_FILTER_SZIP:
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strcat(str,"SZIP ");
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#if defined (PRINT_DEBUG)
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{
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unsigned options_mask=cd_values[0]; /* from dcpl, not filt*/
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unsigned ppb=cd_values[1];
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sprintf(temp,"(%d,",ppb);
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strcat(str,temp);
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if (options_mask & H5_SZIP_EC_OPTION_MASK)
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strcpy(temp,"EC) ");
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else if (options_mask & H5_SZIP_NN_OPTION_MASK)
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strcpy(temp,"NN) ");
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}
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strcat(str,temp);
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#endif
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break;
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case H5Z_FILTER_SHUFFLE:
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strcat(str,"SHUF ");
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break;
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case H5Z_FILTER_FLETCHER32:
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strcat(str,"FLET ");
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break;
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case H5Z_FILTER_NBIT:
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strcat(str,"NBIT ");
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break;
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case H5Z_FILTER_SCALEOFFSET:
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strcat(str,"SCALEOFFSET ");
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break;
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} /* switch */
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}/*i*/
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printf(" %-10s %s %s\n", "dataset",str,name );
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}
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/*-------------------------------------------------------------------------
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* Function: copy_objects
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*
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* Purpose: duplicate all HDF5 objects in the file
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*
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* Return: 0, ok, -1 no
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*
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* Programmer: Pedro Vicente, pvn@ncsa.uiuc.edu
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*
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* Date: October, 23, 2003
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*
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*-------------------------------------------------------------------------
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*/
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int copy_objects(const char* fnamein,
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const char* fnameout,
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pack_opt_t *options,
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int argc,
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const char *argv[])
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{
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hid_t fidin;
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hid_t fidout=(-1);
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trav_table_t *travt=NULL;
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/*-------------------------------------------------------------------------
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* open the files
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*-------------------------------------------------------------------------
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*/
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if ((fidin=h5tools_fopen(fnamein, NULL, NULL, 0, argc, argv))<0 ){
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printf("<%s>: %s\n", fnamein, H5FOPENERROR );
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goto out;
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}
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if ((fidout=H5Fcreate(fnameout,H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT))<0 ){
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printf("<%s>: Could not create file\n", fnameout );
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goto out;
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}
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if (options->verbose)
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printf("Making file <%s>...\n",fnameout);
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/* init table */
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trav_table_init(&travt);
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/* get the list of objects in the file */
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if (h5trav_gettable(fidin,travt)<0)
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goto out;
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/*-------------------------------------------------------------------------
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* do the copy
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*-------------------------------------------------------------------------
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*/
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if(do_copy_objects(fidin,fidout,travt,options)<0) {
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printf("<%s>: Could not copy data to: %s\n", fnamein, fnameout);
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goto out;
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}
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/*-------------------------------------------------------------------------
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* do the copy of referenced objects
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* and create hard links
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*-------------------------------------------------------------------------
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*/
