/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * Copyright by The HDF Group. * * 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 COPYING file, which can be found at the root of the source code * * distribution tree, or in https://www.hdfgroup.org/licenses. * * If you do not have access to either file, you may request a copy from * * help@hdfgroup.org. * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ #include "H5private.h" #include "h5repack.h" #include "h5tools.h" #include "h5tools_utils.h" /*------------------------------------------------------------------------- * File: h5repack.c * Purpose: Public API functions *------------------------------------------------------------------------- */ static int check_options(pack_opt_t *options); static int check_objects(const char *fname, pack_opt_t *options); static const char *get_sfilter(H5Z_filter_t filtn); static int have_request(pack_opt_t *options); /*------------------------------------------------------------------------- * Function: h5repack * * Purpose: locate all high-level HDF5 objects in the file * and compress/chunk them using options * * Algorithm: 2 traversals are made to the file; the 1st builds a list of * the objects, the 2nd makes a copy of them, using the options; * the reason for the 1st traversal is to check for invalid * object name requests * * Return: 0, ok, -1, fail *------------------------------------------------------------------------- */ int h5repack(const char *infile, const char *outfile, pack_opt_t *options) { /* check input */ if (check_options(options) < 0) return -1; /* check for objects in input that are in the file */ if (check_objects(infile, options) < 0) return -1; /* copy the objects */ if (copy_objects(infile, outfile, options) < 0) return -1; return 0; } /* end h5repack() */ /*------------------------------------------------------------------------- * Function: h5repack_init * * Purpose: initialize options * * Return: 0, ok, -1, fail *------------------------------------------------------------------------- */ int h5repack_init(pack_opt_t *options, int verbose, hbool_t latest) { int k, n; HDmemset(options, 0, sizeof(pack_opt_t)); options->min_comp = 0; options->verbose = verbose; options->latest = latest; options->layout_g = H5D_LAYOUT_ERROR; options->low_bound = H5F_LIBVER_EARLIEST; options->high_bound = H5F_LIBVER_LATEST; options->fin_fapl = H5P_DEFAULT; options->fout_fapl = H5P_DEFAULT; for (n = 0; n < H5_REPACK_MAX_NFILTERS; n++) { options->filter_g[n].filtn = -1; options->filter_g[n].cd_nelmts = 0; for (k = 0; k < CD_VALUES; k++) options->filter_g[n].cd_values[k] = 0; } return (options_table_init(&(options->op_tbl))); } /* end h5repack_init() */ /*------------------------------------------------------------------------- * Function: h5repack_end * * Purpose: free options table *------------------------------------------------------------------------- */ int h5repack_end(pack_opt_t *options) { return options_table_free(options->op_tbl); } /* end h5repack_end() */ /*------------------------------------------------------------------------- * Function: h5repack_addfilter * * Purpose: add a compression -f option to table * Example: -f dset:GZIP=6 * * Return: 0, ok, -1, fail *------------------------------------------------------------------------- */ int h5repack_addfilter(const char *str, pack_opt_t *options) { obj_list_t *obj_list = NULL; /* one object list for the -f and -l option entry */ filter_info_t filter; /* filter