mirror of
https://github.com/HDFGroup/hdf5.git
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[svn-r9436] Purpose:
bug fix Description: Description: one case was not handled in the combination of input options (layout and filters) Solution: redo the algorythm that handles all cases Solution: Platforms tested: linux Misc. update:
This commit is contained in:
Pedro Vicente Nunes
parent
a4c0ed0374
commit
8ef059b4f7
1
MANIFEST
1
MANIFEST
@ -1156,7 +1156,6 @@
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./tools/h5repack/h5repack.h
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./tools/h5repack/h5repack_copy.c
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./tools/h5repack/h5repack_filters.c
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./tools/h5repack/h5repack_layout.c
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./tools/h5repack/h5repack_list.c
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./tools/h5repack/h5repack_main.c
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./tools/h5repack/h5repack_opttable.c
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@ -52,10 +52,10 @@ DISTCLEAN=h5repack.sh
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## Source and object files for programs...
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##
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PROG_SRC=h5repack.c h5repack_copy.c h5repack_filters.c h5repack_refs.c h5repack_layout.c h5repack_list.c h5repack_main.c h5repack_opttable.c h5repack_parse.c h5repack_verify.c testh5repack_attr.c testh5repack_dset.c testh5repack_main.c testh5repack_make.c testh5repack_util.c
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PROG_SRC=h5repack.c h5repack_copy.c h5repack_filters.c h5repack_refs.c h5repack_list.c h5repack_main.c h5repack_opttable.c h5repack_parse.c h5repack_verify.c testh5repack_attr.c testh5repack_dset.c testh5repack_main.c testh5repack_make.c testh5repack_util.c
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PROG_OBJ=$(PROG_SRC:.c=.lo)
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OBJS=h5repack.lo h5repack_filters.lo h5repack_copy.lo h5repack_refs.lo h5repack_layout.lo h5repack_list.lo h5repack_main.lo h5repack_opttable.lo h5repack_parse.lo h5repack_verify.lo
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TEST_OBJS=h5repack.lo h5repack_filters.lo h5repack_copy.lo h5repack_refs.lo h5repack_layout.lo h5repack_list.lo h5repack_opttable.lo h5repack_parse.lo h5repack_verify.lo testh5repack_attr.lo testh5repack_dset.lo testh5repack_main.lo testh5repack_make.lo testh5repack_util.lo
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OBJS=h5repack.lo h5repack_filters.lo h5repack_copy.lo h5repack_refs.lo h5repack_list.lo h5repack_main.lo h5repack_opttable.lo h5repack_parse.lo h5repack_verify.lo
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TEST_OBJS=h5repack.lo h5repack_filters.lo h5repack_copy.lo h5repack_refs.lo h5repack_list.lo h5repack_opttable.lo h5repack_parse.lo h5repack_verify.lo testh5repack_attr.lo testh5repack_dset.lo testh5repack_main.lo testh5repack_make.lo testh5repack_util.lo
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PRIVATE_HDR=
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@ -179,18 +179,12 @@ int print_filters(hid_t dcpl_id);
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*-------------------------------------------------------------------------
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*/
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int filter_this(const char* name,
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pack_opt_t *options,
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pack_info_t *pack); /* info about object to filter */
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int apply_filters(const char* name, /* object name from traverse list */
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int rank, /* rank of dataset */
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hsize_t *dims, /* dimensions of dataset */
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hid_t dcpl_id, /* dataset creation property list */
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hid_t type_id, /* datatype */
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pack_opt_t *options, /* repack options */
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int has_layout, /* input chunk */
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pack_info_t *obj); /* info about object to filter */
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pack_opt_t *options); /* repack options */
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int has_filter(hid_t dcpl_id,
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H5Z_filter_t filtnin);
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@ -259,7 +259,6 @@ int do_copy_objects(hid_t fidin,
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#endif /* LATER */
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int i, j;
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int wrote=0;
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int has_layout;
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/*-------------------------------------------------------------------------
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* copy the suppplied object list
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@ -270,7 +269,6 @@ int do_copy_objects(hid_t fidin,
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{
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buf=NULL;
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has_layout=0;
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switch ( travt->objs[i].type )
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{
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/*-------------------------------------------------------------------------
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@ -359,9 +357,6 @@ int do_copy_objects(hid_t fidin,
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*/
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if ( (H5T_REFERENCE!=H5Tget_class(mtype_id)))
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{
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/* the information about the object to be filtered/"layouted" */
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pack_info_t obj;
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init_packobject(&obj);
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/* get the storage size of the input dataset */
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dsize_in=H5Dget_storage_size(dset_in);
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@ -379,24 +374,12 @@ int do_copy_objects(hid_t fidin,
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}
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if (H5Dread(dset_in,mtype_id,H5S_ALL,H5S_ALL,H5P_DEFAULT,buf)<0)
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goto error;
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/*-------------------------------------------------------------------------
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* apply the layout; check first if the object is to be modified.