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if(do_copy_refobjs(fidin,fidout,travt,options)<0) {
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printf("<%s>: Could not copy data to: %s\n", fnamein, fnameout);
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goto out;
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}
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/* free table */
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trav_table_free(travt);
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/*-------------------------------------------------------------------------
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* close
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*-------------------------------------------------------------------------
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*/
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H5Fclose(fidin);
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H5Fclose(fidout);
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return 0;
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/*-------------------------------------------------------------------------
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* out
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*-------------------------------------------------------------------------
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*/
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out:
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H5E_BEGIN_TRY {
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H5Fclose(fidin);
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H5Fclose(fidout);
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} H5E_END_TRY;
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if (travt)
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trav_table_free(travt);
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return -1;
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}
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/*-------------------------------------------------------------------------
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* Function: do_copy_objects
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*
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* Purpose: duplicate all HDF5 objects in the file
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*
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* Return: 0, ok, -1 no
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*
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* Programmer: Pedro Vicente, pvn@ncsa.uiuc.edu
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*
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* Date: October, 23, 2003
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* Modified: December, 03, 2004 - added a check for H5Dcreate; if the dataset
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* cannot be created with the requested filter, use the input one
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*
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*-------------------------------------------------------------------------
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*/
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int do_copy_objects(hid_t fidin,
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hid_t fidout,
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trav_table_t *travt,
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pack_opt_t *options) /* repack options */
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{
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hid_t grp_in=(-1); /* group ID */
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hid_t grp_out=(-1); /* group ID */
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hid_t dset_in=(-1); /* read dataset ID */
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hid_t dset_out=(-1); /* write dataset ID */
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hid_t type_in=(-1); /* named type ID */
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hid_t type_out=(-1); /* named type ID */
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hid_t dcpl_id=(-1); /* dataset creation property list ID */
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hid_t dcpl_out=(-1); /* dataset creation property list ID */
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hid_t space_id=(-1); /* space ID */
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hid_t ftype_id=(-1); /* file data type ID */
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hid_t mtype_id=(-1); /* memory data type ID */
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size_t msize; /* memory size of memory type */
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void *buf=NULL; /* data buffer */
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hsize_t nelmts; /* number of elements in dataset */
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int rank; /* rank of dataset */
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hsize_t dims[H5S_MAX_RANK];/* dimensions of dataset */
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hsize_t dsize_in; /* input dataset size before filter */
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int next; /* external files */
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int i, j;
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/*-------------------------------------------------------------------------
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* copy the suppplied object list
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*-------------------------------------------------------------------------
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*/
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for ( i = 0; i < travt->nobjs; i++)
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{
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buf=NULL;
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switch ( travt->objs[i].type )
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{
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/*-------------------------------------------------------------------------
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* H5G_GROUP
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*-------------------------------------------------------------------------
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*/
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case H5G_GROUP:
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if (options->verbose)
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printf(" %-10s %s\n", "group",travt->objs[i].name );