info for the current -f option entry */ unsigned n_objs; /* number of objects in the current -f or -l option entry */ int is_glb; /* is the filter global */ /* parse the -f (--filter) option */ if (NULL == (obj_list = parse_filter(str, &n_objs, &filter, options, &is_glb))) return -1; /* if it applies to all objects */ if (is_glb) { int n; n = options->n_filter_g++; /* increase # of global filters */ if (options->n_filter_g > H5_REPACK_MAX_NFILTERS) { error_msg("maximum number of filters exceeded for <%s>\n", str); HDfree(obj_list); return -1; } options->filter_g[n] = filter; } else options_add_filter(obj_list, n_objs, filter, options->op_tbl); HDfree(obj_list); return 0; } /* end h5repack_addfilter() */ /*------------------------------------------------------------------------- * Function: h5repack_addlayout * * Purpose: add a layout option * * Return: 0, ok, -1, fail *------------------------------------------------------------------------- */ int h5repack_addlayout(const char *str, pack_opt_t *options) { obj_list_t *obj_list = NULL; /*one object list for the -t and -c option entry */ unsigned n_objs; /*number of objects in the current -t or -c option entry */ pack_info_t pack; /*info about layout to extract from parse */ int j; int ret_value = -1; init_packobject(&pack); if (options->all_layout == 1) { error_msg("invalid layout input: 'all' option is present with other objects <%s>\n", str); return ret_value; } /* parse the layout option */ obj_list = parse_layout(str, &n_objs, &pack, options); if (obj_list) { /* set layout option */ options->layout_g = pack.layout; /* no individual dataset specified */ if (options->all_layout == 1) { if (pack.layout == H5D_CHUNKED) { /* -2 means the NONE option, remove chunking and set the global layout to contiguous */ if (pack.chunk.rank == -2) /* TODO: fix 'magic number' */ options->layout_g = H5D_CONTIGUOUS; /* otherwise set the global chunking type */ else { options->chunk_g.rank = pack.chunk.rank; for (j = 0; j < pack.chunk.rank; j++) options->chunk_g.chunk_lengths[j] = pack.chunk.chunk_lengths[j]; } } } /* individual dataset specified */ if (options->all_layout == 0) ret_value = options_add_layout(obj_list, n_objs, &pack, options->op_tbl); HDfree(obj_list); ret_value = 0; } /* end if obj_list exists */ return ret_value; } /* end h5repack_addlayout() */ /* Note: The below copy_named_datatype(), named_datatype_free(), copy_attr() * were located in h5repack_copy.c as static prior to bugfix1726. * Made shared functions as copy_attr() was needed in h5repack_refs.c. * However copy_attr() may be obsoleted when H5Acopy is available and put back * others to static in h5repack_copy.c. */ /*------------------------------------------------------------------------- * Function: copy_named_datatype * * Purpose: Copies the specified datatype anonymously, and returns an open * id for that datatype in the output file. The first time this * is called it scans every named datatype in travt into a * private stack, afterwards it simply scans that stack. The id * returned must be closed after it is no longer needed. * named_datatype_free must be called before the program exits * to free the stack. *------------------------------------------------------------------------- */ hid_t copy_named_datatype(hid_t type_in, hid_t fidout, named_dt_t **named_dt_head_p, trav_table_t *travt, pack_opt_t *options) { named_dt_t *dt = NULL; /* Stack pointer */ named_dt_t *dt_ret = NULL; /* Datatype to return */ H5O_info2_t