/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * 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 "H5private.h" #include "h5repack.h" #include "h5tools.h" #include "h5tools_utils.h" extern char *progname; /*------------------------------------------------------------------------- * File: h5repack.c * Purpose: Public API functions *------------------------------------------------------------------------- */ static int check_options(pack_opt_t *options); static int check_objects(const char* fname, pack_opt_t *options); static const char* get_sfilter (H5Z_filter_t filtn); static int have_request(pack_opt_t *options); /*------------------------------------------------------------------------- * Function: h5repack * * Purpose: locate all high-level HDF5 objects in the file * and compress/chunk them using options * * Algorithm: 2 traversals are made to the file; the 1st builds a list of * the objects, the 2nd makes a copy of them, using the options; * the reason for the 1st traversal is to check for invalid * object name requests * * Return: 0, ok, -1, fail * * Programmer: 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, H5F_file_space_type_t strategy, hsize_t threshold) { int k, n; memset(options,0,sizeof(pack_opt_t)); options->min_comp = 1024; options->verbose = verbose; for ( n = 0; n < H5_REPACK_MAX_NFILTERS; n++) { options->filter_g[n].filtn = -1; options->filter_g[n].cd_nelmts = 0; for ( k = 0; k < CD_VALUES; k++) options->filter_g[n].cd_values[k] = 0; } options->fs_strategy = strategy; options->fs_threshold = threshold; 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 -f option to table * Example: -f dset:GZIP=6 * * Return: 0, ok, -1, fail * *------------------------------------------------------------------------- */ int h5repack_addfilter(const char* str, pack_opt_t *options) { obj_list_t *obj_list=NULL; /* one object list for the -f and -l option entry */ filter_info_t filter; /* filter info for the current -f option entry */ 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(progname, "maximum number of filters exceeded for <%s>\n", str); free(obj_list); return -1; } options->filter_g[n] = filter; } else options_add_filter(obj_list, n_objs, filter, 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){ error_msg(progname, "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) { /* -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]; } } } 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: pvn@ncsa.uiuc.edu * * Date: September, 22, 2003 * * Modification: * Peter Cao, July 9, 2007 * Add "-L, --latest" and other options to pack a file with the latest file format * *------------------------------------------------------------------------- */ static int check_options(pack_opt_t *options) { unsigned int i; int k, j, has_cp=0, has_ck=0; char slayout[30]; /*------------------------------------------------------------------------- * objects to layout *------------------------------------------------------------------------- */ if (options->verbose && have_request(options) /* only print if requested */) { printf("Objects to modify layout are...\n"); if (options->all_layout==1) { switch (options->layout_g) { case H5D_COMPACT: strcpy(slayout,"compact"); break; case H5D_CONTIGUOUS: strcpy(slayout,"contiguous"); break; case H5D_CHUNKED: strcpy(slayout,"chunked"); break; case H5D_LAYOUT_ERROR: case H5D_NLAYOUTS: error_msg(progname, "invalid layout\n"); return -1; default: strcpy(slayout,"invalid layout\n"); return -1; } printf(" Apply %s layout to all\n", slayout); 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(" <%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(" <%s> %s\n",name,"NONE (contigous)"); has_ck=1; } } if (options->all_layout==1 && has_ck) { error_msg(progname, "invalid chunking input: 'all' option\ is present with other objects\n"); return -1; } /*------------------------------------------------------------------------- * objects to filter *------------------------------------------------------------------------- */ if (options->verbose && have_request(options) /* only print if requested */) { printf("Objects to apply filter are...\n"); if (options->all_filter==1) { for (k = 0; k < options->n_filter_g; k++ ) { H5Z_filter_t filtn=options->filter_g[k].filtn; switch (filtn) { case H5Z_FILTER_NONE: printf(" Uncompress all\n"); break; case H5Z_FILTER_SHUFFLE: case H5Z_FILTER_FLETCHER32: printf(" All with %s\n",get_sfilter(filtn)); break; case H5Z_FILTER_SZIP: case H5Z_FILTER_DEFLATE: printf(" All with %s, parameter %d\n", get_sfilter(filtn), options->filter_g[k].cd_values[0]); break; default: break; } /* k */ }; } } /* 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(" <%s> with %s filter\n", name, get_sfilter(pack.filter[j].filtn)); } has_cp=1; } /* j */ } /* i */ if (options->all_filter==1 && has_cp) { error_msg(progname, "invalid compression input: 'all' option\ is present with other objects\n"); return -1; } /*------------------------------------------------------------------------- * check options for the latest format *------------------------------------------------------------------------- */ if (options->grp_compact < 0) { error_msg(progname, "invalid maximum number of links to store as header messages\n"); return -1; } if (options->grp_indexed < 0) { error_msg(progname, "invalid minimum number of links to store in the indexed format\n"); return -1; } if (options->grp_indexed > options->grp_compact) { error_msg(progname, "minimum indexed size is greater than the maximum compact size\n"); return -1; } for (i=0; i<8; i++) { if (options->msg_size[i]<0) { error_msg(progname, "invalid shared message size\n"); return -1; } } /*-------------------------------------------------------------------------------- * verify new user userblock options; file name must be present *--------------------------------------------------------------------------------- */ if ( options->ublock_filename != NULL && options->ublock_size == 0 ) { if ( options->verbose ) { printf("Warning: user block size missing for file %s. Assigning a default size of 1024...