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*-------------------------------------------------------------------------
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*/
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if (layout_this(dcpl_id,travt->objs[i].name,options,&obj))
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{
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obj.chunk.rank=rank;
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if (apply_layout(dcpl_id,&obj)<0)
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goto error;
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has_layout=1;
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}
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/*-------------------------------------------------------------------------
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* apply the filter; check if the object is to be filtered.
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* apply the filter
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*-------------------------------------------------------------------------
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*/
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if (apply_filters(travt->objs[i].name,rank,dims,dcpl_id,mtype_id,options,has_layout,&obj)<0)
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if (apply_filters(travt->objs[i].name,rank,dims,dcpl_id,mtype_id,options)<0)
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goto error;
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}/*nelmts*/
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@ -18,79 +18,160 @@
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/*-------------------------------------------------------------------------
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* Function: aux_objinsert_filter
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* Function: aux_find_obj
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*
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* Purpose: auxiliary function, inserts the filter in object OBJ
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*
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* Return: void
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* Purpose: find the object name NAME (got from the traverse list)
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* in the repack options list
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*
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*-------------------------------------------------------------------------
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*/
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static void aux_objinsert_filter(pack_info_t *obj,
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filter_info_t filt)
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static
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int aux_find_obj(const char* name, /* object name from traverse list */
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pack_opt_t *options, /* repack options */
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pack_info_t *obj /*OUT*/) /* info about object to filter */
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{
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obj->nfilters=1;
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obj->filter[0]=filt;
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char *pdest;
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int result;
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int i;
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for ( i=0; i<options->op_tbl->nelems; i++)
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{
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if (strcmp(options->op_tbl->objs[i].path,name)==0)
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{
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*obj = options->op_tbl->objs[i];
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return i;
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}
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pdest = strstr(name,options->op_tbl->objs[i].path);
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result = (int)(pdest - name);
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/* found at position 1, meaning without '/' */
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if( pdest != NULL && result==1 )
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{
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*obj = options->op_tbl->objs[i];
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return i;
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}
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}/*i*/
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return -1;
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}
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/*-------------------------------------------------------------------------
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* Function: filter_this
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* Function: aux_assign_obj
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*
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* Purpose: find the object name NAME (got from the traverse list)
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* in the repack options list; assign the filter information OBJ
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*
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* Return: 0 not found, 1 found
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*
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* Programmer: Pedro Vicente, pvn@ncsa.uiuc.edu
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*
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* Date: December 19, 2003
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*
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*-------------------------------------------------------------------------
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*/
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int filter_this(const char* name, /* object name from traverse list */
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pack_opt_t *options, /* repack options */