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if ((grp_out=H5Gcreate(fidout,travt->objs[i].name, 0))<0)
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goto error;
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if((grp_in = H5Gopen (fidin,travt->objs[i].name))<0)
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goto error;
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/*-------------------------------------------------------------------------
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* copy attrs
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*-------------------------------------------------------------------------
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*/
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if (copy_attr(grp_in,grp_out,options)<0)
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goto error;
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if (H5Gclose(grp_out)<0)
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goto error;
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if (H5Gclose(grp_in)<0)
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goto error;
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break;
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/*-------------------------------------------------------------------------
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* H5G_DATASET
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*-------------------------------------------------------------------------
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*/
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case H5G_DATASET:
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if ((dset_in=H5Dopen(fidin,travt->objs[i].name))<0)
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goto error;
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if ((space_id=H5Dget_space(dset_in))<0)
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goto error;
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if ((ftype_id=H5Dget_type (dset_in))<0)
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goto error;
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if ((dcpl_id=H5Dget_create_plist(dset_in))<0)
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goto error;
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if ((dcpl_out = H5Pcopy (dcpl_id))<0)
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goto error;
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if ( (rank=H5Sget_simple_extent_ndims(space_id))<0)
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goto error;
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HDmemset(dims, 0, sizeof dims);
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if ( H5Sget_simple_extent_dims(space_id,dims,NULL)<0)
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goto error;
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nelmts=1;
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for (j=0; j<rank; j++)
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nelmts*=dims[j];
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if (options->verbose)
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print_obj(dcpl_id,travt->objs[i].name );
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if ((mtype_id=h5tools_get_native_type(ftype_id))<0)
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goto error;
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if ((msize=H5Tget_size(mtype_id))==0)
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goto error;
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/*-------------------------------------------------------------------------
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* check for external files
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*-------------------------------------------------------------------------
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*/
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if ((next=H5Pget_external_count (dcpl_id))<0)
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goto error;
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if (next) {
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fprintf(stderr,"Warning: <%s> has external files, ignoring read...\n",travt->objs[i].name );
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}
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/*-------------------------------------------------------------------------
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* check if the dataset creation property list has filters that
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* are not registered in the current configuration
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* 1) the external filters GZIP and SZIP might not be available
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* 2) the internal filters might be turned off
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*-------------------------------------------------------------------------
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*/
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if (next==0 && h5tools_canreadf((travt->objs[i].name),dcpl_id)==1)
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{
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/*-------------------------------------------------------------------------
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* references are a special case
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* we cannot just copy the buffers, but instead we recreate the reference
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* in a second traversal of the output file
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*-------------------------------------------------------------------------
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*/
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if ( (H5T_REFERENCE!=H5Tget_class(mtype_id)))
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{
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/* get the storage size of the input dataset */
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dsize_in=H5Dget_storage_size(dset_in);
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/*-------------------------------------------------------------------------
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* read to memory
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*-------------------------------------------------------------------------
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*/
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if (nelmts)
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{
