From f79eac6049aaf951cbd109214b8c45f6174fd4e7 Mon Sep 17 00:00:00 2001 From: Allen Byrne Date: Mon, 9 Sep 2013 13:30:25 -0500 Subject: [svn-r24116] Correct indentation and create single exit point. Tested : local linux --- tools/h5repack/h5repack.c | 1818 ++++++++++---------- tools/h5repack/h5repack_copy.c | 3243 ++++++++++++++++++------------------ tools/h5repack/h5repack_main.c | 1105 ++++++------ tools/h5repack/h5repack_opttable.c | 530 +++--- 4 files changed, 3270 insertions(+), 3426 deletions(-) diff --git a/tools/h5repack/h5repack.c b/tools/h5repack/h5repack.c index 5c44e1a..742bb06 100644 --- a/tools/h5repack/h5repack.c +++ b/tools/h5repack/h5repack.c @@ -1,17 +1,17 @@ /* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * -* 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. * -* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ + * 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 @@ -23,223 +23,198 @@ #include "h5tools_utils.h" /*------------------------------------------------------------------------- -* File: h5repack.c -* Purpose: Public API functions -*------------------------------------------------------------------------- -*/ + * 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 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; -/*------------------------------------------------------------------------- -* 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; + /* 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; -/*------------------------------------------------------------------------- -* 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; - - HDmemset(options, 0, sizeof(pack_opt_t)); - options->min_comp = 0; - options->verbose = verbose; - options->layout_g = H5D_LAYOUT_ERROR; - - 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))); -} + HDmemset(options, 0, sizeof(pack_opt_t)); + options->min_comp = 0; + options->verbose = verbose; + options->layout_g = H5D_LAYOUT_ERROR; + 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; + } -/*------------------------------------------------------------------------- -* Function: h5repack_end -* -* Purpose: free options table -* -*------------------------------------------------------------------------- -*/ - -int h5repack_end (pack_opt_t *options) -{ - return options_table_free(options->op_tbl); -} + options->fs_strategy = strategy; + options->fs_threshold = threshold; + return (options_table_init(&(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("maximum number of filters exceeded for <%s>\n", str); - HDfree(obj_list); - return -1; - } - - options->filter_g[n] = filter; - } - else - options_add_filter(obj_list, n_objs, filter, options->op_tbl); - - HDfree(obj_list); - return 0; + * 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("maximum number of filters exceeded for <%s>\n", str); + HDfree(obj_list); + return -1; + } + + options->filter_g[n] = filter; + } + else + options_add_filter(obj_list, n_objs, filter, options->op_tbl); + + HDfree(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("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 layout option */ - options->layout_g = pack.layout; - - /* no individual dataset specified */ - if (options->all_layout==1 ) - { - 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]; - } - } - } - - /* individual dataset specified */ - if (options->all_layout==0) - options_add_layout(obj_list, - n_objs, - &pack, - options->op_tbl); - - HDfree(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; + int ret_value = -1; + + init_packobject(&pack); + + if (options->all_layout == 1) { + error_msg( + "invalid layout input: 'all' option \ + is present with other objects <%s>\n", + str); + return ret_value; + } + + /* parse the layout option */ + obj_list = parse_layout(str, &n_objs, &pack, options); + if (obj_list) { + + /* set layout option */ + options->layout_g = pack.layout; + + /* no individual dataset specified */ + if (options->all_layout == 1) { + 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]; + } + } + } + + /* individual dataset specified */ + if (options->all_layout == 0) + ret_value = options_add_layout(obj_list, n_objs, &pack, options->op_tbl); + + HDfree(obj_list); + ret_value = 0; + } + + return ret_value; } /* Note: The below copy_named_datatype(), named_datatype_free(), copy_attr() @@ -249,765 +224,720 @@ int h5repack_addlayout(const char* str, * 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); + * 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 done; + + 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; i < travt->nobjs; 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 done; + } + 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 for */ + } /* 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 done; + } + 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 done; + if (H5Tcommit_anon(fidout, dt_ret->id_out, H5P_DEFAULT, H5P_DEFAULT) < 0) + goto done; + } /* 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) { + ret_value = -1; + } + +done: + return (ret_value); } /* 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; + * 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; + hid_t ret_value = -1; + + while (dt) { + /* Pop the datatype off the stack and free it */ + if (H5Tclose(dt->id_out) < 0 && !ignore_err) + goto done; + dt = dt->next; + HDfree(*named_dt_head_p); + *named_dt_head_p = dt; + } /* end while */ + + ret_value = 0; + +done: + return (ret_value); } /* 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; - hbool_t is_ref=0; - H5T_class_t type_class = -1; - - if(H5Oget_info(loc_in, &oinfo) < 0) - goto error; - - /*------------------------------------------------------------------------- - * copy all attributes - *------------------------------------------------------------------------- - */ - for(u = 0; u < (unsigned)oinfo.num_attrs; u++) { - /* 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 && travt) { - 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 */ - else { - if(options->use_native == 1) - wtype_id = h5tools_get_native_type(ftype_id); - else - wtype_id = H5Tcopy(ftype_id); - } /* end else */ - - - /* 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; j < rank; j++) - nelmts *= dims[j]; - - 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 at copy_refs_attr() - *------------------------------------------------------------------------- - */ - type_class = H5Tget_class(wtype_id); - is_ref = (type_class == H5T_REFERENCE); - if (type_class == H5T_VLEN ||type_class == H5T_ARRAY ) { - hid_t base_type = -1; - base_type = H5Tget_super(ftype_id); - is_ref = (is_ref || (H5Tget_class(base_type)==H5T_REFERENCE)); - H5Tclose(base_type); - } - - if (type_class == H5T_COMPOUND) { - int nmembers = H5Tget_nmembers(wtype_id) ; - for (j=0; jverbose) - 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; + * 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; + hbool_t is_ref = 0; + H5T_class_t type_class = -1; + + if (H5Oget_info(loc_in, &oinfo) < 0) + goto error; + + /*------------------------------------------------------------------------- + * copy all attributes + *------------------------------------------------------------------------- + */ + for (u = 0; u < (unsigned) oinfo.num_attrs; u++) { + /* 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 && travt) { + 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 */ + else { + if (options->use_native == 1) + wtype_id = h5tools_get_native_type(ftype_id); + else + wtype_id = H5Tcopy(ftype_id); + } /* end else */ + + /* 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; j < rank; j++) + nelmts *= dims[j]; + + 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 at copy_refs_attr() + *------------------------------------------------------------------------- + */ + type_class = H5Tget_class(wtype_id); + is_ref = (type_class == H5T_REFERENCE); + if (type_class == H5T_VLEN || type_class == H5T_ARRAY) { + hid_t base_type = -1; + base_type = H5Tget_super(ftype_id); + is_ref = (is_ref || (H5Tget_class(base_type) == H5T_REFERENCE)); + H5Tclose(base_type); + } + + if (type_class == H5T_COMPOUND) { + int nmembers = H5Tget_nmembers(wtype_id); + for (j = 0; j < nmembers; j++) { + hid_t mtid = H5Tget_member_type(wtype_id, (unsigned) j); + H5T_class_t mtclass = H5Tget_class(mtid); + H5Tclose(mtid); + + if (mtclass == H5T_REFERENCE) { + is_ref = 1; + break; + } + } /* for (j=0; iverbose) + 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 { - if(buf) { - /* Check if we have VL data and string in the attribute's datatype that must - * be reclaimed */ - if (TRUE == h5tools_detect_vlen(wtype_id)) - H5Dvlen_reclaim(wtype_id, space_id, H5P_DEFAULT, buf); - - /* Free buf */ - HDfree(buf); - } /* end if */ - - H5Tclose(ftype_id); - H5Tclose(wtype_id); - H5Sclose(space_id); - H5Aclose(attr_id); - H5Aclose(attr_out); - } H5E_END_TRY; - - return -1; + H5E_BEGIN_TRY + { + if (buf) { + /* Check if we have VL data and string in the attribute's datatype that must + * be reclaimed */ + if (TRUE == h5tools_detect_vlen(wtype_id)) + H5Dvlen_reclaim(wtype_id, space_id, H5P_DEFAULT, buf); + + /* Free buf */ + HDfree(buf); + } /* end if */ + + H5Tclose(ftype_id); + H5Tclose(wtype_id); + H5Sclose(space_id); + H5Aclose(attr_id); + H5Aclose(attr_out); + } H5E_END_TRY; + + return -1; } /* end copy_attr() */ /*------------------------------------------------------------------------- -* 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("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("invalid chunking input: 'all' option\ + * 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("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( + "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: - printf(" User Defined %d\n", filtn); - 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("invalid compression input: 'all' option\ + 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: + printf(" User Defined %d\n", filtn); + 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; j < pack.nfilters; j++) { + if (options->verbose) { + 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( + "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("invalid maximum number of links to store as header messages\n"); - return -1; - } - if (options->grp_indexed < 0) - { - error_msg("invalid minimum number of links to store in the indexed format\n"); - return -1; - } - if (options->grp_indexed > options->grp_compact) - { - error_msg("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("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("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("alignment for H5Pset_alignment missing\n"); - return -1; - } - - return 0; + return -1; + } + + /*------------------------------------------------------------------------- + * check options for the latest format + *------------------------------------------------------------------------- + */ + + if (options->grp_compact < 0) { + error_msg( + "invalid maximum number of links to store as header messages\n"); + return -1; + } + if (options->grp_indexed < 0) { + error_msg( + "invalid minimum number of links to store in the indexed format\n"); + return -1; + } + if (options->grp_indexed > options->grp_compact) { + error_msg( + "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("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("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("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("%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; + * 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("%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; + 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; - - -/*------------------------------------------------------------------------- -* 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; + 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 - return "UD"; + * 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 + return "UD"; } diff --git a/tools/h5repack/h5repack_copy.c b/tools/h5repack/h5repack_copy.c index 2133b48..521b9bd 100644 --- a/tools/h5repack/h5repack_copy.c +++ b/tools/h5repack/h5repack_copy.c @@ -1,36 +1,36 @@ /* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * -* 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. * -* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ + * 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 "h5repack.h" #include "h5tools.h" #include "h5tools_utils.h" /*------------------------------------------------------------------------- -* typedefs -*------------------------------------------------------------------------- -*/ + * typedefs + *------------------------------------------------------------------------- + */ /*------------------------------------------------------------------------- -* globals -*------------------------------------------------------------------------- -*/ + * globals + *------------------------------------------------------------------------- + */ /*------------------------------------------------------------------------- -* macros -*------------------------------------------------------------------------- -*/ + * macros + *------------------------------------------------------------------------- + */ /* size of buffer/# of bytes to xfer at a time when copying userblock */ #define USERBLOCK_XFER_SIZE 512 @@ -48,1705 +48,1630 @@ } \ } H5E_END_TRY; \ } - + /*------------------------------------------------------------------------- -* local functions -*------------------------------------------------------------------------- -*/ -static int Get_hyperslab (hid_t dcpl_id, int rank_dset, hsize_t dims_dset[], size_t size_datum, hsize_t dims_hslab[], hsize_t * hslab_nbytes_p); -static void print_dataset_info(hid_t dcpl_id,char *objname,double per, int pr); -static int do_copy_objects(hid_t fidin,hid_t fidout,trav_table_t *travt,pack_opt_t *options); -static int copy_user_block(const char *infile, const char *outfile, hsize_t size); + * local functions + *------------------------------------------------------------------------- + */ +static int Get_hyperslab(hid_t dcpl_id, int rank_dset, hsize_t dims_dset[], + size_t size_datum, hsize_t dims_hslab[], hsize_t * hslab_nbytes_p); +static void print_dataset_info(hid_t dcpl_id, char *objname, double per, int pr); +static int do_copy_objects(hid_t fidin, hid_t fidout, trav_table_t *travt, + pack_opt_t *options); +static int copy_user_block(const char *infile, const char *outfile, + hsize_t size); #if defined (H5REPACK_DEBUG_USER_BLOCK) -static void print_user_block(const char *filename, hid_t fid); +static void print_user_block(const char *filename, hid_t fid); #endif static herr_t walk_error_callback(unsigned n, const H5E_error2_t *err_desc, void *udata); /* get the major number from the error stack. */ -static herr_t walk_error_callback(UNUSED unsigned n, const H5E_error2_t *err_desc, void *udata) -{ - if (err_desc) - *((int *)udata) = err_desc->maj_num; - - return 0; +static herr_t walk_error_callback(UNUSED unsigned n, const H5E_error2_t *err_desc, void *udata) { + if (err_desc) + *((int *) udata) = err_desc->maj_num; + + return 0; } /*------------------------------------------------------------------------- -* Function: copy_objects -* -* Purpose: duplicate all HDF5 objects in the file -* -* Return: 0, ok, -1 no -* -* Programmer: Pedro Vicente, pvn@ncsa.uiuc.edu -* -* Date: October, 23, 2003 -* -* Modification: -* Peter Cao, June 13, 2007 -* Add "-L, --latest" and other options to pack a file with the latest file format -* -* Peter Cao, September 25, 2007 -* Copy user block when repacking a file -* -* Pedro Vicente, August 20, 2008 -* Add a user block to file if requested -* -*------------------------------------------------------------------------- -*/ - -int copy_objects(const char* fnamein, - const char* fnameout, - pack_opt_t *options) -{ - hid_t fidin; - hid_t fidout = -1; - trav_table_t *travt = NULL; - hsize_t ub_size = 0; /* size of user block */ - hid_t fcpl = H5P_DEFAULT; /* file creation property list ID */ - hid_t fapl = H5P_DEFAULT; /* file