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| author | Vailin Choi <vchoi@hdfgroup.org> | 2016-10-17 16:10:22 (GMT) |
|---|---|---|
| committer | Vailin Choi <vchoi@hdfgroup.org> | 2016-10-17 16:10:22 (GMT) |
| commit | 48990d1a91ba6d753d7321e3e348d24fde3669ce (patch) | |
| tree | 79fabd3c34c7316aaadb1c706284a72537bed7c9 /tools | |
| parent | 1c35a6084a70e2dbcc1e0f12c785246bc886fc03 (diff) | |
| parent | 8b4633e99d6e447327526663acd30352b5840446 (diff) | |
| download | hdf5-48990d1a91ba6d753d7321e3e348d24fde3669ce.zip hdf5-48990d1a91ba6d753d7321e3e348d24fde3669ce.tar.gz hdf5-48990d1a91ba6d753d7321e3e348d24fde3669ce.tar.bz2 | |
Merging in latest from upstream (HDFFV/hdf5:refs/heads/hdf5_1_8)
* commit '8b4633e99d6e447327526663acd30352b5840446': (29 commits)
Correct usuage of cmake variable
Correct name of windows variable
Add STGZ to cpack generator list for OSX
Add missing exists check from master project
Check file length before compare
Change check for number of dimensions for old-style arrays in datatype decoding routine from an assertion to an if/HGOTO_ERROR check, since it is inappropriate to assert the contents of a file will be what we expect.
Fix mistakes in porting TALOS-177 fix to 1.8.
Fix bug in "nooptype" decode in fix for TALOS-0177.
Fix issues in H5Znbit.c where the decompression algorithm would not check the compressed data for validity, potentially causing a buffer overflow.
Replace assertion in H5O_dtype_decode_helper for number of array dimensions with a check and error. The assertion was inappropriate because it is operating on data read from the file, which the library does not always have direct control of.
HDFFV-9991: Remove unneeded file
Add new test file to MANIFEST
Fix error reporting
Update new test file references
revert merge change to cleanup files
Fix incorrect use of H5Rdereference2
remove merge typo
Remove unsupported function
Merge/align from trunk(develop)
Merge/align with trunk
...
Diffstat (limited to 'tools')
30 files changed, 3361 insertions, 3480 deletions
diff --git a/tools/h5dump/h5dump.c b/tools/h5dump/h5dump.c index 5b953cb..9efb6db 100644 --- a/tools/h5dump/h5dump.c +++ b/tools/h5dump/h5dump.c @@ -620,10 +620,9 @@ parse_hsize_list(const char *h_list, subset_d *d) size_count++; last_digit = 1; - } - else { - last_digit = 0; } + else + last_digit = 0; if (size_count == 0) /* there aren't any integers to read */ @@ -635,7 +634,7 @@ parse_hsize_list(const char *h_list, subset_d *d) for (ptr = h_list; i < size_count && ptr && *ptr && *ptr != ';' && *ptr != ']'; ptr++) if(HDisdigit(*ptr)) { /* we should have an integer now */ - p_list[i++] = (hsize_t)HDatof(ptr); + p_list[i++] = (hsize_t)HDstrtoull(ptr, NULL, 0); while (HDisdigit(*ptr)) /* scroll to end of integer */ @@ -643,8 +642,6 @@ parse_hsize_list(const char *h_list, subset_d *d) } d->data = p_list; d->len = size_count; - - return; } /*------------------------------------------------------------------------- @@ -667,7 +664,7 @@ static struct subset_t * parse_subset_params(char *dset) { struct subset_t *s = NULL; - register char *brace; + char *brace; if (!disable_compact_subset && ((brace = HDstrrchr(dset, '[')) != NULL)) { *brace++ = '\0'; @@ -705,20 +702,21 @@ parse_subset_params(char *dset) * * Purpose: Parse a list of comma or space separated integers and fill * the packed_bits list and counter. The string being passed into this function - * should be at the start of the list you want to parse. + * should be at the start of the list you want to parse. * * Return: Success: SUCCEED * * Failure: FAIL * - * *------------------------------------------------------------------------- */ static int parse_mask_list(const char *h_list) { - int offset_value; - int length_value; + int soffset_value; + unsigned offset_value; + int slength_value; + unsigned length_value; unsigned long long temp_mask; const char *ptr = NULL; @@ -736,10 +734,11 @@ parse_mask_list(const char *h_list) error_msg("Bad mask list(%s)\n", h_list); return FAIL; } - offset_value = HDatoi(ptr); - if (offset_value < 0 || offset_value >= PACKED_BITS_SIZE_MAX) { - error_msg("Packed Bit offset value(%d) must be between 0 and %d\n", - offset_value, PACKED_BITS_SIZE_MAX - 1); + soffset_value = HDatoi(ptr); + offset_value = (unsigned)soffset_value; + if (soffset_value < 0 || offset_value >= PACKED_BITS_SIZE_MAX) { + error_msg("Packed Bit offset value(%d) must be between 0 and %u\n", + soffset_value, (unsigned)(PACKED_BITS_SIZE_MAX - 1)); return FAIL; } @@ -757,14 +756,15 @@ parse_mask_list(const char *h_list) error_msg("Bad mask list(%s)\n", h_list); return FAIL; } - length_value = HDatoi(ptr); - if (length_value <= 0) { - error_msg("Packed Bit length value(%d) must be positive.\n", length_value); + slength_value = HDatoi(ptr); + if (slength_value <= 0) { + error_msg("Packed Bit length value(%d) must be positive.\n", slength_value); return FAIL; } - if ((offset_value + length_value) > PACKED_BITS_SIZE_MAX){ - error_msg("Packed Bit offset+length value(%d) too large. Max is %d\n", - offset_value+length_value, PACKED_BITS_SIZE_MAX); + length_value = (unsigned)slength_value; + if ((offset_value + length_value) > PACKED_BITS_SIZE_MAX) { + error_msg("Packed Bit offset+length value(%u) too large. Max is %u\n", + offset_value+length_value, (unsigned)PACKED_BITS_SIZE_MAX); return FAIL; } @@ -783,8 +783,8 @@ parse_mask_list(const char *h_list) /* create the bit mask by left shift 1's by length, then negate it. */ /* After packed_mask is calculated, packed_length is not needed but */ /* keep it for debug purpose. */ - temp_mask = ~0L; - if(length_value<8*sizeof(unsigned long long)) { + temp_mask = ~0ULL; + if(length_value < (int)(8 *sizeof(unsigned long long))) { temp_mask = temp_mask << length_value; packed_mask[packed_bits_num] = ~temp_mask; } @@ -831,7 +831,7 @@ static void free_handler(struct handler_t *hand, int len) { int i; - + if(hand) { for (i = 0; i < len; i++) { if(hand[i].obj) { @@ -956,11 +956,15 @@ parse_start: goto done; break; case 'w': - h5tools_nCols = HDatoi(opt_arg); - if (h5tools_nCols <= 0) { - h5tools_nCols = 65535; + { + int sh5tools_nCols = HDatoi(opt_arg); + + if (sh5tools_nCols <= 0) + h5tools_nCols = 65535; + else + h5tools_nCols = (unsigned)sh5tools_nCols; + last_was_dset = FALSE; } - last_was_dset = FALSE; break; case 'N': display_all = 0; @@ -1159,12 +1163,10 @@ parse_start: usage(h5tools_getprogname()); goto error; } - if (HDstrcmp(opt_arg,":") == 0) { + if (HDstrcmp(opt_arg,":") == 0) xmlnsprefix = ""; - } - else { + else xmlnsprefix = opt_arg; - } h5tools_nCols = 0; break; /** end XML parameters **/ @@ -1187,7 +1189,7 @@ parse_start: * the two. */ s = last_dset->subset_info; - } + } else { last_dset->subset_info = s = (struct subset_t *)HDcalloc(1, sizeof(struct subset_t)); } @@ -1358,7 +1360,7 @@ main(int argc, const char *argv[]) /* Disable tools error reporting */ H5Eget_auto2(H5tools_ERR_STACK_g, &tools_func, &tools_edata); H5Eset_auto2(H5tools_ERR_STACK_g, NULL, NULL); - + if((hand = parse_command_line(argc, argv))==NULL) { goto done; } @@ -1444,12 +1446,12 @@ main(int argc, const char *argv[]) if (xml_dtd_uri == NULL) { if (useschema) { xml_dtd_uri = DEFAULT_XSD; - } + } else { xml_dtd_uri = DEFAULT_DTD; xmlnsprefix = ""; } - } + } else { if (useschema && HDstrcmp(xmlnsprefix,"")) { error_msg("Cannot set Schema URL for a qualified namespace--use -X or -U option with -D \n"); @@ -1486,7 +1488,7 @@ main(int argc, const char *argv[]) /* start to dump - display file header information */ if (!doxml) { begin_obj(h5tools_dump_header_format->filebegin, fname, h5tools_dump_header_format->fileblockbegin); - } + } else { PRINTVALSTREAM(rawoutstream, "<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n"); @@ -1495,7 +1497,7 @@ main(int argc, const char *argv[]) if (HDstrcmp(xmlnsprefix,"") == 0) { PRINTSTREAM(rawoutstream, "<HDF5-File xmlns:xsi=\"http://www.w3.org/2001/XMLSchema-instance\" xsi:noNamespaceSchemaLocation=\"%s\">\n", xml_dtd_uri); - } + } else { /* TO DO: make -url option work in this case (may need new option) */ char *ns; @@ -1511,7 +1513,7 @@ main(int argc, const char *argv[]) "http://www.hdfgroup.org/HDF5/XML/schema/HDF5-File.xsd\">\n",xmlnsprefix,ns); HDfree(ns); } - } + } else { PRINTSTREAM(rawoutstream, "<!DOCTYPE HDF5-File PUBLIC \"HDF5-File.dtd\" \"%s\">\n", xml_dtd_uri); PRINTVALSTREAM(rawoutstream, "<HDF5-File>\n"); @@ -1570,7 +1572,7 @@ main(int argc, const char *argv[]) if (!doxml) { end_obj(h5tools_dump_header_format->fileend, h5tools_dump_header_format->fileblockend); PRINTVALSTREAM(rawoutstream, "\n"); - } + } else { PRINTSTREAM(rawoutstream, "</%sHDF5-File>\n", xmlnsprefix); } @@ -1591,7 +1593,7 @@ main(int argc, const char *argv[]) } } /* end while */ - if(hand) + if(hand) free_handler(hand, argc); /* To Do: clean up XML table */ @@ -1615,7 +1617,7 @@ done: fname = NULL; } - if(hand) + if(hand) free_handler(hand, argc); /* To Do: clean up XML table */ @@ -1668,20 +1670,20 @@ h5_fileaccess(void) if (!HDstrcmp(name, "sec2")) { /* Unix read() and write() system calls */ if (H5Pset_fapl_sec2(fapl)<0) return -1; - } + } else if (!HDstrcmp(name, "stdio")) { /* Standard C fread() and fwrite() system calls */ if (H5Pset_fapl_stdio(fapl)<0) return -1; - } + } else if (!HDstrcmp(name, "core")) { /* In-core temporary file with 1MB increment */ if (H5Pset_fapl_core(fapl, 1024*1024, FALSE)<0) return -1; - } + } else if (!HDstrcmp(name, "split")) { /* Split meta data and raw data each using default driver */ if (H5Pset_fapl_split(fapl, "-m.h5", H5P_DEFAULT, "-r.h5", H5P_DEFAULT) < 0) return -1; - } + } else if (!HDstrcmp(name, "multi")) { /* Multi-file driver, general case of the split driver */ H5FD_mem_t memb_map[H5FD_MEM_NTYPES]; @@ -1702,12 +1704,12 @@ h5_fileaccess(void) memb_map[mt] = mt; sprintf(sv[mt], "%%s-%c.h5", multi_letters[mt]); memb_name[mt] = sv[mt]; - memb_addr[mt] = MAX(mt-1,0)*(HADDR_MAX/10); + memb_addr[mt] = (haddr_t)MAX(mt - 1, 0) * (HADDR_MAX / 10); } if (H5Pset_fapl_multi(fapl, memb_map, memb_fapl, memb_name, memb_addr, FALSE) < 0) return -1; - } + } else if (!HDstrcmp(name, "family")) { hsize_t fam_size = 100*1024*1024; /*100 MB*/ @@ -1716,7 +1718,7 @@ h5_fileaccess(void) fam_size = (hsize_t)(HDstrtod(val, NULL) * 1024*1024); if (H5Pset_fapl_family(fapl, fam_size, H5P_DEFAULT)<0) return -1; - } + } else if (!HDstrcmp(name, "log")) { long log_flags = H5FD_LOG_LOC_IO; @@ -1726,12 +1728,12 @@ h5_fileaccess(void) if (H5Pset_fapl_log(fapl, NULL, (unsigned)log_flags, 0) < 0) return -1; - } + } else if (!HDstrcmp(name, "direct")) { /* Substitute Direct I/O driver with sec2 driver temporarily because * some output has sec2 driver as the standard. */ if (H5Pset_fapl_sec2(fapl)<0) return -1; - } + } else { /* Unknown driver */ return -1; diff --git a/tools/h5dump/h5dump.h b/tools/h5dump/h5dump.h index a1f5b22..e9b8233 100644 --- a/tools/h5dump/h5dump.h +++ b/tools/h5dump/h5dump.h @@ -39,11 +39,11 @@ typedef struct dump_functions_t { /* List of table structures. There is one table structure for each file */ typedef struct h5dump_table_items_t { - unsigned long fileno; /* File number that these tables refer to */ - hid_t oid; /* ID of an object in this file, held open so fileno is consistent */ - table_t *group_table; /* Table of groups */ - table_t *dset_table; /* Table of datasets */ - table_t *type_table; /* Table of datatypes */ + unsigned long fileno; /* File number that these tables refer to */ + hid_t oid; /* ID of an object in this file, held open so fileno is consistent */ + table_t *group_table; /* Table of groups */ + table_t *dset_table; /* Table of datasets */ + table_t *type_table; /* Table of datatypes */ } h5dump_table_items_t; typedef struct h5dump_table_list_t { size_t nalloc; @@ -53,7 +53,7 @@ typedef struct h5dump_table_list_t { h5dump_table_list_t table_list = {0, 0, NULL}; table_t *group_table = NULL, *dset_table = NULL, *type_table = NULL; -int dump_indent = 0; /*how far in to indent the line */ +unsigned dump_indent = 0; /*how far in to indent the line */ int unamedtype = 0; /* shared datatype with no name */ hbool_t hit_elink = FALSE; /* whether we have traversed an external link */ @@ -74,7 +74,6 @@ int display_fi = FALSE; /*file index */ int display_ai = TRUE; /*array index */ int display_escape = FALSE; /*escape non printable characters */ int display_region = FALSE; /*print region reference data */ -int enable_error_stack= FALSE; /* re-enable error stack */ int disable_compact_subset= FALSE; /* disable compact form of subset notation */ int display_packed_bits = FALSE; /*print 1-8 byte numbers as packed bits*/ int include_attrs = TRUE; /* Display attributes */ @@ -84,13 +83,13 @@ H5_index_t sort_by = H5_INDEX_NAME; /*sort_by [creation_order | name H5_iter_order_t sort_order = H5_ITER_INC; /*sort_order [ascending | descending] */ #define PACKED_BITS_MAX 8 /* Maximum number of packed-bits to display */ -#define PACKED_BITS_SIZE_MAX 8*sizeof(long long) /* Maximum bits size of integer types of packed-bits */ +#define PACKED_BITS_SIZE_MAX (8*sizeof(long long)) /* Maximum bits size of integer types of packed-bits */ /* mask list for packed bits */ unsigned long long packed_mask[PACKED_BITS_MAX]; /* packed bits are restricted to 8*sizeof(llong) bytes */ /* packed bits display parameters */ -int packed_offset[PACKED_BITS_MAX]; -int packed_length[PACKED_BITS_MAX]; +unsigned packed_offset[PACKED_BITS_MAX]; +unsigned packed_length[PACKED_BITS_MAX]; /* * The global table is set to either ddl_function_table or diff --git a/tools/h5dump/h5dump_ddl.c b/tools/h5dump/h5dump_ddl.c index 0324a52..c0b1833 100644 --- a/tools/h5dump/h5dump_ddl.c +++ b/tools/h5dump/h5dump_ddl.c @@ -26,12 +26,12 @@ typedef struct { hid_t fid; /* File ID being traversed */ - char *op_name; /* Object name wanted */ + const char *op_name; /* Object name wanted */ } trav_handle_udata_t; typedef struct { - char *path; /* Path of object being searched */ - char *op_name; /* Object name wanted */ + const char *path; /* Path of object being searched */ + const char *op_name; /* Object name wanted */ } trav_attr_udata_t; /* callback function used by H5Literate() */ @@ -59,7 +59,7 @@ dump_datatype(hid_t type) h5tool_format_t *outputformat = &h5tools_dataformat; HDmemset(&ctx, 0, sizeof(ctx)); - ctx.indent_level = dump_indent/COL; + ctx.indent_level = dump_indent / COL; ctx.cur_column = dump_indent; h5dump_type_table = type_table; @@ -88,9 +88,9 @@ dump_dataspace(hid_t space) h5tool_format_t *outputformat = &h5tools_dataformat; HDmemset(&ctx, 0, sizeof(ctx)); - ctx.indent_level = dump_indent/COL; + ctx.indent_level = dump_indent / COL; ctx.cur_column = dump_indent; - + h5tools_dump_dataspace(rawoutstream, outputformat, &ctx, space); } @@ -117,19 +117,19 @@ dump_attr_cb(hid_t oid, const char *attr_name, const H5A_info_t H5_ATTR_UNUSED * h5tools_context_t ctx; /* print context */ h5tool_format_t *outputformat = &h5tools_dataformat; h5tool_format_t string_dataformat; - + hid_t attr_id; herr_t ret = SUCCEED; HDmemset(&ctx, 0, sizeof(ctx)); - ctx.indent_level = dump_indent/COL; + ctx.indent_level = dump_indent / COL; ctx.cur_column = dump_indent; - + attr_id = H5Aopen(oid, attr_name, H5P_DEFAULT); oid_output = display_oid; data_output = display_data; attr_data_output = display_attr_data; - + string_dataformat = *outputformat; if (fp_format) { @@ -137,7 +137,7 @@ dump_attr_cb(hid_t oid, const char *attr_name, const H5A_info_t H5_ATTR_UNUSED * string_dataformat.fmt_float = fp_format; } - if (h5tools_nCols==0) { + if (h5tools_nCols == 0) { string_dataformat.line_ncols = 65535; string_dataformat.line_per_line = 1; } @@ -155,7 +155,7 @@ dump_attr_cb(hid_t oid, const char *attr_name, const H5A_info_t H5_ATTR_UNUSED * h5tools_setstatus(EXIT_FAILURE); ret = FAIL; } - + return ret; } @@ -197,9 +197,9 @@ dump_all_cb(hid_t group, const char *name, const H5L_info_t *linfo, void H5_ATTR HDmemset(&buffer, 0, sizeof(h5tools_str_t)); HDmemset(&ctx, 0, sizeof(ctx)); - ctx.indent_level = dump_indent/COL; + ctx.indent_level = dump_indent / COL; ctx.cur_column = dump_indent; - + string_dataformat = *outputformat; if (fp_format) { @@ -207,7 +207,7 @@ dump_all_cb(hid_t group, const char *name, const H5L_info_t *linfo, void H5_ATTR string_dataformat.fmt_float = fp_format; } - if (h5tools_nCols==0) { + if (h5tools_nCols == 0) { string_dataformat.line_ncols = 65535; string_dataformat.line_per_line = 1; } @@ -222,8 +222,8 @@ dump_all_cb(hid_t group, const char *name, const H5L_info_t *linfo, void H5_ATTR if(!obj_path) { ret = FAIL; goto done; - } - + } + HDstrcpy(obj_path, prefix); HDstrcat(obj_path, "/"); HDstrcat(obj_path, name); @@ -310,7 +310,7 @@ dump_all_cb(hid_t group, const char *name, const H5L_info_t *linfo, void H5_ATTR ret = FAIL; H5Dclose(obj); goto done; - } + } else if(found_obj->displayed) { ctx.need_prefix = TRUE; h5tools_simple_prefix(rawoutstream, outputformat, &ctx, (hsize_t)0, 0); @@ -349,7 +349,7 @@ dump_all_cb(hid_t group, const char *name, const H5L_info_t *linfo, void H5_ATTR H5Dclose(obj); goto done; - } + } else { found_obj->displayed = TRUE; } @@ -357,7 +357,7 @@ dump_all_cb(hid_t group, const char *name, const H5L_info_t *linfo, void H5_ATTR dump_function_table->dump_dataset_function(obj, name, NULL); H5Dclose(obj); - } + } else { error_msg("unable to dump dataset \"%s\"\n", name); h5tools_setstatus(EXIT_FAILURE); @@ -370,7 +370,7 @@ dump_all_cb(hid_t group, const char *name, const H5L_info_t *linfo, void H5_ATTR error_msg("unable to dump datatype \"%s\"\n", name); h5tools_setstatus(EXIT_FAILURE); ret = FAIL; - } + } else { dump_function_table->dump_named_datatype_function(obj, name); H5Tclose(obj); @@ -408,7 +408,7 @@ dump_all_cb(hid_t group, const char *name, const H5L_info_t *linfo, void H5_ATTR error_msg("unable to get link value\n"); h5tools_setstatus(EXIT_FAILURE); ret = FAIL; - } + } else { /* print the value of a soft link */ /* Standard DDL: no modification */ @@ -558,7 +558,7 @@ dump_all_cb(hid_t group, const char *name, const H5L_info_t *linfo, void H5_ATTR done: h5tools_str_close(&buffer); - + if(obj_path) HDfree(obj_path); return ret; @@ -648,9 +648,9 @@ dump_named_datatype(hid_t tid, const char *name) HDmemset(&buffer, 0, sizeof(h5tools_str_t)); HDmemset(&ctx, 0, sizeof(ctx)); - ctx.indent_level = dump_indent/COL; + ctx.indent_level = dump_indent / COL; ctx.cur_column = dump_indent; - + string_dataformat = *outputformat; if (fp_format) { @@ -658,7 +658,7 @@ dump_named_datatype(hid_t tid, const char *name) string_dataformat.fmt_float = fp_format; } - if (h5tools_nCols==0) { + if (h5tools_nCols == 0) { string_dataformat.line_ncols = 65535; string_dataformat.line_per_line = 1; } @@ -685,7 +685,7 @@ dump_named_datatype(hid_t tid, const char *name) } ctx.need_prefix = TRUE; - + /* Render the element */ h5tools_str_reset(&buffer); h5tools_str_append(&buffer, "%s \"%s\" %s", @@ -718,7 +718,7 @@ dump_named_datatype(hid_t tid, const char *name) else found_obj->displayed = TRUE; } /* end if */ - + /* Render the element */ h5tools_str_reset(&buffer); h5tools_print_datatype(rawoutstream, &buffer, outputformat, &ctx, tid, FALSE); @@ -726,7 +726,7 @@ dump_named_datatype(hid_t tid, const char *name) if(H5Tget_class(tid) != H5T_COMPOUND) { h5tools_str_append(&buffer, ";"); } - + h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); /* print attributes */ @@ -811,9 +811,9 @@ dump_group(hid_t gid, const char *name) HDmemset(&buffer, 0, sizeof(h5tools_str_t)); HDmemset(&ctx, 0, sizeof(ctx)); - ctx.indent_level = dump_indent/COL; + ctx.indent_level = dump_indent / COL; ctx.cur_column = dump_indent; - + string_dataformat = *outputformat; if (fp_format) { @@ -821,7 +821,7 @@ dump_group(hid_t gid, const char *name) string_dataformat.fmt_float = fp_format; } - if (h5tools_nCols==0) { + if (h5tools_nCols == 0) { string_dataformat.line_ncols = 65535; string_dataformat.line_per_line = 1; } @@ -839,7 +839,7 @@ dump_group(hid_t gid, const char *name) h5tools_dump_header_format->groupbegin, name, h5tools_dump_header_format->groupblockbegin); h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); - + ctx.indent_level++; dump_indent += COL; @@ -858,9 +858,8 @@ dump_group(hid_t gid, const char *name) } } /* end if */ - if(display_oid) { + if(display_oid) h5tools_dump_oid(rawoutstream, outputformat, &ctx, gid); - } h5tools_dump_comment(rawoutstream, outputformat, &ctx, gid); @@ -946,9 +945,9 @@ dump_dataset(hid_t did, const char *name, struct subset_t *sset) hsize_t curr_pos = 0; /* total data element position */ HDmemset(&ctx, 0, sizeof(ctx)); - ctx.indent_level = dump_indent/COL; + ctx.indent_level = dump_indent / COL; ctx.cur_column = dump_indent; - + string_dataformat = *outputformat; if (fp_format) { @@ -956,7 +955,7 @@ dump_dataset(hid_t did, const char *name, struct subset_t *sset) string_dataformat.fmt_float = fp_format; } - if (h5tools_nCols==0) { + if (h5tools_nCols == 0) { string_dataformat.line_ncols = 65535; string_dataformat.line_per_line = 1; } @@ -982,7 +981,7 @@ dump_dataset(hid_t did, const char *name, struct subset_t *sset) ctx.need_prefix = TRUE; h5tools_simple_prefix(rawoutstream, outputformat, &ctx, (hsize_t)0, 0); - + /* Render the element */ h5tools_str_reset(&buffer); h5tools_str_append(&buffer, "%s \"%s\" %s", @@ -994,7 +993,7 @@ dump_dataset(hid_t did, const char *name, struct subset_t *sset) dump_indent += COL; ctx.indent_level++; - + type = H5Dget_type(did); h5dump_type_table = type_table; h5tools_dump_datatype(rawoutstream, outputformat, &ctx, type); @@ -1016,19 +1015,20 @@ dump_dataset(hid_t did, const char *name, struct subset_t *sset) H5Pclose(dcpl_id); if(display_data) { - int data_loop = 1; - int i; + unsigned data_loop = 1; + unsigned u; + if(display_packed_bits) data_loop = packed_bits_num; - for(i=0; i<data_loop; i++) { + for(u = 0; u < data_loop; u++) { if(display_packed_bits) { ctx.need_prefix = TRUE; h5tools_simple_prefix(rawoutstream, outputformat, &ctx, (hsize_t)0, 0); /* Render the element */ h5tools_str_reset(&buffer); - packed_data_mask = packed_mask[i]; - packed_data_offset = packed_offset[i]; - packed_data_length = packed_length[i]; + packed_data_mask = packed_mask[u]; + packed_data_offset = packed_offset[u]; + packed_data_length = packed_length[u]; h5tools_print_packed_bits(&buffer, type); h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); } @@ -1042,7 +1042,7 @@ dump_dataset(hid_t did, const char *name, struct subset_t *sset) h5tools_str_reset(&buffer); h5tools_str_append(&buffer, "DATA{ not yet implemented.}"); h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); - + ctx.indent_level--; break; @@ -1067,7 +1067,7 @@ dump_dataset(hid_t did, const char *name, struct subset_t *sset) HDassert(0); break; } /* end switch */ - } /* for(i=0;i<data_loop;i++) */ + } /* for(u=0; u<data_loop; u++) */ } H5Tclose(type); @@ -1079,7 +1079,7 @@ dump_dataset(hid_t did, const char *name, struct subset_t *sset) ctx.need_prefix = TRUE; h5tools_simple_prefix(rawoutstream, outputformat, &ctx, (hsize_t)0, 0); - + /* Render the element */ h5tools_str_reset(&buffer); if(HDstrlen(h5tools_dump_header_format->datasetblockend)) { @@ -1124,7 +1124,7 @@ dump_data(hid_t obj_id, int obj_data, struct subset_t *sset, int display_index) string_dataformat.fmt_float = fp_format; } - if (h5tools_nCols==0) { + if (h5tools_nCols == 0) { string_dataformat.line_ncols = 65535; string_dataformat.line_per_line = 1; } @@ -1135,7 +1135,7 @@ dump_data(hid_t obj_id, int obj_data, struct subset_t *sset, int display_index) outputformat = &string_dataformat; HDmemset(&ctx, 0, sizeof(ctx)); - ctx.indent_level = dump_indent/COL; + ctx.indent_level = dump_indent / COL; ctx.cur_column = dump_indent; if(obj_data == DATASET_DATA) @@ -1189,7 +1189,7 @@ dump_fcpl(hid_t fid) fdriver=H5Pget_driver(fapl); H5Pclose(fapl); #endif - + /*------------------------------------------------------------------------- * SUPER_BLOCK *------------------------------------------------------------------------- @@ -1279,9 +1279,8 @@ dump_fcontents(hid_t fid) unsigned u; for (u = 0; u < type_table->nobjs; u++) { - if (!type_table->objs[u].recorded) { + if (!type_table->objs[u].recorded) PRINTSTREAM(rawoutstream, " %-10s /#"H5_PRINTF_HADDR_FMT"\n", "datatype", type_table->objs[u].objno); - } } } @@ -1295,54 +1294,54 @@ static herr_t attr_search(hid_t oid, const char *attr_name, const H5A_info_t H5_ATTR_UNUSED *ainfo, void *_op_data) { herr_t ret = SUCCEED; - int i; - int j; - int k; - char *obj_op_name; + int j; + char *obj_op_name; char *obj_name; - trav_attr_udata_t *attr_data = (trav_attr_udata_t*)_op_data; - char *buf = attr_data->path; - char *op_name = attr_data->op_name; + trav_attr_udata_t *attr_data = (trav_attr_udata_t*)_op_data; + const char *buf = attr_data->path; + const char *op_name = attr_data->op_name; j = (int)HDstrlen(op_name) - 1; /* find the last / */ while(j >= 0) { - if (op_name[j] == '/' && (j==0 || (j>0 && op_name[j-1]!='\\'))) - break; - j--; + if(op_name[j] == '/' && (j == 0 || (j > 0 && op_name[j - 1] != '\\'))) + break; + j--; } obj_op_name = h5tools_str_replace(op_name + j + 1, "\\/", "/"); if(obj_op_name == NULL) { - h5tools_setstatus(EXIT_FAILURE); - ret = FAIL; + h5tools_setstatus(EXIT_FAILURE); + ret = FAIL; } else { - if(HDstrcmp(attr_name, obj_op_name)==0) { - /* object name */ - i = (int)HDstrlen(buf); - j = (int)HDstrlen(op_name); - k = (size_t)i + 1 + (size_t)j + 1 + 2; - obj_name = (char *)HDmalloc((size_t)k); - if(obj_name == NULL) { - h5tools_setstatus(EXIT_FAILURE); - ret = FAIL; - } - else { - HDmemset(obj_name, '\0', (size_t)k); - if(op_name[0] != '/') { - HDstrncat(obj_name, buf, (size_t)i + 1); - if(buf[i-1] != '/') - HDstrncat(obj_name, "/", (size_t)2); - } - HDstrncat(obj_name, op_name, (size_t)j + 1); - - handle_attributes(oid, obj_name, NULL, 0, NULL); - HDfree(obj_name); - } - } - HDfree(obj_op_name); + if(HDstrcmp(attr_name, obj_op_name)==0) { + size_t u, v, w; + + /* object name */ + u = HDstrlen(buf); + v = HDstrlen(op_name); + w = u + 1 + v + 1 + 2; + obj_name = (char *)HDmalloc(w); + if(obj_name == NULL) { + h5tools_setstatus(EXIT_FAILURE); + ret = FAIL; + } + else { + HDmemset(obj_name, '\0', w); + if(op_name[0] != '/') { + HDstrncat(obj_name, buf, u + 1); + if(buf[u - 1] != '/') + HDstrncat(obj_name, "/", (size_t)2); + } + HDstrncat(obj_name, op_name, v + 1); + + handle_attributes(oid, obj_name, NULL, 0, NULL); + HDfree(obj_name); + } + } + HDfree(obj_op_name); } return ret; } /* end attr_search() */ @@ -1350,31 +1349,34 @@ attr_search(hid_t oid, const char *attr_name, const H5A_info_t H5_ATTR_UNUSED *a static herr_t obj_search(const char *path, const H5O_info_t *oi, const char H5_ATTR_UNUSED *already_visited, void *_op_data) { - trav_handle_udata_t *handle_data = (trav_handle_udata_t*)_op_data; - char *op_name = (char*)handle_data->op_name; - + trav_handle_udata_t *handle_data = (trav_handle_udata_t*)_op_data; + const char *op_name = handle_data->op_name; trav_attr_udata_t attr_data; - attr_data.path = (char*)path; + + attr_data.path = path; attr_data.op_name = op_name; H5Aiterate_by_name(handle_data->fid, path, H5_INDEX_NAME, H5_ITER_INC, NULL, attr_search, (void*)&attr_data, H5P_DEFAULT); - if(HDstrcmp(path, op_name)==0) { - switch(oi->type) { - case H5O_TYPE_GROUP: - handle_groups(handle_data->fid, path, NULL, 0, NULL); - break; - case H5O_TYPE_DATASET: - handle_datasets(handle_data->fid, path, NULL, 0, NULL); - break; - case H5O_TYPE_NAMED_DATATYPE: - handle_datatypes(handle_data->fid, path, NULL, 0, NULL); - break; - case H5O_TYPE_UNKNOWN: - case H5O_TYPE_NTYPES: - default: - error_msg("unknown object type value\n"); - h5tools_setstatus(EXIT_FAILURE); - } /* end switch */ + if(HDstrcmp(path, op_name) == 0) { + switch(oi->type) { + case H5O_TYPE_GROUP: + handle_groups(handle_data->fid, path, NULL, 0, NULL); + break; + + case H5O_TYPE_DATASET: + handle_datasets(handle_data->fid, path, NULL, 0, NULL); + break; + + case H5O_TYPE_NAMED_DATATYPE: + handle_datatypes(handle_data->fid, path, NULL, 0, NULL); + break; + + case H5O_TYPE_UNKNOWN: + case H5O_TYPE_NTYPES: + default: + error_msg("unknown object type value\n"); + h5tools_setstatus(EXIT_FAILURE); + } /* end switch */ } return 0; @@ -1383,49 +1385,48 @@ obj_search(const char *path, const H5O_info_t *oi, const char H5_ATTR_UNUSED *al static herr_t lnk_search(const char *path, const H5L_info_t *li, void *_op_data) { - int search_len; - int k; + size_t search_len; + size_t k; char *search_name; - trav_handle_udata_t *handle_data = (trav_handle_udata_t*)_op_data; - char *op_name = (char*)handle_data->op_name; + trav_handle_udata_t *handle_data = (trav_handle_udata_t*)_op_data; + const char *op_name = handle_data->op_name; search_len = HDstrlen(op_name); - if(search_len > 0 && op_name[0] != '/') { - k = 2; - } + if(search_len > 0 && op_name[0] != '/') + k = 2; else k = 1; - search_name = (char *)HDmalloc((size_t)(search_len + k)); + search_name = (char *)HDmalloc(search_len + k); if(search_name == NULL) { - error_msg("creating temporary link\n"); - h5tools_setstatus(EXIT_FAILURE); + error_msg("creating temporary link\n"); + h5tools_setstatus(EXIT_FAILURE); } else { - if (k == 2) { - HDstrcpy(search_name, "/"); - HDstrncat(search_name, op_name, (size_t)search_len + 1); - } - else - HDstrncpy(search_name, op_name, (size_t)search_len + 1); - search_name[search_len + k - 1] = '\0'; - - if(HDstrcmp(path, search_name) == 0) { - switch(li->type) { - case H5L_TYPE_SOFT: - case H5L_TYPE_EXTERNAL: - handle_links(handle_data->fid, op_name, NULL, 0, NULL); - break; - - case H5L_TYPE_HARD: - case H5L_TYPE_MAX: - case H5L_TYPE_ERROR: - default: - error_msg("unknown link type value\n"); - h5tools_setstatus(EXIT_FAILURE); - break; - } /* end switch() */ - } - HDfree(search_name); + if (k == 2) { + HDstrcpy(search_name, "/"); + HDstrncat(search_name, op_name, search_len + 1); + } + else + HDstrncpy(search_name, op_name, search_len + 1); + search_name[search_len + k - 1] = '\0'; + + if(HDstrcmp(path, search_name) == 0) { + switch(li->type) { + case H5L_TYPE_SOFT: + case H5L_TYPE_EXTERNAL: + handle_links(handle_data->fid, op_name, NULL, 0, NULL); + break; + + case H5L_TYPE_HARD: + case H5L_TYPE_MAX: + case H5L_TYPE_ERROR: + default: + error_msg("unknown link type value\n"); + h5tools_setstatus(EXIT_FAILURE); + break; + } /* end switch() */ + } + HDfree(search_name); } return 0; } /* end lnk_search() */ @@ -1452,7 +1453,7 @@ handle_paths(hid_t fid, const char *path_name, void H5_ATTR_UNUSED * data, int H hid_t gcpl_id; unsigned crt_order_flags; unsigned attr_crt_order_flags; - trav_handle_udata_t handle_udata; /* User data for traversal */ + trav_handle_udata_t handle_udata; /* User data for traversal */ if ((gcpl_id = H5Gget_create_plist(gid)) < 0) { error_msg("error in getting group creation property list ID\n"); @@ -1476,12 +1477,12 @@ handle_paths(hid_t fid, const char *path_name, void H5_ATTR_UNUSED * data, int H h5tools_setstatus(EXIT_FAILURE); } - handle_udata.fid = fid; - handle_udata.op_name = (char*)path_name; - if(h5trav_visit(fid, "/", TRUE, TRUE, obj_search, lnk_search, &handle_udata) < 0) { - error_msg("error traversing information\n"); - h5tools_setstatus(EXIT_FAILURE); - } + handle_udata.fid = fid; + handle_udata.op_name = path_name; + if(h5trav_visit(fid, "/", TRUE, TRUE, obj_search, lnk_search, &handle_udata) < 0) { + error_msg("error traversing information\n"); + h5tools_setstatus(EXIT_FAILURE); + } } } @@ -1505,8 +1506,8 @@ handle_paths(hid_t fid, const char *path_name, void H5_ATTR_UNUSED * data, int H void handle_attributes(hid_t fid, const char *attr, void H5_ATTR_UNUSED * data, int H5_ATTR_UNUSED pe, const char H5_ATTR_UNUSED *display_name) { - hid_t oid = -1; - hid_t attr_id = -1; + hid_t oid = -1; + hid_t attr_id = -1; char *obj_name = NULL; char *attr_name = NULL; int j; @@ -1523,7 +1524,7 @@ handle_attributes(hid_t fid, const char *attr, void H5_ATTR_UNUSED * data, int H /* find the last / */ while(j >= 0) { - if (attr[j] == '/' && (j==0 || (j>0 && attr[j-1]!='\\'))) + if (attr[j] == '/' && (j==0 || (j>0 && attr[j-1]!='\\'))) break; j--; } @@ -1538,7 +1539,7 @@ handle_attributes(hid_t fid, const char *attr, void H5_ATTR_UNUSED * data, int H dump_indent += COL; HDmemset(&ctx, 0, sizeof(ctx)); - ctx.indent_level = dump_indent/COL; + ctx.indent_level = dump_indent / COL; ctx.cur_column = dump_indent; string_dataformat = *outputformat; @@ -1548,7 +1549,7 @@ handle_attributes(hid_t fid, const char *attr, void H5_ATTR_UNUSED * data, int H string_dataformat.fmt_float = fp_format; } - if (h5tools_nCols==0) { + if (h5tools_nCols == 0) { string_dataformat.line_ncols = 65535; string_dataformat.line_per_line = 1; } @@ -1558,7 +1559,7 @@ handle_attributes(hid_t fid, const char *attr, void H5_ATTR_UNUSED * data, int H string_dataformat.do_escape = display_escape; outputformat = &string_dataformat; - attr_name = h5tools_str_replace(attr + j + 1, "\\/", "/"); + attr_name = h5tools_str_replace(attr + j + 1, "\\/", "/"); /* handle error case: cannot open the object with the attribute */ if((oid = H5Oopen(fid, obj_name, H5P_DEFAULT)) < 0) { @@ -1614,7 +1615,7 @@ handle_attributes(hid_t fid, const char *attr, void H5_ATTR_UNUSED * data, int H } /* end if */ HDfree(obj_name); - HDfree(attr_name); + HDfree(attr_name); dump_indent -= COL; return; @@ -1622,9 +1623,9 @@ error: h5tools_setstatus(EXIT_FAILURE); if(obj_name) HDfree(obj_name); - - if (attr_name) - HDfree(attr_name); + + if (attr_name) + HDfree(attr_name); H5E_BEGIN_TRY { H5Oclose(oid); @@ -1681,8 +1682,7 @@ handle_datasets(hid_t fid, const char *dset, void *data, int pe, const char *dis h5tools_setstatus(EXIT_FAILURE); return; } - else - ndims = ndims_res; + ndims = (unsigned)ndims_res; if(!sset->start.data || !sset->stride.data || !sset->count.data || !sset->block.data) { /* they didn't specify a ``stride'' or ``block''. default to 1 in all @@ -1739,7 +1739,7 @@ handle_datasets(hid_t fid, const char *dset, void *data, int pe, const char *dis h5tools_setstatus(EXIT_FAILURE); return; } - + /*------------------------------------------------------------------------- * check for block overlap *------------------------------------------------------------------------- @@ -1772,7 +1772,7 @@ handle_datasets(hid_t fid, const char *dset, void *data, int pe, const char *dis PRINTSTREAM(rawoutstream, "%s \"%s\"\n", HARDLINK, found_obj->objname); indentation(dump_indent); end_obj(h5tools_dump_header_format->datasetend, h5tools_dump_header_format->datasetblockend); - } + } else { found_obj->displayed = TRUE; dump_indent += COL; @@ -1871,11 +1871,11 @@ handle_links(hid_t fid, const char *links, void H5_ATTR_UNUSED * data, int H5_AT if(H5Lget_info(fid, links, &linfo, H5P_DEFAULT) < 0) { error_msg("unable to get link info from \"%s\"\n", links); h5tools_setstatus(EXIT_FAILURE); - } + } else if(linfo.type == H5L_TYPE_HARD) { error_msg("\"%s\" is a hard link\n", links); h5tools_setstatus(EXIT_FAILURE); - } + } else { char *buf = (char *)HDmalloc(linfo.u.val_size); PRINTVALSTREAM(rawoutstream, "\n"); @@ -1912,12 +1912,12 @@ handle_links(hid_t fid, const char *links, void H5_ATTR_UNUSED * data, int H5_AT PRINTSTREAM(rawoutstream, "TARGETFILE \"%s\"\n", elink_file); indentation(COL); PRINTSTREAM(rawoutstream, "TARGETPATH \"%s\"\n", elink_path); - } + } else { error_msg("h5dump error: unable to unpack external link value for \"%s\"\n", links); h5tools_setstatus(EXIT_FAILURE); } - } + } else { error_msg("h5dump error: unable to get external link value for \"%s\"\n", links); h5tools_setstatus(EXIT_FAILURE); @@ -2091,12 +2091,15 @@ dump_extlink(hid_t group, const char *linkname, const char *objname) case H5O_TYPE_GROUP: handle_groups(group, linkname, NULL, 0, objname); break; + case H5O_TYPE_DATASET: handle_datasets(group, linkname, NULL, 0, objname); break; + case H5O_TYPE_NAMED_DATATYPE: handle_datatypes(group, linkname, NULL, 0, objname); break; + case H5O_TYPE_UNKNOWN: case H5O_TYPE_NTYPES: default: diff --git a/tools/h5repack/CMakeTests.cmake b/tools/h5repack/CMakeTests.cmake index b87de7b..c7171d8 100644 --- a/tools/h5repack/CMakeTests.cmake +++ b/tools/h5repack/CMakeTests.cmake @@ -86,11 +86,13 @@ ${HDF5_TOOLS_H5REPACK_SOURCE_DIR}/testfiles/h5repack.info ${HDF5_TOOLS_H5REPACK_SOURCE_DIR}/testfiles/deflate_limit.h5repack_layout.h5.ddl ${HDF5_TOOLS_H5REPACK_SOURCE_DIR}/testfiles/h5repack_layout.h5.ddl + ${HDF5_TOOLS_H5REPACK_SOURCE_DIR}/testfiles/h5repack_filters.h5-gzip_verbose_filters.tst ${HDF5_TOOLS_H5REPACK_SOURCE_DIR}/testfiles/h5repack_filters.h5.tst ${HDF5_TOOLS_H5REPACK_SOURCE_DIR}/testfiles/h5repack_layout.h5-plugin_test.ddl ${HDF5_TOOLS_H5REPACK_SOURCE_DIR}/testfiles/plugin_test.h5repack_layout.h5.tst ${HDF5_TOOLS_H5REPACK_SOURCE_DIR}/testfiles/h5repack_layout.UD.h5-plugin_none.ddl ${HDF5_TOOLS_H5REPACK_SOURCE_DIR}/testfiles/plugin_none.h5repack_layout.UD.h5.tst + ${HDF5_TOOLS_H5REPACK_SOURCE_DIR}/testfiles/h5repack_layout.h5-plugin_zero.tst ) foreach (h5_file ${LIST_HDF5_TEST_FILES} ${LIST_OTHER_TEST_FILES}) @@ -208,7 +210,7 @@ -D "TEST_OUTPUT=${resultfile}-${testname}.out" -D "TEST_EXPECT=${resultcode}" -D "TEST_FILTER:STRING=${testfilter}" - -D "TEST_REFERENCE=${resultfile}.tst" + -D "TEST_REFERENCE=${resultfile}-${testname}.tst" -P "${HDF_RESOURCES_EXT_DIR}/runTest.cmake" ) endif (HDF5_ENABLE_USING_MEMCHECKER) @@ -988,6 +990,12 @@ ############################################################################## ADD_H5_UD_TEST (plugin_test 0 h5repack_layout.h5 -v -f UD=257,1,9) ADD_H5_UD_TEST (plugin_none 0 h5repack_layout.UD.h5 -v -f NONE) + # check for no parameters + set (TESTRETVAL 255) + if (WIN32) + set (TESTRETVAL -1) + endif() + ADD_H5_CMP_TEST (plugin_zero "" "TEST" ${TESTRETVAL} h5repack_layout.h5 -v -f UD=250,0) if (HDF5_TEST_VFD) # Run test with different Virtual File Driver diff --git a/tools/h5repack/h5repack.c b/tools/h5repack/h5repack.c index 8a9090a..3f99374 100644 --- a/tools/h5repack/h5repack.c +++ b/tools/h5repack/h5repack.c @@ -118,35 +118,36 @@ int h5repack_end(pack_opt_t *options) { * *------------------------------------------------------------------------- */ -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 */ - int n_objs; /* number of objects in the current -f or -l option entry */ - int is_glb; /* is the filter global */ - - /* parse the -f 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; +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 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; } /*------------------------------------------------------------------------- @@ -158,59 +159,53 @@ int h5repack_addfilter(const char* str, pack_opt_t *options) { * *------------------------------------------------------------------------- */ - -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 */ - int 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) { - 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; - } - - return ret_value; +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) + 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; + } + + return ret_value; } /* Note: The below copy_named_datatype(), named_datatype_free(), copy_attr() @@ -366,200 +361,201 @@ done: * *------------------------------------------------------------------------- */ -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 = -1; /* attr ID */ - hid_t attr_out = -1; /* attr ID */ - hid_t space_id = -1; /* space ID */ - hid_t ftype_id = -1; /* file type ID */ - hid_t wtype_id = -1; /* 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 */ - char name[255]; - H5O_info_t oinfo; /* object info */ - int j; - unsigned u; - hbool_t is_ref = 0; - H5T_class_t type_class = -1; - - if (H5Oget_info(loc_in, &oinfo) < 0) - goto error; - - /*------------------------------------------------------------------------- - * 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) - goto error; - - /* get name */ - if (H5Aget_name(attr_id, (size_t) 255, name) < 0) - goto error; - - /* get the file datatype */ - if ((ftype_id = H5Aget_type(attr_id)) < 0) - goto error; - - /* Check if the datatype is committed */ - if ((is_named = H5Tcommitted(ftype_id)) < 0) - goto error; - if (is_named && travt) { - hid_t fidout; - - /* Create out file id */ - if ((fidout = H5Iget_file_id(loc_out)) < 0) - goto error; - - /* Copy named dt */ - if ((wtype_id = copy_named_datatype(ftype_id, fidout, - named_dt_head_p, travt, options)) < 0) { - H5Fclose(fidout); - goto error; - } /* end if */ - - if (H5Fclose(fidout) < 0) - goto error; - } /* end if */ - else { - if (options->use_native == 1) - wtype_id = h5tools_get_native_type(ftype_id); - else - wtype_id = H5Tcopy(ftype_id); - } /* end else */ - - /* get the dataspace handle */ - if ((space_id = H5Aget_space(attr_id)) < 0) - goto error; - - /* get dimensions */ - if ((rank = H5Sget_simple_extent_dims(space_id, dims, NULL)) < 0) - goto error; - - nelmts = 1; - for (j = 0; j < rank; j++) - nelmts *= dims[j]; - - if ((msize = H5Tget_size(wtype_id)) == 0) - goto error; - - /*------------------------------------------------------------------------- - * 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 = -1; - base_type = H5Tget_super(ftype_id); - is_ref = (is_ref || (H5Tget_class(base_type) == H5T_REFERENCE)); - H5Tclose(base_type); - } +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) +{ + 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 type ID */ + hid_t wtype_id = -1; /* 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 */ + char name[255]; + H5O_info_t oinfo; /* object info */ + int j; + unsigned u; + hbool_t is_ref = 0; + H5T_class_t type_class = -1; + + if (H5Oget_info(loc_in, &oinfo) < 0) + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "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) + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Aopen_by_idx failed"); + + /* get name */ + if (H5Aget_name(attr_id, (size_t) 255, name) < 0) + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed"); + + /* get the file datatype */ + if ((ftype_id = H5Aget_type(attr_id)) < 0) + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Aget_type failed"); + + /* Check if the datatype is committed */ + if ((is_named = H5Tcommitted(ftype_id)) < 0) + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Tcommitted failed"); + if (is_named && travt) { + hid_t fidout; + + /* Create out file id */ + if ((fidout = H5Iget_file_id(loc_out)) < 0) + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "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); + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "copy_named_datatype failed"); + } /* end if */ + + if (H5Fclose(fidout) < 0) + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Fclose failed"); + } /* end if */ + else { + if (options->use_native == 1) + wtype_id = h5tools_get_native_type(ftype_id); + else + wtype_id = H5Tcopy(ftype_id); + } /* end else */ + + /* 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"); + + nelmts = 1; + for (j = 0; j < rank; j++) + nelmts *= dims[j]; + + if ((msize = H5Tget_size(wtype_id)) == 0) + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "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 = -1; + + base_type = H5Tget_super(ftype_id); + is_ref = (is_ref || (H5Tget_class(base_type) == H5T_REFERENCE)); + H5Tclose(base_type); + } + + 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); + H5Tclose(mtid); + + if (mtclass == H5T_REFERENCE) { + is_ref = 1; + break; + } + } /* for (j=0; i<nmembers; j++) */ + } /* if (type_class == H5T_COMPOUND) */ + + if (is_ref) { + ; /* handled by copy_refs_attr() */ + } + else { + /*------------------------------------------------------------------------- + * read to memory + *------------------------------------------------------------------------- + */ + + buf = (void *) HDmalloc((size_t)(nelmts * msize)); + if (buf == NULL) { + error_msg("h5repack", "cannot read into memory\n"); + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "HDmalloc failed"); + } /* end if */ + if (H5Aread(attr_id, wtype_id, buf) < 0) + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Aread failed"); + + /*------------------------------------------------------------------------- + * copy + *------------------------------------------------------------------------- + */ + + if ((attr_out = H5Acreate2(loc_out, name, wtype_id, space_id, H5P_DEFAULT, H5P_DEFAULT)) < 0) + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Acreate2 failed"); + if (H5Awrite(attr_out, wtype_id, buf) < 0) + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Awrite failed"); + + /*close*/ + if (H5Aclose(attr_out) < 0) + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "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)) + H5Dvlen_reclaim(wtype_id, space_id, H5P_DEFAULT, buf); + HDfree(buf); + buf = NULL; + } /*H5T_REFERENCE*/ + + if (options->verbose) + printf(FORMAT_OBJ_ATTR, "attr", name); + + /*------------------------------------------------------------------------- + * close + *------------------------------------------------------------------------- + */ + + if (H5Tclose(ftype_id) < 0) + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Tclose failed"); + if (H5Tclose(wtype_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"); + } /* u */ + + return 0; - 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); - H5Tclose(mtid); - - if (mtclass == H5T_REFERENCE) { - is_ref = 1; - break; - } - } /* for (j=0; i<nmembers; j++) */ - } /* if (type_class == H5T_COMPOUND) */ - - if (is_ref) { - ; /* handled by copy_refs_attr() */ - } - else { - /*------------------------------------------------------------------------- - * read to memory - *------------------------------------------------------------------------- - */ - - buf = (void *) HDmalloc((size_t)(nelmts * msize)); - if (buf == NULL) { - error_msg("h5repack", "cannot read into memory\n"); - goto error; - } /* end if */ - if (H5Aread(attr_id, wtype_id, buf) < 0) - goto error; - - /*------------------------------------------------------------------------- - * copy - *------------------------------------------------------------------------- - */ - - if ((attr_out = H5Acreate2(loc_out, name, wtype_id, space_id, - H5P_DEFAULT, H5P_DEFAULT)) < 0) - goto error; - if (H5Awrite(attr_out, wtype_id, buf) < 0) - goto error; - - /*close*/ - if (H5Aclose(attr_out) < 0) - goto error; - - /* Check if we have VL data and string in the attribute's datatype that must - * be reclaimed */ - if (TRUE == h5tools_detect_vlen(wtype_id)) - H5Dvlen_reclaim(wtype_id, space_id, H5P_DEFAULT, buf); - HDfree(buf); - buf = NULL; - } /*H5T_REFERENCE*/ - - if (options->verbose) - printf(FORMAT_OBJ_ATTR, "attr", name); - - /*------------------------------------------------------------------------- - * close - *------------------------------------------------------------------------- - */ - - if (H5Tclose(ftype_id) < 0) - goto error; - if (H5Tclose(wtype_id) < 0) - goto error; - if (H5Sclose(space_id) < 0) - goto error; - if (H5Aclose(attr_id) < 0) - goto error; - } /* u */ - - return 0; - -error: - 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)) - H5Dvlen_reclaim(wtype_id, space_id, H5P_DEFAULT, buf); - - /* Free buf */ - HDfree(buf); - } /* end if */ - - H5Tclose(ftype_id); - H5Tclose(wtype_id); - H5Sclose(space_id); - H5Aclose(attr_id); - H5Aclose(attr_out); - } H5E_END_TRY; - - return -1; +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)) + H5Dvlen_reclaim(wtype_id, space_id, H5P_DEFAULT, buf); + + /* Free buf */ + HDfree(buf); + } /* end if */ + + H5Tclose(ftype_id); + H5Tclose(wtype_id); + H5Sclose(space_id); + H5Aclose(attr_id); + H5Aclose(attr_out); + } H5E_END_TRY; + + return ret_value; } /* end copy_attr() */ /*------------------------------------------------------------------------- diff --git a/tools/h5repack/h5repack.h b/tools/h5repack/h5repack.h index 250121e..6bed05e 100644 --- a/tools/h5repack/h5repack.h +++ b/tools/h5repack/h5repack.h @@ -82,9 +82,9 @@ typedef struct { /* store a table of all objects */ typedef struct { - unsigned int size; - unsigned int nelems; - pack_info_t *objs; + unsigned int size; + unsigned int nelems; + pack_info_t *objs; } pack_opttbl_t; @@ -207,11 +207,11 @@ int apply_filters(const char* name, /* object name from traverse list */ int options_table_init( pack_opttbl_t **tbl ); int options_table_free( pack_opttbl_t *table ); int options_add_layout( obj_list_t *obj_list, - int n_objs, + unsigned n_objs, pack_info_t *pack, pack_opttbl_t *table ); int options_add_filter ( obj_list_t *obj_list, - int n_objs, + unsigned n_objs, filter_info_t filt, pack_opttbl_t *table ); pack_info_t* options_get_object( const char *path, @@ -223,13 +223,13 @@ pack_info_t* options_get_object( const char *path, */ obj_list_t* parse_filter(const char *str, - int *n_objs, + unsigned *n_objs, filter_info_t *filt, pack_opt_t *options, int *is_glb); obj_list_t* parse_layout(const char *str, - int *n_objs, + unsigned *n_objs, pack_info_t *pack, /* info about object */ pack_opt_t *options); diff --git a/tools/h5repack/h5repack_copy.c b/tools/h5repack/h5repack_copy.c index 1963750..9573ee8 100644 --- a/tools/h5repack/h5repack_copy.c +++ b/tools/h5repack/h5repack_copy.c @@ -33,10 +33,10 @@ */ /* size of buffer/# of bytes to xfer at a time when copying userblock */ -#define USERBLOCK_XFER_SIZE 512 +#define USERBLOCK_XFER_SIZE 512 /* check H5Dread()/H5Dwrite() error, e.g. memory allocation error inside the library. */ -#define CHECK_H5DRW_ERROR(_fun, _did, _mtid, _msid, _fsid, _pid, _buf) { \ +#define CHECK_H5DRW_ERROR(_fun, _fail, _did, _mtid, _msid, _fsid, _pid, _buf) { \ H5E_BEGIN_TRY { \ if(_fun(_did, _mtid, _msid, _fsid, _pid, _buf) < 0) { \ hid_t _err_num = 0; \ @@ -44,7 +44,7 @@ H5Ewalk2(H5E_DEFAULT, H5E_WALK_DOWNWARD, walk_error_callback, &_err_num); \ H5Eget_msg(_err_num, NULL, _msg, (size_t)80); \ error_msg("%s %s -- %s\n", #_fun, "failed", _msg); \ - goto error; \ + HGOTO_DONE(_fail) \ } \ } H5E_END_TRY; \ } @@ -54,12 +54,12 @@ *------------------------------------------------------------------------- */ static int Get_hyperslab(hid_t dcpl_id, int rank_dset, hsize_t dims_dset[], - size_t size_datum, hsize_t dims_hslab[], hsize_t * hslab_nbytes_p); + size_t size_datum, hsize_t dims_hslab[], hsize_t * hslab_nbytes_p); static void print_dataset_info(hid_t dcpl_id, char *objname, double per, int pr); static int do_copy_objects(hid_t fidin, hid_t fidout, trav_table_t *travt, - pack_opt_t *options); + pack_opt_t *options); static int copy_user_block(const char *infile, const char *outfile, - hsize_t size); + hsize_t size); #if defined (H5REPACK_DEBUG_USER_BLOCK) static void print_user_block(const char *filename, hid_t fid); #endif @@ -67,10 +67,10 @@ static herr_t walk_error_callback(unsigned n, const H5E_error2_t *err_desc, void /* get the major number from the error stack. */ static herr_t walk_error_callback(H5_ATTR_UNUSED unsigned n, const H5E_error2_t *err_desc, void *udata) { - if (err_desc) - *((int *) udata) = err_desc->maj_num; + if (err_desc) + *((hid_t *) udata) = err_desc->maj_num; - return 0; + return 0; } /*------------------------------------------------------------------------- @@ -97,306 +97,311 @@ static herr_t walk_error_callback(H5_ATTR_UNUSED unsigned n, const H5E_error2_t *------------------------------------------------------------------------- */ -int copy_objects(const char* fnamein, const char* fnameout, pack_opt_t *options) { - hid_t fidin; - hid_t fidout = -1; - trav_table_t *travt = NULL; - hsize_t ub_size = 0; /* size of user block */ - hid_t fcpl = H5P_DEFAULT; /* file creation property list ID */ - hid_t fapl = H5P_DEFAULT; /* file access property list ID */ - - /*------------------------------------------------------------------------- - * open input file - *------------------------------------------------------------------------- - */ - if ((fidin = h5tools_fopen(fnamein, H5F_ACC_RDONLY, H5P_DEFAULT, NULL, NULL, - (size_t) 0)) < 0) { - error_msg("<%s>: %s\n", fnamein, H5FOPENERROR); - goto out; - } - - /* get user block size and file space strategy/threshold */ - { - hid_t fcpl_in; /* file creation property list ID for input file */ - - if ((fcpl_in = H5Fget_create_plist(fidin)) < 0) { - error_msg("failed to retrieve file creation property list\n"); - goto out; - } - - if (H5Pget_userblock(fcpl_in, &ub_size) < 0) { - error_msg("failed to retrieve userblock size\n"); - goto out; - } - - if (H5Pclose(fcpl_in) < 0) { - error_msg("failed to close property list\n"); - goto out; - } - } - - /* Check if we need to create a non-default file creation property list */ - if (options->latest || ub_size > 0) { - /* Create file creation property list */ - if ((fcpl = H5Pcreate(H5P_FILE_CREATE)) < 0) { - error_msg("fail to create a file creation property list\n"); - goto out; - } - - if (ub_size > 0) { - if (H5Pset_userblock(fcpl, ub_size) < 0) { - error_msg("failed to set non-default userblock size\n"); - goto out; - } - } - - if (options->latest) { - unsigned i = 0, nindex = 0, mesg_type_flags[5], min_mesg_sizes[5]; - - /* Adjust group creation parameters for root group */ - /* (So that it is created in "dense storage" form) */ - if (H5Pset_link_phase_change(fcpl, (unsigned) options->grp_compact, - (unsigned) options->grp_indexed) < 0) { - error_msg( - "fail to adjust group creation parameters for root group\n"); - goto out; - } - - for (i = 0; i < 5; i++) { - if (options->msg_size[i] > 0) { - switch (i) { - case 0: - mesg_type_flags[nindex] = H5O_SHMESG_SDSPACE_FLAG; - break; - - case 1: - mesg_type_flags[nindex] = H5O_SHMESG_DTYPE_FLAG; - break; - - case 2: - mesg_type_flags[nindex] = H5O_SHMESG_FILL_FLAG; - break; - - case 3: - mesg_type_flags[nindex] = H5O_SHMESG_PLINE_FLAG; - break; - - case 4: - mesg_type_flags[nindex] = H5O_SHMESG_ATTR_FLAG; - break; - default: - break; - } /* end switch */ - min_mesg_sizes[nindex] = (unsigned) options->msg_size[i]; - - nindex++; - } /* end if */ - } /* end for */ - - if (nindex > 0) { - if (H5Pset_shared_mesg_nindexes(fcpl, nindex) < 0) { - error_msg( - "fail to set the number of shared object header message indexes\n"); - goto out; - } - - /* msg_size[0]=dataspace, 1=datatype, 2=file value, 3=filter pipleline, 4=attribute */ - for (i = 0; i < (nindex - 1); i++) { - if (H5Pset_shared_mesg_index(fcpl, i, mesg_type_flags[i], - min_mesg_sizes[i]) < 0) { - error_msg( - "fail to configure the specified shared object header message index\n"); - goto out; - } /* end if */ - } /* end for */ - } /* if (nindex>0) */ - - /* Create file access property list */ - if ((fapl = H5Pcreate(H5P_FILE_ACCESS)) < 0) { - error_msg("Could not create file access property list\n"); - goto out; - } /* end if */ - - if (H5Pset_libver_bounds(fapl, H5F_LIBVER_LATEST, H5F_LIBVER_LATEST) < 0) { - error_msg( - "Could not set property for using latest version of the format\n"); - goto out; - } /* end if */ - } /* end if */ - } /* end if */ +int copy_objects(const char* fnamein, const char* fnameout, pack_opt_t *options) +{ + int ret_value = 0; /*no need to LEAVE() on ERROR: HERR_INIT(int, SUCCEED) */ + hid_t fidin; + hid_t fidout = -1; + trav_table_t *travt = NULL; + hsize_t ub_size = 0; /* size of user block */ + hid_t fcpl = H5P_DEFAULT; /* file creation property list ID */ + hid_t fapl = H5P_DEFAULT; /* file access property list ID */ + + /*------------------------------------------------------------------------- + * open input file + *------------------------------------------------------------------------- + */ + if ((fidin = h5tools_fopen(fnamein, H5F_ACC_RDONLY, H5P_DEFAULT, NULL, NULL, (size_t) 0)) < 0) { + error_msg("<%s>: %s\n", fnamein, H5FOPENERROR); + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed"); + } + + /* get user block size and file space strategy/threshold */ + { + hid_t fcpl_in; /* file creation property list ID for input file */ + + if ((fcpl_in = H5Fget_create_plist(fidin)) < 0) { + error_msg("failed to retrieve file creation property list\n"); + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed"); + } + + if (H5Pget_userblock(fcpl_in, &ub_size) < 0) { + error_msg("failed to retrieve userblock size\n"); + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed"); + } + + if (H5Pclose(fcpl_in) < 0) { + error_msg("failed to close property list\n"); + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed"); + } + } + + /* Check if we need to create a non-default file creation property list */ + if (options->latest || ub_size > 0) { + /* Create file creation property list */ + if ((fcpl = H5Pcreate(H5P_FILE_CREATE)) < 0) { + error_msg("fail to create a file creation property list\n"); + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed"); + } + + if (ub_size > 0) { + if (H5Pset_userblock(fcpl, ub_size) < 0) { + error_msg("failed to set non-default userblock size\n"); + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed"); + } + } + + if (options->latest) { + unsigned i = 0, nindex = 0, mesg_type_flags[5], min_mesg_sizes[5]; + + /* Adjust group creation parameters for root group */ + /* (So that it is created in "dense storage" form) */ + if (H5Pset_link_phase_change(fcpl, (unsigned) options->grp_compact, + (unsigned) options->grp_indexed) < 0) { + error_msg("fail to adjust group creation parameters for root group\n"); + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed"); + } + + for (i = 0; i < 5; i++) { + if (options->msg_size[i] > 0) { + switch (i) { + case 0: + mesg_type_flags[nindex] = H5O_SHMESG_SDSPACE_FLAG; + break; + + case 1: + mesg_type_flags[nindex] = H5O_SHMESG_DTYPE_FLAG; + break; + + case 2: + mesg_type_flags[nindex] = H5O_SHMESG_FILL_FLAG; + break; + + case 3: + mesg_type_flags[nindex] = H5O_SHMESG_PLINE_FLAG; + break; + + case 4: + mesg_type_flags[nindex] = H5O_SHMESG_ATTR_FLAG; + break; + + default: + break; + } /* end switch */ + min_mesg_sizes[nindex] = (unsigned) options->msg_size[i]; + + nindex++; + } /* end if */ + } /* end for */ + + if (nindex > 0) { + if (H5Pset_shared_mesg_nindexes(fcpl, nindex) < 0) { + error_msg("fail to set the number of shared object header message indexes\n"); + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed"); + } + + /* msg_size[0]=dataspace, 1=datatype, 2=file value, 3=filter pipleline, 4=attribute */ + for (i = 0; i < (nindex - 1); i++) { + if (H5Pset_shared_mesg_index(fcpl, i, mesg_type_flags[i], min_mesg_sizes[i]) < 0) { + error_msg("fail to configure the specified shared object header message index\n"); + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed"); + } /* end if */ + } /* end for */ + } /* if (nindex>0) */ + + /* Create file access property list */ + if ((fapl = H5Pcreate(H5P_FILE_ACCESS)) < 0) { + error_msg("Could not create file access property list\n"); + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed"); + } /* end if */ + + if (H5Pset_libver_bounds(fapl, H5F_LIBVER_LATEST, H5F_LIBVER_LATEST) < 0) { + error_msg("Could not set property for using latest version of the format\n"); + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed"); + } /* end if */ + } /* end if */ + } /* end if */ #if defined (H5REPACK_DEBUG_USER_BLOCK) - print_user_block(fnamein, fidin); +print_user_block(fnamein, fidin); #endif - /*------------------------------------------------------------------------- - * set the new user userblock options in the FCPL (before H5Fcreate ) - *------------------------------------------------------------------------- - */ - if (options->ublock_size > 0) { - /* either use the FCPL already created or create a new one */ - if (fcpl == H5P_DEFAULT) { - /* create a file creation property list */ - if ((fcpl = H5Pcreate(H5P_FILE_CREATE)) < 0) { - error_msg("fail to create a file creation property list\n"); - goto out; - } - } - - /* set user block size */ - if (H5Pset_userblock(fcpl, options->ublock_size) < 0) { - error_msg("failed to set userblock size\n"); - goto out; - } - } - - /*------------------------------------------------------------------------- - * set alignment options - *------------------------------------------------------------------------- - */ - if (options->alignment > 0) { - /* either use the FAPL already created or create a new one */ - if (fapl == H5P_DEFAULT) { - /* create a file access property list */ - if ((fapl = H5Pcreate(H5P_FILE_ACCESS)) < 0) { - error_msg("Could not create file access property list\n"); - goto out; - } - } - - if (H5Pset_alignment(fapl, options->threshold, options->alignment) < 0) { - error_msg("failed to set alignment\n"); - goto out; - } - } - - /*------------------------------------------------------------------------- - * set metadata block size option - *------------------------------------------------------------------------- - */ - if (options->meta_block_size > 0) { - /* either use the FAPL already created or create a new one */ - if (fapl == H5P_DEFAULT) { - /* create a file access property list */ - if ((fapl = H5Pcreate(H5P_FILE_ACCESS)) < 0) { - error_msg("Could not create file access property list\n"); - goto out; - } - } - - if (H5Pset_meta_block_size(fapl, options->meta_block_size) < 0) { - error_msg("failed to set metadata block size\n"); - goto out; - } - } - - - /*------------------------------------------------------------------------- - * create the output file - *------------------------------------------------------------------------- - */ - if (options->verbose) - printf("Making file <%s>...\n", fnameout); - - if ((fidout = H5Fcreate(fnameout, H5F_ACC_TRUNC, fcpl, fapl)) < 0) { - error_msg("<%s>: Could not create file\n", fnameout); - goto out; - } - - /*------------------------------------------------------------------------- - * write a new user block if requested - *------------------------------------------------------------------------- - */ - if (options->ublock_size > 0) { - if (copy_user_block(options->ublock_filename, fnameout, - options->ublock_size) < 0) { - error_msg("Could not copy user block. Exiting...\n"); - goto out; - - } - } - - /*------------------------------------------------------------------------- - * get list of objects - *------------------------------------------------------------------------- - */ - - /* init table */ - trav_table_init(&travt); - - /* get the list of objects in the file */ - if (h5trav_gettable(fidin, travt) < 0) - goto out; - - /*------------------------------------------------------------------------- - * do the copy - *------------------------------------------------------------------------- - */ - if (do_copy_objects(fidin, fidout, travt, options) < 0) { - error_msg("<%s>: Could not copy data to: %s\n", fnamein, fnameout); - goto out; - } /* end if */ - - /*------------------------------------------------------------------------- - * do the copy of referenced objects - * and create hard links - *------------------------------------------------------------------------- - */ - if (do_copy_refobjs(fidin, fidout, travt, options) < 0) { - printf("h5repack: <%s>: Could not copy data to: %s\n", fnamein, - fnameout); - goto out; - } - - /*------------------------------------------------------------------------- - * close - *------------------------------------------------------------------------- - */ - - if (fapl > 0) - H5Pclose(fapl); - - if (fcpl > 0) - H5Pclose(fcpl); - - H5Fclose(fidin); - H5Fclose(fidout); - - /* free table */ - trav_table_free(travt); - travt = NULL; - - /*------------------------------------------------------------------------- - * write only the input file user block if there is no user block file input - *------------------------------------------------------------------------- - */ - - if (ub_size > 0 && options->ublock_size == 0) { - if (copy_user_block(fnamein, fnameout, ub_size) < 0) { - error_msg("Could not copy user block. Exiting...\n"); - goto out; - - } - } - - return 0; - - /*------------------------------------------------------------------------- - * out - *------------------------------------------------------------------------- - */ - -out: - H5E_BEGIN_TRY - { - H5Pclose(fapl); - H5Pclose(fcpl); - H5Fclose(fidin); - H5Fclose(fidout); - }H5E_END_TRY; - if (travt) - trav_table_free(travt); - - return -1; + /*------------------------------------------------------------------------- + * set the new user userblock options in the FCPL (before H5Fcreate ) + *------------------------------------------------------------------------- + */ + if (options->ublock_size > 0) { + /* either use the FCPL already created or create a new one */ + if (fcpl == H5P_DEFAULT) { + /* create a file creation property list */ + if ((fcpl = H5Pcreate(H5P_FILE_CREATE)) < 0) { + error_msg("fail to create a file creation property list\n"); + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed"); + } + } + + /* set user block size */ + if (H5Pset_userblock(fcpl, options->ublock_size) < 0) { + error_msg("failed to set userblock size\n"); + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed"); + } + } + + /*------------------------------------------------------------------------- + * set alignment options + *------------------------------------------------------------------------- + */ + if (options->alignment > 0) { + /* either use the FAPL already created or create a new one */ + if (fapl == H5P_DEFAULT) { + /* create a file access property list */ + if ((fapl = H5Pcreate(H5P_FILE_ACCESS)) < 0) { + error_msg("Could not create file access property list\n"); + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed"); + } + } + + if (H5Pset_alignment(fapl, options->threshold, options->alignment) < 0) { + error_msg("failed to set alignment\n"); + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed"); + } + } + + /*------------------------------------------------------------------------- + * set metadata block size option + *------------------------------------------------------------------------- + */ + if (options->meta_block_size > 0) { + /* either use the FAPL already created or create a new one */ + if (fapl == H5P_DEFAULT) { + /* create a file access property list */ + if ((fapl = H5Pcreate(H5P_FILE_ACCESS)) < 0) { + error_msg("Could not create file access property list\n"); + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed"); + } + } + + if (H5Pset_meta_block_size(fapl, options->meta_block_size) < 0) { + error_msg("failed to set metadata block size\n"); + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed"); + } + } + + /*------------------------------------------------------------------------- + * set free-space strategy options + *------------------------------------------------------------------------- + */ + + /* either use the FCPL already created or create a new one */ + if (fcpl == H5P_DEFAULT) { + /* create a file creation property list */ + if ((fcpl = H5Pcreate(H5P_FILE_CREATE)) < 0) { + error_msg("fail to create a file creation property list\n"); + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed"); + } + } + + /*------------------------------------------------------------------------- + * create the output file + *------------------------------------------------------------------------- + */ + if (options->verbose) + printf("Making file <%s>...\n", fnameout); + + if ((fidout = H5Fcreate(fnameout, H5F_ACC_TRUNC, fcpl, fapl)) < 0) { + error_msg("<%s>: Could not create file\n", fnameout); + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed"); + } + + /*------------------------------------------------------------------------- + * write a new user block if requested + *------------------------------------------------------------------------- + */ + if (options->ublock_size > 0) { + if (copy_user_block(options->ublock_filename, fnameout, options->ublock_size) < 0) { + error_msg("Could not copy user block. Exiting...\n"); + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed"); + } + } + + /*------------------------------------------------------------------------- + * get list of objects + *------------------------------------------------------------------------- + */ + + /* init table */ + trav_table_init(&travt); + + /* get the list of objects in the file */ + if (h5trav_gettable(fidin, travt) < 0) + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed"); + + /*------------------------------------------------------------------------- + * do the copy + *------------------------------------------------------------------------- + */ + if (do_copy_objects(fidin, fidout, travt, options) < 0) { + error_msg("<%s>: Could not copy data to: %s\n", fnamein, fnameout); + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed"); + } /* end if */ + + /*------------------------------------------------------------------------- + * do the copy of referenced objects + * and create hard links + *------------------------------------------------------------------------- + */ + if (do_copy_refobjs(fidin, fidout, travt, options) < 0) { + printf("h5repack: <%s>: Could not copy data to: %s\n", fnamein, fnameout); + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed"); + } + + /*------------------------------------------------------------------------- + * close + *------------------------------------------------------------------------- + */ + + if (fapl > 0) + H5Pclose(fapl); + + if (fcpl > 0) + H5Pclose(fcpl); + + H5Fclose(fidin); + H5Fclose(fidout); + + /* free table */ + trav_table_free(travt); + travt = NULL; + + /*------------------------------------------------------------------------- + * write only the input file user block if there is no user block file input + *------------------------------------------------------------------------- + */ + + if (ub_size > 0 && options->ublock_size == 0) { + if (copy_user_block(fnamein, fnameout, ub_size) < 0) { + error_msg("Could not copy user block. Exiting...\n"); + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed"); + } + } + + return 0; + + /*------------------------------------------------------------------------- + * out + *------------------------------------------------------------------------- + */ + +done: + H5E_BEGIN_TRY { + H5Pclose(fapl); + H5Pclose(fcpl); + H5Fclose(fidin); + H5Fclose(fidout); + } H5E_END_TRY; + if (travt) + trav_table_free(travt); + + return ret_value; } /*------------------------------------------------------------------------- @@ -437,132 +442,126 @@ out: *-----------------------------------------*/ int Get_hyperslab(hid_t dcpl_id, int rank_dset, hsize_t dims_dset[], - size_t size_datum, hsize_t dims_hslab[], hsize_t * hslab_nbytes_p) { - int status = 0; - int k; - H5D_layout_t dset_layout; - int rank_chunk; - hsize_t dims_chunk[H5S_MAX_RANK]; - hsize_t size_chunk = 1; - hsize_t nchunk_fit; /* number of chunks that fits in hyperslab buffer (H5TOOLS_BUFSIZE) */ - hsize_t ndatum_fit; /* number of dataum that fits in hyperslab buffer (H5TOOLS_BUFSIZE) */ - hsize_t chunk_dims_map[H5S_MAX_RANK]; /* mapped chunk dimentions */ - hsize_t hs_dims_map[H5S_MAX_RANK]; /* mapped hyperslab dimentions */ - hsize_t hslab_nbytes; /* size of hyperslab in byte */ - - /* init to set as size of a data element */ - hslab_nbytes = size_datum; - - /* get layout of dataset */ - dset_layout = H5Pget_layout(dcpl_id); - - /* if dataset is chunked */ - if (dset_layout == H5D_CHUNKED) { - /* get chunk dims */ - rank_chunk = H5Pget_chunk(dcpl_id, rank_dset, dims_chunk); - if (rank_chunk < 0) { - status = -1; - goto out; - } - - for (k = rank_dset; k > 0; --k) - size_chunk *= dims_chunk[k - 1]; - - /* figure out how many chunks can fit in the hyperslab buffer */ - nchunk_fit = (H5TOOLS_BUFSIZE / size_datum) / size_chunk; - - /* 1. if a chunk fit in hyperslab buffer */ - if (nchunk_fit >= 1) { - /* Calulate a hyperslab that contains as many chunks that can fit - * in hyperslab buffer. Hyperslab will be increased starting from - * the last dimention of the dataset (see h5dump's dims output). - * The calculation boundary is dataset dims. - * In the loop, used mapping from a datum to a chunk to figure out - * chunk based hyperslab. - */ - for (k = rank_dset; k > 0; --k) { - /* map dataset dimentions with a chunk dims */ - chunk_dims_map[k - 1] = dims_dset[k - 1] / dims_chunk[k - 1]; - - /* if reminder exist, increse by 1 to cover partial edge chunks */ - if (dims_dset[k - 1] % dims_chunk[k - 1] > 0) - chunk_dims_map[k - 1]++; - - /* get mapped hyperslab dims */ - hs_dims_map[k - 1] = MIN (nchunk_fit, chunk_dims_map[k-1]); - - /* prepare next round */ - nchunk_fit = nchunk_fit / chunk_dims_map[k - 1]; - /* if a chunk is bigger than the rest of buffer */ - if (nchunk_fit == 0) - nchunk_fit = 1; - - /* get hyperslab dimentions as unmapping to actual size */ - dims_hslab[k - 1] = - MIN( (hs_dims_map[k-1] * dims_chunk[k-1]), dims_dset[k-1]); - - /* calculate total size for the hyperslab */ - hslab_nbytes *= dims_hslab[k - 1]; - } - } - /* 2. if a chunk is bigger than hyperslab buffer */ - else { - /* Calulate a hyperslab that contains as many data elements that - * can fit in hyperslab buffer. Hyperslab will be increased - * starting from the last dimention of the chunk (see h5dump's dims - * output). - * The calculation boundary is a chunk dims. - */ - for (k = rank_dset; k > 0; --k) { - ndatum_fit = H5TOOLS_BUFSIZE / hslab_nbytes; - - /* if a datum is bigger than rest of buffer */ - if (ndatum_fit == 0) - ndatum_fit = 1; - /* get hyperslab dimentions within a chunk boundary */ - dims_hslab[k - 1] = MIN (dims_chunk[k-1], ndatum_fit); - - /* calculate total size for the hyperslab */ - hslab_nbytes *= dims_hslab[k - 1]; - - if (hslab_nbytes <= 0) { - status = -1; - goto out; - } - } - } - } - /* 3. if dataset is not chunked */ - else { - /* Calulate a hyperslab that contains as many data elements that can - * fit in hyperslab buffer. Hyperslab will be increased starting from - * the last dimention of the dataset (see h5dump's dims output). - * The calculation boundary is dataset dims. - */ - for (k = rank_dset; k > 0; --k) { - ndatum_fit = H5TOOLS_BUFSIZE / hslab_nbytes; - - /* if a datum is bigger than rest of buffer */ - if (ndatum_fit == 0) - ndatum_fit = 1; - /* get hyperslab dimentions within dataset boundary */ - dims_hslab[k - 1] = MIN(dims_dset[k - 1], ndatum_fit); - - /* calculate total size for the hyperslab */ - hslab_nbytes *= dims_hslab[k - 1]; - - if (hslab_nbytes <= 0) { - status = -1; - goto out; - } - } - } - - /* pass out the hyperslab size*/ - *hslab_nbytes_p = hslab_nbytes; - -out: - return status; + size_t size_datum, hsize_t dims_hslab[], hsize_t * hslab_nbytes_p) +{ + int ret_value = 0; /*no need to LEAVE() on ERROR: HERR_INIT(int, SUCCEED) */ + int k; + H5D_layout_t dset_layout; + int rank_chunk; + hsize_t dims_chunk[H5S_MAX_RANK]; + hsize_t size_chunk = 1; + hsize_t nchunk_fit; /* number of chunks that fits in hyperslab buffer (H5TOOLS_BUFSIZE) */ + hsize_t ndatum_fit; /* number of dataum that fits in hyperslab buffer (H5TOOLS_BUFSIZE) */ + hsize_t chunk_dims_map[H5S_MAX_RANK]; /* mapped chunk dimentions */ + hsize_t hs_dims_map[H5S_MAX_RANK]; /* mapped hyperslab dimentions */ + hsize_t hslab_nbytes; /* size of hyperslab in byte */ + + /* init to set as size of a data element */ + hslab_nbytes = size_datum; + + /* get layout of dataset */ + dset_layout = H5Pget_layout(dcpl_id); + + /* if dataset is chunked */ + if (dset_layout == H5D_CHUNKED) { + /* get chunk dims */ + rank_chunk = H5Pget_chunk(dcpl_id, rank_dset, dims_chunk); + if (rank_chunk < 0) + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed"); + + for (k = rank_dset; k > 0; --k) + size_chunk *= dims_chunk[k - 1]; + + /* figure out how many chunks can fit in the hyperslab buffer */ + nchunk_fit = (H5TOOLS_BUFSIZE / size_datum) / size_chunk; + + /* 1. if a chunk fit in hyperslab buffer */ + if (nchunk_fit >= 1) { + /* Calulate a hyperslab that contains as many chunks that can fit + * in hyperslab buffer. Hyperslab will be increased starting from + * the last dimention of the dataset (see h5dump's dims output). + * The calculation boundary is dataset dims. + * In the loop, used mapping from a datum to a chunk to figure out + * chunk based hyperslab. + */ + for (k = rank_dset; k > 