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pack_info_t *obj /*OUT*/) /* info about object to filter */
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static
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int aux_assign_obj(const char* name, /* object name from traverse list */
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pack_opt_t *options, /* repack options */
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pack_info_t *obj /*OUT*/) /* info about object to filter */
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{
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char *pdest;
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int result;
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int i, j;
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int index, i;
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pack_info_t tmp;
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init_packobject(&tmp);
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index = aux_find_obj(name,options,&tmp);
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/* name was on input */
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if (index>=0)
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{
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/* applying to all objects */
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if (options->all_layout)
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{
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/* assign the global layout info to the OBJ info */
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tmp.layout=options->layout_g;
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switch (options->layout_g)
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{
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case H5D_CHUNKED:
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tmp.chunk.rank=options->chunk_g.rank;
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for ( i=0; i<tmp.chunk.rank; i++)
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tmp.chunk.chunk_lengths[i]=options->chunk_g.chunk_lengths[i];
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break;
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default:
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break;
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}/*switch*/
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}
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else
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{
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tmp.layout = options->op_tbl->objs[index].layout;
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switch (tmp.layout)
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{
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case H5D_CHUNKED:
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tmp.chunk.rank = options->op_tbl->objs[index].chunk.rank;
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for ( i=0; i<tmp.chunk.rank; i++)
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tmp.chunk.chunk_lengths[i]=options->op_tbl->objs[index].chunk.chunk_lengths[i];
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break;
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default:
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break;
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}/*switch*/
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}
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/* applying to all objects */
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if (options->all_filter)
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{
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/* assign the global filter */
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tmp.nfilters=1;
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tmp.filter[0]=options->filter_g;
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} /* if all */
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else
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{
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tmp.nfilters=options->op_tbl->objs[index].nfilters;
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for ( i=0; i<tmp.nfilters; i++)
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{
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tmp.filter[i] = options->op_tbl->objs[index].filter[i];
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}
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}
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} /* if index */
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/* no input name */
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else
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{
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if (options->all_filter)
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{
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/* assign the global filter */
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tmp.nfilters=1;
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tmp.filter[0]=options->filter_g;
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}
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if (options->all_layout)
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{
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/* assign the global layout info to the OBJ info */
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tmp.layout=options->layout_g;
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switch (options->layout_g)
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{
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case H5D_CHUNKED:
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tmp.chunk.rank=options->chunk_g.rank;
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for ( i=0; i<tmp.chunk.rank; i++)
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tmp.chunk.chunk_lengths[i]=options->chunk_g.chunk_lengths[i];
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break;
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default:
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break;
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}/*switch*/
