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hdf5/tools/h5repack/h5repack_copy.c
Pedro Vicente Nunes 50c658d66d [svn-r12884] 
h5repack support for H5Ocopy in the copy of objects. The old method
for recreating references was dropped (references recreated in a second
traversal of the file)
The logic for using H5Ocopy or not is
if the input DCPL has filters or non default layout OR these are
requested by the user THEN
use the old h5repack read / write
ELSE
use H5Ocopy
2006-11-08 16:34:21 -05:00

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/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
* Copyright by the Board of Trustees of the University of Illinois. *
* All rights reserved. *
* *
* This file is part of HDF5. The full HDF5 copyright notice, including *
* terms governing use, modification, and redistribution, is contained in *
* the files COPYING and Copyright.html. COPYING can be found at the root *
* of the source code distribution tree; Copyright.html can be found at the *
* root level of an installed copy of the electronic HDF5 document set and *
* is linked from the top-level documents page. It can also be found at *
* http://hdf.ncsa.uiuc.edu/HDF5/doc/Copyright.html. If you do not have *
* access to either file, you may request a copy from hdfhelp@ncsa.uiuc.edu. *
* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
#include <stdlib.h>
#include <string.h>
#include <stdio.h>
#include "H5private.h"
#include "h5tools.h"
#include "h5tools_utils.h"
#include "h5repack.h"
extern char *progname;
#define PER(A,B) { per = 0; \
if (A!=0) \
per = (float)fabs(1-( (float)B / (float)A )); \
}
#define FORMAT_OBJ " %-21s %s\n" /* obj type, name */
#define FORMAT_OBJ_ATTR " %-21s %s\n" /* obj type, name */
static
int do_hardlinks(hid_t fidout,trav_table_t *travt);
/*-------------------------------------------------------------------------
* Function: print_dataset_info
*
* Purpose: print name, filters, percentage compression of a dataset
*
*-------------------------------------------------------------------------
*/
static void print_dataset_info(hid_t dcpl_id,
char *objname,
float per)
{
char strfilter[255];
#if defined (PRINT_DEBUG )
char temp[255];
#endif
int nfilters; /* number of filters */
unsigned filt_flags; /* filter flags */
H5Z_filter_t filtn; /* filter identification number */
unsigned cd_values[20]; /* filter client data values */
size_t cd_nelmts; /* filter client number of values */
char f_objname[256]; /* filter objname */
int i;
strcpy(strfilter,"\0");
/* get information about input filters */
if ((nfilters = H5Pget_nfilters(dcpl_id))<0)
return;
for ( i=0; i<nfilters; i++)
{
cd_nelmts = NELMTS(cd_values);
#ifdef H5_WANT_H5_V1_6_COMPAT
filtn = H5Pget_filter(dcpl_id,
(unsigned)i,
&filt_flags,
&cd_nelmts,
cd_values,
sizeof(f_objname),
f_objname);
#else
filtn = H5Pget_filter(dcpl_id,
(unsigned)i,
&filt_flags,
&cd_nelmts,
cd_values,
sizeof(f_objname),
f_objname,
NULL);
#endif /* H5_WANT_H5_V1_6_COMPAT */
switch (filtn)
{
default:
break;
case H5Z_FILTER_DEFLATE:
strcat(strfilter,"GZIP ");
#if defined (PRINT_DEBUG)
{
unsigned level=cd_values[0];
sprintf(temp,"(%d)",level);
strcat(strfilter,temp);
}
#endif
break;
case H5Z_FILTER_SZIP:
strcat(strfilter,"SZIP ");
#if defined (PRINT_DEBUG)
{
unsigned options_mask=cd_values[0]; /* from dcpl, not filt*/
unsigned ppb=cd_values[1];
sprintf(temp,"(%d,",ppb);
strcat(strfilter,temp);
if (options_mask & H5_SZIP_EC_OPTION_MASK)
