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-rw-r--r--tools/h5repack/h5repack.h8
-rw-r--r--tools/h5repack/h5repack_copy.c604
-rw-r--r--tools/h5repack/h5repack_main.c4
-rw-r--r--tools/h5repack/h5repack_refs.c720
4 files changed, 369 insertions, 967 deletions
diff --git a/tools/h5repack/h5repack.h b/tools/h5repack/h5repack.h
index da82a05..0f5ccfe 100644
--- a/tools/h5repack/h5repack.h
+++ b/tools/h5repack/h5repack.h
@@ -102,6 +102,7 @@ typedef struct {
int verbose; /*verbose mode */
hsize_t threshold; /*minimum size to compress, in bytes */
int use_native; /*use a native type in write */
+ int have_fc_f; /*has input to use filter/chunking flag */
} pack_opt_t;
@@ -158,13 +159,6 @@ int copy_attr(hid_t loc_in,
pack_opt_t *options
);
-int do_copy_refobjs(hid_t fidin,
- hid_t fidout,
- trav_table_t *travt,
- pack_opt_t *options); /* repack options */
-
-
-
void read_info(const char *filename,pack_opt_t *options);
void init_packobject(pack_info_t *obj);
int print_filters(hid_t dcpl_id);
diff --git a/tools/h5repack/h5repack_copy.c b/tools/h5repack/h5repack_copy.c
index 03edd01..6b3e4d0 100644
--- a/tools/h5repack/h5repack_copy.c
+++ b/tools/h5repack/h5repack_copy.c
@@ -33,6 +33,8 @@ extern char *progname;
#define FORMAT_OBJ_ATTR " %-21s %s\n" /* obj type, name */
+static
+int do_hardlinks(hid_t fidout,trav_table_t *travt);
/*-------------------------------------------------------------------------
* Function: print_dataset_info
@@ -148,12 +150,8 @@ static void print_dataset_info(hid_t dcpl_id,
strcat(str,temp);
printf(FORMAT_OBJ,str,objname);
}
-
-
-
}
-
/*-------------------------------------------------------------------------
* Function: copy_objects
*
@@ -209,11 +207,11 @@ int copy_objects(const char* fnamein,
}
/*-------------------------------------------------------------------------
- * do the copy of referenced objects
- * and create hard links
+ * create hard links
*-------------------------------------------------------------------------
*/
- if(do_copy_refobjs(fidin,fidout,travt,options)<0) {
+
+ if(do_hardlinks(fidout,travt)<0) {
error_msg(progname, "<%s>: Could not copy data to: %s\n", fnamein, fnameout);
goto out;
}
@@ -299,6 +297,8 @@ int do_copy_objects(hid_t fidin,
void *buf=NULL; /* buffer for raw data */
void *sm_buf=NULL; /* buffer for raw data */
int i, j;
+ int nfilters; /* number of filters in DCPL */
+ H5D_layout_t layout;
/*-------------------------------------------------------------------------
* copy the suppplied object list
@@ -351,268 +351,337 @@ int do_copy_objects(hid_t fidin,
*-------------------------------------------------------------------------
*/
case H5G_DATASET:
-
+
+/*-------------------------------------------------------------------------
+ * early check for filters or a non default layout
+ *-------------------------------------------------------------------------
+ */
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;
+
+ /* get information about input filters */
+ if ((nfilters = H5Pget_nfilters(dcpl_id))<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 for external files
- *-------------------------------------------------------------------------
- */
- if ((next=H5Pget_external_count (dcpl_id))<0)
+ if ((layout = H5Pget_layout(dcpl_id))<0)
goto error;
- if (next)
- fprintf(stderr," <warning: %s has external files, ignoring read...>\n",
- travt->objs[i].name );
-
-/*-------------------------------------------------------------------------
- * check if the dataset creation property list has filters that
- * are not registered in the current configuration
- * 1) the external filters GZIP and SZIP might not be available
- * 2) the internal filters might be turned off
- *-------------------------------------------------------------------------
- */
- if (next==0 && h5tools_canreadf((travt->objs[i].name),dcpl_id)==1)
- {
- apply_s=1;
- apply_f=1;
-
+ if (H5Dclose(dset_in)<0)
+ goto error;
+ if (H5Pclose(dcpl_id)<0)
+ goto error;
+
/*-------------------------------------------------------------------------
- * 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
+ * check if we should use H5Ocopy or not
+ * if the DCPL has filters or a non default layout, we read/write the object