access property list ID */ - - /*------------------------------------------------------------------------- - * open input file - *------------------------------------------------------------------------- - */ - if((fidin = h5tools_fopen(fnamein, H5F_ACC_RDONLY, H5P_DEFAULT, NULL, NULL, (size_t)0)) < 0) - { - error_msg("<%s>: %s\n", fnamein, H5FOPENERROR ); - goto out; - } - - /* get user block size and file space strategy/threshold */ - { - hid_t fcpl_in; /* file creation property list ID for input file */ - - if((fcpl_in = H5Fget_create_plist(fidin)) < 0) - { - error_msg("failed to retrieve file creation property list\n"); - goto out; - } - - if(H5Pget_userblock(fcpl_in, &ub_size) < 0) - { - error_msg("failed to retrieve userblock size\n"); - goto out; - } - - if(!options->fs_strategy) - { - if(H5Pget_file_space(fcpl_in, &options->fs_strategy, NULL) < 0) - { - error_msg("failed to retrieve file space strategy\n"); - goto out; - } - } - - if(!options->fs_threshold) - { - if(H5Pget_file_space(fcpl_in, NULL, &options->fs_threshold) < 0) - { - error_msg("failed to retrieve file space threshold\n"); - goto out; - } - } - - if(H5Pclose(fcpl_in) < 0) - { - error_msg("failed to close property list\n"); - goto out; - } - } - - /* Check if we need to create a non-default file creation property list */ - if(options->latest || ub_size > 0) - { - /* Create file creation property list */ - if((fcpl = H5Pcreate(H5P_FILE_CREATE)) < 0) - { - error_msg("fail to create a file creation property list\n"); - goto out; - } - - if(ub_size > 0) - { - if(H5Pset_userblock(fcpl, ub_size) < 0) - { - error_msg("failed to set non-default userblock size\n"); - goto out; - } - } - - if(options->latest) - { - unsigned i = 0, nindex = 0, mesg_type_flags[5], min_mesg_sizes[5]; - - /* Adjust group creation parameters for root group */ - /* (So that it is created in "dense storage" form) */ - if(H5Pset_link_phase_change(fcpl, (unsigned)options->grp_compact, (unsigned)options->grp_indexed) < 0) - { - error_msg("fail to adjust group creation parameters for root group\n"); - goto out; - } - - for(i = 0; i < 5; i++) - { - if(options->msg_size[i] > 0) - { - switch(i) - { - case 0: - mesg_type_flags[nindex] = H5O_SHMESG_SDSPACE_FLAG; - break; - - case 1: - mesg_type_flags[nindex] = H5O_SHMESG_DTYPE_FLAG; - break; - - case 2: - mesg_type_flags[nindex] = H5O_SHMESG_FILL_FLAG; - break; - - case 3: - mesg_type_flags[nindex] = H5O_SHMESG_PLINE_FLAG; - break; - - case 4: - mesg_type_flags[nindex] = H5O_SHMESG_ATTR_FLAG; - break; - default: - break; - } /* end switch */ - min_mesg_sizes[nindex] = (unsigned)options->msg_size[i]; - - nindex++; - } /* end if */ - } /* end for */ - - if(nindex > 0) - { - if(H5Pset_shared_mesg_nindexes(fcpl, nindex) < 0) - { - error_msg("fail to set the number of shared object header message indexes\n"); - goto out; - } - - /* msg_size[0]=dataspace, 1=datatype, 2=file value, 3=filter pipleline, 4=attribute */ - for(i = 0; i < (nindex - 1); i++) - { - if(H5Pset_shared_mesg_index(fcpl, i, mesg_type_flags[i], min_mesg_sizes[i]) < 0) { - error_msg("fail to configure the specified shared object header message index\n"); - goto out; - } /* end if */ - } /* end for */ - } /* if (nindex>0) */ - - /* Create file access property list */ - if((fapl = H5Pcreate(H5P_FILE_ACCESS)) < 0) - { - error_msg("Could not create file access property list\n"); - goto out; - } /* end if */ - - if(H5Pset_libver_bounds(fapl, H5F_LIBVER_LATEST, H5F_LIBVER_LATEST) < 0) - { - error_msg("Could not set property for using latest version of the format\n"); - goto out; - } /* end if */ - } /* end if */ - } /* end if */ + * Function: copy_objects + * + * Purpose: duplicate all HDF5 objects in the file + * + * Return: 0, ok, -1 no + * + * Programmer: Pedro Vicente, pvn@ncsa.uiuc.edu + * + * Date: October, 23, 2003 + * + * Modification: + * Peter Cao, June 13, 2007 + * Add "-L, --latest" and other options to pack a file with the latest file format + * + * Peter Cao, September 25, 2007 + * Copy user block when repacking a file + * + * Pedro Vicente, August 20, 2008 + * Add a user block to file if requested + * + *------------------------------------------------------------------------- + */ + +int copy_objects(const char* fnamein, const char* fnameout, pack_opt_t *options) { + hid_t fidin; + hid_t fidout = -1; + trav_table_t *travt = NULL; + hsize_t ub_size = 0; /* size of user block */ + hid_t fcpl = H5P_DEFAULT; /* file creation property list ID */ + hid_t fapl = H5P_DEFAULT; /* file access property list ID */ + + /*------------------------------------------------------------------------- + * open input file + *------------------------------------------------------------------------- + */ + if ((fidin = h5tools_fopen(fnamein, H5F_ACC_RDONLY, H5P_DEFAULT, NULL, NULL, + (size_t) 0)) < 0) { + error_msg("<%s>: %s\n", fnamein, H5FOPENERROR); + goto out; + } + + /* get user block size and file space strategy/threshold */ + { + hid_t fcpl_in; /* file creation property list ID for input file */ + + if ((fcpl_in = H5Fget_create_plist(fidin)) < 0) { + error_msg("failed to retrieve file creation property list\n"); + goto out; + } + + if (H5Pget_userblock(fcpl_in, &ub_size) < 0) { + error_msg("failed to retrieve userblock size\n"); + goto out; + } + + if (!options->fs_strategy) { + if (H5Pget_file_space(fcpl_in, &options->fs_strategy, NULL) < 