oinfo; /* Object info of input dtype */ int token_cmp; hid_t ret_value = H5I_INVALID_HID; if (H5Oget_info3(type_in, &oinfo, H5O_INFO_BASIC) < 0) H5TOOLS_GOTO_ERROR(H5I_INVALID_HID, "H5Oget_info failed"); if (*named_dt_head_p) { /* Search the stack for the datatype. */ for (dt = *named_dt_head_p; dt != NULL; dt = dt->next) { if (H5Otoken_cmp(type_in, &dt->obj_token, &oinfo.token, &token_cmp) < 0) H5TOOLS_GOTO_ERROR(H5I_INVALID_HID, "failed to compare object tokens"); if (token_cmp == 0) break; // found it! } dt_ret = dt; } else { /* Create the stack */ size_t i; for (i = 0; i < travt->nobjs; i++) { if (travt->objs[i].type == H5TRAV_TYPE_NAMED_DATATYPE) { /* Push onto the stack */ if (NULL == (dt = (named_dt_t *)HDmalloc(sizeof(named_dt_t)))) H5TOOLS_GOTO_ERROR(H5I_INVALID_HID, "buffer allocation failed failed"); dt->next = *named_dt_head_p; *named_dt_head_p = dt; /* Update the token/address and id */ HDmemcpy(&dt->obj_token, &travt->objs[i].obj_token, sizeof(H5O_token_t)); dt->id_out = H5I_INVALID_HID; /* Check if this type is the one requested */ if (H5Otoken_cmp(type_in, &oinfo.token, &dt->obj_token, &token_cmp) < 0) H5TOOLS_GOTO_ERROR(H5I_INVALID_HID, "failed to compare object tokens"); if (!token_cmp) dt_ret = dt; } /* end if named datatype */ } /* end for each object in traversal table */ } /* end else (create the stack) */ /* Handle the case that the requested datatype was not found. This is * possible if the datatype was committed anonymously in the input file. */ if (!dt_ret) { /* Push the new datatype onto the stack */ if (NULL == (dt_ret = (named_dt_t *)HDmalloc(sizeof(named_dt_t)))) H5TOOLS_GOTO_ERROR(H5I_INVALID_HID, "buffer allocation failed failed"); dt_ret->next = *named_dt_head_p; *named_dt_head_p = dt_ret; /* Update the token/address and id */ HDmemcpy(&dt_ret->obj_token, &oinfo.token, sizeof(H5O_token_t)); dt_ret->id_out = H5I_INVALID_HID; } /* end if requested datatype not found */ /* If the requested datatype does not yet exist in the output file, copy it * anonymously */ if (dt_ret->id_out < 0) { if (options->use_native == 1) dt_ret->id_out = H5Tget_native_type(type_in, H5T_DIR_DEFAULT); else dt_ret->id_out = H5Tcopy(type_in); if (dt_ret->id_out < 0) H5TOOLS_GOTO_ERROR(H5I_INVALID_HID, "H5Tget_native_type-H5Tcopy failed"); if (H5Tcommit_anon(fidout, dt_ret->id_out, H5P_DEFAULT, H5P_DEFAULT) < 0) H5TOOLS_GOTO_ERROR(H5I_INVALID_HID, "H5Tcommit_anon failed"); } /* end if named datatype not yet in output file */ /* Set return value */ ret_value = dt_ret->id_out; /* Increment the ref count on id_out, because the calling function will try * to close it. (TODO: fix scope envy) */ if (H5Iinc_ref(ret_value) < 0) H5TOOLS_GOTO_ERROR(H5I_INVALID_HID, "H5Iinc_ref failed"); done: return ret_value; } /* end copy_named_datatype() */ /*------------------------------------------------------------------------- * Function: named_datatype_free * * Purpose: Frees the stack of named datatypes. *------------------------------------------------------------------------- */ int named_datatype_free(named_dt_t **named_dt_head_p, int ignore_err) { named_dt_t *dt = *named_dt_head_p; int ret_value = -1; while (dt) { /* Pop the datatype off the stack and free it */ if (H5Tclose(dt->id_out) < 0 && !ignore_err) H5TOOLS_GOTO_ERROR((-1), "H5Tclose failed"); dt = dt->next; HDfree(*named_dt_head_p); *named_dt_head_p = dt; } ret_value = 0; done: return (ret_value); } /* end named_datatype_free() */ /*------------------------------------------------------------------------- * Function: copy_attr * * Purpose: copy attributes located in LOC_IN, which is obtained either from * loc_id = H5Gopen2( fid, name); * loc_id = H5Dopen2( fid, name); * loc_id = H5Topen2( fid, name); * * Return: 0, ok, -1 no *------------------------------------------------------------------------- */ int copy_attr(hid_t loc_in, hid_t loc_out, named_dt_t **named_dt_head_p, trav_table_t *travt, pack_opt_t *options) { hid_t attr_id = H5I_INVALID_HID; /* attr ID */ hid_t attr_out = H5I_INVALID_HID; /* attr ID */ hid_t space_id = H5I_INVALID_HID; /* space ID */ hid_t ftype_id = H5I_INVALID_HID; /* file type ID */ hid_t wtype_id = H5I_INVALID_HID; /* read/write type ID */ size_t msize; /* size of type */ void *buf = NULL; /* data buffer */ hsize_t nelmts; /* number of elements in dataset */ int rank; /* rank of dataset */ htri_t is_named; /* Whether the datatype is named */ hsize_t dims[H5S_MAX_RANK]; /* dimensions of dataset */ H5_timer_t timer; /* Timer for read/write operations */ H5_timevals_t times; /* Elapsed time for each operation */ static double read_time = 0; static double write_time = 0; char name[255]; H5O_info2_t oinfo; /* object info */ int j; unsigned u; hbool_t is_ref = 0; H5T_class_t type_class = -1; int ret_value = 0; if (H5Oget_info3(loc_in, &oinfo, H5O_INFO_NUM_ATTRS) < 0) H5TOOLS_GOTO_ERROR((-1), "H5Oget_info failed"); /*------------------------------------------------------------------------- * copy all attributes *------------------------------------------------------------------------- */ for (u = 0; u < (unsigned)oinfo.num_attrs; u++) { /* 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) H5TOOLS_GOTO_ERROR((-1), "H5Aopen_by_idx failed"); if (H5Aget_name(attr_id, (size_t)255, name) < 0) H5TOOLS_GOTO_ERROR((-1), "H5Pclose failed"); /* get the file datatype */ if ((ftype_id = H5Aget_type(attr_id)) < 0) H5TOOLS_GOTO_ERROR((-1), "H5Aget_type failed"); /* Check if the datatype is committed */ if ((is_named = H5Tcommitted(ftype_id)) < 0) H5TOOLS_GOTO_ERROR((-1), "H5Tcommitted failed"); if (is_named && travt) { hid_t fidout = H5I_INVALID_HID; /* Create out file id */ if ((fidout = H5Iget_file_id(loc_out)) < 0) H5TOOLS_GOTO_ERROR((-1), "H5Iget_file_id failed"); /* Copy named dt */ if ((wtype_id = copy_named_datatype(ftype_id, fidout, named_dt_head_p, travt, options)) < 0) { H5Fclose(fidout); H5TOOLS_GOTO_ERROR((-1), "copy_named_datatype failed"); } if (H5Fclose(fidout) < 0) H5TOOLS_GOTO_ERROR((-1), "H5Fclose failed"); } /* end if datatype is committed and we have a traversal table */ else { if (options->use_native == 1) wtype_id = H5Tget_native_type(ftype_id, H5T_DIR_DEFAULT); else wtype_id = H5Tcopy(ftype_id); } /* end else: uncommitted datatype and/or no traversal table */ /* get the dataspace handle */ if ((space_id = H5Aget_space(attr_id)) < 0) H5TOOLS_GOTO_ERROR((-1), "H5Aget_space failed"); /* get dimensions */ if ((rank = H5Sget_simple_extent_dims(space_id, dims, NULL)) < 0) H5TOOLS_GOTO_ERROR((-1), "H5Sget_simple_extent_dims failed"); nelmts = 1; for (j = 0; j < rank; j++) nelmts *= dims[j]; if ((msize = H5Tget_size(wtype_id)) == 0) H5TOOLS_GOTO_ERROR((-1), "H5Tget_size failed"); /*--------------------------------------------------------------------- * object references are a special case. We cannot just copy the * buffers, but instead we recreate the reference. * This is done on a second sweep of the file that just copies the * referenced objects at