diff options
Diffstat (limited to 'tools/src/h5repack/h5repack_refs.c')
| -rw-r--r-- | tools/src/h5repack/h5repack_refs.c | 259 |
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) |