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Diffstat (limited to 'tools/src/h5repack/h5repack_refs.c')
-rw-r--r--tools/src/h5repack/h5repack_refs.c259
1 files changed, 122 insertions, 137 deletions
diff --git a/tools/src/h5repack/h5repack_refs.c b/tools/src/h5repack/h5repack_refs.c
index 36038b5..376ab92 100644
--- a/tools/src/h5repack/h5repack_refs.c
+++ b/tools/src/h5repack/h5repack_refs.c
@@ -30,15 +30,10 @@ static herr_t update_ref_value(hid_t obj_id, H5R_type_t ref_type, void *ref_in,
/*-------------------------------------------------------------------------
* 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
+ * Purpose: duplicate all referenced HDF5 objects in the file
+ * and create hard links
*
+ * Return: 0, ok, -1 no
*-------------------------------------------------------------------------
*/
@@ -47,41 +42,39 @@ int do_copy_refobjs(hid_t fidin,
trav_table_t *travt,
pack_opt_t *options) /* repack options */
{
- int ret_value = 0; /*no need to LEAVE() on ERROR: HERR_INIT(int, SUCCEED) */
- 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 */
+ int ret_value = 0; /*no need to LEAVE() on ERROR: HERR_INIT(int, SUCCEED) */
+ 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;
- named_dt_t *named_dt_head=NULL; /* Pointer to the stack of named datatypes
- copied */
+ named_dt_t *named_dt_head = NULL; /* Pointer to the stack of named datatypes copied */
/*-------------------------------------------------------------------------
* browse
*-------------------------------------------------------------------------
*/
for(i = 0; i < travt->nobjs; i++) {
- switch(travt->objs[i].type)
- {
+ switch(travt->objs[i].type) {
/*-------------------------------------------------------------------------
- * H5TRAV_TYPE_GROUP
- *-------------------------------------------------------------------------
- */
+ * H5TRAV_TYPE_GROUP
+ *-------------------------------------------------------------------------
+ */
case H5TRAV_TYPE_GROUP:
/*-------------------------------------------------------------------------
- * copy referenced objects in attributes
- *-------------------------------------------------------------------------
- */
+ * copy referenced objects in attributes
+ *-------------------------------------------------------------------------
+ */
if((grp_out = H5Gopen2(fidout, travt->objs[i].name, H5P_DEFAULT)) < 0)
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Gopen2 failed");
@@ -97,18 +90,18 @@ int do_copy_refobjs(hid_t fidin,
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Gclose failed");
/*-------------------------------------------------------------------------
- * check for hard links
- *-------------------------------------------------------------------------
- */
+ * check for hard links
+ *-------------------------------------------------------------------------
+ */
if(travt->objs[i].nlinks)
for(j = 0; j < travt->objs[i].nlinks; j++)
H5Lcreate_hard(fidout, travt->objs[i].name, H5L_SAME_LOC, travt->objs[i].links[j].new_name, H5P_DEFAULT, H5P_DEFAULT);
break;
/*-------------------------------------------------------------------------
- * H5TRAV_TYPE_DATASET
- *-------------------------------------------------------------------------
- */
+ * H5TRAV_TYPE_DATASET
+ *-------------------------------------------------------------------------
+ */
case H5TRAV_TYPE_DATASET:
if((dset_in = H5Dopen2(fidin, travt->objs[i].name, H5P_DEFAULT)) < 0)
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dopen2 failed");
@@ -141,16 +134,16 @@ int do_copy_refobjs(hid_t fidin,
*/
if(h5tools_canreadf(NULL, dcpl_id) == 1) {
/*-------------------------------------------------------------------------
- * test for a valid output dataset
- *-------------------------------------------------------------------------
- */
+ * 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
- *-------------------------------------------------------------------------
- */
+ * 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)) {
hid_t refobj_id;
hobj_ref_t *refbuf = NULL; /* buffer for object references */
@@ -159,9 +152,9 @@ int do_copy_refobjs(hid_t fidin,
unsigned u;
/*-------------------------------------------------------------------------
- * read to memory