copy_refs_attr(). *--------------------------------------------------------------------- */ type_class = H5Tget_class(wtype_id); is_ref = (type_class == H5T_REFERENCE); if (type_class == H5T_VLEN || type_class == H5T_ARRAY) { hid_t base_type = H5I_INVALID_HID; base_type = H5Tget_super(ftype_id); is_ref = (is_ref || (H5Tget_class(base_type) == H5T_REFERENCE)); if (H5Tclose(base_type) < 0) H5TOOLS_ERROR((-1), "H5Tclose base_type failed"); } /* end if type_class is variable length or array */ if (type_class == H5T_COMPOUND) { int nmembers = H5Tget_nmembers(wtype_id); for (j = 0; j < nmembers; j++) { hid_t mtid = H5Tget_member_type(wtype_id, (unsigned)j); H5T_class_t mtclass = H5Tget_class(mtid); if (H5Tclose(mtid) < 0) H5TOOLS_ERROR((-1), "H5Tclose mtid failed"); if (mtclass == H5T_REFERENCE) { is_ref = 1; break; } } /* end for each member */ } /* end if type_class is H5T_COMPOUND */ read_time = 0; write_time = 0; if (!is_ref) { /*----------------------------------------------------------------- * read to memory *----------------------------------------------------------------- */ buf = (void *)HDmalloc((size_t)(nelmts * msize)); if (buf == NULL) { H5TOOLS_GOTO_ERROR((-1), "HDmalloc failed"); } /* end if */ if (options->verbose == 2) { H5_timer_init(&timer); H5_timer_start(&timer); } if (H5Aread(attr_id, wtype_id, buf) < 0) H5TOOLS_GOTO_ERROR((-1), "H5Aread failed"); if (options->verbose == 2) { H5_timer_stop(&timer); H5_timer_get_times(timer, ×); read_time += times.elapsed; } /*----------------------------------------------------------------- * copy *----------------------------------------------------------------- */ if ((attr_out = H5Acreate2(loc_out, name, wtype_id, space_id, H5P_DEFAULT, H5P_DEFAULT)) < 0) H5TOOLS_GOTO_ERROR((-1), "H5Acreate2 failed on ,%s>", name); if (options->verbose == 2) { H5_timer_init(&timer); H5_timer_start(&timer); } if (H5Awrite(attr_out, wtype_id, buf) < 0) H5TOOLS_GOTO_ERROR((-1), "H5Awrite failed"); if (options->verbose == 2) { H5_timer_stop(&timer); H5_timer_get_times(timer, ×); write_time += times.elapsed; } /*close*/ if (H5Aclose(attr_out) < 0) H5TOOLS_GOTO_ERROR((-1), "H5Aclose failed"); /* Check if we have VL data and string in the attribute's datatype that must * be reclaimed */ if (TRUE == h5tools_detect_vlen(wtype_id)) H5Treclaim(wtype_id, space_id, H5P_DEFAULT, buf); HDfree(buf); buf = NULL; } /*H5T_REFERENCE*/ if (options->verbose > 0) { if (options->verbose == 2) HDprintf(FORMAT_OBJ_ATTR_TIME, "attr", read_time, write_time, name); else HDprintf(FORMAT_OBJ_ATTR, "attr", name); } /*--------------------------------------------------------------------- * close *--------------------------------------------------------------------- */ if (H5Sclose(space_id) < 0) H5TOOLS_GOTO_ERROR((-1), "H5Sclose failed"); space_id = H5I_INVALID_HID; if (H5Tclose(wtype_id) < 0) H5TOOLS_GOTO_ERROR((-1), "H5Tclose failed"); wtype_id = H5I_INVALID_HID; if (H5Tclose(ftype_id) < 0) H5TOOLS_GOTO_ERROR((-1), "H5Tclose failed"); ftype_id = H5I_INVALID_HID; if (H5Aclose(attr_id) < 0) H5TOOLS_GOTO_ERROR((-1), "H5Aclose failed"); attr_id = H5I_INVALID_HID; } /* for u (each attribute) */ done: H5E_BEGIN_TRY { if (buf) { /* Check if we have VL data and string in the attribute's * datatype that must be reclaimed */ if (TRUE == h5tools_detect_vlen(wtype_id)) H5Treclaim(wtype_id, space_id, H5P_DEFAULT, buf); /* Free buf */ HDfree(buf); } H5Aclose(attr_out); H5Sclose(space_id); H5Tclose(wtype_id); H5Tclose(ftype_id); H5Aclose(attr_id); } H5E_END_TRY; return