+ * otherwise we do a copy using H5Ocopy
*-------------------------------------------------------------------------
*/
- if ( (H5T_REFERENCE!=H5Tget_class(wtype_id)))
+
+ if (nfilters || layout!=H5D_CONTIGUOUS
+ /* does the dcpl has filters or non default layout ? */
+ ||
+ options->op_tbl->nelems
+ /* do we have input request for filter/chunking */
+ ||
+ options->all_filter==1 || options->all_layout==1
+ )
{
- /* 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;
+ 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];
- /* apply the filter */
- if (apply_s){
- if (apply_filters(travt->objs[i].name,rank,dims,dcpl_out,options)<0)
- goto error;
- }
+ if (options->use_native==1)
+ wtype_id = h5tools_get_native_type(ftype_id);
+ else
+ wtype_id = H5Tcopy(ftype_id);
- /*-------------------------------------------------------------------------
- * 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
- *-------------------------------------------------------------------------
+ if ((msize=H5Tget_size(wtype_id))==0)
+ goto error;
+
+ /*-------------------------------------------------------------------------
+ * check for external files
+ *-------------------------------------------------------------------------
+ */
+ if ((next=H5Pget_external_count (dcpl_id))<0)
+ goto error;
+
+ if (next)
+ fprintf(stderr," <warning: %s has external files, ignoring read...>\n",
+ travt->objs[i].name );
+
+ /*-------------------------------------------------------------------------
+ * 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
+ *-------------------------------------------------------------------------
*/
- 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 (next==0 && h5tools_canreadf((travt->objs[i].name),dcpl_id)==1)
{
- 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;
- }
+ apply_s=1;
+ apply_f=1;
- else /* possibly not enough memory, read/write by hyperslabs */
-
+ /*-------------------------------------------------------------------------
+ * 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)))
{
- 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 */
+ /* get the storage size of the input dataset */
+ dsize_in=H5Dget_storage_size(dset_in);
- /* 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 */
+ /* check for datasets too small */
+ if (nelmts*msize < options->threshold )
+ apply_s=0;
- /* 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 */
+ /* apply the filter */
+ if (apply_s){
+ if (apply_filters(travt->objs[i].name,rank,dims,dcpl_out,options)<0)
+ goto error;
+ }
- /* 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.
+ /*-------------------------------------------------------------------------
+ * 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
+ *-------------------------------------------------------------------------
*/
- sm_nbytes = p_type_nbytes;
-
- for (i = rank; i > 0; --i) {
- sm_size[i - 1] = MIN(dims[i - 1], H5TOOLS_BUFSIZE / sm_nbytes);
- sm_nbytes *= sm_size[i - 1];
- assert(sm_nbytes > 0);
+ 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;
}
- 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)
+ /*-------------------------------------------------------------------------
+ * read/write
+ *-------------------------------------------------------------------------
+ */
+ if (nelmts)
{
- /* calculate the hyperslab size */
- if (rank > 0)
+ size_t need = (size_t)(nelmts*msize); /* bytes needed */
+ if ( need < H5TOOLS_MALLOCSIZE )
+ buf = HDmalloc(need);
+
+ if (buf != NULL )
{
- for (i = 0, hs_nelmts = 1; i < rank; i++)
- {
- hs_size[i] = MIN(dims[i] - hs_offset[i], sm_size[i]);
- hs_nelmts *= hs_size[i];
- }
-
- if (H5Sselect_hyperslab(f_space_id, H5S_SELECT_SET, hs_offset, NULL, hs_size, NULL)<0)
+ if (H5Dread(dset_in,wtype_id,H5S_ALL,H5S_ALL,H5P_DEFAULT,buf)<0)
goto error;
- if (H5Sselect_hyperslab(sm_space, H5S_SELECT_SET, zero, NULL, &hs_nelmts, NULL)<0)
+ if (H5Dwrite(dset_out,wtype_id,H5S_ALL,H5S_ALL,H5P_DEFAULT,buf)<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 (i = rank, carry = 1; i > 0 && carry; --i)
+ else /* possibly not enough memory, read/write by hyperslabs */
+
{
- hs_offset[i - 1] += hs_size[i - 1];
- if (hs_offset[i - 1] == dims[i - 1])
- hs_offset[i - 1] = 0;
