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|
/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
* Copyright by The HDF Group. *
* 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://hdfgroup.org/HDF5/doc/Copyright.html. If you do not have *
* access to either file, you may request a copy from help@hdfgroup.org. *
* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
#include "h5repack.h"
#include "h5diff.h"
#include "h5tools.h"
/*-------------------------------------------------------------------------
* local functions
*-------------------------------------------------------------------------
*/
static const char* MapIdToName(hid_t refobj_id,trav_table_t *travt);
static int copy_refs_attr(hid_t loc_in, hid_t loc_out, pack_opt_t *options,
trav_table_t *travt, hid_t fidout);
/*-------------------------------------------------------------------------
* Function: do_copy_refobjs
*
* Purpose: duplicate all referenced HDF5 objects in the file
* and create hard links
*
* Return: 0, ok, -1 no
*
* Programmer: Pedro Vicente, pvn@ncsa.uiuc.edu
*
* Date: December, 10, 2003
*
*-------------------------------------------------------------------------
*/
int do_copy_refobjs(hid_t fidin,
hid_t fidout,
trav_table_t *travt,
pack_opt_t *options) /* repack options */
{
hid_t grp_in = (-1); /* read group ID */
hid_t grp_out = (-1); /* write 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 dcpl_id = (-1); /* dataset creation property list ID */
hid_t space_id = (-1); /* space ID */
hid_t ftype_id = (-1); /* file data type ID */
hid_t mtype_id = (-1); /* memory data type ID */
size_t msize; /* memory size of memory type */
hsize_t nelmts; /* number of elements in dataset */
int rank; /* rank of dataset */
hsize_t dims[H5S_MAX_RANK]; /* dimensions of dataset */
unsigned int i, j;
int k;
named_dt_t *named_dt_head=NULL; /* Pointer to the stack of named datatypes
copied */
/*-------------------------------------------------------------------------
* browse
*-------------------------------------------------------------------------
*/
for(i = 0; i < travt->nobjs; i++) {
switch(travt->objs[i].type)
{
/*-------------------------------------------------------------------------
* H5TRAV_TYPE_GROUP
*-------------------------------------------------------------------------
*/
case H5TRAV_TYPE_GROUP:
/*-------------------------------------------------------------------------
* copy referenced objects in attributes
*-------------------------------------------------------------------------
*/
if((grp_out = H5Gopen2(fidout, travt->objs[i].name, H5P_DEFAULT)) < 0)
goto error;
if((grp_in = H5Gopen2(fidin, travt->objs[i].name, H5P_DEFAULT)) < 0)
goto error;
if(copy_refs_attr(grp_in, grp_out, options, travt, fidout) < 0)
goto error;
if(H5Gclose(grp_out) < 0)
goto error;
if(H5Gclose(grp_in) < 0)
goto error;
/*-------------------------------------------------------------------------
* check for hard links
*-------------------------------------------------------------------------
*/
if(travt->objs[i].nlinks)
for(j = 0; j < travt->objs[i].nlinks; j++)
H5Lcreate_hard(fidout, travt->objs[i].name, H5L_SAME_LOC, travt->objs[i].links[j].new_name, H5P_DEFAULT, H5P_DEFAULT);
break;
/*-------------------------------------------------------------------------
* H5TRAV_TYPE_DATASET
*-------------------------------------------------------------------------
*/
case H5TRAV_TYPE_DATASET:
if((dset_in = H5Dopen2(fidin, travt->objs[i].name, H5P_DEFAULT)) < 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(k = 0; k < rank; k++)
nelmts *= dims[k];
if((mtype_id = h5tools_get_native_type(ftype_id)) < 0)
goto error;
if((msize = H5Tget_size(mtype_id)) == 0)
goto error;