ret_value; } /* end copy_attr() */ /*----------------------------------------------------------------------------- * Function: check_options * * Purpose: print options, checks for invalid options * * Return: void, return -1 on error *----------------------------------------------------------------------------- */ static int check_options(pack_opt_t *options) { unsigned int i; int k, j, has_cp = 0, has_ck = 0; char slayout[30]; int ret_value = 0; /*------------------------------------------------------------------------- * Objects to layout *------------------------------------------------------------------------- */ if (options->verbose > 0 && have_request(options)) { if (options->all_layout == 1) { HDprintf("All objects to modify layout are...\n"); switch (options->layout_g) { case H5D_COMPACT: strcpy(slayout, "compact"); break; case H5D_CONTIGUOUS: strcpy(slayout, "contiguous"); break; case H5D_CHUNKED: strcpy(slayout, "chunked"); break; case H5D_VIRTUAL: strcpy(slayout, "virtual"); break; case H5D_LAYOUT_ERROR: case H5D_NLAYOUTS: H5TOOLS_GOTO_ERROR((-1), "invalid layout"); break; default: strcpy(slayout, "invalid layout\n"); H5TOOLS_GOTO_DONE((-1)); } HDprintf(" Apply %s layout to all", slayout); if (H5D_CHUNKED == options->layout_g) { HDprintf("with dimension [ "); for (j = 0; j < options->chunk_g.rank; j++) HDprintf("%d ", (int)options->chunk_g.chunk_lengths[j]); HDprintf("]"); } HDprintf("\n"); } else HDprintf("No all objects to modify layout\n"); } /* end if verbose */ for (i = 0; i < options->op_tbl->nelems; i++) { char *name = options->op_tbl->objs[i].path; if (options->op_tbl->objs[i].chunk.rank > 0) { if (options->verbose > 0) { HDprintf(" <%s> with chunk size ", name); for (k = 0; k < options->op_tbl->objs[i].chunk.rank; k++) HDprintf("%d ", (int)options->op_tbl->objs[i].chunk.chunk_lengths[k]); HDprintf("\n"); } has_ck = 1; } else if (options->op_tbl->objs[i].chunk.rank == -2) { /* TODO: replace 'magic number' */ if (options->verbose > 0) HDprintf(" <%s> %s\n", name, "NONE (contiguous)"); has_ck = 1; } } /* end for each object in options */ if (options->all_layout == 1 && has_ck) H5TOOLS_GOTO_ERROR((-1), "invalid chunking input: 'all' option is present with other objects"); /*------------------------------------------------------------------------- * Objects to filter *------------------------------------------------------------------------- */ if (options->verbose > 0 && have_request(options)) { if (options->all_filter == 1) { HDprintf("All objects to apply filter are...\n"); for (k = 0; k < options->n_filter_g; k++) { H5Z_filter_t filtn = options->filter_g[k].filtn; if (filtn < 0) { HDprintf(" Unknown\n"); continue; } switch (filtn) { case H5Z_FILTER_NONE: HDprintf(" Uncompress all\n"); break; case H5Z_FILTER_SHUFFLE: case H5Z_FILTER_FLETCHER32: HDprintf(" All with %s\n", get_sfilter(filtn)); break; case H5Z_FILTER_SZIP: case H5Z_FILTER_DEFLATE: HDprintf(" All with %s, parameter %d\n", get_sfilter(filtn), options->filter_g[k].cd_values[0]); break; default: HDprintf(" User Defined %d\n", filtn); break; } /* end switch */ } /* end for each filter */ } /* end if options->all_filter == 1 (TODO: meaning) */ else HDprintf("No all objects to apply filter\n"); } /* end if verbose */ for (i = 0; i < options->op_tbl->nelems; i++) { pack_info_t pack = options->op_tbl->objs[i]; char *name = pack.path; for (j = 0; j < pack.nfilters; j++) { if (options->verbose > 0) { if (pack.filter[j].filtn >= 0) { if (pack.filter[j].filtn > H5Z_FILTER_SCALEOFFSET) { HDprintf(" <%s> with %s filter %d\n", name, get_sfilter(pack.filter[j].filtn), pack.filter[j].filtn); } else { HDprintf(" <%s> with %s filter\n", name, get_sfilter(pack.filter[j].filtn)); } } } has_cp = 1; } /* end for each filter */ } /* end for each object in options table */ if (options->all_filter == 1 && has_cp) H5TOOLS_GOTO_ERROR((-1), "invalid compression input: 'all' option is present with other objects"); /*------------------------------------------------------------------------- * Check options for the latest format *------------------------------------------------------------------------- */ if (options->grp_compact < 0) H5TOOLS_GOTO_ERROR((-1), "invalid maximum number of links to store as header messages"); if (options->grp_indexed < 0) H5TOOLS_GOTO_ERROR((-1), "invalid minimum number of links to store in the indexed format"); if (options->grp_indexed > options->grp_compact) H5TOOLS_GOTO_ERROR((-1), "minimum indexed size is greater than the maximum compact size"); for (i = 0; i < 8; i++) if (options->msg_size[i] < 0) H5TOOLS_GOTO_ERROR((-1), "invalid shared message size"); /*------------------------------------------------------------------------ * Verify new user userblock options; file name must be present *------------------------------------------------------------------------ */ if (options->ublock_filename != NULL && options->ublock_size == 0) { if (options->verbose > 0) { HDprintf("Warning: user block size missing for file %s. Assigning a default size of 1024...\n", options->ublock_filename); options->ublock_size = 1024; } } if (options->ublock_filename == NULL && options->ublock_size != 0) H5TOOLS_GOTO_ERROR((-1), "file name missing for user block"); /*------------------------------------------------------------------------ * Verify alignment options; threshold is zero default but alignment not *------------------------------------------------------------------------ */ if (options->alignment == 0 && options->threshold != 0) H5TOOLS_GOTO_ERROR((-1), "alignment for H5Pset_alignment missing"); done: return ret_value; } /* end check_options() */ /*------------------------------------------------------------------------- * Function: check_objects * * Purpose: Locate all HDF5 objects in the file and compare with user-supplied * list. * * Return: 0, ok, -1 no *------------------------------------------------------------------------- */ static int check_objects(const char *fname, pack_opt_t *options) { hid_t fid = H5I_INVALID_HID; hid_t did = H5I_INVALID_HID; hid_t sid = H5I_INVALID_HID; unsigned int i; int ifil; trav_table_t *travt = NULL; int ret_value = 0; /* nothing to do */ if (options->op_tbl->nelems == 0) H5TOOLS_GOTO_DONE(0); /*------------------------------------------------------------------------- * open the file *------------------------------------------------------------------------- */ if ((fid = h5tools_fopen(fname, H5F_ACC_RDONLY, options->fin_fapl, (options->fin_fapl != H5P_DEFAULT), NULL, 0)) < 0) H5TOOLS_GOTO_ERROR((-1), "h5tools_fopen failed <%s>: %s", fname, H5FOPENERROR); /*------------------------------------------------------------------------- * get the list of objects in the file *------------------------------------------------------------------------- */ /* Initialize indexing options */ h5trav_set_index(sort_by, sort_order); /* init table */ trav_table_init(fid, &travt); /* get the list of objects in the file */ if (h5trav_gettable(fid, travt) < 0) H5TOOLS_GOTO_ERROR((-1), "h5trav_gettable failed"); /*------------------------------------------------------------------------- * compare with user supplied list *------------------------------------------------------------------------- */ if (options->verbose > 0) HDprintf("Opening file. Searching %zu objects to modify ...