- else
- carry = 0;
- } /* i */
- } /* elmtno */
-
- H5Sclose(sm_space);
- /* free */
- if (sm_buf!=NULL)
- {
- HDfree(sm_buf);
- sm_buf=NULL;
- }
- } /* hyperslab read */
+ 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 */
+
+ /* 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 (i = rank; i > 0; --i) {
+ sm_size[i - 1] = MIN(dims[i - 1], H5TOOLS_BUFSIZE / sm_nbytes);
+ sm_nbytes *= sm_size[i - 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 (i = 0, hs_nelmts = 1; i < rank; i++)
+ {
+ hs_size[i] = MIN(dims[i] - hs_offset[i], sm_size[i]);
+ hs_nelmts *= hs_size[i];
+ }
+
+ 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 (i = rank, carry = 1; i > 0 && carry; --i)
+ {
+ hs_offset[i - 1] += hs_size[i - 1];
+ if (hs_offset[i - 1] == dims[i - 1])
+ hs_offset[i - 1] = 0;
+ else
+ carry = 0;
+ } /* i */
+ } /* 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)
+
+ /*-------------------------------------------------------------------------
+ * amount of compression used
+ *-------------------------------------------------------------------------
+ */
+ if (options->verbose)
{
- /* 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*(float)100.0);
+ 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*(float)100.0);
+ }
+ else
+ print_dataset_info(dcpl_id,travt->objs[i].name,0);
}
- else
- print_dataset_info(dcpl_id,travt->objs[i].name,0);
- }
-
- if (apply_s==0 && options->verbose)
- printf(" <warning: filter not applied to %s. dataset smaller than %d bytes>\n",
- travt->objs[i].name,
- (int)options->threshold);
-
- if (apply_f==0 && options->verbose)
+
+ if (apply_s==0 && options->verbose)
+ printf(" <warning: filter not applied to %s. dataset smaller than %d bytes>\n",
+ travt->objs[i].name,
+ (int)options->threshold);
+
+ if (apply_f==0 && options->verbose)
printf(" <warning: could not apply the filter to %s>\n",
travt->objs[i].name);
-
- /*-------------------------------------------------------------------------
- * copy attrs
- *-------------------------------------------------------------------------
- */
- if (copy_attr(dset_in,dset_out,options)<0)
- goto error;
-
- /*close */
- if (H5Dclose(dset_out)<0)
- goto error;
-
+
+ /*-------------------------------------------------------------------------
+ * copy attrs
+ *-------------------------------------------------------------------------
+ */
+ if (copy_attr(dset_in,dset_out,options)<0)
+ goto error;
+
+ /*close */
+ if (H5Dclose(dset_out)<0)
+ goto error;
+
}/*H5T_STD_REF_OBJ*/
}/*can_read*/
+
+
+ /*-------------------------------------------------------------------------
+ * close
+ *-------------------------------------------------------------------------
+ */
+ if (H5Tclose(ftype_id)<0)
+ goto error;
+ if (H5Tclose(wtype_id)<0)
+ goto error;
+ if (H5Pclose(dcpl_id)<0)
+ goto error;
+ if (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;
+
+ /*-------------------------------------------------------------------------
+ * 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;
+
+ } /* end do we have request for filter/chunking */
-/*-------------------------------------------------------------------------
- * 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;
break;
@@ -686,8 +755,6 @@ int do_copy_objects(hid_t fidin,
/*-------------------------------------------------------------------------
* 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
*-------------------------------------------------------------------------
*/
@@ -827,8 +894,6 @@ int copy_attr(hid_t loc_in,
*/
if ( ! H5Tequal(wtype_id, H5T_STD_REF_OBJ))
{
-
-
/*-------------------------------------------------------------------------
* read to memory
*-------------------------------------------------------------------------
@@ -894,6 +959,73 @@ error:
return -1;
}
+/*-------------------------------------------------------------------------
+ * Function: do_hardlinks
+ *
+ * Purpose: duplicate hard links
+ *
+ * Return: 0, ok, -1 no
+ *
+ * Programmer: Pedro Vicente, pvn@ncsa.uiuc.edu
+ *
+ * Date: December, 10, 2003
+ *
+ *-------------------------------------------------------------------------
+ */
+
+static
+int do_hardlinks(hid_t fidout,trav_table_t *travt)
+{
+ int i, j;
