/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * 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://hdf.ncsa.uiuc.edu/HDF5/doc/Copyright.html. If you do not have * * access to either file, you may request a copy from hdfhelp@ncsa.uiuc.edu. * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ #include #include "h5repack.h" /*------------------------------------------------------------------------- * File: h5repack.c * Purpose: Public API functions *------------------------------------------------------------------------- */ static int check_options(pack_opt_t *options); /*------------------------------------------------------------------------- * Function: aux_initglb_filter * * Purpose: auxiliary function, initialize the options global filter * * Return: void * *------------------------------------------------------------------------- */ static void aux_initglb_filter(pack_opt_t *options) { int k; options->filter_g.filtn = -1; for ( k=0; kfilter_g.cd_values[k] = -1; } /*------------------------------------------------------------------------- * Function: h5repack * * Purpose: locate all high-level HDF5 objects in the file * and compress/chunk them using options * * Algorythm: 2 traversals are made to the file; the 1st builds a list of * the objects, the 2nd makes a copy of them, using the options; * the reason for the 1st traversal is to check for invalid * object name requests * * Return: 0, ok, -1, fail * * Programmer: Pedro Vicente, pvn@ncsa.uiuc.edu * * Date: September, 22, 2003 * *------------------------------------------------------------------------- */ int h5repack(const char* infile, const char* outfile, pack_opt_t *options) { /* check input */ if (check_options(options)<0) return -1; /* check for objects in input that are in the file */ if (check_objects(infile,options)<0) return -1; /* copy the objects */ if (copy_objects(infile,outfile,options)<0) return -1; return 0; } /*------------------------------------------------------------------------- * Function: h5repack_init * * Purpose: initialize options * * Return: 0, ok, -1, fail * *------------------------------------------------------------------------- */ int h5repack_init (pack_opt_t *options, int verbose) { memset(options,0,sizeof(pack_opt_t)); options->threshold = 1024; options->verbose = verbose; return (options_table_init(&(options->op_tbl))); } /*------------------------------------------------------------------------- * Function: h5repack_end * * Purpose: free options table * *------------------------------------------------------------------------- */ int h5repack_end (pack_opt_t *options) { return options_table_free(options->op_tbl); } /*------------------------------------------------------------------------- * Function: h5repack_addfilter * * Purpose: add a compression -t option to table * Example: -t "*:GZIP 6" , STR = "*:GZIP 6" * * Return: 0, ok, -1, fail * *------------------------------------------------------------------------- */ int h5repack_addfilter(const char* str, pack_opt_t *options) { obj_list_t *obj_list=NULL; /*one object list for the -f and -c option entry */ filter_info_t filt; /*filter info for the current -f option entry */ int n_objs; /*number of objects in the current -f or -c option entry */ if (options->all_filter==1){ printf("Error: Invalid compression input: all option is present \ with other objects <%s>\n",str); return -1; } /* parse the -f option */ obj_list=parse_filter(str,&n_objs,&filt,options); if (obj_list==NULL) { return -1; } if (options->all_filter==1) { /* if we are compressing all set the global filter type */ aux_initglb_filter(options); options->filter_g=filt; } if (options->all_filter==0) options_add_filter(obj_list,n_objs,filt,options->op_tbl); free(obj_list); return 0; } /*------------------------------------------------------------------------- * Function: h5repack_addlayout * * Purpose: add a layout option * * Return: 0, ok, -1, fail * *------------------------------------------------------------------------- */ int h5repack_addlayout(const char* str, pack_opt_t *options) { obj_list_t *obj_list=NULL; /*one object list for the -t and -c option entry */ 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; init_packobject(&pack); if (options->all_layout==1){ printf("Error: Invalid layout input: all option \ is present with other objects <%s>\n",str); return -1; } /* parse the layout option */ obj_list=parse_layout(str,&n_objs,&pack,options); if (obj_list==NULL) return -1; /* set global layout option */ if (options->all_layout==1 ) { options->layout_g=pack.layout; if (pack.layout==H5D_CHUNKED) { /* if we are chunking all set the global chunking type */ 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]; } } if (options->all_layout==0) options_add_layout(obj_list, n_objs, &pack, options->op_tbl); free(obj_list); return 0; } /*------------------------------------------------------------------------- * Function: check_options * * Purpose: print options, checks for invalid options * * Return: void, return -1 on error * * Programmer: Pedro Vicente, pvn@ncsa.uiuc.edu * * Date: September, 22, 2003 * *------------------------------------------------------------------------- */ static int check_options(pack_opt_t *options) { int i, k, j, has_cp=0, has_ck=0; unsigned szip_options_mask=H5_SZIP_NN_OPTION_MASK; unsigned szip_pixels_per_block; /*------------------------------------------------------------------------- * objects to layout *------------------------------------------------------------------------- */ if (options->verbose) { printf("\n"); printf("Objects to modify are...