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hdf5/tools/h5repack/h5repack_copy.c
Pedro Vicente Nunes 796fe1c402 [svn-r8122] Purpose: 
h5repack new feature

Description:
in the SZIP settings, when the requested pixels per block parameter does not conform
to the SZIP specifications, instead of returning without applying the filter,
do an attempt to set this parameter to a valid value, issuing a warning in the process

Solution:

Platforms tested:
linux
solaris
AIX

Misc. update:
2004-01-28 17:48:47 -05:00

622 lines
17 KiB
C
Raw Blame History

/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
* 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 "h5repack.h"
/*-------------------------------------------------------------------------
* 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;
trav_table_t *travt=NULL;
/*-------------------------------------------------------------------------
* open the files
*-------------------------------------------------------------------------
*/
/* disable error reporting */
H5E_BEGIN_TRY {
/* Open the files */
if ((fidin=H5Fopen(fnamein,H5F_ACC_RDONLY,H5P_DEFAULT))<0 ){
printf("h5repack: <%s>: %s\n", fnamein, H5FOPENERROR );
exit(1);
}
if ((fidout=H5Fcreate(fnameout,H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT))<0 ){
printf("h5repack: <%s>: Could not create file\n", fnameout );
exit(1);
}
/* enable error reporting */
} H5E_END_TRY;
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) {
printf("h5repack: <%s>: Could not copy data to: %s\n", fnamein, fnameout);
goto out;
}
/*-------------------------------------------------------------------------
* do the copy of referenced objects
* and create hard links
*-------------------------------------------------------------------------
*/
if(do_copy_refobjs(fidin,fidout,travt,options)<0) {
printf("h5repack: <%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);
trav_table_free(travt);
} H5E_END_TRY;
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
*
*-------------------------------------------------------------------------
*/
int do_copy_objects(hid_t fidin,
hid_t fidout,
trav_table_t *travt,
pack_opt_t *options) /* repack options */
{
hid_t grp_in; /* group ID */
hid_t grp_out; /* group ID */
hid_t dset_in; /* read dataset ID */
hid_t dset_out; /* write dataset ID */
hid_t type_in; /* named type ID */
hid_t type_out; /* named type ID */
hid_t dcpl_id; /* dataset creation property list ID */
hid_t space_id; /* space ID */
hid_t ftype_id; /* file data type ID */
hid_t mtype_id; /* memory data type ID */
size_t msize; /* memory size of memory 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 */
hsize_t dsize_in; /* input dataset size before filter */
hsize_t dsize_out; /* output dataset size after filter */
int i, j;
/*-------------------------------------------------------------------------
* copy the suppplied object list
*-------------------------------------------------------------------------
*/
for ( i = 0; i < travt->nobjs; i++)
{
buf=NULL;
switch ( travt->objs[i].type )
{
/*-------------------------------------------------------------------------
* H5G_GROUP
*-------------------------------------------------------------------------
*/
case H5G_GROUP:
if (options->verbose)
printf(" %-10s %s\n", "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:
if (options->verbose)
printf(" %-10s %s\n", "dataset",travt->objs[i].name );
if ((dset_in=H5Dopen(fidin,travt->objs[i].name))<0)
goto error;
if ((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 ( (rank=H5Sget_simple_extent_ndims(space_id))<0)
goto error;
HDmemset(dims, 0, sizeof dims);
if ( 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=H5Tget_native_type(ftype_id,H5T_DIR_DEFAULT))<0)
goto error;
if ((msize=H5Tget_size(mtype_id))==0)
goto error;
if (options->verbose)
print_filters(dcpl_id);
/*-------------------------------------------------------------------------
* 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(mtype_id)))
{
/* the information about the object to be filtered/"layouted" */
pack_info_t obj;
init_packobject(&obj);
/* get the storage size of the input dataset */