- *-------------------------------------------------------------------------
- */
+ * read to memory
+ *-------------------------------------------------------------------------
+ */
if(nelmts) {
buf = (hobj_ref_t *)HDmalloc((unsigned)(nelmts * msize));
if(buf==NULL) {
@@ -201,9 +194,9 @@ int do_copy_refobjs(hid_t fidin,
} /*nelmts*/
/*-------------------------------------------------------------------------
- * create/write dataset/close
- *-------------------------------------------------------------------------
- */
+ * create/write dataset/close
+ *-------------------------------------------------------------------------
+ */
if((dset_out = H5Dcreate2(fidout, travt->objs[i].name, mtype_id, space_id, H5P_DEFAULT, dcpl_id, H5P_DEFAULT)) < 0)
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dcreate2 failed");
if(nelmts)
@@ -223,11 +216,10 @@ int do_copy_refobjs(hid_t fidin,
} /*H5T_STD_REF_OBJ*/
/*-------------------------------------------------------------------------
- * dataset region references
- *-------------------------------------------------------------------------
- */
- else if(H5Tequal(mtype_id, H5T_STD_REF_DSETREG))
- {
+ * dataset region references
+ *-------------------------------------------------------------------------
+ */
+ else if(H5Tequal(mtype_id, H5T_STD_REF_DSETREG)) {
hid_t refobj_id;
hdset_reg_ref_t *refbuf = NULL; /* input buffer for region references */
hdset_reg_ref_t *buf = NULL; /* output buffer */
@@ -235,9 +227,9 @@ int do_copy_refobjs(hid_t fidin,
unsigned u;
/*-------------------------------------------------------------------------
- * read input to memory
- *-------------------------------------------------------------------------
- */
+ * read input to memory
+ *-------------------------------------------------------------------------
+ */
if(nelmts) {
buf = (hdset_reg_ref_t *)HDmalloc((unsigned)(nelmts * msize));
if(buf == NULL) {
@@ -248,9 +240,9 @@ int do_copy_refobjs(hid_t fidin,
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dread failed");
/*-------------------------------------------------------------------------
- * create output
- *-------------------------------------------------------------------------
- */
+ * create output
+ *-------------------------------------------------------------------------
+ */
refbuf = (hdset_reg_ref_t *)HDcalloc(sizeof(hdset_reg_ref_t), (size_t)nelmts); /*init to zero */
if(refbuf == NULL) {
printf("cannot allocate memory\n");
@@ -289,9 +281,9 @@ int do_copy_refobjs(hid_t fidin,
} /*nelmts*/
/*-------------------------------------------------------------------------
- * create/write dataset/close
- *-------------------------------------------------------------------------
- */
+ * create/write dataset/close
+ *-------------------------------------------------------------------------
+ */
if((dset_out = H5Dcreate2(fidout, travt->objs[i].name, mtype_id, space_id, H5P_DEFAULT, dcpl_id, H5P_DEFAULT)) < 0)
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dcreate2 failed");
if(nelmts)
@@ -310,25 +302,25 @@ int do_copy_refobjs(hid_t fidin,
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "copy_attr failed");
} /* H5T_STD_REF_DSETREG */
/*-------------------------------------------------------------------------
- * not references, open previously created object in 1st traversal
- *-------------------------------------------------------------------------
- */
+ * not references, open previously created object in 1st traversal
+ *-------------------------------------------------------------------------
+ */
else {
if((dset_out = H5Dopen2(fidout, travt->objs[i].name, H5P_DEFAULT)) < 0)
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dopen2 failed");
} /* end else */
/*-------------------------------------------------------------------------
- * copy referenced objects in attributes
- *-------------------------------------------------------------------------
- */
+ * copy referenced objects in attributes
+ *-------------------------------------------------------------------------
+ */
if(copy_refs_attr(dset_in, dset_out, options, travt, fidout) < 0)
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "copy_refs_attr failed");
/*-------------------------------------------------------------------------