0; --k) { + /* map dataset dimentions with a chunk dims */ + chunk_dims_map[k - 1] = dims_dset[k - 1] / dims_chunk[k - 1]; + + /* if reminder exist, increse by 1 to cover partial edge chunks */ + if (dims_dset[k - 1] % dims_chunk[k - 1] > 0) + chunk_dims_map[k - 1]++; + + /* get mapped hyperslab dims */ + hs_dims_map[k - 1] = MIN (nchunk_fit, chunk_dims_map[k-1]); + + /* prepare next round */ + nchunk_fit = nchunk_fit / chunk_dims_map[k - 1]; + /* if a chunk is bigger than the rest of buffer */ + if (nchunk_fit == 0) + nchunk_fit = 1; + + /* get hyperslab dimentions as unmapping to actual size */ + dims_hslab[k - 1] = MIN( (hs_dims_map[k-1] * dims_chunk[k-1]), dims_dset[k-1]); + + /* calculate total size for the hyperslab */ + hslab_nbytes *= dims_hslab[k - 1]; + } + } + /* 2. if a chunk is bigger than hyperslab buffer */ + else { + /* Calulate a hyperslab that contains as many data elements that + * can fit in hyperslab buffer. Hyperslab will be increased + * starting from the last dimention of the chunk (see h5dump's dims + * output). + * The calculation boundary is a chunk dims. + */ + for (k = rank_dset; k > 0; --k) { + ndatum_fit = H5TOOLS_BUFSIZE / hslab_nbytes; + + /* if a datum is bigger than rest of buffer */ + if (ndatum_fit == 0) + ndatum_fit = 1; + /* get hyperslab dimentions within a chunk boundary */ + dims_hslab[k - 1] = MIN (dims_chunk[k-1], ndatum_fit); + + /* calculate total size for the hyperslab */ + hslab_nbytes *= dims_hslab[k - 1]; + + if (hslab_nbytes <= 0) + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed"); + } + } + } + /* 3. if dataset is not chunked */ + else { + /* Calulate a hyperslab that contains as many data elements that can + * fit in hyperslab buffer. Hyperslab will be increased starting from + * the last dimention of the dataset (see h5dump's dims output). + * The calculation boundary is dataset dims. + */ + for (k = rank_dset; k > 0; --k) { + ndatum_fit = H5TOOLS_BUFSIZE / hslab_nbytes; + + /* if a datum is bigger than rest of buffer */ + if (ndatum_fit == 0) + ndatum_fit = 1; + /* get hyperslab dimentions within dataset boundary */ + dims_hslab[k - 1] = MIN(dims_dset[k - 1], ndatum_fit); + + /* calculate total size for the hyperslab */ + hslab_nbytes *= dims_hslab[k - 1]; + + if (hslab_nbytes <= 0) + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed"); + } + } + + /* pass out the hyperslab size*/ + *hslab_nbytes_p = hslab_nbytes; + +done: + return ret_value; } /*------------------------------------------------------------------------- @@ -660,718 +659,641 @@ out: */ int do_copy_objects(hid_t fidin, hid_t fidout, trav_table_t *travt, - pack_opt_t *options) /* repack options */ + pack_opt_t *options) /* repack options */ { - hid_t grp_in = -1; /* group ID */ - hid_t grp_out = -1; /* group ID */ - hid_t dset_in = -1; /* read dataset ID */ - hid_t dset_out = -1; /* write dataset ID */ - hid_t gcpl_in = -1; /* group creation property list */ - hid_t gcpl_out = -1; /* group creation property list */ - hid_t type_in = -1; /* named type ID */ - hid_t type_out = -1; /* named type ID */ - hid_t dcpl_in = -1; /* dataset creation property list ID */ - hid_t dcpl_out = -1; /* dataset creation property list ID */ - hid_t f_space_id = -1; /* file space ID */ - hid_t ftype_id = -1; /* file type ID */ - hid_t wtype_id = -1; /* read/write type ID */ - named_dt_t *named_dt_head = NULL; /* Pointer to the stack of named datatypes copied */ - size_t msize; /* size of type */ - hsize_t nelmts; /* number of elements in dataset */ - H5D_space_status_t space_status; /* determines whether space has been allocated for the dataset */ - int rank; /* rank of dataset */ - hsize_t dims[H5S_MAX_RANK];/* dimensions of dataset */ - hsize_t dsize_in; /* input dataset size before filter */ - hsize_t dsize_out; /* output dataset size after filter */ - int apply_s; /* flag for apply filter to small dataset sizes */ - int apply_f; /* flag for apply filter to return error on H5Dcreate */ - void *buf = NULL; /* buffer for raw data */ - void *hslab_buf = NULL; /* hyperslab buffer for raw data */ - int has_filter; /* current object has a filter */ - int req_filter; /* there was a request for a filter */ - int req_obj_layout = 0; /* request layout to current object */ - unsigned crt_order_flags; /* group creation order flag */ - unsigned i; - unsigned u; - int is_ref = 0; - htri_t is_named; - hbool_t limit_maxdims; - hsize_t size_dset; - - /*------------------------------------------------------------------------- - * copy the suppplied object list - *------------------------------------------------------------------------- - */ - - if (options->verbose) { - printf("-----------------------------------------\n"); - printf(" Type Filter (Compression) Name\n"); - printf("-----------------------------------------\n"); - } - - for (i = 0; i < travt->nobjs; i++) { - /* init variables per obj */ - buf = NULL; - limit_maxdims = FALSE; - - switch (travt->objs[i].type) { - - case H5TRAV_TYPE_UNKNOWN: - HDassert(0); - break; - /*------------------------------------------------------------------------- - * H5TRAV_TYPE_GROUP - *------------------------------------------------------------------------- - */ - case H5TRAV_TYPE_GROUP: - - if (options->verbose) { - printf(FORMAT_OBJ, "group", travt->objs[i].name); - } - - /* open input group */ - if ((grp_in = H5Gopen2(fidin, travt->objs[i].name, H5P_DEFAULT)) - < 0) - goto error; - - /* get input group creation property list */ - if ((gcpl_in = H5Gget_create_plist(grp_in)) < 0) - goto error; - - /* query and set the group creation properties */ - if (H5Pget_link_creation_order(gcpl_in, &crt_order_flags) < 0) - goto error; - - /* set up group creation property list */ - if ((gcpl_out = H5Pcreate(H5P_GROUP_CREATE)) < 0) - goto error; - - if (H5Pset_link_creation_order(gcpl_out, crt_order_flags) < 0) - goto error; - - /*------------------------------------------------------------------------- - * the root is a special case, we get an ID for the root group - * and copy its attributes using that ID - *------------------------------------------------------------------------- - */ - if (HDstrcmp(travt->objs[i].name, "/") == 0) { - if ((grp_out = H5Gopen2(fidout, "/", H5P_DEFAULT)) < 0) - goto error; - } - else { - - if (options->grp_compact > 0 || options->grp_indexed > 0) { - if (H5Pset_link_phase_change(gcpl_out, - (unsigned) options->grp_compact, - (unsigned) options->grp_indexed) < 0) - goto error; - } - - if ((grp_out = H5Gcreate2(fidout, travt->objs[i].name, - H5P_DEFAULT, gcpl_out, H5P_DEFAULT)) < 0) - goto error; - - } - - /*------------------------------------------------------------------------- - * copy attrs - *------------------------------------------------------------------------- - */ - if (copy_attr(grp_in, grp_out, &named_dt_head, travt, options) < 0) - goto error; - - if (H5Pclose(gcpl_out) < 0) - goto error; - if (H5Pclose(gcpl_in) < 0) - goto error; - if (H5Gclose(grp_out) < 0) - goto error; - if (H5Gclose(grp_in) < 0) - goto error; - - break; - - /*------------------------------------------------------------------------- - * H5TRAV_TYPE_DATASET - *------------------------------------------------------------------------- - */ - case H5TRAV_TYPE_DATASET: - - has_filter = 0; - req_filter = 0; - - /* check if global filters were requested */ - if (options->n_filter_g) - req_filter = 1; - - /* check if filters were requested for individual objects */ - for (u = 0; u < options->op_tbl->nelems; u++) { - - if (HDstrcmp(travt->objs[i].name, options->op_tbl->objs[u].path) == 0) { - if (options->op_tbl->objs[u].filter->filtn > 0) { - req_filter = 1; - } - } - } - - /* check if layout change requested individual object */ - if (options->layout_g != H5D_LAYOUT_ERROR) { - pack_info_t *pckinfo; - /* any dataset is specified */ - if (options->op_tbl->nelems > 0) { - /* check if object exist */ - pckinfo = options_get_object(travt->objs[i].name, - options->op_tbl); - if (pckinfo) { - req_obj_layout = 1; - } - } - } - - /* early detection of references */ - if ((dset_in = H5Dopen2(fidin, travt->objs[i].name, H5P_DEFAULT)) - < 0) - goto error; - if ((ftype_id = H5Dget_type(dset_in)) < 0) - goto error; - if (H5T_REFERENCE == H5Tget_class(ftype_id)) - is_ref = 1; - - /* Check if the datatype is committed */ - if ((is_named = H5Tcommitted(ftype_id)) < 0) - goto error; - if (is_named) - if ((wtype_id = copy_named_datatype(ftype_id, fidout, - &named_dt_head, travt, options)) < 0) - goto error; - - if (H5Tclose(ftype_id) < 0) - goto error; - if (H5Dclose(dset_in) < 0) - goto error; - - /*------------------------------------------------------------------------- - * check if we should use H5Ocopy or not - * if there is a request for filters/layout, we read/write the object - * otherwise we do a copy using H5Ocopy - *------------------------------------------------------------------------- - */ - if (options->op_tbl->nelems || options->all_filter == 1 - || options->all_layout == 1 || is_ref || is_named) { - - int j; - - if ((dset_in = H5Dopen2(fidin, travt->objs[i].name, H5P_DEFAULT)) < 0) - goto error; - if ((f_space_id = H5Dget_space(dset_in)) < 0) - goto error; - if ((ftype_id = H5Dget_type(dset_in)) < 0) - goto error; - if ((dcpl_in = H5Dget_create_plist(dset_in)) < 0) - goto error; - if ((dcpl_out = H5Pcopy(dcpl_in)) < 0) - goto error; - if ((rank = H5Sget_simple_extent_ndims(f_space_id)) < 0) - goto error; - HDmemset(dims, 0, sizeof dims); - if (H5Sget_simple_extent_dims(f_space_id, dims, NULL) < 0) - goto error; - - if (H5Dget_space_status(dset_in, &space_status) < 0) - goto error; - - nelmts = 1; - for (j = 0; j < rank; j++) - nelmts *= dims[j]; - - /* wtype_id will have already been set if using a named dtype */ - if (!is_named) { - if (options->use_native == 1) - wtype_id = h5tools_get_native_type(ftype_id); - else - wtype_id = H5Tcopy(ftype_id); - } /* end if */ - - if ((msize = H5Tget_size(wtype_id)) == 0) - goto error; - - /* size of current dset */ - size_dset = nelmts * msize; - - /*------------------------------------------------------------------------- - * 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((travt->objs[i].name), dcpl_in) == 1) { - apply_s = 1; - apply_f = 1; - - /*------------------------------------------------------------------------- - * references are a special case - * we cannot just copy the buffers, but instead we recreate the reference - * in a second traversal of the output file - *------------------------------------------------------------------------- - */ - if (H5T_REFERENCE != H5Tget_class(wtype_id)) { - /* get the storage size of the input dataset */ - dsize_in = H5Dget_storage_size(dset_in); - - /* check for small size datasets (less than 1k) except - * changing to COMPACT. For the reference, COMPACT is limited - * by size 64K by library. - */ - if (options->layout_g != H5D_COMPACT) { - if (size_dset < options->min_comp) - apply_s = 0; - } - - /* apply the filter */ - if (apply_s) { - if (apply_filters(travt->objs[i].name, rank, dims, - msize, dcpl_out, options, &has_filter) < 0) - goto error; - } - - /* only if layout change requested for entire file or - * individual obj */ - if (options->all_layout > 0 || req_obj_layout == 1) - /*------------------------------------------------- - * Unset the unlimited max dims if convert to other - * than chunk layouts, because unlimited max dims - * only can be applied to chunk layout. - * Also perform only for targeted dataset - * Also check for size limit to convert to compact - *-------------------------------------------------*/ - if (options->layout_g != H5D_CHUNKED) { - /* any dataset is specified */ - if (options->op_tbl->nelems > 0) { - /* if current obj match specified obj */ - if (options_get_object(travt->objs[i].name, - options->op_tbl)) - limit_maxdims = TRUE; - } - else { /* no dataset is specified */ - limit_maxdims = TRUE; - } - - /* if convert to COMPACT */ - if (options->layout_g == H5D_COMPACT) { - /* should be smaller than 64K */ - if (size_dset > MAX_COMPACT_DSIZE) - limit_maxdims = FALSE; - } - - /* unset unlimited max dims */ - if (limit_maxdims) - H5Sset_extent_simple(f_space_id, rank, dims, - NULL); - } - - /*------------------------------------------------------------------------- - * create the output dataset; - * disable error checking in case the dataset cannot be created with the - * modified dcpl; in that case use the original instead - *------------------------------------------------------------------------- - */ - H5E_BEGIN_TRY - { - dset_out = H5Dcreate2(fidout, - travt->objs[i].name, wtype_id, - f_space_id, H5P_DEFAULT, dcpl_out, - H5P_DEFAULT); - }H5E_END_TRY; - - if (dset_out == FAIL) { - if (options->verbose) - printf( - " warning: could not create dataset <%s>. Applying original settings\n", - travt->objs[i].name); - - if ((dset_out = H5Dcreate2(fidout, - travt->objs[i].name, wtype_id, f_space_id, - H5P_DEFAULT, dcpl_in, H5P_DEFAULT)) < 0) - goto error; - apply_f = 0; - } - - /*------------------------------------------------------------------------- - * read/write - *------------------------------------------------------------------------- - */ - if (nelmts > 0 && space_status != H5D_SPACE_STATUS_NOT_ALLOCATED) { - size_t need = (size_t)(nelmts * msize); /* bytes needed */ - - /* have to read the whole dataset if there is only one element in the dataset */ - if (need < H5TOOLS_MALLOCSIZE) - buf = HDmalloc(need); - - if (buf != NULL) { - /* read/write: use the macro to check error, e.g. memory allocation error inside the library. */ - CHECK_H5DRW_ERROR(H5Dread, dset_in, wtype_id, - H5S_ALL, H5S_ALL, H5P_DEFAULT, buf); - CHECK_H5DRW_ERROR(H5Dwrite, dset_out, wtype_id, - H5S_ALL, H5S_ALL, H5P_DEFAULT, buf); - - /* Check if we have VL data in the dataset's - * datatype that must be reclaimed */ - if (TRUE == H5Tdetect_class(wtype_id, H5T_VLEN)) - if (H5Dvlen_reclaim(wtype_id, f_space_id, - H5P_DEFAULT, buf) < 0) - goto error; - } - else { /* possibly not enough memory, read/write by hyperslabs */ - size_t p_type_nbytes = msize; /*size of memory type */ - hsize_t p_nelmts = nelmts; /*total elements */ - hsize_t elmtno; /*counter */ - int carry; /*counter carry value */ - unsigned int vl_data = 0; /*contains VL datatypes */ - - /* hyperslab info */ - hsize_t hslab_dims[H5S_MAX_RANK]; /*hyperslab dims */ - hsize_t hslab_nbytes; /*bytes per hyperslab */ - hsize_t hslab_nelmts; /*elements per hyperslab*/ - hid_t hslab_space; /*hyperslab data space */ - - /* hyperslab selection info */ - hsize_t hs_sel_offset[H5S_MAX_RANK];/* selection offset */ - hsize_t hs_sel_count[H5S_MAX_RANK]; /* selection count */ - hsize_t hs_select_nelmts; /* selected elements */ - hsize_t zero[8]; /*vector of zeros */ - int k; - H5D_layout_t dset_layout; - hid_t dcpl_tmp = -1; /* dataset creation property list ID */ - - /* check if we have VL data in the dataset's datatype */ - if (H5Tdetect_class(wtype_id, H5T_VLEN) == TRUE) - vl_data = TRUE; - - /* check first if writing dataset is chunked, - * if so use its chunk layout for better performance. */ - dset_layout = H5Pget_layout(dcpl_out); - if (dset_layout == H5D_CHUNKED) - dcpl_tmp = dcpl_out; /* writing dataset */ - else { /* if reading dataset is chunked */ - dset_layout = H5Pget_layout(dcpl_in); - if (dset_layout == H5D_CHUNKED) - dcpl_tmp = dcpl_in; /* reading dataset */ - } - - /* get hyperslab dims and size in byte */ - if (Get_hyperslab(dcpl_tmp, rank, dims, - p_type_nbytes, hslab_dims, - &hslab_nbytes) < 0) - goto error; - - hslab_buf = HDmalloc((size_t)hslab_nbytes); - - hslab_nelmts = hslab_nbytes / p_type_nbytes; - hslab_space = H5Screate_simple(1, &hslab_nelmts, - NULL); - - /* the hyperslab selection loop */ - HDmemset(hs_sel_offset, 0, - sizeof hs_sel_offset); - HDmemset(zero, 0, sizeof zero); - - for (elmtno = 0; elmtno < p_nelmts; elmtno += - hs_select_nelmts) { - if (rank > 0) { - /* calculate the hyperslab selections. The selection would be same as the hyperslab except for remaining edge portion of the dataset which is smaller then the hyperslab. - */ - for (k = 0, hs_select_nelmts = 1; - k < rank; k++) { - /* MIN() is used to get the remaining edge portion if exist. - * "dims[k] - hs_sel_offset[k]" is remaining edge portion that is smaller then the hyperslab.*/ - hs_sel_count[k] = - MIN(dims[k] - hs_sel_offset[k], hslab_dims[k]); - hs_select_nelmts *= hs_sel_count[k]; - } - - if (H5Sselect_hyperslab(f_space_id, - H5S_SELECT_SET, hs_sel_offset, - NULL, hs_sel_count, NULL) < 0) - goto error; - if (H5Sselect_hyperslab(hslab_space, - H5S_SELECT_SET, zero, NULL, - &hs_select_nelmts, NULL) < 0) - goto error; - } - else { - H5Sselect_all(f_space_id); - H5Sselect_all(hslab_space); - hs_select_nelmts = 1; - } /* rank */ - - /* read/write: use the macro to check error, e.g. memory allocation error inside the library. */ - CHECK_H5DRW_ERROR(H5Dread, dset_in, - wtype_id, hslab_space, f_space_id, - H5P_DEFAULT, hslab_buf); - CHECK_H5DRW_ERROR(H5Dwrite, dset_out, - wtype_id, hslab_space, f_space_id, - H5P_DEFAULT, hslab_buf); - - /* reclaim any VL memory, if necessary */ - if (vl_data) - H5Dvlen_reclaim(wtype_id, hslab_space, - H5P_DEFAULT, hslab_buf); - - /* calculate the next hyperslab offset */ - for (k = rank, carry = 1; k > 0 && carry; - --k) { - hs_sel_offset[k - 1] += hs_sel_count[k - - 1]; - /* if reached the end of a dim */ - if (hs_sel_offset[k - 1] == dims[k - 1]) - hs_sel_offset[k - 1] = 0; - else - carry = 0; - } /* k */ - } /* elmtno */ - - H5Sclose(hslab_space); - /* free */ - if (hslab_buf != NULL) { - HDfree(hslab_buf); - hslab_buf = NULL; - } - } /* hyperslab read */ - } /* if (nelmts>0 && space_status==H5D_SPACE_STATUS_NOT_ALLOCATED) */ - - /*------------------------------------------------------------------------- - * amount of compression used - *------------------------------------------------------------------------- - */ - if (options->verbose) { - double ratio = 0; - - /* only print the compression ration if there was a filter request */ - if (apply_s && apply_f && req_filter) { - /* get the storage size of the output dataset */ - dsize_out = H5Dget_storage_size(dset_out); - - /* compression ratio = uncompressed size / compressed size */ - if (dsize_out != 0) - ratio = (double) dsize_in - / (double) dsize_out; - - print_dataset_info(dcpl_out, - travt->objs[i].name, ratio, 1); - } - else - print_dataset_info(dcpl_in, travt->objs[i].name, - ratio, 0); - - /* print a message that the filter was not applied - (in case there was a filter) - */ - if (has_filter && apply_s == 0) - printf( - " <warning: filter not applied to %s. dataset smaller than %d bytes>\n", - travt->objs[i].name, - (int) options->min_comp); - - if (has_filter && apply_f == 0) - printf( - " <warning: could not apply the filter to %s>\n", - travt->objs[i].name); - - } /* verbose */ - - /*------------------------------------------------------------------------- - * copy attrs - *------------------------------------------------------------------------- - */ - if (copy_attr(dset_in, dset_out, &named_dt_head, travt, - options) < 0) - goto error; - /*close */ - if (H5Dclose(dset_out) < 0) - goto error; - - }/*!H5T_REFERENCE*/ - }/*h5tools_canreadf*/ - - /*------------------------------------------------------------------------- - * close - *------------------------------------------------------------------------- - */ - if (H5Tclose(ftype_id) < 0) - goto error; - if (H5Tclose(wtype_id) < 0) - goto error; - if (H5Pclose(dcpl_in) < 0) - goto error; - if (H5Pclose(dcpl_out) < 0) - goto error; - if (H5Sclose(f_space_id) < 0) - goto error; - if (H5Dclose(dset_in) < 0) - goto error; - - } - /*------------------------------------------------------------------------- - * we do not have request for filter/chunking use H5Ocopy instead - *------------------------------------------------------------------------- - */ - else { - hid_t pid; - - /* create property to pass copy options */ - if ((pid = H5Pcreate(H5P_OBJECT_COPY)) < 0) - goto error; - - /* set options for object copy */ - if (H5Pset_copy_object(pid, H5O_COPY_WITHOUT_ATTR_FLAG) < 0) - goto error; - - /*------------------------------------------------------------------------- - * do the copy - *------------------------------------------------------------------------- - */ - - if (H5Ocopy(fidin, /* Source file or group identifier */ - travt->objs[i].name, /* Name of the source object to be copied */ - fidout, /* Destination file or group identifier */ - travt->objs[i].name, /* Name of the destination object */ - pid, /* Properties which apply to the copy */ - H5P_DEFAULT) < 0) /* Properties which apply to the new hard link */ - goto error; - - /* close property */ - if (H5Pclose(pid) < 0) - goto error; - - /*------------------------------------------------------------------------- - * copy attrs manually - *------------------------------------------------------------------------- - */ - if ((dset_in = H5Dopen2(fidin, travt->objs[i].name, H5P_DEFAULT)) - < 0) - goto error; - if ((dset_out = H5Dopen2(fidout, travt->objs[i].name, - H5P_DEFAULT)) < 0) - goto error; - if (copy_attr(dset_in, dset_out, &named_dt_head, travt, options) - < 0) - goto error; - if (H5Dclose(dset_in) < 0) - goto error; - if (H5Dclose(dset_out) < 0) - goto error; - - if (options->verbose) - printf(FORMAT_OBJ, "dset", travt->objs[i].name); - - } /* end do we have request for filter/chunking */ - - break; - - /*------------------------------------------------------------------------- - * H5TRAV_TYPE_NAMED_DATATYPE - *------------------------------------------------------------------------- - */ - case H5TRAV_TYPE_NAMED_DATATYPE: - - if (options->verbose) - printf(FORMAT_OBJ, "type", travt->objs[i].name); - - if ((type_in = H5Topen2(fidin, travt->objs[i].name, H5P_DEFAULT)) - < 0) - goto error; - - /* Copy the datatype anonymously */ - if ((type_out = copy_named_datatype(type_in, fidout, &named_dt_head, - travt, options)) < 0) - goto error; - - /* Link in to group structure */ - if (H5Lcreate_hard(type_out, ".", fidout, travt->objs[i].name, - H5P_DEFAULT, H5P_DEFAULT) < 0) - goto error; - - /*------------------------------------------------------------------------- - * copy attrs - *------------------------------------------------------------------------- - */ - if (copy_attr(type_in, type_out, &named_dt_head, travt, options) - < 0) - goto error; - - if (H5Tclose(type_in) < 0) - goto error; - if (H5Tclose(type_out) < 0) - goto error; - - break; - - /*------------------------------------------------------------------------- - * H5TRAV_TYPE_LINK - * H5TRAV_TYPE_UDLINK - * - * Only handles external links; H5Lcopy will fail for other UD link types - * since we don't have creation or copy callbacks for them. - *------------------------------------------------------------------------- - */ - - case H5TRAV_TYPE_LINK: - case H5TRAV_TYPE_UDLINK: { - - if (options->verbose) - printf(FORMAT_OBJ, "link", travt->objs[i].name); - - if (H5Lcopy(fidin, travt->objs[i].name, fidout, travt->objs[i].name, - H5P_DEFAULT, H5P_DEFAULT) < 0) - goto error; - - if (options->verbose) - printf(FORMAT_OBJ, "link", travt->objs[i].name); - - } - break; - - default: - goto error; - } /* switch */ - - /* free */ - if (buf != NULL) { - HDfree(buf); - buf = NULL; - } - - } /* i */ - - /* Finalize (link) the stack of named datatypes (if any) */ - named_datatype_free(&named_dt_head, 0); - - return 0; - -error: - H5E_BEGIN_TRY - { - H5Gclose(grp_in); - H5Gclose(grp_out); - H5Pclose(dcpl_in); - H5Pclose(gcpl_in); - H5Pclose(gcpl_out); - H5Sclose(f_space_id); - H5Dclose(dset_in); - H5Dclose(dset_out); - H5Tclose(ftype_id); - H5Tclose(wtype_id); - H5Tclose(type_in); - H5Tclose(type_out); - named_datatype_free(&named_dt_head, 1); - }H5E_END_TRY; - /* free */ - if (buf != NULL) - HDfree(buf); - if (hslab_buf != NULL) - HDfree(hslab_buf); - return -1; + int ret_value = 0; /*no need to LEAVE() on ERROR: HERR_INIT(int, SUCCEED) */ + hid_t grp_in = -1; /* group ID */ + hid_t grp_out = -1; /* group ID */ + hid_t dset_in = -1; /* read dataset ID */ + hid_t dset_out = -1; /* write dataset ID */ + hid_t gcpl_in = -1; /* group creation property list */ + hid_t gcpl_out = -1; /* group creation property list */ + hid_t type_in = -1; /* named type ID */ + hid_t type_out = -1; /* named type ID */ + hid_t dcpl_in = -1; /* dataset creation property list ID */ + hid_t dcpl_out = -1; /* dataset creation property list ID */ + hid_t f_space_id = -1; /* file space ID */ + hid_t ftype_id = -1; /* file type ID */ + hid_t wtype_id = -1; /* read/write type ID */ + named_dt_t *named_dt_head = NULL; /* Pointer to the stack of named datatypes copied */ + size_t msize; /* size of type */ + hsize_t nelmts; /* number of elements in dataset */ + H5D_space_status_t space_status; /* determines whether space has been allocated for the dataset */ + int rank; /* rank of dataset */ + hsize_t dims[H5S_MAX_RANK];/* dimensions of dataset */ + hsize_t dsize_in; /* input dataset size before filter */ + hsize_t dsize_out; /* output dataset size after filter */ + int apply_s; /* flag for apply filter to small dataset sizes */ + int apply_f; /* flag for apply filter to return error on H5Dcreate */ + void *buf = NULL; /* buffer for raw data */ + void *hslab_buf = NULL; /* hyperslab buffer for raw data */ + int has_filter; /* current object has a filter */ + int req_filter; /* there was a request for a filter */ + int req_obj_layout = 0; /* request layout to current object */ + unsigned crt_order_flags; /* group creation order flag */ + unsigned i; + unsigned u; + int is_ref = 0; + htri_t is_named; + hbool_t limit_maxdims; + hsize_t size_dset; + + /*------------------------------------------------------------------------- + * copy the suppplied object list + *------------------------------------------------------------------------- + */ + + if (options->verbose) { + printf("-----------------------------------------\n"); + printf(" Type Filter (Compression) Name\n"); + printf("-----------------------------------------\n"); + } + + for (i = 0; i < travt->nobjs; i++) { + /* init variables per obj */ + buf = NULL; + limit_maxdims = FALSE; + + switch (travt->objs[i].type) { + case H5TRAV_TYPE_UNKNOWN: + HDassert(0); + break; + + /*------------------------------------------------------------------------- + * H5TRAV_TYPE_GROUP + *------------------------------------------------------------------------- + */ + case H5TRAV_TYPE_GROUP: + if (options->verbose) + printf(FORMAT_OBJ, "group", travt->objs[i].name); + + /* open input group */ + if ((grp_in = H5Gopen2(fidin, travt->objs[i].name, H5P_DEFAULT)) < 0) + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Gopen2 failed"); + + /* get input group creation property list */ + if ((gcpl_in = H5Gget_create_plist(grp_in)) < 0) + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Gget_create_plist failed"); + + /* query and set the group creation properties */ + if (H5Pget_link_creation_order(gcpl_in, &crt_order_flags) < 0) + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pget_link_creation_order failed"); + + /* set up group creation property list */ + if ((gcpl_out = H5Pcreate(H5P_GROUP_CREATE)) < 0) + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pcreate failed"); + + if (H5Pset_link_creation_order(gcpl_out, crt_order_flags) < 0) + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pset_link_creation_order failed"); + + /*------------------------------------------------------------------------- + * the root is a special case, we get an ID for the root group + * and copy its attributes using that ID + *------------------------------------------------------------------------- + */ + if (HDstrcmp(travt->objs[i].name, "/") == 0) { + if ((grp_out = H5Gopen2(fidout, "/", H5P_DEFAULT)) < 0) + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Gopen2 failed"); + } + else { + if (options->grp_compact > 0 || options->grp_indexed > 0) + if (H5Pset_link_phase_change(gcpl_out, (unsigned) options->grp_compact, (unsigned) options->grp_indexed) < 0) + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pset_link_phase_change failed"); + + if ((grp_out = H5Gcreate2(fidout, travt->objs[i].name, H5P_DEFAULT, gcpl_out, H5P_DEFAULT)) < 0) + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Gcreate2 failed"); + } + + /*------------------------------------------------------------------------- + * copy attrs + *------------------------------------------------------------------------- + */ + if (copy_attr(grp_in, grp_out, &named_dt_head, travt, options) < 0) + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "copy_attr failed"); + + if (H5Pclose(gcpl_out) < 0) + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed"); + if (H5Pclose(gcpl_in) < 0) + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose 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"); + + break; + + /*------------------------------------------------------------------------- + * H5TRAV_TYPE_DATASET + *------------------------------------------------------------------------- + */ + case H5TRAV_TYPE_DATASET: + has_filter = 0; + req_filter = 0; + + /* check if global filters were requested */ + if (options->n_filter_g) + req_filter = 1; + + /* check if filters were requested for individual objects */ + for (u = 0; u < options->op_tbl->nelems; u++) + if (HDstrcmp(travt->objs[i].name, options->op_tbl->objs[u].path) == 0) + if (options->op_tbl->objs[u].filter->filtn > 0) + req_filter = 1; + + /* check if layout change requested individual object */ + if (options->layout_g != H5D_LAYOUT_ERROR) { + pack_info_t *pckinfo; + + /* any dataset is specified */ + if (options->op_tbl->nelems > 0) { + /* check if object exist */ + pckinfo = options_get_object(travt->objs[i].name, options->op_tbl); + if (pckinfo) + req_obj_layout = 1; + } + } + + /* early detection of references */ + if ((dset_in = H5Dopen2(fidin, travt->objs[i].name, H5P_DEFAULT)) < 0) + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dopen2 failed"); + if ((ftype_id = H5Dget_type(dset_in)) < 0) + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dget_type failed"); + if (H5T_REFERENCE == H5Tget_class(ftype_id)) + is_ref = 1; + + /* Check if the datatype is committed */ + if ((is_named = H5Tcommitted(ftype_id)) < 0) + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Tcommitted failed"); + if (is_named) + if ((wtype_id = copy_named_datatype(ftype_id, fidout, &named_dt_head, travt, options)) < 0) + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "copy_named_datatype failed"); + + if (H5Tclose(ftype_id) < 0) + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Tclose failed"); + if (H5Dclose(dset_in) < 0) + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dclose failed"); + + /*------------------------------------------------------------------------- + * check if we should use H5Ocopy or not + * if there is a request for filters/layout, we read/write the object + * otherwise we do a copy using H5Ocopy + *------------------------------------------------------------------------- + */ + if (options->op_tbl->nelems || options->all_filter == 1 + || options->all_layout == 1 || is_ref || is_named) { + + int j; + + if ((dset_in = H5Dopen2(fidin, travt->objs[i].name, H5P_DEFAULT)) < 0) + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dopen2 failed"); + if ((f_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_in = H5Dget_create_plist(dset_in)) < 0) + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dget_create_plist failed"); + if ((dcpl_out = H5Pcopy(dcpl_in)) < 0) + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pcopy failed"); + if ((rank = H5Sget_simple_extent_ndims(f_space_id)) < 0) + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Sget_simple_extent_ndims failed"); + HDmemset(dims, 0, sizeof dims); + if (H5Sget_simple_extent_dims(f_space_id, dims, NULL) < 0) + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Sget_simple_extent_dims failed"); + if (H5Dget_space_status(dset_in, &space_status) < 0) + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dget_space_status failed"); + + nelmts = 1; + for (j = 0; j < rank; j++) + nelmts *= dims[j]; + + /* wtype_id will have already been set if using a named dtype */ + if (!is_named) { + if (options->use_native == 1) + wtype_id = h5tools_get_native_type(ftype_id); + else + wtype_id = H5Tcopy(ftype_id); + } /* end if */ + + if ((msize = H5Tget_size(wtype_id)) == 0) + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Tget_size failed"); + + /* size of current dset */ + size_dset = nelmts * msize; + + /*------------------------------------------------------------------------- + * 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((travt->objs[i].name), dcpl_in) == 1) { + apply_s = 1; + apply_f = 1; + + /*------------------------------------------------------------------------- + * references are a special case + * we cannot just copy the buffers, but instead we recreate the reference + * in a second traversal of the output file + *------------------------------------------------------------------------- + */ + if (H5T_REFERENCE != H5Tget_class(wtype_id)) { + /* get the storage size of the input dataset */ + dsize_in = H5Dget_storage_size(dset_in); + + /* check for small size datasets (less than 1k) except + * changing to COMPACT. For the reference, COMPACT is limited + * by size 64K by library. + */ + if (options->layout_g != H5D_COMPACT) + if (size_dset < options->min_comp) + apply_s = 0; + + /* apply the filter */ + if (apply_s) + if (apply_filters(travt->objs[i].name, rank, dims, msize, dcpl_out, options, &has_filter) < 0) + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "apply_filters failed"); + + /* only if layout change requested for entire file or + * individual obj */ + if (options->all_layout > 0 || req_obj_layout == 1) + /*------------------------------------------------- + * Unset the unlimited max dims if convert to other + * than chunk layouts, because unlimited max dims + * only can be applied to chunk layout. + * Also perform only for targeted dataset + * Also check for size limit to convert to compact + *-------------------------------------------------*/ + if (options->layout_g != H5D_CHUNKED) { + /* any dataset is specified */ + if (options->op_tbl->nelems > 0) { + /* if current obj match specified obj */ + if (options_get_object(travt->objs[i].name, options->op_tbl)) + limit_maxdims = TRUE; + } + else /* no dataset is specified */ + limit_maxdims = TRUE; + + /* if convert to COMPACT */ + if (options->layout_g == H5D_COMPACT) + /* should be smaller than 64K */ + if (size_dset > MAX_COMPACT_DSIZE) + limit_maxdims = FALSE; + + /* unset unlimited max dims */ + if (limit_maxdims) + H5Sset_extent_simple(f_space_id, rank, dims, NULL); + } + + /*------------------------------------------------------------------------- + * create the output dataset; + * disable error checking in case the dataset cannot be created with the + * modified dcpl; in that case use the original instead + *------------------------------------------------------------------------- + */ + dset_out = H5Dcreate2(fidout, travt->objs[i].name, wtype_id, f_space_id, H5P_DEFAULT, dcpl_out, H5P_DEFAULT); + if (dset_out == FAIL) { + H5Epush2(H5tools_ERR_STACK_g, __FILE__, FUNC, __LINE__, H5tools_ERR_CLS_g, H5E_tools_g, H5E_tools_min_id_g, "H5Dcreate2 failed"); + if (options->verbose) + printf(" warning: could not create dataset <%s>. Applying original settings\n", travt->objs[i].name); + + if ((dset_out = H5Dcreate2(fidout, travt->objs[i].name, wtype_id, f_space_id, H5P_DEFAULT, dcpl_in, H5P_DEFAULT)) < 0) + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dcreate2 failed"); + apply_f = 0; + } + + /*------------------------------------------------------------------------- + * read/write + *------------------------------------------------------------------------- + */ + if (nelmts > 0 && space_status != H5D_SPACE_STATUS_NOT_ALLOCATED) { + size_t need = (size_t)(nelmts * msize); /* bytes needed */ + + /* have to read the whole dataset if there is only one element in the dataset */ + if (need < H5TOOLS_MALLOCSIZE) + buf = HDmalloc(need); + + if (buf != NULL) { + /* read/write: use the macro to check error, e.g. memory allocation error inside the library. */ + CHECK_H5DRW_ERROR(H5Dread, FAIL, dset_in, wtype_id, H5S_ALL, H5S_ALL, H5P_DEFAULT, buf); + CHECK_H5DRW_ERROR(H5Dwrite, FAIL, dset_out, wtype_id, H5S_ALL, H5S_ALL, H5P_DEFAULT, buf); + + /* Check if we have VL data in the dataset's + * datatype that must be reclaimed */ + if (TRUE == H5Tdetect_class(wtype_id, H5T_VLEN)) + if (H5Dvlen_reclaim(wtype_id, f_space_id, H5P_DEFAULT, buf) < 0) + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dvlen_reclaim failed"); + } + else { /* possibly not enough memory, read/write by hyperslabs */ + size_t p_type_nbytes = msize; /*size of memory type */ + hsize_t p_nelmts = nelmts; /*total elements */ + hsize_t elmtno; /*counter */ + int carry; /*counter carry value */ + unsigned int vl_data = 0; /*contains VL datatypes */ + + /* hyperslab info */ + hsize_t hslab_dims[H5S_MAX_RANK]; /*hyperslab dims */ + hsize_t hslab_nbytes; /*bytes per hyperslab */ + hsize_t hslab_nelmts; /*elements per hyperslab*/ + hid_t hslab_space; /*hyperslab data space */ + + /* hyperslab selection info */ + hsize_t hs_sel_offset[H5S_MAX_RANK];/* selection offset */ + hsize_t hs_sel_count[H5S_MAX_RANK]; /* selection count */ + hsize_t hs_select_nelmts; /* selected elements */ + hsize_t zero[8]; /*vector of zeros */ + int k; + H5D_layout_t dset_layout; + hid_t dcpl_tmp = -1; /* dataset creation property list ID */ + + /* check if we have VL data in the dataset's datatype */ + if (H5Tdetect_class(wtype_id, H5T_VLEN) == TRUE) + vl_data = TRUE; + + /* check first if writing dataset is chunked, + * if so use its chunk layout for better performance. */ + dset_layout = H5Pget_layout(dcpl_out); + if (dset_layout == H5D_CHUNKED) + dcpl_tmp = dcpl_out; /* writing dataset */ + else { /* if reading dataset is chunked */ + dset_layout = H5Pget_layout(dcpl_in); + if (dset_layout == H5D_CHUNKED) + dcpl_tmp = dcpl_in; /* reading dataset */ + } + + /* get hyperslab dims and size in byte */ + if (Get_hyperslab(dcpl_tmp, rank, dims, p_type_nbytes, hslab_dims, &hslab_nbytes) < 0) + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "Get_hyperslab failed"); + + hslab_buf = HDmalloc((size_t)hslab_nbytes); + + hslab_nelmts = hslab_nbytes / p_type_nbytes; + hslab_space = H5Screate_simple(1, &hslab_nelmts, NULL); + + /* the hyperslab selection loop */ + HDmemset(hs_sel_offset, 0, sizeof hs_sel_offset); + HDmemset(zero, 0, sizeof zero); + + for (elmtno = 0; elmtno < p_nelmts; elmtno += hs_select_nelmts) { + if (rank > 0) { + /* calculate the hyperslab selections. + * The selection would be same as the hyperslab + * except for remaining edge portion of the dataset + * which is smaller then the hyperslab. + */ + for (k = 0, hs_select_nelmts = 1; k < rank; k++) { + /* MIN() is used to get the remaining edge portion if exist. + * "dims[k] - hs_sel_offset[k]" is remaining edge portion that is smaller then the hyperslab.