+
+ for ( i = 0; i < travt->nobjs; i++)
+ {
+ switch ( travt->objs[i].type )
+ {
+ case H5G_GROUP:
+
+ if (travt->objs[i].nlinks)
+ {
+ for ( j=0; j<travt->objs[i].nlinks; j++)
+ {
+ if (H5Glink(fidout,
+ H5L_TYPE_HARD,
+ travt->objs[i].name,
+ travt->objs[i].links[j].new_name)<0)
+ return -1;
+ }
+ }
+
+ break;
+
+ case H5G_DATASET:
+ if (travt->objs[i].nlinks)
+ {
+ for ( j=0; j<travt->objs[i].nlinks; j++){
+ if (H5Glink(fidout,
+ H5L_TYPE_HARD,
+ travt->objs[i].name,
+ travt->objs[i].links[j].new_name)<0)
+ return -1;
+ }
+ }
+ break;
+ case H5G_TYPE:
+ case H5G_LINK:
+ case H5G_UDLINK:
+
+ /*nothing to do */
+ break;
+
+ default:
+
+ break;
+ }
+ }
+
+ return 0;
+
+}
diff --git a/tools/h5repack/h5repack_main.c b/tools/h5repack/h5repack_main.c
index 1d2ec98..5a0f8d6 100644
--- a/tools/h5repack/h5repack_main.c
+++ b/tools/h5repack/h5repack_main.c
@@ -106,10 +106,6 @@ void usage(void)
printf("\n");
}
-
-
-
-
/*-------------------------------------------------------------------------
* Function: main
*
diff --git a/tools/h5repack/h5repack_refs.c b/tools/h5repack/h5repack_refs.c
index 7fce723..e01af2d 100644
--- a/tools/h5repack/h5repack_refs.c
+++ b/tools/h5repack/h5repack_refs.c
@@ -24,728 +24,8 @@ extern char *progname;
static const char* MapIdToName(hid_t refobj_id,
trav_table_t *travt);
-static void close_obj(H5G_obj_t obj_type, hid_t obj_id);
-static int copy_refs_attr(hid_t loc_in,
- hid_t loc_out,
- pack_opt_t *options,
- trav_table_t *travt,
- hid_t fidout /* for saving references */
- );
-
-/*-------------------------------------------------------------------------
- * Function: do_copy_refobjs
- *
- * Purpose: duplicate all referenced HDF5 objects in the file
- * and create hard links
- *
- * Return: 0, ok, -1 no
- *
- * Programmer: Pedro Vicente, pvn@ncsa.uiuc.edu
- *
- * Date: December, 10, 2003
- *
- *-------------------------------------------------------------------------
- */
-
-int do_copy_refobjs(hid_t fidin,
- hid_t fidout,
- trav_table_t *travt,
- pack_opt_t *options) /* repack options */
-{
- hid_t grp_in=-1; /* read group ID */
- hid_t grp_out=-1; /* write group ID */
- hid_t dset_in=-1; /* read dataset ID */
- hid_t dset_out=-1; /* write dataset ID */
- hid_t type_in=-1; /* named type ID */
- hid_t dcpl_id=-1; /* dataset creation property list ID */
- hid_t space_id=-1; /* space ID */
- hid_t ftype_id=-1; /* file type ID */
- hid_t wtype_id=-1; /* read/write type ID */
- size_t msize; /* size of type */
- hsize_t nelmts; /* number of elements in dataset */
- int rank; /* rank of dataset */
- hsize_t dims[H5S_MAX_RANK];/* dimensions of dataset */
- int next; /* external files */
- int i, j;
-
-/*-------------------------------------------------------------------------
- * browse
- *-------------------------------------------------------------------------
- */
-
- for ( i = 0; i < travt->nobjs; i++)
- {
- switch ( travt->objs[i].type )
- {
- /*-------------------------------------------------------------------------
- * H5G_GROUP
- *-------------------------------------------------------------------------
- */
- case H5G_GROUP:
-
- /*-------------------------------------------------------------------------
- * check for hard links
- *-------------------------------------------------------------------------
- */
-
- if (travt->objs[i].nlinks)
- {
- for ( j=0; j<travt->objs[i].nlinks; j++)
- {
- H5Glink(fidout,
- H5L_TYPE_HARD,
- travt->objs[i].name,
- travt->objs[i].links[j].new_name);
- }
- }
-
- break;
-
- /*-------------------------------------------------------------------------
- * H5G_DATASET
- *-------------------------------------------------------------------------
- */
- case H5G_DATASET:
-
- if ((dset_in=H5Dopen(fidin,travt->objs[i].name))<0)
- goto error;
- if ((space_id=H5Dget_space(dset_in))<0)
- goto error;
- if ((ftype_id=H5Dget_type (dset_in))<0)
- goto error;
- if ((dcpl_id=H5Dget_create_plist(dset_in))<0)
- goto error;
- if ( (rank=H5Sget_simple_extent_ndims(space_id))<0)
- goto error;
- if ( H5Sget_simple_extent_dims(space_id,dims,NULL)<0)
- goto error;
- nelmts=1;
- for (j=0; j<rank; j++)
- nelmts*=dims[j];
-
- if (options->use_native==1)
- wtype_id = h5tools_get_native_type(ftype_id);
- else
