/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * 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" /*------------------------------------------------------------------------- * 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) { 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; } 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(h5tools_getprogname(), "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(h5tools_getprogname(), "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; } /* Note: The below copy_named_datatype(), named_datatype_free(), copy_attr() * were located in h5repack_copy.c as static prior to bugfix1726. * Made shared functions as copy_attr() was needed in h5repack_refs.c. * However copy_attr() may be obsoleted when H5Acopy is available and put back * others to static in h5repack_copy.c. */ /*------------------------------------------------------------------------- * Function: copy_named_datatype * * Purpose: Copies the specified datatype anonymously, and returns an open * id for that datatype in the output file. The first time this * is called it scans every named datatype in travt into a * private stack, afterwards it simply scans that stack. The id * returned must be closed after it is no longer needed. * named_datatype_free must be called before the program exits * to free the stack. * * Programmer: Neil Fortner * * Date: April 14, 2009 * *------------------------------------------------------------------------- */ hid_t copy_named_datatype(hid_t type_in, hid_t fidout, named_dt_t **named_dt_head_p, trav_table_t *travt, pack_opt_t *options) { named_dt_t *dt = *named_dt_head_p; /* Stack pointer */ named_dt_t *dt_ret = NULL; /* Datatype to return */ H5O_info_t oinfo; /* Object info of input dtype */ hid_t ret_value = -1; /* The identifier of the named dtype in the out file */ if(H5Oget_info(type_in, &oinfo) < 0) goto error; if(*named_dt_head_p) { /* Stack already exists, search for the datatype */ while(dt && dt->addr_in != oinfo.addr) dt = dt->next; dt_ret = dt; } else { /* Create the stack */ size_t i; for(i=0; inobjs; i++) if(travt->objs[i].type == H5TRAV_TYPE_NAMED_DATATYPE) { /* Push onto the stack */ if(NULL == (dt = (named_dt_t *) HDmalloc(sizeof(named_dt_t)))) goto error; dt->next = *named_dt_head_p; *named_dt_head_p = dt; /* Update the address and id */ dt->addr_in = travt->objs[i].objno; dt->id_out = -1; /* Check if this type is the one requested */ if(oinfo.addr == dt->addr_in) { HDassert(!dt_ret); dt_ret = dt; } /* end if */ } /* end if */ } /* end else */ /* Handle the case that the requested datatype was not found. This is * possible if the datatype was committed anonymously in the input file. */ if(!dt_ret) { /* Push the new datatype onto the stack */ if(NULL == (dt_ret = (named_dt_t *) HDmalloc(sizeof(named_dt_t)))) goto error; dt_ret->next = *named_dt_head_p; *named_dt_head_p = dt_ret; /* Update the address and id */ dt_ret->addr_in = oinfo.addr; dt_ret->id_out = -1; } /* end if */ /* If the requested datatype does not yet exist in the output file, copy it * anonymously */ if(dt_ret->id_out < 0) { if (options->use_native==1) dt_ret->id_out = h5tools_get_native_type(type_in); else dt_ret->id_out = H5Tcopy(type_in); if(dt_ret->id_out < 0) goto error; if(H5Tcommit_anon(fidout, dt_ret->id_out, H5P_DEFAULT, H5P_DEFAULT) < 0) goto error; } /* end if */ /* Set return value */ ret_value = dt_ret->id_out; /* Increment the ref count on id_out, because the calling function will try * to close it */ if(H5Iinc_ref(ret_value) < 0) goto error; return(ret_value); error: return(-1); } /* end copy_named_datatype */ /*------------------------------------------------------------------------- * Function: named_datatype_free * * Purpose: Frees the stack of named datatypes. * * Programmer: Neil Fortner * * Date: April 14, 2009 * *------------------------------------------------------------------------- */ int named_datatype_free(named_dt_t **named_dt_head_p, int ignore_err) { named_dt_t *dt = *named_dt_head_p; while(dt) { /* Pop the datatype off the stack and free it */ if(H5Tclose(dt->id_out) < 0 && !ignore_err) goto error; dt = dt->next; HDfree(*named_dt_head_p); *named_dt_head_p = dt; } /* end while */ return 0; error: return -1; } /* end named_datatype_free */ /*------------------------------------------------------------------------- * Function: copy_attr * * Purpose: copy attributes located in LOC_IN, which is obtained either from * loc_id = H5Gopen2( fid, name); * loc_id = H5Dopen2( fid, name); * loc_id = H5Topen2( fid, name); * * Return: 0, ok, -1 no * * Programmer: Pedro Vicente, pvn@ncsa.uiuc.edu * * Date: October, 28, 2003 * *------------------------------------------------------------------------- */ 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; if(H5Oget_info(loc_in, &oinfo) < 0) goto error; /*------------------------------------------------------------------------- * copy all attributes *------------------------------------------------------------------------- */ for ( u = 0; u < (unsigned)oinfo.num_attrs; u++) { buf=NULL; /* 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) { 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 */ /* 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; juse_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; /*------------------------------------------------------------------------- * 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 *------------------------------------------------------------------------- */ if (H5T_REFERENCE==H5Tget_class(wtype_id)) { ; } else { /*------------------------------------------------------------------------- * read to memory *------------------------------------------------------------------------- */ buf = (void *)HDmalloc((size_t)(nelmts * msize)); if(buf == NULL) { error_msg(h5tools_getprogname(), "cannot read into memory\n" ); goto error; } 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; if(buf) free(buf); } /*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 { H5Tclose(ftype_id); H5Tclose(wtype_id); H5Sclose(space_id); H5Aclose(attr_id); H5Aclose(attr_out); if (buf) free(buf); } H5E_END_TRY; return -1; } /*------------------------------------------------------------------------- * 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(h5tools_getprogname(), "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(h5tools_getprogname(), "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(h5tools_getprogname(), "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(h5tools_getprogname(), "invalid maximum number of links to store as header messages\n"); return -1; } if (options->grp_indexed < 0) { error_msg(h5tools_getprogname(), "invalid minimum number of links to store in the indexed format\n"); return -1; } if (options->grp_indexed > options->grp_compact) { error_msg(h5tools_getprogname(), "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(h5tools_getprogname(), "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(h5tools_getprogname(), "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(h5tools_getprogname(), "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(h5tools_getprogname(), "%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(h5tools_getprogname(), "input error in filter type\n"); exit(EXIT_FAILURE); } }