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d83a48e4f9
hdf5/tools/h5repack/h5repack_copy.c
Pedro Vicente Nunes d83a48e4f9 [svn-r8056] Purpose: 
h5repack change

Description:
changed the default size of chunks when defining a new dataset to apply a filter
this size is now equal to the current dimensions. previously , it was set to half this
value, and it was causing write calls to fail on some files (probably a bug)

Solution:

Platforms tested:
linux
solaris
AIX

Misc. update:
2004-01-13 13:12:47 -05:00

623 lines
17 KiB
C
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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 "h5repack.h"
/*-------------------------------------------------------------------------
* Function: copy_file
*
* 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_file(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>: No such file or directory\n", fnamein );
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;
#if defined (H5_REPACK_DEBUG)
h5trav_printtable(travt);
#endif
/*-------------------------------------------------------------------------
* do the copy
*-------------------------------------------------------------------------
*/
if(do_copy_file(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_file
*
* 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_file(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++)
{
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;
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);
/*-------------------------------------------------------------------------
* object 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 ( ! H5Tequal(mtype_id, H5T_STD_REF_OBJ) )
{
/* 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
*-------------------------------------------------------------------------
*/
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 the layout could not be applied, continue
*-------------------------------------------------------------------------
*/
if (layout_this(dcpl_id,travt->objs[i].name,options,&obj))
{
if (apply_layout(dcpl_id,&obj)<0)
continue;
}
/*-------------------------------------------------------------------------
* apply the filter; check first if the object is to be filtered.
* if the filter could not be applied, continue
*-------------------------------------------------------------------------
*/
if (filter_this(travt->objs[i].name,options,&obj))
{
/* 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,H5Tget_size(mtype_id),options,&obj)<0)
continue;
}
/*-------------------------------------------------------------------------
* create/write dataset/close
*-------------------------------------------------------------------------
*/
if ((dset_out=H5Dcreate(fidout,travt->objs[i].name,ftype_id,space_id,dcpl_id))<0)
goto error;
if (dsize_in) {
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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