- wtype_id = H5Tcopy(ftype_id);
-
- if ((msize=H5Tget_size(wtype_id))==0)
- goto error;
-
-/*-------------------------------------------------------------------------
- * check for external files
- *-------------------------------------------------------------------------
- */
- if ((next=H5Pget_external_count (dcpl_id))<0)
- goto error;
-/*-------------------------------------------------------------------------
- * check if the dataset creation property list has filters that
- * are not registered in the current configuration
- * 1) the external filters GZIP and SZIP might not be available
- * 2) the internal filters might be turned off
- *-------------------------------------------------------------------------
- */
- if (next==0 && h5tools_canreadf((NULL),dcpl_id)==1)
- {
-/*-------------------------------------------------------------------------
- * test for a valid output dataset
- *-------------------------------------------------------------------------
- */
- dset_out = FAIL;
-
-/*-------------------------------------------------------------------------
- * object references are a special case
- * we cannot just copy the buffers, but instead we recreate the reference
- *-------------------------------------------------------------------------
- */
- if (H5Tequal(wtype_id, H5T_STD_REF_OBJ))
- {
- H5G_obj_t obj_type;
- hid_t refobj_id;
- hobj_ref_t *refbuf=NULL; /* buffer for object references */
- hobj_ref_t *buf=NULL;
- const char* refname;
- unsigned u;
-
- /*-------------------------------------------------------------------------
- * read to memory
- *-------------------------------------------------------------------------
- */
-
- if (nelmts)
- {
- buf=(void *) HDmalloc((unsigned)(nelmts*msize));
- if ( buf==NULL){
- error_msg(progname, "cannot read into memory\n" );
- goto error;
- }
- if (H5Dread(dset_in,wtype_id,H5S_ALL,H5S_ALL,H5P_DEFAULT,buf)<0)
- goto error;
-
- if ((obj_type = H5Rget_obj_type(dset_in,H5R_OBJECT,buf))<0)
- goto error;
- refbuf=HDmalloc((unsigned)nelmts*msize);
- if ( refbuf==NULL){
- error_msg(progname, "cannot allocate memory\n" );
- goto error;
- }
- for ( u=0; u<nelmts; u++)
- {
- H5E_BEGIN_TRY {
- if ((refobj_id = H5Rdereference(dset_in,H5R_OBJECT,&buf[u]))<0)
- continue;
- } H5E_END_TRY;
- /* get the name. a valid name could only occur in the
- second traversal of the file */
- if ((refname=MapIdToName(refobj_id,travt))!=NULL)
- {
- /* create the reference, -1 parameter for objects */
- if (H5Rcreate(&refbuf[u],fidout,refname,H5R_OBJECT,-1)<0)
- goto error;
- if (options->verbose)
- printf("object <%s> object reference created to <%s>\n",
- travt->objs[i].name,
- refname);
- }/*refname*/
- close_obj(obj_type,refobj_id);
- }/* u */
- }/*nelmts*/
-
- /*-------------------------------------------------------------------------
- * create/write dataset/close
- *-------------------------------------------------------------------------
- */
- if ((dset_out=H5Dcreate(fidout,travt->objs[i].name,wtype_id,space_id,dcpl_id))<0)
- goto error;
- if (nelmts) {
- if (H5Dwrite(dset_out,wtype_id,H5S_ALL,H5S_ALL,H5P_DEFAULT,refbuf)<0)
- goto error;
- }
-
- if (buf)
- free(buf);
- if (refbuf)
- free(refbuf);
-
- }/*H5T_STD_REF_OBJ*/
-
-/*-------------------------------------------------------------------------
- * dataset region references
- *-------------------------------------------------------------------------
- */
- else if (H5Tequal(wtype_id, H5T_STD_REF_DSETREG))
- {
- H5G_obj_t obj_type;
- hid_t refobj_id;
- hdset_reg_ref_t *refbuf=NULL; /* input buffer for region references */
- hdset_reg_ref_t *buf=NULL; /* output buffer */
- const char* refname;
- unsigned u;
-
- /*-------------------------------------------------------------------------
- * read input to memory
- *-------------------------------------------------------------------------
- */
- if (nelmts)
- {
- buf=(void *) HDmalloc((unsigned)(nelmts*msize));
- if ( buf==NULL){
- error_msg(progname, "cannot read into memory\n" );
- goto error;
- }
- if (H5Dread(dset_in,wtype_id,H5S_ALL,H5S_ALL,H5P_DEFAULT,buf)<0)
- goto error;
- if ((obj_type = H5Rget_obj_type(dset_in,H5R_DATASET_REGION,buf))<0)
- goto error;
-
- /*-------------------------------------------------------------------------