- * check for hard links
- *-------------------------------------------------------------------------
- */
+ * check for hard links
+ *-------------------------------------------------------------------------
+ */
if(travt->objs[i].nlinks)
for(j = 0; j < travt->objs[i].nlinks; j++)
H5Lcreate_hard(fidout, travt->objs[i].name, H5L_SAME_LOC, travt->objs[i].links[j].new_name, H5P_DEFAULT, H5P_DEFAULT);
@@ -338,9 +330,9 @@ int do_copy_refobjs(hid_t fidin,
} /*can_read*/
/*-------------------------------------------------------------------------
- * close
- *-------------------------------------------------------------------------
- */
+ * close
+ *-------------------------------------------------------------------------
+ */
if(H5Tclose(ftype_id) < 0)
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Tclose failed");
if(H5Tclose(mtype_id) < 0)
@@ -354,9 +346,9 @@ int do_copy_refobjs(hid_t fidin,
break;
/*-------------------------------------------------------------------------
- * H5TRAV_TYPE_NAMED_DATATYPE
- *-------------------------------------------------------------------------
- */
+ * H5TRAV_TYPE_NAMED_DATATYPE
+ *-------------------------------------------------------------------------
+ */
case H5TRAV_TYPE_NAMED_DATATYPE:
if((type_in = H5Topen2(fidin, travt->objs[i].name, H5P_DEFAULT)) < 0)
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Topen2 failed");
@@ -365,9 +357,9 @@ int do_copy_refobjs(hid_t fidin,
break;
/*-------------------------------------------------------------------------
- * H5TRAV_TYPE_LINK
- *-------------------------------------------------------------------------
- */
+ * H5TRAV_TYPE_LINK
+ *-------------------------------------------------------------------------
+ */
case H5TRAV_TYPE_LINK:
/*nothing to do */
break;
@@ -410,27 +402,22 @@ done:
/*-------------------------------------------------------------------------
* Function: copy_refs_attr
*
- * Purpose: duplicate all referenced HDF5 located in attributes
- * relative to LOC_IN, which is obtained either from
- * loc_id = H5Gopen2(fid, name, H5P_DEFAULT);
- * loc_id = H5Dopen2(fid, name, H5P_DEFAULT);
- * loc_id = H5Topen2(fid, name, H5P_DEFAULT);
- *
- * Return: 0, ok, -1 no
+ * Purpose: duplicate all referenced HDF5 located in attributes
+ * relative to LOC_IN, which is obtained either from
+ * loc_id = H5Gopen2(fid, name, H5P_DEFAULT);
+ * loc_id = H5Dopen2(fid, name, H5P_DEFAULT);
+ * loc_id = H5Topen2(fid, name, H5P_DEFAULT);
*
- * Programmer: Pedro Vicente, pvn@ncsa.uiuc.edu
+ * Return: 0, ok, -1 no
*
- * Modifier: xcao@hdfgroup.org, 9/12/2011
- * Update values of references(object and region) for the following types:
+ * Modified:
+ * Update values of references(object and region) for the following types:
* 1) References,
* 2) ARRAY of reference,
* 3) VLEN of references.
* 4) COMPOUND of references.
- * This function does not handle references in other complicated structures,
- * such as references in nested compound datatypes.
- *
- * Date: October, 28, 2003
- *
+ * This function does not handle references in other complicated structures,
+ * such as references in nested compound datatypes.
*-------------------------------------------------------------------------
*/
@@ -438,30 +425,32 @@ 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 fidout) /* for saving references */
{
- int ret_value = 0; /*no need to LEAVE() on ERROR: HERR_INIT(int, SUCCEED) */
- hid_t attr_id = -1; /* attr ID */
- hid_t attr_out = -1; /* attr 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 type */
- hsize_t nelmts; /* number of elements in dataset */
- hsize_t dims[H5S_MAX_RANK];/* dimensions of dataset */
- char name[255];
- H5O_info_t oinfo; /* Object info */
- unsigned u, i, j;
- int rank;
+ int ret_value = 0; /*no need to LEAVE() on ERROR: HERR_INIT(int, SUCCEED) */
+ hid_t attr_id = -1; /* attr ID */
+ hid_t attr_out = -1; /* attr 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 type */
+ hsize_t nelmts; /* number of elements in dataset */
+ hsize_t dims[H5S_MAX_RANK];/* dimensions of dataset */
+ char name[255];
+ H5O_info_t oinfo; /* Object info */
+ unsigned u, i, j;
+ int rank;
H5T_class_t type_class = -1;
- hbool_t is_ref=0, is_ref_vlen=0, is_ref_array=0, is_ref_comp=0;
- void *refbuf = NULL;