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buf=(void *) HDmalloc((unsigned)(nelmts*msize));
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if ( buf==NULL){
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printf( "cannot read into memory\n" );
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goto error;
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}
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if (H5Dread(dset_in,mtype_id,H5S_ALL,H5S_ALL,H5P_DEFAULT,buf)<0)
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goto error;
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/*-------------------------------------------------------------------------
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* apply the filter
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*-------------------------------------------------------------------------
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*/
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if (apply_filters(travt->objs[i].name,rank,dims,dcpl_out,mtype_id,options)<0)
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goto error;
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}/*nelmts*/
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/*-------------------------------------------------------------------------
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* create;
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* disable error checking in case the dataset cannot be created with the
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* modified dcpl; in that case use the original instead
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*-------------------------------------------------------------------------
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*/
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H5E_BEGIN_TRY {
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dset_out=H5Dcreate(fidout,travt->objs[i].name,mtype_id,space_id,dcpl_out);
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} H5E_END_TRY;
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if (dset_out==FAIL)
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{
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if ((dset_out=H5Dcreate(fidout,travt->objs[i].name,mtype_id,space_id,dcpl_id))<0)
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goto error;
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if (options->verbose)
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printf("Warning: Could not apply the filter to <%s>\n", travt->objs[i].name);
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}
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/*-------------------------------------------------------------------------
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* write dataset
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*-------------------------------------------------------------------------
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*/
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|
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if (dsize_in && nelmts) {
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if (H5Dwrite(dset_out,mtype_id,H5S_ALL,H5S_ALL,H5P_DEFAULT,buf)<0)
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goto error;
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}
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/*-------------------------------------------------------------------------
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* copy attrs
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*-------------------------------------------------------------------------
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*/
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if (copy_attr(dset_in,dset_out,options)<0)
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goto error;
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|
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/*close */
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if (H5Dclose(dset_out)<0)
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goto error;
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|
|
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if (buf)
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free(buf);
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|
|
|
}/*H5T_STD_REF_OBJ*/
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}/*can_read*/
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|
|
|
|
|
/*-------------------------------------------------------------------------
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* close
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|
*-------------------------------------------------------------------------
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*/
|
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if (H5Tclose(ftype_id)<0)
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goto error;
|
|
if (H5Tclose(mtype_id)<0)
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goto error;
|
|
if (H5Pclose(dcpl_id)<0)
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goto error;
|
|
if (H5Pclose(dcpl_out)<0)
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goto error;
|
|
if (H5Sclose(space_id)<0)
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goto error;
|
|
if (H5Dclose(dset_in)<0)
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goto error;
|
|
|
|
break;
|
|
|
|
/*-------------------------------------------------------------------------
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|
* H5G_TYPE
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|
*-------------------------------------------------------------------------
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|
*/
|
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case H5G_TYPE:
|
|
|
|
if ((type_in = H5Topen (fidin,travt->objs[i].name))<0)
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goto error;
|
|
|
|
if ((type_out = H5Tcopy(type_in))<0)
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goto error;
|
|
|
|
if ((H5Tcommit(fidout,travt->objs[i].name,type_out))<0)
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|
goto error;
|
|
|
|
/*-------------------------------------------------------------------------
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|
* copy attrs
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|
*-------------------------------------------------------------------------
|
|
*/
|
|
if (copy_attr(type_in,type_out,options)<0)
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goto error;
|
|
|
|
if (H5Tclose(type_in)<0)
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|
goto error;
|
|