- * create output
- *-------------------------------------------------------------------------
- */
-
- refbuf=HDcalloc(sizeof(hdset_reg_ref_t),(size_t)nelmts); /*init to zero */
- if ( refbuf==NULL){
- error_msg(progname, "cannot allocate memory\n" );
- goto error;
- }
- for ( u=0; u<nelmts; u++)
- {
- H5E_BEGIN_TRY {
- if ((refobj_id = H5Rdereference(dset_in,H5R_DATASET_REGION,&buf[u]))<0)
- continue;
- } H5E_END_TRY;
-
- /* get the name. a valid name could only occur in the
- second traversal of the file */
- if ((refname=MapIdToName(refobj_id,travt))!=NULL)
- {
- hid_t region_id; /* region id of the referenced dataset */
- if ((region_id = H5Rget_region(dset_in,H5R_DATASET_REGION,&buf[u]))<0)
- goto error;
- /* create the reference, we need the space_id */
- if (H5Rcreate(&refbuf[u],fidout,refname,H5R_DATASET_REGION,region_id)<0)
- goto error;
- if (H5Sclose(region_id)<0)
- goto error;
- if (options->verbose)
- printf("object <%s> region reference created to <%s>\n",
- travt->objs[i].name,
- refname);
- }/*refname*/
- close_obj(obj_type,refobj_id);
- }/* u */
- }/*nelmts*/
-
- /*-------------------------------------------------------------------------
- * create/write dataset/close
- *-------------------------------------------------------------------------
- */
- if ((dset_out=H5Dcreate(fidout,travt->objs[i].name,wtype_id,space_id,dcpl_id))<0)
- goto error;
- if (nelmts) {
- if (H5Dwrite(dset_out,wtype_id,H5S_ALL,H5S_ALL,H5P_DEFAULT,refbuf)<0)
- goto error;
- }
-
- if (buf)
- free(buf);
- if (refbuf)
- free(refbuf);
- } /* H5T_STD_REF_DSETREG */
-
-
-/*-------------------------------------------------------------------------
- * not references, open previously created object in 1st traversal
- *-------------------------------------------------------------------------
- */
- else
- {
- if ((dset_out=H5Dopen(fidout,travt->objs[i].name))<0)
- goto error;
- }
-
- assert(dset_out!=FAIL);
-
-/*-------------------------------------------------------------------------
- * copy referenced objects in attributes
- *-------------------------------------------------------------------------
- */
- if (copy_refs_attr(dset_in,dset_out,options,travt,fidout)<0)
- goto error;
-
-
-/*-------------------------------------------------------------------------
- * check for hard links
- *-------------------------------------------------------------------------
- */
- if (travt->objs[i].nlinks)
- {
- for ( j=0; j<travt->objs[i].nlinks; j++){
- H5Glink(fidout,
- H5L_TYPE_HARD,
- travt->objs[i].name,
- travt->objs[i].links[j].new_name);
- }
- }
-
- if (H5Dclose(dset_out)<0)
- goto error;
-
- }/*can_read*/
-
- /*-------------------------------------------------------------------------
- * close
- *-------------------------------------------------------------------------
- */
-
- if (H5Tclose(ftype_id)<0)
- goto error;
- if (H5Tclose(wtype_id)<0)
- goto error;
- if (H5Pclose(dcpl_id)<0)
- goto error;
- if (H5Sclose(space_id)<0)
- goto error;
- if (H5Dclose(dset_in)<0)
- goto error;
-
- break;
-
- /*-------------------------------------------------------------------------
- * H5G_TYPE
- *-------------------------------------------------------------------------
- */
- case H5G_TYPE:
-
- if ((type_in = H5Topen (fidin,travt->objs[i].name))<0)
- goto error;
-
- if (H5Tclose(type_in)<0)
- goto error;
-
- break;
-
- /*-------------------------------------------------------------------------
- * H5G_LINK
- * H5G_UDLINK
- *-------------------------------------------------------------------------
- */
-
- case H5G_LINK:
- case H5G_UDLINK:
-
- /*nothing to do */
- break;
-
- default:
-
- break;
- }
- }
-
-
-
-/*-------------------------------------------------------------------------
- * the root is a special case, we get an ID for the root group
- * and copy its attributes using that ID
- * it must be done last, because the attributes might contain references to
- * objects in the object list
- *-------------------------------------------------------------------------
- */
-
- if ((grp_out = H5Gopen(fidout,"/"))<0)
- goto error;
-
- if ((grp_in = H5Gopen(fidin,"/"))<0)
- goto error;
-
- if (copy_refs_attr(grp_in,grp_out,options,travt,fidout)<0)