0) { + error_msg("failed to retrieve file space strategy\n"); + goto out; + } + } + + if (!options->fs_threshold) { + if (H5Pget_file_space(fcpl_in, NULL, &options->fs_threshold) < 0) { + error_msg("failed to retrieve file space threshold\n"); + goto out; + } + } + + if (H5Pclose(fcpl_in) < 0) { + error_msg("failed to close property list\n"); + goto out; + } + } + + /* Check if we need to create a non-default file creation property list */ + if (options->latest || ub_size > 0) { + /* Create file creation property list */ + if ((fcpl = H5Pcreate(H5P_FILE_CREATE)) < 0) { + error_msg("fail to create a file creation property list\n"); + goto out; + } + + if (ub_size > 0) { + if (H5Pset_userblock(fcpl, ub_size) < 0) { + error_msg("failed to set non-default userblock size\n"); + goto out; + } + } + + if (options->latest) { + unsigned i = 0, nindex = 0, mesg_type_flags[5], min_mesg_sizes[5]; + + /* Adjust group creation parameters for root group */ + /* (So that it is created in "dense storage" form) */ + if (H5Pset_link_phase_change(fcpl, (unsigned) options->grp_compact, + (unsigned) options->grp_indexed) < 0) { + error_msg( + "fail to adjust group creation parameters for root group\n"); + goto out; + } + + for (i = 0; i < 5; i++) { + if (options->msg_size[i] > 0) { + switch (i) { + case 0: + mesg_type_flags[nindex] = H5O_SHMESG_SDSPACE_FLAG; + break; + + case 1: + mesg_type_flags[nindex] = H5O_SHMESG_DTYPE_FLAG; + break; + + case 2: + mesg_type_flags[nindex] = H5O_SHMESG_FILL_FLAG; + break; + + case 3: + mesg_type_flags[nindex] = H5O_SHMESG_PLINE_FLAG; + break; + + case 4: + mesg_type_flags[nindex] = H5O_SHMESG_ATTR_FLAG; + break; + default: + break; + } /* end switch */ + min_mesg_sizes[nindex] = (unsigned) options->msg_size[i]; + + nindex++; + } /* end if */ + } /* end for */ + + if (nindex > 0) { + if (H5Pset_shared_mesg_nindexes(fcpl, nindex) < 0) { + error_msg( + "fail to set the number of shared object header message indexes\n"); + goto out; + } + + /* msg_size[0]=dataspace, 1=datatype, 2=file value, 3=filter pipleline, 4=attribute */ + for (i = 0; i < (nindex - 1); i++) { + if (H5Pset_shared_mesg_index(fcpl, i, mesg_type_flags[i], + min_mesg_sizes[i]) < 0) { + error_msg( + "fail to configure the specified shared object header message index\n"); + goto out; + } /* end if */ + } /* end for */ + } /* if (nindex>0) */ + + /* Create file access property list */ + if ((fapl = H5Pcreate(H5P_FILE_ACCESS)) < 0) { + error_msg("Could not create file access property list\n"); + goto out; + } /* end if */ + + if (H5Pset_libver_bounds(fapl, H5F_LIBVER_LATEST, H5F_LIBVER_LATEST) < 0) { + error_msg( + "Could not set property for using latest version of the format\n"); + goto out; + } /* end if */ + } /* end if */ + } /* end if */ #if defined (H5REPACK_DEBUG_USER_BLOCK) - print_user_block(fnamein, fidin); + print_user_block(fnamein, fidin); #endif - /*------------------------------------------------------------------------- - * set the new user userblock options in the FCPL (before H5Fcreate ) - *------------------------------------------------------------------------- - */ - if ( options->ublock_size > 0 ) - { - /* either use the FCPL already created or create a new one */ - if(fcpl == H5P_DEFAULT) - { - /* create a file creation property list */ - if((fcpl = H5Pcreate(H5P_FILE_CREATE)) < 0) - { - error_msg("fail to create a file creation property list\n"); - goto out; - } - } - - /* set user block size */ - if(H5Pset_userblock(fcpl, options->ublock_size) < 0) - { - error_msg("failed to set userblock size\n"); - goto out; - } - } - - /*------------------------------------------------------------------------- - * set alignment options - *------------------------------------------------------------------------- - */ - if ( options->alignment > 0 ) - { - /* either use the FAPL already created or create a new one */ - if (fapl == H5P_DEFAULT) - { - /* create a file access property list */ - if ((fapl = H5Pcreate(H5P_FILE_ACCESS)) < 0) - { - error_msg("Could not create file access property list\n"); - goto out; - } - } - - if (H5Pset_alignment(fapl, options->threshold, options->alignment) < 0) - { - error_msg("failed to set alignment\n"); - goto out; - } - } - - /*------------------------------------------------------------------------- - * set metadata block size option - *------------------------------------------------------------------------- - */ - if ( options->meta_block_size > 0 ) - { - /* either use the FAPL already created or create a new one */ - if (fapl == H5P_DEFAULT) - { - /* create a file access property list */ - if ((fapl = H5Pcreate(H5P_FILE_ACCESS)) < 0) - { - error_msg("Could not create file access property list\n"); - goto out; - } - } - - if (H5Pset_meta_block_size(fapl, options->meta_block_size) < 0) - { - error_msg("failed to set metadata block size\n"); - goto out; - } - } - - /*------------------------------------------------------------------------- - * set free-space strategy options - *------------------------------------------------------------------------- - */ - - /* either use the FCPL already created or create a new one */ - if(fcpl == H5P_DEFAULT) - { - /* create a file creation property list */ - if((fcpl = H5Pcreate(H5P_FILE_CREATE)) < 0) - { - error_msg("fail to create a file creation property list\n"); - goto out; - } - } - - /* set file space strategy and free space threshold */ - if(H5Pset_file_space(fcpl, options->fs_strategy, options->fs_threshold) < 0) - { - error_msg("failed to set file space strategy & threshold \n"); - goto out; - } - - /*------------------------------------------------------------------------- - * create the output file - *------------------------------------------------------------------------- - */ - if(options->verbose) - printf("Making file <%s>...