\n"); if (options->all_layout==1) { printf("\tApply layout to all\n "); if (H5D_CHUNKED==options->layout_g) { printf("with dimension ["); for ( j = 0; j < options->chunk_g.rank; j++) printf("%d ",(int)options->chunk_g.chunk_lengths[j]); printf("]\n"); } } }/* verbose */ for ( i = 0; i < options->op_tbl->nelems; i++) { char* name=options->op_tbl->objs[i].path; if (options->op_tbl->objs[i].chunk.rank>0) { if (options->verbose){ printf("\t<%s> with chunk size ",name); for ( k = 0; k < options->op_tbl->objs[i].chunk.rank; k++) printf("%d ",(int)options->op_tbl->objs[i].chunk.chunk_lengths[k]); printf("\n"); } has_ck=1; } else if (options->op_tbl->objs[i].chunk.rank==-2) { if (options->verbose) printf("\t%s %s\n",name,"NONE"); has_ck=1; } } if (options->all_layout==1 && has_ck){ printf("Error: Invalid chunking input: all option\ is present with other objects\n"); return -1; } /*------------------------------------------------------------------------- * objects to compress/uncompress *------------------------------------------------------------------------- */ if (options->verbose) { printf("Objects to filter are...\n"); if (options->all_filter==1) { H5Z_filter_t filtn=options->filter_g.filtn; switch (filtn) { case H5Z_FILTER_NONE: printf("\tUncompress all %s\n",get_sfilter(filtn)); break; case H5Z_FILTER_SZIP: printf("\tCompress all with %s compression\n",get_sfilter(filtn)); break; case H5Z_FILTER_DEFLATE: printf("\tCompress all with %s compression, parameter %d\n", get_sfilter(filtn), options->filter_g.cd_values[0]); break; }; } } /* verbose */ for ( i = 0; i < options->op_tbl->nelems; i++) { pack_info_t pack = options->op_tbl->objs[i]; char* name = pack.path; for ( j=0; jverbose) { printf("\t<%s> with %s filter", name, get_sfilter(pack.filter[j].filtn)); } has_cp=1; /*check for invalid combination of options */ switch (pack.filter[j].filtn) { default: break; case H5Z_FILTER_SZIP: szip_pixels_per_block=pack.filter[j].cd_values[0]; /* check szip parameters */ if (check_szip(pack.chunk.rank, pack.chunk.chunk_lengths, 0, /* do not test size */ szip_options_mask, szip_pixels_per_block)==0) { /* Return: 1=can apply the filter 0=cannot apply the filter Reset this object filter info */ options->op_tbl->objs[i].filter[j].filtn=-1; options->op_tbl->objs[i].chunk.rank=-1; printf("\tObject <%s> cannot be filtered\n",name); } break; } /* switch */ } /* j */ } /* i */ if (options->all_filter==1 && has_cp){ printf("Error: Invalid compression input: all option\ is present with other objects\n"); return -1; } return 0; } /*------------------------------------------------------------------------- * Function: read_info * * Purpose: read comp and chunk options from file * * Return: void, exit on error * * Programmer: Pedro Vicente, pvn@ncsa.uiuc.edu * * Date: September, 22, 2003 * *------------------------------------------------------------------------- */ 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) { printf( "Cannot open options file %s", filename); exit(1); } /* Cycle until end of file reached */ while( 1 ) { rc=fscanf(fp, "%s", stype); if (rc==-1) break; /*------------------------------------------------------------------------- * comp *------------------------------------------------------------------------- */ if (strcmp(stype,"-t") == 0) { /* find begining of info */ i=0; c='0'; while( c!='"' ) { fscanf(fp, "%c", &c); } c='0'; /* go until end */ while( c!='"' ) { fscanf(fp, "%c", &c); comp_info[i]=c; i++; } comp_info[i-1]='\0'; /*cut the last " */ if (h5repack_addfilter(comp_info,options)==-1){ printf( "Could not add compression option. Exiting\n"); exit(1); } } /*------------------------------------------------------------------------- * chunk *------------------------------------------------------------------------- */ else if (strcmp(stype,"-c") == 0) { /* find begining of info */ i=0; c='0'; while( c!='"' ) { fscanf(fp, "%c", &c); } c='0'; /* go until end */ while( c!='"' ) { fscanf(fp, "%c", &c); comp_info[i]=c; i++; } comp_info[i-1]='\0'; /*cut the last " */ if (h5repack_addlayout(comp_info,options)==-1){ printf( "Could not add chunck option. Exiting\n"); exit(1); } } /*------------------------------------------------------------------------- * not valid *------------------------------------------------------------------------- */ else { printf( "Bad file format for %s", filename); exit(1); } } fclose(fp); return; }