/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * Copyright by The HDF Group. * * Copyright by the Board of Trustees of the University of Illinois. * * All rights reserved. * * * * This file is part of HDF5. The full HDF5 copyright notice, including * * terms governing use, modification, and redistribution, is contained in * * the COPYING file, which can be found at the root of the source code * * distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases. * * If you do not have access to either file, you may request a copy from * * help@hdfgroup.org. * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ #include "h5tools.h" #include "h5tools_utils.h" #include "h5repack.h" /* Name of tool */ #define PROGRAMNAME "h5repack" static int parse_command_line(int argc, const char **argv, pack_opt_t* options); static void leave(int ret) H5_ATTR_NORETURN; /* module-scoped variables */ static int has_i_o = 0; const char *infile = NULL; 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:q:z: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 */ { "sort_by", require_arg, 'q' }, { "sort_order", require_arg, 'z' }, { "enable-error-stack", no_arg, 'E' }, { NULL, 0, '\0' } }; /*------------------------------------------------------------------------- * Function: usage * * Purpose: print usage * * Return: void * *------------------------------------------------------------------------- */ static void usage(const char *prog) { 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, " -q Q, --sort_by=Q Sort groups and attributes by index Q\n"); PRINTVALSTREAM(rawoutstream, " -z Z, --sort_order=Z Sort groups and attributes by order Z\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, " Q - is the sort index type for the input file. It can be \"name\" or \"creation_order\" (default)\n"); PRINTVALSTREAM(rawoutstream, " Z - is the sort order type for the input file. It can be \"descending\" or \"ascending\" (default)\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 . 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, " :=\n"); PRINTVALSTREAM(rawoutstream, "\n"); PRINTVALSTREAM(rawoutstream, " 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, " 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, " is optional filter parameter information\n"); PRINTVALSTREAM(rawoutstream, " GZIP= from 1-9\n"); PRINTVALSTREAM(rawoutstream, " SZIP= 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 is an integer and scale_type\n"); PRINTVALSTREAM(rawoutstream, " is either IN or DS\n"); PRINTVALSTREAM(rawoutstream, " UD=\n"); PRINTVALSTREAM(rawoutstream, " required values for filter_number,filter_flag,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, " :=\n"); PRINTVALSTREAM(rawoutstream, "\n"); PRINTVALSTREAM(rawoutstream, " 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, " 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, " 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=307,0,1,9 file1 file2\n"); PRINTVALSTREAM(rawoutstream, "\n"); PRINTVALSTREAM(rawoutstream, " Add bzip2 filter to all datasets\n"); PRINTVALSTREAM(rawoutstream, "\n"); } /*------------------------------------------------------------------------- * Function: leave * * Purpose: Shutdown MPI & HDF5 and call exit() * * Return: Does not return *------------------------------------------------------------------------- */ static void leave(int ret) { h5tools_close(); HDexit(ret); } /*------------------------------------------------------------------------- * Function: read_info * * Purpose: read comp and chunk options from a file * * Return: void, exit on error *------------------------------------------------------------------------- */ static int read_info(const char *filename, pack_opt_t *options) { char stype[10] = {0, 0, 0, 0, 0, 0, 0, 0, 0, 0}; char comp_info[1024]; FILE *fp = NULL; char c; int i, rc = 1; int ret_value = EXIT_SUCCESS; if ((fp = HDfopen(filename, "r")) == (FILE *) NULL) { error_msg("cannot open options file %s\n", filename); h5tools_setstatus(EXIT_FAILURE); ret_value = EXIT_FAILURE; goto done; } /* cycle until end of file reached */ while (1) { rc = fscanf(fp, "%s", stype); if (rc == -1) break; /*------------------------------------------------------------------------- * filter *------------------------------------------------------------------------- */ if (HDstrcmp(stype,"-f") == 0) { /* find begining of info */ i = 0; c = '0'; while (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 != ' ') { 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)) break; if (c == 10 /*eol*/) break; } comp_info[i - 1] = '\0'; /*cut the last " */ if (h5repack_addfilter(comp_info, options) == -1) { error_msg("could not add compression option\n"); h5tools_setstatus(EXIT_FAILURE); ret_value = EXIT_FAILURE; goto done; } } /*------------------------------------------------------------------------- * layout *------------------------------------------------------------------------- */ else if (HDstrcmp(stype,"-l") == 0) { /* find begining of info */ i = 0; c = '0'; while (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 != ' ') { 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)) break; if (c == 10 /*eol*/) break; } comp_info[i - 1] = '\0'; /*cut the last " */ if (h5repack_addlayout(comp_info, options) == -1) { error_msg("could not add chunck option\n"); h5tools_setstatus(EXIT_FAILURE); ret_value = EXIT_FAILURE; goto done; } } /*------------------------------------------------------------------------- * not valid *------------------------------------------------------------------------- */ else { error_msg("bad file format for %s", filename); h5tools_setstatus(EXIT_FAILURE); ret_value = EXIT_FAILURE; goto done; } } done: if (fp) HDfclose(fp); return ret_value; } /*------------------------------------------------------------------------- * Function: set_sort_by * * Purpose: set the "by" form of sorting by translating from a string input * parameter to a H5_index_t return value * current sort values are [creation_order | name] * * Return: H5_index_t form of sort or H5_INDEX_UNKNOWN if none found *------------------------------------------------------------------------- */ static H5_index_t set_sort_by(const char *form) { H5_index_t idx_type = H5_INDEX_UNKNOWN; if (HDstrcmp(form,"name")==0) /* H5_INDEX_NAME */ idx_type = H5_INDEX_NAME; else if (HDstrcmp(form,"creation_order")==0) /* H5_INDEX_CRT_ORDER */ idx_type = H5_INDEX_CRT_ORDER; return idx_type; } /*------------------------------------------------------------------------- * Function: set_sort_order * * Purpose: set the order of sorting by translating from a string input * parameter to a H5_iter_order_t return value * current order values are [ascending | descending ] * * Return: H5_iter_order_t form of order or H5_ITER_UNKNOWN if none found *------------------------------------------------------------------------- */ static H5_iter_order_t set_sort_order(const char *form) { H5_iter_order_t iter_order = H5_ITER_UNKNOWN; if (HDstrcmp(form,"ascending")==0) /* H5_ITER_INC */ iter_order = H5_ITER_INC; else if (HDstrcmp(form,"descending")==0) /* H5_ITER_DEC */ iter_order = H5_ITER_DEC; return iter_order; } /*------------------------------------------------------------------------- * Function: parse_command_line * * Purpose: parse command line input *------------------------------------------------------------------------- */ static int parse_command_line(int argc, const char **argv, pack_opt_t* options) { int opt; int ret_value = 0; /* parse command line options */ while ((opt = get_option(argc, argv, s_opts, l_opts)) != EOF) { switch ((char) opt) { /* -i for backward compatibility */ case 'i': infile = opt_arg; has_i_o = 1; break; /* -o for backward compatibility */ case 'o': outfile = opt_arg; has_i_o = 1; break; case 'h': usage(h5tools_getprogname()); h5tools_setstatus(EXIT_SUCCESS); ret_value = -1; goto done; case 'V': print_version(h5tools_getprogname()); h5tools_setstatus(EXIT_SUCCESS); ret_value = -1; goto done; case 'v': options->verbose = 1; break; case 'f': /* parse the -f filter option */ if (h5repack_addfilter(opt_arg, options) < 0) { error_msg("in parsing filter\n"); h5tools_setstatus(EXIT_FAILURE); ret_value = -1; goto done; } break; case 'l': /* parse the -l layout option */ if (h5repack_addlayout(opt_arg, options) < 0) { error_msg("in parsing layout\n"); h5tools_setstatus(EXIT_FAILURE); ret_value = -1; goto done; } break; case 'm': 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); ret_value = -1; goto done; } break; case 'e': ret_value = read_info(opt_arg, options); if (ret_value < 0) goto done; break; case 'n': options->use_native = 1; break; case 'L': options->latest = TRUE; break; case 'c': options->grp_compact = HDatoi( opt_arg ); if (options->grp_compact > 0) options->latest = TRUE; /* must use latest format */ break; case 'd': options->grp_indexed = HDatoi( opt_arg ); if (options->grp_indexed > 0) options->latest = TRUE; /* must use latest format */ break; case 's': { int idx = 0; int ssize = 0; char *msgPtr = HDstrchr( opt_arg, ':'); options->latest = TRUE; /* must use latest format */ if (msgPtr == NULL) { ssize = HDatoi( opt_arg ); for (idx = 0; idx < 5; idx++) options->msg_size[idx] = ssize; } else { char msgType[10]; HDstrcpy(msgType, msgPtr + 1); msgPtr[0] = '\0'; ssize = HDatoi( opt_arg ); if (HDstrncmp(msgType, "dspace",6) == 0) options->msg_size[0] = ssize; else if (HDstrncmp(msgType, "dtype", 5) == 0) options->msg_size[1] = ssize; else if (HDstrncmp(msgType, "fill", 4) == 0) options->msg_size[2] = ssize; else if (HDstrncmp(msgType, "pline", 5) == 0) options->msg_size[3] = ssize; else if (HDstrncmp(msgType, "attr", 4) == 0) options->msg_size[4] = ssize; } } break; case 'u': options->ublock_filename = opt_arg; break; case 'b': options->ublock_size = (hsize_t) HDatol( opt_arg ); break; case 'M': options->meta_block_size = (hsize_t) HDatol( opt_arg ); break; case 't': options->threshold = (hsize_t) HDatol( opt_arg ); break; case 'a': options->alignment = HDstrtoull(opt_arg , NULL, 0); if (options->alignment < 1) { error_msg("invalid alignment size\n", opt_arg); h5tools_setstatus(EXIT_FAILURE); ret_value = -1; goto done; } break; case 'q': if((sort_by = set_sort_by(opt_arg)) < 0) { error_msg(" failed to set sort by form <%s>\n", opt_arg); h5tools_setstatus(EXIT_FAILURE); ret_value = -1; goto done; } break; case 'z': if((sort_order = set_sort_order(opt_arg)) < 0) { error_msg(" failed to set sort order form <%s>\n", opt_arg); h5tools_setstatus(EXIT_FAILURE); ret_value = -1; goto done; } break; case 'E': enable_error_stack = TRUE; break; default: break; } /* switch */ } /* while */ 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"); usage(h5tools_getprogname()); h5tools_setstatus(EXIT_FAILURE); ret_value = -1; } } done: return ret_value; } /*------------------------------------------------------------------------- * Function: main * * Purpose: h5repack main program * * Return: Success: EXIT_SUCCESS(0) * * Failure: EXIT_FAILURE(1) *------------------------------------------------------------------------- */ int main(int argc, const char **argv) { pack_opt_t options; /*the global options */ H5E_auto2_t func; H5E_auto2_t tools_func; void *edata; void *tools_edata; h5tools_setprogname(PROGRAMNAME); h5tools_setstatus(EXIT_SUCCESS); /* 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 */ if (h5repack_init(&options, 0, FALSE) < 0) { h5tools_setstatus(EXIT_FAILURE); goto done; } /* Initialize default indexing options */ sort_by = H5_INDEX_CRT_ORDER; 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: /* free tables */ h5repack_end(&options); leave(h5tools_getstatus()); }