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}
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}
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/* if we are applying to all objects just return true */
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if (options->all_filter)
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{
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/* assign the global filter and chunk info to the OBJ info */
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aux_objinsert_filter( obj, options->filter_g );
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obj->chunk=options->chunk_g;
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return 1;
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}
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for ( i=0; i<options->op_tbl->nelems; i++)
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{
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for ( j=0; j<options->op_tbl->objs[i].nfilters; j++)
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{
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if (options->op_tbl->objs[i].filter[j].filtn != -1 )
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{
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if (strcmp(options->op_tbl->objs[i].path,name)==0)
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{
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*obj=options->op_tbl->objs[i];
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return 1;
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}
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pdest = strstr(name,options->op_tbl->objs[i].path);
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result = (int)(pdest - name);
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/* found at position 1, meaning without '/' */
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if( pdest != NULL && result==1 )
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{
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*obj=options->op_tbl->objs[i];
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return 1;
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}
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} /*if*/
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}/*j*/
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}/*i*/
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return 0;
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*obj = tmp;
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return 1;
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}
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@ -115,37 +196,31 @@ int apply_filters(const char* name, /* object name from traverse list */
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hsize_t *dims, /* dimensions of dataset */
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hid_t dcpl_id, /* dataset creation property list */
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hid_t type_id, /* dataset datatype */
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pack_opt_t *options, /* repack options */
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int has_layout, /* input chunk */
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pack_info_t *obj) /* info about object to filter */
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{
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int nfilters; /* number of filters in DCPL */
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pack_opt_t *options) /* repack options */
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{
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int nfilters; /* number of filters in DCPL */
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unsigned aggression; /* the deflate level */
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hsize_t nelmts; /* number of elements in dataset */
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size_t size; /* size of datatype in bytes */
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int i;
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/* check first if the object is to be filtered */
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if (filter_this(name,options,obj)==0)
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return 0;
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pack_info_t obj;
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if (rank==0)
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goto out;
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/*-------------------------------------------------------------------------
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* filters require CHUNK layout; if we do not have one define a default
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* initialize the assigment object
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*-------------------------------------------------------------------------
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*/
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if (has_layout)
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{
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layout_this(dcpl_id,name,options,obj);
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}
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else
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{
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obj->chunk.rank=rank;
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for (i=0; i<rank; i++)
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obj->chunk.chunk_lengths[i] = dims[i];
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}
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init_packobject(&obj);
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/*-------------------------------------------------------------------------
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* find options
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*-------------------------------------------------------------------------
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*/
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if (aux_assign_obj(name,options,&obj)==0)
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return 0;