/*-------------------------------------------------------------------------
* 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(h5tools_canreadf(NULL, dcpl_id) == 1) {
/*-------------------------------------------------------------------------
* test for a valid output dataset
*-------------------------------------------------------------------------
*/
dset_out = FAIL;
/*-------------------------------------------------------------------------
* object references are a special case
* we cannot just copy the buffers, but instead we recreate the reference
*-------------------------------------------------------------------------
*/
if(H5Tequal(mtype_id, H5T_STD_REF_OBJ)) {
hid_t refobj_id;
hobj_ref_t *refbuf = NULL; /* buffer for object references */
hobj_ref_t *buf = NULL;
const char* refname;
unsigned u;
/*-------------------------------------------------------------------------
* read to memory
*-------------------------------------------------------------------------
*/
if(nelmts) {
buf = (hobj_ref_t *)HDmalloc((unsigned)(nelmts * msize));
if(buf==NULL) {
printf("cannot read into memory\n" );
goto error;
} /* end if */
if(H5Dread(dset_in, mtype_id, H5S_ALL, H5S_ALL, H5P_DEFAULT, buf) < 0)
goto error;
refbuf = (hobj_ref_t*) HDcalloc((unsigned)nelmts, msize);
if(refbuf == NULL){
printf("cannot allocate memory\n" );
goto error;
} /* end if */
for(u = 0; u < nelmts; u++) {
H5E_BEGIN_TRY {
if((refobj_id = H5Rdereference2(dset_in, H5P_DEFAULT, H5R_OBJECT, &buf[u])) < 0)
continue;
} H5E_END_TRY;
/* get the name. a valid name could only occur
* in the second traversal of the file
*/
if((refname = MapIdToName(refobj_id, travt)) != NULL) {
/* create the reference, -1 parameter for objects */
if(H5Rcreate(&refbuf[u], fidout, refname, H5R_OBJECT, -1) < 0)
goto error;
if(options->verbose)
{
printf(FORMAT_OBJ,"dset",travt->objs[i].name );
printf("object <%s> object reference created to <%s>\n",
travt->objs[i].name,
refname);
}
} /*refname*/
H5Oclose(refobj_id);
} /* u */
} /*nelmts*/
/*-------------------------------------------------------------------------
* create/write dataset/close
*-------------------------------------------------------------------------
*/
if((dset_out = H5Dcreate2(fidout, travt->objs[i].name, mtype_id, space_id, H5P_DEFAULT, dcpl_id, H5P_DEFAULT)) < 0)
goto error;
if(nelmts)
if(H5Dwrite(dset_out, mtype_id, H5S_ALL, H5S_ALL, H5P_DEFAULT, refbuf) < 0)
goto error;
if(buf)
HDfree(buf);
if(refbuf)
HDfree(refbuf);
/*------------------------------------------------------
* copy attrs
*----------------------------------------------------*/
if(copy_attr(dset_in, dset_out, &named_dt_head, travt, options) < 0)
goto error;
} /*H5T_STD_REF_OBJ*/
/*-------------------------------------------------------------------------
* dataset region references
*-------------------------------------------------------------------------
*/
else if(H5Tequal(mtype_id, H5T_STD_REF_DSETREG))
{
hid_t refobj_id;
hdset_reg_ref_t *refbuf = NULL; /* input buffer for region references */
hdset_reg_ref_t *buf = NULL; /* output buffer */
const char* refname;
unsigned u;
/*-------------------------------------------------------------------------
* read input to memory
*-------------------------------------------------------------------------
*/
if(nelmts) {
buf = (hdset_reg_ref_t *)HDmalloc((unsigned)(nelmts * msize));
if(buf == NULL) {
printf("cannot read into memory\n");
goto error;
} /* end if */
if(H5Dread(dset_in, mtype_id, H5S_ALL, H5S_ALL, H5P_DEFAULT, buf) < 0)
goto error;
/*-------------------------------------------------------------------------
* create output
*-------------------------------------------------------------------------
*/
