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-rw-r--r--tools/h5repack/h5repack_refs.c720
1 files changed, 0 insertions, 720 deletions
diff --git a/tools/h5repack/h5repack_refs.c b/tools/h5repack/h5repack_refs.c
index 7fce723..e01af2d 100644
--- a/tools/h5repack/h5repack_refs.c
+++ b/tools/h5repack/h5repack_refs.c
@@ -24,728 +24,8 @@ extern char *progname;
static const char* MapIdToName(hid_t refobj_id,
trav_table_t *travt);
-static void close_obj(H5G_obj_t obj_type, hid_t obj_id);
-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 */
- );
-
-/*-------------------------------------------------------------------------
- * 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 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 */
- int next; /* external files */
- int i, j;
-
-/*-------------------------------------------------------------------------
- * browse
- *-------------------------------------------------------------------------
- */
-
- for ( i = 0; i < travt->nobjs; i++)
- {
- switch ( travt->objs[i].type )
- {
- /*-------------------------------------------------------------------------
- * H5G_GROUP
- *-------------------------------------------------------------------------
- */
- case H5G_GROUP:
-
- /*-------------------------------------------------------------------------
- * check for hard links
- *-------------------------------------------------------------------------
- */
-
- if (travt->objs[i].nlinks)
- {
- for ( j=0; j<travt->objs[i].nlinks; j++)
- {
- H5Glink(fidout,
- H5L_TYPE_HARD,
- travt->objs[i].name,
- travt->objs[i].links[j].new_name);
- }
- }
-
- break;
-
- /*-------------------------------------------------------------------------
- * H5G_DATASET
- *-------------------------------------------------------------------------
- */
- case H5G_DATASET:
-
- 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 (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;
-/*-------------------------------------------------------------------------
- * 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((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(wtype_id, H5T_STD_REF_OBJ))
- {
- H5G_obj_t obj_type;
- 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=(void *) HDmalloc((unsigned)(nelmts*msize));
- if ( buf==NULL){
- error_msg(progname, "cannot read into memory\n" );
- goto error;
- }
- if (H5Dread(dset_in,wtype_id,H5S_ALL,H5S_ALL,H5P_DEFAULT,buf)<0)
- goto error;
-
- if ((obj_type = H5Rget_obj_type(dset_in,H5R_OBJECT,buf))<0)
- goto error;
- refbuf=HDmalloc((unsigned)nelmts*msize);
- if ( refbuf==NULL){
- error_msg(progname, "cannot allocate memory\n" );
- goto error;
- }
- for ( u=0; u<nelmts; u++)
- {
- H5E_BEGIN_TRY {
- if ((refobj_id = H5Rdereference(dset_in,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("object <%s> object reference created to <%s>\n",
- travt->objs[i].name,
- refname);
- }/*refname*/
- close_obj(obj_type,refobj_id);
- }/* u */
- }/*nelmts*/
-
- /*-------------------------------------------------------------------------
- * create/write dataset/close
- *-------------------------------------------------------------------------
- */
- if ((dset_out=H5Dcreate(fidout,travt->objs[i].name,wtype_id,space_id,dcpl_id))<0)
- goto error;
- if (nelmts) {
- if (H5Dwrite(dset_out,wtype_id,H5S_ALL,H5S_ALL,H5P_DEFAULT,refbuf)<0)
- goto error;
- }
-
- if (buf)
- free(buf);
- if (refbuf)
- free(refbuf);
-
- }/*H5T_STD_REF_OBJ*/
-
-/*-------------------------------------------------------------------------
- * dataset region references
- *-------------------------------------------------------------------------
- */
- else if (H5Tequal(wtype_id, H5T_STD_REF_DSETREG))
- {
- H5G_obj_t obj_type;
- 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=(void *) HDmalloc((unsigned)(nelmts*msize));
- if ( buf==NULL){
- error_msg(progname, "cannot read into memory\n" );
- goto error;
- }
- if (H5Dread(dset_in,wtype_id,H5S_ALL,H5S_ALL,H5P_DEFAULT,buf)<0)
- goto error;
- if ((obj_type = H5Rget_obj_type(dset_in,H5R_DATASET_REGION,buf))<0)
- goto error;
-
- /*-------------------------------------------------------------------------
- * create output
- *-------------------------------------------------------------------------
- */
-
- refbuf=HDcalloc(sizeof(hdset_reg_ref_t),(size_t)nelmts); /*init to zero */
- if ( refbuf==NULL){
- error_msg(progname, "cannot allocate memory\n" );
- goto error;
- }
- for ( u=0; u<nelmts; u++)
- {
- H5E_BEGIN_TRY {
- if ((refobj_id = H5Rdereference(dset_in,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("object <%s> region reference created to <%s>\n",
- travt->objs[i].name,
- refname);
- }/*refname*/
- close_obj(obj_type,refobj_id);
- }/* u */
- }/*nelmts*/
-
- /*-------------------------------------------------------------------------
- * create/write dataset/close
- *-------------------------------------------------------------------------
- */
- if ((dset_out=H5Dcreate(fidout,travt->objs[i].name,wtype_id,space_id,dcpl_id))<0)
- goto error;
- if (nelmts) {
- if (H5Dwrite(dset_out,wtype_id,H5S_ALL,H5S_ALL,H5P_DEFAULT,refbuf)<0)
- goto error;
- }
-
- if (buf)
- free(buf);
- if (refbuf)
- free(refbuf);
- } /* H5T_STD_REF_DSETREG */
-
-
-/*-------------------------------------------------------------------------
- * not references, open previously created object in 1st traversal