*/ + hs_sel_count[k] = MIN(dims[k] - hs_sel_offset[k], hslab_dims[k]); + hs_select_nelmts *= hs_sel_count[k]; + } + + if (H5Sselect_hyperslab(f_space_id, H5S_SELECT_SET, hs_sel_offset, NULL, hs_sel_count, NULL) < 0) + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Sselect_hyperslab failed"); + if (H5Sselect_hyperslab(hslab_space, H5S_SELECT_SET, zero, NULL, &hs_select_nelmts, NULL) < 0) + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Sselect_hyperslab failed"); + } + else { + H5Sselect_all(f_space_id); + H5Sselect_all(hslab_space); + hs_select_nelmts = 1; + } /* rank */ + + /* read/write: use the macro to check error, e.g. memory allocation error inside the library. */ + CHECK_H5DRW_ERROR(H5Dread, FAIL, dset_in, wtype_id, hslab_space, f_space_id, H5P_DEFAULT, hslab_buf); + CHECK_H5DRW_ERROR(H5Dwrite, FAIL, dset_out, wtype_id, hslab_space, f_space_id, H5P_DEFAULT, hslab_buf); + + /* reclaim any VL memory, if necessary */ + if (vl_data) + H5Dvlen_reclaim(wtype_id, hslab_space, H5P_DEFAULT, hslab_buf); + + /* calculate the next hyperslab offset */ + for (k = rank, carry = 1; k > 0 && carry; --k) { + hs_sel_offset[k - 1] += hs_sel_count[k - 1]; + /* if reached the end of a dim */ + if (hs_sel_offset[k - 1] == dims[k - 1]) + hs_sel_offset[k - 1] = 0; + else + carry = 0; + } /* k */ + } /* elmtno */ + + H5Sclose(hslab_space); + /* free */ + if (hslab_buf != NULL) { + HDfree(hslab_buf); + hslab_buf = NULL; + } + } /* hyperslab read */ + } /* if (nelmts>0 && space_status==H5D_SPACE_STATUS_NOT_ALLOCATED) */ + + /*------------------------------------------------------------------------- + * amount of compression used + *------------------------------------------------------------------------- + */ + if (options->verbose) { + double ratio = 0; + + /* only print the compression ration if there was a filter request */ + if (apply_s && apply_f && req_filter) { + /* get the storage size of the output dataset */ + dsize_out = H5Dget_storage_size(dset_out); + + /* compression ratio = uncompressed size / compressed size */ + if (dsize_out != 0) + ratio = (double) dsize_in / (double) dsize_out; + print_dataset_info(dcpl_out, travt->objs[i].name, ratio, 1); + } + else + print_dataset_info(dcpl_in, travt->objs[i].name, ratio, 0); + + /* print a message that the filter was not applied + (in case there was a filter) + */ + if (has_filter && apply_s == 0) + printf(" <warning: filter not applied to %s. dataset smaller than %d bytes>\n", travt->objs[i].name, (int) options->min_comp); + + if (has_filter && apply_f == 0) + printf(" <warning: could not apply the filter to %s>\n", travt->objs[i].name); + } /* verbose */ + + /*------------------------------------------------------------------------- + * 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"); + + /*close */ + if (H5Dclose(dset_out) < 0) + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dclose failed"); + }/*!H5T_REFERENCE*/ + }/*h5tools_canreadf*/ + + /*------------------------------------------------------------------------- + * close + *------------------------------------------------------------------------- + */ + if (H5Tclose(ftype_id) < 0) + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Tclose failed"); + if (H5Tclose(wtype_id) < 0) + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Tclose failed"); + if (H5Pclose(dcpl_in) < 0) + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed"); + if (H5Pclose(dcpl_out) < 0) + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed"); + if (H5Sclose(f_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"); + } + /*------------------------------------------------------------------------- + * we do not have request for filter/chunking use H5Ocopy instead + *------------------------------------------------------------------------- + */ + else { + hid_t pid; + + /* create property to pass copy options */ + if ((pid = H5Pcreate(H5P_OBJECT_COPY)) < 0) + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pcreate failed"); + + /* set options for object copy */ + if (H5Pset_copy_object(pid, H5O_COPY_WITHOUT_ATTR_FLAG) < 0) + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pset_copy_object failed"); + + /*------------------------------------------------------------------------- + * do the copy + *------------------------------------------------------------------------- + */ + + if (H5Ocopy(fidin, /* Source file or group identifier */ + travt->objs[i].name, /* Name of the source object to be copied */ + fidout, /* Destination file or group identifier */ + travt->objs[i].name, /* Name of the destination object */ + pid, /* Properties which apply to the copy */ + H5P_DEFAULT) < 0) /* Properties which apply to the new hard link */ + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Ocopy failed"); + + /* close property */ + if (H5Pclose(pid) < 0) + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed"); + + /*------------------------------------------------------------------------- + * copy attrs manually + *------------------------------------------------------------------------- + */ + if ((dset_in = H5Dopen2(fidin, travt->objs[i].name, H5P_DEFAULT)) < 0) + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dopen2 failed"); + if ((dset_out = H5Dopen2(fidout, travt->objs[i].name, H5P_DEFAULT)) < 0) + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dopen2 failed"); + if (copy_attr(dset_in, dset_out, &named_dt_head, travt, options) < 0) + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "copy_attr failed"); + if (H5Dclose(dset_in) < 0) + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dclose failed"); + if (H5Dclose(dset_out) < 0) + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dclose failed"); + + if (options->verbose) + printf(FORMAT_OBJ, "dset", travt->objs[i].name); + + } /* end do we have request for filter/chunking */ + break; + + /*------------------------------------------------------------------------- + * H5TRAV_TYPE_NAMED_DATATYPE + *------------------------------------------------------------------------- + */ + case H5TRAV_TYPE_NAMED_DATATYPE: + if (options->verbose) + printf(FORMAT_OBJ, "type", travt->objs[i].name); + + if ((type_in = H5Topen2(fidin, travt->objs[i].name, H5P_DEFAULT)) < 0) + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Topen2 failed"); + + /* Copy the datatype anonymously */ + if ((type_out = copy_named_datatype(type_in, fidout, &named_dt_head, travt, options)) < 0) + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "copy_named_datatype failed"); + + /* Link in to group structure */ + if (H5Lcreate_hard(type_out, ".", fidout, travt->objs[i].name, H5P_DEFAULT, H5P_DEFAULT) < 0) + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Lcreate_hard failed"); + + /*------------------------------------------------------------------------- + * copy attrs + *------------------------------------------------------------------------- + */ + if (copy_attr(type_in, type_out, &named_dt_head, travt, options) < 0) + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "copy_attr failed"); + + if (H5Tclose(type_in) < 0) + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Tclose failed"); + if (H5Tclose(type_out) < 0) + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Tclose failed"); + + break; + + /*------------------------------------------------------------------------- + * H5TRAV_TYPE_LINK + * H5TRAV_TYPE_UDLINK + * + * Only handles external links; H5Lcopy will fail for other UD link types + * since we don't have creation or copy callbacks for them. + *------------------------------------------------------------------------- + */ + case H5TRAV_TYPE_LINK: + case H5TRAV_TYPE_UDLINK: + if (options->verbose) + printf(FORMAT_OBJ, "link", travt->objs[i].name); + + if (H5Lcopy(fidin, travt->objs[i].name, fidout, travt->objs[i].name, H5P_DEFAULT, H5P_DEFAULT) < 0) + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Lcopy failed"); + + if (options->verbose) + printf(FORMAT_OBJ, "link", travt->objs[i].name); + break; + + default: + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "Object type not found"); + } /* switch */ + + /* free */ + if (buf != NULL) { + HDfree(buf); + buf = NULL; + } + } /* i */ + + /* Finalize (link) the stack of named datatypes (if any) */ + named_datatype_free(&named_dt_head, 0); + + return ret_value; + +done: + H5E_BEGIN_TRY + { + H5Gclose(grp_in); + H5Gclose(grp_out); + H5Pclose(dcpl_in); + H5Pclose(gcpl_in); + H5Pclose(gcpl_out); + H5Sclose(f_space_id); + H5Dclose(dset_in); + H5Dclose(dset_out); + H5Tclose(ftype_id); + H5Tclose(wtype_id); + H5Tclose(type_in); + H5Tclose(type_out); + named_datatype_free(&named_dt_head, 1); + }H5E_END_TRY; + + /* free */ + if (buf != NULL) + HDfree(buf); + if (hslab_buf != NULL) + HDfree(hslab_buf); + + return ret_value; } /*------------------------------------------------------------------------- @@ -1382,101 +1304,102 @@ error: *------------------------------------------------------------------------- */ static void print_dataset_info(hid_t dcpl_id, char *objname, double ratio, - int pr) { - char strfilter[255]; + int pr) +{ + char strfilter[255]; #if defined (PRINT_DEBUG ) - char temp[255]; + char temp[255]; #endif - int nfilters; /* number of filters */ - unsigned filt_flags; /* filter flags */ - H5Z_filter_t filtn; /* filter identification number */ - unsigned cd_values[20]; /* filter client data values */ - size_t cd_nelmts; /* filter client number of values */ - char f_objname[256]; /* filter objname */ - int i; - - HDstrcpy(strfilter, "\0"); + int nfilters; /* number of filters */ + unsigned filt_flags; /* filter flags */ + H5Z_filter_t filtn; /* filter identification number */ + unsigned cd_values[20]; /* filter client data values */ + size_t cd_nelmts; /* filter client number of values */ + char f_objname[256]; /* filter objname */ + int i; - /* get information about input filters */ - if ((nfilters = H5Pget_nfilters(dcpl_id)) < 0) - return; + HDstrcpy(strfilter, "\0"); - for (i = 0; i < nfilters; i++) { - cd_nelmts = NELMTS(cd_values); + /* get information about input filters */ + if ((nfilters = H5Pget_nfilters(dcpl_id)) < 0) + return; - filtn = H5Pget_filter2(dcpl_id, (unsigned) i, &filt_flags, &cd_nelmts, - cd_values, sizeof(f_objname), f_objname, NULL); + for (i = 0; i < nfilters; i++) { + cd_nelmts = NELMTS(cd_values); - switch (filtn) { + filtn = H5Pget_filter2(dcpl_id, (unsigned) i, &filt_flags, &cd_nelmts, + cd_values, sizeof(f_objname), f_objname, NULL); - case H5Z_FILTER_NONE: - HDstrcat(strfilter, "NONE "); - break; + switch (filtn) { + case H5Z_FILTER_NONE: + HDstrcat(strfilter, "NONE "); + break; - case H5Z_FILTER_DEFLATE: - HDstrcat(strfilter, "GZIP "); + case H5Z_FILTER_DEFLATE: + HDstrcat(strfilter, "GZIP "); #if defined (PRINT_DEBUG) - { - unsigned level=cd_values[0]; - sprintf(temp,"(%d)",level); - HDstrcat(strfilter,temp); - } + { + unsigned level = cd_values[0]; + + sprintf(temp,"(%d)", level); + HDstrcat(strfilter, temp); + } #endif - break; + break; - case H5Z_FILTER_SZIP: - HDstrcat(strfilter, "SZIP "); + case H5Z_FILTER_SZIP: + HDstrcat(strfilter, "SZIP "); #if defined (PRINT_DEBUG) - { - unsigned options_mask=cd_values[0]; /* from dcpl, not filt*/ - unsigned ppb=cd_values[1]; - sprintf(temp,"(%d,",ppb); - HDstrcat(strfilter,temp); - if (options_mask & H5_SZIP_EC_OPTION_MASK) - HDstrcpy(temp,"EC) "); - else if (options_mask & H5_SZIP_NN_OPTION_MASK) - HDstrcpy(temp,"NN) "); - } - HDstrcat(strfilter,temp); - + { + unsigned options_mask = cd_values[0]; /* from dcpl, not filt*/ + unsigned ppb = cd_values[1]; + + sprintf(temp,"(%d,", ppb); + HDstrcat(strfilter, temp); + if (options_mask & H5_SZIP_EC_OPTION_MASK) + HDstrcpy(temp, "EC) "); + else if (options_mask & H5_SZIP_NN_OPTION_MASK) + HDstrcpy(temp, "NN) "); + } + HDstrcat(strfilter, temp); #endif - - break; - - case H5Z_FILTER_SHUFFLE: - HDstrcat(strfilter, "SHUF "); - break; - - case H5Z_FILTER_FLETCHER32: - HDstrcat(strfilter, "FLET "); - break; - - case H5Z_FILTER_NBIT: - HDstrcat(strfilter, "NBIT "); - break; - - case H5Z_FILTER_SCALEOFFSET: - HDstrcat(strfilter, "SCALEOFFSET "); - break; - - default: - HDstrcat(strfilter, "UD "); - break; - } /* switch */ - }/*i*/ - - if (!pr) - printf(FORMAT_OBJ, "dset", objname); - else { - char str[255], temp[28]; - HDstrcpy(str, "dset "); - HDstrcat(str, strfilter); - sprintf(temp, " (%.3f:1)", ratio); - HDstrcat(str, temp); - printf(FORMAT_OBJ, str, objname); - } + break; + + case H5Z_FILTER_SHUFFLE: + HDstrcat(strfilter, "SHUF "); + break; + + case H5Z_FILTER_FLETCHER32: + HDstrcat(strfilter, "FLET "); + break; + + case H5Z_FILTER_NBIT: + HDstrcat(strfilter, "NBIT "); + break; + + case H5Z_FILTER_SCALEOFFSET: + HDstrcat(strfilter, "SCALEOFFSET "); + break; + + default: + HDstrcat(strfilter, "UD "); + break; + } /* switch */ + }/*i*/ + + if (!pr) + printf(FORMAT_OBJ, "dset", objname); + else { + char str[255], temp[28]; + + HDstrcpy(str, "dset "); + HDstrcat(str, strfilter); + sprintf(temp, " (%.3f:1)", ratio); + HDstrcat(str, temp); + printf(FORMAT_OBJ, str, objname); + } } /*------------------------------------------------------------------------- @@ -1493,73 +1416,66 @@ static void print_dataset_info(hid_t dcpl_id, char *objname, double ratio, *------------------------------------------------------------------------- */ static int copy_user_block(const char *infile, const char *outfile, - hsize_t size) { - int infid = -1, outfid = -1; /* File descriptors */ - int status = 0; /* Return value */ - - /* User block must be any power of 2 equal to 512 or greater (512, 1024, 2048, etc.) */ - HDassert(size > 0); - - /* Open files */ - if ((infid = HDopen(infile, O_RDONLY, 0)) < 0) { - status = -1; - goto done; - } - if ((outfid = HDopen(outfile, O_WRONLY, 0644)) < 0) { - status = -1; - goto done; - } - - /* Copy the userblock from the input file to the output file */ - while (size > 0) { - ssize_t nread, nbytes; /* # of bytes transfered, etc. */ - char rbuf[USERBLOCK_XFER_SIZE]; /* Buffer for reading */ - const char *wbuf; /* Pointer into buffer, for writing */ - - /* Read buffer from source file */ - if (size > USERBLOCK_XFER_SIZE) - nread = HDread(infid, rbuf, (size_t)USERBLOCK_XFER_SIZE); - else - nread = HDread(infid, rbuf, (size_t)size); - if (nread < 0) { - status = -1; - goto done; - } /* end if */ - - /* Write buffer to destination file */ - /* (compensating for interrupted writes & checking for errors, etc.) */ - nbytes = nread; - wbuf = rbuf; - while (nbytes > 0) { - ssize_t nwritten; /* # of bytes written */ - - do { - nwritten = HDwrite(outfid, wbuf, (size_t)nbytes); - } while (-1 == nwritten && EINTR == errno); - if (-1 == nwritten) { /* error */ - status = -1; - goto done; - } /* end if */ - HDassert(nwritten > 0); - HDassert(nwritten <= nbytes); - - /* Update # of bytes left & offset in buffer */ - nbytes -= nwritten; - wbuf += nwritten; - HDassert(nbytes == 0 || wbuf < (rbuf + USERBLOCK_XFER_SIZE)); - } /* end while */ - - /* Update size of userblock left to transfer */ - size = size - (hsize_t) nread; - } /* end while */ + hsize_t size) +{ + int ret_value = 0; /*no need to LEAVE() on ERROR: HERR_INIT(int, SUCCEED) */ + int infid = -1, outfid = -1; /* File descriptors */ + + /* User block must be any power of 2 equal to 512 or greater (512, 1024, 2048, etc.) */ + HDassert(size > 0); + + /* Open files */ + if ((infid = HDopen(infile, O_RDONLY, 0)) < 0) + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "HDopen failed"); + if ((outfid = HDopen(outfile, O_WRONLY, 0644)) < 0) + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "HDopen failed"); + + /* Copy the userblock from the input file to the output file */ + while (size > 0) { + ssize_t nread, nbytes; /* # of bytes transfered, etc. */ + char rbuf[USERBLOCK_XFER_SIZE]; /* Buffer for reading */ + const char *wbuf; /* Pointer into buffer, for writing */ + + /* Read buffer from source file */ + if (size > USERBLOCK_XFER_SIZE) + nread = HDread(infid, rbuf, (size_t)USERBLOCK_XFER_SIZE); + else + nread = HDread(infid, rbuf, (size_t)size); + if (nread < 0) + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "HDread failed"); + + /* Write buffer to destination file */ + /* (compensating for interrupted writes & checking for errors, etc.) */ + nbytes = nread; + wbuf = rbuf; + while (nbytes > 0) { + ssize_t nwritten; /* # of bytes written */ + + do { + nwritten = HDwrite(outfid, wbuf, (size_t)nbytes); + } while (-1 == nwritten && EINTR == errno); + if (-1 == nwritten) /* error */ + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "HDwrite failed"); + HDassert(nwritten > 0); + HDassert(nwritten <= nbytes); + + /* Update # of bytes left & offset in buffer */ + nbytes -= nwritten; + wbuf += nwritten; + HDassert(nbytes == 0 || wbuf < (rbuf + USERBLOCK_XFER_SIZE)); + } /* end while */ + + /* Update size of userblock left to transfer */ + size = size - (hsize_t) nread; + } /* end while */ done: - if (infid > 0) - HDclose(infid); - if (outfid > 0) - HDclose(outfid); + if (infid > 0) + HDclose(infid); + if (outfid > 0) + HDclose(outfid); - return status; + return ret_value; } /*------------------------------------------------------------------------- @@ -1579,66 +1495,67 @@ done: static void print_user_block(const char *filename, hid_t fid) { - int fh; /* file handle */ - hsize_t ub_size; /* user block size */ - hsize_t size; /* size read */ - hid_t fcpl; /* file creation property list ID for HDF5 file */ - int i; - - /* get user block size */ - if(( fcpl = H5Fget_create_plist(fid)) < 0) { - error_msg("failed to retrieve file creation property list\n"); - goto done; - } - - if(H5Pget_userblock(fcpl, &ub_size) < 0) { - error_msg("failed to retrieve userblock size\n"); - goto done; - } - - if(H5Pclose(fcpl) < 0) { - error_msg("failed to close property list\n"); - goto done; - } - - /* open file */ - if((fh = HDopen(filename, O_RDONLY, 0)) < 0) { - goto done; - } - - size = ub_size; - - /* read file */ - while(size > 0) { - ssize_t nread; /* # of bytes read */ - char rbuf[USERBLOCK_XFER_SIZE]; /* buffer for reading */ - - /* read buffer */ - if(size > USERBLOCK_XFER_SIZE) - nread = HDread(fh, rbuf, (size_t)USERBLOCK_XFER_SIZE); - else - nread = HDread(fh, rbuf, (size_t)size); - - for(i = 0; i < nread; i++) { - - printf("%c ", rbuf[i]); - - } - printf("\n"); - - if(nread < 0) { - goto done; - } - - /* update size of userblock left to transfer */ - size -= nread; - } + int ret_value = 0; /*no need to LEAVE() on ERROR: HERR_INIT(int, SUCCEED) */ + int fh; /* file handle */ + hsize_t ub_size; /* user block size */ + hsize_t size; /* size read */ + hid_t fcpl; /* file creation property list ID for HDF5 file */ + int i; + + /* get user block size */ + if(( fcpl = H5Fget_create_plist(fid)) < 0) { + error_msg("failed to retrieve file creation property list\n"); + HGOTO_ERROR(H5E_tools_g, H5E_tools_min_id_g, "H5Fget_create_plist failed"); + } + + if(H5Pget_userblock(fcpl, &ub_size) < 0) { + error_msg("failed to retrieve userblock size\n"); + HGOTO_ERROR(H5E_tools_g, H5E_tools_min_id_g, "H5Pget_userblock failed"); + } + + if(H5Pclose(fcpl) < 0) { + error_msg("failed to close property list\n"); + HGOTO_ERROR(H5E_tools_g, H5E_tools_min_id_g, "H5Pclose failed"); + } + + /* open file */ + if((fh = HDopen(filename, O_RDONLY, 0)) < 0) { + HGOTO_ERROR(H5E_tools_g, H5E_tools_min_id_g, "HDopen failed"); + } + + size = ub_size; + + /* read file */ + while(size > 0) { + ssize_t nread; /* # of bytes read */ + char rbuf[USERBLOCK_XFER_SIZE]; /* buffer for reading */ + + /* read buffer */ + if(size > USERBLOCK_XFER_SIZE) + nread = HDread(fh, rbuf, (size_t)USERBLOCK_XFER_SIZE); + else + nread = HDread(fh, rbuf, (size_t)size); + + for(i = 0; i < nread; i++) { + + printf("%c ", rbuf[i]); + + } + printf("\n"); + + if(nread < 0) { + HGOTO_ERROR(H5E_tools_g, H5E_tools_min_id_g, "nread < 0"); + } + + /* update size of userblock left to transfer */ + size -= nread; + } done: - if(fh > 0) - HDclose(fh); + if(fh > 0) + HDclose(fh); - return; + return; } #endif diff --git a/tools/h5repack/h5repack_filters.c b/tools/h5repack/h5repack_filters.c index 56e08ef..e873a53 100644 --- a/tools/h5repack/h5repack_filters.c +++ b/tools/h5repack/h5repack_filters.c @@ -34,8 +34,8 @@ * *------------------------------------------------------------------------- */ -static -int aux_find_obj(const char* name, /* object name from traverse list */ +static int +aux_find_obj(const char* name, /* object name from traverse list */ pack_opt_t *options, /* repack options */ pack_info_t *obj /*OUT*/) /* info about object to filter */ { @@ -48,7 +48,7 @@ int aux_find_obj(const char* name, /* object name from traverse list */ if (HDstrcmp(options->op_tbl->objs[i].path,name)==0) { *obj = options->op_tbl->objs[i]; - return i; + return (int)i; } pdest = HDstrstr(name,options->op_tbl->objs[i].path); @@ -58,7 +58,7 @@ int aux_find_obj(const char* name, /* object name from traverse list */ if( pdest != NULL && result==1 ) { *obj = options->op_tbl->objs[i]; - return i; + return (int)i; } }/*i*/ @@ -76,8 +76,8 @@ int aux_find_obj(const char* name, /* object name from traverse list */ * *------------------------------------------------------------------------- */ -static -int aux_assign_obj(const char* name, /* object name from traverse list */ +static int +aux_assign_obj(const char* name, /* object name from traverse list */ pack_opt_t *options, /* repack options */ pack_info_t *obj /*OUT*/) /* info about object to filter */ { @@ -433,7 +433,7 @@ int apply_filters(const char* name, /* object name from traverse list */ int scale_factor; scale_type = (H5Z_SO_scale_type_t)obj.filter[i].cd_values[0]; - scale_factor = obj.filter[i].cd_values[1]; + scale_factor = (int)obj.filter[i].cd_values[1]; if(H5Pset_chunk(dcpl_id, obj.chunk.rank, obj.chunk.chunk_lengths)<0) return -1; diff --git a/tools/h5repack/h5repack_main.c b/tools/h5repack/h5repack_main.c index f3fd469..7998ae8 100644 --- a/tools/h5repack/h5repack_main.c +++ b/tools/h5repack/h5repack_main.c @@ -33,28 +33,29 @@ const char *outfile = NULL; * Command-line options: The user can specify short or long-named * parameters. */ -static const char *s_opts = "hVvf:l:m:e:nLc:d:s:u:b:M:t:a:i:o:"; +static const char *s_opts = "hVvf:l:m:e:nLc:d:s:u:b:M:t:a:i:o:E"; static struct long_options l_opts[] = { - { "help", no_arg, 'h' }, - { "version", no_arg, 'V' }, - { "verbose", no_arg, 'v' }, - { "filter", require_arg, 'f' }, - { "layout", require_arg, 'l' }, - { "minimum", require_arg, 'm' }, - { "file", require_arg, 'e' }, - { "native", no_arg, 'n' }, - { "latest", no_arg, 'L' }, - { "compact", require_arg, 'c' }, - { "indexed", require_arg, 'd' }, - { "ssize", require_arg, 's' }, - { "ublock", require_arg, 'u' }, - { "block", require_arg, 'b' }, - { "metadata_block_size", require_arg, 'M' }, - { "threshold", require_arg, 't' }, - { "alignment", require_arg, 'a' }, - { "infile", require_arg, 'i' }, /* -i for backward compability */ - { "outfile", require_arg, 'o' }, /* -o for backward compability */ - { NULL, 0, '\0' } + { "help", no_arg, 'h' }, + { "version", no_arg, 'V' }, + { "verbose", no_arg, 'v' }, + { "filter", require_arg, 'f' }, + { "layout", require_arg, 'l' }, + { "minimum", require_arg, 'm' }, + { "file", require_arg, 'e' }, + { "native", no_arg, 'n' }, + { "latest", no_arg, 'L' }, + { "compact", require_arg, 'c' }, + { "indexed", require_arg, 'd' }, + { "ssize", require_arg, 's' }, + { "ublock", require_arg, 'u' }, + { "block", require_arg, 'b' }, + { "metadata_block_size", require_arg, 'M' }, + { "threshold", require_arg, 't' }, + { "alignment", require_arg, 'a' }, + { "infile", require_arg, 'i' }, /* -i for backward compability */ + { "outfile", require_arg, 'o' }, /* -o for backward compability */ + { "enable-error-stack", no_arg, 'E' }, + { NULL, 0, '\0' } }; /*------------------------------------------------------------------------- @@ -67,113 +68,117 @@ static struct long_options l_opts[] = { *------------------------------------------------------------------------- */ static void usage(const char *prog) { - printf("usage: %s [OPTIONS] file1 file2\n", prog); - printf(" file1 Input HDF5 File\n"); - printf(" file2 Output HDF5 File\n"); - printf(" OPTIONS\n"); - printf(" -h, --help Print a usage message and exit\n"); - printf(" -v, --verbose Verbose mode, print object information\n"); - printf(" -V, --version Print version number and exit\n"); - printf(" -n, --native Use a native HDF5 type when repacking\n"); - printf(" -L, --latest Use latest version of file format\n"); - printf(" -c L1, --compact=L1 Maximum number of links in header messages\n"); - printf(" -d L2, --indexed=L2 Minimum number of links in the indexed format\n"); - printf(" -s S[:F], --ssize=S[:F] Shared object header message minimum size\n"); - printf(" -m M, --minimum=M Do not apply the filter to datasets smaller than M\n"); - printf(" -e E, --file=E Name of file E with the -f and -l options\n"); - printf(" -u U, --ublock=U Name of file U with user block data to be added\n"); - printf(" -b B, --block=B Size of user block to be added\n"); - printf(" -M A, --metadata_block_size=A Metadata block size for H5Pset_meta_block_size\n"); - printf(" -t T, --threshold=T Threshold value for H5Pset_alignment\n"); - printf(" -a A, --alignment=A Alignment value for H5Pset_alignment\n"); - printf(" -f FILT, --filter=FILT Filter type\n"); - printf(" -l LAYT, --layout=LAYT Layout type\n"); - printf("\n"); - printf(" M - is an integer greater than 1, size of dataset in bytes (default is 0) \n"); - printf(" E - is a filename.\n"); - printf(" S - is an integer\n"); - printf(" U - is a filename.\n"); - printf(" T - is an integer\n"); - printf(" A - is an integer greater than zero\n"); - printf(" B - is the user block size, any value that is 512 or greater and is\n"); - printf(" a power of 2 (1024 default)\n"); - printf(" F - is the shared object header message type, any of <dspace|dtype|fill|\n"); - printf(" pline|attr>. If F is not specified, S applies to all messages\n"); - printf("\n"); - printf(" FILT - is a string with the format:\n"); - printf("\n"); - printf(" <list of objects>:<name of filter>=<filter parameters>\n"); - printf("\n"); - printf(" <list of objects> is a comma separated list of object names, meaning apply\n"); - printf(" compression only to those objects. If no names are specified, the filter\n"); - printf(" is applied to all objects\n"); - printf(" <name of filter> can be:\n"); - printf(" GZIP, to apply the HDF5 GZIP filter (GZIP compression)\n"); - printf(" SZIP, to apply the HDF5 SZIP filter (SZIP compression)\n"); - printf(" SHUF, to apply the HDF5 shuffle filter\n"); - printf(" FLET, to apply the HDF5 checksum filter\n"); - printf(" NBIT, to apply the HDF5 NBIT filter (NBIT compression)\n"); - printf(" SOFF, to apply the HDF5 Scale/Offset filter\n"); - printf(" UD, to apply a user defined filter\n"); - printf(" NONE, to remove all filters\n"); - printf(" <filter parameters> is optional filter parameter information\n"); - printf(" GZIP=<deflation level> from 1-9\n"); - printf(" SZIP=<pixels per block,coding> pixels per block is a even number in\n"); - printf(" 2-32 and coding method is either EC or NN\n"); - printf(" SHUF (no parameter)\n"); - printf(" FLET (no parameter)\n"); - printf(" NBIT (no parameter)\n"); - printf(" SOFF=<scale_factor,scale_type> scale_factor is an integer and scale_type\n"); - printf(" is either IN or DS\n"); - printf(" UD=<filter_number,cd_value_count,value_1[,value_2,...,value_N]>\n"); - printf(" required values for filter_number,cd_value_count,value_1\n"); - printf(" optional values for value_2 to value_N\n"); - printf(" NONE (no parameter)\n"); - printf("\n"); - printf(" LAYT - is a string with the format:\n"); - printf("\n"); - printf(" <list of objects>:<layout type>=<layout parameters>\n"); - printf("\n"); - printf(" <list of objects> is a comma separated list of object names, meaning that\n"); - printf(" layout information is supplied for those objects. If no names are\n"); - printf(" specified, the layout type is applied to all objects\n"); - printf(" <layout type> can be:\n"); - printf(" CHUNK, to apply chunking layout\n"); - printf(" COMPA, to apply compact layout\n"); - printf(" CONTI, to apply contiguous layout\n"); - printf(" <layout parameters> is optional layout information\n"); - printf(" CHUNK=DIM[xDIM...xDIM], the chunk size of each dimension\n"); - printf(" COMPA (no parameter)\n"); - printf(" CONTI (no parameter)\n"); - printf("\n"); - printf("Examples of use:\n"); - printf("\n"); - printf("1) h5repack -v -f GZIP=1 file1 file2\n"); - printf("\n"); - printf(" GZIP compression with level 1 to all objects\n"); - printf("\n"); - printf("2) h5repack -v -f dset1:SZIP=8,NN file1 file2\n"); - printf("\n"); - printf(" SZIP compression with 8 pixels per block and NN coding method to object dset1\n"); - printf("\n"); - printf("3) h5repack -v -l dset1,dset2:CHUNK=20x10 -f dset3,dset4,dset5:NONE file1 file2\n"); - printf("\n"); - printf(" Chunked layout, with a layout size of 20x10, to objects dset1 and dset2\n"); - printf(" and remove filters to objects dset3, dset4, dset5\n"); - printf("\n"); - printf("4) h5repack -L -c 10 -s 20:dtype file1 file2 \n"); - printf("\n"); - printf(" Using latest file format with maximum compact group size of 10 and\n"); - printf(" and minimum shared datatype size of 20\n"); - printf("\n"); - printf("5) h5repack -f SHUF -f GZIP=1 file1 file2 \n"); - printf("\n"); - printf(" Add both filters SHUF and GZIP in this order to all datasets\n"); - printf("\n"); - printf("6) h5repack -f UD=307,1,9 file1 file2 \n"); - printf("\n"); - printf(" Add bzip2 filter to all datasets\n"); - printf("\n"); + FLUSHSTREAM(rawoutstream); + PRINTSTREAM(rawoutstream, "usage: %s [OPTIONS] file1 file2\n", prog); + PRINTVALSTREAM(rawoutstream, " file1 Input HDF5 File\n"); + PRINTVALSTREAM(rawoutstream, " file2 Output HDF5 File\n"); + PRINTVALSTREAM(rawoutstream, " OPTIONS\n"); + PRINTVALSTREAM(rawoutstream, " -h, --help Print a usage message and exit\n"); + PRINTVALSTREAM(rawoutstream, " -v, --verbose Verbose mode, print object information\n"); + PRINTVALSTREAM(rawoutstream, " -V, --version Print version number and exit\n"); + PRINTVALSTREAM(rawoutstream, " -n, --native Use a native HDF5 type when repacking\n"); + PRINTVALSTREAM(rawoutstream, " -L, --latest Use latest version of file format\n"); + PRINTVALSTREAM(rawoutstream, " -c L1, --compact=L1 Maximum number of links in header messages\n"); + PRINTVALSTREAM(rawoutstream, " -d L2, --indexed=L2 Minimum number of links in the indexed format\n"); + PRINTVALSTREAM(rawoutstream, " -s S[:F], --ssize=S[:F] Shared object header message minimum size\n"); + PRINTVALSTREAM(rawoutstream, " -m M, --minimum=M Do not apply the filter to datasets smaller than M\n"); + PRINTVALSTREAM(rawoutstream, " -e E, --file=E Name of file E with the -f and -l options\n"); + PRINTVALSTREAM(rawoutstream, " -u U, --ublock=U Name of file U with user block data to be added\n"); + PRINTVALSTREAM(rawoutstream, " -b B, --block=B Size of user block to be added\n"); + PRINTVALSTREAM(rawoutstream, " -M A, --metadata_block_size=A Metadata block size for H5Pset_meta_block_size\n"); + PRINTVALSTREAM(rawoutstream, " -t T, --threshold=T Threshold value for H5Pset_alignment\n"); + PRINTVALSTREAM(rawoutstream, " -a A, --alignment=A Alignment value for H5Pset_alignment\n"); + PRINTVALSTREAM(rawoutstream, " -f FILT, --filter=FILT Filter type\n"); + PRINTVALSTREAM(rawoutstream, " -l LAYT, --layout=LAYT Layout type\n"); + PRINTVALSTREAM(rawoutstream, "\n"); + PRINTVALSTREAM(rawoutstream, " M - is an integer greater than 1, size of dataset in bytes (default is 0) \n"); + PRINTVALSTREAM(rawoutstream, " E - is a filename.\n"); + PRINTVALSTREAM(rawoutstream, " S - is an integer\n"); + PRINTVALSTREAM(rawoutstream, " U - is a filename.\n"); + PRINTVALSTREAM(rawoutstream, " T - is an integer\n"); + PRINTVALSTREAM(rawoutstream, " A - is an integer greater than zero\n"); + PRINTVALSTREAM(rawoutstream, " B - is the user block size, any value that is 512 or greater and is\n"); + PRINTVALSTREAM(rawoutstream, " a power of 2 (1024 default)\n"); + PRINTVALSTREAM(rawoutstream, " F - is the shared object header message type, any of <dspace|dtype|fill|\n"); + PRINTVALSTREAM(rawoutstream, " pline|attr>. If F is not specified, S applies to all messages\n"); + PRINTVALSTREAM(rawoutstream, "\n"); + PRINTVALSTREAM(rawoutstream, " --enable-error-stack Prints messages from the HDF5 error stack as they\n"); + PRINTVALSTREAM(rawoutstream, " occur.