refbuf = (hdset_reg_ref_t *)HDcalloc(sizeof(hdset_reg_ref_t), (size_t)nelmts); /*init to zero */
if(refbuf == NULL) {
printf("cannot allocate memory\n");
goto error;
} /* end if */
for(u = 0; u < nelmts; u++) {
H5E_BEGIN_TRY {
if((refobj_id = H5Rdereference2(dset_in, H5P_DEFAULT, H5R_DATASET_REGION, &buf[u])) < 0)
continue;
} H5E_END_TRY;
/* get the name. a valid name could only occur
* in the second traversal of the file
*/
if((refname = MapIdToName(refobj_id, travt)) != NULL) {
hid_t region_id; /* region id of the referenced dataset */
if((region_id = H5Rget_region(dset_in, H5R_DATASET_REGION, &buf[u])) < 0)
goto error;
/* create the reference, we need the space_id */
if(H5Rcreate(&refbuf[u], fidout, refname, H5R_DATASET_REGION, region_id) < 0)
goto error;
if(H5Sclose(region_id) < 0)
goto error;
if(options->verbose)
{
printf(FORMAT_OBJ,"dset",travt->objs[i].name );
printf("object <%s> region reference created to <%s>\n",
travt->objs[i].name,
refname);
}
} /*refname*/
H5Oclose(refobj_id);
} /* u */
} /*nelmts*/
/*-------------------------------------------------------------------------
* create/write dataset/close
*-------------------------------------------------------------------------
*/
if((dset_out = H5Dcreate2(fidout, travt->objs[i].name, mtype_id, space_id, H5P_DEFAULT, dcpl_id, H5P_DEFAULT)) < 0)
goto error;
if(nelmts)
if(H5Dwrite(dset_out, mtype_id, H5S_ALL, H5S_ALL, H5P_DEFAULT, refbuf) < 0)
goto error;
if(buf)
HDfree(buf);
if(refbuf)
HDfree(refbuf);
/*-----------------------------------------------------
* copy attrs
*----------------------------------------------------*/
if(copy_attr(dset_in, dset_out, &named_dt_head, travt, options) < 0)
goto error;
} /* H5T_STD_REF_DSETREG */
/*-------------------------------------------------------------------------
* not references, open previously created object in 1st traversal
*-------------------------------------------------------------------------
*/
else {
if((dset_out = H5Dopen2(fidout, travt->objs[i].name, H5P_DEFAULT)) < 0)
goto error;
} /* end else */
assert(dset_out != FAIL);
/*-------------------------------------------------------------------------
* copy referenced objects in attributes
*-------------------------------------------------------------------------
*/
if(copy_refs_attr(dset_in, dset_out, options, travt, fidout) < 0)
goto error;
/*-------------------------------------------------------------------------
* check for hard links
*-------------------------------------------------------------------------
*/
if(travt->objs[i].nlinks)
for(j = 0; j < travt->objs[i].nlinks; j++)
H5Lcreate_hard(fidout, travt->objs[i].name, H5L_SAME_LOC, travt->objs[i].links[j].new_name, H5P_DEFAULT, H5P_DEFAULT);
if(H5Dclose(dset_out) < 0)
goto error;
} /*can_read*/
/*-------------------------------------------------------------------------
* 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;
/*-------------------------------------------------------------------------
* H5TRAV_TYPE_NAMED_DATATYPE
*-------------------------------------------------------------------------
*/
case H5TRAV_TYPE_NAMED_DATATYPE:
if((type_in = H5Topen2(fidin, travt->objs[i].name, H5P_DEFAULT)) < 0)
goto error;
if(H5Tclose(type_in) < 0)
goto error;
break;
/*-------------------------------------------------------------------------
* H5TRAV_TYPE_LINK
*-------------------------------------------------------------------------
*/
case H5TRAV_TYPE_LINK:
/*nothing to do */
break;
case H5TRAV_TYPE_UNKNOWN:
case H5TRAV_TYPE_UDLINK:
goto error;
default:
break;
} /* end switch */
} /* end for */
/* Finalize (link) the stack of named datatypes (if any)
* This function is paired with copy_named_datatype() which is called
* in copy_attr(), so need to free.