- goto error;
-
- if (H5Gclose(grp_out)<0)
- goto error;
- if (H5Gclose(grp_in)<0)
- goto error;
-
- return 0;
-
-error:
- H5E_BEGIN_TRY {
- H5Gclose(grp_in);
- H5Gclose(grp_out);
- H5Pclose(dcpl_id);
- H5Sclose(space_id);
- H5Dclose(dset_in);
- H5Dclose(dset_out);
- H5Tclose(ftype_id);
- H5Tclose(wtype_id);
- H5Tclose(type_in);
- } H5E_END_TRY;
- return -1;
-
-}
-
-
-/*-------------------------------------------------------------------------
- * Function: copy_refs_attr
- *
- * Purpose: duplicate all referenced HDF5 located in attributes
- * relative to LOC_IN, which is obtained either from
- * loc_id = H5Gopen( fid, name);
- * loc_id = H5Dopen( fid, name);
- * loc_id = H5Topen( fid, name);
- *
- * Return: 0, ok, -1 no
- *
- * Programmer: Pedro Vicente, pvn@ncsa.uiuc.edu
- *
- * Date: October, 28, 2003
- *
- *-------------------------------------------------------------------------
- */
-
-static int copy_refs_attr(hid_t loc_in,
- hid_t loc_out,
- pack_opt_t *options,
- trav_table_t *travt,
- hid_t fidout /* for saving references */
- )
-{
- hid_t attr_id; /* attr ID */
- hid_t attr_out; /* attr ID */
- hid_t space_id; /* space ID */
- hid_t ftype_id; /* file type ID */
- hid_t wtype_id; /* read/write type ID */
- size_t msize; /* size of type */
- hsize_t nelmts; /* number of elements in dataset */
- int rank; /* rank of dataset */
- hsize_t dims[H5S_MAX_RANK];/* dimensions of dataset */
- char name[255];
- int n, j;
- unsigned u;
-
- if ((n = H5Aget_num_attrs(loc_in))<0)
- goto error;
-
- for ( u = 0; u < (unsigned)n; u++)
- {
-
-/*-------------------------------------------------------------------------
- * open
- *-------------------------------------------------------------------------
- */
- /* open attribute */
- if ((attr_id = H5Aopen_idx(loc_in, u))<0)
- goto error;
-
- /* get name */
- if (H5Aget_name( attr_id, 255, name )<0)
- goto error;
-
- /* get the file datatype */
- if ((ftype_id = H5Aget_type( attr_id )) < 0 )
- goto error;
-
- /* get the dataspace handle */
- if ((space_id = H5Aget_space( attr_id )) < 0 )
- goto error;
-
- /* get dimensions */
- if ( (rank = H5Sget_simple_extent_dims(space_id, dims, NULL)) < 0 )
- goto error;
-
-
- /*-------------------------------------------------------------------------
- * elements
- *-------------------------------------------------------------------------
- */
- nelmts=1;
- for (j=0; j<rank; j++)
- nelmts*=dims[j];
-
- if (options->use_native==1)
- wtype_id = h5tools_get_native_type(ftype_id);
- else
- wtype_id = H5Tcopy(ftype_id);
-
- if ((msize=H5Tget_size(wtype_id))==0)
- goto error;
-
-/*-------------------------------------------------------------------------
- * object references are a special case
- * we cannot just copy the buffers, but instead we recreate the reference
- *-------------------------------------------------------------------------
- */
- if (H5Tequal(wtype_id, H5T_STD_REF_OBJ))
- {
- H5G_obj_t obj_type;
- hid_t refobj_id;
- hobj_ref_t *refbuf=NULL;
- unsigned k;
- const char* refname;
- hobj_ref_t *buf=NULL;
-
- /*-------------------------------------------------------------------------
- * read input to memory
- *-------------------------------------------------------------------------
- */
-
- if (nelmts)
- {
- buf=(void *) HDmalloc((unsigned)(nelmts*msize));
- if ( buf==NULL){
- error_msg(progname, "cannot read into memory\n" );
- goto error;
- }
- if (H5Aread(attr_id,wtype_id,buf)<0)
- goto error;
-
- if ((obj_type = H5Rget_obj_type(attr_id,H5R_OBJECT,buf))<0)
- goto error;
- refbuf=HDmalloc((unsigned)nelmts*msize);
- if ( refbuf==NULL){
- error_msg(progname, "cannot allocate memory\n" );
- goto error;
- }
- for ( k=0; k<nelmts; k++)
- {
- H5E_BEGIN_TRY {
- if ((refobj_id = H5Rdereference(attr_id,H5R_OBJECT,&buf[k]))<0)
- goto error;
- } H5E_END_TRY;
- /* get the name. a valid name could only occur in the
- second traversal of the file */
- if ((refname=MapIdToName(refobj_id,travt))!=NULL)
- {
- /* create the reference */
- if (H5Rcreate(&refbuf[k],fidout,refname,H5R_OBJECT,-1)<0)
- goto error;
- if (options->verbose)
- printf("object <%s> reference created to <%s>\n",name,refname);
- }
- close_obj(obj_type,refobj_id);
- }/* k */
- }/*nelmts*/
