diff options
Diffstat (limited to 'tools/src/h5repack/h5repack_refs.c')
| -rw-r--r-- | tools/src/h5repack/h5repack_refs.c | 877 |
1 files changed, 877 insertions, 0 deletions
diff --git a/tools/src/h5repack/h5repack_refs.c b/tools/src/h5repack/h5repack_refs.c new file mode 100644 index 0000000..f0f32c3 --- /dev/null +++ b/tools/src/h5repack/h5repack_refs.c @@ -0,0 +1,877 @@ +/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * + * Copyright by The HDF Group. * + * Copyright by the Board of Trustees of the University of Illinois. * + * All rights reserved. * + * * + * This file is part of HDF5. The full HDF5 copyright notice, including * + * terms governing use, modification, and redistribution, is contained in * + * the files COPYING and Copyright.html. COPYING can be found at the root * + * of the source code distribution tree; Copyright.html can be found at the * + * root level of an installed copy of the electronic HDF5 document set and * + * is linked from the top-level documents page. It can also be found at * + * http://hdfgroup.org/HDF5/doc/Copyright.html. If you do not have * + * access to either file, you may request a copy from help@hdfgroup.org. * + * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ + +#include "h5repack.h" +#include "h5diff.h" +#include "h5tools.h" + + +/*------------------------------------------------------------------------- + * local functions + *------------------------------------------------------------------------- + */ + +static const char* MapIdToName(hid_t refobj_id,trav_table_t *travt); +static int copy_refs_attr(hid_t loc_in, hid_t loc_out, pack_opt_t *options, + trav_table_t *travt, hid_t fidout); +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); + +/*------------------------------------------------------------------------- + * 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 */ +{ + 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 */ + + /*------------------------------------------------------------------------- + * browse + *------------------------------------------------------------------------- + */ + for(i = 0; i < travt->nobjs; i++) { + switch(travt->objs[i].type) + { + /*------------------------------------------------------------------------- + * H5TRAV_TYPE_GROUP + *------------------------------------------------------------------------- + */ + case H5TRAV_TYPE_GROUP: + /*------------------------------------------------------------------------- + * 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"); + + if((grp_in = H5Gopen2(fidin, travt->objs[i].name, H5P_DEFAULT)) < 0) + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Gopen2 failed"); + + if(copy_refs_attr(grp_in, grp_out, options, travt, fidout) < 0) + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "copy_refs_attr failed"); + + if(H5Gclose(grp_out) < 0) + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Gclose failed"); + if(H5Gclose(grp_in) < 0) + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Gclose failed"); + + /*------------------------------------------------------------------------- + * 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 + *------------------------------------------------------------------------- + */ + 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"); + if((space_id = H5Dget_space(dset_in)) < 0) + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dget_space failed"); + if((ftype_id = H5Dget_type(dset_in)) < 0) + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dget_type failed"); + if((dcpl_id = H5Dget_create_plist(dset_in)) < 0) + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dget_create_plist failed"); + if((rank = H5Sget_simple_extent_ndims(space_id)) < 0) + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Sget_simple_extent_ndims failed"); + if(H5Sget_simple_extent_dims(space_id, dims, NULL) < 0) + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Sget_simple_extent_dims failed"); + nelmts = 1; + for(k = 0; k < rank; k++) + nelmts *= dims[k]; + + if((mtype_id = h5tools_get_native_type(ftype_id)) < 0) + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "h5tools_get_native_type failed"); + + if((msize = H5Tget_size(mtype_id)) == 0) + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Tget_size failed"); + + /*------------------------------------------------------------------------- + * 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)) { + 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 = (hobj_ref_t *)HDmalloc((unsigned)(nelmts * msize)); + if(buf==NULL) { + printf("cannot read into memory\n" ); + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "HDmalloc failed"); + } /* end