*/
named_datatype_free(&named_dt_head, 0);
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);
named_datatype_free(&named_dt_head, 0);
} H5E_END_TRY;
return -1;
}
/*-------------------------------------------------------------------------
* Function: copy_refs_attr
*
* Purpose: duplicate all referenced HDF5 located in attributes
* relative to LOC_IN, which is obtained either from
* loc_id = H5Gopen2(fid, name, H5P_DEFAULT);
* loc_id = H5Dopen2(fid, name, H5P_DEFAULT);
* loc_id = H5Topen2(fid, name, H5P_DEFAULT);
*
* Return: 0, ok, -1 no
*
* Programmer: Pedro Vicente, pvn@ncsa.uiuc.edu
*
* Date: October, 28, 2003
*
*-------------------------------------------------------------------------
*/
static int copy_refs_attr(hid_t loc_in,
hid_t loc_out,
pack_opt_t *options,
trav_table_t *travt,
hid_t fidout /* for saving references */
)
{
hid_t attr_id = -1; /* attr ID */
hid_t attr_out = -1; /* attr ID */
hid_t space_id = -1; /* space ID */
hid_t ftype_id = -1; /* file data type ID */
hid_t mtype_id = -1; /* memory data type ID */
size_t msize; /* memory size of type */
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];
H5O_info_t oinfo; /* Object info */
int j;
unsigned u;
if(H5Oget_info(loc_in, &oinfo) < 0)
goto error;
for(u = 0; u < (unsigned)oinfo.num_attrs; u++)
{
/*-------------------------------------------------------------------------
* open
*-------------------------------------------------------------------------
*/
/* open attribute */
if((attr_id = H5Aopen_by_idx(loc_in, ".", H5_INDEX_CRT_ORDER, H5_ITER_INC, (hsize_t)u, H5P_DEFAULT, H5P_DEFAULT)) < 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;
/*-------------------------------------------------------------------------
* elements
*-------------------------------------------------------------------------
*/
nelmts = 1;
for(j = 0; j < rank; j++)
nelmts *= dims[j];
if((mtype_id = h5tools_get_native_type(ftype_id)) < 0)
goto error;
if((msize = H5Tget_size(mtype_id)) == 0)
goto error;
/*-------------------------------------------------------------------------
* object references are a special case
* we cannot just copy the buffers, but instead we recreate the reference
*-------------------------------------------------------------------------
*/
if(H5Tequal(mtype_id, H5T_STD_REF_OBJ))
{
hid_t refobj_id;
hobj_ref_t *refbuf = NULL;
unsigned k;
const char* refname;
hobj_ref_t *buf = NULL;
/*-------------------------------------------------------------------------
* read input to memory
*-------------------------------------------------------------------------
*/
if (nelmts)
{
buf = (hobj_ref_t *)HDmalloc((unsigned)(nelmts * msize));
if(buf == NULL)
{
printf("cannot read into memory\n");
goto error;
} /* end if */
if(H5Aread(attr_id, mtype_id, buf) < 0)
goto error;
refbuf = (hobj_ref_t *)HDcalloc((unsigned)nelmts, msize);
if(refbuf == NULL)
{
printf( "cannot allocate memory\n" );
goto error;
} /* end if */
for(k = 0; k < nelmts; k++)
{
H5E_BEGIN_TRY
{
if((refobj_id = H5Rdereference2(attr_id, H5P_DEFAULT, H5R_OBJECT, &buf[k])) < 0)
goto error;
} H5E_END_TRY;
/* get the name. a valid name could only occur in the
* second traversal of the file
*/
if((refname = MapIdToName(refobj_id, travt)) != NULL)
{
/* create the reference */
if(H5Rcreate(&refbuf[k], fidout, refname, H5R_OBJECT, -1) < 0)
goto error;
if(options->verbose)
printf("object <%s> reference created to <%s>\n", name, refname);
}
H5Oclose(refobj_id);
} /* k */
} /*nelmts*/
/*-------------------------------------------------------------------------
* copy
*-------------------------------------------------------------------------
*/
if((attr_out = H5Acreate2(loc_out, name, ftype_id, space_id, H5P_DEFAULT, H5P_DEFAULT)) < 0)