- void *buf = NULL;
- const char* refname = NULL;
- unsigned *ref_comp_index = NULL;
- size_t *ref_comp_size = NULL;
- int ref_comp_field_n = 0;
+ hbool_t is_ref = 0,
+ is_ref_vlen = 0,
+ is_ref_array = 0,
+ is_ref_comp = 0;
+ void *refbuf = NULL;
+ void *buf = NULL;
+ const char *refname = NULL;
+ unsigned *ref_comp_index = NULL;
+ size_t *ref_comp_size = NULL;
+ int ref_comp_field_n = 0;
if(H5Oget_info(loc_in, &oinfo) < 0)
@@ -492,7 +481,7 @@ static int copy_refs_attr(hid_t loc_in,
hid_t base_type;
base_type = H5Tget_super(ftype_id);
- is_ref_vlen = (H5Tget_class(base_type)==H5T_REFERENCE);
+ is_ref_vlen = (H5Tget_class(base_type) == H5T_REFERENCE);
msize = H5Tget_size(base_type);
H5Tclose(base_type);
}
@@ -500,7 +489,7 @@ static int copy_refs_attr(hid_t loc_in,
hid_t base_type;
base_type = H5Tget_super(ftype_id);
- is_ref_array = (H5Tget_class(base_type)==H5T_REFERENCE);
+ is_ref_array = (H5Tget_class(base_type) == H5T_REFERENCE);
msize = H5Tget_size(base_type);
H5Tclose(base_type);
}
@@ -515,9 +504,9 @@ static int copy_refs_attr(hid_t loc_in,
ref_comp_field_n = 0;
for (i=0; i<(unsigned)nmembers; i++) {
- hid_t mtid = H5Tget_member_type( ftype_id, i );
+ hid_t mtid = H5Tget_member_type(ftype_id, i);
- if ((H5Tget_class(mtid)==H5T_REFERENCE)) {
+ if ((H5Tget_class(mtid) == H5T_REFERENCE)) {
ref_comp_index[ref_comp_field_n] = i;
ref_comp_size[ref_comp_field_n] = H5Tget_size(mtid);
ref_comp_field_n++;
@@ -627,9 +616,9 @@ static int copy_refs_attr(hid_t loc_in,
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Aread failed");
/*-------------------------------------------------------------------------
- * create output
- *-------------------------------------------------------------------------
- */
+ * create output
+ *-------------------------------------------------------------------------
+ */
refbuf = (hdset_reg_ref_t *)HDcalloc(sizeof(hdset_reg_ref_t), (size_t)nelmts); /*init to zero */
if(refbuf == NULL) {
printf( "cannot allocate memory\n" );
@@ -669,7 +658,8 @@ static int copy_refs_attr(hid_t loc_in,
HDmemcpy(&(ptr[j]), &ref_out, msize);
}
} /* for (i=0; i<nelems; i++) */
- } else if (H5R_DSET_REG_REF_BUF_SIZE == msize) {
+ }
+ else if (H5R_DSET_REG_REF_BUF_SIZE == msize) {
hdset_reg_ref_t ref_out;
for (i=0; i<(unsigned)nelmts; i++) {
@@ -689,8 +679,7 @@ static int copy_refs_attr(hid_t loc_in,
buf = HDmalloc((unsigned)(nelmts * msize));
refbuf = buf; /* reuse the read buffer for write */
- if(buf == NULL)
- {
+ if(buf == NULL) {
printf( "cannot read into memory\n" );
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "HDmalloc failed");
} /* end if */
@@ -767,8 +756,6 @@ static int copy_refs_attr(hid_t loc_in,
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Aclose failed");
} /* for(u = 0; u < (unsigned)oinfo.num_attrs; u++) */
- return ret_value;
-
done:
if(refbuf)
HDfree(refbuf);
@@ -795,7 +782,7 @@ done:
/*-------------------------------------------------------------------------
* Function: MapIdToName
*
- * Purpose: map a ID from a reference to a dataset name
+ * Purpose: map a ID from a reference to a dataset name
*
*-------------------------------------------------------------------------
*/
@@ -803,7 +790,7 @@ static const char*
MapIdToName(hid_t refobj_id, trav_table_t *travt)
{
unsigned int u;
- const char* ret = NULL;
+ const char *ret = NULL;
/* linear search */
for(u = 0; u < travt->nobjs; u++) {
@@ -830,18 +817,16 @@ out:
/*-------------------------------------------------------------------------
* Function: Update_Ref_value
*
- * Purpose: Update a reference value
- *
- * Programmer: xcao@hdfgroup.org 9/12/2011
- *
+ * Purpose: Update a reference value
*-------------------------------------------------------------------------
*/
static herr_t update_ref_value(hid_t obj_id, H5R_type_t ref_type, void *ref_in,
hid_t fid_out, void *ref_out, trav_table_t *travt)
{
- int ret_value = 0; /*no need to LEAVE() on ERROR: HERR_INIT(int, SUCCEED) */
- const char* ref_obj_name;
- hid_t space_id=-1, ref_obj_id=-1;
+ int ret_value = 0; /*no need to LEAVE() on ERROR: HERR_INIT(int, SUCCEED) */
+ const char *ref_obj_name;
+ hid_t space_id = -1;
+ hid_t ref_obj_id = -1;
ref_obj_id = H5Rdereference2(obj_id, H5P_DEFAULT, ref_type, ref_in);
if (ref_obj_id < 0)