- *-------------------------------------------------------------------------
- */
- else
- {
- if ((dset_out=H5Dopen(fidout,travt->objs[i].name))<0)
- goto error;
- }
-
- 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++){
- H5Glink(fidout,
- H5L_TYPE_HARD,
- travt->objs[i].name,
- travt->objs[i].links[j].new_name);
- }
- }
-
- if (H5Dclose(dset_out)<0)
- goto error;
-
- }/*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 (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 (H5Tclose(type_in)<0)
- goto error;
-
- break;
-
- /*-------------------------------------------------------------------------
- * H5G_LINK
- * H5G_UDLINK
- *-------------------------------------------------------------------------
- */
-
- case H5G_LINK:
- case H5G_UDLINK:
-
- /*nothing to do */
- break;
-
- default:
-
- 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_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;
-
- 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(wtype_id);
- H5Tclose(type_in);
- } 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 = 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
- *
- *-------------------------------------------------------------------------
- */
-
-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; /* attr ID */
- hid_t attr_out; /* attr ID */
- hid_t space_id; /* space ID */
- hid_t ftype_id; /* file type ID */
- hid_t wtype_id; /* 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 */
- 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++)
- {
-
-/*-------------------------------------------------------------------------
- * 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;
-
-
- /*-------------------------------------------------------------------------
- * elements
- *-------------------------------------------------------------------------
- */
- 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
- *-------------------------------------------------------------------------
- */
- if (H5Tequal(wtype_id, H5T_STD_REF_OBJ))
- {
- H5G_obj_t obj_type;
- 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=(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;
-
- if ((obj_type = H5Rget_obj_type(attr_id,H5R_OBJECT,buf))<0)
- goto error;
- refbuf=HDmalloc((unsigned)nelmts*msize);
- if ( refbuf==NULL){
- error_msg(progname, "cannot allocate memory\n" );
- goto error;
- }
- for ( k=0; k<nelmts; k++)
- {
- H5E_BEGIN_TRY {
- if ((refobj_id = H5Rdereference(attr_id,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);
- }
- close_obj(obj_type,refobj_id);
- }/* k */
- }/*nelmts*/
-
- /*-------------------------------------------------------------------------
- * copy
- *-------------------------------------------------------------------------
- */
-
- if ((attr_out=H5Acreate(loc_out,name,ftype_id,space_id,H5P_DEFAULT))<0)
- goto error;
- if (nelmts) {
- if(H5Awrite(attr_out,wtype_id,refbuf)<0)
- goto error;
- }
-
- if (H5Aclose(attr_out)<0)
- goto error;
-
- if (refbuf)
- free(refbuf);
- if (buf)
- free(buf);
-
- }/*H5T_STD_REF_OBJ*/
-
-/*-------------------------------------------------------------------------
- * dataset region references
- *-------------------------------------------------------------------------
- */
- else if (H5Tequal(wtype_id, H5T_STD_REF_DSETREG))
- {
- H5G_obj_t obj_type;
- 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=(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;
- if ((obj_type = H5Rget_obj_type(attr_id,H5R_DATASET_REGION,buf))<0)
- goto error;
-
- /*-------------------------------------------------------------------------
- * create output
- *-------------------------------------------------------------------------
- */
-
- refbuf=HDcalloc(sizeof(hdset_reg_ref_t),(size_t)nelmts); /*init to zero */
- if ( refbuf==NULL){
- error_msg(progname, "cannot allocate memory\n" );
- goto error;
- }
- for ( k=0; k<nelmts; k++)
- {
- H5E_BEGIN_TRY {
- if ((refobj_id = H5Rdereference(attr_id,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);
- }
- close_obj(obj_type,refobj_id);
- }/* k */
- }/*nelmts */
-
- /*-------------------------------------------------------------------------
- * copy
- *-------------------------------------------------------------------------
- */
-
- if ((attr_out=H5Acreate(loc_out,name,ftype_id,space_id,H5P_DEFAULT))<0)
- goto error;
- if (nelmts) {
- if(H5Awrite(attr_out,wtype_id,refbuf)<0)
- goto error;
- }
- if (H5Aclose(attr_out)<0)
- goto error;
- if (refbuf)
- free(refbuf);
- if (buf)
- free(buf);
- } /* H5T_STD_REF_DSETREG */
-
-/*-------------------------------------------------------------------------
- * 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);
- } H5E_END_TRY;
- return -1;
-}
-
-/*-------------------------------------------------------------------------
- * Function: close_obj
- *
- * Purpose: Auxiliary function to close an object
- *
- *-------------------------------------------------------------------------
- */
-
-static void close_obj(H5G_obj_t obj_type, hid_t obj_id)
-{
- H5E_BEGIN_TRY
- {
- switch (obj_type)
- {
- case H5G_GROUP:
- H5Gclose(obj_id);
- break;
- case H5G_DATASET:
- H5Dclose(obj_id);
- break;
- case H5G_TYPE:
- H5Tclose(obj_id);
- break;
- default:
- break;
- }
- } H5E_END_TRY;
-}
/*-------------------------------------------------------------------------
* Function: MapIdToName