\n"); + PRINTVALSTREAM(rawoutstream, "\n"); + PRINTVALSTREAM(rawoutstream, " FILT - is a string with the format:\n"); + PRINTVALSTREAM(rawoutstream, "\n"); + PRINTVALSTREAM(rawoutstream, " <list of objects>:<name of filter>=<filter parameters>\n"); + PRINTVALSTREAM(rawoutstream, "\n"); + PRINTVALSTREAM(rawoutstream, " <list of objects> is a comma separated list of object names, meaning apply\n"); + PRINTVALSTREAM(rawoutstream, " compression only to those objects. If no names are specified, the filter\n"); + PRINTVALSTREAM(rawoutstream, " is applied to all objects\n"); + PRINTVALSTREAM(rawoutstream, " <name of filter> can be:\n"); + PRINTVALSTREAM(rawoutstream, " GZIP, to apply the HDF5 GZIP filter (GZIP compression)\n"); + PRINTVALSTREAM(rawoutstream, " SZIP, to apply the HDF5 SZIP filter (SZIP compression)\n"); + PRINTVALSTREAM(rawoutstream, " SHUF, to apply the HDF5 shuffle filter\n"); + PRINTVALSTREAM(rawoutstream, " FLET, to apply the HDF5 checksum filter\n"); + PRINTVALSTREAM(rawoutstream, " NBIT, to apply the HDF5 NBIT filter (NBIT compression)\n"); + PRINTVALSTREAM(rawoutstream, " SOFF, to apply the HDF5 Scale/Offset filter\n"); + PRINTVALSTREAM(rawoutstream, " UD, to apply a user defined filter\n"); + PRINTVALSTREAM(rawoutstream, " NONE, to remove all filters\n"); + PRINTVALSTREAM(rawoutstream, " <filter parameters> is optional filter parameter information\n"); + PRINTVALSTREAM(rawoutstream, " GZIP=<deflation level> from 1-9\n"); + PRINTVALSTREAM(rawoutstream, " SZIP=<pixels per block,coding> pixels per block is a even number in\n"); + PRINTVALSTREAM(rawoutstream, " 2-32 and coding method is either EC or NN\n"); + PRINTVALSTREAM(rawoutstream, " SHUF (no parameter)\n"); + PRINTVALSTREAM(rawoutstream, " FLET (no parameter)\n"); + PRINTVALSTREAM(rawoutstream, " NBIT (no parameter)\n"); + PRINTVALSTREAM(rawoutstream, " SOFF=<scale_factor,scale_type> scale_factor is an integer and scale_type\n"); + PRINTVALSTREAM(rawoutstream, " is either IN or DS\n"); + PRINTVALSTREAM(rawoutstream, " UD=<filter_number,cd_value_count,value_1[,value_2,...,value_N]>\n"); + PRINTVALSTREAM(rawoutstream, " required values for filter_number,cd_value_count,value_1\n"); + PRINTVALSTREAM(rawoutstream, " optional values for value_2 to value_N\n"); + PRINTVALSTREAM(rawoutstream, " NONE (no parameter)\n"); + PRINTVALSTREAM(rawoutstream, "\n"); + PRINTVALSTREAM(rawoutstream, " LAYT - is a string with the format:\n"); + PRINTVALSTREAM(rawoutstream, "\n"); + PRINTVALSTREAM(rawoutstream, " <list of objects>:<layout type>=<layout parameters>\n"); + PRINTVALSTREAM(rawoutstream, "\n"); + PRINTVALSTREAM(rawoutstream, " <list of objects> is a comma separated list of object names, meaning that\n"); + PRINTVALSTREAM(rawoutstream, " layout information is supplied for those objects. If no names are\n"); + PRINTVALSTREAM(rawoutstream, " specified, the layout type is applied to all objects\n"); + PRINTVALSTREAM(rawoutstream, " <layout type> can be:\n"); + PRINTVALSTREAM(rawoutstream, " CHUNK, to apply chunking layout\n"); + PRINTVALSTREAM(rawoutstream, " COMPA, to apply compact layout\n"); + PRINTVALSTREAM(rawoutstream, " CONTI, to apply contiguous layout\n"); + PRINTVALSTREAM(rawoutstream, " <layout parameters> is optional layout information\n"); + PRINTVALSTREAM(rawoutstream, " CHUNK=DIM[xDIM...xDIM], the chunk size of each dimension\n"); + PRINTVALSTREAM(rawoutstream, " COMPA (no parameter)\n"); + PRINTVALSTREAM(rawoutstream, " CONTI (no parameter)\n"); + PRINTVALSTREAM(rawoutstream, "\n"); + PRINTVALSTREAM(rawoutstream, "Examples of use:\n"); + PRINTVALSTREAM(rawoutstream, "\n"); + PRINTVALSTREAM(rawoutstream, "1) h5repack -v -f GZIP=1 file1 file2\n"); + PRINTVALSTREAM(rawoutstream, "\n"); + PRINTVALSTREAM(rawoutstream, " GZIP compression with level 1 to all objects\n"); + PRINTVALSTREAM(rawoutstream, "\n"); + PRINTVALSTREAM(rawoutstream, "2) h5repack -v -f dset1:SZIP=8,NN file1 file2\n"); + PRINTVALSTREAM(rawoutstream, "\n"); + PRINTVALSTREAM(rawoutstream, " SZIP compression with 8 pixels per block and NN coding method to object dset1\n"); + PRINTVALSTREAM(rawoutstream, "\n"); + PRINTVALSTREAM(rawoutstream, "3) h5repack -v -l dset1,dset2:CHUNK=20x10 -f dset3,dset4,dset5:NONE file1 file2\n"); + PRINTVALSTREAM(rawoutstream, "\n"); + PRINTVALSTREAM(rawoutstream, " Chunked layout, with a layout size of 20x10, to objects dset1 and dset2\n"); + PRINTVALSTREAM(rawoutstream, " and remove filters to objects dset3, dset4, dset5\n"); + PRINTVALSTREAM(rawoutstream, "\n"); + PRINTVALSTREAM(rawoutstream, "4) h5repack -L -c 10 -s 20:dtype file1 file2 \n"); + PRINTVALSTREAM(rawoutstream, "\n"); + PRINTVALSTREAM(rawoutstream, " Using latest file format with maximum compact group size of 10 and\n"); + PRINTVALSTREAM(rawoutstream, " and minimum shared datatype size of 20\n"); + PRINTVALSTREAM(rawoutstream, "\n"); + PRINTVALSTREAM(rawoutstream, "5) h5repack -f SHUF -f GZIP=1 file1 file2 \n"); + PRINTVALSTREAM(rawoutstream, "\n"); + PRINTVALSTREAM(rawoutstream, " Add both filters SHUF and GZIP in this order to all datasets\n"); + PRINTVALSTREAM(rawoutstream, "\n"); + PRINTVALSTREAM(rawoutstream, "6) h5repack -f UD=307,1,9 file1 file2 \n"); + PRINTVALSTREAM(rawoutstream, "\n"); + PRINTVALSTREAM(rawoutstream, " Add bzip2 filter to all datasets\n"); + PRINTVALSTREAM(rawoutstream, "\n"); } /*------------------------------------------------------------------------- @@ -242,14 +247,24 @@ int read_info(const char *filename, pack_opt_t *options) { i = 0; c = '0'; while (c != ' ') { - fscanf(fp, "%c", &c); + if(fscanf(fp, "%c", &c) < 0 && HDferror(fp)) { + error_msg("fscanf error\n"); + h5tools_setstatus(EXIT_FAILURE); + ret_value = EXIT_FAILURE; + goto done; + } /* end if */ if (HDfeof(fp)) break; } c = '0'; /* go until end */ while (c != ' ') { - fscanf(fp, "%c", &c); + if(fscanf(fp, "%c", &c) < 0 && HDferror(fp)) { + error_msg("fscanf error\n"); + h5tools_setstatus(EXIT_FAILURE); + ret_value = EXIT_FAILURE; + goto done; + } /* end if */ comp_info[i] = c; i++; if (HDfeof(fp)) @@ -276,14 +291,24 @@ int read_info(const char *filename, pack_opt_t *options) { i = 0; c = '0'; while (c != ' ') { - fscanf(fp, "%c", &c); + if(fscanf(fp, "%c", &c) < 0 && HDferror(fp)) { + error_msg("fscanf error\n"); + h5tools_setstatus(EXIT_FAILURE); + ret_value = EXIT_FAILURE; + goto done; + } /* end if */ if (HDfeof(fp)) break; } c = '0'; /* go until end */ while (c != ' ') { - fscanf(fp, "%c", &c); + if(fscanf(fp, "%c", &c) < 0 && HDferror(fp)) { + error_msg("fscanf error\n"); + h5tools_setstatus(EXIT_FAILURE); + ret_value = EXIT_FAILURE; + goto done; + } /* end if */ comp_info[i] = c; i++; if (HDfeof(fp)) @@ -343,7 +368,7 @@ int parse_command_line(int argc, const char **argv, pack_opt_t* options) { has_i_o = 1; break; - /* -o for backward compability */ + /* -o for backward compability */ case 'o': outfile = opt_arg; has_i_o = 1; @@ -386,7 +411,7 @@ int parse_command_line(int argc, const char **argv, pack_opt_t* options) { break; case 'm': - options->min_comp = HDatoi( opt_arg ); + options->min_comp = HDstrtoull(opt_arg , NULL, 0); if ((int) options->min_comp <= 0) { error_msg("invalid minimum compress size <%s>\n", opt_arg); h5tools_setstatus(EXIT_FAILURE); @@ -473,7 +498,7 @@ int parse_command_line(int argc, const char **argv, pack_opt_t* options) { break; case 'a': - options->alignment = HDatol( opt_arg ); + options->alignment = HDstrtoull(opt_arg , NULL, 0); if (options->alignment < 1) { error_msg("invalid alignment size\n", opt_arg); h5tools_setstatus(EXIT_FAILURE); @@ -482,13 +507,17 @@ int parse_command_line(int argc, const char **argv, pack_opt_t* options) { } break; - default: - break; - } /* switch */ + case 'E': + enable_error_stack = TRUE; + break; + + default: + break; + } /* switch */ - } /* while */ + } /* while */ - if (has_i_o == 0) { + if (has_i_o == 0) { /* check for file names to be processed */ if (argc <= opt_ind || argv[opt_ind + 1] == NULL) { error_msg("missing file names\n"); @@ -520,50 +549,67 @@ done: *------------------------------------------------------------------------- */ int main(int argc, const char **argv) { + H5E_auto2_t func; + H5E_auto2_t tools_func; + void *edata; + void *tools_edata; pack_opt_t options; /*the global options */ h5tools_setprogname(PROGRAMNAME); h5tools_setstatus(EXIT_SUCCESS); - /* Initialize h5tools lib */ - h5tools_init(); - - /* update hyperslab buffer size from H5TOOLS_BUFSIZE env if exist */ - if (h5tools_getenv_update_hyperslab_bufsize() < 0) { - h5tools_setstatus(EXIT_FAILURE); - goto done; - } - - /* initialize options */ - h5repack_init(&options, 0); - - if (parse_command_line(argc, argv, &options) < 0) - goto done; - - /* get file names if they were not yet got */ - if (has_i_o == 0) { - - if (argv[opt_ind] != NULL && argv[opt_ind + 1] != NULL) { - infile = argv[opt_ind]; - outfile = argv[opt_ind + 1]; - - if ( HDstrcmp( infile, outfile ) == 0) { - error_msg("file names cannot be the same\n"); - usage(h5tools_getprogname()); - h5tools_setstatus(EXIT_FAILURE); - goto done; - } - } - else { - error_msg("file names missing\n"); - usage(h5tools_getprogname()); - h5tools_setstatus(EXIT_FAILURE); - goto done; - } - } - - /* pack it */ + /* Disable error reporting */ + H5Eget_auto2(H5E_DEFAULT, &func, &edata); + H5Eset_auto2(H5E_DEFAULT, NULL, NULL); + + /* Initialize h5tools lib */ + h5tools_init(); + + /* Disable tools error reporting */ + H5Eget_auto2(H5tools_ERR_STACK_g, &tools_func, &tools_edata); + H5Eset_auto2(H5tools_ERR_STACK_g, NULL, NULL); + + /* update hyperslab buffer size from H5TOOLS_BUFSIZE env if exist */ + if (h5tools_getenv_update_hyperslab_bufsize() < 0) { + h5tools_setstatus(EXIT_FAILURE); + goto done; + } + + /* initialize options */ + h5repack_init(&options, 0); + + if (parse_command_line(argc, argv, &options) < 0) + goto done; + + /* get file names if they were not yet got */ + if (has_i_o == 0) { + + if (argv[opt_ind] != NULL && argv[opt_ind + 1] != NULL) { + infile = argv[opt_ind]; + outfile = argv[opt_ind + 1]; + + if ( HDstrcmp( infile, outfile ) == 0) { + error_msg("file names cannot be the same\n"); + usage(h5tools_getprogname()); + h5tools_setstatus(EXIT_FAILURE); + goto done; + } + } + else { + error_msg("file names missing\n"); + usage(h5tools_getprogname()); + h5tools_setstatus(EXIT_FAILURE); + goto done; + } + } + + if (enable_error_stack) { + H5Eset_auto2(H5E_DEFAULT, func, edata); + H5Eset_auto2(H5tools_ERR_STACK_g, tools_func, tools_edata); + } + + /* pack it */ h5tools_setstatus(h5repack(infile, outfile, &options)); done: diff --git a/tools/h5repack/h5repack_opttable.c b/tools/h5repack/h5repack_opttable.c index b54e887..dd0a0e9 100644 --- a/tools/h5repack/h5repack_opttable.c +++ b/tools/h5repack/h5repack_opttable.c @@ -105,21 +105,22 @@ static void aux_tblinsert_layout(pack_opttbl_t *table, unsigned int I, * *------------------------------------------------------------------------- */ - -static int aux_inctable(pack_opttbl_t *table, int n_objs) { - unsigned int i; - - table->size += n_objs; - table->objs = - (pack_info_t*) HDrealloc(table->objs, table->size * sizeof(pack_info_t)); - if (table->objs == NULL) { - error_msg("not enough memory for options table\n"); - return -1; - } - for (i = table->nelems; i < table->size; i++) { - init_packobject(&table->objs[i]); - } - return 0; +static int +aux_inctable(pack_opttbl_t *table, unsigned n_objs) +{ + unsigned u; + + table->size += n_objs; + table->objs = (pack_info_t*) HDrealloc(table->objs, table->size * sizeof(pack_info_t)); + if (table->objs == NULL) { + error_msg("not enough memory for options table\n"); + return -1; + } + + for (u = table->nelems; u < table->size; u++) + init_packobject(&table->objs[u]); + + return 0; } @@ -183,80 +184,77 @@ int options_table_free(pack_opttbl_t *table) { * *------------------------------------------------------------------------- */ - -int options_add_layout(obj_list_t *obj_list, int n_objs, pack_info_t *pack, - pack_opttbl_t *table) { - unsigned int i, I; - int j, added = 0, found = 0; - - /* increase the size of the collection by N_OBJS if necessary */ - if (table->nelems + n_objs >= table->size) { - if (aux_inctable(table, n_objs) < 0) - return -1; - } - - /* search if this object is already in the table; "path" is the key */ - if (table->nelems > 0) { - /* go tru the supplied list of names */ - for (j = 0; j < n_objs; j++) { - /* linear table search */ - for (i = 0; i < table->nelems; i++) { - /*already on the table */ - if (HDstrcmp(obj_list[j].obj,table->objs[i].path) == 0) { - /* already chunk info inserted for this one; exit */ - if (table->objs[i].chunk.rank > 0) { - error_msg( - "chunk information already inserted for <%s>\n", - obj_list[j].obj); - HDexit(EXIT_FAILURE); - } - /* insert the layout info */ - else { - aux_tblinsert_layout(table, i, pack); - found = 1; - break; - } - } /* if */ - } /* i */ - - if (found == 0) { - /* keep the grow in a temp var */ - I = table->nelems + added; - added++; - HDstrcpy(table->objs[I].path, obj_list[j].obj); - aux_tblinsert_layout(table, I, pack); - } - /* cases where we have an already inserted name but there is a new name also - example: - -f dset1:GZIP=1 -l dset1,dset2:CHUNK=20x20 - dset1 is already inserted, but dset2 must also be - */ - else if (found == 1 - && HDstrcmp(obj_list[j].obj,table->objs[i].path) != 0) { - /* keep the grow in a temp var */ - I = table->nelems + added; - added++; - HDstrcpy(table->objs[I].path, obj_list[j].obj); - aux_tblinsert_layout(table, I, pack); - } - } /* j */ - } - - /* first time insertion */ - else { - /* go tru the supplied list of names */ - for (j = 0; j < n_objs; j++) { - I = table->nelems + added; - added++; - HDstrcpy(table->objs[I].path, obj_list[j].obj); - aux_tblinsert_layout(table, I, pack); - - } - } - - table->nelems += added; - - return 0; +int +options_add_layout(obj_list_t *obj_list, unsigned n_objs, pack_info_t *pack, + pack_opttbl_t *table) +{ + unsigned i, j, I; + unsigned added = 0; + int found = FALSE; + + /* increase the size of the collection by N_OBJS if necessary */ + if (table->nelems + n_objs >= table->size) + if (aux_inctable(table, n_objs) < 0) + return -1; + + /* search if this object is already in the table; "path" is the key */ + if (table->nelems > 0) { + /* go tru the supplied list of names */ + for (j = 0; j < n_objs; j++) { + /* linear table search */ + for (i = 0; i < table->nelems; i++) { + /*already on the table */ + if (HDstrcmp(obj_list[j].obj,table->objs[i].path) == 0) { + /* already chunk info inserted for this one; exit */ + if (table->objs[i].chunk.rank > 0) { + error_msg("chunk information already inserted for <%s>\n", obj_list[j].obj); + HDexit(EXIT_FAILURE); + } + /* insert the layout info */ + else { + aux_tblinsert_layout(table, i, pack); + found = TRUE; + break; + } + } /* if */ + } /* i */ + + if (!found) { + /* keep the grow in a temp var */ + I = table->nelems + added; + added++; + HDstrcpy(table->objs[I].path, obj_list[j].obj); + aux_tblinsert_layout(table, I, pack); + } + /* cases where we have an already inserted name but there is a new name also + example: + -f dset1:GZIP=1 -l dset1,dset2:CHUNK=20x20 + dset1 is already inserted, but dset2 must also be + */ + else + if(found && HDstrcmp(obj_list[j].obj,table->objs[i].path) != 0) { + /* keep the grow in a temp var */ + I = table->nelems + added; + added++; + HDstrcpy(table->objs[I].path, obj_list[j].obj); + aux_tblinsert_layout(table, I, pack); + } + } /* j */ + } + /* first time insertion */ + else { + /* go tru the supplied list of names */ + for (j = 0; j < n_objs; j++) { + I = table->nelems + added; + added++; + HDstrcpy(table->objs[I].path, obj_list[j].obj); + aux_tblinsert_layout(table, I, pack); + } + } + + table->nelems += added; + + return 0; } /*------------------------------------------------------------------------- @@ -268,71 +266,71 @@ int options_add_layout(obj_list_t *obj_list, int n_objs, pack_info_t *pack, * *------------------------------------------------------------------------- */ - -int options_add_filter(obj_list_t *obj_list, int n_objs, filter_info_t filt, - pack_opttbl_t *table) { - - unsigned int i, I; - int j, added = 0, found = 0; - - /* increase the size of the collection by N_OBJS if necessary */ - if (table->nelems + n_objs >= table->size) { - if (aux_inctable(table, n_objs) < 0) - return -1; - } - - /* search if this object is already in the table; "path" is the key */ - if (table->nelems > 0) { - /* go tru the supplied list of names */ - for (j = 0; j < n_objs; j++) { - /* linear table search */ - for (i = 0; i < table->nelems; i++) { - /*already on the table */ - if (HDstrcmp(obj_list[j].obj,table->objs[i].path) == 0) { - /* insert */ - aux_tblinsert_filter(table, i, filt); - found = 1; - break; - } /* if */ - } /* i */ - - if (found == 0) { - /* keep the grow in a temp var */ - I = table->nelems + added; - added++; - HDstrcpy(table->objs[I].path, obj_list[j].obj); - aux_tblinsert_filter(table, I, filt); - } - /* cases where we have an already inserted name but there is a new name also - example: - -l dset1:CHUNK=20x20 -f dset1,dset2:GZIP=1 - dset1 is already inserted, but dset2 must also be - */ - else if (found == 1 - && HDstrcmp(obj_list[j].obj,table->objs[i].path) != 0) { - /* keep the grow in a temp var */ - I = table->nelems + added; - added++; - HDstrcpy(table->objs[I].path, obj_list[j].obj); - aux_tblinsert_filter(table, I, filt); - } - } /* j */ - } - - /* first time insertion */ - else { - /* go tru the supplied list of names */ - for (j = 0; j < n_objs; j++) { - I = table->nelems + added; - added++; - HDstrcpy(table->objs[I].path, obj_list[j].obj); - aux_tblinsert_filter(table, I, filt); - } - } - - table->nelems += added; - - return 0; +int +options_add_filter(obj_list_t *obj_list, unsigned n_objs, filter_info_t filt, + pack_opttbl_t *table) +{ + unsigned int i, j, I; + unsigned added = 0; + int found = FALSE; + + /* increase the size of the collection by N_OBJS if necessary */ + if (table->nelems + n_objs >= table->size) + if (aux_inctable(table, n_objs) < 0) + return -1; + + /* search if this object is already in the table; "path" is the key */ + if (table->nelems > 0) { + /* go tru the supplied list of names */ + for (j = 0; j < n_objs; j++) { + /* linear table search */ + for (i = 0; i < table->nelems; i++) { + /*already on the table */ + if (HDstrcmp(obj_list[j].obj, table->objs[i].path) == 0) { + /* insert */ + aux_tblinsert_filter(table, i, filt); + found = TRUE; + break; + } /* if */ + } /* i */ + + if (!found) { + /* keep the grow in a temp var */ + I = table->nelems + added; + added++; + HDstrcpy(table->objs[I].path, obj_list[j].obj); + aux_tblinsert_filter(table, I, filt); + } + /* cases where we have an already inserted name but there is a new name also + example: + -l dset1:CHUNK=20x20 -f dset1,dset2:GZIP=1 + dset1 is already inserted, but dset2 must also be + */ + else + if(found && HDstrcmp(obj_list[j].obj,table->objs[i].path) != 0) { + /* keep the grow in a temp var */ + I = table->nelems + added; + added++; + HDstrcpy(table->objs[I].path, obj_list[j].obj); + aux_tblinsert_filter(table, I, filt); + } + } /* j */ + } + + /* first time insertion */ + else { + /* go tru the supplied list of names */ + for (j = 0; j < n_objs; j++) { + I = table->nelems + added; + added++; + HDstrcpy(table->objs[I].path, obj_list[j].obj); + aux_tblinsert_filter(table, I, filt); + } + } + + table->nelems += added; + + return 0; } /*------------------------------------------------------------------------- diff --git a/tools/h5repack/h5repack_parse.c b/tools/h5repack/h5repack_parse.c index 1d71c13..004b9e4 100644 --- a/tools/h5repack/h5repack_parse.c +++ b/tools/h5repack/h5repack_parse.c @@ -31,493 +31,425 @@ * FLET, to apply the HDF5 checksum filter * NBIT, to apply the HDF5 NBIT filter (NBIT compression) * SOFF, to apply the HDF5 scale+offset filter (compression) - * UD, to apply a User Defined filter k, m, n1[,…,nm] + * UD, to apply a User Defined filter k,m,n1[,…,nm] * NONE, to remove the filter * * Examples: * "GZIP=6" * "A,B:NONE" - * - * Programmer: Pedro Vicente, pvn@ncsa.uiuc.edu - * - * Date: September, 23, 2003 - * *------------------------------------------------------------------------- */ - - -obj_list_t* parse_filter(const char *str, - int *n_objs, - filter_info_t *filt, - pack_opt_t *options, - int *is_glb) -{ - unsigned i, u; +obj_list_t* parse_filter(const char *str, unsigned *n_objs, filter_info_t *filt, + pack_opt_t *options, int *is_glb) { + size_t i, m, u; char c; - size_t len=HDstrlen(str); - int j, m, n, k, l, p, r, q, end_obj=-1, no_param=0; + size_t len = HDstrlen(str); + int k, l, p, q, end_obj = -1, no_param = 0; + unsigned j, n; char sobj[MAX_NC_NAME]; char scomp[10]; char stype[6]; char smask[3]; - obj_list_t* obj_list=NULL; + obj_list_t* obj_list = NULL; unsigned pixels_per_block; - /* initialize compression info */ - HDmemset(filt,0,sizeof(filter_info_t)); + HDmemset(filt, 0, sizeof(filter_info_t)); *is_glb = 0; /* check for the end of object list and number of objects */ - for ( i = 0, n = 0; i < len; i++) - { + for (i = 0, n = 0; i < len; i++) { c = str[i]; - if ( c==':' ) - { - end_obj=i; - } - if ( c==',' ) - { + if (c == ':') + end_obj = (int) i; + if (c == ',') n++; - } } - if (end_obj==-1) /* missing : */ - { + /* Check for missing : */ + if (end_obj == -1) { /* apply to all objects */ - options->all_filter=1; + options->all_filter = 1; *is_glb = 1; } n++; - obj_list = (obj_list_t*) HDmalloc(n*sizeof(obj_list_t)); - if (obj_list==NULL) - { + obj_list = (obj_list_t *) HDmalloc(n * sizeof(obj_list_t)); + if (obj_list == NULL) { error_msg("could not allocate object list\n"); return NULL; } - *n_objs=n; + *n_objs = n; /* get object list */ - for ( j = 0, k = 0, n = 0; j < end_obj; j++, k++) - { - c = str[j]; - sobj[k] = c; - if ( c==',' || j==end_obj-1) - { - if ( c==',') sobj[k]='\0'; else sobj[k+1]='\0'; - HDstrcpy(obj_list[n].obj,sobj); - HDmemset(sobj,0,sizeof(sobj)); - n++; - k=-1; + if (end_obj > 0) + for (j = 0, k = 0, n = 0; j < (unsigned) end_obj; j++, k++) { + c = str[j]; + sobj[k] = c; + if (c == ',' || j == (unsigned) (end_obj - 1)) { + if (c == ',') + sobj[k] = '\0'; + else + sobj[k + 1] = '\0'; + HDstrcpy(obj_list[n].obj, sobj); + HDmemset(sobj, 0, sizeof(sobj)); + n++; + k = -1; + } } - } /* nothing after : */ - if (end_obj+1==(int)len) - { - if (obj_list) HDfree(obj_list); - error_msg("input Error: Invalid compression type in <%s>\n",str); + if (end_obj + 1 == (int) len) { + if (obj_list) + HDfree(obj_list); + error_msg("input Error: Invalid compression type in <%s>\n", str); HDexit(EXIT_FAILURE); } - /* get filter additional parameters */ - m=0; - for ( i=end_obj+1, k=0, j=0; i<len; i++,k++) - { + m = 0; + for (i = (size_t)(end_obj + 1), k = 0, j = 0; i < len; i++, k++) { c = str[i]; - scomp[k]=c; - if ( c=='=' || i==len-1) - { - if ( c=='=') /*one more parameter */ - { - scomp[k]='\0'; /*cut space */ + scomp[k] = c; + if (c == '=' || i == len - 1) { + if (c == '=') { /*one more parameter */ + scomp[k] = '\0'; /*cut space */ /*------------------------------------------------------------------------- - * H5Z_FILTER_SZIP - * szip has the format SZIP=<pixels per block,coding> - * pixels per block is a even number in 2-32 and coding method is 'EC' or 'NN' - * example SZIP=8,NN - *------------------------------------------------------------------------- - */ - if (HDstrcmp(scomp,"SZIP")==0) - { - l=-1; /* mask index check */ - for ( m=0,u=i+1; u<len; u++,m++) - { - if (str[u]==',') - { - stype[m]='\0'; /* end digit of szip */ - l=0; /* start EC or NN search */ - u++; /* skip ',' */ + * H5Z_FILTER_SZIP + * szip has the format SZIP=<pixels per block,coding> + * pixels per block is a even number in 2-32 and coding method is 'EC' or 'NN' + * example SZIP=8,NN + *------------------------------------------------------------------------- + */ + if (HDstrcmp(scomp, "SZIP") == 0) { + l = -1; /* mask index check */ + for (m = 0, u = i + 1; u < len; u++, m++) { + if (str[u] == ',') { + stype[m] = '\0'; /* end digit of szip */ + l = 0; /* start EC or NN search */ + u++; /* skip ',' */ } c = str[u]; - if (!isdigit(c) && l==-1) - { - if (obj_list) HDfree(obj_list); - error_msg("compression parameter not digit in <%s>\n",str); + if (!HDisdigit(c) && l == -1) { + if (obj_list) + HDfree(obj_list); + error_msg("compression parameter not digit in <%s>\n", str); HDexit(EXIT_FAILURE); } - if (l==-1) - stype[m]=c; - else - { - smask[l]=c; + if (l == -1) + stype[m] = c; + else { + smask[l] = c; l++; - if (l==2) - { - smask[l]='\0'; - i=len-1; /* end */ + if (l == 2) { + smask[l] = '\0'; + i = len - 1; /* end */ (*n_objs)--; /* we counted an extra ',' */ - if (HDstrcmp(smask,"NN")==0) - filt->cd_values[j++]=H5_SZIP_NN_OPTION_MASK; - else if (HDstrcmp(smask,"EC")==0) - filt->cd_values[j++]=H5_SZIP_EC_OPTION_MASK; - else - { + if (HDstrcmp(smask,"NN") == 0) + filt->cd_values[j++] = H5_SZIP_NN_OPTION_MASK; + else if (HDstrcmp(smask,"EC") == 0) + filt->cd_values[j++] = H5_SZIP_EC_OPTION_MASK; + else { error_msg("szip mask must be 'NN' or 'EC' \n"); HDexit(EXIT_FAILURE); } - - } } - - } /* u */ + } /* u */ } /*if */ /*------------------------------------------------------------------------- - * H5Z_FILTER_SCALEOFFSET - * scaleoffset has the format SOFF=<scale_factor,scale_type> - * scale_type can be - * integer datatype, H5Z_SO_INT (IN) - * float datatype using D-scaling method, H5Z_SO_FLOAT_DSCALE (DS) - * float datatype using E-scaling method, H5Z_SO_FLOAT_ESCALE (ES) , not yet implemented - * for integer datatypes, scale_factor denotes Minimum Bits - * for float datatypes, scale_factor denotes decimal scale factor - * examples - * SOFF=31,IN - * SOFF=3,DF - *------------------------------------------------------------------------- - */ - - else if (HDstrcmp(scomp,"SOFF")==0) - { - l=-1; /* mask index check */ - for ( m=0,u=i+1; u<len; u++,m++) - { - if (str[u]==',') - { - stype[m]='\0'; /* end digit */ - l=0; /* start 'IN' , 'DS', or 'ES' search */ - u++; /* skip ',' */ + * H5Z_FILTER_SCALEOFFSET + * scaleoffset has the format SOFF=<scale_factor,scale_type> + * scale_type can be + * integer datatype, H5Z_SO_INT (IN) + * float datatype using D-scaling method, H5Z_SO_FLOAT_DSCALE (DS) + * float datatype using E-scaling method, H5Z_SO_FLOAT_ESCALE (ES) , not yet implemented + * for integer datatypes, scale_factor denotes Minimum Bits + * for float datatypes, scale_factor denotes decimal scale factor + * examples + * SOFF=31,IN + * SOFF=3,DF + *------------------------------------------------------------------------- + */ + else if (HDstrcmp(scomp, "SOFF") == 0) { + l = -1; /* mask index check */ + for (m = 0, u = i + 1; u < len; u++, m++) { + if (str[u] == ',') { + stype[m] = '\0'; /* end digit */ + l = 0; /* start 'IN' , 'DS', or 'ES' search */ + u++; /* skip ',' */ } c = str[u]; - if (!isdigit(c) && l==-1) - { - if (obj_list) HDfree(obj_list); - error_msg("compression parameter is not a digit in <%s>\n",str); + if (!HDisdigit(c) && l == -1) { + if (obj_list) + HDfree(obj_list); + error_msg("compression parameter is not a digit in <%s>\n", str); HDexit(EXIT_FAILURE); } - if (l==-1) - stype[m]=c; - else - { - smask[l]=c; + if (l == -1) + stype[m] = c; + else { + smask[l] = c; l++; - if (l==2) - { - smask[l]='\0'; - i=len-1; /* end */ + if (l == 2) { + smask[l] = '\0'; + i = len - 1; /* end */ (*n_objs)--; /* we counted an extra ',' */ - if (HDstrcmp(smask,"IN")==0) - filt->cd_values[j++]=H5Z_SO_INT; - else if (HDstrcmp(smask,"DS")==H5Z_SO_FLOAT_DSCALE) - filt->cd_values[j++]=H5Z_SO_FLOAT_DSCALE; - else - { + if (HDstrcmp(smask,"IN") == 0) + filt->cd_values[j++] = H5Z_SO_INT; + else if (HDstrcmp(smask, "DS") == H5Z_SO_FLOAT_DSCALE) + filt->cd_values[j++] = H5Z_SO_FLOAT_DSCALE; + else { error_msg("scale type must be 'IN' or 'DS' \n"); HDexit(EXIT_FAILURE); } - } } - - } /* u */ + } /* u */ } /*if */ + /*------------------------------------------------------------------------- - * User Defined - * has the format UD=<filter_number,cd_value_count,value_1[,value_2,...,value_N]> - * BZIP2 example - * UD=307,1,9 - *------------------------------------------------------------------------- - */ - - else if (HDstrcmp(scomp,"UD")==0) - { - l=-1; /* filter number index check */ - p=-1; /* CD_VAL count check */ - r=-1; /* CD_VAL check */ - for ( m=0,q=0,u=i+1; u<len; u++,m++,q++) - { - if (str[u]==',') - { - stype[q]='\0'; /* end digit */ - if (l==-1) - { - filt->filtn=atoi(stype); - l=0; + * User Defined + * has the format UD=<filter_number,cd_value_count,value_1[,value_2,...,value_N]> + * BZIP2 example + * UD=307,1,9 + *------------------------------------------------------------------------- + */ + else if (HDstrcmp(scomp, "UD") == 0) { + l = -1; /* filter number index check */ + p = -1; /* CD_VAL count check */ + for (m = 0, q = 0, u = i + 1; u < len; u++, m++, q++) { + if (str[u] == ',') { + stype[q] = '\0'; /* end digit */ + if (l == -1) { + filt->filtn = HDatoi(stype); + l = 0; } - else if (p==-1) - { - filt->cd_nelmts=atoi(stype); - p=0; + else if (p == -1) { + filt->cd_nelmts = HDstrtoull(stype, NULL, 0); + p = 0; } else - r=0; - q=0; - u++; /* skip ',' */ + filt->cd_values[j++] = (unsigned)HDstrtoul(stype, NULL, 0); + q = 0; + u++; /* skip ',' */ } c = str[u]; - if (!isdigit(c) && l==-1) - { - if (obj_list) HDfree(obj_list); - error_msg("filter number parameter is not a digit in <%s>\n",str); + if (!HDisdigit(c) && l == -1) { + if (obj_list) + HDfree(obj_list); + error_msg("filter number parameter is not a digit in <%s>\n", str); HDexit(EXIT_FAILURE); } - stype[q]=c; - if (l==0 && p==0) - { - if (r==0) - filt->cd_values[j++]=atoi(stype); - } - - } /* u */ - - stype[q]='\0'; + stype[q] = c; + } /* for u */ + stype[q] = '\0'; } /*if */ - /*------------------------------------------------------------------------- - * all other filters - *------------------------------------------------------------------------- - */ - - else - { + * all other filters + *------------------------------------------------------------------------- + */ + else { /* here we could have 1 or 2 digits */ - for ( m=0,u=i+1; u<len; u++,m++) - { + for (m = 0, u = i + 1; u < len; u++, m++) { c = str[u]; - if (!isdigit(c)){ - if (obj_list) HDfree(obj_list); - error_msg("compression parameter is not a digit in <%s>\n",str); + if (!HDisdigit(c)) { + if (obj_list) + HDfree(obj_list); + error_msg("compression parameter is not a digit in <%s>\n", str); HDexit(EXIT_FAILURE); } - stype[m]=c; + stype[m] = c; } /* u */ - stype[m]='\0'; + stype[m] = '\0'; } /*if */ - - - filt->cd_values[j++]=atoi(stype); - i+=m; /* jump */ + filt->cd_values[j++] = (unsigned) HDstrtoul(stype, NULL, 0); + if(filt->cd_nelmts == 0) + j = 0; + i += m; /* jump */ } - else if (i==len-1) - { /*no more parameters */ - scomp[k+1]='\0'; - no_param=1; + else if (i == len - 1) { /*no more parameters */ + scomp[k + 1] = '\0'; + no_param = 1; } /*------------------------------------------------------------------------- - * translate from string to filter symbol - *------------------------------------------------------------------------- - */ + * translate from string to filter symbol + *------------------------------------------------------------------------- + */ /*------------------------------------------------------------------------- - * H5Z_FILTER_NONE - *------------------------------------------------------------------------- - */ - if (HDstrcmp(scomp,"NONE")==0) - { - filt->filtn=H5Z_FILTER_NONE; + * H5Z_FILTER_NONE + *------------------------------------------------------------------------- + */ + if (HDstrcmp(scomp, "NONE") == 0) { + filt->filtn = H5Z_FILTER_NONE; filt->cd_nelmts = 0; } /*------------------------------------------------------------------------- - * H5Z_FILTER_DEFLATE - *------------------------------------------------------------------------- - */ - else if (HDstrcmp(scomp,"GZIP")==0) - { - filt->filtn=H5Z_FILTER_DEFLATE; + * H5Z_FILTER_DEFLATE + *------------------------------------------------------------------------- + */ + else if (HDstrcmp(scomp, "GZIP") == 0) { + filt->filtn = H5Z_FILTER_DEFLATE; filt->cd_nelmts = 1; - if (no_param) - { /*no more parameters, GZIP must have parameter */ - if (obj_list) HDfree(obj_list); - error_msg("missing compression parameter in <%s>\n",str); + if (no_param) { /*no more parameters, GZIP must have parameter */ + if (obj_list) + HDfree(obj_list); + error_msg("missing compression parameter in <%s>\n", str); HDexit(EXIT_FAILURE); } } /*------------------------------------------------------------------------- - * H5Z_FILTER_SZIP - *------------------------------------------------------------------------- - */ - else if (HDstrcmp(scomp,"SZIP")==0) - { - filt->filtn=H5Z_FILTER_SZIP; + * H5Z_FILTER_SZIP + *------------------------------------------------------------------------- + */ + else if (HDstrcmp(scomp, "SZIP") == 0) { + filt->filtn = H5Z_FILTER_SZIP; filt->cd_nelmts = 2; - if (no_param) - { /*no more parameters, SZIP must have parameter */ - if (obj_list) HDfree(obj_list); - error_msg("missing compression parameter in <%s>\n",str); + if (no_param) { /*no more parameters, SZIP must have parameter */ + if (obj_list) + HDfree(obj_list); + error_msg("missing compression parameter in <%s>\n", str); HDexit(EXIT_FAILURE); } } /*------------------------------------------------------------------------- - * H5Z_FILTER_SHUFFLE - *------------------------------------------------------------------------- - */ - else if (HDstrcmp(scomp,"SHUF")==0) - { - filt->filtn=H5Z_FILTER_SHUFFLE; + * H5Z_FILTER_SHUFFLE + *------------------------------------------------------------------------- + */ + else if (HDstrcmp(scomp, "SHUF") == 0) { + filt->filtn = H5Z_FILTER_SHUFFLE; filt->cd_nelmts = 0; - if (m>0) - { /*shuffle does not have parameter */ - if (obj_list) HDfree(obj_list); - error_msg("extra parameter in SHUF <%s>\n",str); + if (m > 0) { /*shuffle does not have parameter */ + if (obj_list) + HDfree(obj_list); + error_msg("extra parameter in SHUF <%s>\n", str); HDexit(EXIT_FAILURE); } } /*------------------------------------------------------------------------- - * H5Z_FILTER_FLETCHER32 - *------------------------------------------------------------------------- - */ - else if (HDstrcmp(scomp,"FLET")==0) - { - filt->filtn=H5Z_FILTER_FLETCHER32; + * H5Z_FILTER_FLETCHER32 + *------------------------------------------------------------------------- + */ + else if (HDstrcmp(scomp, "FLET") == 0) { + filt->filtn = H5Z_FILTER_FLETCHER32; filt->cd_nelmts = 0; - if (m>0) - { /*shuffle does not have parameter */ - if (obj_list) HDfree(obj_list); - error_msg("extra parameter in FLET <%s>\n",str); + if (m > 0) { /*shuffle does not have parameter */ + if (obj_list) + HDfree(obj_list); + error_msg("extra parameter in FLET <%s>\n", str); HDexit(EXIT_FAILURE); } } /*------------------------------------------------------------------------- - * H5Z_FILTER_NBIT - *------------------------------------------------------------------------- - */ - else if (HDstrcmp(scomp,"NBIT")==0) - { - filt->filtn=H5Z_FILTER_NBIT; + * H5Z_FILTER_NBIT + *------------------------------------------------------------------------- + */ + else if (HDstrcmp(scomp, "NBIT") == 0) { + filt->filtn = H5Z_FILTER_NBIT; filt->cd_nelmts = 0; - if (m>0) - { /*nbit does not have parameter */ - if (obj_list) HDfree(obj_list); - error_msg("extra parameter in NBIT <%s>\n",str); + if (m > 0) { /*nbit does not have parameter */ + if (obj_list) + HDfree(obj_list); + error_msg("extra parameter in NBIT <%s>\n", str); HDexit(EXIT_FAILURE); } } /*------------------------------------------------------------------------- - * H5Z_FILTER_SCALEOFFSET - *------------------------------------------------------------------------- - */ - else if (HDstrcmp(scomp,"SOFF")==0) - { - filt->filtn=H5Z_FILTER_SCALEOFFSET; + * H5Z_FILTER_SCALEOFFSET + *------------------------------------------------------------------------- + */ + else if (HDstrcmp(scomp, "SOFF") == 0) { + filt->filtn = H5Z_FILTER_SCALEOFFSET; filt->cd_nelmts = 2; - if (no_param) - { /*no more parameters, SOFF must have parameter */ - if (obj_list) HDfree(obj_list); - error_msg("missing compression parameter in <%s>\n",str); + if (no_param) { /*no more parameters, SOFF must have parameter */ + if (obj_list) + HDfree(obj_list); + error_msg("missing compression parameter in <%s>\n", str); HDexit(EXIT_FAILURE); } } /*------------------------------------------------------------------------- - * User Defined Filter - *------------------------------------------------------------------------- - */ - else if (HDstrcmp(scomp,"UD")==0) - { - if (filt->cd_nelmts != j) - { /* parameters does not match count */ - if (obj_list) HDfree(obj_list); - error_msg("incorrect number of compression parameters in <%s>\n",str); + * User Defined Filter + *------------------------------------------------------------------------- + */ + else if (HDstrcmp(scomp, "UD") == 0) { + /* parameters does not match count */ + if (filt->cd_nelmts != j) { + if (obj_list) + HDfree(obj_list); + error_msg("incorrect number of compression parameters in <%s>\n", str); HDexit(EXIT_FAILURE); } } else { - if (obj_list) HDfree(obj_list); - error_msg("invalid filter type in <%s>\n",str); + if (obj_list) + HDfree(obj_list); + error_msg("invalid filter type in <%s>\n", str); HDexit(EXIT_FAILURE); } } } /*i*/ /*------------------------------------------------------------------------- - * check valid parameters - *------------------------------------------------------------------------- - */ - - switch (filt->filtn) - { + * check valid parameters + *------------------------------------------------------------------------- + */ + switch (filt->filtn) { /*------------------------------------------------------------------------- - * H5Z_FILTER_DEFLATE - *------------------------------------------------------------------------- - */ - + * H5Z_FILTER_DEFLATE + *------------------------------------------------------------------------- + */ case H5Z_FILTER_DEFLATE: - if (filt->cd_values[0]>9 ) - { - if (obj_list) HDfree(obj_list); - error_msg("invalid compression parameter in <%s>\n",str); + if (filt->cd_values[0] > 9) { + if (obj_list) + HDfree(obj_list); + error_msg("invalid compression parameter in <%s>\n", str); HDexit(EXIT_FAILURE); } break; - /*------------------------------------------------------------------------- - * H5Z_FILTER_SZIP - *------------------------------------------------------------------------- - */ - + * H5Z_FILTER_SZIP + *------------------------------------------------------------------------- + */ case H5Z_FILTER_SZIP: - pixels_per_block=filt->cd_values[0]; - if ((pixels_per_block%2)==1) - { - if (obj_list) HDfree(obj_list); - error_msg("pixels_per_block is not even in <%s>\n",str); + pixels_per_block = filt->cd_values[0]; + if ((pixels_per_block % 2) == 1) { + if (obj_list) + HDfree(obj_list); + error_msg("pixels_per_block is not even in <%s>\n", str); HDexit(EXIT_FAILURE); } - if (pixels_per_block>H5_SZIP_MAX_PIXELS_PER_BLOCK) - { - if (obj_list) HDfree(obj_list); - error_msg("pixels_per_block is too large in <%s>\n",str); + if (pixels_per_block > H5_SZIP_MAX_PIXELS_PER_BLOCK) { + if (obj_list) + HDfree(obj_list); + error_msg("pixels_per_block is too large in <%s>\n", str); HDexit(EXIT_FAILURE); } - if ( (HDstrcmp(smask,"NN")!=0) && (HDstrcmp(smask,"EC")!=0) ) - { - if (obj_list) HDfree(obj_list); + if ((HDstrcmp(smask,"NN") != 0) && (HDstrcmp(smask,"EC") != 0)) { + if (obj_list) + HDfree(obj_list); error_msg("szip mask must be 'NN' or 'EC' \n"); HDexit(EXIT_FAILURE); } break; default: break; - - }; return obj_list; } - - + /*------------------------------------------------------------------------- * Function: parse_layout * @@ -539,176 +471,146 @@ obj_list_t* parse_filter(const char *str, * *------------------------------------------------------------------------- */ -obj_list_t* parse_layout(const char *str, - int *n_objs, - pack_info_t *pack, /* info about layout needed */ - pack_opt_t *options) -{ - obj_list_t* obj_list=NULL; - unsigned i; +obj_list_t* parse_layout(const char *str, unsigned *n_objs, pack_info_t *pack, /* info about layout needed */ +pack_opt_t *options) { + obj_list_t* obj_list = NULL; + unsigned i, j, n; char c; - size_t len=HDstrlen(str); - int j, n, k, end_obj=-1, c_index; + size_t len = HDstrlen(str); + int k, end_obj = -1, c_index; char sobj[MAX_NC_NAME]; char sdim[10]; char slayout[10]; - HDmemset(sdim, '\0', sizeof(sdim)); HDmemset(sobj, '\0', sizeof(sobj)); HDmemset(slayout, '\0', sizeof(slayout)); /* check for the end of object list and number of objects */ - for ( i=0, n=0; i<len; i++) - { + for (i = 0, n = 0; i < len; i++) { c = str[i]; - if ( c==':' ) - { - end_obj=i; - } - if ( c==',' ) - { + if (c == ':') + end_obj = (int) i; + if (c == ',') n++; - } } - if (end_obj==-1) { /* missing : chunk all */ - options->all_layout=1; + if (end_obj == -1) { /* missing : chunk all */ + options->all_layout = 1; } n++; - obj_list = (obj_list_t*) HDmalloc(n*sizeof(obj_list_t)); - if (obj_list==NULL) - { + obj_list = (obj_list_t*) HDmalloc(n * sizeof(obj_list_t)); + if (obj_list == NULL) { error_msg("could not allocate object list\n"); return NULL; } - *n_objs=n; + *n_objs = n; /* get object list */ - for ( j=0, k=0, n=0; j<end_obj; j++,k++) - { - c = str[j]; - sobj[k]=c; - if ( c==',' || j==end_obj-1) - { - if ( c==',') sobj[k]='\0'; else sobj[k+1]='\0'; - HDstrcpy(obj_list[n].obj,sobj); - HDmemset(sobj,0,sizeof(sobj)); - n++; - k=-1; + if (end_obj > 0) + for (j = 0, k = 0, n = 0; j < (unsigned) end_obj; j++, k++) { + c = str[j]; + sobj[k] = c; + if (c == ',' || j == (unsigned) (end_obj - 1)) { + if (c == ',') + sobj[k] = '\0'; + else + sobj[k + 1] = '\0'; + HDstrcpy(obj_list[n].obj, sobj); + HDmemset(sobj, 0, sizeof(sobj)); + n++; + k = -1; + } } - } /* nothing after : */ - if (end_obj+1==(int)len) - { - if (obj_list) HDfree(obj_list); - error_msg("in parse layout, no characters after : in <%s>\n",str); + if (end_obj + 1 == (int) len) { + if (obj_list) + HDfree(obj_list); + error_msg("in parse layout, no characters after : in <%s>\n", str); HDexit(EXIT_FAILURE); } /* get layout info */ - for ( j=end_obj+1, n=0; n<=5; j++,n++) - { - if (n==5) - { - slayout[n]='\0'; /*cut string */ - if (HDstrcmp(slayout,"COMPA")==0) - pack->layout=H5D_COMPACT; - else if (HDstrcmp(slayout,"CONTI")==0) - pack->layout=H5D_CONTIGUOUS; - else if (HDstrcmp(slayout,"CHUNK")==0) - pack->layout=H5D_CHUNKED; + for (j = (unsigned) (end_obj + 1), n = 0; n <= 5; j++, n++) { + if (n == 5) { + slayout[n] = '\0'; /*cut string */ + if (HDstrcmp(slayout, "COMPA") == 0) + pack->layout = H5D_COMPACT; + else if (HDstrcmp(slayout, "CONTI") == 0) + pack->layout = H5D_CONTIGUOUS; + else if (HDstrcmp(slayout, "CHUNK") == 0) + pack->layout = H5D_CHUNKED; else { - error_msg("in parse layout, not a valid layout in <%s>\n",str); + error_msg("in parse layout, not a valid layout in <%s>\n", str); HDexit(EXIT_FAILURE); } } - else - { + else { c = str[j]; - slayout[n]=c; + slayout[n] = c; } } /* j */ - - if ( pack->layout==H5D_CHUNKED ) - { - + if (pack->layout == H5D_CHUNKED) { /*------------------------------------------------------------------------- - * get chunk info - *------------------------------------------------------------------------- - */ - k=0; - - if (j>(int)len) - { - if (obj_list) HDfree(obj_list); - error_msg("in parse layout, <%s> Chunk dimensions missing\n",str); + * get chunk info + *------------------------------------------------------------------------- + */ + k = 0; + if (j > len) { + if (obj_list) + HDfree(obj_list); + error_msg("in parse layout, <%s> Chunk dimensions missing\n", str); HDexit(EXIT_FAILURE); } - for ( i=j, c_index=0; i<len; i++) - { + for (i = j, c_index = 0; i < len; i++) { c = str[i]; - sdim[k]=c; + sdim[k] = c; k++; /*increment sdim index */ - if (!isdigit(c) && c!