\n", travt->nobjs); for (i = 0; i < options->op_tbl->nelems; i++) { pack_info_t obj = options->op_tbl->objs[i]; char *name = obj.path; if (options->verbose > 0) HDprintf(" <%s>", name); /* the input object names are present in the file and are valid */ if (h5trav_getindext(name, travt) < 0) H5TOOLS_GOTO_ERROR((-1), "%s Could not find <%s> in file <%s>. Exiting...\n", (options->verbose > 0 ? "\n" : ""), name, fname); if (options->verbose > 0) HDprintf("...Found\n"); for (ifil = 0; ifil < obj.nfilters; ifil++) { if (obj.filter[ifil].filtn < 0) H5TOOLS_GOTO_ERROR((-1), "invalid filter"); /* check for extra filter conditions */ switch (obj.filter[ifil].filtn) { /* chunk size must be smaller than pixels per block */ case H5Z_FILTER_SZIP: { int j; hsize_t csize = 1; unsigned ppb = obj.filter[ifil].cd_values[0]; hsize_t dims[H5S_MAX_RANK]; int rank; if (obj.chunk.rank > 0) { rank = obj.chunk.rank; for (j = 0; j < rank; j++) csize *= obj.chunk.chunk_lengths[j]; } else { if ((did = H5Dopen2(fid, name, H5P_DEFAULT)) < 0) H5TOOLS_GOTO_ERROR((-1), "H5Dopen2 failed"); if ((sid = H5Dget_space(did)) < 0) H5TOOLS_GOTO_ERROR((-1), "H5Dget_space failed"); if ((rank = H5Sget_simple_extent_ndims(sid)) < 0) H5TOOLS_GOTO_ERROR((-1), "H5Sget_simple_extent_ndims failed"); HDmemset(dims, 0, sizeof dims); if (H5Sget_simple_extent_dims(sid, dims, NULL) < 0) H5TOOLS_GOTO_ERROR((-1), "H5Sget_simple_extent_dims failed"); for (j = 0; j < rank; j++) csize *= dims[j]; if (H5Sclose(sid) < 0) H5TOOLS_GOTO_ERROR((-1), "H5Sclose failed"); if (H5Dclose(did) < 0) H5TOOLS_GOTO_ERROR((-1), "H5Dclose failed"); } if (csize < ppb) { HDprintf(" \n"); H5TOOLS_GOTO_DONE(0); } } /* end case SZIP */ break; default: break; } /* end switch */ } /* for ifil (each user-defined filter) */ } /* for i (each object in options traversal table) */ done: H5E_BEGIN_TRY { H5Sclose(sid); H5Dclose(did); H5Fclose(fid); } H5E_END_TRY; if (travt) trav_table_free(travt); return ret_value; } /* end check_objects() */ /*------------------------------------------------------------------------- * Function: have_request * * Purpose: check if a filter or layout was requested * * Return: 1 yes, 0 no *------------------------------------------------------------------------- */ static int have_request(pack_opt_t *options) { if (options->all_filter || options->all_layout || options->op_tbl->nelems) return 1; return 0; } /* end have_request() */ /*------------------------------------------------------------------------- * Function: get_sfilter * * Purpose: return the filter as a string name * * Return: name of filter, exit on error *------------------------------------------------------------------------- */ static const char * get_sfilter(H5Z_filter_t filtn) { if (filtn < 0) return NULL; else if (filtn == H5Z_FILTER_NONE) return "NONE"; else if (filtn == H5Z_FILTER_DEFLATE) return "GZIP"; else if (filtn == H5Z_FILTER_SZIP) return "SZIP"; else if (filtn == H5Z_FILTER_SHUFFLE) return "SHUFFLE"; else if (filtn == H5Z_FILTER_FLETCHER32) return "FLETCHER32"; else if (filtn == H5Z_FILTER_NBIT) return "NBIT"; else if (filtn == H5Z_FILTER_SCALEOFFSET) return "SOFF"; else return "UD"; } /* end get_sfilter() */