mirror of
https://github.com/HDFGroup/hdf5.git
synced 2024-11-21 01:04:10 +08:00
28e43d818f
code clean Description: separated the h5repack code in several modules Solution: Platforms tested: linux IRIX solaris Misc. update:
517 lines
14 KiB
C
517 lines
14 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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/*-------------------------------------------------------------------------
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* Function: copy_file
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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_file(const char* fnamein,
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const char* fnameout,
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pack_opt_t *options)
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{
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hid_t fidin;
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hid_t fidout;
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int nobjects;
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trav_info_t *info=NULL;
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/*-------------------------------------------------------------------------
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* open the files
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*-------------------------------------------------------------------------
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*/
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/* disable error reporting */
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H5E_BEGIN_TRY {
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/* Open the files */
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if ((fidin=H5Fopen(fnamein,H5F_ACC_RDONLY,H5P_DEFAULT))<0 ){
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printf("h5repack: <%s>: No such file or directory\n", fnamein );
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exit(1);
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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("h5repack: <%s>: Could not create file\n", fnameout );
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exit(1);
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}
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/* enable error reporting */
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} H5E_END_TRY;
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if (options->verbose)
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printf("Making file <%s>...\n",fnameout);
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/*-------------------------------------------------------------------------
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* get the number of objects in the file
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*-------------------------------------------------------------------------
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*/
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if ((nobjects = h5trav_getinfo(fidin, NULL ))<0) {
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printf("h5repack: <%s>: Could not obtain object list\n", fnamein );
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return -1;
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}
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/*-------------------------------------------------------------------------
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* get the list of objects in the file
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*-------------------------------------------------------------------------
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*/
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if ((info = (trav_info_t*) malloc( nobjects * sizeof(trav_info_t)))==NULL){
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printf("h5repack: <%s>: Could not allocate object list\n", fnamein );
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return -1;
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}
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if (h5trav_getinfo(fidin, info )<0) {
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printf("h5repack: <%s>: Could not obtain object list\n", fnamein );
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return -1;
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}
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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_file(fidin,fidout,nobjects,info,options)<0) {
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printf("h5repack: <%s>: Could not copy data to: %s\n", fnamein, fnameout);
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return -1;
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}
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/*-------------------------------------------------------------------------
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* free
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*-------------------------------------------------------------------------
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*/
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H5Fclose(fidin);
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H5Fclose(fidout);
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h5trav_freeinfo(info,nobjects);
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return 0;
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}
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/*-------------------------------------------------------------------------
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* Function: do_copy_file
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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 do_copy_file(hid_t fidin,
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hid_t fidout,
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int nobjects,
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trav_info_t *info,
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pack_opt_t *options)
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{
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hid_t grp_in; /* group ID */
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hid_t grp_out; /* group ID */
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hid_t dset_in; /* read dataset ID */
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hid_t dset_out; /* write dataset ID */
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hid_t type_in; /* named type ID */
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hid_t type_out; /* named type ID */
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hid_t dcpl_id; /* dataset creation property list ID */
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hid_t space_id; /* space ID */
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hid_t ftype_id; /* file data type ID */
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hid_t mtype_id; /* 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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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 < nobjects; i++)
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{
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switch ( info[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",info[i].name );
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if ((grp_out=H5Gcreate(fidout, info[i].name, 0))<0)
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goto error;
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if((grp_in = H5Gopen (fidin, info[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 (options->verbose)
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printf(" %-10s %s\n", "dataset",info[i].name );
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if ((dset_in=H5Dopen(fidin,info[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 ( (rank=H5Sget_simple_extent_ndims(space_id))<0)
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goto error;
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if ( H5Sget_simple_extent_dims(space_id,dims,NULL)<0)
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goto error;
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/*-------------------------------------------------------------------------
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* read to memory
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*-------------------------------------------------------------------------
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*/
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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 ((mtype_id=H5Tget_native_type(ftype_id,H5T_DIR_DEFAULT))<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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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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* create/write dataset/close
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*-------------------------------------------------------------------------
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*/
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if ((dset_out=H5Dcreate(fidout,info[i].name,ftype_id,space_id,dcpl_id))<0)
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goto error;
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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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* 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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*-------------------------------------------------------------------------
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*/
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if (H5Tclose(ftype_id)<0)
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goto error;
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if (H5Tclose(mtype_id)<0)
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goto error;
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if (H5Pclose(dcpl_id)<0)
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goto error;
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if (H5Sclose(space_id)<0)
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goto error;
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if (H5Dclose(dset_in)<0)
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goto error;
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if (H5Dclose(dset_out)<0)
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goto error;
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if (buf)
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free(buf);
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break;
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/*-------------------------------------------------------------------------
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* H5G_TYPE
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*-------------------------------------------------------------------------
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*/
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case H5G_TYPE:
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if ((type_in = H5Topen (fidin, info[i].name))<0)
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goto error;
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if ((type_out = H5Tcopy(type_in))<0)
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goto error;
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if ((H5Tcommit(fidout, info[i].name, type_out))<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(type_in,type_out,options)<0)
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goto error;