strcpy(temp,"EC) ");
else if (options_mask & H5_SZIP_NN_OPTION_MASK)
strcpy(temp,"NN) ");
}
strcat(strfilter,temp);
#endif
break;
case H5Z_FILTER_SHUFFLE:
strcat(strfilter,"SHUF ");
break;
case H5Z_FILTER_FLETCHER32:
strcat(strfilter,"FLET ");
break;
case H5Z_FILTER_NBIT:
strcat(strfilter,"NBIT ");
break;
case H5Z_FILTER_SCALEOFFSET:
strcat(strfilter,"SCALEOFFSET ");
break;
} /* switch */
}/*i*/
if (strcmp(strfilter,"\0")==0)
printf(FORMAT_OBJ,"dset",objname );
else
{
char str[255], temp[20];
strcpy(str,"dset ");
strcat(str,strfilter);
sprintf(temp,"(%.2f%%)",per);
strcat(str,temp);
printf(FORMAT_OBJ,str,objname);
}
}
/*-------------------------------------------------------------------------
* Function: copy_objects
*
* Purpose: duplicate all HDF5 objects in the file
*
* Return: 0, ok, -1 no
*
* Programmer: Pedro Vicente, pvn@ncsa.uiuc.edu
*
* Date: October, 23, 2003
*
*-------------------------------------------------------------------------
*/
int copy_objects(const char* fnamein,
const char* fnameout,
pack_opt_t *options)
{
hid_t fidin;
hid_t fidout=-1;
trav_table_t *travt=NULL;
/*-------------------------------------------------------------------------
* open the files
*-------------------------------------------------------------------------
*/
if ((fidin=h5tools_fopen(fnamein, NULL, NULL, 0))<0 ){
error_msg(progname, "<%s>: %s\n", fnamein, H5FOPENERROR );
goto out;
}
if ((fidout=H5Fcreate(fnameout,H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT))<0 ){
error_msg(progname, "<%s>: Could not create file\n", fnameout );
goto out;
}
if (options->verbose)
printf("Making file <%s>...\n",fnameout);
/* init table */
trav_table_init(&travt);
/* get the list of objects in the file */
if (h5trav_gettable(fidin,travt)<0)
goto out;
/*-------------------------------------------------------------------------
* do the copy
*-------------------------------------------------------------------------
*/
if(do_copy_objects(fidin,fidout,travt,options)<0) {
error_msg(progname, "<%s>: Could not copy data to: %s\n", fnamein, fnameout);
goto out;
}
/*-------------------------------------------------------------------------
* create hard links
*-------------------------------------------------------------------------
*/
if(do_hardlinks(fidout,travt)<0) {
error_msg(progname, "<%s>: Could not copy data to: %s\n", fnamein, fnameout);
goto out;
}
/* free table */
trav_table_free(travt);
/*-------------------------------------------------------------------------
* close
*-------------------------------------------------------------------------
*/
H5Fclose(fidin);
H5Fclose(fidout);
return 0;
/*-------------------------------------------------------------------------
* out
*-------------------------------------------------------------------------
*/
out:
H5E_BEGIN_TRY {
H5Fclose(fidin);
H5Fclose(fidout);
} H5E_END_TRY;
if (travt)
trav_table_free(travt);
return -1;
}
/*-------------------------------------------------------------------------
* Function: do_copy_objects
*
* Purpose: duplicate all HDF5 objects in the file
*
* Return: 0, ok, -1 no
*
* Programmer: Pedro Vicente, pvn@ncsa.uiuc.edu
*
* Date: October, 23, 2003
*
* Modifications:
*
* July 2004: Introduced the extra EC or NN option for SZIP
*
* December 2004: Added a check for H5Dcreate; if the dataset cannot be created
* with the requested filter, use the input one
*
* October 2006: Read/write using the file type by default.
* Read/write by hyperslabs for big datasets.
