diff options
Diffstat (limited to 'tools/h5repack/h5repack_refs.c')
| -rw-r--r-- | tools/h5repack/h5repack_refs.c | 877 |
1 files changed, 0 insertions, 877 deletions
diff --git a/tools/h5repack/h5repack_refs.c b/tools/h5repack/h5repack_refs.c deleted file mode 100644 index f0f32c3..0000000 --- a/tools/h5repack/h5repack_refs.c +++ /dev/null @@ -1,877 +0,0 @@ -/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * - * 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; -} - |