if (H5Tclose(type_out)<0)
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|
goto error;
|
|
|
|
if (options->verbose)
|
|
printf(" %-10s %s\n","datatype",travt->objs[i].name );
|
|
|
|
break;
|
|
|
|
|
|
/*-------------------------------------------------------------------------
|
|
* H5G_LINK
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|
*-------------------------------------------------------------------------
|
|
*/
|
|
|
|
case H5G_LINK:
|
|
{
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|
H5G_stat_t statbuf;
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|
char *targbuf=NULL;
|
|
|
|
if (H5Gget_objinfo(fidin,travt->objs[i].name,FALSE,&statbuf)<0)
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|
goto error;
|
|
|
|
targbuf = malloc(statbuf.u.slink.linklen);
|
|
|
|
if (H5Gget_linkval(fidin,travt->objs[i].name,statbuf.u.slink.linklen,targbuf)<0)
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goto error;
|
|
|
|
if (H5Glink(fidout,
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|
H5G_LINK_SOFT,
|
|
targbuf, /* current name of object */
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|
travt->objs[i].name /* new name of object */
|
|
)<0)
|
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goto error;
|
|
|
|
free(targbuf);
|
|
|
|
if (options->verbose)
|
|
printf(" %-10s %s\n","link",travt->objs[i].name );
|
|
|
|
}
|
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break;
|
|
|
|
default:
|
|
if (options->verbose)
|
|
printf(" %-10s %s\n","User defined object",travt->objs[i].name);
|
|
goto error;
|
|
}
|
|
}
|
|
|
|
/*-------------------------------------------------------------------------
|
|
* the root is a special case, we get an ID for the root group
|
|
* and copy its attributes using that ID
|
|
* it must be done last, because the attributes might contain references to
|
|
* objects in the object list
|
|
*-------------------------------------------------------------------------
|
|
*/
|
|
|
|
if ((grp_out = H5Gopen(fidout,"/"))<0)
|
|
goto error;
|
|
|
|
if ((grp_in = H5Gopen(fidin,"/"))<0)
|
|
goto error;
|
|
|
|
if (copy_attr(grp_in,grp_out,options)<0)
|
|
goto error;
|
|
|
|
if (H5Gclose(grp_out)<0)
|
|
goto error;
|
|
if (H5Gclose(grp_in)<0)
|
|
goto error;
|
|
|
|
return 0;
|
|
|
|
error:
|
|
H5E_BEGIN_TRY {
|
|
H5Gclose(grp_in);
|
|
H5Gclose(grp_out);
|
|
H5Pclose(dcpl_id);
|
|
H5Sclose(space_id);
|
|
H5Dclose(dset_in);
|
|
H5Dclose(dset_out);
|
|
H5Tclose(ftype_id);
|
|
H5Tclose(mtype_id);
|
|
H5Tclose(type_in);
|
|
H5Tclose(type_out);
|
|
if (buf)
|
|
free(buf);
|
|
} H5E_END_TRY;
|
|
return -1;
|
|
|
|
}
|
|
|
|
|
|
/*-------------------------------------------------------------------------
|
|
* Function: copy_attr
|
|
*
|
|
* Purpose: copy attributes located in LOC_IN, which is obtained either from
|
|
* loc_id = H5Gopen( fid, name);
|
|
* loc_id = H5Dopen( fid, name);
|
|
* loc_id = H5Topen( fid, name);
|
|
*
|
|
* Return: 0, ok, -1 no
|
|
*
|
|
* Programmer: Pedro Vicente, pvn@ncsa.uiuc.edu
|
|
*
|
|
* Date: October, 28, 2003
|
|
*
|
|
*-------------------------------------------------------------------------
|
|
*/
|
|
|
|
int copy_attr(hid_t loc_in,
|
|
hid_t loc_out,
|
|
pack_opt_t *options
|
|
)
|
|
{
|
|
hid_t attr_id=-1; /* attr ID */
|
|
hid_t attr_out=-1; /* attr ID */
|
|
hid_t space_id=-1; /* space ID */
|
|
hid_t ftype_id=-1; /* file data type ID */
|
|
hid_t mtype_id=-1; /* memory data type ID */
|
|
size_t msize; /* memory size of type */
|
|
void *buf=NULL; /* data buffer */
|
|
hsize_t nelmts; /* number of elements in dataset */
|
|
int rank; /* rank of dataset */
|
|
hsize_t dims[H5S_MAX_RANK];/* dimensions of dataset */
|
|
char name[255];
|
|
int n, j;
|
|
unsigned u;
|
|
|
|
if ((n = H5Aget_num_attrs(loc_in))<0)
|
|
goto error;
|
|
|
|
for ( u = 0; u < (unsigned)n; u++)
|
|
{
|
|
|
|
/* set data buffer to NULL each iteration
|
|
we might not use it in the case of references
|
|
*/
|
|
buf=NULL;
|
|
/*-------------------------------------------------------------------------
|
|
* open
|
|
*-------------------------------------------------------------------------
|
|
*/
|
|
/* open attribute */
|
|
if ((attr_id = H5Aopen_idx(loc_in, u))<0)
|
|
goto error;
|
|
|
|
/* get name */
|
|
if (H5Aget_name( attr_id, 255, name )<0)
|
|
goto error;
|
|
|
|
/* get the file datatype */
|
|
if ((ftype_id = H5Aget_type( attr_id )) < 0 )
|
|
goto error;
|
|
|
|
/* get the dataspace handle */
|
|
if ((space_id = H5Aget_space( attr_id )) < 0 )
|
|
goto error;
|
|
|
|
/* get dimensions */
|
|
if ( (rank = H5Sget_simple_extent_dims(space_id, dims, NULL)) < 0 )
|
|
goto error;
|
|
|
|
nelmts=1;
|
|
for (j=0; j<rank; j++)
|
|
nelmts*=dims[j];
|
|
|
|
if ((mtype_id=h5tools_get_native_type(ftype_id))<0)
|
|
goto error;
|
|
|
|
if ((msize=H5Tget_size(mtype_id))==0)
|
|
goto error;
|
|
|
|
/*-------------------------------------------------------------------------
|
|
* object references are a special case
|
|
* we cannot just copy the buffers, but instead we recreate the reference
|
|
* this is done on a second sweep of the file that just copies
|
|
* the referenced objects
|
|
*-------------------------------------------------------------------------
|
|
*/
|
|
if ( ! H5Tequal(mtype_id, H5T_STD_REF_OBJ))
|
|
{
|
|
|
|
|
|
/*-------------------------------------------------------------------------
|
|
* read to memory
|
|
*-------------------------------------------------------------------------
|
|
*/
|
|
|
|
buf=(void *) HDmalloc((unsigned)(nelmts*msize));
|
|
if ( buf==NULL){
|
|
printf( "cannot read into memory\n" );
|
|
goto error;
|
|
}
|
|
if (H5Aread(attr_id,mtype_id,buf)<0)
|
|
goto error;
|
|
|
|
/*-------------------------------------------------------------------------
|
|
* copy
|
|
*-------------------------------------------------------------------------
|
|
*/
|
|
|
|
if ((attr_out=H5Acreate(loc_out,name,ftype_id,space_id,H5P_DEFAULT))<0)
|
|
goto error;
|
|
if(H5Awrite(attr_out,mtype_id,buf)<0)
|
|
goto error;
|
|
|
|
/*close*/
|
|
if (H5Aclose(attr_out)<0)
|
|
goto error;
|
|
|
|
|
|
if (buf)
|
|
free(buf);
|
|
|
|
|
|
} /*H5T_STD_REF_OBJ*/
|
|
|
|
|
|
if (options->verbose)
|
|
printf(" %-13s %s\n", "attr", name);
|
|
|
|
/*-------------------------------------------------------------------------
|
|
* close
|
|
*-------------------------------------------------------------------------
|
|
*/
|
|
|
|
if (H5Tclose(ftype_id)<0) goto error;
|
|
if (H5Tclose(mtype_id)<0) goto error;
|
|
if (H5Sclose(space_id)<0) goto error;
|
|
if (H5Aclose(attr_id)<0) goto error;
|
|
|
|
} /* u */
|
|
|
|
return 0;
|
|
|
|
error:
|
|
H5E_BEGIN_TRY {
|
|
H5Tclose(ftype_id);
|
|
H5Tclose(mtype_id);
|
|
H5Sclose(space_id);
|
|
H5Aclose(attr_id);
|
|
H5Aclose(attr_out);
|
|
if (buf)
|
|
free(buf);
|
|
} H5E_END_TRY;
|
|
return -1;
|
|
}
|
|
|
|
|
|
|
|
|