*
*-------------------------------------------------------------------------
*/
int do_copy_objects(hid_t fidin,
hid_t fidout,
trav_table_t *travt,
pack_opt_t *options) /* repack options */
{
hid_t grp_in=-1; /* group ID */
hid_t grp_out=-1; /* group ID */
hid_t dset_in=-1; /* read dataset ID */
hid_t dset_out=-1; /* write dataset ID */
hid_t type_in=-1; /* named type ID */
hid_t type_out=-1; /* named type ID */
hid_t dcpl_id=-1; /* dataset creation property list ID */
hid_t dcpl_out=-1; /* dataset creation property list ID */
hid_t f_space_id=-1; /* file space ID */
hid_t ftype_id=-1; /* file type ID */
hid_t wtype_id=-1; /* read/write type ID */
size_t msize; /* size of type */
hsize_t nelmts; /* number of elements in dataset */
int rank; /* rank of dataset */
hsize_t dims[H5S_MAX_RANK];/* dimensions of dataset */
hsize_t dsize_in; /* input dataset size before filter */
hsize_t dsize_out; /* output dataset size after filter */
int next; /* external files */
int apply_s; /* flag for apply filter to small dataset sizes */
int apply_f; /* flag for apply filter to return error on H5Dcreate */
float per; /* percent utilization of storage */
void *buf=NULL; /* buffer for raw data */
void *sm_buf=NULL; /* buffer for raw data */
int i, j;
int nfilters; /* number of filters in DCPL */
H5D_layout_t layout;
/*-------------------------------------------------------------------------
* copy the suppplied object list
*-------------------------------------------------------------------------
*/
if (options->verbose) {
printf("-----------------------------------------\n");
printf(" Type Filter (Ratio) Name\n");
printf("-----------------------------------------\n");
}
for ( i = 0; i < travt->nobjs; i++)
{
buf = NULL;
switch ( travt->objs[i].type )
{
/*-------------------------------------------------------------------------
* H5G_GROUP
*-------------------------------------------------------------------------
*/
case H5G_GROUP:
if (options->verbose)
printf(FORMAT_OBJ,"group",travt->objs[i].name );
if ((grp_out=H5Gcreate(fidout,travt->objs[i].name, 0))<0)
goto error;
if((grp_in = H5Gopen (fidin,travt->objs[i].name))<0)
goto error;
/*-------------------------------------------------------------------------
* copy attrs
*-------------------------------------------------------------------------
*/
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;
break;
/*-------------------------------------------------------------------------
* H5G_DATASET
*-------------------------------------------------------------------------
*/
case H5G_DATASET:
/*-------------------------------------------------------------------------
* early check for filters or a non default layout
*-------------------------------------------------------------------------
*/
if ((dset_in=H5Dopen(fidin,travt->objs[i].name))<0)
goto error;
if ((dcpl_id=H5Dget_create_plist(dset_in))<0)
goto error;
/* get information about input filters */
if ((nfilters = H5Pget_nfilters(dcpl_id))<0)
goto error;
if ((layout = H5Pget_layout(dcpl_id))<0)
goto error;
if (H5Dclose(dset_in)<0)
goto error;
if (H5Pclose(dcpl_id)<0)
goto error;
/*-------------------------------------------------------------------------
* check if we should use H5Ocopy or not
* if the DCPL has filters or a non default layout, we read/write the object
* otherwise we do a copy using H5Ocopy
*-------------------------------------------------------------------------
*/
if (nfilters || layout!=H5D_CONTIGUOUS
/* does the dcpl has filters or non default layout ? */
||
options->op_tbl->nelems
/* do we have input request for filter/chunking */
||
options->all_filter==1 || options->all_layout==1
)
{
if ((dset_in=H5Dopen(fidin,travt->objs[i].name))<0)
goto error;
if ((f_space_id=H5Dget_space(dset_in))<0)
goto error;
if ((ftype_id=H5Dget_type (dset_in))<0)
goto error;
if ((dcpl_id=H5Dget_create_plist(dset_in))<0)