\n", options->ublock_filename); options->ublock_size = 1024; } } if ( options->ublock_filename == NULL && options->ublock_size != 0 ) { error_msg(progname, "file name missing for user block\n", options->ublock_filename); return -1; } /*-------------------------------------------------------------------------------- * verify alignment options; threshold is zero default but alignment not *--------------------------------------------------------------------------------- */ if ( options->alignment == 0 && options->threshold != 0 ) { error_msg(progname, "alignment for H5Pset_alignment missing\n"); return -1; } return 0; } /*------------------------------------------------------------------------- * Function: check_objects * * Purpose: locate all HDF5 objects in the file and compare with user * supplied list * * Return: 0, ok, -1 no * * Programmer: Pedro Vicente, pvn@ncsa.uiuc.edu * * Date: September, 23, 2003 * *------------------------------------------------------------------------- */ static int check_objects(const char* fname, pack_opt_t *options) { hid_t fid; unsigned int i; trav_table_t *travt = NULL; /* nothing to do */ if(options->op_tbl->nelems == 0) return 0; /*------------------------------------------------------------------------- * open the file *------------------------------------------------------------------------- */ if((fid = h5tools_fopen(fname, H5F_ACC_RDONLY, H5P_DEFAULT, NULL, NULL, 0)) < 0) { printf("<%s>: %s\n", fname, H5FOPENERROR ); return -1; } /*------------------------------------------------------------------------- * get the list of objects in the file *------------------------------------------------------------------------- */ /* init table */ trav_table_init(&travt); /* get the list of objects in the file */ if(h5trav_gettable(fid, travt) < 0) goto out; /*------------------------------------------------------------------------- * compare with user supplied list *------------------------------------------------------------------------- */ if(options->verbose) printf("Opening file <%s>. Searching for objects to modify...\n", fname); for(i = 0; i < options->op_tbl->nelems; i++) { char* name=options->op_tbl->objs[i].path; if(options->verbose) printf(" <%s>",name); /* the input object names are present in the file and are valid */ if(h5trav_getindext(name, travt) < 0) { error_msg(progname, "%s Could not find <%s> in file <%s>. Exiting...\n", (options->verbose?"\n":""),name,fname); goto out; } if(options->verbose) printf("...Found\n"); /* check for extra filter conditions */ switch(options->op_tbl->objs[i].filter->filtn) { /* chunk size must be smaller than pixels per block */ case H5Z_FILTER_SZIP: { int j; hsize_t csize = 1; unsigned ppb = options->op_tbl->objs[i].filter->cd_values[0]; hsize_t dims[H5S_MAX_RANK]; int rank; hid_t did; hid_t sid; if(options->op_tbl->objs[i].chunk.rank > 0) { rank = options->op_tbl->objs[i].chunk.rank; for(j = 0; j < rank; j++) csize *= options->op_tbl->objs[i].chunk.chunk_lengths[j]; } else { if((did = H5Dopen2(fid, name, H5P_DEFAULT)) < 0) goto out; if((sid = H5Dget_space(did)) < 0) goto out; if((rank = H5Sget_simple_extent_ndims(sid)) < 0) goto out; HDmemset(dims, 0, sizeof dims); if(H5Sget_simple_extent_dims(sid, dims, NULL) < 0) goto out; for(j = 0; j < rank; j++) csize *= dims[j]; if(H5Sclose(sid) < 0) goto out; if(H5Dclose(did) < 0) goto out; } if (csize < ppb ) { printf(" \n"); goto out; } } break; default: break; } } /* i */ /*------------------------------------------------------------------------- * close *------------------------------------------------------------------------- */ H5Fclose(fid); trav_table_free(travt); return 0; out: H5Fclose(fid); trav_table_free(travt); return -1; } /*------------------------------------------------------------------------- * Function: have_request * * Purpose: check if a filter or layout was requested * * Return: 1 yes, 0 no * * Date: May, 24, 2007 * *------------------------------------------------------------------------- */ static int have_request(pack_opt_t *options) { if (options->all_filter || options->all_layout || options->op_tbl->nelems) return 1; return 0; } /*------------------------------------------------------------------------- * Function: get_sfilter * * Purpose: return the filter as a string name * * Return: name of filter, exit on error * *------------------------------------------------------------------------- */ static const char* get_sfilter(H5Z_filter_t filtn) { if (filtn==H5Z_FILTER_NONE) return "NONE"; else if (filtn==H5Z_FILTER_DEFLATE) return "GZIP"; else if (filtn==H5Z_FILTER_SZIP) return "SZIP"; else if (filtn==H5Z_FILTER_SHUFFLE) return "SHUFFLE"; else if (filtn==H5Z_FILTER_FLETCHER32) return "FLETCHER32"; else if (filtn==H5Z_FILTER_NBIT) return "NBIT"; else if (filtn==H5Z_FILTER_SCALEOFFSET) return "SOFF"; else { error_msg(progname, "input error in filter type\n"); exit(EXIT_FAILURE); } }