-
- /*-------------------------------------------------------------------------
- * copy
- *-------------------------------------------------------------------------
- */
-
- if ((attr_out=H5Acreate(loc_out,name,ftype_id,space_id,H5P_DEFAULT))<0)
- goto error;
- if (nelmts) {
- if(H5Awrite(attr_out,wtype_id,refbuf)<0)
- goto error;
- }
-
- if (H5Aclose(attr_out)<0)
- goto error;
-
- if (refbuf)
- free(refbuf);
- if (buf)
- free(buf);
-
- }/*H5T_STD_REF_OBJ*/
-
-/*-------------------------------------------------------------------------
- * dataset region references
- *-------------------------------------------------------------------------
- */
- else if (H5Tequal(wtype_id, H5T_STD_REF_DSETREG))
- {
- H5G_obj_t obj_type;
- hid_t refobj_id;
- hdset_reg_ref_t *refbuf=NULL; /* input buffer for region references */
- hdset_reg_ref_t *buf=NULL; /* output buffer */
- const char* refname;
- unsigned k;
-
- /*-------------------------------------------------------------------------
- * read input to memory
- *-------------------------------------------------------------------------
- */
-
- if (nelmts)
- {
- buf=(void *) HDmalloc((unsigned)(nelmts*msize));
- if ( buf==NULL){
- error_msg(progname, "cannot read into memory\n" );
- goto error;
- }
- if (H5Aread(attr_id,wtype_id,buf)<0)
- goto error;
- if ((obj_type = H5Rget_obj_type(attr_id,H5R_DATASET_REGION,buf))<0)
- goto error;
-
- /*-------------------------------------------------------------------------
- * create output
- *-------------------------------------------------------------------------
- */
-
- refbuf=HDcalloc(sizeof(hdset_reg_ref_t),(size_t)nelmts); /*init to zero */
- if ( refbuf==NULL){
- error_msg(progname, "cannot allocate memory\n" );
- goto error;
- }
- for ( k=0; k<nelmts; k++)
- {
- H5E_BEGIN_TRY {
- if ((refobj_id = H5Rdereference(attr_id,H5R_DATASET_REGION,&buf[k]))<0)
- continue;
- } H5E_END_TRY;
- /* get the name. a valid name could only occur in the
- second traversal of the file */
- if ((refname=MapIdToName(refobj_id,travt))!=NULL)
- {
- hid_t region_id; /* region id of the referenced dataset */
- if ((region_id = H5Rget_region(attr_id,H5R_DATASET_REGION,&buf[k]))<0)
- goto error;
- /* create the reference, we need the space_id */
- if (H5Rcreate(&refbuf[k],fidout,refname,H5R_DATASET_REGION,region_id)<0)
- goto error;
- if (H5Sclose(region_id)<0)
- goto error;
- if (options->verbose)
- printf("object <%s> region reference created to <%s>\n",name,refname);
- }
- close_obj(obj_type,refobj_id);
- }/* k */
- }/*nelmts */
-
- /*-------------------------------------------------------------------------
- * copy
- *-------------------------------------------------------------------------
- */
-
- if ((attr_out=H5Acreate(loc_out,name,ftype_id,space_id,H5P_DEFAULT))<0)
- goto error;
- if (nelmts) {
- if(H5Awrite(attr_out,wtype_id,refbuf)<0)
- goto error;
- }
- if (H5Aclose(attr_out)<0)
- goto error;
- if (refbuf)
- free(refbuf);
- if (buf)
- free(buf);
- } /* H5T_STD_REF_DSETREG */
-
-/*-------------------------------------------------------------------------
- * close
- *-------------------------------------------------------------------------
- */
-
- if (H5Tclose(ftype_id)<0) goto error;
- if (H5Tclose(wtype_id)<0) goto error;
- if (H5Sclose(space_id)<0) goto error;
- if (H5Aclose(attr_id)<0) goto error;
- } /* u */
-
- return 0;
-
-error:
- H5E_BEGIN_TRY {
- H5Tclose(ftype_id);
- H5Tclose(wtype_id);
- H5Sclose(space_id);
- H5Aclose(attr_id);
- H5Aclose(attr_out);
- } H5E_END_TRY;
- return -1;
-}
-
-/*-------------------------------------------------------------------------
- * Function: close_obj
- *
- * Purpose: Auxiliary function to close an object
- *
- *-------------------------------------------------------------------------
- */
-
-static void close_obj(H5G_obj_t obj_type, hid_t obj_id)
-{
- H5E_BEGIN_TRY
- {
- switch (obj_type)
- {
- case H5G_GROUP:
- H5Gclose(obj_id);
- break;
- case H5G_DATASET:
- H5Dclose(obj_id);
- break;
- case H5G_TYPE:
- H5Tclose(obj_id);
- break;
- default:
- break;
- }
- } H5E_END_TRY;
-}
/*-------------------------------------------------------------------------
* Function: MapIdToName
generated by cgit v0.12 at 2024-11-16 20:44:36 (GMT)