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/* check for datasets too small */
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@ -175,8 +250,6 @@ int apply_filters(const char* name, /* object name from traverse list */
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return -1;
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}
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/*-------------------------------------------------------------------------
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* the type of filter and additional parameter
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* type can be one of the filters
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@ -187,9 +260,24 @@ int apply_filters(const char* name, /* object name from traverse list */
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* H5Z_FILTER_SZIP 4 , szip compression
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*-------------------------------------------------------------------------
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*/
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for ( i=0; i<obj->nfilters; i++)
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if (obj.nfilters)
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{
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/*-------------------------------------------------------------------------
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* filters require CHUNK layout; if we do not have one define a default
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*-------------------------------------------------------------------------
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*/
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if (obj.layout==-1)
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{
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obj.chunk.rank=rank;
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for (i=0; i<rank; i++)
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obj.chunk.chunk_lengths[i] = dims[i];
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}
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for ( i=0; i<obj.nfilters; i++)
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{
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switch (obj->filter[i].filtn)
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switch (obj.filter[i].filtn)
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{
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default:
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break;
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@ -199,9 +287,9 @@ int apply_filters(const char* name, /* object name from traverse list */
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*-------------------------------------------------------------------------
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*/
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case H5Z_FILTER_DEFLATE:
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aggression=obj->filter[i].cd_values[0];
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aggression=obj.filter[i].cd_values[0];
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/* set up for deflated data */
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if(H5Pset_chunk(dcpl_id, obj->chunk.rank, obj->chunk.chunk_lengths)<0)
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if(H5Pset_chunk(dcpl_id, obj.chunk.rank, obj.chunk.chunk_lengths)<0)
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return -1;
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if(H5Pset_deflate(dcpl_id,aggression)<0)
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return -1;
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@ -216,14 +304,14 @@ int apply_filters(const char* name, /* object name from traverse list */
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unsigned options_mask;
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unsigned pixels_per_block;
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pixels_per_block=obj->filter[i].cd_values[0];
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if (obj->filter[i].szip_coding==0)
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pixels_per_block=obj.filter[i].cd_values[0];
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if (obj.filter[i].szip_coding==0)
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options_mask=H5_SZIP_NN_OPTION_MASK;
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else
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options_mask=H5_SZIP_EC_OPTION_MASK;
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/* set up for szip data */
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if(H5Pset_chunk(dcpl_id,obj->chunk.rank,obj->chunk.chunk_lengths)<0)
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if(H5Pset_chunk(dcpl_id,obj.chunk.rank,obj.chunk.chunk_lengths)<0)
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return -1;
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if (H5Pset_szip(dcpl_id,options_mask,pixels_per_block)<0)
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return -1;
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@ -236,7 +324,7 @@ int apply_filters(const char* name, /* object name from traverse list */
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*-------------------------------------------------------------------------
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*/
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case H5Z_FILTER_SHUFFLE:
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if(H5Pset_chunk(dcpl_id, obj->chunk.rank, obj->chunk.chunk_lengths)<0)
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if(H5Pset_chunk(dcpl_id, obj.chunk.rank, obj.chunk.chunk_lengths)<0)
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return -1;
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if (H5Pset_shuffle(dcpl_id)<0)
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return -1;
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@ -247,7 +335,7 @@ int apply_filters(const char* name, /* object name from traverse list */
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*-------------------------------------------------------------------------
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*/