if */ + if(H5Dread(dset_in, mtype_id, H5S_ALL, H5S_ALL, H5P_DEFAULT, buf) < 0) + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dread failed"); + + refbuf = (hobj_ref_t*) HDcalloc((unsigned)nelmts, msize); + if(refbuf == NULL){ + printf("cannot allocate memory\n" ); + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "HDcalloc failed"); + } /* end if */ + for(u = 0; u < nelmts; u++) { + H5E_BEGIN_TRY { + if((refobj_id = H5Rdereference2(dset_in, H5P_DEFAULT, 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, (hid_t)-1) < 0) + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Rcreate failed"); + if(options->verbose) + { + printf(FORMAT_OBJ,"dset",travt->objs[i].name ); + printf("object <%s> object reference created to <%s>\n", + travt->objs[i].name, + refname); + } + } /*refname*/ + H5Oclose(refobj_id); + } /* u */ + } /*nelmts*/ + + /*------------------------------------------------------------------------- + * 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) + if(H5Dwrite(dset_out, mtype_id, H5S_ALL, H5S_ALL, H5P_DEFAULT, refbuf) < 0) + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dwrite failed"); + + if(buf) + HDfree(buf); + if(refbuf) + HDfree(refbuf); + + /*------------------------------------------------------ + * copy attrs + *----------------------------------------------------*/ + if(copy_attr(dset_in, dset_out, &named_dt_head, travt, options) < 0) + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "copy_attr failed"); + } /*H5T_STD_REF_OBJ*/ + + /*------------------------------------------------------------------------- + * 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 */ + const char* refname; + unsigned u; + + /*------------------------------------------------------------------------- + * read input to memory + *------------------------------------------------------------------------- + */ + if(nelmts) { + buf = (hdset_reg_ref_t *)HDmalloc((unsigned)(nelmts * msize)); + if(buf == NULL) { + printf("cannot read into memory\n"); + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "HDmalloc failed"); + } /* end if */ + if(H5Dread(dset_in, mtype_id, H5S_ALL, H5S_ALL, H5P_DEFAULT, buf) < 0) + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dread failed"); + + /*------------------------------------------------------------------------- + * 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"); + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "HDcalloc failed"); + } /* end if */ + + for(u = 0; u < nelmts; u++) { + H5E_BEGIN_TRY { + if((refobj_id = H5Rdereference2(dset_in, H5P_DEFAULT, 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) + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Rget_region failed"); + + /* create the reference, we need the space_id */ + if(H5Rcreate(&refbuf[u], fidout, refname, H5R_DATASET_REGION, region_id) < 0) + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Rcreate failed"); + if(H5Sclose(region_id) < 0) + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Sclose failed"); + if(options->verbose) + { + printf(FORMAT_OBJ,"dset",travt->objs[i].name ); + printf("object <%s> region reference created to <%s>\n", + travt->objs[i].name, + refname); + } + } /*refname*/ + H5Oclose(refobj_id); + } /* u */ + } /*nelmts*/ + + /*------------------------------------------------------------------------- + * 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) + if(H5Dwrite(dset_out, mtype_id, H5S_ALL, H5S_ALL, H5P_DEFAULT, refbuf) < 0) + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dwrite failed"); + + if(buf) + HDfree(buf); + if(refbuf) + HDfree(refbuf); + + /*----------------------------------------------------- + * copy attrs + *----------------------------------------------------*/ + if(copy_attr(dset_in, dset_out, &named_dt_head, travt, options) < 0) + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "copy_attr failed"); + } /* H5T_STD_REF_DSETREG */ + /*------------------------------------------------------------------------- + * 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 */ + + HDassert(dset_out != FAIL); + + /*------------------------------------------------------------------------- + * 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 + *------------------------------------------------------------------------- + */ + 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); + + if(H5Dclose(dset_out) < 0) + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dclose failed"); + } /*can_read*/ + + /*------------------------------------------------------------------------- + * close + *------------------------------------------------------------------------- + */ + if(H5Tclose(ftype_id) < 0) + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Tclose failed"); + if(H5Tclose(mtype_id) < 0) + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Tclose failed"); + if(H5Pclose(dcpl_id) < 0) + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed"); + if(H5Sclose(space_id) < 0) + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Sclose failed"); + if(H5Dclose(dset_in) < 0) + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dclose failed"); + break; + + /*------------------------------------------------------------------------- + * 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"); + if(H5Tclose(type_in) < 0) + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Tclose failed"); + break; + + /*------------------------------------------------------------------------- + * H5TRAV_TYPE_LINK + *------------------------------------------------------------------------- + */ + case H5TRAV_TYPE_LINK: + /*nothing to do */ + break; + + case H5TRAV_TYPE_UNKNOWN: + case H5TRAV_TYPE_UDLINK: + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5TRAV invalid type"); + + default: + break; + } /* end switch */ + } /* end for */ + + /* Finalize (link) the stack of named datatypes (if any) + * This function is paired with copy_named_datatype() which is called + * in copy_attr(), so need to free. + */ + named_datatype_free(&named_dt_head, 0); + + return ret_value; + +done: + 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); + named_datatype_free(&named_dt_head, 0); + } H5E_END_TRY; + + return ret_value; +} + + +/*------------------------------------------------------------------------- + * 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 + * + * Programmer: Pedro Vicente, pvn@ncsa.uiuc.edu + * + * Modifier: xcao@hdfgroup.org, 9/12/2011 + * 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 + * + *------------------------------------------------------------------------- + */ + +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 */ + ) +{ + 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; + + + if(H5Oget_info(loc_in, &oinfo) < 0) + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Oget_info failed"); + + for(u = 0; u < (unsigned)oinfo.num_attrs; u++) { + is_ref = is_ref_vlen = is_ref_array = is_ref_comp = 0; + + /* open attribute */ + if((attr_id = H5Aopen_by_idx(loc_in, ".", H5_INDEX_CRT_ORDER, H5_ITER_INC, (hsize_t)u, H5P_DEFAULT, H5P_DEFAULT)) < 0) + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Aopen_by_idx failed"); + + /* get the file datatype */ + if((ftype_id = H5Aget_type(attr_id)) < 0) + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Aget_type failed"); + + type_class = H5Tget_class(ftype_id); + + if((mtype_id = h5tools_get_native_type(ftype_id)) < 0) + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "h5tools_get_native_type failed"); + + if((msize = H5Tget_size(mtype_id)) == 0) + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Tget_size failed"); + + is_ref = (type_class == H5T_REFERENCE); + + if(type_class == H5T_VLEN ) { + hid_t base_type; + + base_type = H5Tget_super(ftype_id); + is_ref_vlen = (H5Tget_class(base_type)==H5T_REFERENCE); + msize = H5Tget_size(base_type); + H5Tclose(base_type); + } + else if(type_class == H5T_ARRAY ) { + hid_t base_type; + + base_type = H5Tget_super(ftype_id); + is_ref_array = (H5Tget_class(base_type)==H5T_REFERENCE); + msize = H5Tget_size(base_type); + H5Tclose(base_type); + } + else if(type_class == H5T_COMPOUND) { + int nmembers = H5Tget_nmembers(ftype_id) ; + + if (nmembers < 1) + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Tget_nmembers failed"); + + ref_comp_index = (unsigned *)HDmalloc((size_t)nmembers*sizeof(unsigned)); + ref_comp_size = (size_t *)HDmalloc((size_t)nmembers*sizeof(ref_comp_size)); + ref_comp_field_n = 0; + + for (i=0; i<(unsigned)nmembers; i++) { + hid_t mtid = H5Tget_member_type( ftype_id, i ); + + 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++; + } + H5Tclose(mtid); + } + + /* if compound don't contain reference type member, free the above + * mallocs. Otherwise there can be memory leaks by the 'continue' + * statement below. */ + if (!ref_comp_field_n) { + if (ref_comp_index) { + HDfree(ref_comp_index); + ref_comp_index = NULL; + } + + if (ref_comp_size) { + HDfree(ref_comp_size); + ref_comp_size = NULL; + } + } + } + + is_ref_comp = (ref_comp_field_n > 0); + + if (!