='x' - && c!='N' && c!='O' && c!='N' && c!='E' - ){ - if (obj_list) HDfree(obj_list); - error_msg("in parse layout, <%s> Not a valid character in <%s>\n", - sdim,str); + if (!HDisdigit(c) && c != 'x' && c != 'N' && c != 'O' && c != 'N' && c != 'E') { + if (obj_list) + HDfree(obj_list); + error_msg("in parse layout, <%s> Not a valid character in <%s>\n", sdim, str); HDexit(EXIT_FAILURE); } - if ( c=='x' || i==len-1) - { - if ( c=='x') { - sdim[k-1]='\0'; - k=0; - pack->chunk.chunk_lengths[c_index]=atoi(sdim); - if (pack->chunk.chunk_lengths[c_index]==0) { - if (obj_list) HDfree(obj_list); - error_msg("in parse layout, <%s> conversion to number in <%s>\n", - sdim,str); + if (c == 'x' || i == len - 1) { + if (c == 'x') { + sdim[k - 1] = '\0'; + k = 0; + pack->chunk.chunk_lengths[c_index] = HDstrtoull(sdim, NULL, 0); + if (pack->chunk.chunk_lengths[c_index] == 0) { + if (obj_list) + HDfree(obj_list); + error_msg("in parse layout, <%s> conversion to number in <%s>\n", sdim, str); HDexit(EXIT_FAILURE); } c_index++; } - else if (i==len-1) { /*no more parameters */ - sdim[k]='\0'; - k=0; - if (HDstrcmp(sdim,"NONE")==0) - { - pack->chunk.rank=-2; + else if (i == len - 1) { /*no more parameters */ + sdim[k] = '\0'; + k = 0; + if (HDstrcmp(sdim,"NONE") == 0) { + pack->chunk.rank = -2; } - else - { - pack->chunk.chunk_lengths[c_index]=atoi(sdim); - if (pack->chunk.chunk_lengths[c_index]==0){ - if (obj_list) HDfree(obj_list); - error_msg("in parse layout, <%s> conversion to number in <%s>\n", - sdim,str); + else { + pack->chunk.chunk_lengths[c_index] = HDstrtoull(sdim, NULL, 0); + if (pack->chunk.chunk_lengths[c_index] == 0) { + if (obj_list) + HDfree(obj_list); + error_msg("in parse layout, <%s> conversion to number in <%s>\n", sdim, str); HDexit(EXIT_FAILURE); } - pack->chunk.rank=c_index+1; + pack->chunk.rank = c_index + 1; } } /*if */ } /*if c=='x' || i==len-1 */ } /*i*/ - - } /*H5D_CHUNKED*/ - return obj_list; } - - - - - - diff --git a/tools/h5repack/h5repack_plugin.sh.in b/tools/h5repack/h5repack_plugin.sh.in index 7502397..a064db6 100644 --- a/tools/h5repack/h5repack_plugin.sh.in +++ b/tools/h5repack/h5repack_plugin.sh.in @@ -127,7 +127,7 @@ CLEAN_TESTFILES_AND_TESTDIR() # skip rm if srcdir is same as destdir # this occurs when build/test performed in source dir and # make cp fail - SDIR=`$DIRNAME $tstfile` + SDIR=$SRC_H5REPACK_TESTFILES INODE_SDIR=`$LS -i -d $SDIR | $AWK -F' ' '{print $1}'` INODE_DDIR=`$LS -i -d $TESTDIR | $AWK -F' ' '{print $1}'` if [ "$INODE_SDIR" != "$INODE_DDIR" ]; then diff --git a/tools/h5repack/h5repack_refs.c b/tools/h5repack/h5repack_refs.c index 2b39249..fbaeada 100644 --- a/tools/h5repack/h5repack_refs.c +++ b/tools/h5repack/h5repack_refs.c @@ -1,4 +1,3 @@ - /* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * Copyright by The HDF Group. * * Copyright by the Board of Trustees of the University of Illinois. * @@ -50,6 +49,7 @@ 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 */ @@ -85,18 +85,18 @@ int do_copy_refobjs(hid_t fidin, *------------------------------------------------------------------------- */ if((grp_out = H5Gopen2(fidout, travt->objs[i].name, H5P_DEFAULT)) < 0) - goto error; + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Gopen2 failed"); if((grp_in = H5Gopen2(fidin, travt->objs[i].name, H5P_DEFAULT)) < 0) - goto error; + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Gopen2 failed"); if(copy_refs_attr(grp_in, grp_out, options, travt, fidout) < 0) - goto error; + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "copy_refs_attr failed"); if(H5Gclose(grp_out) < 0) - goto error; + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Gclose failed"); if(H5Gclose(grp_in) < 0) - goto error; + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Gclose failed"); /*------------------------------------------------------------------------- * check for hard links @@ -113,26 +113,26 @@ int do_copy_refobjs(hid_t fidin, */ case H5TRAV_TYPE_DATASET: if((dset_in = H5Dopen2(fidin, travt->objs[i].name, H5P_DEFAULT)) < 0) - goto error; + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dopen2 failed"); if((space_id = H5Dget_space(dset_in)) < 0) - goto error; + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dget_space failed"); if((ftype_id = H5Dget_type(dset_in)) < 0) - goto error; + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dget_type failed"); if((dcpl_id = H5Dget_create_plist(dset_in)) < 0) - goto error; + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dget_create_plist failed"); if((rank = H5Sget_simple_extent_ndims(space_id)) < 0) - goto error; + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Sget_simple_extent_ndims failed"); if(H5Sget_simple_extent_dims(space_id, dims, NULL) < 0) - goto error; + 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) - goto error; + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "h5tools_get_native_type failed"); if((msize = H5Tget_size(mtype_id)) == 0) - goto error; + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Tget_size failed"); /*------------------------------------------------------------------------- * check if the dataset creation property list has filters that @@ -168,15 +168,15 @@ int do_copy_refobjs(hid_t fidin, buf = (hobj_ref_t *)HDmalloc((unsigned)(nelmts * msize)); if(buf==NULL) { printf("cannot read into memory\n" ); - goto error; + 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) - goto error; + 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" ); - goto error; + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "HDcalloc failed"); } /* end if */ for(u = 0; u < nelmts; u++) { H5E_BEGIN_TRY { @@ -190,7 +190,7 @@ int do_copy_refobjs(hid_t fidin, 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) - goto error; + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Rcreate failed"); if(options->verbose) { printf(FORMAT_OBJ,"dset",travt->objs[i].name ); @@ -208,10 +208,10 @@ int do_copy_refobjs(hid_t fidin, *------------------------------------------------------------------------- */ if((dset_out = H5Dcreate2(fidout, travt->objs[i].name, mtype_id, space_id, H5P_DEFAULT, dcpl_id, H5P_DEFAULT)) < 0) - goto error; + 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) - goto error; + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dwrite failed"); if(buf) HDfree(buf); @@ -222,7 +222,7 @@ int do_copy_refobjs(hid_t fidin, * copy attrs *----------------------------------------------------*/ if(copy_attr(dset_in, dset_out, &named_dt_head, travt, options) < 0) - goto error; + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "copy_attr failed"); } /*H5T_STD_REF_OBJ*/ /*------------------------------------------------------------------------- @@ -245,10 +245,10 @@ int do_copy_refobjs(hid_t fidin, buf = (hdset_reg_ref_t *)HDmalloc((unsigned)(nelmts * msize)); if(buf == NULL) { printf("cannot read into memory\n"); - goto error; + 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) - goto error; + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dread failed"); /*------------------------------------------------------------------------- * create output @@ -257,7 +257,7 @@ int do_copy_refobjs(hid_t fidin, 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"); - goto error; + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "HDcalloc failed"); } /* end if */ for(u = 0; u < nelmts; u++) { @@ -273,18 +273,15 @@ int do_copy_refobjs(hid_t fidin, hid_t region_id; /* region id of the referenced dataset */ if((region_id = H5Rget_region(dset_in, H5R_DATASET_REGION, &buf[u])) < 0) - goto error; + 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) - goto error; + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Rcreate failed"); if(H5Sclose(region_id) < 0) - goto error; + 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, @@ -300,10 +297,10 @@ int do_copy_refobjs(hid_t fidin, *------------------------------------------------------------------------- */ if((dset_out = H5Dcreate2(fidout, travt->objs[i].name, mtype_id, space_id, H5P_DEFAULT, dcpl_id, H5P_DEFAULT)) < 0) - goto error; + 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) - goto error; + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dwrite failed"); if(buf) HDfree(buf); @@ -314,7 +311,7 @@ int do_copy_refobjs(hid_t fidin, * copy attrs *----------------------------------------------------*/ if(copy_attr(dset_in, dset_out, &named_dt_head, travt, options) < 0) - goto error; + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "copy_attr failed"); } /* H5T_STD_REF_DSETREG */ /*------------------------------------------------------------------------- * not references, open previously created object in 1st traversal @@ -322,7 +319,7 @@ int do_copy_refobjs(hid_t fidin, */ else { if((dset_out = H5Dopen2(fidout, travt->objs[i].name, H5P_DEFAULT)) < 0) - goto error; + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dopen2 failed"); } /* end else */ HDassert(dset_out != FAIL); @@ -332,7 +329,7 @@ int do_copy_refobjs(hid_t fidin, *------------------------------------------------------------------------- */ if(copy_refs_attr(dset_in, dset_out, options, travt, fidout) < 0) - goto error; + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "copy_refs_attr failed"); /*------------------------------------------------------------------------- * check for hard links @@ -343,7 +340,7 @@ int do_copy_refobjs(hid_t fidin, 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) - goto error; + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dclose failed"); } /*can_read*/ /*------------------------------------------------------------------------- @@ -351,15 +348,15 @@ int do_copy_refobjs(hid_t fidin, *------------------------------------------------------------------------- */ if(H5Tclose(ftype_id) < 0) - goto error; + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Tclose failed"); if(H5Tclose(mtype_id) < 0) - goto error; + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Tclose failed"); if(H5Pclose(dcpl_id) < 0) - goto error; + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed"); if(H5Sclose(space_id) < 0) - goto error; + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Sclose failed"); if(H5Dclose(dset_in) < 0) - goto error; + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dclose failed"); break; /*------------------------------------------------------------------------- @@ -368,9 +365,9 @@ int do_copy_refobjs(hid_t fidin, */ case H5TRAV_TYPE_NAMED_DATATYPE: if((type_in = H5Topen2(fidin, travt->objs[i].name, H5P_DEFAULT)) < 0) - goto error; + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Topen2 failed"); if(H5Tclose(type_in) < 0) - goto error; + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Tclose failed"); break; /*------------------------------------------------------------------------- @@ -383,7 +380,7 @@ int do_copy_refobjs(hid_t fidin, case H5TRAV_TYPE_UNKNOWN: case H5TRAV_TYPE_UDLINK: - goto error; + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5TRAV invalid type"); default: break; @@ -396,9 +393,9 @@ int do_copy_refobjs(hid_t fidin, */ named_datatype_free(&named_dt_head, 0); - return 0; + return ret_value; -error: +done: H5E_BEGIN_TRY { H5Gclose(grp_in); H5Gclose(grp_out); @@ -412,7 +409,7 @@ error: named_datatype_free(&named_dt_head, 0); } H5E_END_TRY; - return -1; + return ret_value; } @@ -450,6 +447,7 @@ static int copy_refs_attr(hid_t loc_in, 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 */ @@ -467,32 +465,32 @@ static int copy_refs_attr(hid_t loc_in, void *refbuf = NULL; void *buf = NULL; const char* refname = NULL; - int *ref_comp_index = 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) - goto error; + 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) - goto error; + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Aopen_by_idx failed"); /* get the file datatype */ if((ftype_id = H5Aget_type(attr_id)) < 0) - goto error; + 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) - goto error; + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "h5tools_get_native_type failed"); if((msize = H5Tget_size(mtype_id)) == 0) - goto error; + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Tget_size failed"); is_ref = (type_class == H5T_REFERENCE); @@ -516,10 +514,10 @@ static int copy_refs_attr(hid_t loc_in, int nmembers = H5Tget_nmembers(ftype_id) ; if (nmembers < 1) - goto error; + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Tget_nmembers failed"); - ref_comp_index = (int *)HDmalloc(nmembers*sizeof (int)); - ref_comp_size = (size_t *)HDmalloc(nmembers*sizeof(ref_comp_size)); + 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++) { @@ -560,15 +558,15 @@ static int copy_refs_attr(hid_t loc_in, /* get name */ if(H5Aget_name(attr_id, 255, name) < 0) - goto error; + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Aget_name failed"); /* get the dataspace handle */ if((space_id = H5Aget_space(attr_id)) < 0) - goto error; + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Aget_space failed"); /* get dimensions */ if((rank = H5Sget_simple_extent_dims(space_id, dims, NULL)) < 0) - goto error; + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Sget_simple_extent_dims failed"); /*------------------------------------------------------------------------- @@ -580,8 +578,8 @@ static int copy_refs_attr(hid_t loc_in, nelmts *= dims[j]; if (is_ref_array) { - unsigned array_rank = 0; - hsize_t array_size = 1; + unsigned array_rank = 0; + hsize_t array_size = 1; hsize_t array_dims[H5S_MAX_RANK]; hid_t base_type; @@ -589,7 +587,7 @@ static int copy_refs_attr(hid_t loc_in, msize = H5Tget_size(base_type); H5Tclose(base_type); - array_rank = H5Tget_array_ndims(mtype_id); + 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]; @@ -597,7 +595,7 @@ static int copy_refs_attr(hid_t loc_in, } if((attr_out = H5Acreate2(loc_out, name, ftype_id, space_id, H5P_DEFAULT, H5P_DEFAULT)) < 0) - goto error; + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Acreate2 failed"); if (nelmts>0) { /* handle object references */ @@ -605,15 +603,15 @@ static int copy_refs_attr(hid_t loc_in, buf = (hobj_ref_t *)HDmalloc((unsigned)(nelmts * msize)); if(buf == NULL) { printf("cannot read into memory\n"); - goto error; + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "HDmalloc failed"); } /* end if */ if(H5Aread(attr_id, mtype_id, buf) < 0) - goto error; + 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"); - goto error; + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "HDcalloc failed"); } /* end if */ for(i = 0; i < (unsigned)nelmts; i++) { @@ -629,10 +627,10 @@ static int copy_refs_attr(hid_t loc_in, if(buf == NULL) { printf( "cannot read into memory\n" ); - goto error; + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "HDmalloc failed"); } /* end if */ if(H5Aread(attr_id, mtype_id, buf) < 0) - goto error; + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Aread failed"); /*------------------------------------------------------------------------- * create output @@ -641,7 +639,7 @@ static int copy_refs_attr(hid_t loc_in, 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" ); - goto error; + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "HDcalloc failed"); } /* end if */ for(i = 0; i < (unsigned)nelmts; i++) { @@ -659,11 +657,11 @@ static int copy_refs_attr(hid_t loc_in, if(buf == NULL) { printf( "cannot read into memory\n" ); - goto error; + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "HDmalloc failed"); } /* end if */ if(H5Aread(attr_id, mtype_id, buf) < 0) - goto error; + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Aread failed"); if (H5R_OBJ_REF_BUF_SIZE==msize) { hobj_ref_t ref_out; @@ -700,41 +698,43 @@ static int copy_refs_attr(hid_t loc_in, if(buf == NULL) { printf( "cannot read into memory\n" ); - goto error; + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "HDmalloc failed"); } /* end if */ if(H5Aread(attr_id, mtype_id, buf) < 0) - goto error; + 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) { - int idx = i*msize+H5Tget_member_offset( mtype_id, (unsigned)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) { - int idx = i*msize+H5Tget_member_offset( mtype_id, (unsigned)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 */ + 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) - goto error; + 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. */ + refbuf = NULL; /* set it to NULL to avoid double free since buf and refbuf are the same. */ if(buf) { HDfree(buf); @@ -747,39 +747,39 @@ static int copy_refs_attr(hid_t loc_in, } if (ref_comp_index) { - HDfree(ref_comp_index); - ref_comp_index = NULL; + HDfree(ref_comp_index); + ref_comp_index = NULL; } if (ref_comp_size) { - HDfree(ref_comp_size); - ref_comp_size = NULL; + HDfree(ref_comp_size); + ref_comp_size = NULL; } if(H5Aclose(attr_out) < 0) - goto error; + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Aclose failed"); /*------------------------------------------------------------------------- * close *------------------------------------------------------------------------- */ if(H5Tclose(ftype_id) < 0) - goto error; + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Tclose failed"); if(H5Tclose(mtype_id) < 0) - goto error; + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Tclose failed"); if(H5Sclose(space_id) < 0) - goto error; + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Sclose failed"); if(H5Aclose(attr_id) < 0) - goto error; + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Aclose failed"); } /* for(u = 0; u < (unsigned)oinfo.num_attrs; u++) */ - return 0; + return ret_value; -error: - if(refbuf) - HDfree(refbuf); - if(buf) - HDfree(buf); +done: + if(refbuf) + HDfree(refbuf); + if(buf) + HDfree(buf); if (ref_comp_index) HDfree(ref_comp_index); @@ -795,7 +795,7 @@ error: H5Aclose(attr_out); } H5E_END_TRY; - return -1; + return ret_value; } /*------------------------------------------------------------------------- @@ -845,30 +845,26 @@ out: 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) { - herr_t ret = -1; - 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, ref_obj_id=-1; ref_obj_id = H5Rdereference(obj_id, ref_type, ref_in); - if (ref_obj_id<0) - goto done; - - ref_obj_name = MapIdToName(ref_obj_id, travt); - if (ref_obj_name == NULL) - goto done; - - if (ref_type == H5R_DATASET_REGION) { - space_id = H5Rget_region(obj_id, H5R_DATASET_REGION, ref_in); - if (space_id < 0) - goto done; - } + if (ref_obj_id < 0) + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Rdereference2 failed"); - ret = H5Rcreate(ref_out, fid_out, ref_obj_name, ref_type, space_id); + ref_obj_name = MapIdToName(ref_obj_id, travt); + if (ref_obj_name == NULL) + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "MapIdToName failed"); - if (ret < 0) - goto done; + 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"); + } - ret = 0; + 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 { @@ -876,6 +872,6 @@ done: H5Oclose(ref_obj_id); } H5E_END_TRY; - return ret; + return ret_value; } diff --git a/tools/h5repack/h5repack_verify.c b/tools/h5repack/h5repack_verify.c index cec9c86..60962aa 100644 --- a/tools/h5repack/h5repack_verify.c +++ b/tools/h5repack/h5repack_verify.c @@ -51,11 +51,12 @@ static int verify_filters(hid_t pid, hid_t tid, int nfilters, filter_info_t *fil int h5repack_verify(const char *out_fname, pack_opt_t *options) { - hid_t fidout; /* file ID for output file*/ - hid_t did; /* dataset ID */ - hid_t pid; /* dataset creation property list ID */ - hid_t sid; /* space ID */ - hid_t tid; /* type ID */ + int ret_value = 0; /*no need to LEAVE() on ERROR: HERR_INIT(int, SUCCEED) */ + hid_t fidout = -1; /* file ID for output file*/ + hid_t did = -1; /* dataset ID */ + hid_t pid = -1; /* dataset creation property list ID */ + hid_t sid = -1; /* space ID */ + hid_t tid = -1; /* type ID */ unsigned int i; trav_table_t *travt = NULL; int ok = 1; @@ -74,20 +75,20 @@ h5repack_verify(const char *out_fname, pack_opt_t *options) *------------------------------------------------------------------------- */ if((did = H5Dopen2(fidout, name, H5P_DEFAULT)) < 0) - goto error; + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dopen2 failed"); if((sid = H5Dget_space(did)) < 0) - goto error; + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dget_space failed"); if((pid = H5Dget_create_plist(did)) < 0) - goto error; + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dget_create_plist failed"); if((tid = H5Dget_type(did)) < 0) - goto error; + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dget_type failed"); /*------------------------------------------------------------------------- * filter check *------------------------------------------------------------------------- */ if(verify_filters(pid, tid, obj->nfilters, obj->filter) <= 0) - ok = 0; + ok = 0; /*------------------------------------------------------------------------- @@ -102,13 +103,13 @@ h5repack_verify(const char *out_fname, pack_opt_t *options) *------------------------------------------------------------------------- */ if(H5Pclose(pid) < 0) - goto error; + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed"); if (H5Sclose(sid) < 0) - goto error; + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Sclose failed"); if (H5Dclose(did) < 0) - goto error; + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dclose failed"); if (H5Tclose(tid) < 0) - goto error; + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Tclose failed"); } @@ -126,7 +127,7 @@ h5repack_verify(const char *out_fname, pack_opt_t *options) /* get the list of objects in the file */ if(h5trav_gettable(fidout, travt) < 0) - goto error; + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "h5trav_gettable failed"); for(i = 0; i < travt->nobjs; i++) { @@ -140,13 +141,13 @@ h5repack_verify(const char *out_fname, pack_opt_t *options) *------------------------------------------------------------------------- */ if((did = H5Dopen2(fidout, name, H5P_DEFAULT)) < 0) - goto error; + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dopen2 failed"); if((sid = H5Dget_space(did)) < 0) - goto error; + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dget_space failed"); if((pid = H5Dget_create_plist(did)) < 0) - goto error; + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dget_create_plist failed"); if((tid = H5Dget_type(did)) < 0) - goto error; + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dget_type failed"); /*------------------------------------------------------------------------- * filter check @@ -154,7 +155,6 @@ h5repack_verify(const char *out_fname, pack_opt_t *options) */ if(options->all_filter == 1) { - if(verify_filters(pid, tid, options->n_filter_g, options->filter_g) <= 0) ok = 0; } @@ -166,6 +166,7 @@ h5repack_verify(const char *out_fname, pack_opt_t *options) if(options->all_layout == 1) { pack_info_t pack; + init_packobject(&pack); pack.layout = options->layout_g; pack.chunk = options->chunk_g; @@ -179,13 +180,13 @@ h5repack_verify(const char *out_fname, pack_opt_t *options) *------------------------------------------------------------------------- */ if (H5Pclose(pid) < 0) - goto error; + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed"); if (H5Sclose(sid) < 0) - goto error; + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Sclose failed"); if (H5Dclose(did) < 0) - goto error; + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dclose failed"); if (H5Tclose(tid) < 0) - goto error; + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Tclose failed"); } /* if */ } /* i */ @@ -200,11 +201,11 @@ h5repack_verify(const char *out_fname, pack_opt_t *options) */ if (H5Fclose(fidout) < 0) - goto error; + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Fclose failed"); return ok; -error: +done: H5E_BEGIN_TRY { H5Pclose(pid); H5Sclose(sid); @@ -213,7 +214,8 @@ error: if (travt) trav_table_free(travt); } H5E_END_TRY; - return -1; + + return ret_value; } /* h5repack_verify() */ @@ -291,6 +293,7 @@ int verify_layout(hid_t pid, int h5repack_cmp_pl(const char *fname1, const char *fname2) { + int ret_value = 0; /*no need to LEAVE() on ERROR: HERR_INIT(int, SUCCEED) */ hid_t fid1=-1; /* file ID */ hid_t fid2=-1; /* file ID */ hid_t dset1=-1; /* dataset ID */ @@ -315,12 +318,12 @@ int h5repack_cmp_pl(const char *fname1, { /* Open the files */ - if ((fid1=H5Fopen(fname1,H5F_ACC_RDONLY,H5P_DEFAULT)) < 0 ) + if ((fid1 = H5Fopen(fname1,H5F_ACC_RDONLY,H5P_DEFAULT)) < 0 ) { error_msg("<%s>: %s\n", fname1, H5FOPENERROR ); return -1; } - if ((fid2=H5Fopen(fname2,H5F_ACC_RDONLY,H5P_DEFAULT)) < 0 ) + if ((fid2 = H5Fopen(fname2,H5F_ACC_RDONLY,H5P_DEFAULT)) < 0 ) { error_msg("<%s>: %s\n", fname2, H5FOPENERROR ); H5Fclose(fid1); @@ -335,7 +338,7 @@ int h5repack_cmp_pl(const char *fname1, */ trav_table_init(&trav); if(h5trav_gettable(fid1, trav) < 0) - goto error; + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "h5trav_gettable failed"); /*------------------------------------------------------------------------- * traverse the suppplied object list @@ -348,31 +351,30 @@ int h5repack_cmp_pl(const char *fname1, { if ((gid = H5Gopen2(fid1, trav->objs[i].name, H5P_DEFAULT)) < 0) - goto error; + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Gopen2 failed"); if ((gcplid = H5Gget_create_plist(gid)) < 0) - goto error; + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Gget_create_plist failed"); if (H5Pget_link_creation_order(gcplid, &crt_order_flag1) < 0) - goto error; + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pget_link_creation_order failed"); if (H5Pclose(gcplid) < 0) - goto error; + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed"); if (H5Gclose(gid) < 0) - goto error; + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Gclose failed"); if ((gid = H5Gopen2(fid2, trav->objs[i].name, H5P_DEFAULT)) < 0) - goto error; + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Gopen2 failed"); if ((gcplid = H5Gget_create_plist(gid)) < 0) - goto error; + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Gget_create_plist failed"); if (H5Pget_link_creation_order(gcplid, &crt_order_flag2) < 0) - goto error; + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pget_link_creation_order failed"); if (H5Pclose(gcplid) < 0) - goto error; + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed"); if (H5Gclose(gid) < 0) - goto error; + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Gclose failed"); - if ( crt_order_flag1 != crt_order_flag2 ) - { + if (crt_order_flag1 != crt_order_flag2) { error_msg("property lists for <%s> are different\n",trav->objs[i].name); - goto error; + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "property lists failed"); } } @@ -382,25 +384,24 @@ int h5repack_cmp_pl(const char *fname1, else if(trav->objs[i].type == H5TRAV_TYPE_DATASET) { if((dset1 = H5Dopen2(fid1, trav->objs[i].name, H5P_DEFAULT)) < 0) - goto error; + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dopen2 failed"); if((dset2 = H5Dopen2(fid2, trav->objs[i].name, H5P_DEFAULT)) < 0) - goto error; + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dopen2 failed"); if((dcpl1 = H5Dget_create_plist(dset1)) < 0) - goto error; + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dget_create_plist failed"); if((dcpl2 = H5Dget_create_plist(dset2)) < 0) - goto error; + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dget_create_plist failed"); /*------------------------------------------------------------------------- * compare the property lists *------------------------------------------------------------------------- */ if((ret = H5Pequal(dcpl1, dcpl2)) < 0) - goto error; + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pequal failed"); - if(ret == 0) - { + if(ret == 0) { error_msg("property lists for <%s> are different\n",trav->objs[i].name); - goto error; + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "property lists failed"); } /*------------------------------------------------------------------------- @@ -408,13 +409,13 @@ int h5repack_cmp_pl(const char *fname1, *------------------------------------------------------------------------- */ if(H5Pclose(dcpl1) < 0) - goto error; + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed"); if(H5Pclose(dcpl2) < 0) - goto error; + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed"); if(H5Dclose(dset1) < 0) - goto error; + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dclose failed"); if(H5Dclose(dset2) < 0) - goto error; + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dclose failed"); } /*if*/ } /*i*/ @@ -432,14 +433,14 @@ int h5repack_cmp_pl(const char *fname1, H5Fclose(fid1); H5Fclose(fid2); - return ret; - /*------------------------------------------------------------------------- - * error - *------------------------------------------------------------------------- - */ + return ret; -error: +/*------------------------------------------------------------------------- +* error +*------------------------------------------------------------------------- +*/ +done: H5E_BEGIN_TRY { H5Pclose(dcpl1); @@ -452,8 +453,8 @@ error: H5Gclose(gid); trav_table_free(trav); } H5E_END_TRY; - return -1; + return ret_value; } @@ -522,100 +523,71 @@ int verify_filters(hid_t pid, hid_t tid, int nfilters, filter_info_t *filter) switch (filtn) { - case H5Z_FILTER_NONE: - break; - - case H5Z_FILTER_SHUFFLE: - - /* 1 private client value is returned by DCPL */ - if ( cd_nelmts != H5Z_SHUFFLE_TOTAL_NPARMS && filter[i].cd_nelmts != H5Z_SHUFFLE_USER_NPARMS ) - return 0; - - /* get dataset's type size */ - if((size = H5Tget_size(tid)) <= 0) - return -1; - - /* the private client value holds the dataset's type size */ - if ( size != cd_values[0] ) - return 0; - - + case H5Z_FILTER_NONE: break; - case H5Z_FILTER_SZIP: - - /* 4 private client values are returned by DCPL */ - if ( cd_nelmts != H5Z_SZIP_TOTAL_NPARMS && filter[i].cd_nelmts != H5Z_SZIP_USER_NPARMS ) - return 0; - - /* "User" parameter for pixels-per-block (index 1) */ - if ( cd_values[H5Z_SZIP_PARM_PPB] != filter[i].cd_values[H5Z_SZIP_PARM_PPB] ) - return 0; - - - break; - - case H5Z_FILTER_NBIT: - - /* only client data values number of values checked */ - if ( H5Z_NBIT_USER_NPARMS != filter[i].cd_nelmts) - return 0; - - - - break; + case H5Z_FILTER_SHUFFLE: + /* 1 private client value is returned by DCPL */ + if ( cd_nelmts != H5Z_SHUFFLE_TOTAL_NPARMS && filter[i].cd_nelmts != H5Z_SHUFFLE_USER_NPARMS ) + return 0; - case H5Z_FILTER_SCALEOFFSET: + /* get dataset's type size */ + if((size = H5Tget_size(tid)) <= 0) + return -1; - /* only client data values checked */ - for( j = 0; j < H5Z_SCALEOFFSET_USER_NPARMS; j++) - { - if (cd_values[j] != filter[i].cd_values[j]) - { + /* the private client value holds the dataset's type size */ + if ( size != cd_values[0] ) return 0; - } - - } + break; - break; + case H5Z_FILTER_SZIP: + /* 4 private client values are returned by DCPL */ + if ( cd_nelmts != H5Z_SZIP_TOTAL_NPARMS && filter[i].cd_nelmts != H5Z_SZIP_USER_NPARMS ) + return 0; - /* for these filters values must match, no local values set in DCPL */ - case H5Z_FILTER_FLETCHER32: - case H5Z_FILTER_DEFLATE: + /* "User" parameter for pixels-per-block (index 1) */ + if ( cd_values[H5Z_SZIP_PARM_PPB] != filter[i].cd_values[H5Z_SZIP_PARM_PPB] ) + return 0; - if ( cd_nelmts != filter[i].cd_nelmts) - return 0; + break; - for( j = 0; j < cd_nelmts; j++) - { - if (cd_values[j] != filter[i].cd_values[j]) - { + case H5Z_FILTER_NBIT: + /* only client data values number of values checked */ + if ( H5Z_NBIT_USER_NPARMS != filter[i].cd_nelmts) return 0; - } + break; - } + case H5Z_FILTER_SCALEOFFSET: + /* only client data values checked */ + for( j = 0; j < H5Z_SCALEOFFSET_USER_NPARMS; j++) + if (cd_values[j] != filter[i].cd_values[j]) + return 0; + break; + /* for these filters values must match, no local values set in DCPL */ + case H5Z_FILTER_FLETCHER32: + case H5Z_FILTER_DEFLATE: + if ( cd_nelmts != filter[i].cd_nelmts) + return 0; - break; + for( j = 0; j < cd_nelmts; j++) + if (cd_values[j] != filter[i].cd_values[j]) + return 0; - default: - if ( cd_nelmts != filter[i].cd_nelmts) - return 0; + break; - for( j = 0; j < cd_nelmts; j++) - { - if (cd_values[j] != filter[i].cd_values[j]) - { - return 0; - } + default: + if ( cd_nelmts != filter[i].cd_nelmts) + return 0; - } - break; + for( j = 0; j < cd_nelmts; j++) + if (cd_values[j] != filter[i].cd_values[j]) + return 0; + break; } /* switch */ - } return 1; diff --git a/tools/h5repack/h5repacktst.c b/tools/h5repack/h5repacktst.c index f49e587..0d43576 100644 --- a/tools/h5repack/h5repacktst.c +++ b/tools/h5repack/h5repacktst.c @@ -1545,6 +1545,8 @@ int main (void) puts("All h5repack tests passed."); + h5tools_close(); + return 0; error: @@ -3361,7 +3363,7 @@ make_userblock(void) /* Initialize userblock data */ for(u = 0; u < USERBLOCK_SIZE; u++) - ub[u] = 'a' + (char)(u % 26); + ub[u] = (char)('a' + (char)(u % 26)); /* Re-open HDF5 file, as "plain" file */ if((fd = HDopen(FNAME16, O_WRONLY, 0644)) < 0) @@ -3474,7 +3476,7 @@ make_userblock_file(void) /* initialize userblock data */ for(u = 0; u < USERBLOCK_SIZE; u++) - ub[u] = 'a' + (char)(u % 26); + ub[u] = (char)('a' + (char)(u % 26)); /* open file */ if((fd = HDopen(FNAME_UB,O_WRONLY|O_CREAT|O_TRUNC, 0644 )) < 0) @@ -3531,7 +3533,8 @@ int write_dset_in(hid_t loc_id, hid_t sid=-1; hid_t tid=-1; hid_t pid=-1; - int val, i, j, k, n; + unsigned i, j; + int val, k, n; float f; /* create 1D attributes with dimension [2], 2 elements */ @@ -3586,13 +3589,10 @@ int write_dset_in(hid_t loc_id, */ - if (make_diffs) - { - for (i=0; i<2; i++) - for (j=0; j<2; j++) - { - buf1[i][j]='z'; - } + if(make_diffs) { + for(i = 0; i < 2; i++) + for(j = 0; j < 2; j++) + buf1[i][j] = 'z'; } @@ -3615,10 +3615,9 @@ int write_dset_in(hid_t loc_id, *------------------------------------------------------------------------- */ - if (make_diffs) - { - for (i=0; i<2; i++) - buf2[i]=buf2[1]=0; + if(make_diffs) { + for(i = 0; i < 2; i++) + buf2[i] = buf2[1] = 0; } if ((tid = H5Tcopy(H5T_STD_B8LE)) < 0) @@ -3633,11 +3632,10 @@ int write_dset_in(hid_t loc_id, *------------------------------------------------------------------------- */ - if (make_diffs) - { - for (i=0; i<2; i++) - { - buf3[i].a=0; buf3[i].b=0; + if(make_diffs) { + for(i = 0; i < 2; i++) { + buf3[i].a = 0; + buf3[i].b = 0; } } @@ -3656,12 +3654,9 @@ int write_dset_in(hid_t loc_id, */ - if (make_diffs) - { - for (i=0; i<2; i++) - { - buf45[i]=GREEN; - } + if(make_diffs) { + for(i = 0; i < 2; i++) + buf45[i] = GREEN; } if ((tid = H5Tcreate (H5T_COMPOUND, sizeof(s_t))) < 0) @@ -3753,13 +3748,10 @@ int write_dset_in(hid_t loc_id, *------------------------------------------------------------------------- */ - if (make_diffs) - { - for (i=0; i<2; i++) - for (j=0; j<3; j++) - { - buf6[i][j]=0; - } + if(make_diffs) { + for(i = 0; i < 2; i++) + for(j = 0; j < 3; j++) + buf6[i][j] = 0; } if ((tid = H5Tarray_create2(H5T_NATIVE_INT, 1, dimarray)) < 0) @@ -3820,12 +3812,10 @@ int write_dset_in(hid_t loc_id, *------------------------------------------------------------------------- */ - if (make_diffs) - { - for (i=0; i<2; i++) - { - buf7[i]=0; - buf8[i]=0; + if(make_diffs) { + for(i = 0; i < 2; i++) { + buf7[i] = 0; + buf8[i] = 0; } } @@ -3948,16 +3938,13 @@ int write_dset_in(hid_t loc_id, /* Allocate and initialize VL dataset to write */ n = 0; - for(i = 0; i < 3; i++) - { - for(j = 0; j < 2; j++) - { - int l; + for(i = 0; i < 3; i++) { + for(j = 0; j < 2; j++) { + unsigned l; buf52[i][j].p = HDmalloc((i + 1) * sizeof(int)); buf52[i][j].len = (size_t)(i + 1); - for(l = 0; l < i + 1; l++) - { + for(l = 0; l < i + 1; l++) { if(make_diffs) ((int *)buf52[i][j].p)[l] = 0; else @@ -4068,11 +4055,13 @@ int write_dset_in(hid_t loc_id, n=1; - for (i = 0; i < 4; i++) { - for (j = 0; j < 3; j++) { - for (k = 0; k < 2; k++) { - if (make_diffs) buf23[i][j][k]=0; - else buf23[i][j][k]=n++; + for(i = 0; i < 4; i++) { + for(j = 0; j < 3; j++) { + for(k = 0; k < 2; k++) { + if(make_diffs) + buf23[i][j][k] = 0; + else + buf23[i][j][k] = (char)(n++); } } } @@ -4104,16 +4093,16 @@ int write_dset_in(hid_t loc_id, */ n=1; - for (i = 0; i < 4; i++) { - for (j = 0; j < 3; j++) { - for (k = 0; k < 2; k++) { - if (make_diffs) { - buf33[i][j][k].a=0; - buf33[i][j][k].b=0; + for(i = 0; i < 4; i++) { + for(j = 0; j < 3; j++) { + for(k = 0; k < 2; k++) { + if(make_diffs) { + buf33[i][j][k].a = 0; + buf33[i][j][k].b = 0; } else { - buf33[i][j][k].a=n++; - buf33[i][j][k].b=n++; + buf33[i][j][k].a = (char)(n++); + buf33[i][j][k].b = n++; } } } @@ -4167,18 +4156,14 @@ int write_dset_in(hid_t loc_id, /* Allocate and initialize VL dataset to write */ n = 0; - for(i = 0; i < 4; i++) - { - for(j = 0; j < 3; j++) - { - for(k = 0; k < 2; k++) - { - int l; + for(i = 0; i < 4; i++) { + for(j = 0; j < 3; j++) { + for(k = 0; k < 2; k++) { + unsigned l; buf53[i][j][k].p = HDmalloc((i + 1) * sizeof(int)); buf53[i][j][k].len = (size_t)(i + 1); - for(l = 0; l < i + 1; l++) - { + for(l = 0; l < i + 1; l++) { if(make_diffs) ((int *)buf53[i][j][k].p)[l] = 0; else @@ -4214,10 +4199,8 @@ int write_dset_in(hid_t loc_id, n = 1; - for(i = 0; i < 24; i++) - { - for(j = 0; j < (int)dimarray[0]; j++) - { + for(i = 0; i < 24; i++) { + for(j = 0; j < dimarray[0]; j++) { if(make_diffs) buf63[i][j] = 0; else @@ -4256,13 +4239,10 @@ int write_dset_in(hid_t loc_id, if (write_dset(loc_id,3,dims3,"float3D",H5T_NATIVE_FLOAT,buf83) < 0) goto out; - return 0; - out: - H5E_BEGIN_TRY - { + H5E_BEGIN_TRY { H5Pclose(pid); H5Sclose(sid); H5Dclose(did); @@ -4411,7 +4391,8 @@ int write_attr_in(hid_t loc_id, hid_t aid = -1; hid_t sid = -1; hid_t tid = -1; - int val, i, j, k, n; + int val, j, k, n; + unsigned i; float f; /* create 1D attributes with dimension [2], 2 elements */ @@ -4961,16 +4942,17 @@ int write_attr_in(hid_t loc_id, /* Allocate and initialize VL dataset to write */ n=0; - for (i = 0; i < 3; i++) - { - for (j = 0; j < 2; j++) - { - int l; + for(i = 0; i < 3; i++) { + for(j = 0; j < 2; j++) { + unsigned l; + buf52[i][j].p = HDmalloc((i + 1) * sizeof(int)); buf52[i][j].len = (size_t)(i + 1); - for (l = 0; l < i + 1; l++) - if (make_diffs)((int *)buf52[i][j].p)[l] = 0; - else ((int *)buf52[i][j].p)[l] = n++; + for(l = 0; l < i + 1; l++) + if(make_diffs) + ((int *)buf52[i][j].p)[l] = 0; + else + ((int *)buf52[i][j].p)[l] = n++; } } @@ -5179,14 +5161,13 @@ int write_attr_in(hid_t loc_id, */ n=1; - for (i = 0; i < 4; i++) - { - for (j = 0; j < 3; j++) - { - for (k = 0; k < 2; k++) - { - if (make_diffs) buf23[i][j][k]=0; - else buf23[i][j][k]=n++; + for(i = 0; i < 4; i++) { + for(j = 0; j < 3; j++) { + for(k = 0; k < 2; k++) { + if(make_diffs) + buf23[i][j][k] = 0; + else + buf23[i][j][k] = (char)(n++); } } } @@ -5248,21 +5229,16 @@ int write_attr_in(hid_t loc_id, */ n=1; - for (i = 0; i < 4; i++) - { - for (j = 0; j < 3; j++) - { - for (k = 0; k < 2; k++) - { - if (make_diffs) - { - buf33[i][j][k].a=0; - buf33[i][j][k].b=0; + for(i = 0; i < 4; i++) { + for(j = 0; j < 3; j++) { + for(k = 0; k < 2; k++) { + if(make_diffs) { + buf33[i][j][k].a = 0; + buf33[i][j][k].b = 0; } - else - { - buf33[i][j][k].a=n++; - buf33[i][j][k].b=n++; + else { + buf33[i][j][k].a = (char)(n++); + buf33[i][j][k].b = n++; } } } @@ -5431,14 +5407,13 @@ int write_attr_in(hid_t loc_id, { for (k = 0; k < 2; k++) { - int l; + unsigned l; + buf53[i][j][k].p = HDmalloc((i + 1) * sizeof(int)); buf53[i][j][k].len = (size_t)i + 1; for (l = 0; l < i + 1; l++) if (make_diffs) - { ((int *)buf53[i][j][k].p)[l] = 0; - } else ((int *)buf53[i][j][k].p)[l] = n++; } @@ -5562,8 +5537,7 @@ int write_attr_in(hid_t loc_id, return 0; out: - H5E_BEGIN_TRY - { + H5E_BEGIN_TRY { H5Aclose(aid); H5Sclose(sid); H5Tclose(tid); diff --git a/tools/h5repack/testfiles/h5repack-help.txt b/tools/h5repack/testfiles/h5repack-help.txt index ba58bc6..5c30ce8 100644 --- a/tools/h5repack/testfiles/h5repack-help.txt +++ b/tools/h5repack/testfiles/h5repack-help.txt @@ -31,6 +31,9 @@ usage: h5repack [OPTIONS] file1 file2 F - is the shared object header message type, any of <dspace|dtype|fill| pline|attr>. If F is not specified, S applies to all messages + --enable-error-stack Prints messages from the HDF5 error stack as they + occur. + FILT - is a string with the format: <list of objects>:<name of filter>=<filter parameters> diff --git a/tools/h5repack/testfiles/h5repack_filters.h5-gzip_verbose_filters.tst b/tools/h5repack/testfiles/h5repack_filters.h5-gzip_verbose_filters.tst new file mode 100644 index 0000000..36e65b9 --- /dev/null +++ b/tools/h5repack/testfiles/h5repack_filters.h5-gzip_verbose_filters.tst @@ -0,0 +1,13 @@ +Objects to modify layout are... +Objects to apply filter are... + </dset_deflate> with GZIP filter + </dset_deflate>...Found +----------------------------------------- + Type Filter (Compression) Name +----------------------------------------- + group / + dset /dset_all + dset GZIP (0.995:1) /dset_deflate + dset /dset_fletcher32 + dset /dset_nbit + dset /dset_shuffle diff --git a/tools/h5repack/testfiles/h5repack_layout.h5-plugin_zero.tst b/tools/h5repack/testfiles/h5repack_layout.h5-plugin_zero.tst new file mode 100644 index 0000000..0993d5b --- /dev/null +++ b/tools/h5repack/testfiles/h5repack_layout.h5-plugin_zero.tst @@ -0,0 +1,9 @@ +Objects to modify layout are... +Objects to apply filter are... + User Defined 250 +Making file <out-plugin_zero.h5repack_layout.h5>... +----------------------------------------- + Type Filter (Compression) Name +----------------------------------------- + group / +h5repack error: <h5repack_layout.h5>: Could not copy data to: out-plugin_zero.h5repack_layout.h5 diff --git a/tools/lib/h5diff_util.c b/tools/lib/h5diff_util.c index aefd641..ab3e1ce 100644 --- a/tools/lib/h5diff_util.c +++ b/tools/lib/h5diff_util.c @@ -78,8 +78,6 @@ void print_type(hid_t type) { switch (H5Tget_class(type)) { - default: - return; case H5T_INTEGER: if (H5Tequal(type, H5T_STD_I8BE)) { parallel_print("H5T_STD_I8BE"); @@ -160,7 +158,21 @@ void print_type(hid_t type) } break; - }/*switch*/ + case H5T_TIME: + case H5T_STRING: + case H5T_BITFIELD: + case H5T_OPAQUE: + case H5T_COMPOUND: + case H5T_REFERENCE: + case H5T_ENUM: + case H5T_VLEN: + case H5T_ARRAY: + case H5T_NO_CLASS: + case H5T_NCLASSES: + default: + return; + + } /* end switch */ } /*------------------------------------------------------------------------- @@ -179,16 +191,16 @@ diff_basename(const char *name) { size_t i; - if (name==NULL) + if (name == NULL) return NULL; /* Find the end of the base name */ i = HDstrlen(name); - while (i>0 && '/'==name[i-1]) + while (i > 0 && '/' == name[i - 1]) --i; /* Skip backward over base name */ - while (i>0 && '/'!=name[i-1]) + while (i > 0 && '/' != name[i - 1]) --i; return(name+i); @@ -211,14 +223,20 @@ get_type(h5trav_type_t type) switch(type) { case H5TRAV_TYPE_DATASET: return("H5G_DATASET"); + case H5TRAV_TYPE_GROUP: return("H5G_GROUP"); + case H5TRAV_TYPE_NAMED_DATATYPE: return("H5G_TYPE"); + case H5TRAV_TYPE_LINK: return("H5G_LINK"); + case H5TRAV_TYPE_UDLINK: return("H5G_UDLINK"); + + case H5TRAV_TYPE_UNKNOWN: default: return("unknown type"); } @@ -242,13 +260,22 @@ get_sign(H5T_sign_t sign) { switch (sign) { - default: - return("H5T_SGN_ERROR"); - case H5T_SGN_NONE: - return("H5T_SGN_NONE"); - case H5T_SGN_2: - return("H5T_SGN_2"); - } + case H5T_SGN_NONE: + return "H5T_SGN_NONE"; + + case H5T_SGN_2: + return "H5T_SGN_2"; + + case H5T_SGN_ERROR: + return "H5T_SGN_ERROR"; + + case H5T_NSGN: + return "H5T_NSGN"; + + default: + HDassert(0); + return "unknown sign value"; + } /* end switch */ } @@ -266,34 +293,47 @@ get_sign(H5T_sign_t sign) const char* get_class(H5T_class_t tclass) { - switch (tclass) - { - default: - return("Invalid class"); - case H5T_TIME: - return("H5T_TIME"); - case H5T_INTEGER: - return("H5T_INTEGER"); - case H5T_FLOAT: - return("H5T_FLOAT"); - case H5T_STRING: - return("H5T_STRING"); - case H5T_BITFIELD: - return("H5T_BITFIELD"); - case H5T_OPAQUE: - return("H5T_OPAQUE"); - case H5T_COMPOUND: - return("H5T_COMPOUND"); - case H5T_REFERENCE: - return("H5T_REFERENCE"); - case H5T_ENUM: - return("H5T_ENUM"); - case H5T_VLEN: - return("H5T_VLEN"); - case H5T_ARRAY: - return("H5T_ARRAY"); - } -} + switch (tclass) { + case H5T_TIME: + return("H5T_TIME"); + + case H5T_INTEGER: + return("H5T_INTEGER"); + + case H5T_FLOAT: + return("H5T_FLOAT"); + + case H5T_STRING: + return("H5T_STRING"); + + case H5T_BITFIELD: + return("H5T_BITFIELD"); + + case H5T_OPAQUE: + return("H5T_OPAQUE"); + + case H5T_COMPOUND: + return("H5T_COMPOUND"); + + case H5T_REFERENCE: + return("H5T_REFERENCE"); + + case H5T_ENUM: + return("H5T_ENUM"); + + case H5T_VLEN: + return("H5T_VLEN"); + + case H5T_ARRAY: + return("H5T_ARRAY"); + + case H5T_NO_CLASS: + case H5T_NCLASSES: + default: + HDassert(0); + return("Invalid class"); + } /* end switch */ +} /* end get_class() */ /*------------------------------------------------------------------------- * Function: print_found @@ -304,10 +344,10 @@ get_class(H5T_class_t tclass) */ void print_found(hsize_t nfound) { - if(g_Parallel) - parallel_print("%"H5_PRINTF_LL_WIDTH"u differences found\n", (unsigned long long)nfound); - else - HDfprintf(stdout,"%Hu differences found\n",nfound); + if(g_Parallel) + parallel_print("%"H5_PRINTF_LL_WIDTH"u differences found\n", (unsigned long long)nfound); + else + HDfprintf(stdout,"%Hu differences found\n",nfound); } @@ -354,3 +394,4 @@ herr_t match_up_memsize (hid_t f_tid1_id, hid_t f_tid2_id, out: return ret; } + diff --git a/tools/lib/h5tools.c b/tools/lib/h5tools.c index a21dea7..f2123fb 100644 --- a/tools/lib/h5tools.c +++ b/tools/lib/h5tools.c @@ -47,10 +47,11 @@ int region_output; /* region output */ int oid_output; /* oid output */ int data_output; /* data output */ int attr_data_output; /* attribute data output */ -int packed_bits_num; /* number of packed bits to display */ -int packed_data_offset; /* offset of packed bits to display */ -int packed_data_length; /* lengtht of packed bits to display */ +unsigned packed_bits_num; /* number of packed bits to display */ +unsigned packed_data_offset; /* offset of packed bits to display */ +unsigned packed_data_length; /* length of packed bits to display */ unsigned long long packed_data_mask; /* mask in which packed bits to display */ +int enable_error_stack= FALSE; /* re-enable error stack */ /* module-scoped variables */ static int h5tools_init_g; /* if h5tools lib has been initialized */ @@ -805,7 +806,7 @@ h5tools_simple_prefix(FILE *stream, const h5tool_format_t *info, h5tools_str_t prefix; h5tools_str_t str; /*temporary for indentation */ size_t templength = 0; - int i, indentlevel = 0; + unsigned u, indentlevel = 0; if (stream == NULL) return; @@ -827,10 +828,9 @@ h5tools_simple_prefix(FILE *stream, const h5tool_format_t *info, h5tools_str_prefix(&prefix, info, elmtno, ctx->ndims, ctx); /* Write new prefix to output */ - if (ctx->indent_level >= 0) { + if (ctx->indent_level > 0) indentlevel = ctx->indent_level; - } - else { + else /* * This is because sometimes we don't print out all the header * info for the data (like the tattr-2.ddl example). If that happens @@ -838,29 +838,23 @@ h5tools_simple_prefix(FILE *stream, const h5tool_format_t *info, * just print out the default indent levels. */ indentlevel = ctx->default_indent_level; - } /* when printing array indices, print the indentation before the prefix the prefix is printed one indentation level before */ - if (info->pindex) { - for (i = 0; i < indentlevel - 1; i++) { + if (info->pindex) + for (u = 0; u < indentlevel - 1; u++) PUTSTREAM(h5tools_str_fmt(&str, (size_t)0, info->line_indent), stream); - } - } - if (elmtno == 0 && secnum == 0 && info->line_1st) { + if (elmtno == 0 && secnum == 0 && info->line_1st) PUTSTREAM(h5tools_str_fmt(&prefix, (size_t)0, info->line_1st), stream); - } - else if (secnum && info->line_cont) { + else if (secnum && info->line_cont) PUTSTREAM(h5tools_str_fmt(&prefix, (size_t)0, info->line_cont), stream); - } - else { + else PUTSTREAM(h5tools_str_fmt(&prefix, (size_t)0, info->line_pre), stream); - } templength = h5tools_str_len(&prefix); - for (i = 0; i < indentlevel; i++) { + for (u = 0; u < indentlevel; u++) /*we already made the indent for the array indices case */ if (!info->pindex) { PUTSTREAM(h5tools_str_fmt(&prefix, (size_t)0, info->line_indent), stream); @@ -870,7 +864,6 @@ h5tools_simple_prefix(FILE *stream, const h5tool_format_t *info, /*we cannot count the prefix for the array indices case */ templength += h5tools_str_len(&str); } - } ctx->cur_column = ctx->prev_prefix_len = templength; ctx->cur_elmt = 0; @@ -900,7 +893,7 @@ h5tools_region_simple_prefix(FILE *stream, const h5tool_format_t *info, h5tools_str_t prefix; h5tools_str_t str; /*temporary for indentation */ size_t templength = 0; - int i, indentlevel = 0; + unsigned u, indentlevel = 0; if (stream == NULL) return; @@ -922,7 +915,7 @@ h5tools_region_simple_prefix(FILE *stream, const h5tool_format_t *info, h5tools_str_region_prefix(&prefix, info, elmtno, ptdata, ctx->ndims, ctx->p_max_idx, ctx); /* Write new prefix to output */ - if (ctx->indent_level >= 0) + if (ctx->indent_level > 0) indentlevel = ctx->indent_level; else /* @@ -936,20 +929,19 @@ h5tools_region_simple_prefix(FILE *stream, const h5tool_format_t *info, /* when printing array indices, print the indentation before the prefix the prefix is printed one indentation level before */ if (info->pindex) - for (i = 0; i < indentlevel - 1; i++) { + for (u = 0; u < indentlevel - 1; u++) PUTSTREAM(h5tools_str_fmt(&str, (size_t)0, info->line_indent), stream); - } - if (elmtno == 0 && secnum == 0 && info->line_1st) { + if (elmtno == 0 && secnum == 0 && info->line_1st) PUTSTREAM(h5tools_str_fmt(&prefix, (size_t)0, info->line_1st), stream); - } else if (secnum && info->line_cont) { + else if (secnum && info->line_cont) PUTSTREAM(h5tools_str_fmt(&prefix, (size_t)0, info->line_cont), stream); - } else + else PUTSTREAM(h5tools_str_fmt(&prefix, (size_t)0, info->line_pre), stream); templength = h5tools_str_len(&prefix); - for (i = 0; i < indentlevel; i++) { + for (u = 0; u < indentlevel; u++) /*we already made the indent for the array indices case */ if (!info->pindex) { PUTSTREAM(h5tools_str_fmt(&prefix, (size_t)0, info->line_indent), stream); @@ -959,7 +951,6 @@ h5tools_region_simple_prefix(FILE *stream, const h5tool_format_t *info, /*we cannot count the prefix for the array indices case */ templength += h5tools_str_len(&str); } - } ctx->cur_column = ctx->prev_prefix_len = templength; ctx->cur_elmt = 0; @@ -1299,9 +1290,8 @@ init_acc_pos(h5tools_context_t *ctx, hsize_t *dims) HDassert(ctx->ndims); ctx->acc[ctx->ndims - 1] = 1; - for (i = (ctx->ndims - 2); i >= 0; i--) { + for (i = ((int)ctx->ndims - 2); i >= 0; i--) ctx->acc[i] = ctx->acc[i + 1] * dims[i + 1]; - } for (j = 0; j < ctx->ndims; j++) ctx->pos[j] = 0; } @@ -1536,18 +1526,18 @@ CATCH */ int render_bin_output_region_data_blocks(hid_t region_id, FILE *stream, - hid_t container, int ndims, hid_t type_id, hssize_t nblocks, hsize_t *ptdata) + hid_t container, unsigned ndims, hid_t type_id, hsize_t nblocks, hsize_t *ptdata) { hsize_t *dims1 = NULL; hsize_t *start = NULL; hsize_t *count = NULL; hsize_t numelem; hsize_t total_size[H5S_MAX_RANK]; - int jndx; + unsigned jndx; size_t type_size; hid_t mem_space = -1; void *region_buf = NULL; - int blkndx; + hsize_t blkndx; hid_t sid1 = -1; int ret_value = SUCCEED; @@ -1567,7 +1557,7 @@ render_bin_output_region_data_blocks(hid_t region_id, FILE *stream, } /* Create dataspace for reading buffer */ - if((mem_space = H5Screate_simple(ndims, dims1, NULL)) < 0) + if((mem_space = H5Screate_simple((int)ndims, dims1, NULL)) < 0) HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Screate_simple failed"); if((type_size = H5Tget_size(type_id)) == 0) @@ -1640,7 +1630,8 @@ render_bin_output_region_blocks(hid_t region_space, hid_t region_id, hsize_t nblocks; hsize_t alloc_size; hsize_t *ptdata; - int ndims; + int sndims; + unsigned ndims; hid_t dtype = -1; hid_t type_id = -1; @@ -1649,16 +1640,16 @@ render_bin_output_region_blocks(hid_t region_space, hid_t region_id, nblocks = (hsize_t)snblocks; /* Print block information */ - if((ndims = H5Sget_simple_extent_ndims(region_space)) < 0) + if((sndims = H5Sget_simple_extent_ndims(region_space)) < 0) H5E_THROW(FALSE, H5E_tools_min_id_g, "H5Sget_simple_extent_ndims failed"); + ndims = (unsigned)sndims; alloc_size = nblocks * ndims * 2 * sizeof(ptdata[0]); HDassert(alloc_size == (hsize_t) ((size_t) alloc_size)); /*check for overflow*/ if((ptdata = (hsize_t*) HDmalloc((size_t) alloc_size)) == NULL) HGOTO_ERROR(FALSE, H5E_tools_min_id_g, "Could not allocate buffer for ptdata"); - H5_CHECK_OVERFLOW(nblocks, hssize_t, hsize_t); - if(H5Sget_select_hyper_blocklist(region_space, (hsize_t) 0, (hsize_t) nblocks, ptdata) < 0) + if(H5Sget_select_hyper_blocklist(region_space, (hsize_t) 0, nblocks, ptdata) < 0) HGOTO_ERROR(FALSE, H5E_tools_min_id_g, "H5Rget_select_hyper_blocklist failed"); if((dtype = H5Dget_type(region_id)) < 0) @@ -1705,10 +1696,10 @@ render_bin_output_region_blocks(hid_t region_space, hid_t region_id, int render_bin_output_region_data_points(hid_t region_space, hid_t region_id, FILE *stream, hid_t container, - int ndims, hid_t type_id, hssize_t npoints) + unsigned ndims, hid_t type_id, hsize_t npoints) { hsize_t *dims1 = NULL; - int type_size; + size_t type_size; hid_t mem_space = -1; void *region_buf = NULL; int ret_value = SUCCEED; @@ -1763,17 +1754,21 @@ render_bin_output_region_points(hid_t region_space, hid_t region_id, FILE *stream, hid_t container) { HERR_INIT(hbool_t, TRUE) - hssize_t npoints; - int ndims; + hssize_t snpoints; + hsize_t npoints; + int sndims; + unsigned ndims; hid_t dtype = -1; hid_t type_id = -1; - if((npoints = H5Sget_select_elem_npoints(region_space)) <= 0) + if((snpoints = H5Sget_select_elem_npoints(region_space)) <= 0) H5E_THROW(FALSE, H5E_tools_min_id_g, "H5Sget_select_elem_npoints failed"); + npoints = (hsize_t)snpoints; /* Allocate space for the dimension array */ - if((ndims = H5Sget_simple_extent_ndims(region_space)) < 0) + if((sndims = H5Sget_simple_extent_ndims(region_space)) < 0) H5E_THROW(FALSE, H5E_tools_min_id_g, "H5Sget_simple_extent_ndims failed"); + ndims = (unsigned)sndims; if((dtype = H5Dget_type(region_id)) < 0) HGOTO_ERROR(FALSE, H5E_tools_min_id_g, "H5Dget_type failed"); diff --git a/tools/lib/h5tools.h b/tools/lib/h5tools.h index 5c08f33..b548100 100644 --- a/tools/lib/h5tools.h +++ b/tools/lib/h5tools.h @@ -37,10 +37,10 @@ #define H5TOOLS_DUMP_MAX_RANK H5S_MAX_RANK /* Stream macros */ -#define FLUSHSTREAM(S) {if(S != NULL) HDfflush(S);} -#define PRINTSTREAM(S, F, ...) {if(S != NULL) HDfprintf(S, F, __VA_ARGS__);} -#define PRINTVALSTREAM(S, V) {if(S != NULL) HDfprintf(S, V);} -#define PUTSTREAM(X,S) {if(S != NULL) HDfputs(X, S);} +#define FLUSHSTREAM(S) if(S != NULL) HDfflush(S) +#define PRINTSTREAM(S, F, ...) if(S != NULL) HDfprintf(S, F, __VA_ARGS__) +#define PRINTVALSTREAM(S, V) if(S != NULL) HDfprintf(S, V) +#define PUTSTREAM(X,S) do { if(S != NULL) HDfputs(X, S); } while(0) /* * Strings for output - these were duplicated from the h5dump.h @@ -81,7 +81,7 @@ #define FLETCHER32 "CHECKSUM FLETCHER32" #define SZIP "COMPRESSION SZIP" #define NBIT "COMPRESSION NBIT" -#define SCALEOFFSET "COMPRESSION SCALEOFFSET" +#define SCALEOFFSET "COMPRESSION SCALEOFFSET" #define SCALEOFFSET_MINBIT "MIN BITS" #define STORAGE_LAYOUT "STORAGE_LAYOUT" #define CONTIGUOUS "CONTIGUOUS" @@ -275,7 +275,7 @@ typedef struct h5tool_format_t { const char *fmt_float; int ascii; int str_locale; - int str_repeat; + unsigned str_repeat; /* * Fields associated with compound array members. @@ -491,9 +491,9 @@ typedef struct h5tools_context_t { hsize_t size_last_dim; /*the size of the last dimension, *needed so we can break after each *row */ - int indent_level; /*the number of times we need some + unsigned indent_level; /*the number of times we need some *extra indentation */ - int default_indent_level; /*this is used when the indent level gets changed */ + unsigned default_indent_level; /*this is used when the indent level gets changed */ hsize_t acc[H5S_MAX_RANK]; /* accumulator position */ hsize_t pos[H5S_MAX_RANK]; /* matrix position */ hsize_t sm_pos; /* current stripmine element position */ @@ -526,9 +526,9 @@ H5TOOLS_DLLVAR const h5tools_dump_header_t* h5tools_dump_header_format; extern "C" { #endif -H5TOOLS_DLLVAR int packed_bits_num; /* number of packed bits to display */ -H5TOOLS_DLLVAR int packed_data_offset; /* offset of packed bits to display */ -H5TOOLS_DLLVAR int packed_data_length; /* lengtht of packed bits to display */ +H5TOOLS_DLLVAR unsigned packed_bits_num; /* number of packed bits to display */ +H5TOOLS_DLLVAR unsigned packed_data_offset; /* offset of packed bits to display */ +H5TOOLS_DLLVAR unsigned packed_data_length; /* length of packed bits to display */ H5TOOLS_DLLVAR unsigned long long packed_data_mask; /* mask in which packed bits to display */ H5TOOLS_DLLVAR FILE *rawattrstream; /* output stream for raw attribute data */ H5TOOLS_DLLVAR FILE *rawdatastream; /* output stream for raw data */ @@ -542,6 +542,9 @@ H5TOOLS_DLLVAR int oid_output; /* oid output */ H5TOOLS_DLLVAR int data_output; /* data output */ H5TOOLS_DLLVAR int attr_data_output; /* attribute data output */ +/* things to display or which are set via command line parameters */ +H5TOOLS_DLLVAR int enable_error_stack; /* re-enable error stack */ + /* Strings for output */ #define H5_TOOLS_GROUP "GROUP" #define H5_TOOLS_DATASET "DATASET" @@ -550,11 +553,11 @@ H5TOOLS_DLLVAR int attr_data_output; /* attribute data output */ /* Definitions of useful routines */ H5TOOLS_DLL void h5tools_init(void); H5TOOLS_DLL void h5tools_close(void); -H5TOOLS_DLL int h5tools_set_data_output_file(const char *fname, int is_bin); -H5TOOLS_DLL int h5tools_set_attr_output_file(const char *fname, int is_bin); -H5TOOLS_DLL int h5tools_set_input_file(const char *fname, int is_bin); -H5TOOLS_DLL int h5tools_set_output_file(const char *fname, int is_bin); -H5TOOLS_DLL int h5tools_set_error_file(const char *fname, int is_bin); +H5TOOLS_DLL int h5tools_set_data_output_file(const char *fname, int is_bin); +H5TOOLS_DLL int h5tools_set_attr_output_file(const char *fname, int is_bin); +H5TOOLS_DLL int h5tools_set_input_file(const char *fname, int is_bin); +H5TOOLS_DLL int h5tools_set_output_file(const char *fname, int is_bin); +H5TOOLS_DLL int h5tools_set_error_file(const char *fname, int is_bin); H5TOOLS_DLL hid_t h5tools_fopen(const char *fname, unsigned flags, hid_t fapl, const char *driver, char *drivername, size_t drivername_len); H5TOOLS_DLL hid_t h5tools_get_native_type(hid_t type); @@ -574,8 +577,12 @@ H5TOOLS_DLL void h5tools_region_simple_prefix(FILE *stream, const h5tool_form h5tools_context_t *ctx, hsize_t elmtno, hsize_t *ptdata, int secnum); H5TOOLS_DLL int render_bin_output(FILE *stream, hid_t container, hid_t tid, void *_mem, hsize_t nelmts); +H5TOOLS_DLL int render_bin_output_region_data_blocks(hid_t region_id, FILE *stream, + hid_t container, unsigned ndims, hid_t type_id, hsize_t nblocks, hsize_t *ptdata); H5TOOLS_DLL hbool_t render_bin_output_region_blocks(hid_t region_space, hid_t region_id, FILE *stream, hid_t container); +H5TOOLS_DLL int render_bin_output_region_data_points(hid_t region_space, hid_t region_id, + FILE* stream, hid_t container, unsigned ndims, hid_t type_id, hsize_t npoints); H5TOOLS_DLL hbool_t render_bin_output_region_points(hid_t region_space, hid_t region_id, FILE *stream, hid_t container); diff --git a/tools/lib/h5tools_dump.c b/tools/lib/h5tools_dump.c index 2c2a06f..3928837 100644 --- a/tools/lib/h5tools_dump.c +++ b/tools/lib/h5tools_dump.c @@ -198,10 +198,10 @@ hbool_t h5tools_dump_region_data_points(hid_t region_space, hid_t region_id, size_t ncols, hsize_t region_elmt_counter/*element counter*/, hsize_t elmt_counter); -int h5tools_print_region_data_points(hid_t region_space, hid_t region_id, +static int h5tools_print_region_data_points(hid_t region_space, hid_t region_id, FILE *stream, const h5tool_format_t *info, h5tools_context_t *cur_ctx, h5tools_str_t *buffer, size_t ncols, - int ndims, hid_t type_id, hssize_t npoints, hsize_t *ptdata); + unsigned ndims, hid_t type_id, hsize_t npoints, hsize_t *ptdata); hbool_t h5tools_dump_region_data_blocks(hid_t region_space, hid_t region_id, FILE *stream, const h5tool_format_t *info, @@ -634,10 +634,10 @@ h5tools_dump_region_data_blocks(hid_t region_space, hid_t region_id, alloc_size = nblocks * ndims * 2 * sizeof(ptdata[0]); HDassert(alloc_size == (hsize_t) ((size_t) alloc_size)); /*check for overflow*/ if((ptdata = (hsize_t*) HDmalloc((size_t) alloc_size)) == NULL) -{ + { HERROR(H5E_tools_g, H5E_tools_min_id_g, "Could not allocate buffer for ptdata"); HGOTO_DONE(dimension_break); -} + } if(H5Sget_select_hyper_blocklist(region_space, (hsize_t)0, nblocks, ptdata) < 0) HGOTO_ERROR(dimension_break, H5E_tools_min_id_g, "H5Rget_select_hyper_blocklist failed"); @@ -779,20 +779,20 @@ h5tools_dump_region_data_blocks(hid_t region_space, hid_t region_id, * hssize_t npoints is the number of points in the region *------------------------------------------------------------------------- */ -int +static int h5tools_print_region_data_points(hid_t region_space, hid_t region_id, FILE *stream, const h5tool_format_t *info, h5tools_context_t *cur_ctx, h5tools_str_t *buffer, size_t ncols, - int ndims, hid_t type_id, hssize_t npoints, hsize_t *ptdata) + unsigned ndims, hid_t type_id, hsize_t npoints, hsize_t *ptdata) { hbool_t dimension_break = TRUE; hsize_t *dims1 = NULL; hsize_t elmtno; /* elemnt index */ hsize_t curr_pos = 0; hsize_t total_size[H5S_MAX_RANK]; - size_t jndx; + hsize_t jndx; unsigned indx; - int type_size; + size_t type_size; int ret_value = SUCCEED; unsigned int region_flags; /* buffer extent flags */ hid_t mem_space = -1; @@ -807,7 +807,7 @@ h5tools_print_region_data_points(hid_t region_space, hid_t region_id, HDmemset(&ctx, 0, sizeof(ctx)); /* Allocate space for the dimension array */ - if((dims1 = (hsize_t *) HDmalloc(sizeof(hsize_t) * (size_t)ndims)) == NULL) + if((dims1 = (hsize_t *) HDmalloc(sizeof(hsize_t) * ndims)) == NULL) HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "Could not allocate buffer for dims"); dims1[0] = npoints; @@ -841,7 +841,7 @@ h5tools_print_region_data_points(hid_t region_space, hid_t region_id, HERROR(H5E_tools_g, H5E_tools_min_id_g, "H5Sget_simple_extent_dims failed"); /* assume entire data space to be printed */ - for (indx = 0; indx < (size_t) ctx.ndims; indx++) + for (indx = 0; indx < ctx.ndims; indx++) ctx.p_min_idx[indx] = 0; init_acc_pos(&ctx, total_size); @@ -850,13 +850,12 @@ h5tools_print_region_data_points(hid_t region_space, hid_t region_id, if (jndx == npoints - 1) region_flags |= END_OF_DATA; - for (indx = 0; indx < (size_t)ctx.ndims; indx++) + for (indx = 0; indx < ctx.ndims; indx++) ctx.p_max_idx[indx] = cur_ctx->p_max_idx[indx]; ctx.sm_pos = jndx * ndims; - if (ctx.ndims > 0) { - ctx.size_last_dim = (int) (ctx.p_max_idx[ctx.ndims - 1]); - } + if (ctx.ndims > 0) + ctx.size_last_dim = ctx.p_max_idx[ctx.ndims - 1]; else ctx.size_last_dim = 0; @@ -922,11 +921,13 @@ h5tools_dump_region_data_points(hid_t region_space, hid_t region_id, hsize_t elmt_counter) { HERR_INIT(hbool_t, TRUE) hbool_t dimension_break = TRUE; - hssize_t npoints; + hssize_t snpoints; + hsize_t npoints; hsize_t alloc_size; hsize_t *ptdata; - int ndims; - hssize_t indx; + int sndims; + unsigned ndims; + hsize_t indx; hid_t dtype = -1; hid_t type_id = -1; @@ -934,12 +935,14 @@ h5tools_dump_region_data_points(hid_t region_space, hid_t region_id, HDassert(ctx); HDassert(buffer); - if((npoints = H5Sget_select_elem_npoints(region_space)) <= 0) + if((snpoints = H5Sget_select_elem_npoints(region_space)) <= 0) H5E_THROW(dimension_break, H5E_tools_min_id_g, "H5Sget_select_elem_npoints failed"); + npoints = (hsize_t)snpoints; /* Allocate space for the dimension array */ - if((ndims = H5Sget_simple_extent_ndims(region_space)) < 0) + if((sndims = H5Sget_simple_extent_ndims(region_space)) < 0) H5E_THROW(dimension_break, H5E_tools_min_id_g, "H5Sget_simple_extent_ndims failed"); + ndims = (unsigned)sndims; /* Render the region { element begin */ h5tools_str_reset(buffer); @@ -960,12 +963,11 @@ h5tools_dump_region_data_points(hid_t region_space, hid_t region_id, if(NULL == (ptdata = (hsize_t *)HDmalloc((size_t) alloc_size))) HGOTO_ERROR(dimension_break, H5E_tools_min_id_g, "Could not allocate buffer for ptdata"); - H5_CHECK_OVERFLOW(npoints, hssize_t, hsize_t); - if(H5Sget_select_elem_pointlist(region_space, (hsize_t) 0, (hsize_t) npoints, ptdata) < 0) + if(H5Sget_select_elem_pointlist(region_space, (hsize_t) 0, npoints, ptdata) < 0) HGOTO_ERROR(dimension_break, H5E_tools_min_id_g, "H5Sget_select_elem_pointlist failed"); for (indx = 0; indx < npoints; indx++) { - int loop_indx; + unsigned loop_indx; h5tools_str_append(buffer, info->dset_ptformat_pre, indx ? "," OPTIONAL_LINE_BREAK " " : "", (unsigned long) indx); @@ -1249,7 +1251,7 @@ h5tools_print_simple_subset(FILE *stream, const h5tool_format_t *info, h5tools_c H5Dvlen_reclaim(p_type, sm_space, H5P_DEFAULT, sm_buf); if(H5Sclose(sm_space) < 0) - H5E_THROW(H5E_tools_g, H5E_tools_min_id_g, "H5Sclose failed"); + H5E_THROW(FAIL, H5E_tools_min_id_g, "H5Sclose failed"); if(sm_buf) HDfree(sm_buf); sm_buf = NULL; @@ -1333,7 +1335,7 @@ h5tools_display_simple_subset(FILE *stream, const h5tool_format_t *info, h5tools } /* initialize temporary start, count and maximum start */ - for (i = 0; i < (size_t) ctx->ndims; i++) { + for (i = 0; i < ctx->ndims; i++) { temp_start[i] = sset->start.data[i]; temp_count[i] = sset->count.data[i]; temp_block[i] = sset->block.data[i]; @@ -1375,12 +1377,11 @@ h5tools_display_simple_subset(FILE *stream, const h5tool_format_t *info, h5tools if (ctx->ndims > 2) { /* dimension for start */ - current_outer_dim = (ctx->ndims - 2) - 1; + current_outer_dim = (int)(ctx->ndims - 2) - 1; /* set start to original from current_outer_dim up */ - for (i = current_outer_dim + 1; i < ctx->ndims; i++) { + for (i = (size_t)(current_outer_dim + 1); i < ctx->ndims; i++) temp_start[i] = sset->start.data[i]; - } /* increment start dimension */ do { @@ -1472,7 +1473,7 @@ h5tools_dump_simple_subset(FILE *stream, const h5tool_format_t *info, h5tools_co CATCH if(f_space >= 0 && H5Sclose(f_space) < 0) - H5E_THROW(H5E_tools_g, H5E_tools_min_id_g, "H5Sclose failed"); + H5E_THROW(FAIL, H5E_tools_min_id_g, "H5Sclose failed"); return ret_value; } @@ -1500,6 +1501,7 @@ h5tools_dump_simple_dset(FILE *stream, const h5tool_format_t *info, h5tools_cont hid_t f_space = -1; /* file data space */ hsize_t elmtno; /* counter */ size_t i; /* counter */ + int sndims; /* rank of dataspace */ int carry; /* counter carry value */ hsize_t zero[8]; /* vector of zeros */ unsigned int flags; /* buffer extent flags */ @@ -1529,11 +1531,13 @@ h5tools_dump_simple_dset(FILE *stream, const h5tool_format_t *info, h5tools_cont if (f_space == FAIL) H5E_THROW(FAIL, H5E_tools_min_id_g, "H5Dget_space failed"); - ctx->ndims = H5Sget_simple_extent_ndims(f_space); + sndims = H5Sget_simple_extent_ndims(f_space); + if(sndims < 0) + H5E_THROW(FAIL, H5E_tools_min_id_g, "H5Dget_simple_extent_ndims failed"); + ctx->ndims = (unsigned)sndims; - if ((size_t)ctx->ndims > NELMTS(sm_size)) { + if ((size_t)ctx->ndims > NELMTS(sm_size)) H5E_THROW(FAIL, H5E_tools_min_id_g, "ctx->ndims > NELMTS(sm_size) failed"); - } /* Assume entire data space to be printed */ if (ctx->ndims > 0) @@ -1652,9 +1656,9 @@ CATCH done: if(sm_space >= 0 && H5Sclose(sm_space) < 0) - H5E_THROW(H5E_tools_g, H5E_tools_min_id_g, "H5Sclose failed"); + H5E_THROW(FAIL, H5E_tools_min_id_g, "H5Sclose failed"); if(f_space >= 0 && H5Sclose(f_space) < 0) - H5E_THROW(H5E_tools_g, H5E_tools_min_id_g, "H5Sclose failed"); + H5E_THROW(FAIL, H5E_tools_min_id_g, "H5Sclose failed"); return ret_value; } @@ -1675,10 +1679,14 @@ h5tools_dump_simple_mem(FILE *stream, const h5tool_format_t *info, h5tools_conte hid_t type, hid_t space, void *mem) { HERR_INIT(herr_t, SUCCEED) + int sndims; /* rank of dataspace */ unsigned i; /*counters */ hsize_t nelmts; /*total selected elmts */ - ctx->ndims = H5Sget_simple_extent_ndims(space); + sndims = H5Sget_simple_extent_ndims(space); + if(sndims < 0) + H5E_THROW(FAIL, H5E_tools_min_id_g, "H5Dget_simple_extent_ndims failed"); + ctx->ndims = (unsigned)sndims; if ((size_t) ctx->ndims > NELMTS(ctx->p_min_idx)) H5E_THROW(FAIL, H5E_tools_min_id_g, "ctx->ndims > NELMTS(ctx->p_min_idx) failed"); @@ -1696,7 +1704,7 @@ h5tools_dump_simple_mem(FILE *stream, const h5tool_format_t *info, h5tools_conte H5_LEAVE(SUCCEED); /* nothing to print */ if (ctx->ndims > 0) { HDassert(ctx->p_max_idx[ctx->ndims - 1] == (hsize_t) ((int) ctx->p_max_idx[ctx->ndims - 1])); - ctx->size_last_dim = (int) (ctx->p_max_idx[ctx->ndims - 1]); + ctx->size_last_dim = ctx->p_max_idx[ctx->ndims - 1]; } /* end if */ else ctx->size_last_dim = 0; @@ -2583,7 +2591,6 @@ h5tools_print_enum(FILE *stream, h5tools_str_t *buffer, const h5tool_format_t *i unsigned i; unsigned nmembs = 0; /*number of members */ int snmembs; - int nchars; /*number of output characters */ hid_t super = -1; /*enum base integer type */ hid_t native = -1; /*native integer datatype */ H5T_sign_t sign_type; /*sign of value type */ @@ -2650,12 +2657,14 @@ h5tools_print_enum(FILE *stream, h5tools_str_t *buffer, const h5tool_format_t *i /* Print members */ for (i = 0; i < nmembs; i++) { + int nchars; /*number of output characters */ + ctx->need_prefix = TRUE; h5tools_simple_prefix(stream, info, ctx, (hsize_t)0, 0); h5tools_str_reset(buffer); h5tools_str_append(buffer, "\"%s\"", name[i]); - nchars = HDstrlen(name[i]); + nchars = (int)HDstrlen(name[i]); h5tools_str_append(buffer, "%*s ", MAX(0, 16 - nchars), ""); if (native < 0) { @@ -2900,7 +2909,7 @@ h5tools_dump_dcpl(FILE *stream, const h5tool_format_t *info, size_t cd_nelmts; /* filter client number of values */ off_t offset; /* offset of external file */ char f_name[256]; /* filter name */ - char name[256]; /* external file name */ + char name[256]; /* external or virtual file name */ hsize_t chsize[64]; /* chunk size in elements */ hsize_t size; /* size of external file */ hsize_t storage_size; @@ -2942,7 +2951,7 @@ h5tools_dump_dcpl(FILE *stream, const h5tool_format_t *info, for(i = 1; i < rank; i++) h5tools_str_append(&buffer, ", " HSIZE_T_FORMAT, chsize[i]); h5tools_str_append(&buffer, " %s", h5tools_dump_header_format->dataspacedimend); - h5tools_render_element(stream, info, ctx, &buffer, &curr_pos, (size_t)ncols, (hsize_t)0, (hsize_t)0); + h5tools_render_element(stream, info, ctx, &buffer, &curr_pos, (size_t) ncols, (hsize_t) 0, (hsize_t) 0); ctx->need_prefix = TRUE; h5tools_simple_prefix(stream, info, ctx, curr_pos, 0); @@ -2995,8 +3004,7 @@ h5tools_dump_dcpl(FILE *stream, const h5tool_format_t *info, else { h5tools_str_append(&buffer, "SIZE " HSIZE_T_FORMAT, storage_size); } - h5tools_render_element(stream, info, ctx, &buffer, &curr_pos, (size_t)ncols, (hsize_t)0, (hsize_t)0); - + h5tools_render_element(stream, info, ctx, &buffer, &curr_pos, (size_t) ncols, (hsize_t) 0, (hsize_t) 0); ctx->indent_level--; break; case H5D_COMPACT: @@ -3006,15 +3014,14 @@ h5tools_dump_dcpl(FILE *stream, const h5tool_format_t *info, h5tools_str_reset(&buffer); h5tools_str_append(&buffer, "%s", COMPACT); - h5tools_render_element(stream, info, ctx, &buffer, &curr_pos, (size_t)ncols, (hsize_t)0, (hsize_t)0); + h5tools_render_element(stream, info, ctx, &buffer, &curr_pos, (size_t) ncols, (hsize_t) 0, (hsize_t) 0); ctx->need_prefix = TRUE; h5tools_simple_prefix(stream, info, ctx, curr_pos, 0); h5tools_str_reset(&buffer); h5tools_str_append(&buffer, "SIZE " HSIZE_T_FORMAT, storage_size); - h5tools_render_element(stream, info, ctx, &buffer, &curr_pos, (size_t)ncols, (hsize_t)0, (hsize_t)0); - + h5tools_render_element(stream, info, ctx, &buffer, &curr_pos, (size_t) ncols, (hsize_t) 0, (hsize_t) 0); ctx->indent_level--; break; case H5D_CONTIGUOUS: @@ -3034,14 +3041,14 @@ h5tools_dump_dcpl(FILE *stream, const h5tool_format_t *info, h5tools_str_reset(&buffer); h5tools_str_append(&buffer, "%s", CONTIGUOUS); - h5tools_render_element(stream, info, ctx, &buffer, &curr_pos, (size_t)ncols, (hsize_t)0, (hsize_t)0); + h5tools_render_element(stream, info, ctx, &buffer, &curr_pos, (size_t) ncols, (hsize_t) 0, (hsize_t) 0); ctx->need_prefix = TRUE; h5tools_simple_prefix(stream, info, ctx, curr_pos, 0); h5tools_str_reset(&buffer); h5tools_str_append(&buffer, "%s %s", EXTERNAL, BEGIN); - h5tools_render_element(stream, info, ctx, &buffer, &curr_pos, (size_t)ncols, (hsize_t)0, (hsize_t)0); + h5tools_render_element(stream, info, ctx, &buffer, &curr_pos, (size_t) ncols, (hsize_t) 0, (hsize_t) 0); ctx->indent_level++; for (j = 0; j < (unsigned) next; j++) { @@ -3053,7 +3060,7 @@ h5tools_dump_dcpl(FILE *stream, const h5tool_format_t *info, h5tools_str_reset(&buffer); h5tools_str_append(&buffer, "FILENAME %s SIZE " HSIZE_T_FORMAT, name, size); h5tools_str_append(&buffer, " OFFSET %ld", offset); - h5tools_render_element(stream, info, ctx, &buffer, &curr_pos, (size_t)ncols, (hsize_t)0, (hsize_t)0); + h5tools_render_element(stream, info, ctx, &buffer, &curr_pos, (size_t) ncols, (hsize_t) 0, (hsize_t) 0); } ctx->indent_level--; @@ -3072,14 +3079,14 @@ h5tools_dump_dcpl(FILE *stream, const h5tool_format_t *info, h5tools_str_reset(&buffer); h5tools_str_append(&buffer, "%s", CONTIGUOUS); - h5tools_render_element(stream, info, ctx, &buffer, &curr_pos, (size_t)ncols, (hsize_t)0, (hsize_t)0); + h5tools_render_element(stream, info, ctx, &buffer, &curr_pos, (size_t) ncols, (hsize_t) 0, (hsize_t) 0); ctx->need_prefix = TRUE; h5tools_simple_prefix(stream, info, ctx, curr_pos, 0); h5tools_str_reset(&buffer); h5tools_str_append(&buffer,"SIZE " HSIZE_T_FORMAT, storage_size); - h5tools_render_element(stream, info, ctx, &buffer, &curr_pos, (size_t)ncols, (hsize_t)0, (hsize_t)0); + h5tools_render_element(stream, info, ctx, &buffer, &curr_pos, (size_t) ncols, (hsize_t) 0, (hsize_t) 0); ctx->need_prefix = TRUE; h5tools_simple_prefix(stream, info, ctx, curr_pos, 0); @@ -3437,7 +3444,7 @@ h5tools_dump_comment(FILE *stream, const h5tool_format_t *info, if (cmt_bufsize > 0) { comment = (char *)HDmalloc((size_t)(cmt_bufsize+1)); /* new_size including null