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case H5Z_FILTER_FLETCHER32:
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if(H5Pset_chunk(dcpl_id, obj->chunk.rank, obj->chunk.chunk_lengths)<0)
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if(H5Pset_chunk(dcpl_id, obj.chunk.rank, obj.chunk.chunk_lengths)<0)
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return -1;
|
||||
if (H5Pset_fletcher32(dcpl_id)<0)
|
||||
return -1;
|
||||
@ -255,6 +343,32 @@ int apply_filters(const char* name, /* object name from traverse list */
|
||||
} /* switch */
|
||||
}/*i*/
|
||||
|
||||
}
|
||||
/*obj.nfilters*/
|
||||
else
|
||||
{
|
||||
/* just apply layout */
|
||||
|
||||
/* no layout info was found, define the default */
|
||||
if (obj.layout==-1)
|
||||
obj.layout = H5D_CONTIGUOUS;
|
||||
|
||||
|
||||
if (H5Pset_layout(dcpl_id, obj.layout)<0)
|
||||
return -1;
|
||||
|
||||
if (H5D_CHUNKED==obj.layout) { /* set up chunk */
|
||||
if(H5Pset_chunk(dcpl_id, obj.chunk.rank, obj.chunk.chunk_lengths)<0)
|
||||
return -1;
|
||||
}
|
||||
else if (H5D_COMPACT==obj.layout) {
|
||||
if (H5Pset_alloc_time(dcpl_id, H5D_ALLOC_TIME_EARLY)<0)
|
||||
return -1;
|
||||
}
|
||||
|
||||
|
||||
}
|
||||
|
||||
return 0;
|
||||
|
||||
out:
|
||||
@ -264,6 +378,7 @@ out:
|
||||
}
|
||||
|
||||
|
||||
|
||||
/*-------------------------------------------------------------------------
|
||||
* Function: print_filters
|
||||
*
|
||||
@ -271,10 +386,6 @@ out:
|
||||
*
|
||||
* Return: 0, ok, -1 no
|
||||
*
|
||||
* Programmer: Pedro Vicente, pvn@ncsa.uiuc.edu
|
||||
*
|
||||
* Date: December 19, 2003
|
||||
*
|
||||
*-------------------------------------------------------------------------
|
||||
*/
|
||||
|
||||
|
||||
@ -1,175 +0,0 @@
|
||||
/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
|
||||
* 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 "hdf5.h"
|
||||
#include "h5test.h"
|
||||
#include "h5repack.h"
|
||||
|
||||
|
||||
static void CANNOT_LAYOUT(pack_opt_t *options)
|
||||
{
|
||||
if (options->verbose)
|
||||
printf("Warning: This layout cannot be applied, this object\
|
||||
requires chunked layout\n");
|
||||
}
|
||||
|
||||
|
||||
|
||||
/*-------------------------------------------------------------------------
|
||||
* Function: layout_this
|
||||
*
|
||||
* Purpose: check if the layout can be applied;
|
||||
* find the object name NAME (got from the traverse list)
|
||||
* in the repack options list; assign the layout information OBJ
|
||||
*
|
||||
* Return: 0 cannot apply, 1 can, -1 error
|
||||
*
|
||||
* Programmer: Pedro Vicente, pvn@ncsa.uiuc.edu
|
||||
*
|
||||
* Date: December 30, 2003
|
||||
*
|
||||
*-------------------------------------------------------------------------
|
||||
*/
|
||||
|
||||
int layout_this(hid_t dcpl_id, /* DCPL from input object */
|
||||
const char* name, /* object name from traverse list */
|
||||
pack_opt_t *options, /* repack options */
|
||||
pack_info_t *pack /*OUT*/) /* object to apply layout */
|
||||
{
|
||||
int nfilters; /* number of filters in the input object */
|
||||
H5D_layout_t layout; /* layout */
|
||||
char *pdest;
|
||||
int result;
|
||||
int i, ret=1;
|
||||
|
||||
/* check if we have filters in the input object */
|
||||
if ((nfilters = H5Pget_nfilters(dcpl_id))<0)
|
||||
return -1;
|
||||
|
||||
/* applying to all objects */
|
||||
if (options->all_layout)
|
||||
{
|
||||
/* assign the global layout info to the OBJ info */
|
||||
pack->layout=options->layout_g;
|
||||
|
||||
switch (options->layout_g)
|
||||
{
|
||||
case H5D_CHUNKED:
|
||||
pack->chunk.rank=options->chunk_g.rank;
|
||||
for ( i=0; i<pack->chunk.rank; i++)
|
||||
pack->chunk.chunk_lengths[i]=options->chunk_g.chunk_lengths[i];
|
||||
break;
|
||||
|
||||
case H5D_CONTIGUOUS:
|
||||
case H5D_COMPACT:
|
||||
if (nfilters)
|
||||
{
|
||||
CANNOT_LAYOUT(options);
|
||||
ret=0;
|
||||
}
|
||||
break;
|
||||
|
||||
default:
|
||||
ret=0;
|
||||
break;
|
||||
}/*switch*/
|
||||
return ret;
|
||||
}
|
||||
|
||||
/* find the object */
|
||||
for ( i=0; i<options->op_tbl->nelems; i++)
|
||||
{
|
||||
layout=options->op_tbl->objs[i].layout;
|
||||
if ( layout != -1 )
|
||||
{
|
||||
if (strcmp(options->op_tbl->objs[i].path,name)==0)
|
||||
{
|
||||
if (nfilters && layout!=H5D_CHUNKED)
|
||||
{
|
||||
CANNOT_LAYOUT(options);
|
||||
return 0;
|
||||
}
|
||||
else
|
||||
{
|
||||
*pack=options->op_tbl->objs[i];
|
||||
return 1;
|
||||
}
|
||||
}
|
||||
|
||||
pdest = strstr(name,options->op_tbl->objs[i].path);
|
||||
result = (int)(pdest - name);
|
||||
|
||||
/* found at position 1, meaning without '/' */
|
||||
if( pdest != NULL && result==1 )
|
||||
{
|
||||
if (nfilters && layout!=H5D_CHUNKED)
|
||||
{
|
||||
CANNOT_LAYOUT(options);
|
||||
return 0;
|
||||
}
|
||||
else
|
||||
{
|
||||
*pack=options->op_tbl->objs[i];
|
||||
return 1;
|
||||
}
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
return 0;
|
||||
}
|
||||
/*-------------------------------------------------------------------------
|
||||
* Function: apply_layout
|
||||
*
|
||||
* Purpose: apply a layout to the property list. Valid values for layout are:
|
||||
*
|
||||
* H5D_COMPACT
|
||||
* Store raw data in the dataset object header in file.
|
||||
* This should only be used for very small amounts of raw data.
|
||||
* H5D_CONTIGUOUS
|
||||
* Store raw data separately from the object header in one large chunk
|
||||
* in the file.
|
||||
* H5D_CHUNKED
|
||||
* Store raw data separately from the object header as chunks of data in
|
||||
* separate locations in the file.
|
||||
*
|
||||
* Return: 0, ok, -1 no
|
||||
*
|
||||
* Programmer: Pedro Vicente, pvn@ncsa.uiuc.edu
|
||||
*
|
||||
* Date: December 30, 2003
|
||||
*
|
||||
*-------------------------------------------------------------------------
|
||||
*/
|
||||
|
||||
int apply_layout(hid_t dcpl_id,
|
||||
pack_info_t *obj) /* info about object */
|
||||
{
|
||||
|
||||
|
||||
if (H5Pset_layout(dcpl_id, obj->layout)<0)
|
||||
return -1;
|
||||
|
||||
if (H5D_CHUNKED==obj->layout) { /* set up chunk */
|
||||
if(H5Pset_chunk(dcpl_id, obj->chunk.rank, obj->chunk.chunk_lengths)<0)
|
||||
return -1;
|
||||
}
|
||||
else if (H5D_COMPACT==obj->layout) {
|
||||
if (H5Pset_alloc_time(dcpl_id, H5D_ALLOC_TIME_EARLY)<0)
|
||||
return -1;
|
||||
}
|
||||
|
||||
return 0;
|
||||
}
|
||||
|
||||
Loading…
x
Reference in New Issue
Block a user