(is_ref || is_ref_vlen || is_ref_array || is_ref_comp)) { + H5Tclose(mtype_id); + H5Tclose(ftype_id); + H5Aclose(attr_id); + continue; + } + + /* get name */ + if(H5Aget_name(attr_id, 255, name) < 0) + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Aget_name failed"); + + /* get the dataspace handle */ + if((space_id = H5Aget_space(attr_id)) < 0) + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Aget_space failed"); + + /* get dimensions */ + if((rank = H5Sget_simple_extent_dims(space_id, dims, NULL)) < 0) + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Sget_simple_extent_dims failed"); + + + /*------------------------------------------------------------------------- + * elements + *------------------------------------------------------------------------- + */ + nelmts = 1; + for(j = 0; j < (unsigned)rank; j++) + nelmts *= dims[j]; + + if (is_ref_array) { + unsigned array_rank = 0; + hsize_t array_size = 1; + hsize_t array_dims[H5S_MAX_RANK]; + hid_t base_type; + + base_type = H5Tget_super(ftype_id); + msize = H5Tget_size(base_type); + H5Tclose(base_type); + + array_rank = (unsigned)H5Tget_array_ndims(mtype_id); + H5Tget_array_dims2(mtype_id, array_dims); + for(j = 0; j <array_rank; j++) + array_size *= array_dims[j]; + nelmts *= array_size; + } + + if((attr_out = H5Acreate2(loc_out, name, ftype_id, space_id, H5P_DEFAULT, H5P_DEFAULT)) < 0) + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Acreate2 failed"); + + if (nelmts>0) { + /* handle object references */ + if((is_ref || is_ref_array) && (H5R_OBJ_REF_BUF_SIZE==msize)) { + buf = (hobj_ref_t *)HDmalloc((unsigned)(nelmts * msize)); + if(buf == NULL) { + printf("cannot read into memory\n"); + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "HDmalloc failed"); + } /* end if */ + if(H5Aread(attr_id, mtype_id, buf) < 0) + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Aread failed"); + + refbuf = (hobj_ref_t *)HDcalloc((unsigned)nelmts, msize); + if(refbuf == NULL) { + printf("cannot allocate memory\n"); + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "HDcalloc failed"); + } /* end if */ + + for(i = 0; i < (unsigned)nelmts; i++) { + if (update_ref_value(attr_id, H5R_OBJECT, &((hobj_ref_t *)buf)[i], fidout, &((hobj_ref_t *)refbuf)[i], travt)<0) + continue; + if(options->verbose) + printf("object <%s> reference created to <%s>\n", name, refname); + } /* i */ + } /* H5T_STD_REF_OBJ */ + /* handle region references */ + else if((is_ref || is_ref_array) && (H5R_DSET_REG_REF_BUF_SIZE == msize)) { + buf = (hdset_reg_ref_t *)HDmalloc((unsigned)(nelmts * msize)); + + if(buf == NULL) { + printf( "cannot read into memory\n" ); + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "HDmalloc failed"); + } /* end if */ + if(H5Aread(attr_id, mtype_id, buf) < 0) + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Aread failed"); + + /*------------------------------------------------------------------------- + * 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" ); + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "HDcalloc failed"); + } /* end if */ + + for(i = 0; i < (unsigned)nelmts; i++) { + if (update_ref_value(attr_id, H5R_DATASET_REGION, &((hdset_reg_ref_t *)buf)[i], fidout, &((hdset_reg_ref_t *)refbuf)[i], travt)<0) + continue; + if(options->verbose) + printf("object <%s> region reference created to <%s>\n", name, refname); + } + } /* H5T_STD_REF_DSETREG */ + else if (is_ref_vlen) { + /* handle VLEN of references */ + + buf = (hvl_t *)HDmalloc((unsigned)(nelmts * sizeof(hvl_t))); + refbuf = buf; /* reuse the read buffer for write */ + + if(buf == NULL) { + printf( "cannot read into memory\n" ); + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "HDmalloc failed"); + } /* end if */ + + if(H5Aread(attr_id, mtype_id, buf) < 0) + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Aread failed"); + + if (H5R_OBJ_REF_BUF_SIZE==msize) { + hobj_ref_t ref_out; + + for (i=0; i<(unsigned)nelmts; i++) { + hobj_ref_t *ptr = (hobj_ref_t *)((hvl_t *)buf)[i].p; + + for (j=0; j<((hvl_t *)buf)[i].len; j++ ) { + if (update_ref_value(attr_id, H5R_OBJECT, &(ptr[j]), fidout, &ref_out, travt)<0) + continue; + HDmemcpy(&(ptr[j]), &ref_out, msize); + } + } /* for (i=0; i<nelems; i++) */ + } else if (H5R_DSET_REG_REF_BUF_SIZE == msize) { + hdset_reg_ref_t ref_out; + + for (i=0; i<(unsigned)nelmts; i++) { + hdset_reg_ref_t *ptr = (hdset_reg_ref_t *)((hvl_t *)buf)[i].p; + + for (j=0; j<((hvl_t *)buf)[i].len; j++ ) { + if (update_ref_value(attr_id, H5R_DATASET_REGION, &(ptr[j]), fidout, &ref_out, travt)<0) + continue; + HDmemcpy(&(ptr[j]), &ref_out, msize); + } + } /* for (i=0; i<nelems; i++) */ + } + } /* else if (is_ref_vlen) */ + else if (is_ref_comp) { + /* handle ref fields in a compound */ + + buf = HDmalloc((unsigned)(nelmts * msize)); + refbuf = buf; /* reuse the read buffer for write */ + + if(buf == NULL) + { + printf( "cannot read into memory\n" ); + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "HDmalloc