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-rw-r--r--tools/h5repack/h5repack.h4
-rw-r--r--tools/h5repack/h5repack_copy.c1067
-rw-r--r--tools/h5repack/h5repack_list.c49
-rw-r--r--tools/h5repack/h5repack_refs.c744
-rw-r--r--tools/h5repack/h5repack_verify.c4
-rw-r--r--tools/h5repack/h5repacktst.c4
6 files changed, 892 insertions, 980 deletions
diff --git a/tools/h5repack/h5repack.h b/tools/h5repack/h5repack.h
index f8f642b..d986cc0 100644
--- a/tools/h5repack/h5repack.h
+++ b/tools/h5repack/h5repack.h
@@ -174,10 +174,6 @@ int apply_filters(const char* name, /* object name from traverse list */
pack_opt_t *options, /* repack options */
int *has_filter); /* (OUT) object NAME has a filter */
-int has_filter(hid_t dcpl_id,
- H5Z_filter_t filtnin);
-
-
int can_read(const char* name, /* object name from traverse list */
hid_t dcpl_id, /* dataset creation property list */
pack_opt_t *options); /* repack options */
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
*
diff --git a/tools/h5repack/h5repack_list.c b/tools/h5repack/h5repack_list.c
index 3de8101..78b8858 100644
--- a/tools/h5repack/h5repack_list.c
+++ b/tools/h5repack/h5repack_list.c
@@ -165,52 +165,3 @@ out:
return -1;
}
-
-
-/*-------------------------------------------------------------------------
- * Function: print_objlist
- *
- * Purpose: print list of objects in file
- *
- * Return: void
- *
- * Programmer: Pedro Vicente, pvn@ncsa.uiuc.edu
- *
- * Date: October 23, 2003
- *
- *-------------------------------------------------------------------------
- */
-void print_objlist(const char *filename,
- int nobjects,
- trav_info_t *info )
-{
- int i;
-
- printf("File <%s>: # of entries = %d\n", filename, nobjects );
- for ( i = 0; i < nobjects; i++)
- {
- switch ( info[i].type )
- {
- case H5G_GROUP:
- printf(" %-10s %s\n", "group", info[i].name );
- break;
- case H5G_DATASET:
- printf(" %-10s %s\n", "dataset", info[i].name );
- break;
- case H5G_TYPE:
- printf(" %-10s %s\n", "datatype", info[i].name );
- break;
- case H5G_LINK:
- printf(" %-10s %s\n", "link", info[i].name );
- break;
- case H5G_UDLINK:
- printf(" %-10s %s\n", "User defined link", info[i].name );
- break;
- default:
- printf(" %-10s %s\n", "User defined object", info[i].name );
- break;
- }
- }
-
-}
-
diff --git a/tools/h5repack/h5repack_refs.c b/tools/h5repack/h5repack_refs.c
index 538c99f..71e42bb 100644
--- a/tools/h5repack/h5repack_refs.c
+++ b/tools/h5repack/h5repack_refs.c
@@ -53,406 +53,390 @@ int do_copy_refobjs(hid_t fidin,
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;
+ 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;
-/*-------------------------------------------------------------------------
- * browse
- *-------------------------------------------------------------------------
- */
-
- for ( i = 0; i < travt->nobjs; i++)
- {
- switch ( travt->objs[i].type )
- {
- /*-------------------------------------------------------------------------
- * H5G_GROUP
- *-------------------------------------------------------------------------
- */
- case H5G_GROUP:
-
- /*-------------------------------------------------------------------------
- * copy referenced objects in attributes
- *-------------------------------------------------------------------------
- */
-
- if ((grp_out=H5Gopen(fidout,travt->objs[i].name))<0)
- goto error;
-
- if((grp_in = H5Gopen (fidin,travt->objs[i].name))<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
+ /*-------------------------------------------------------------------------
+ * browse
*-------------------------------------------------------------------------
*/
- if (travt->objs[i].nlinks)
- {
- for ( j=0; j<travt->objs[i].nlinks; j++)
+ for ( i = 0; i < travt->nobjs; i++)
{
- H5Glink(fidout,
- H5G_LINK_HARD,
- travt->objs[i].name,
- travt->objs[i].links[j].new_name);
+ switch ( travt->objs[i].type )
+ {
+ /*-------------------------------------------------------------------------
+ * H5G_GROUP
+ *-------------------------------------------------------------------------
+ */
+ case H5G_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++)
+ H5Glink(fidout, H5G_LINK_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 (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))
+ {
+ H5G_obj_t1 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){
+ printf( "cannot read into memory\n" );
+ goto error;
+ }
+ if (H5Dread(dset_in,mtype_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=HDcalloc((unsigned)nelmts,msize);
+ if ( refbuf==NULL){
+ printf( "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,mtype_id,space_id,dcpl_id))<0)
+ goto error;
+ if (nelmts) {
+ if (H5Dwrite(dset_out,mtype_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(mtype_id, H5T_STD_REF_DSETREG))
+ {
+ H5G_obj_t1 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){
+ printf( "cannot read into memory\n" );
+ goto error;
+ }
+ if (H5Dread(dset_in,mtype_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){
+ printf( "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,mtype_id,space_id,dcpl_id))<0)
+ goto error;
+ if (nelmts) {
+ if (H5Dwrite(dset_out,mtype_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, H5G_LINK_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(mtype_id)<0)
+ goto error;
+ if (H5Pclose(dcpl_id)<0)
+ goto error;
+ if (H5Sclose(space_id)<0)
+ goto error;
+ if (H5Dclose(dset_in)<0)
+ goto error;
+
+ break;
+
+ /*-------------------------------------------------------------------------