goto error;
if(nelmts)
if(H5Awrite(attr_out, mtype_id, refbuf) < 0)
goto error;
if(H5Aclose(attr_out) < 0)
goto error;
if(refbuf)
HDfree(refbuf);
if(buf)
HDfree(buf);
}/*H5T_STD_REF_OBJ*/
/*-------------------------------------------------------------------------
* dataset region references
*-------------------------------------------------------------------------
*/
else if(H5Tequal(mtype_id, H5T_STD_REF_DSETREG))
{
hid_t refobj_id;
hdset_reg_ref_t *refbuf = NULL; /* input buffer for region references */
hdset_reg_ref_t *buf = NULL; /* output buffer */
const char* refname;
unsigned k;
/*-------------------------------------------------------------------------
* read input to memory
*-------------------------------------------------------------------------
*/
if(nelmts)
{
buf = (hdset_reg_ref_t *)HDmalloc((unsigned)(nelmts * msize));
if(buf == NULL)
{
printf( "cannot read into memory\n" );
goto error;
} /* end if */
if(H5Aread(attr_id, mtype_id, buf) < 0)
goto error;
/*-------------------------------------------------------------------------
* create output
*-------------------------------------------------------------------------
*/
refbuf = (hdset_reg_ref_t *)HDcalloc(sizeof(hdset_reg_ref_t), (size_t)nelmts); /*init to zero */
if(refbuf == NULL)
{
printf( "cannot allocate memory\n" );
goto error;
} /* end if */
for(k = 0; k < nelmts; k++)
{
H5E_BEGIN_TRY
{
if((refobj_id = H5Rdereference2(attr_id, H5P_DEFAULT, H5R_DATASET_REGION, &buf[k])) < 0)
continue;
} H5E_END_TRY;
/* get the name. a valid name could only occur in the
* second traversal of the file
*/
if((refname = MapIdToName(refobj_id, travt)) != NULL)
{
hid_t region_id; /* region id of the referenced dataset */
if((region_id = H5Rget_region(attr_id, H5R_DATASET_REGION, &buf[k])) < 0)
goto error;
/* create the reference, we need the space_id */
if(H5Rcreate(&refbuf[k], fidout, refname, H5R_DATASET_REGION, region_id) < 0)
goto error;
if(H5Sclose(region_id) < 0)
goto error;
if(options->verbose)
printf("object <%s> region reference created to <%s>\n", name, refname);
} /* end if */
H5Oclose(refobj_id);
} /* k */
} /*nelmts */
/*-------------------------------------------------------------------------
* copy
*-------------------------------------------------------------------------
*/
if((attr_out = H5Acreate2(loc_out, name, ftype_id, space_id, H5P_DEFAULT, H5P_DEFAULT)) < 0)
goto error;
if(nelmts)
{
if(H5Awrite(attr_out, mtype_id, refbuf) < 0)
goto error;
}
if(H5Aclose(attr_out) < 0)
goto error;
if(refbuf)
HDfree(refbuf);
if(buf)
HDfree(buf);
} /* H5T_STD_REF_DSETREG */
/*-------------------------------------------------------------------------
* 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);
} H5E_END_TRY;
return -1;
}
/*-------------------------------------------------------------------------
* Function: MapIdToName
*
* Purpose: map a ID from a reference to a dataset name
*
*-------------------------------------------------------------------------
*/
static const char*
MapIdToName(hid_t refobj_id, trav_table_t *travt)
{
unsigned int u;
const char* ret = NULL;
/* linear search */
for(u = 0; u < travt->nobjs; u++) {
if(travt->objs[u].type == H5O_TYPE_DATASET ||
travt->objs[u].type == H5O_TYPE_GROUP ||
travt->objs[u].type == H5O_TYPE_NAMED_DATATYPE) {
H5O_info_t ref_oinfo; /* Stat for the refobj id */
/* obtain information to identify the referenced object uniquely */
if(H5Oget_info(refobj_id, &ref_oinfo) < 0)
goto out;
if(ref_oinfo.addr == travt->objs[u].objno) {
ret = travt->objs[u].name;
goto out;
} /* end if */
} /* end if */
} /* u */
out:
return ret;
}
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