failed"); + } /* end if */ + + if(H5Aread(attr_id, mtype_id, buf) < 0) + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Aread failed"); + + for (i=0; i<(unsigned)nelmts; i++) { + for (j=0; j<(unsigned)ref_comp_field_n; j++) { + if (ref_comp_size[j] == H5R_OBJ_REF_BUF_SIZE) { + size_t idx = (i * msize) + H5Tget_member_offset(mtype_id, ref_comp_index[j]); + hobj_ref_t ref_out; + + if (update_ref_value(attr_id, H5R_OBJECT, (hobj_ref_t *)(((char *)buf)+idx), fidout, &ref_out, travt)<0) + continue; + HDmemcpy(((char *)buf)+idx, &ref_out, ref_comp_size[j]); + } /* if */ + else if (ref_comp_size[j] == H5R_DSET_REG_REF_BUF_SIZE) { + size_t idx = i * msize + H5Tget_member_offset(mtype_id, ref_comp_index[j]); + hdset_reg_ref_t ref_out; + + if (update_ref_value(attr_id, H5R_DATASET_REGION, (hdset_reg_ref_t *)(((char *)buf)+idx), fidout, &ref_out, travt)<0) + continue; + HDmemcpy(((char *)buf)+idx, &ref_out, ref_comp_size[j]); + } /* else if */ + } /* j */ + } /* i */ + } /* else if (is_ref_comp) */ + + if(H5Awrite(attr_out, mtype_id, refbuf) < 0) + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Awrite failed"); + + if (is_ref_vlen && buf) + H5Dvlen_reclaim (mtype_id, space_id, H5P_DEFAULT, buf); + } /* if (nelmts) */ + + if (refbuf == buf) + refbuf = NULL; /* set it to NULL to avoid double free since buf and refbuf are the same. */ + + if(buf) { + HDfree(buf); + buf = NULL; + } + + if(refbuf) { + HDfree(refbuf); + refbuf = NULL; + } + + if (ref_comp_index) { + HDfree(ref_comp_index); + ref_comp_index = NULL; + } + + if (ref_comp_size) { + HDfree(ref_comp_size); + ref_comp_size = NULL; + } + + if(H5Aclose(attr_out) < 0) + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Aclose failed"); + + /*------------------------------------------------------------------------- + * close + *------------------------------------------------------------------------- + */ + if(H5Tclose(ftype_id) < 0) + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Tclose failed"); + if(H5Tclose(mtype_id) < 0) + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Tclose failed"); + if(H5Sclose(space_id) < 0) + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Sclose failed"); + if(H5Aclose(attr_id) < 0) + 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); + if(buf) + HDfree(buf); + + if (ref_comp_index) + HDfree(ref_comp_index); + + if (ref_comp_size) + HDfree(ref_comp_size); + + H5E_BEGIN_TRY { + H5Tclose(ftype_id); + H5Tclose(mtype_id); + H5Sclose(space_id); + H5Aclose(attr_id); + H5Aclose(attr_out); + } H5E_END_TRY; + + return ret_value; +} + +/*------------------------------------------------------------------------- + * Function: MapIdToName + * + * Purpose: map a ID from a reference to a dataset name + * + *------------------------------------------------------------------------- + */ +static const char* +MapIdToName(hid_t refobj_id, trav_table_t *travt) +{ + unsigned int u; + const char* ret = NULL; + + /* linear search */ + for(u = 0; u < travt->nobjs; u++) { + if(travt->objs[u].type == (h5trav_type_t)H5O_TYPE_DATASET || + travt->objs[u].type == (h5trav_type_t)H5O_TYPE_GROUP || + travt->objs[u].type == (h5trav_type_t)H5O_TYPE_NAMED_DATATYPE) { + H5O_info_t ref_oinfo; /* Stat for the refobj id */ + + /* obtain information to identify the referenced object uniquely */ + if(H5Oget_info(refobj_id, &ref_oinfo) < 0) + goto out; + + if(ref_oinfo.addr == travt->objs[u].objno) { + ret = travt->objs[u].name; + goto out; + } /* end if */ + } /* end if */ + } /* u */ + +out: + return ret; +} + +/*------------------------------------------------------------------------- + * Function: Update_Ref_value + * + * Purpose: Update a reference value + * + * Programmer: xcao@hdfgroup.org 9/12/2011 + * + *------------------------------------------------------------------------- + */ +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; + + ref_obj_id = H5Rdereference2(obj_id, H5P_DEFAULT, ref_type, ref_in); + if (ref_obj_id < 0) + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Rdereference2 failed"); + + ref_obj_name = MapIdToName(ref_obj_id, travt); + if (ref_obj_name == NULL) + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "MapIdToName failed"); + + if (ref_type == H5R_DATASET_REGION) { + space_id = H5Rget_region(obj_id, H5R_DATASET_REGION, ref_in); + if (space_id < 0) + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Rget_region failed"); + } + + if(H5Rcreate(ref_out, fid_out, ref_obj_name, ref_type, space_id) < 0) + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Rcreate failed"); + +done: + H5E_BEGIN_TRY { + H5Sclose(space_id); + H5Oclose(ref_obj_id); + } H5E_END_TRY; + + return ret_value; +} + |