dsize_in=H5Dget_storage_size(dset_in);
/*-------------------------------------------------------------------------
* read to memory
*-------------------------------------------------------------------------
*/
if (nelmts)
{
buf=(void *) HDmalloc((unsigned)(nelmts*msize));
if ( buf==NULL){
printf( "cannot read into memory\n" );
goto error;
}
if (H5Dread(dset_in,mtype_id,H5S_ALL,H5S_ALL,H5P_DEFAULT,buf)<0)
goto error;
/*-------------------------------------------------------------------------
* apply the layout; check first if the object is to be modified.
*-------------------------------------------------------------------------
*/
if (layout_this(dcpl_id,travt->objs[i].name,options,&obj))
{
if (apply_layout(dcpl_id,&obj)<0)
goto error;
}
/*-------------------------------------------------------------------------
* apply the filter; check first if the object is to be filtered.
*-------------------------------------------------------------------------
*/
if (filter_this(travt->objs[i].name,options,&obj))
{
if (rank)
{
/* filters require CHUNK layout; if we do not have one define a default */
if (obj.chunk.rank<=0)
{
obj.chunk.rank=rank;
for (j=0; j<rank; j++)
obj.chunk.chunk_lengths[j] = dims[j];
}
if (apply_filters(dcpl_id,msize,options,&obj)<0)
goto error;
}
else
{
if (options->verbose)
printf("Warning: Filter could not be applied to <%s>\n",
travt->objs[i].name);
}/*rank*/
}/*filter_this*/
}/*nelmts*/
/*-------------------------------------------------------------------------
* create/write dataset/close
*-------------------------------------------------------------------------
*/
if ((dset_out=H5Dcreate(fidout,travt->objs[i].name,mtype_id,space_id,dcpl_id))<0)
goto error;
if (dsize_in && nelmts) {
if (H5Dwrite(dset_out,mtype_id,H5S_ALL,H5S_ALL,H5P_DEFAULT,buf)<0)
goto error;
}
/*-------------------------------------------------------------------------
* copy attrs
*-------------------------------------------------------------------------
*/
if (copy_attr(dset_in,dset_out,options)<0)
goto error;
/*-------------------------------------------------------------------------
* store the storage sizes
*-------------------------------------------------------------------------
*/
dsize_out=H5Dget_storage_size(dset_out);
/*close */
if (H5Dclose(dset_out)<0)
goto error;
if (buf)
free(buf);
}/*H5T_STD_REF_OBJ*/
/*-------------------------------------------------------------------------
* close
*-------------------------------------------------------------------------
*/
if (H5Tclose(ftype_id)<0)
goto error;
if (H5Tclose(mtype_id)<0)
goto error;
if (H5Pclose(dcpl_id)<0)
goto error;
if (H5Sclose(space_id)<0)
goto error;
if (H5Dclose(dset_in)<0)
goto error;
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(" %-10s %s\n","datatype",travt->objs[i].name );
break;
/*-------------------------------------------------------------------------
* H5G_LINK
*-------------------------------------------------------------------------
*/
case H5G_LINK:
{
H5G_stat_t statbuf;
char *targbuf=NULL;
if (H5Gget_objinfo(fidin,travt->objs[i].name,FALSE,&statbuf)<0)
goto error;
targbuf = malloc(statbuf.linklen);
if (H5Gget_linkval(fidin,travt->objs[i].name,statbuf.linklen,targbuf)<0)
goto error;
if (H5Glink(fidout,
H5G_LINK_SOFT,
targbuf, /* current name of object */
travt->objs[i].name /* new name of object */
)<0)
goto error;
free(targbuf);
if (options->verbose)
printf(" %-10s %s\n","link",travt->objs[i].name );
}
break;
default:
if (options->verbose)
printf(" %-10s %s\n","User defined object",travt->objs[i].name);
break;
}
}
/*-------------------------------------------------------------------------
* 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; /* attr ID */
hid_t attr_out; /* attr ID */
hid_t space_id; /* space ID */
hid_t ftype_id; /* file data type ID */
hid_t mtype_id; /* memory data type ID */
size_t msize; /* memory size of type */
void *buf; /* 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=H5Tget_native_type(ftype_id,H5T_DIR_DEFAULT))<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;
}
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