\n",fnameout); - - if((fidout = H5Fcreate(fnameout,H5F_ACC_TRUNC, fcpl, fapl)) < 0) - { - error_msg("<%s>: Could not create file\n", fnameout ); - goto out; - } - - - /*------------------------------------------------------------------------- - * write a new user block if requested - *------------------------------------------------------------------------- - */ - if ( options->ublock_size > 0 ) - { - if ( copy_user_block( options->ublock_filename, fnameout, options->ublock_size) < 0 ) - { - error_msg("Could not copy user block. Exiting...\n"); - goto out; - - } - } - - /*------------------------------------------------------------------------- - * get list of objects - *------------------------------------------------------------------------- - */ - - /* init table */ - trav_table_init(&travt); - - /* get the list of objects in the file */ - if(h5trav_gettable(fidin, travt) < 0) - goto out; - - /*------------------------------------------------------------------------- - * do the copy - *------------------------------------------------------------------------- - */ - if(do_copy_objects(fidin, fidout, travt, options) < 0) - { - error_msg("<%s>: Could not copy data to: %s\n", fnamein, fnameout); - goto out; - } /* end if */ - - /*------------------------------------------------------------------------- - * do the copy of referenced objects - * and create hard links - *------------------------------------------------------------------------- - */ - if ( do_copy_refobjs(fidin, fidout, travt, options) < 0 ) - { - printf("h5repack: <%s>: Could not copy data to: %s\n", fnamein, fnameout); - goto out; - } - - /*------------------------------------------------------------------------- - * close - *------------------------------------------------------------------------- - */ - - if(fapl > 0) - H5Pclose(fapl); - - if(fcpl > 0) - H5Pclose(fcpl); - - H5Fclose(fidin); - H5Fclose(fidout); - - /* free table */ - trav_table_free(travt); - travt = NULL; - - /*------------------------------------------------------------------------- - * write only the input file user block if there is no user block file input - *------------------------------------------------------------------------- - */ - - if( ub_size > 0 && options->ublock_size == 0 ) - { - if ( copy_user_block(fnamein, fnameout, ub_size) < 0 ) - { - error_msg("Could not copy user block. Exiting...\n"); - goto out; - - } - } - - return 0; - - /*------------------------------------------------------------------------- - * out - *------------------------------------------------------------------------- - */ + /*------------------------------------------------------------------------- + * set the new user userblock options in the FCPL (before H5Fcreate ) + *------------------------------------------------------------------------- + */ + if (options->ublock_size > 0) { + /* either use the FCPL already created or create a new one */ + if (fcpl == H5P_DEFAULT) { + /* create a file creation property list */ + if ((fcpl = H5Pcreate(H5P_FILE_CREATE)) < 0) { + error_msg("fail to create a file creation property list\n"); + goto out; + } + } + + /* set user block size */ + if (H5Pset_userblock(fcpl, options->ublock_size) < 0) { + error_msg("failed to set userblock size\n"); + goto out; + } + } + + /*------------------------------------------------------------------------- + * set alignment options + *------------------------------------------------------------------------- + */ + if (options->alignment > 0) { + /* either use the FAPL already created or create a new one */ + if (fapl == H5P_DEFAULT) { + /* create a file access property list */ + if ((fapl = H5Pcreate(H5P_FILE_ACCESS)) < 0) { + error_msg("Could not create file access property list\n"); + goto out; + } + } + + if (H5Pset_alignment(fapl, options->threshold, options->alignment) < 0) { + error_msg("failed to set alignment\n"); + goto out; + } + } + + /*------------------------------------------------------------------------- + * set metadata block size option + *------------------------------------------------------------------------- + */ + if (options->meta_block_size > 0) { + /* either use the FAPL already created or create a new one */ + if (fapl == H5P_DEFAULT) { + /* create a file access property list */ + if ((fapl = H5Pcreate(H5P_FILE_ACCESS)) < 0) { + error_msg("Could not create file access property list\n"); + goto out; + } + } + + if (H5Pset_meta_block_size(fapl, options->meta_block_size) < 0) { + error_msg("failed to set metadata block size\n"); + goto out; + } + } + + /*------------------------------------------------------------------------- + * set free-space strategy options + *------------------------------------------------------------------------- + */ + + /* either use the FCPL already created or create a new one */ + if (fcpl == H5P_DEFAULT) { + /* create a file creation property list */ + if ((fcpl = H5Pcreate(H5P_FILE_CREATE)) < 0) { + error_msg("fail to create a file creation property list\n"); + goto out; + } + } + + /* set file space strategy and free space threshold */ + if (H5Pset_file_space(fcpl, options->fs_strategy, options->fs_threshold) < 0) { + error_msg("failed to set file space strategy & threshold \n"); + goto out; + } + + /*------------------------------------------------------------------------- + * create the output file + *------------------------------------------------------------------------- + */ + if (options->verbose) + printf("Making file <%s>...