diff options
Diffstat (limited to 'tools/h5repack/h5repack_copy.c')
| -rw-r--r-- | tools/h5repack/h5repack_copy.c | 1067 |
1 files changed, 524 insertions, 543 deletions
diff --git a/tools/h5repack/h5repack_copy.c b/tools/h5repack/h5repack_copy.c index e9a89e2..f32d15d 100644 --- a/tools/h5repack/h5repack_copy.c +++ b/tools/h5repack/h5repack_copy.c @@ -281,566 +281,547 @@ int do_copy_objects(hid_t fidin, trav_table_t *travt, pack_opt_t *options) /* repack options */ { - hid_t grp_in=-1; /* group ID */ - hid_t grp_out=-1; /* group ID */ - hid_t dset_in=-1; /* read dataset ID */ - hid_t dset_out=-1; /* write dataset ID */ - hid_t gcpl_id=-1; /* group creation property list */ - hid_t type_in=-1; /* named type ID */ - hid_t type_out=-1; /* named type ID */ - hid_t dcpl_id=-1; /* dataset creation property list ID */ - hid_t dcpl_out=-1; /* dataset creation property list ID */ - hid_t f_space_id=-1; /* file 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 */ - hsize_t dsize_in; /* input dataset size before filter */ - hsize_t dsize_out; /* output dataset size after filter */ - int apply_s; /* flag for apply filter to small dataset sizes */ - int apply_f; /* flag for apply filter to return error on H5Dcreate */ - double per; /* percent utilization of storage */ - void *buf=NULL; /* buffer for raw data */ - void *sm_buf=NULL; /* buffer for raw data */ - int has_filter; /* current object has a filter */ - unsigned i; - int is_ref=0; + hid_t grp_in=-1; /* group ID */ + hid_t grp_out=-1; /* group ID */ + hid_t dset_in=-1; /* read dataset ID */ + hid_t dset_out=-1; /* write dataset ID */ + hid_t gcpl_id=-1; /* group creation property list */ + hid_t type_in=-1; /* named type ID */ + hid_t type_out=-1; /* named type ID */ + hid_t dcpl_id=-1; /* dataset creation property list ID */ + hid_t dcpl_out=-1; /* dataset creation property list ID */ + hid_t f_space_id=-1; /* file 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 */ + hsize_t dsize_in; /* input dataset size before filter */ + hsize_t dsize_out; /* output dataset size after filter */ + int apply_s; /* flag for apply filter to small dataset sizes */ + int apply_f; /* flag for apply filter to return error on H5Dcreate */ + double per; /* percent utilization of storage */ + void *buf=NULL; /* buffer for raw data */ + void *sm_buf=NULL; /* buffer for raw data */ + int has_filter; /* current object has a filter */ + unsigned i; + int is_ref=0; -/*------------------------------------------------------------------------- - * copy the suppplied object list - *------------------------------------------------------------------------- - */ - - if (options->verbose) { - printf("-----------------------------------------\n"); - printf(" Type Filter (Ratio) Name\n"); - printf("-----------------------------------------\n"); - } - - for ( i = 0; i < travt->nobjs; i++) - { - - buf = NULL; - - switch ( travt->objs[i].type ) - { -/*------------------------------------------------------------------------- - * H5G_GROUP - *------------------------------------------------------------------------- - */ - case H5G_GROUP: - if (options->verbose) - printf(FORMAT_OBJ,"group",travt->objs[i].name ); - - if (options->grp_compact>0 || options->grp_indexed>0) { - /* Set up group creation property list */ - if((gcpl_id = H5Pcreate(H5P_GROUP_CREATE)) < 0) - goto error; - - if(H5Pset_link_phase_change(gcpl_id, (unsigned)options->grp_compact, (unsigned)options->grp_indexed) < 0) - goto error; - - if((grp_out = H5Gcreate2(fidout, travt->objs[i].name, H5P_DEFAULT, gcpl_id, H5P_DEFAULT)) < 0) - goto error; - } - else { - if((grp_out = H5Gcreate2(fidout, travt->objs[i].name, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT)) < 0) - goto error; - } - - if((grp_in = H5Gopen (fidin,travt->objs[i].name))<0) - goto error; - - /*------------------------------------------------------------------------- - * copy attrs + /*------------------------------------------------------------------------- + * copy the suppplied object list *------------------------------------------------------------------------- */ - if (copy_attr(grp_in,grp_out,options)<0) - goto error; - if (gcpl_id>0) { - if (H5Pclose(gcpl_id)<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("-----------------------------------------\n"); + printf(" Type Filter (Ratio) Name\n"); + printf("-----------------------------------------\n"); + } - has_filter = 0; + for ( i = 0; i < travt->nobjs; i++) { + + buf = NULL; + switch ( travt->objs[i].type ) { + /*------------------------------------------------------------------------- + * H5G_GROUP + *------------------------------------------------------------------------- + */ + case H5G_GROUP: + if (options->verbose) + printf(FORMAT_OBJ,"group",travt->objs[i].name ); + + if (options->grp_compact>0 || options->grp_indexed>0) { + /* Set up group creation property list */ + if((gcpl_id = H5Pcreate(H5P_GROUP_CREATE)) < 0) + goto error; + + if(H5Pset_link_phase_change(gcpl_id, (unsigned)options->grp_compact, (unsigned)options->grp_indexed) < 0) + goto error; + + if((grp_out = H5Gcreate2(fidout, travt->objs[i].name, H5P_DEFAULT, gcpl_id, H5P_DEFAULT)) < 0) + goto error; + } + else { + if((grp_out = H5Gcreate2(fidout, travt->objs[i].name, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT)) < 0) + goto error; + } + + if((grp_in = H5Gopen2(fidin, travt->objs[i].name, H5P_DEFAULT)) < 0) + goto error; + + /*------------------------------------------------------------------------- + * copy attrs + *------------------------------------------------------------------------- + */ + if (copy_attr(grp_in,grp_out,options)<0) + goto error; + + if (gcpl_id>0) { + if (H5Pclose(gcpl_id)<0) + goto error; + } + if (H5Gclose(grp_out)<0) + goto error; + if (H5Gclose(grp_in)<0) + goto error; + + break; + + /*------------------------------------------------------------------------- + * H5G_DATASET + *------------------------------------------------------------------------- + */ + case H5G_DATASET: + + has_filter = 0; + + /* early detection of references */ + if ((dset_in=H5Dopen(fidin,travt->objs[i].name))<0) + goto error; + if ((ftype_id=H5Dget_type (dset_in))<0) + goto error; + if (H5T_REFERENCE==H5Tget_class(ftype_id)) + is_ref=1; + if (H5Tclose(ftype_id)<0) + goto error; + if (H5Dclose(dset_in)<0) + goto error; + + + /*------------------------------------------------------------------------- + * check if we should use H5Ocopy or not + * if there is a request for filters/layout, we read/write the object + * otherwise we do a copy using H5Ocopy + *------------------------------------------------------------------------- + */ + if (options->op_tbl->nelems + || + options->all_filter==1 || options->all_layout==1 + || is_ref + ) + { + int j; + + if ((dset_in=H5Dopen(fidin,travt->objs[i].name))<0) + goto error; + if ((f_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 ((dcpl_out = H5Pcopy (dcpl_id))<0) + goto error; + if ( (rank=H5Sget_simple_extent_ndims(f_space_id))<0) + goto error; + HDmemset(dims, 0, sizeof dims); + if ( H5Sget_simple_extent_dims(f_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 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((travt->objs[i].name),dcpl_id)==1) + { + apply_s=1; + apply_f=1; + + /*------------------------------------------------------------------------- + * references are a special case + * we cannot just copy the buffers, but instead we recreate the reference + * in a second traversal of the output file + *------------------------------------------------------------------------- + */ + if (H5T_REFERENCE!