/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * Copyright by The HDF Group. * * Copyright by the Board of Trustees of the University of Illinois. * * All rights reserved. * * * * This file is part of HDF5. The full HDF5 copyright notice, including * * terms governing use, modification, and redistribution, is contained in * * the files COPYING and Copyright.html. COPYING can be found at the root * * of the source code distribution tree; Copyright.html can be found at the * * root level of an installed copy of the electronic HDF5 document set and * * is linked from the top-level documents page. It can also be found at * * http://hdfgroup.org/HDF5/doc/Copyright.html. If you do not have * * access to either file, you may request a copy from help@hdfgroup.org. * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ #include #include #include #include "h5tools_utils.h" #include "h5repack.h" static void usage(const char *prog); static void parse_command_line(int argc, const char **argv, pack_opt_t* options); static void read_info(const char *filename,pack_opt_t *options); /* module-scoped variables */ const char *progname = "h5repack"; int d_status = EXIT_SUCCESS; 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:t:a:i:o:S:T:"; 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' }, { "threshold", require_arg, 't' }, { "alignment", require_arg, 'a' }, { "infile", require_arg, 'i' }, /* -i for backward compability */ { "outfile", require_arg, 'o' }, /* -o for backward compability */ { "fs_strategy", require_arg, 'S' }, { "fs_threshold", require_arg, 'T' }, { NULL, 0, '\0' } }; /*------------------------------------------------------------------------- * Function: main * * Purpose: h5repack main program * * Return: Success: EXIT_SUCCESS(0) * * Failure: EXIT_FAILURE(1) * * Programmer: Pedro Vicente, pvn@ncsa.uiuc.edu * * Date: May 9, 2003 * * Comments: * * Modifications: * July 2004: Introduced the extra EC or NN option for SZIP * October 2006: Added a new switch -n, that allows to write the dataset * using a native type. The default to write is the file type. * * Modification: * Peter Cao, June 13, 2007 * Add "-L, --latest" option to pack a file with the latest file format * PVN, November 19, 2007 * adopted the syntax h5repack [OPTIONS] file1 file2 * PVN, November 28, 2007 * added support for multiple global filters * PVN, May 16, 2008 * added backward compatibility for -i infile -o outfile * PVN, August 20, 2008 * add a user block to repacked file (switches -u -b) * PVN, August 28, 2008 * add options to set alignment (H5Pset_alignment) (switches -t -a) *------------------------------------------------------------------------- */ int main(int argc, const char **argv) { pack_opt_t options; /*the global options */ int ret=-1; /* initialize options */ h5repack_init(&options, 0, 0, (hsize_t)0); parse_command_line(argc, argv, &options); /* 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 ( strcmp( infile, outfile ) == 0 ) { error_msg(progname, "file names cannot be the same\n"); usage(progname); exit(EXIT_FAILURE); } } else { error_msg(progname, "file names missing\n"); usage(progname); exit(EXIT_FAILURE); } } /* pack it */ ret=h5repack(infile,outfile,&options); /* free tables */ h5repack_end(&options); if (ret==-1) return 1; else return 0; } /*------------------------------------------------------------------------- * Function: usage * * Purpose: print usage * * Return: void * *------------------------------------------------------------------------- */ 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(" -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(" -S FS_STRGY, --fs_strategy=FS_STRGY File space management strategy\n"); printf(" -T FS_THRD, --fs_threshold=FS_THRD Free-space section threshold\n"); printf("\n"); printf(" M - is an integer greater than 1, size of dataset in bytes (default is 1024) \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 . If F is not specified, S applies to all messages\n"); printf("\n"); printf(" FS_STRGY is the file space management strategy to use for the output file.