\n", fnameout); + + if ((fidout = H5Fcreate(fnameout, H5F_ACC_TRUNC, fcpl, fapl)) < 0) { + error_msg("<%s>: Could not create file\n", fnameout); + goto out; + } + + /*------------------------------------------------------------------------- + * write a new user block if requested + *------------------------------------------------------------------------- + */ + if (options->ublock_size > 0) { + if (copy_user_block(options->ublock_filename, fnameout, + options->ublock_size) < 0) { + error_msg("Could not copy user block. Exiting...\n"); + goto out; + + } + } + + /*------------------------------------------------------------------------- + * get list of objects + *------------------------------------------------------------------------- + */ + + /* init table */ + trav_table_init(&travt); + + /* get the list of objects in the file */ + if (h5trav_gettable(fidin, travt) < 0) + goto out; + + /*------------------------------------------------------------------------- + * do the copy + *------------------------------------------------------------------------- + */ + if (do_copy_objects(fidin, fidout, travt, options) < 0) { + error_msg("<%s>: Could not copy data to: %s\n", fnamein, fnameout); + goto out; + } /* end if */ + + /*------------------------------------------------------------------------- + * do the copy of referenced objects + * and create hard links + *------------------------------------------------------------------------- + */ + if (do_copy_refobjs(fidin, fidout, travt, options) < 0) { + printf("h5repack: <%s>: Could not copy data to: %s\n", fnamein, + fnameout); + goto out; + } + + /*------------------------------------------------------------------------- + * close + *------------------------------------------------------------------------- + */ + + if (fapl > 0) + H5Pclose(fapl); + + if (fcpl > 0) + H5Pclose(fcpl); + + H5Fclose(fidin); + H5Fclose(fidout); + + /* free table */ + trav_table_free(travt); + travt = NULL; + + /*------------------------------------------------------------------------- + * write only the input file user block if there is no user block file input + *------------------------------------------------------------------------- + */ + + if (ub_size > 0 && options->ublock_size == 0) { + if (copy_user_block(fnamein, fnameout, ub_size) < 0) { + error_msg("Could not copy user block. Exiting...\n"); + goto out; + + } + } + + return 0; + + /*------------------------------------------------------------------------- + * out + *------------------------------------------------------------------------- + */ out: - H5E_BEGIN_TRY - { - H5Pclose(fapl); - H5Pclose(fcpl); - H5Fclose(fidin); - H5Fclose(fidout); - } H5E_END_TRY; - if(travt) - trav_table_free(travt); - - return -1; + H5E_BEGIN_TRY + { + H5Pclose(fapl); + H5Pclose(fcpl); + H5Fclose(fidin); + H5Fclose(fidout); + }H5E_END_TRY; + if (travt) + trav_table_free(travt); + + return -1; } /*------------------------------------------------------------------------- -* Function: Get_hyperslab -* -* Purpose: Calulate a hyperslab from a dataset for higher performance. -* The size of hyperslab is limitted by H5TOOLS_BUFSIZE. -* Return the hyperslab dimentions and size in byte. -* -* Return: 0 - SUCCEED, -1 FAILED -* -* Parameters: -* dcpl_id : [IN] dataset creation property. -* rank_dset : [IN] dataset rank -* dims_dset[] : [IN] dataset dimentions -* size_datum : [IN] size of a data element in byte -* dims_hslab[] : [OUT] calculated hyperslab dimentions -* * hslab_nbytes_p : [OUT] total byte of the hyperslab -* -* Programmer: Jonathan Kim -* Date: Feburary, 2012 -* Update: -* The hyperslab calucation would be depend on if the dataset is chunked -* or not. -* -* There care 3 conditions to cover: -* 1. If chunked and a chunk fits in buffer, each chunk would be a unit of -* collection and the boundary would be dataset's dims. -* 2. If chunked but a chunk doesn't fit in buffer, each data element would -* be a unit of collection and the boundary would be the chunk itself. -* 3. If not chunked, each data element would be a unit of collection and -* the boundary would be dataset's dims. -* -* The calulation starts from the last dimention (h5dump dims output). -* -* Note: -* Added for JIRA HDFFV-7862. -*-----------------------------------------*/ - -int Get_hyperslab (hid_t dcpl_id, int rank_dset, hsize_t dims_dset[], - size_t size_datum, - hsize_t dims_hslab[], hsize_t * hslab_nbytes_p) -{ - int status = 0; - int k; - H5D_layout_t dset_layout; - int rank_chunk; - hsize_t dims_chunk[H5S_MAX_RANK]; - hsize_t size_chunk=1; - hsize_t nchunk_fit; /* number of chunks that fits in hyperslab buffer (H5TOOLS_BUFSIZE) */ - hsize_t ndatum_fit; /* number of dataum that fits in hyperslab buffer (H5TOOLS_BUFSIZE) */ - hsize_t chunk_dims_map[H5S_MAX_RANK]; /* mapped chunk dimentions */ - hsize_t hs_dims_map[H5S_MAX_RANK]; /* mapped