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if (H5Tclose(type_in)<0)
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goto error;
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if (H5Tclose(type_out)<0)
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goto error;
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if (options->verbose)
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printf(" %-10s %s\n", "datatype",info[i].name );
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break;
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case H5G_LINK:
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{
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H5G_stat_t statbuf;
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char *targbuf=NULL;
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if (H5Gget_objinfo(fidin,info[i].name,FALSE,&statbuf)<0)
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goto error;
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targbuf = malloc(statbuf.linklen);
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if (H5Gget_linkval(fidin,info[i].name,statbuf.linklen,targbuf)<0)
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goto error;
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if (H5Glink(fidout,
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H5G_LINK_SOFT,
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targbuf, /* current name of object */
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info[i].name /* new name of object */
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)<0)
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goto error;
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free(targbuf);
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if (options->verbose)
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printf(" %-10s %s\n", "link",info[i].name );
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}
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break;
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default:
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if (options->verbose)
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printf(" %-10s %s\n", "User defined object", info[i].name);
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break;
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}
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}
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/*-------------------------------------------------------------------------
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* the root is a special case, we get an ID for the root group
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* and copy its attributes using that ID
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* it must be done last, because the attributes might contain references to
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* objects in the object list
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*-------------------------------------------------------------------------
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*/
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if ((grp_out = H5Gopen(fidout,"/"))<0)
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goto error;
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if ((grp_in = H5Gopen(fidin,"/"))<0)
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goto error;
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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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return 0;
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error:
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H5E_BEGIN_TRY {
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H5Gclose(grp_in);
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H5Gclose(grp_out);
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H5Pclose(dcpl_id);
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H5Sclose(space_id);
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H5Dclose(dset_in);
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H5Dclose(dset_out);
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H5Tclose(ftype_id);
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H5Tclose(mtype_id);
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H5Tclose(type_in);
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H5Tclose(type_out);
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if (buf)
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free(buf);
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} H5E_END_TRY;
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return -1;
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}
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/*-------------------------------------------------------------------------
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* Function: copy_attr
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*
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* Purpose: copy attributes located in LOC_IN, which is obtained either from
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* loc_id = H5Gopen( fid, name);
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* loc_id = H5Dopen( fid, name);
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* loc_id = H5Topen( fid, name);
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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, 28, 2003
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*
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*-------------------------------------------------------------------------
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*/
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int copy_attr(hid_t loc_in,
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hid_t loc_out,
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pack_opt_t *options
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)
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{
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hid_t attr_id; /* attr ID */
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hid_t attr_out; /* attr ID */
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hid_t space_id; /* space ID */
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hid_t ftype_id; /* file data type ID */
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hid_t mtype_id; /* 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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char name[255];
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int n, j;
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unsigned u;
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if ((n = H5Aget_num_attrs(loc_in))<0)
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goto error;
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for ( u = 0; u < (unsigned)n; u++)
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{
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/*-------------------------------------------------------------------------
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* open
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*-------------------------------------------------------------------------
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*/
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/* open attribute */
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if ((attr_id = H5Aopen_idx(loc_in, u))<0)
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goto error;
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/* get name */
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if (H5Aget_name( attr_id, 255, name )<0)
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goto error;
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/* get the file datatype */
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if ((ftype_id = H5Aget_type( attr_id )) < 0 )
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goto error;
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/* get the dataspace handle */
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if ((space_id = H5Aget_space( attr_id )) < 0 )
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goto error;
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/* get dimensions */
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if ( (rank = H5Sget_simple_extent_dims(space_id, dims, NULL)) < 0 )
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goto error;
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/*-------------------------------------------------------------------------
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* read to memory
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*-------------------------------------------------------------------------
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*/
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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 ((mtype_id=H5Tget_native_type(ftype_id,H5T_DIR_DEFAULT))<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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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 (H5Aread(attr_id,mtype_id,buf)<0)
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goto error;
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/*-------------------------------------------------------------------------
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* copy
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*-------------------------------------------------------------------------
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*/
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if ((attr_out=H5Acreate(loc_out,name,ftype_id,space_id,H5P_DEFAULT))<0)
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goto error;
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if(H5Awrite(attr_out,mtype_id,buf)<0)
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goto error;
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if (options->verbose)
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printf(" %-13s %s\n", "attr", name);
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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) goto error;
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if (H5Tclose(mtype_id)<0) goto error;
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if (H5Sclose(space_id)<0) goto error;
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if (H5Aclose(attr_id)<0) goto error;
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if (H5Aclose(attr_out)<0) goto error;
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if (buf)
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free(buf);
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} /* u */
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return 0;
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error:
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H5E_BEGIN_TRY {
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H5Tclose(ftype_id);
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H5Tclose(mtype_id);
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H5Sclose(space_id);
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H5Aclose(attr_id);
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H5Aclose(attr_out);
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if (buf)
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free(buf);
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} H5E_END_TRY;
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return -1;
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}
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