=H5Tget_class(wtype_id)) + { + /* get the storage size of the input dataset */ + dsize_in=H5Dget_storage_size(dset_in); + + /* check for datasets too small */ + if (nelmts*msize < options->threshold ) + apply_s=0; + + /* apply the filter */ + if (apply_s) { + if (apply_filters(travt->objs[i].name,rank,dims,dcpl_out,options,&has_filter)<0) + goto error; + } + + /*------------------------------------------------------------------------- + * create the output dataset; + * disable error checking in case the dataset cannot be created with the + * modified dcpl; in that case use the original instead + *------------------------------------------------------------------------- + */ + H5E_BEGIN_TRY { + dset_out=H5Dcreate(fidout,travt->objs[i].name,wtype_id,f_space_id,dcpl_out); + } H5E_END_TRY; + if (dset_out==FAIL) + { + if ((dset_out=H5Dcreate(fidout,travt->objs[i].name,wtype_id,f_space_id,dcpl_id))<0) + goto error; + apply_f=0; + } + + /*------------------------------------------------------------------------- + * read/write + *------------------------------------------------------------------------- + */ + if (nelmts) + { + size_t need = (size_t)(nelmts*msize); /* bytes needed */ + if ( need < H5TOOLS_MALLOCSIZE ) + buf = HDmalloc(need); + + if (buf != NULL ) + { + if (H5Dread(dset_in,wtype_id,H5S_ALL,H5S_ALL,H5P_DEFAULT,buf)<0) + goto error; + if (H5Dwrite(dset_out,wtype_id,H5S_ALL,H5S_ALL,H5P_DEFAULT,buf)<0) + goto error; + } + + else /* possibly not enough memory, read/write by hyperslabs */ + { + size_t p_type_nbytes = msize; /*size of memory type */ + hsize_t p_nelmts = nelmts; /*total selected elmts */ + hsize_t elmtno; /*counter */ + int carry; /*counter carry value */ + unsigned int vl_data = 0; /*contains VL datatypes */ + + /* stripmine info */ + hsize_t sm_size[H5S_MAX_RANK]; /*stripmine size */ + hsize_t sm_nbytes; /*bytes per stripmine */ + hsize_t sm_nelmts; /*elements per stripmine*/ + hid_t sm_space; /*stripmine data space */ + + /* hyperslab info */ + hsize_t hs_offset[H5S_MAX_RANK];/*starting offset */ + hsize_t hs_size[H5S_MAX_RANK]; /*size this pass */ + hsize_t hs_nelmts; /*elements in request */ + hsize_t zero[8]; /*vector of zeros */ + int k; + + /* check if we have VL data in the dataset's datatype */ + if (H5Tdetect_class(wtype_id, H5T_VLEN) == TRUE) + vl_data = TRUE; + + /* + * determine the strip mine size and allocate a buffer. The strip mine is + * a hyperslab whose size is manageable. + */ + sm_nbytes = p_type_nbytes; + + for (k = rank; k > 0; --k) { + sm_size[k - 1] = MIN(dims[k - 1], H5TOOLS_BUFSIZE / sm_nbytes); + sm_nbytes *= sm_size[k - 1]; + assert(sm_nbytes > 0); + } + sm_buf = HDmalloc((size_t)sm_nbytes); + + sm_nelmts = sm_nbytes / p_type_nbytes; + sm_space = H5Screate_simple(1, &sm_nelmts, NULL); + + /* the stripmine loop */ + memset(hs_offset, 0, sizeof hs_offset); + memset(zero, 0, sizeof zero); + + for (elmtno = 0; elmtno < p_nelmts; elmtno += hs_nelmts) + { + /* calculate the hyperslab size */ + if (rank > 0) + { + for (k = 0, hs_nelmts = 1; k < rank; k++) + { + hs_size[k] = MIN(dims[k] - hs_offset[k], sm_size[k]); + hs_nelmts *= hs_size[k]; + } + + if (H5Sselect_hyperslab(f_space_id, H5S_SELECT_SET, hs_offset, NULL, hs_size, NULL)<0) + goto error; + if (H5Sselect_hyperslab(sm_space, H5S_SELECT_SET, zero, NULL, &hs_nelmts, NULL)<0) + goto error; + } + else + { + H5Sselect_all(f_space_id); + H5Sselect_all(sm_space); + hs_nelmts = 1; + } /* rank */ + + /* read/write */ + if (H5Dread(dset_in, wtype_id, sm_space, f_space_id, H5P_DEFAULT, sm_buf) < 0) + goto error; + if (H5Dwrite(dset_out, wtype_id, sm_space, f_space_id, H5P_DEFAULT, sm_buf) < 0) + goto error; + + /* reclaim any VL memory, if necessary */ + if(vl_data) + H5Dvlen_reclaim(wtype_id, sm_space, H5P_DEFAULT, sm_buf); + + /* calculate the next hyperslab offset */ + for (k = rank, carry = 1; k > 0 && carry; --k) + { + hs_offset[k - 1] += hs_size[k - 1]; + if (hs_offset[k - 1] == dims[k - 1]) + hs_offset[k - 1] = 0; + else + carry = 0; + } /* k */ + } /* elmtno */ + + H5Sclose(sm_space); + /* free */ + if (sm_buf!