terminator */ if(comment) { - cmt_bufsize = H5Oget_comment(obj_id, comment, cmt_bufsize); + cmt_bufsize = H5Oget_comment(obj_id, comment, (size_t)cmt_bufsize); if(cmt_bufsize > 0) { comment[cmt_bufsize] = '\0'; /* necessary because null char is not returned */ @@ -3576,49 +3583,39 @@ h5tools_print_dims(h5tools_str_t *buffer, hsize_t *s, int dims) void h5tools_print_packed_bits(h5tools_str_t *buffer, hid_t type) { - int packed_bits_size = 0; - + unsigned packed_bits_size = 0; hid_t n_type = h5tools_get_native_type(type); - if(H5Tget_class(n_type)==H5T_INTEGER) { - if(H5Tequal(n_type, H5T_NATIVE_SCHAR) == TRUE) { + + if(H5Tget_class(n_type) == H5T_INTEGER) { + if(H5Tequal(n_type, H5T_NATIVE_SCHAR) == TRUE) packed_bits_size = 8 * sizeof(char); - } - else if(H5Tequal(n_type, H5T_NATIVE_UCHAR) == TRUE) { + else if(H5Tequal(n_type, H5T_NATIVE_UCHAR) == TRUE) packed_bits_size = 8 * sizeof(unsigned char); - } - else if(H5Tequal(n_type, H5T_NATIVE_SHORT) == TRUE) { + else if(H5Tequal(n_type, H5T_NATIVE_SHORT) == TRUE) packed_bits_size = 8 * sizeof(short); - } - else if(H5Tequal(n_type, H5T_NATIVE_USHORT) == TRUE) { + else if(H5Tequal(n_type, H5T_NATIVE_USHORT) == TRUE) packed_bits_size = 8 * sizeof(unsigned short); - } - else if(H5Tequal(n_type, H5T_NATIVE_INT) == TRUE) { + else if(H5Tequal(n_type, H5T_NATIVE_INT) == TRUE) packed_bits_size = 8 * sizeof(int); - } - else if(H5Tequal(n_type, H5T_NATIVE_UINT) == TRUE) { + else if(H5Tequal(n_type, H5T_NATIVE_UINT) == TRUE) packed_bits_size = 8 * sizeof(unsigned int); - } - else if(H5Tequal(n_type, H5T_NATIVE_LONG) == TRUE) { + else if(H5Tequal(n_type, H5T_NATIVE_LONG) == TRUE) packed_bits_size = 8 * sizeof(long); - } - else if(H5Tequal(n_type, H5T_NATIVE_ULONG) == TRUE) { + else if(H5Tequal(n_type, H5T_NATIVE_ULONG) == TRUE) packed_bits_size = 8 * sizeof(unsigned long); - } - else if(H5Tequal(n_type, H5T_NATIVE_LLONG) == TRUE) { + else if(H5Tequal(n_type, H5T_NATIVE_LLONG) == TRUE) packed_bits_size = 8 * sizeof(long long); - } - else if(H5Tequal(n_type, H5T_NATIVE_ULLONG) == TRUE) { + else if(H5Tequal(n_type, H5T_NATIVE_ULLONG) == TRUE) packed_bits_size = 8 * sizeof(unsigned long long); - } else error_msg("Packed Bit not valid for this datatype"); } - if ((packed_bits_size>0) && (packed_data_offset + packed_data_length) > packed_bits_size) { - error_msg("Packed Bit offset+length value(%d) too large. Max is %d\n", packed_data_offset+packed_data_length, packed_bits_size); + if((packed_bits_size > 0) && (packed_data_offset + packed_data_length) > packed_bits_size) { + error_msg("Packed Bit offset+length value(%u) too large. Max is %d\n", packed_data_offset + packed_data_length, packed_bits_size); packed_data_mask = 0; }; - h5tools_str_append(buffer, "%s %s=%d %s=%d", PACKED_BITS, PACKED_OFFSET, packed_data_offset, PACKED_LENGTH, packed_data_length); + h5tools_str_append(buffer, "%s %s=%u %s=%u", PACKED_BITS, PACKED_OFFSET, packed_data_offset, PACKED_LENGTH, packed_data_length); } /*------------------------------------------------------------------------- diff --git a/tools/lib/h5tools_error.h b/tools/lib/h5tools_error.h index ae549fd..749157e 100644 --- a/tools/lib/h5tools_error.h +++ b/tools/lib/h5tools_error.h @@ -98,7 +98,7 @@ H5TOOLS_DLLVAR hid_t H5E_tools_min_id_g; * to the `catch_except' label, if we're not already past it. */ #define H5E_THROW(fail_value, min_id, str) { \ - HERROR(H5E_tools_g, min_id, str); \ + H5Epush2(H5tools_ERR_STACK_g, __FILE__, FUNC, __LINE__, H5tools_ERR_CLS_g, H5E_tools_g, min_id, str); \ H5_LEAVE(fail_value) \ } diff --git a/tools/lib/h5tools_filters.c b/tools/lib/h5tools_filters.c index ccdba26..0b42124 100644 --- a/tools/lib/h5tools_filters.c +++ b/tools/lib/h5tools_filters.c @@ -13,7 +13,7 @@ * access to either file, you may request a copy from help@hdfgroup.org. * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ -#include "hdf5.h" +#include "H5private.h" #include "h5tools.h" /*------------------------------------------------------------------------- @@ -151,54 +151,60 @@ int h5tools_can_encode(H5Z_filter_t filtn) { switch (filtn) { /* user defined filter */ default: - return 0; + return 0; case H5Z_FILTER_DEFLATE: #ifndef H5_HAVE_FILTER_DEFLATE - return 0; + return 0; #endif - break; + break; + case H5Z_FILTER_SZIP: #ifndef H5_HAVE_FILTER_SZIP - return 0; + return 0; #else { - unsigned int filter_config_flags; + unsigned int filter_config_flags; - if (H5Zget_filter_info(filtn, &filter_config_flags) < 0) - return -1; - if ((filter_config_flags - & (H5Z_FILTER_CONFIG_ENCODE_ENABLED | H5Z_FILTER_CONFIG_DECODE_ENABLED)) == 0) { - /* filter present but neither encode nor decode is supported (???) */ - return -1; - } - else if ((filter_config_flags - & (H5Z_FILTER_CONFIG_ENCODE_ENABLED | H5Z_FILTER_CONFIG_DECODE_ENABLED)) == H5Z_FILTER_CONFIG_DECODE_ENABLED) { - /* decoder only: read but not write */ - return 0; - } - else if ((filter_config_flags - & (H5Z_FILTER_CONFIG_ENCODE_ENABLED | H5Z_FILTER_CONFIG_DECODE_ENABLED)) == H5Z_FILTER_CONFIG_ENCODE_ENABLED) { - /* encoder only: write but not read (???) */ - return -1; - } - else if ((filter_config_flags - & (H5Z_FILTER_CONFIG_ENCODE_ENABLED | H5Z_FILTER_CONFIG_DECODE_ENABLED)) - == (H5Z_FILTER_CONFIG_ENCODE_ENABLED | H5Z_FILTER_CONFIG_DECODE_ENABLED)) { - return 1; - } + if (H5Zget_filter_info(filtn, &filter_config_flags) < 0) + return -1; + if ((filter_config_flags + & (H5Z_FILTER_CONFIG_ENCODE_ENABLED | H5Z_FILTER_CONFIG_DECODE_ENABLED)) == 0) { + /* filter present but neither encode nor decode is supported (???) */ + return -1; + } + else if ((filter_config_flags + & (H5Z_FILTER_CONFIG_ENCODE_ENABLED | H5Z_FILTER_CONFIG_DECODE_ENABLED)) == H5Z_FILTER_CONFIG_DECODE_ENABLED) { + /* decoder only: read but not write */ + return 0; + } + else if ((filter_config_flags + & (H5Z_FILTER_CONFIG_ENCODE_ENABLED | H5Z_FILTER_CONFIG_DECODE_ENABLED)) == H5Z_FILTER_CONFIG_ENCODE_ENABLED) { + /* encoder only: write but not read (???) */ + return -1; + } + else if ((filter_config_flags + & (H5Z_FILTER_CONFIG_ENCODE_ENABLED | H5Z_FILTER_CONFIG_DECODE_ENABLED)) + == (H5Z_FILTER_CONFIG_ENCODE_ENABLED | H5Z_FILTER_CONFIG_DECODE_ENABLED)) { + return 1; + } } #endif - break; + break; + case H5Z_FILTER_SHUFFLE: - break; + break; + case H5Z_FILTER_FLETCHER32: - break; + break; + case H5Z_FILTER_NBIT: - break; + break; + case H5Z_FILTER_SCALEOFFSET: - break; - }/*switch*/ + break; + }/*switch*/ - return 1; + return 1; } + diff --git a/tools/lib/h5tools_ref.c b/tools/lib/h5tools_ref.c index 3a4183b..8c869c8 100644 --- a/tools/lib/h5tools_ref.c +++ b/tools/lib/h5tools_ref.c @@ -39,7 +39,7 @@ typedef struct { haddr_t objno; /* Object ID (i.e. address) */ - const char *path; /* Object path */ + char *path; /* Object path */ } ref_path_node_t; static H5SL_t *ref_path_table = NULL; /* the "table" (implemented with a skip list) */ @@ -65,7 +65,7 @@ free_ref_path_info(void *item, void H5_ATTR_UNUSED *key, void H5_ATTR_UNUSED *op { ref_path_node_t *node = (ref_path_node_t *)item; - HDfree((void *)node->path); + HDfree(node->path); HDfree(node); return(0); @@ -218,7 +218,7 @@ ref_path_table_put(const char *path, haddr_t objno) HDassert(ref_path_table); HDassert(path); - if((new_node = HDmalloc(sizeof(ref_path_node_t))) == NULL) + if((new_node = (ref_path_node_t *)HDmalloc(sizeof(ref_path_node_t))) == NULL) return(-1); new_node->objno = objno; @@ -300,7 +300,7 @@ lookup_ref_path(haddr_t ref) if(ref_path_table == NULL) init_ref_path_table(); - node = H5SL_search(ref_path_table, &ref); + node = (ref_path_node_t *)H5SL_search(ref_path_table, &ref); return(node ? node->path : NULL); } diff --git a/tools/lib/h5tools_str.c b/tools/lib/h5tools_str.c index a92568a..7f65c91 100644 --- a/tools/lib/h5tools_str.c +++ b/tools/lib/h5tools_str.c @@ -126,14 +126,12 @@ h5tools_str_append(h5tools_str_t *str/*in,out*/, const char *fmt, ...) va_list ap; /* Make sure we have some memory into which to print */ - if (!str->s || str->nalloc <= 0) { + if (!str->s || str->nalloc <= 0) h5tools_str_reset(str); - } - if (HDstrlen(fmt) == 0) { + if (HDstrlen(fmt) == 0) /* nothing to print */ return str->s; - } /* Format the arguments and append to the value already in `str' */ while (1) { @@ -156,19 +154,18 @@ h5tools_str_append(h5tools_str_t *str/*in,out*/, const char *fmt, ...) * to lack of buffer size, so try one more time after realloc more * buffer size before return NULL. */ - if (nchars < 0) { + if (nchars < 0) /* failure, such as bad format */ return NULL; - } - if (nchars < 0 || (size_t) nchars >= avail || (0 == nchars && (HDstrcmp(fmt, "%s")))) { + if ((size_t) nchars >= avail || (0 == nchars && (HDstrcmp(fmt, "%s")))) { /* Truncation return value as documented by C99, or zero return value with either of the * following conditions, each of which indicates that the proper C99 return value probably * should have been positive when the format string is * something other than "%s" * Alocate at least twice as much space and try again. */ - size_t newsize = MAX(str->len + nchars + 1, 2 * str->nalloc); + size_t newsize = MAX(str->len + (size_t)nchars + 1, 2 * str->nalloc); HDassert(newsize > str->nalloc); /*overflow*/ str->s = (char*)HDrealloc(str->s, newsize); HDassert(str->s); @@ -176,7 +173,7 @@ h5tools_str_append(h5tools_str_t *str/*in,out*/, const char *fmt, ...) } else { /* Success */ - str->len += nchars; + str->len += (size_t)nchars; break; } } @@ -267,6 +264,9 @@ h5tools_str_fmt(h5tools_str_t *str/*in,out*/, size_t start, const char *fmt) { char _temp[1024], *temp = _temp; + HDassert(str); + HDassert(fmt); + /* If the format string is simply "%s" then don't bother doing anything */ if (!HDstrcmp(fmt, "%s")) return str->s; @@ -413,58 +413,57 @@ h5tools_str_region_prefix(h5tools_str_t *str, const h5tool_format_t *info, } /*------------------------------------------------------------------------- - * Function: h5tools_str_dump_region_blocks + * Function: h5tools_str_dump_space_blocks * - * Purpose: Prints information about a dataspace region by appending + * Purpose: Prints information about a dataspace selection by appending * the information to the specified string. * * Return: none * * In/Out: - * h5tools_context_t *ctx * h5tools_str_t *str *------------------------------------------------------------------------- */ void -h5tools_str_dump_region_blocks(h5tools_str_t *str, hid_t region, +h5tools_str_dump_space_blocks(h5tools_str_t *str, hid_t rspace, const h5tool_format_t *info) { - hssize_t nblocks; - hsize_t alloc_size; - hsize_t *ptdata; - int ndims = H5Sget_simple_extent_ndims(region); + hssize_t snblocks; /* - * This function fails if the region does not have blocks. + * This function fails if the rspace does not have blocks. */ H5E_BEGIN_TRY { - nblocks = H5Sget_select_hyper_nblocks(region); + snblocks = H5Sget_select_hyper_nblocks(rspace); } H5E_END_TRY; /* Print block information */ - if (nblocks > 0) { - int i; - + if (snblocks > 0) { + hsize_t nblocks; + hsize_t *ptdata; + hsize_t alloc_size; + unsigned ndims = (unsigned)H5Sget_simple_extent_ndims(rspace); + hsize_t u; + + nblocks = (hsize_t)snblocks; alloc_size = nblocks * ndims * 2 * sizeof(ptdata[0]); HDassert(alloc_size == (hsize_t) ((size_t) alloc_size)); /*check for overflow*/ ptdata = (hsize_t *)HDmalloc((size_t) alloc_size); - H5_CHECK_OVERFLOW(nblocks, hssize_t, hsize_t); - H5Sget_select_hyper_blocklist(region, (hsize_t)0, (hsize_t)nblocks, ptdata); + H5Sget_select_hyper_blocklist(rspace, (hsize_t)0, nblocks, ptdata); - for (i = 0; i < nblocks; i++) { - int j; + for (u = 0; u < nblocks; u++) { + unsigned v; - h5tools_str_append(str, info->dset_blockformat_pre, i ? "," OPTIONAL_LINE_BREAK " " : "", - (unsigned long)i); + h5tools_str_append(str, info->dset_blockformat_pre, u ? "," OPTIONAL_LINE_BREAK " " : "", (unsigned long)u); /* Start coordinates and opposite corner */ - for (j = 0; j < ndims; j++) - h5tools_str_append(str, "%s" HSIZE_T_FORMAT, j ? "," : "(", - ptdata[i * 2 * ndims + j]); + for (v = 0; v < ndims; v++) + h5tools_str_append(str, "%s" HSIZE_T_FORMAT, v ? "," : "(", + ptdata[u * 2 * ndims + v]); - for (j = 0; j < ndims; j++) - h5tools_str_append(str, "%s" HSIZE_T_FORMAT, j ? "," : ")-(", - ptdata[i * 2 * ndims + j + ndims]); + for (v = 0; v < ndims; v++) + h5tools_str_append(str, "%s" HSIZE_T_FORMAT, v ? "," : ")-(", + ptdata[u * 2 * ndims + v + ndims]); h5tools_str_append(str, ")"); } @@ -474,53 +473,53 @@ h5tools_str_dump_region_blocks(h5tools_str_t *str, hid_t region, } /*------------------------------------------------------------------------- - * Function: h5tools_str_dump_region_points + * Function: h5tools_str_dump_space_points * - * Purpose: Prints information about a dataspace region by appending + * Purpose: Prints information about a dataspace selection by appending * the information to the specified string. * * Return: none * * In/Out: - * h5tools_context_t *ctx * h5tools_str_t *str *------------------------------------------------------------------------- */ void -h5tools_str_dump_region_points(h5tools_str_t *str, hid_t region, +h5tools_str_dump_space_points(h5tools_str_t *str, hid_t rspace, const h5tool_format_t *info) { - hssize_t npoints; - hsize_t alloc_size; - hsize_t *ptdata; - int ndims = H5Sget_simple_extent_ndims(region); + hssize_t snpoints; /* - * This function fails if the region does not have points. + * This function fails if the rspace does not have points. */ H5E_BEGIN_TRY { - npoints = H5Sget_select_elem_npoints(region); + snpoints = H5Sget_select_elem_npoints(rspace); } H5E_END_TRY; /* Print point information */ - if (npoints > 0) { - int i; - + if (snpoints > 0) { + hsize_t npoints; + hsize_t alloc_size; + hsize_t *ptdata; + unsigned ndims = (unsigned)H5Sget_simple_extent_ndims(rspace); + hsize_t u; + + npoints = (hsize_t)snpoints; alloc_size = npoints * ndims * sizeof(ptdata[0]); HDassert(alloc_size == (hsize_t) ((size_t) alloc_size)); /*check for overflow*/ ptdata = (hsize_t *)HDmalloc((size_t) alloc_size); - H5_CHECK_OVERFLOW(npoints, hssize_t, hsize_t); - H5Sget_select_elem_pointlist(region, (hsize_t)0, (hsize_t)npoints, ptdata); + H5Sget_select_elem_pointlist(rspace, (hsize_t)0, npoints, ptdata); - for (i = 0; i < npoints; i++) { - int j; + for (u = 0; u < npoints; u++) { + unsigned v; - h5tools_str_append(str, info->dset_ptformat_pre, i ? "," OPTIONAL_LINE_BREAK " " : "", - (unsigned long)i); + h5tools_str_append(str, info->dset_ptformat_pre, u ? "," OPTIONAL_LINE_BREAK " " : "", + (unsigned long)u); - for (j = 0; j < ndims; j++) - h5tools_str_append(str, "%s" HSIZE_T_FORMAT, j ? "," : "(", - (ptdata[i * ndims + j])); + for (v = 0; v < ndims; v++) + h5tools_str_append(str, "%s" HSIZE_T_FORMAT, v ? "," : "(", + (ptdata[u * ndims + v])); h5tools_str_append(str, ")"); } @@ -609,13 +608,12 @@ void h5tools_str_indent(h5tools_str_t *str, const h5tool_format_t *info, h5tools_context_t *ctx) { - int i, indentlevel = 0; + unsigned u, indentlevel = 0; /* Write new prefix */ - if (ctx->indent_level >= 0) { + if (ctx->indent_level > 0) indentlevel = ctx->indent_level; - } - else { + else /* * This is because sometimes we don't print out all the header * info for the data (like the tattr-2.ddl example). If that happens @@ -623,11 +621,9 @@ h5tools_str_indent(h5tools_str_t *str, const h5tool_format_t *info, * just print out the default indent levels. */ indentlevel = ctx->default_indent_level; - } - for (i = 0; i < indentlevel; i++) { + for (u = 0; u < indentlevel; u++) h5tools_str_append(str, "%s", OPT(info->line_indent, "")); - } } /*------------------------------------------------------------------------- @@ -686,22 +682,10 @@ h5tools_str_sprint(h5tools_str_t *str, const h5tool_format_t *info, hid_t contai unsigned char *ucp_vp = (unsigned char *)vp; char *cp_vp = (char *)vp; hid_t memb, obj; - unsigned nmembs; static char fmt_llong[8], fmt_ullong[8]; H5T_str_t pad; H5T_class_t type_class; - /* - * some tempvars to store the value before we append it to the string to - * get rid of the memory alignment problem - */ - unsigned long long tempullong; - long long templlong; - unsigned long tempulong; - long templong; - unsigned int tempuint; - int tempint; - /* Build default formats for long long types */ if (!fmt_llong[0]) { HDsnprintf(fmt_llong, sizeof(fmt_llong), "%%%sd", H5_PRINTF_LL_WIDTH); @@ -737,7 +721,7 @@ h5tools_str_sprint(h5tools_str_t *str, const h5tool_format_t *info, hid_t contai float tempfloat; HDmemcpy(&tempfloat, vp, sizeof(float)); - h5tools_str_append(str, OPT(info->fmt_float, "%g"), tempfloat); + h5tools_str_append(str, OPT(info->fmt_float, "%g"), (double)tempfloat); } else if (sizeof(double) == nsize) { /* if (H5Tequal(type, H5T_NATIVE_DOUBLE)) */ @@ -756,6 +740,7 @@ h5tools_str_sprint(h5tools_str_t *str, const h5tool_format_t *info, hid_t contai #endif } break; + case H5T_STRING: { unsigned int i; @@ -776,12 +761,11 @@ h5tools_str_sprint(h5tools_str_t *str, const h5tool_format_t *info, hid_t contai pad = H5Tget_strpad(type); /* Check for NULL pointer for string */ - if (s == NULL) { + if (s == NULL) h5tools_str_append(str, "NULL"); - } else { for (i = 0; i < size && (s[i] || pad != H5T_STR_NULLTERM); i++) { - int j = 1; + unsigned j = 1; /* * Count how many times the next character repeats. If the @@ -798,7 +782,8 @@ h5tools_str_sprint(h5tools_str_t *str, const h5tool_format_t *info, hid_t contai * in it's own quote. */ if (info->str_repeat > 0 && j > info->str_repeat) { - if (quote) h5tools_str_append(str, "%c", quote); + if (quote) + h5tools_str_append(str, "%c", quote); quote = '\''; h5tools_str_append(str, "%s%c", i ? " " : "", quote); @@ -821,10 +806,10 @@ h5tools_str_sprint(h5tools_str_t *str, const h5tool_format_t *info, hid_t contai quote = '\0'; i += j - 1; } - } - if (quote) h5tools_str_append(str, "%c", quote); + if (quote) + h5tools_str_append(str, "%c", quote); if (i == 0) /*empty string*/ @@ -832,64 +817,64 @@ h5tools_str_sprint(h5tools_str_t *str, const h5tool_format_t *info, hid_t contai } /* end else */ } break; + case H5T_INTEGER: if (sizeof(char) == nsize) { - /* if ((H5Tequal(type, H5T_NATIVE_SCHAR) || H5Tequal(type, H5T_NATIVE_UCHAR))) */ - if (info->ascii) { + if (info->ascii) h5tools_print_char(str, info, (char) (*ucp_vp)); - } else if(H5T_SGN_NONE == nsign) { - /* if (H5Tequal(type, H5T_NATIVE_UCHAR)) */ unsigned char tempuchar; + HDmemcpy(&tempuchar, ucp_vp, sizeof(unsigned char)); if (packed_bits_num) { if (packed_data_offset >= 8 * sizeof(unsigned char)) tempuchar = 0; else - tempuchar = (tempuchar >> packed_data_offset) & packed_data_mask; + tempuchar = (unsigned char)((unsigned long long)(tempuchar >> packed_data_offset) & packed_data_mask); } - h5tools_str_append(str, OPT(info->fmt_uchar, "%u"), tempuchar); + h5tools_str_append(str, OPT(info->fmt_uchar, "%hhu"), tempuchar); } else { - /* if (H5Tequal(type, H5T_NATIVE_SCHAR)) */ signed char tempchar; + HDmemcpy(&tempchar, cp_vp, sizeof(char)); if (packed_bits_num) { if (packed_data_offset >= 8 * sizeof(char)) tempchar = 0; else - tempchar = (tempchar >> packed_data_offset) & packed_data_mask; + tempchar = (signed char)((unsigned long long)(tempchar >> packed_data_offset) & packed_data_mask); } h5tools_str_append(str, OPT(info->fmt_schar, "%hhd"), tempchar); } } /* end if (sizeof(char) == nsize) */ else if (sizeof(int) == nsize) { if(H5T_SGN_NONE == nsign) { - /* if (H5Tequal(type, H5T_NATIVE_UINT)) */ + unsigned int tempuint; + HDmemcpy(&tempuint, vp, sizeof(unsigned int)); if (packed_bits_num) { if (packed_data_offset >= 8 * sizeof(unsigned int)) tempuint = 0; else - tempuint = (tempuint >> packed_data_offset) & packed_data_mask; + tempuint = (unsigned)((tempuint >> packed_data_offset) & packed_data_mask); } h5tools_str_append(str, OPT(info->fmt_uint, "%u"), tempuint); } else { - /* if (H5Tequal(type, H5T_NATIVE_INT)) */ + int tempint; + HDmemcpy(&tempint, vp, sizeof(int)); if (packed_bits_num) { if (packed_data_offset >= 8 * sizeof(int)) tempint = 0; else - tempint = (tempint >> packed_data_offset) & packed_data_mask; + tempint = (int)((unsigned long long)(tempint >> packed_data_offset) & packed_data_mask); } h5tools_str_append(str, OPT(info->fmt_int, "%d"), tempint); } } /* end if (sizeof(int) == nsize) */ else if (sizeof(short) == nsize) { if(H5T_SGN_NONE == nsign) { - /* if (H5Tequal(type, H5T_NATIVE_USHORT)) */ unsigned short tempushort; HDmemcpy(&tempushort, vp, sizeof(unsigned short)); @@ -897,12 +882,11 @@ h5tools_str_sprint(h5tools_str_t *str, const h5tool_format_t *info, hid_t contai if (packed_data_offset >= 8 * sizeof(unsigned short)) tempushort = 0; else - tempushort = (tempushort >> packed_data_offset) & packed_data_mask; + tempushort = (unsigned short)((unsigned long long)(tempushort >> packed_data_offset) & packed_data_mask); } - h5tools_str_append(str, OPT(info->fmt_ushort, "%u"), tempushort); + h5tools_str_append(str, OPT(info->fmt_ushort, "%hu"), tempushort); } else { - /* if (H5Tequal(type, H5T_NATIVE_SHORT)) */ short tempshort; HDmemcpy(&tempshort, vp, sizeof(short)); @@ -910,14 +894,15 @@ h5tools_str_sprint(h5tools_str_t *str, const h5tool_format_t *info, hid_t contai if (packed_data_offset >= 8 * sizeof(short)) tempshort = 0; else - tempshort = (tempshort >> packed_data_offset) & packed_data_mask; + tempshort = (short)((unsigned long long)(tempshort >> packed_data_offset) & packed_data_mask); } - h5tools_str_append(str, OPT(info->fmt_short, "%d"), tempshort); + h5tools_str_append(str, OPT(info->fmt_short, "%hd"), tempshort); } } /* end if (sizeof(short) == nsize) */ else if (sizeof(long) == nsize) { if(H5T_SGN_NONE == nsign) { - /* if (H5Tequal(type, H5T_NATIVE_ULONG)) */ + unsigned long tempulong; + HDmemcpy(&tempulong, vp, sizeof(unsigned long)); if (packed_bits_num) { if (packed_data_offset >= 8 * sizeof(unsigned long)) @@ -928,20 +913,23 @@ h5tools_str_sprint(h5tools_str_t *str, const h5tool_format_t *info, hid_t contai h5tools_str_append(str, OPT(info->fmt_ulong, "%lu"), tempulong); } else { - /* if (H5Tequal(type, H5T_NATIVE_LONG)) */ + long templong; + HDmemcpy(&templong, vp, sizeof(long)); if (packed_bits_num) { if (packed_data_offset >= 8 * sizeof(long)) templong = 0; else - templong = (templong >> packed_data_offset) & packed_data_mask; + templong = (long)((unsigned long long)(templong >> packed_data_offset) & packed_data_mask); } h5tools_str_append(str, OPT(info->fmt_long, "%ld"), templong); } } /* end if (sizeof(long) == nsize) */ +#if H5_SIZEOF_LONG != H5_SIZEOF_LONG_LONG else if (sizeof(long long) == nsize) { if(H5T_SGN_NONE == nsign) { - /* if (H5Tequal(type, H5T_NATIVE_ULLONG)) */ + unsigned long long tempullong; + HDmemcpy(&tempullong, vp, sizeof(unsigned long long)); if (packed_bits_num) { if (packed_data_offset >= 8 * sizeof(unsigned long long)) @@ -952,7 +940,8 @@ h5tools_str_sprint(h5tools_str_t *str, const h5tool_format_t *info, hid_t contai h5tools_str_append(str, OPT(info->fmt_ullong, fmt_ullong), tempullong); } else { - /* if (H5Tequal(type, H5T_NATIVE_LLONG)) */ + long long templlong; + HDmemcpy(&templlong, vp, sizeof(long long)); if (packed_bits_num) { if (packed_data_offset >= 8 * sizeof(long long)) @@ -963,12 +952,15 @@ h5tools_str_sprint(h5tools_str_t *str, const h5tool_format_t *info, hid_t contai h5tools_str_append(str, OPT(info->fmt_llong, fmt_llong), templlong); } } /* end if (sizeof(long long) == nsize) */ +#endif /* H5_SIZEOF_LONG != H5_SIZEOF_LONG_LONG */ break; + case H5T_COMPOUND: { + unsigned nmembs; unsigned j; - nmembs = H5Tget_nmembers(type); + nmembs = (unsigned)H5Tget_nmembers(type); h5tools_str_append(str, "%s", OPT(info->cmpd_pre, "{")); ctx->indent_level++; @@ -979,7 +971,8 @@ h5tools_str_sprint(h5tools_str_t *str, const h5tool_format_t *info, hid_t contai else h5tools_str_append(str, "%s", OPT(info->cmpd_end, "")); - if (info->arr_linebreak) h5tools_str_indent(str, info, ctx); + if (info->arr_linebreak) + h5tools_str_indent(str, info, ctx); /* The name */ name = H5Tget_member_name(type, j); @@ -1001,9 +994,9 @@ h5tools_str_sprint(h5tools_str_t *str, const h5tool_format_t *info, hid_t contai h5tools_str_indent(str, info, ctx); } h5tools_str_append(str, "%s", OPT(info->cmpd_suf, "}")); - } break; + case H5T_ENUM: { char enum_name[1024]; @@ -1023,10 +1016,10 @@ h5tools_str_sprint(h5tools_str_t *str, const h5tool_format_t *info, hid_t contai } } break; + case H5T_REFERENCE: - if (h5tools_str_is_zero(vp, nsize)) { + if (h5tools_str_is_zero(vp, nsize)) h5tools_str_append(str, "NULL"); - } else { if (nsize == H5R_DSET_REG_REF_BUF_SIZE) { /* if (H5Tequal(type, H5T_STD_REF_DSETREG)) */ @@ -1082,6 +1075,7 @@ h5tools_str_sprint(h5tools_str_t *str, const h5tool_format_t *info, hid_t contai } /* end else if (H5Tequal(type, H5T_STD_REF_OBJ)) */ } break; + case H5T_ARRAY: { int k, ndims; @@ -1108,7 +1102,8 @@ h5tools_str_sprint(h5tools_str_t *str, const h5tool_format_t *info, hid_t contai ctx->indent_level++; for (i = 0; i < nelmts; i++) { - if (i) h5tools_str_append(str, "%s", OPT(info->arr_sep, "," OPTIONAL_LINE_BREAK)); + if (i) + h5tools_str_append(str, "%s", OPT(info->arr_sep, "," OPTIONAL_LINE_BREAK)); if (info->arr_linebreak && i && i % dims[ndims - 1] == 0) { h5tools_str_append(str, "%s", "\n"); @@ -1143,6 +1138,7 @@ h5tools_str_sprint(h5tools_str_t *str, const h5tool_format_t *info, hid_t contai H5Tclose(memb); } break; + case H5T_VLEN: { unsigned int i; @@ -1244,9 +1240,9 @@ h5tools_str_sprint_region(h5tools_str_t *str, const h5tool_format_t *info, region_type = H5Sget_select_type(region); if(region_type==H5S_SEL_POINTS) - h5tools_str_dump_region_points(str, region, info); + h5tools_str_dump_space_points(str, region, info); else - h5tools_str_dump_region_blocks(str, region, info); + h5tools_str_dump_space_blocks(str, region, info); h5tools_str_append(str, "}"); @@ -1392,31 +1388,33 @@ h5tools_str_is_zero(const void *_mem, size_t size) char * h5tools_str_replace ( const char *string, const char *substr, const char *replacement ) { - char *tok = NULL; - char *newstr = NULL; - char *oldstr = NULL; - char *head = NULL; - - if ( substr == NULL || replacement == NULL ) - return HDstrdup (string); - newstr = HDstrdup (string); - head = newstr; - while ( (tok = HDstrstr ( head, substr ))){ - oldstr = newstr; - newstr = (char *)HDmalloc( HDstrlen( oldstr ) - HDstrlen( substr ) + HDstrlen( replacement ) + 1 ); - - if ( newstr == NULL ){ - HDfree (oldstr); - return NULL; + char *tok = NULL; + char *newstr = NULL; + char *head = NULL; + + if(substr == NULL || replacement == NULL) + return HDstrdup(string); + newstr = HDstrdup(string); + head = newstr; + while((tok = HDstrstr(head, substr))) { + char *oldstr; + + oldstr = newstr; + newstr = (char *)HDmalloc(HDstrlen(oldstr) - HDstrlen(substr) + HDstrlen(replacement) + 1); + + if(newstr == NULL) { + HDfree(oldstr); + return NULL; } - HDmemcpy ( newstr, oldstr, tok - oldstr ); - HDmemcpy ( newstr + (tok - oldstr), replacement, HDstrlen ( replacement ) ); - HDmemcpy ( newstr + (tok - oldstr) + HDstrlen( replacement ), tok + HDstrlen ( substr ), HDstrlen ( oldstr ) - HDstrlen ( substr ) - ( tok - oldstr ) ); - HDmemset ( newstr + HDstrlen ( oldstr ) - HDstrlen ( substr ) + HDstrlen ( replacement ) , 0, 1 ); + HDmemcpy(newstr, oldstr, (size_t)(tok - oldstr)); + HDmemcpy(newstr + (tok - oldstr), replacement, HDstrlen(replacement)); + HDmemcpy(newstr + (tok - oldstr) + HDstrlen(replacement), tok + HDstrlen(substr), HDstrlen(oldstr) - HDstrlen(substr) - (size_t)(tok - oldstr)); + HDmemset(newstr + HDstrlen (oldstr) - HDstrlen(substr) + HDstrlen(replacement) , 0, 1); /* move back head right after the last replacement */ - head = newstr + (tok - oldstr) + HDstrlen( replacement ); - HDfree (oldstr); + head = newstr + (tok - oldstr) + HDstrlen(replacement); + HDfree(oldstr); } return newstr; } + diff --git a/tools/lib/h5tools_str.h b/tools/lib/h5tools_str.h index 38697c6..8d4c042 100644 --- a/tools/lib/h5tools_str.h +++ b/tools/lib/h5tools_str.h @@ -40,8 +40,8 @@ H5TOOLS_DLL char *h5tools_str_prefix(h5tools_str_t *str, const h5tool_format_ H5TOOLS_DLL char *h5tools_str_region_prefix(h5tools_str_t *str, const h5tool_format_t *info, hsize_t elmtno, hsize_t *ptdata, unsigned ndims, hsize_t max_idx[], h5tools_context_t *ctx); -H5TOOLS_DLL void h5tools_str_dump_region_blocks(h5tools_str_t *, hid_t, const h5tool_format_t *); -H5TOOLS_DLL void h5tools_str_dump_region_points(h5tools_str_t *, hid_t, const h5tool_format_t *); +H5TOOLS_DLL void h5tools_str_dump_space_blocks(h5tools_str_t *, hid_t, const h5tool_format_t *); +H5TOOLS_DLL void h5tools_str_dump_space_points(h5tools_str_t *, hid_t, const h5tool_format_t *); H5TOOLS_DLL void h5tools_str_sprint_region(h5tools_str_t *str, const h5tool_format_t *info, hid_t container, void *vp); H5TOOLS_DLL char *h5tools_str_sprint(h5tools_str_t *str, const h5tool_format_t *info, diff --git a/tools/lib/h5tools_type.c b/tools/lib/h5tools_type.c index d68d3c5..8a56d29 100644 --- a/tools/lib/h5tools_type.c +++ b/tools/lib/h5tools_type.c @@ -13,6 +13,7 @@ * access to either file, you may request a copy from help@hdfgroup.org. * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ +#include "H5private.h" #include "h5tools.h" /*------------------------------------------------------------------------- @@ -75,54 +76,54 @@ h5tools_get_little_endian_type(hid_t tid) size = H5Tget_size(tid); sign = H5Tget_sign(tid); - switch( type_class ) - { - case H5T_INTEGER: - { - if ( size == 1 && sign == H5T_SGN_2) - p_type=H5Tcopy(H5T_STD_I8LE); - else if ( size == 2 && sign == H5T_SGN_2) - p_type=H5Tcopy(H5T_STD_I16LE); - else if ( size == 4 && sign == H5T_SGN_2) - p_type=H5Tcopy(H5T_STD_I32LE); - else if ( size == 8 && sign == H5T_SGN_2) - p_type=H5Tcopy(H5T_STD_I64LE); - else if ( size == 1 && sign == H5T_SGN_NONE) - p_type=H5Tcopy(H5T_STD_U8LE); - else if ( size == 2 && sign == H5T_SGN_NONE) - p_type=H5Tcopy(H5T_STD_U16LE); - else if ( size == 4 && sign == H5T_SGN_NONE) - p_type=H5Tcopy(H5T_STD_U32LE); - else if ( size == 8 && sign == H5T_SGN_NONE) - p_type=H5Tcopy(H5T_STD_U64LE); - } - break; - - case H5T_FLOAT: - if ( size == 4) - p_type=H5Tcopy(H5T_IEEE_F32LE); - else if ( size == 8) - p_type=H5Tcopy(H5T_IEEE_F64LE); - break; - - case H5T_TIME: - case H5T_BITFIELD: - case H5T_OPAQUE: - case H5T_STRING: - case H5T_COMPOUND: - case H5T_REFERENCE: - case H5T_ENUM: - case H5T_VLEN: - case H5T_ARRAY: - break; - - default: - break; - - } - - return(p_type); -} + switch(type_class) { + case H5T_INTEGER: + if ( size == 1 && sign == H5T_SGN_2) + p_type=H5Tcopy(H5T_STD_I8LE); + else if ( size == 2 && sign == H5T_SGN_2) + p_type=H5Tcopy(H5T_STD_I16LE); + else if ( size == 4 && sign == H5T_SGN_2) + p_type=H5Tcopy(H5T_STD_I32LE); + else if ( size == 8 && sign == H5T_SGN_2) + p_type=H5Tcopy(H5T_STD_I64LE); + else if ( size == 1 && sign == H5T_SGN_NONE) + p_type=H5Tcopy(H5T_STD_U8LE); + else if ( size == 2 && sign == H5T_SGN_NONE) + p_type=H5Tcopy(H5T_STD_U16LE); + else if ( size == 4 && sign == H5T_SGN_NONE) + p_type=H5Tcopy(H5T_STD_U32LE); + else if ( size == 8 && sign == H5T_SGN_NONE) + p_type=H5Tcopy(H5T_STD_U64LE); + break; + + case H5T_FLOAT: + if ( size == 4) + p_type=H5Tcopy(H5T_IEEE_F32LE); + else if ( size == 8) + p_type=H5Tcopy(H5T_IEEE_F64LE); + break; + + case H5T_TIME: + case H5T_BITFIELD: + case H5T_OPAQUE: + case H5T_STRING: + case H5T_COMPOUND: + case H5T_REFERENCE: + case H5T_ENUM: + case H5T_VLEN: + case H5T_ARRAY: + break; + + case H5T_NO_CLASS: + case H5T_NCLASSES: + default: + HDassert(0); + break; + + } /* end switch */ + + return p_type; +} /* end h5tools_get_little_endian_type() */ /*------------------------------------------------------------------------- @@ -152,53 +153,51 @@ h5tools_get_big_endian_type(hid_t tid) size = H5Tget_size(tid); sign = H5Tget_sign(tid); - switch( type_class ) - { - case H5T_INTEGER: - { - if ( size == 1 && sign == H5T_SGN_2) - p_type=H5Tcopy(H5T_STD_I8BE); - else if ( size == 2 && sign == H5T_SGN_2) - p_type=H5Tcopy(H5T_STD_I16BE); - else if ( size == 4 && sign == H5T_SGN_2) - p_type=H5Tcopy(H5T_STD_I32BE); - else if ( size == 8 && sign == H5T_SGN_2) - p_type=H5Tcopy(H5T_STD_I64BE); - else if ( size == 1 && sign == H5T_SGN_NONE) - p_type=H5Tcopy(H5T_STD_U8BE); - else if ( size == 2 && sign == H5T_SGN_NONE) - p_type=H5Tcopy(H5T_STD_U16BE); - else if ( size == 4 && sign == H5T_SGN_NONE) - p_type=H5Tcopy(H5T_STD_U32BE); - else if ( size == 8 && sign == H5T_SGN_NONE) - p_type=H5Tcopy(H5T_STD_U64BE); - } - break; - - case H5T_FLOAT: - if ( size == 4) - p_type=H5Tcopy(H5T_IEEE_F32BE); - else if ( size == 8) - p_type=H5Tcopy(H5T_IEEE_F64BE); - break; - - case H5T_TIME: - case H5T_BITFIELD: - case H5T_OPAQUE: - case H5T_STRING: - case H5T_COMPOUND: - case H5T_REFERENCE: - case H5T_ENUM: - case H5T_VLEN: - case H5T_ARRAY: - break; - - default: - break; - - } - - - return(p_type); -} + switch(type_class) { + case H5T_INTEGER: + if ( size == 1 && sign == H5T_SGN_2) + p_type=H5Tcopy(H5T_STD_I8BE); + else if ( size == 2 && sign == H5T_SGN_2) + p_type=H5Tcopy(H5T_STD_I16BE); + else if ( size == 4 && sign == H5T_SGN_2) + p_type=H5Tcopy(H5T_STD_I32BE); + else if ( size == 8 && sign == H5T_SGN_2) + p_type=H5Tcopy(H5T_STD_I64BE); + else if ( size == 1 && sign == H5T_SGN_NONE) + p_type=H5Tcopy(H5T_STD_U8BE); + else if ( size == 2 && sign == H5T_SGN_NONE) + p_type=H5Tcopy(H5T_STD_U16BE); + else if ( size == 4 && sign == H5T_SGN_NONE) + p_type=H5Tcopy(H5T_STD_U32BE); + else if ( size == 8 && sign == H5T_SGN_NONE) + p_type=H5Tcopy(H5T_STD_U64BE); + break; + + case H5T_FLOAT: + if ( size == 4) + p_type=H5Tcopy(H5T_IEEE_F32BE); + else if ( size == 8) + p_type=H5Tcopy(H5T_IEEE_F64BE); + break; + + case H5T_TIME: + case H5T_BITFIELD: + case H5T_OPAQUE: + case H5T_STRING: + case H5T_COMPOUND: + case H5T_REFERENCE: + case H5T_ENUM: + case H5T_VLEN: + case H5T_ARRAY: + break; + + case H5T_NO_CLASS: + case H5T_NCLASSES: + default: + HDassert(0); + break; + } /* end switch */ + + return p_type; +} /* end h5tools_get_big_endian_type() */ diff --git a/tools/lib/h5tools_utils.c b/tools/lib/h5tools_utils.c index b87abf6..e19926b 100644 --- a/tools/lib/h5tools_utils.c +++ b/tools/lib/h5tools_utils.c @@ -34,7 +34,7 @@ #include "h5trav.h" /* global variables */ -int h5tools_nCols = 80; +unsigned h5tools_nCols = 80; /* ``get_option'' variables */ int opt_err = 1; /*get_option prints errors if this is on */ int opt_ind = 1; /*token pointer */ @@ -57,7 +57,7 @@ hsize_t H5TOOLS_BUFSIZE = ( 32 * 1024 * 1024); /* 32 MB */ /* ``parallel_print'' variables */ unsigned char g_Parallel = 0; /*0 for serial, 1 for parallel */ char outBuff[OUTBUFF_SIZE]; -int outBuffOffset; +unsigned outBuffOffset; FILE* overflow_file = NULL; /* local functions */ @@ -89,11 +89,11 @@ void parallel_print(const char* format, ...) HDvprintf(format, ap); else { if(overflow_file == NULL) /*no overflow has occurred yet */ { - bytes_written = HDvsnprintf(outBuff+outBuffOffset, OUTBUFF_SIZE-outBuffOffset, format, ap); + bytes_written = HDvsnprintf(outBuff + outBuffOffset, OUTBUFF_SIZE - outBuffOffset, format, ap); HDva_end(ap); HDva_start(ap, format); - if((bytes_written < 0) || (bytes_written >= (OUTBUFF_SIZE - outBuffOffset))) { + if((bytes_written < 0) || ((unsigned)bytes_written >= (OUTBUFF_SIZE - outBuffOffset))) { /* Terminate the outbuff at the end of the previous output */ outBuff[outBuffOffset] = '\0'; @@ -104,7 +104,7 @@ void parallel_print(const char* format, ...) bytes_written = HDvfprintf(overflow_file, format, ap); } else - outBuffOffset += bytes_written; + outBuffOffset += (unsigned)bytes_written; } else bytes_written = HDvfprintf(overflow_file, format, ap); @@ -376,7 +376,7 @@ get_option(int argc, const char **argv, const char *opts, const struct long_opti *------------------------------------------------------------------------- */ void -indentation(int x) +indentation(unsigned x) { if (x < h5tools_nCols) { while (x-- > 0) @@ -408,7 +408,7 @@ print_version(const char *progname) { PRINTSTREAM(rawoutstream, "%s: Version %u.%u.%u%s%s\n", progname, H5_VERS_MAJOR, H5_VERS_MINOR, H5_VERS_RELEASE, - ((char *)H5_VERS_SUBRELEASE)[0] ? "-" : "", H5_VERS_SUBRELEASE); + ((const char *)H5_VERS_SUBRELEASE)[0] ? "-" : "", H5_VERS_SUBRELEASE); } @@ -680,7 +680,7 @@ init_objs(hid_t fid, find_objs_t *info, table_t **group_table, static void add_obj(table_t *table, haddr_t objno, const char *objname, hbool_t record) { - unsigned u; + size_t u; /* See if we need to make table larger */ if(table->nobjs == table->size) { @@ -912,7 +912,6 @@ int h5tools_getenv_update_hyperslab_bufsize(void) hyperslab_bufsize_mb = HDstrtol(env_str, (char**)NULL, 10); if (errno != 0 || hyperslab_bufsize_mb <= 0) { - /* TODO: later when pubilshed HDfprintf(rawerrorstream,"Error: Invalid environment variable \"H5TOOLS_BUFSIZE\" : %s\n", env_str); */ @@ -922,13 +921,14 @@ int h5tools_getenv_update_hyperslab_bufsize(void) /* convert MB to byte */ - H5TOOLS_BUFSIZE = hyperslab_bufsize_mb * 1024 * 1024; + H5TOOLS_BUFSIZE = (hsize_t)hyperslab_bufsize_mb * 1024 * 1024; H5TOOLS_MALLOCSIZE = MAX(H5TOOLS_BUFSIZE, H5TOOLS_MALLOCSIZE); } - return (1); + error: return (-1); } + diff --git a/tools/lib/h5tools_utils.h b/tools/lib/h5tools_utils.h index 3285278..f7ab65b 100644 --- a/tools/lib/h5tools_utils.h +++ b/tools/lib/h5tools_utils.h @@ -35,7 +35,7 @@ extern "C" { H5TOOLS_DLLVAR int g_nTasks; H5TOOLS_DLLVAR unsigned char g_Parallel; H5TOOLS_DLLVAR char outBuff[]; -H5TOOLS_DLLVAR int outBuffOffset; +H5TOOLS_DLLVAR unsigned outBuffOffset; H5TOOLS_DLLVAR FILE * overflow_file; /* Maximum size used in a call to malloc for a dataset */ @@ -119,10 +119,10 @@ typedef struct find_objs_t { table_t *dset_table; } find_objs_t; -H5TOOLS_DLLVAR int h5tools_nCols; /*max number of columns for outputting */ +H5TOOLS_DLLVAR unsigned h5tools_nCols; /*max number of columns for outputting */ /* Definitions of useful routines */ -H5TOOLS_DLL void indentation(int); +H5TOOLS_DLL void indentation(unsigned); H5TOOLS_DLL void print_version(const char *progname); H5TOOLS_DLL void parallel_print(const char* format, ... ); H5TOOLS_DLL void error_msg(const char *fmt, ...); |