goto error;
if ((dcpl_out = H5Pcopy (dcpl_id))<0)
goto error;
if ( (rank=H5Sget_simple_extent_ndims(f_space_id))<0)
goto error;
HDmemset(dims, 0, sizeof dims);
if ( H5Sget_simple_extent_dims(f_space_id,dims,NULL)<0)
goto error;
nelmts=1;
for (j=0; j<rank; j++)
nelmts*=dims[j];
if (options->use_native==1)
wtype_id = h5tools_get_native_type(ftype_id);
else
wtype_id = H5Tcopy(ftype_id);
if ((msize=H5Tget_size(wtype_id))==0)
goto error;
/*-------------------------------------------------------------------------
* check for external files
*-------------------------------------------------------------------------
*/
if ((next=H5Pget_external_count (dcpl_id))<0)
goto error;
if (next)
fprintf(stderr," <warning: %s has external files, ignoring read...>\n",
travt->objs[i].name );
/*-------------------------------------------------------------------------
* check if the dataset creation property list has filters that
* are not registered in the current configuration
* 1) the external filters GZIP and SZIP might not be available
* 2) the internal filters might be turned off
*-------------------------------------------------------------------------
*/
if (next==0 && h5tools_canreadf((travt->objs[i].name),dcpl_id)==1)
{
apply_s=1;
apply_f=1;
/*-------------------------------------------------------------------------
* references are a special case
* we cannot just copy the buffers, but instead we recreate the reference
* in a second traversal of the output file
*-------------------------------------------------------------------------
*/
if ( (H5T_REFERENCE!=H5Tget_class(wtype_id)))
{
/* get the storage size of the input dataset */
dsize_in=H5Dget_storage_size(dset_in);
/* check for datasets too small */
if (nelmts*msize < options->threshold )
apply_s=0;
/* apply the filter */
if (apply_s){
if (apply_filters(travt->objs[i].name,rank,dims,dcpl_out,options)<0)
goto error;
}
/*-------------------------------------------------------------------------
* create the output dataset;
* disable error checking in case the dataset cannot be created with the
* modified dcpl; in that case use the original instead
*-------------------------------------------------------------------------
*/
H5E_BEGIN_TRY {
dset_out=H5Dcreate(fidout,travt->objs[i].name,wtype_id,f_space_id,dcpl_out);
} H5E_END_TRY;
if (dset_out==FAIL)
{
if ((dset_out=H5Dcreate(fidout,travt->objs[i].name,wtype_id,f_space_id,dcpl_id))<0)
goto error;
apply_f=0;
}
/*-------------------------------------------------------------------------
* read/write
*-------------------------------------------------------------------------
*/
if (nelmts)
{
size_t need = (size_t)(nelmts*msize); /* bytes needed */
if ( need < H5TOOLS_MALLOCSIZE )
buf = HDmalloc(need);
if (buf != NULL )
{
if (H5Dread(dset_in,wtype_id,H5S_ALL,H5S_ALL,H5P_DEFAULT,buf)<0)
goto error;
if (H5Dwrite(dset_out,wtype_id,H5S_ALL,H5S_ALL,H5P_DEFAULT,buf)<0)
goto error;
}
else /* possibly not enough memory, read/write by hyperslabs */
{
size_t p_type_nbytes = msize; /*size of memory type */
hsize_t p_nelmts = nelmts; /*total selected elmts */
hsize_t elmtno; /*counter */
int carry; /*counter carry value */
unsigned int vl_data = 0; /*contains VL datatypes */
/* stripmine info */
hsize_t sm_size[H5S_MAX_RANK]; /*stripmine size */
hsize_t sm_nbytes; /*bytes per stripmine */
hsize_t sm_nelmts; /*elements per stripmine*/
hid_t sm_space; /*stripmine data space */
/* hyperslab info */
hsize_t hs_offset[H5S_MAX_RANK];/*starting offset */
hsize_t hs_size[H5S_MAX_RANK]; /*size this pass */
hsize_t hs_nelmts; /*elements in request */
hsize_t zero[8]; /*vector of zeros */
/* check if we have VL data in the dataset's datatype */
if (H5Tdetect_class(wtype_id, H5T_VLEN) == TRUE)
vl_data = TRUE;
/*
* determine the strip mine size and allocate a buffer. The strip mine is
* a hyperslab whose size is manageable.