=NULL) + { + HDfree(sm_buf); + sm_buf=NULL; + } + } /* hyperslab read */ + }/*nelmts*/ + + /*------------------------------------------------------------------------- + * amount of compression used + *------------------------------------------------------------------------- + */ + if (options->verbose) + { + if (apply_s && apply_f) + { + /* get the storage size of the input dataset */ + dsize_out=H5Dget_storage_size(dset_out); + PER((hssize_t)dsize_in,(hssize_t)dsize_out); + print_dataset_info(dcpl_out,travt->objs[i].name,per*100.0); + } + else + print_dataset_info(dcpl_id,travt->objs[i].name,0.0); + + /* print a message that the filter was not applied + (in case there was a filter) + */ + if ( has_filter && apply_s == 0 ) + printf(" <warning: filter not applied to %s. dataset smaller than %d bytes>\n", + travt->objs[i].name, + (int)options->threshold); + + if ( has_filter && apply_f == 0 ) + printf(" <warning: could not apply the filter to %s>\n", + travt->objs[i].name); + + } /* verbose */ + + /*------------------------------------------------------------------------- + * copy attrs + *------------------------------------------------------------------------- + */ + if (copy_attr(dset_in,dset_out,options)<0) + goto error; + + /*close */ + if (H5Dclose(dset_out)<0) + goto error; + + }/*!H5T_REFERENCE*/ + }/*h5tools_canreadf*/ + + + /*------------------------------------------------------------------------- + * close + *------------------------------------------------------------------------- + */ + if (H5Tclose(ftype_id)<0) + goto error; + if (H5Tclose(wtype_id)<0) + goto error; + if (H5Pclose(dcpl_id)<0) + goto error; + if (H5Pclose(dcpl_out)<0) + goto error; + if (H5Sclose(f_space_id)<0) + goto error; + if (H5Dclose(dset_in)<0) + goto error; + + } + /*------------------------------------------------------------------------- + * we do not have request for filter/chunking use H5Ocopy instead + *------------------------------------------------------------------------- + */ + else + { + hid_t pid; + + /* create property to pass copy options */ + if ( (pid = H5Pcreate(H5P_OBJECT_COPY)) < 0) + goto error; + + /* set options for object copy */ + if(H5Pset_copy_object(pid, H5O_COPY_WITHOUT_ATTR_FLAG) < 0) + goto error; + + /*------------------------------------------------------------------------- + * do the copy + *------------------------------------------------------------------------- + */ + + if (H5Ocopy(fidin, /* Source file or group identifier */ + travt->objs[i].name, /* Name of the source object to be copied */ + fidout, /* Destination file or group identifier */ + travt->objs[i].name, /* Name of the destination object */ + pid, /* Properties which apply to the copy */ + H5P_DEFAULT)<0) /* Properties which apply to the new hard link */ + goto error; + + /* close property */ + if (H5Pclose(pid)<0) + goto error; + + + /*------------------------------------------------------------------------- + * copy attrs manually + *------------------------------------------------------------------------- + */ + if ((dset_in=H5Dopen(fidin,travt->objs[i].name))<0) + goto error; + if ((dset_out=H5Dopen(fidout,travt->objs[i].name))<0) + goto error; + if (copy_attr(dset_in,dset_out,options)<0) + goto error; + if (H5Dclose(dset_in)<0) + goto error; + if (H5Dclose(dset_out)<0) + goto error; + + } /* end do we have request for filter/chunking */ + + + 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(FORMAT_OBJ,"type",travt->objs[i].name ); + + break; + + + /*------------------------------------------------------------------------- + * H5G_LINK + * H5G_UDLINK + * + * Only handles external links; H5Lcopy will fail for other UD link types + * since we don't have creation or copy callbacks for them. + *------------------------------------------------------------------------- + */ + + case H5G_LINK: + case H5G_UDLINK: + { + if(H5Lcopy(fidin, travt->objs[i].name,fidout, travt->objs[i].name, H5P_DEFAULT, H5P_DEFAULT) < 0) + goto error; + + if (options->verbose) + printf(FORMAT_OBJ,"link",travt->objs[i].name ); + + } + break; + + default: + goto error; + } /* switch */ - /* early detection of references */ - if ((dset_in=H5Dopen(fidin,travt->objs[i].name))<0) - goto error; - if ((ftype_id=H5Dget_type (dset_in))<0) - goto error; - if (H5T_REFERENCE==H5Tget_class(ftype_id)) - { - is_ref=1; - } - if (H5Tclose(ftype_id)<0) - goto error; - if (H5Dclose(dset_in)<0) - goto error; - - -/*------------------------------------------------------------------------- - * check if we should use H5Ocopy or not - * if there is a request for filters/layout, we read/write the object - * otherwise we do a copy using H5Ocopy - *------------------------------------------------------------------------- - */ - if (options->op_tbl->nelems - || - options->all_filter==1 || options->all_layout==1 - || is_ref - ) - { - int j; - - if ((dset_in=H5Dopen(fidin,travt->objs[i].name))<0) - goto error; - if ((f_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 ((dcpl_out = H5Pcopy (dcpl_id))<0) - goto error; - if ( (rank=H5Sget_simple_extent_ndims(f_space_id))<0) - goto error; - HDmemset(dims, 0, sizeof dims); - if ( H5Sget_simple_extent_dims(f_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 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((travt->objs[i].name),dcpl_id)==1) - { - apply_s=1; - apply_f=1; - - /*------------------------------------------------------------------------- - * references are a special case - * we cannot just copy the buffers, but instead we recreate the reference - * in a second traversal of the output file - *------------------------------------------------------------------------- - */ - if (H5T_REFERENCE==H5Tget_class(wtype_id)) - { - ; - } - else /* H5T_REFERENCE */ - { - /* get the storage size of the input dataset */ - dsize_in=H5Dget_storage_size(dset_in); - - /* check for datasets too small */ - if (nelmts*msize < options->threshold ) - apply_s=0; - - /* apply the filter */ - if (apply_s){ - if (apply_filters(travt->objs[i].name,rank,dims,dcpl_out,options,&has_filter)<0) - goto error; - } - - /*------------------------------------------------------------------------- - * create the output dataset; - * disable error checking in case the dataset cannot be created with the - * modified dcpl; in that case use the original instead - *------------------------------------------------------------------------- - */ - H5E_BEGIN_TRY { - dset_out=H5Dcreate(fidout,travt->objs[i].name,wtype_id,f_space_id,dcpl_out); - } H5E_END_TRY; - if (dset_out==FAIL) - { - if ((dset_out=H5Dcreate(fidout,travt->objs[i].name,wtype_id,f_space_id,dcpl_id))<0) - goto error; - apply_f=0; - } - - /*------------------------------------------------------------------------- - * read/write - *------------------------------------------------------------------------- - */ - if (nelmts) - { - size_t need = (size_t)(nelmts*msize); /* bytes needed */ - if ( need < H5TOOLS_MALLOCSIZE ) - buf = HDmalloc(need); - - if (buf != NULL ) - { - if (H5Dread(dset_in,wtype_id,H5S_ALL,H5S_ALL,H5P_DEFAULT,buf)<0) - goto error; - if (H5Dwrite(dset_out,wtype_id,H5S_ALL,H5S_ALL,H5P_DEFAULT,buf)<0) - goto error; - } - - else /* possibly not enough memory, read/write by hyperslabs */ - - { - size_t p_type_nbytes = msize; /*size of memory type */ - hsize_t p_nelmts = nelmts; /*total selected elmts */ - hsize_t elmtno; /*counter */ - int carry; /*counter carry value */ - unsigned int vl_data = 0; /*contains VL datatypes */ - - /* stripmine info */ - hsize_t sm_size[H5S_MAX_RANK]; /*stripmine size */ - hsize_t sm_nbytes; /*bytes per stripmine */ - hsize_t sm_nelmts; /*elements per stripmine*/ - hid_t sm_space; /*stripmine data space */ - - /* hyperslab info */ - hsize_t hs_offset[H5S_MAX_RANK];/*starting offset */ - hsize_t hs_size[H5S_MAX_RANK]; /*size this pass */ - hsize_t hs_nelmts; /*elements in request */ - hsize_t zero[8]; /*vector of zeros */ - int k; - - /* check if we have VL data in the dataset's datatype */ - if (H5Tdetect_class(wtype_id, H5T_VLEN) == TRUE) - vl_data = TRUE; - - /* - * determine the strip mine size and allocate a buffer. The strip mine is - * a hyperslab whose size is manageable. - */ - sm_nbytes = p_type_nbytes; - - for (k = rank; k > 0; --k) { - sm_size[k - 1] = MIN(dims[k - 1], H5TOOLS_BUFSIZE / sm_nbytes); - sm_nbytes *= sm_size[k - 1]; - assert(sm_nbytes > 0); - } - sm_buf = HDmalloc((size_t)sm_nbytes); - - sm_nelmts = sm_nbytes / p_type_nbytes; - sm_space = H5Screate_simple(1, &sm_nelmts, NULL); - - /* the stripmine loop */ - memset(hs_offset, 0, sizeof hs_offset); - memset(zero, 0, sizeof zero); - - for (elmtno = 0; elmtno < p_nelmts; elmtno += hs_nelmts) - { - /* calculate the hyperslab size */ - if (rank > 0) - { - for (k = 0, hs_nelmts = 1; k < rank; k++) - { - hs_size[k] = MIN(dims[k] - hs_offset[k], sm_size[k]); - hs_nelmts *= hs_size[k]; - } - - if (H5Sselect_hyperslab(f_space_id, H5S_SELECT_SET, hs_offset, NULL, hs_size, NULL)<0) - goto error; - if (H5Sselect_hyperslab(sm_space, H5S_SELECT_SET, zero, NULL, &hs_nelmts, NULL)<0) - goto error; - } - else - { - H5Sselect_all(f_space_id); - H5Sselect_all(sm_space); - hs_nelmts = 1; - } /* rank */ - - /* read/write */ - if (H5Dread(dset_in, wtype_id, sm_space, f_space_id, H5P_DEFAULT, sm_buf) < 0) - goto error; - if (H5Dwrite(dset_out, wtype_id, sm_space, f_space_id, H5P_DEFAULT, sm_buf) < 0) - goto error; - - /* reclaim any VL memory, if necessary */ - if(vl_data) - H5Dvlen_reclaim(wtype_id, sm_space, H5P_DEFAULT, sm_buf); - - /* calculate the next hyperslab offset */ - for (k = rank, carry = 1; k > 0 && carry; --k) - { - hs_offset[k - 1] += hs_size[k - 1]; - if (hs_offset[k - 1] == dims[k - 1]) - hs_offset[k - 1] = 0; - else - carry = 0; - } /* k */ - } /* elmtno */ - - H5Sclose(sm_space); /* free */ - if (sm_buf!=NULL) + if (buf!=NULL) { - HDfree(sm_buf); - sm_buf=NULL; + HDfree(buf); + buf=NULL; } - } /* hyperslab read */ - }/*nelmts*/ - + + } /* i */ + /*------------------------------------------------------------------------- - * amount of compression used - *------------------------------------------------------------------------- - */ - if (options->verbose) - { - if (apply_s && apply_f) - { - /* get the storage size of the input dataset */ - dsize_out=H5Dget_storage_size(dset_out); - PER((hssize_t)dsize_in,(hssize_t)dsize_out); - print_dataset_info(dcpl_out,travt->objs[i].name,per*100.0); - } - else - print_dataset_info(dcpl_id,travt->objs[i].name,0.0); - - /* print a message that the filter was not applied - (in case there was a filter) - */ - if ( has_filter && apply_s == 0 ) - printf(" <warning: filter not applied to %s. dataset smaller than %d bytes>\n", - travt->objs[i].name, - (int)options->threshold); - - if ( has_filter && apply_f == 0 ) - printf(" <warning: could not apply the filter to %s>\n", - travt->objs[i].name); - - } /* verbose */ - - /*------------------------------------------------------------------------- - * copy attrs - *------------------------------------------------------------------------- - */ - if (copy_attr(dset_in,dset_out,options)<0) - goto error; - - /*close */ - if (H5Dclose(dset_out)<0) - goto error; - - }/*H5T_REFERENCE*/ - }/*h5tools_canreadf*/ - - - /*------------------------------------------------------------------------- - * close + * the root is a special case, we get an ID for the root group + * and copy its attributes using that ID *------------------------------------------------------------------------- */ - if (H5Tclose(ftype_id)<0) - goto error; - if (H5Tclose(wtype_id)<0) - goto error; - if (H5Pclose(dcpl_id)<0) - goto error; - if (H5Pclose(dcpl_out)<0) - goto error; - if (H5Sclose(f_space_id)<0) - goto error; - if (H5Dclose(dset_in)<0) - goto error; - - } - /*------------------------------------------------------------------------- - * we do not have request for filter/chunking use H5Ocopy instead - *------------------------------------------------------------------------- - */ - else - { - hid_t pid; - - /* create property to pass copy options */ - if ( (pid = H5Pcreate(H5P_OBJECT_COPY)) < 0) - goto error; - - /* set options for object copy */ - if(H5Pset_copy_object(pid, H5O_COPY_WITHOUT_ATTR_FLAG) < 0) - goto error; - - /*------------------------------------------------------------------------- - * do the copy - *------------------------------------------------------------------------- - */ - - if (H5Ocopy(fidin, /* Source file or group identifier */ - travt->objs[i].name, /* Name of the source object to be copied */ - fidout, /* Destination file or group identifier */ - travt->objs[i].name, /* Name of the destination object */ - pid, /* Properties which apply to the copy */ - H5P_DEFAULT)<0) /* Properties which apply to the new hard link */ - goto error; - - /* close property */ - if (H5Pclose(pid)<0) - goto error; - - - /*------------------------------------------------------------------------- - * copy attrs manually - *------------------------------------------------------------------------- - */ - if ((dset_in=H5Dopen(fidin,travt->objs[i].name))<0) - goto error; - if ((dset_out=H5Dopen(fidout,travt->objs[i].name))<0) - goto error; - if (copy_attr(dset_in,dset_out,options)<0) - goto error; - if (H5Dclose(dset_in)<0) - goto error; - if (H5Dclose(dset_out)<0) - goto error; - - - } /* end do we have request for filter/chunking */ - - - 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(FORMAT_OBJ,"type",travt->objs[i].name ); - break; - - -/*------------------------------------------------------------------------- - * H5G_LINK - * H5G_UDLINK - * - * Only handles external links; H5Lcopy will fail for other UD link types - * since we don't have creation or copy callbacks for them. - *------------------------------------------------------------------------- - */ - - case H5G_LINK: - case H5G_UDLINK: - { - if(H5Lcopy(fidin, travt->objs[i].name,fidout, travt->objs[i].name, H5P_DEFAULT, H5P_DEFAULT) < 0) + if ((grp_out = H5Gopen2(fidout, "/", H5P_DEFAULT)) < 0) goto error; - if (options->verbose) - printf(FORMAT_OBJ,"link",travt->objs[i].name ); - - } - break; - - default: - goto error; - } /* switch */ - - /* free */ - if (buf!=NULL) - { - HDfree(buf); - buf=NULL; - } - - } /* i */ - -/*------------------------------------------------------------------------- - * the root is a special case, we get an ID for the root group - * and copy its attributes using that ID - *------------------------------------------------------------------------- - */ - - if ((grp_out = H5Gopen(fidout,"/"))<0) - goto error; - - if ((grp_in = H5Gopen(fidin,"/"))<0) - goto error; + if ((grp_in = H5Gopen2(fidin, "/", H5P_DEFAULT)) < 0) + goto error; - if (copy_attr(grp_in,grp_out,options)<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; + if (H5Gclose(grp_out)<0) + goto error; + if (H5Gclose(grp_in)<0) + goto error; - return 0; + return 0; error: - H5E_BEGIN_TRY { - H5Gclose(grp_in); - H5Gclose(grp_out); - H5Pclose(dcpl_id); - H5Pclose(gcpl_id); - H5Sclose(f_space_id); - H5Dclose(dset_in); - H5Dclose(dset_out); - H5Tclose(ftype_id); - H5Tclose(wtype_id); - H5Tclose(type_in); - H5Tclose(type_out); - /* free */ - if (buf!=NULL) - { - HDfree(buf); - buf=NULL; - } - if (sm_buf!=NULL) - { - HDfree(sm_buf); - sm_buf=NULL; - } - } H5E_END_TRY; - return -1; - + H5E_BEGIN_TRY { + H5Gclose(grp_in); + H5Gclose(grp_out); + H5Pclose(dcpl_id); + H5Pclose(gcpl_id); + H5Sclose(f_space_id); + H5Dclose(dset_in); + H5Dclose(dset_out); + H5Tclose(ftype_id); + H5Tclose(wtype_id); + H5Tclose(type_in); + H5Tclose(type_out); + } H5E_END_TRY; + /* free */ + if (buf!=NULL) + HDfree(buf); + if (sm_buf!=NULL) + HDfree(sm_buf); + return -1; } @@ -848,9 +829,9 @@ error: * 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); + * loc_id = H5Gopen2( fid, name); + * loc_id = H5Dopen2( fid, name); + * loc_id = H5Topen2( fid, name); * * Return: 0, ok, -1 no * |