\n"); printf(" It is a string as listed below:\n"); printf(" ALL_PERSIST - Use persistent free-space managers, aggregators and virtual file driver\n"); printf(" for file space allocation\n"); printf(" ALL - Use non-persistent free-space managers, aggregators and virtual file driver\n"); printf(" for file space allocation\n"); printf(" AGGR_VFD - Use aggregators and virtual file driver for file space allocation\n"); printf(" VFD - Use virtual file driver for file space allocation\n"); printf("\n"); printf(" FS_THRD is the free-space section threshold to use for the output file.\n"); printf(" It is the minimum size (in bytes) of free-space sections to be tracked\n"); printf(" by the the library's free-space managers.\n"); printf("\n"); printf(" FILT - is a string with the format:\n"); printf("\n"); printf(" :=\n"); printf("\n"); printf(" 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(" 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(" NONE, to remove all filters\n"); printf(" is optional filter parameter information\n"); printf(" GZIP= from 1-9\n"); printf(" SZIP= 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 is an integer and scale_type\n"); printf(" is either IN or DS\n"); printf(" NONE (no parameter)\n"); printf("\n"); printf(" LAYT - is a string with the format:\n"); printf("\n"); printf(" :=\n"); printf("\n"); printf(" 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(" can be:\n"); printf(" CHUNK, to apply chunking layout\n"); printf(" COMPA, to apply compact layout\n"); printf(" CONTI, to apply continuous layout\n"); printf(" 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 A:SZIP=8,NN file1 file2\n"); printf("\n"); printf(" SZIP compression with 8 pixels per block and NN coding method to object A\n"); printf("\n"); printf("3) h5repack -v -l A,B:CHUNK=20x10 -f C,D,F:NONE file1 file2\n"); printf("\n"); printf(" Chunked layout, with a layout size of 20x10, to objects A and B\n"); printf(" and remove filters to objects C, D, F\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"); } /*------------------------------------------------------------------------- * Function: parse_command_line * * Purpose: parse command line input * *------------------------------------------------------------------------- */ static void parse_command_line(int argc, const char **argv, pack_opt_t* options) { int opt; /* parse command line options */ while ((opt = get_option(argc, argv, s_opts, l_opts)) != EOF) { switch ((char)opt) { /* -i for backward compability */ case 'i': infile = opt_arg; has_i_o = 1; break; /* -o for backward compability */ case 'o': outfile = opt_arg; has_i_o = 1; break; case 'h': usage(progname); exit(EXIT_SUCCESS); case 'V': print_version(progname); exit(EXIT_SUCCESS); case 'v': options->verbose = 1; break; case 'f': /* parse the -f filter option */ if (h5repack_addfilter( opt_arg, options)<0) { error_msg(progname, "in parsing filter\n"); exit(EXIT_FAILURE); } break; case 'l': /* parse the -l layout option */ if (h5repack_addlayout( opt_arg, options)<0) { error_msg(progname, "in parsing layout\n"); exit(EXIT_FAILURE); } break; case 'm': options->min_comp = atoi( opt_arg ); if ((int)options->min_comp<=0) { error_msg(progname, "invalid minimum compress size <%s>\n", opt_arg ); exit(EXIT_FAILURE); } break; case 'e': read_info( opt_arg, options); break; case 'n': options->use_native = 1; break; case 'L': options->latest = 1; break; case 'c': options->grp_compact = atoi( opt_arg ); if (options->grp_compact>0) options->latest = 1; /* must use latest format */ break; case 'd': options->grp_indexed = atoi( opt_arg ); if (options->grp_indexed>0) options->latest = 1; /* must