*/
sm_nbytes = p_type_nbytes;
for (i = rank; i > 0; --i) {
sm_size[i - 1] = MIN(dims[i - 1], H5TOOLS_BUFSIZE / sm_nbytes);
sm_nbytes *= sm_size[i - 1];
assert(sm_nbytes > 0);
}
sm_buf = HDmalloc((size_t)sm_nbytes);
sm_nelmts = sm_nbytes / p_type_nbytes;
sm_space = H5Screate_simple(1, &sm_nelmts, NULL);
/* the stripmine loop */
memset(hs_offset, 0, sizeof hs_offset);
memset(zero, 0, sizeof zero);
for (elmtno = 0; elmtno < p_nelmts; elmtno += hs_nelmts)
{
/* calculate the hyperslab size */
if (rank > 0)
{
for (i = 0, hs_nelmts = 1; i < rank; i++)
{
hs_size[i] = MIN(dims[i] - hs_offset[i], sm_size[i]);
hs_nelmts *= hs_size[i];
}
if (H5Sselect_hyperslab(f_space_id, H5S_SELECT_SET, hs_offset, NULL, hs_size, NULL)<0)
goto error;
if (H5Sselect_hyperslab(sm_space, H5S_SELECT_SET, zero, NULL, &hs_nelmts, NULL)<0)
goto error;
}
else
{
H5Sselect_all(f_space_id);
H5Sselect_all(sm_space);
hs_nelmts = 1;
} /* rank */
/* read/write */
if (H5Dread(dset_in, wtype_id, sm_space, f_space_id, H5P_DEFAULT, sm_buf) < 0)
goto error;
if (H5Dwrite(dset_out, wtype_id, sm_space, f_space_id, H5P_DEFAULT, sm_buf) < 0)
goto error;
/* reclaim any VL memory, if necessary */
if(vl_data)
H5Dvlen_reclaim(wtype_id, sm_space, H5P_DEFAULT, sm_buf);
/* calculate the next hyperslab offset */
for (i = rank, carry = 1; i > 0 && carry; --i)
{
hs_offset[i - 1] += hs_size[i - 1];
if (hs_offset[i - 1] == dims[i - 1])
hs_offset[i - 1] = 0;
else
carry = 0;
} /* i */
} /* elmtno */
H5Sclose(sm_space);
/* free */
if (sm_buf!=NULL)
{
HDfree(sm_buf);
sm_buf=NULL;
}
} /* hyperslab read */
}/*nelmts*/
/*-------------------------------------------------------------------------
* amount of compression used
*-------------------------------------------------------------------------
*/
if (options->verbose)
{
if (apply_s && apply_f)
{
/* get the storage size of the input dataset */
dsize_out=H5Dget_storage_size(dset_out);
PER((hssize_t)dsize_in,(hssize_t)dsize_out);
print_dataset_info(dcpl_out,travt->objs[i].name,per*(float)100.0);
}
else
print_dataset_info(dcpl_id,travt->objs[i].name,0);
}
if (apply_s==0 && options->verbose)
printf(" <warning: filter not applied to %s. dataset smaller than %d bytes>\n",
travt->objs[i].name,
(int)options->threshold);
if (apply_f==0 && options->verbose)
printf(" <warning: could not apply the filter to %s>\n",
travt->objs[i].name);
/*-------------------------------------------------------------------------
* copy attrs
*-------------------------------------------------------------------------
*/
if (copy_attr(dset_in,dset_out,options)<0)
goto error;
/*close */
if (H5Dclose(dset_out)<0)
goto error;
}/*H5T_STD_REF_OBJ*/
}/*can_read*/
/*-------------------------------------------------------------------------
* close
*-------------------------------------------------------------------------
*/
if (H5Tclose(ftype_id)<0)
goto error;
if (H5Tclose(wtype_id)<0)
goto error;
if (H5Pclose(dcpl_id)<0)
goto error;
if (H5Pclose(dcpl_out)<0)
goto error;
if (H5Sclose(f_space_id)<0)
goto error;
if (H5Dclose(dset_in)<0)
goto error;
}
/*-------------------------------------------------------------------------
* we do not have request for filter/chunking use H5Ocopy instead
*-------------------------------------------------------------------------
*/
else
{
hid_t pid;
/* create property to pass copy options */
if ( (pid = H5Pcreate(H5P_OBJECT_COPY)) < 0)
goto error;
/*-------------------------------------------------------------------------
* do the copy
*-------------------------------------------------------------------------
*/
if (H5Ocopy(fidin, /* Source file or group identifier */
travt->objs[i].name, /* Name of the source object to be copied */
fidout, /* Destination file or group identifier */
travt->objs[i].name, /* Name of the destination object */
pid, /* Properties which apply to the copy */
H5P_DEFAULT)<0) /* Properties which apply to the new hard link */
goto error;
/* close property */
if (H5Pclose(pid)<0)
goto error;
} /* end do we have request for filter/chunking */
break;
/*-------------------------------------------------------------------------
* H5G_TYPE
*-------------------------------------------------------------------------
*/
case H5G_TYPE:
if ((type_in = H5Topen (fidin,travt->objs[i].name))<0)
goto error;
if ((type_out = H5Tcopy(type_in))<0)
goto error;
if ((H5Tcommit(fidout,travt->objs[i].name,type_out))<0)
goto error;
/*-------------------------------------------------------------------------
* copy attrs
*-------------------------------------------------------------------------
*/
if (copy_attr(type_in,type_out,options)<0)
goto error;
if (H5Tclose(type_in)<0)
goto error;
if (H5Tclose(type_out)<0)
goto error;
if (options->verbose)
printf(FORMAT_OBJ,"type",travt->objs[i].name );
break;
/*-------------------------------------------------------------------------
* H5G_LINK
* H5G_UDLINK
*
* Only handles external links; H5Lcopy will fail for other UD link types
* since we don't have creation or copy callbacks for them.