+ * H5G_TYPE
+ *-------------------------------------------------------------------------
+ */
+ case H5G_TYPE:
+
+ if ((type_in = H5Topen (fidin,travt->objs[i].name))<0)
+ goto error;
+
+ if (H5Tclose(type_in)<0)
+ goto error;
+
+ break;
+
+ /*-------------------------------------------------------------------------
+ * H5G_LINK
+ *-------------------------------------------------------------------------
+ */
+
+ case H5G_LINK:
+
+ /*nothing to do */
+ break;
+
+ default:
+
+ break;
+ }
}
- }
-
- 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 (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))
- {
- H5G_obj_t1 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){
- printf( "cannot read into memory\n" );
- goto error;
- }
- if (H5Dread(dset_in,mtype_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=HDcalloc((unsigned)nelmts,msize);
- if ( refbuf==NULL){
- printf( "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,mtype_id,space_id,dcpl_id))<0)
- goto error;
- if (nelmts) {
- if (H5Dwrite(dset_out,mtype_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(mtype_id, H5T_STD_REF_DSETREG))
- {
- H5G_obj_t1 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
+ * 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 (nelmts)
- {
- buf=(void *) HDmalloc((unsigned)(nelmts*msize));
- if ( buf==NULL){
- printf( "cannot read into memory\n" );
- goto error;
- }
- if (H5Dread(dset_in,mtype_id,H5S_ALL,H5S_ALL,H5P_DEFAULT,buf)<0)
- goto error;
- if ((obj_type = H5Rget_obj_type(dset_in,H5R_DATASET_REGION,buf))<0)
- goto error;
- /*-------------------------------------------------------------------------
- * create output
- *-------------------------------------------------------------------------
- */
+ if ((grp_out = H5Gopen2(fidout, "/", H5P_DEFAULT)) < 0)
+ goto error;
- refbuf=HDcalloc(sizeof(hdset_reg_ref_t),(size_t)nelmts); /*init to zero */
- if ( refbuf==NULL){
- printf( "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;
+ if ((grp_in = H5Gopen2(fidin, "/", H5P_DEFAULT)) < 0)
+ goto error;
- /* 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)
+ if (copy_refs_attr(grp_in, grp_out, options, travt, fidout) < 0)
goto error;
- /* create the reference, we need the space_id */
- if (H5Rcreate(&refbuf[u],fidout,refname,H5R_DATASET_REGION,region_id)<0)
+
+ if (H5Gclose(grp_out) < 0)
goto error;
- if (H5Sclose(region_id)<0)
+ if (H5Gclose(grp_in) < 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,mtype_id,space_id,dcpl_id))<0)
- goto error;
- if (nelmts) {
- if (H5Dwrite(dset_out,mtype_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,
- H5G_LINK_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(mtype_id)<0)
- goto error;
- if (H5Pclose(dcpl_id)<0)
- goto error;
- if (H5Sclose(space_id)<0)
- goto error;
- if (H5Dclose(dset_in)<0)
- goto error;
-
- break;
-
- /*-------------------------------------------------------------------------
- * H5G_TYPE
- *-------------------------------------------------------------------------
- */
- case H5G_TYPE:
-
- if ((type_in = H5Topen (fidin,travt->objs[i].name))<0)
- goto error;
-
- if (H5Tclose(type_in)<0)
- goto error;
-
- break;
-
- /*-------------------------------------------------------------------------
- * H5G_LINK
- *-------------------------------------------------------------------------
- */
-
- case H5G_LINK:
-
- /*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;
+ 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);
- } H5E_END_TRY;
- return -1;
-
+ 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);
+ } H5E_END_TRY;
+ return -1;
}
@@ -461,7 +445,7 @@ error:
*
* Purpose: duplicate all referenced HDF5 located in attributes
* relative to LOC_IN, which is obtained either from
- * loc_id = H5Gopen( fid, name);
+ * loc_id = H5Gopen2( fid, name, H5P_DEFAULT);
* loc_id = H5Dopen( fid, name);
* loc_id = H5Topen( fid, name);
*
diff --git a/tools/h5repack/h5repack_verify.c b/tools/h5repack/h5repack_verify.c
index 049e059..6c02e92 100644
--- a/tools/h5repack/h5repack_verify.c
+++ b/tools/h5repack/h5repack_verify.c
@@ -34,8 +34,8 @@ extern char *progname;
*-------------------------------------------------------------------------
*/
-int has_filter(hid_t dcpl_id,
- H5Z_filter_t filtnin)
+static int
+has_filter(hid_t dcpl_id, H5Z_filter_t filtnin)
{
int nfilters; /* number of filters */
diff --git a/tools/h5repack/h5repacktst.c b/tools/h5repack/h5repacktst.c
index 3328c70..b8c7948 100644
--- a/tools/h5repack/h5repacktst.c
+++ b/tools/h5repack/h5repacktst.c
@@ -1570,7 +1570,7 @@ int make_all_objects(hid_t loc_id)
*-------------------------------------------------------------------------
*/
group_id = H5Gcreate2(loc_id, "g1", H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
- root_id = H5Gopen(loc_id, "/");
+ root_id = H5Gopen2(loc_id, "/", H5P_DEFAULT);
/*-------------------------------------------------------------------------
* H5G_TYPE
@@ -1645,7 +1645,7 @@ int make_attributes(hid_t loc_id)
*-------------------------------------------------------------------------
*/
group_id = H5Gcreate2(loc_id, "g1", H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
- root_id = H5Gopen(loc_id, "/");
+ root_id = H5Gopen2(loc_id, "/", H5P_DEFAULT);
/*-------------------------------------------------------------------------
* write a series of attributes on the dataset, group, and root group
generated by cgit v0.12 at 2024-07-16 23:12:47 (GMT)