use latest format */ break; case 's': { int idx = 0; int ssize = 0; char *msgPtr = strchr( opt_arg, ':'); options->latest = 1; /* must use latest format */ if (msgPtr == NULL) { ssize = atoi( opt_arg ); for (idx=0; idx<5; idx++) options->msg_size[idx] = ssize; } else { char msgType[10]; strcpy(msgType, msgPtr+1); msgPtr[0] = '\0'; ssize = atoi( opt_arg ); if (strncmp(msgType, "dspace",6) == 0) { options->msg_size[0] = ssize; } else if (strncmp(msgType, "dtype", 5) == 0) { options->msg_size[1] = ssize; } else if (strncmp(msgType, "fill", 4) == 0) { options->msg_size[2] = ssize; } else if (strncmp(msgType, "pline", 5) == 0) { options->msg_size[3] = ssize; } else if (strncmp(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)atol( opt_arg ); break; case 't': options->threshold = (hsize_t)atol( opt_arg ); break; case 'a': options->alignment = atol( opt_arg ); if ( options->alignment < 1 ) { error_msg(progname, "invalid alignment size\n", opt_arg ); exit(EXIT_FAILURE); } break; case 'S': { char strategy[MAX_NC_NAME]; strcpy(strategy, opt_arg); if(!strcmp(strategy, "ALL_PERSIST")) options->fs_strategy = H5F_FILE_SPACE_ALL_PERSIST; else if(!strcmp(strategy, "ALL")) options->fs_strategy = H5F_FILE_SPACE_ALL; else if(!strcmp(strategy, "AGGR_VFD")) options->fs_strategy = H5F_FILE_SPACE_AGGR_VFD; else if(!strcmp(strategy, "VFD")) options->fs_strategy = H5F_FILE_SPACE_VFD; else { error_msg(progname, "invalid file space management strategy\n", opt_arg ); exit(EXIT_FAILURE); } break; } case 'T': options->fs_threshold = (hsize_t)atol( opt_arg ); 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(progname, "missing file names\n"); usage(progname); exit(EXIT_FAILURE); } } } /*------------------------------------------------------------------------- * Function: read_info * * Purpose: read comp and chunk options from a file * * Return: void, exit on error * * Programmer: pvn@ncsa.uiuc.edu * * Date: September, 22, 2003 * *------------------------------------------------------------------------- */ static void read_info(const char *filename, pack_opt_t *options) { char stype[10]; char comp_info[1024]; FILE *fp; char c; int i, rc=1; if ((fp = fopen(filename, "r")) == (FILE *)NULL) { error_msg(progname, "cannot open options file %s\n", filename); exit(EXIT_FAILURE); } /* cycle until end of file reached */ while( 1 ) { rc=fscanf(fp, "%s", stype); if (rc==-1) break; /*------------------------------------------------------------------------- * filter *------------------------------------------------------------------------- */ if (strcmp(stype,"-f") == 0) { /* find begining of info */ i=0; c='0'; while( c!=' ' ) { fscanf(fp, "%c", &c); if (feof(fp)) break; } c='0'; /* go until end */ while( c!=' ' ) { fscanf(fp, "%c", &c); comp_info[i]=c; i++; if (feof(fp)) break; if (c==10 /*eol*/) break; } comp_info[i-1]='\0'; /*cut the last " */ if (h5repack_addfilter(comp_info,options)==-1){ error_msg(progname, "could not add compression option\n"); exit(EXIT_FAILURE); } } /*------------------------------------------------------------------------- * layout *------------------------------------------------------------------------- */ else if (strcmp(stype,"-l") == 0) { /* find begining of info */ i=0; c='0'; while( c!=' ' ) { fscanf(fp, "%c", &c); if (feof(fp)) break; } c='0'; /* go until end */ while( c!=' ' ) { fscanf(fp, "%c", &c); comp_info[i]=c; i++; if (feof(fp)) break; if (c==10 /*eol*/) break; } comp_info[i-1]='\0'; /*cut the last " */ if (h5repack_addlayout(comp_info,options)==-1){ error_msg(progname, "could not add chunck option\n"); exit(EXIT_FAILURE); } } /*------------------------------------------------------------------------- * not valid *------------------------------------------------------------------------- */ else { error_msg(progname, "bad file format for %s", filename); exit(EXIT_FAILURE); } } fclose(fp); return; }