*-------------------------------------------------------------------------
*/
case H5G_LINK:
case H5G_UDLINK:
{
if(H5Lcopy(fidin, travt->objs[i].name,fidout, travt->objs[i].name, H5P_DEFAULT, H5P_DEFAULT) < 0)
goto error;
if (options->verbose)
printf(FORMAT_OBJ,"link",travt->objs[i].name );
}
break;
default:
goto error;
} /* switch */
/* free */
if (buf!=NULL)
{
HDfree(buf);
buf=NULL;
}
} /* i */
/*-------------------------------------------------------------------------
* the root is a special case, we get an ID for the root group
* and copy its attributes using that ID
*-------------------------------------------------------------------------
*/
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(f_space_id);
H5Dclose(dset_in);
H5Dclose(dset_out);
H5Tclose(ftype_id);
H5Tclose(wtype_id);
H5Tclose(type_in);
H5Tclose(type_out);
/* free */
if (buf!=NULL)
{
HDfree(buf);
buf=NULL;
}
if (sm_buf!=NULL)
{
HDfree(sm_buf);
sm_buf=NULL;
}
} 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 type ID */
hid_t wtype_id=-1; /* read/write type ID */
size_t msize; /* 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 (options->use_native==1)
wtype_id = h5tools_get_native_type(ftype_id);
else
wtype_id = H5Tcopy(ftype_id);
if ((msize=H5Tget_size(wtype_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(wtype_id, H5T_STD_REF_OBJ))
{
/*-------------------------------------------------------------------------
* read to memory
*-------------------------------------------------------------------------
*/
buf=(void *) HDmalloc((unsigned)(nelmts*msize));
if ( buf==NULL){
error_msg(progname, "cannot read into memory\n" );
goto error;
}
if (H5Aread(attr_id,wtype_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,wtype_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(FORMAT_OBJ_ATTR, "attr", name);
/*-------------------------------------------------------------------------
* close
*-------------------------------------------------------------------------
*/
if (H5Tclose(ftype_id)<0) goto error;
if (H5Tclose(wtype_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(wtype_id);
H5Sclose(space_id);
H5Aclose(attr_id);
H5Aclose(attr_out);
if (buf)
free(buf);
} H5E_END_TRY;
return -1;
}
/*-------------------------------------------------------------------------
* Function: do_hardlinks
*
* Purpose: duplicate hard links
*
* Return: 0, ok, -1 no
*
* Programmer: Pedro Vicente, pvn@ncsa.uiuc.edu
*
* Date: December, 10, 2003
*
*-------------------------------------------------------------------------
*/
static
int do_hardlinks(hid_t fidout,trav_table_t *travt)
{
int i, j;
for ( i = 0; i < travt->nobjs; i++)
{
switch ( travt->objs[i].type )
{
case H5G_GROUP:
if (travt->objs[i].nlinks)
{
for ( j=0; j<travt->objs[i].nlinks; j++)
{
if (H5Glink(fidout,
H5L_TYPE_HARD,
travt->objs[i].name,
travt->objs[i].links[j].new_name)<0)
return -1;
}
}
break;
case H5G_DATASET:
if (travt->objs[i].nlinks)
{
for ( j=0; j<travt->objs[i].nlinks; j++){
if (H5Glink(fidout,
H5L_TYPE_HARD,
travt->objs[i].name,
travt->objs[i].links[j].new_name)<0)
return -1;
}
}
break;
case H5G_TYPE:
case H5G_LINK:
case H5G_UDLINK:
/*nothing to do */
break;
default:
break;
}
}
return 0;
}
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