hyperslab dimentions */ - hsize_t hslab_nbytes; /* size of hyperslab in byte */ - - /* init to set as size of a data element */ - hslab_nbytes = size_datum; - - /* get layout of dataset */ - dset_layout = H5Pget_layout(dcpl_id); - - /* if dataset is chunked */ - if ( dset_layout == H5D_CHUNKED ) - { - /* get chunk dims */ - rank_chunk = H5Pget_chunk(dcpl_id, rank_dset, dims_chunk); - if (rank_chunk < 0) - { - status = -1; - goto out; - } - - for (k = rank_dset; k > 0; --k) - size_chunk *= dims_chunk[k-1]; - - /* figure out how many chunks can fit in the hyperslab buffer */ - nchunk_fit = (H5TOOLS_BUFSIZE / size_datum) / size_chunk; - - - /* 1. if a chunk fit in hyperslab buffer */ - if (nchunk_fit >= 1) - { - /* Calulate a hyperslab that contains as many chunks that can fit - * in hyperslab buffer. Hyperslab will be increased starting from - * the last dimention of the dataset (see h5dump's dims output). - * The calculation boundary is dataset dims. - * In the loop, used mapping from a datum to a chunk to figure out - * chunk based hyperslab. - */ - for (k = rank_dset; k > 0; --k) - { - /* map dataset dimentions with a chunk dims */ - chunk_dims_map[k-1]= dims_dset[k-1] / dims_chunk[k-1]; - - /* if reminder exist, increse by 1 to cover partial edge chunks */ - if (dims_dset[k-1] % dims_chunk[k-1] > 0) - chunk_dims_map[k-1]++; - - /* get mapped hyperslab dims */ - hs_dims_map[k-1] = MIN (nchunk_fit, chunk_dims_map[k-1]); - - /* prepare next round */ - nchunk_fit = nchunk_fit / chunk_dims_map[k-1]; - /* if a chunk is bigger than the rest of buffer */ - if (nchunk_fit == 0) - nchunk_fit=1; - - /* get hyperslab dimentions as unmapping to actual size */ - dims_hslab[k-1] = MIN( (hs_dims_map[k-1] * dims_chunk[k-1]), dims_dset[k-1]); - - /* calculate total size for the hyperslab */ - hslab_nbytes *= dims_hslab[k-1]; - } - } - /* 2. if a chunk is bigger than hyperslab buffer */ - else - { - /* Calulate a hyperslab that contains as many data elements that - * can fit in hyperslab buffer. Hyperslab will be increased - * starting from the last dimention of the chunk (see h5dump's dims - * output). - * The calculation boundary is a chunk dims. - */ - for (k = rank_dset; k > 0; --k) - { - ndatum_fit = H5TOOLS_BUFSIZE / hslab_nbytes; - - /* if a datum is bigger than rest of buffer */ - if ( ndatum_fit == 0) - ndatum_fit = 1; - /* get hyperslab dimentions within a chunk boundary */ - dims_hslab[k - 1] = MIN (dims_chunk[k-1], ndatum_fit); - - /* calculate total size for the hyperslab */ - hslab_nbytes *= dims_hslab[k - 1]; - - if (hslab_nbytes <= 0) - { - status = -1; - goto out; - } - } - } - } - /* 3. if dataset is not chunked */ - else - { - /* Calulate a hyperslab that contains as many data elements that can - * fit in hyperslab buffer. Hyperslab will be increased starting from - * the last dimention of the dataset (see h5dump's dims output). - * The calculation boundary is dataset dims. - */ - for (k = rank_dset; k > 0; --k) - { - ndatum_fit = H5TOOLS_BUFSIZE / hslab_nbytes; - - /* if a datum is bigger than rest of buffer */ - if ( ndatum_fit == 0) - ndatum_fit = 1; - /* get hyperslab dimentions within dataset boundary */ - dims_hslab[k - 1] = MIN(dims_dset[k - 1], ndatum_fit); - - /* calculate total size for the hyperslab */ - hslab_nbytes *= dims_hslab[k - 1]; - - if (hslab_nbytes <= 0) - { - status = -1; - goto out; - } - } - } - - /* pass out the hyperslab size*/ - *hslab_nbytes_p = hslab_nbytes; + * Function: Get_hyperslab + * + * Purpose: Calulate a hyperslab from a dataset for higher performance. + * The size of hyperslab is limitted by H5TOOLS_BUFSIZE. + * Return the hyperslab dimentions and size in byte. + * + * Return: 0 - SUCCEED, -1 FAILED + * + * Parameters: + * dcpl_id : [IN] dataset creation property. + * rank_dset : [IN] dataset rank + * dims_dset[] : [IN] dataset dimentions + * size_datum : [IN] size of a data element in byte + * dims_hslab[] : [OUT] calculated hyperslab dimentions + * * hslab_nbytes_p : [OUT] total byte of the hyperslab + * + * Programmer: Jonathan Kim + * Date: Feburary, 2012 + * Update: + * The hyperslab calucation would be depend on if the dataset is chunked + * or not. + * + * There care 3 conditions to cover: + * 1. If chunked and a chunk fits in buffer, each chunk would be a unit of + * collection and the boundary would be dataset's dims. + * 2. If chunked but a chunk doesn't fit in buffer, each data element would + * be a unit of collection and the boundary would be the chunk itself. + * 3. If not chunked, each data element would be a unit of collection and + * the boundary would be dataset's dims. + * + * The calulation starts from the last dimention (h5dump dims output). + * + * Note: + * Added for JIRA HDFFV-7862. + *-----------------------------------------*/ + +int Get_hyperslab(hid_t dcpl_id, int rank_dset, hsize_t dims_dset[], + size_t size_datum, hsize_t dims_hslab[], hsize_t * hslab_nbytes_p) { + int status = 0; + int k; + H5D_layout_t dset_layout; + int rank_chunk; + hsize_t dims_chunk[H5S_MAX_RANK]; + hsize_t size_chunk = 1; + hsize_t nchunk_fit; /* number of chunks that fits in hyperslab buffer (H5TOOLS_BUFSIZE) */ + hsize_t ndatum_fit; /* number of dataum that fits in hyperslab buffer (H5TOOLS_BUFSIZE) */ + hsize_t chunk_dims_map[H5S_MAX_RANK]; /* mapped chunk dimentions */ + hsize_t hs_dims_map[H5S_MAX_RANK]; /* mapped hyperslab dimentions */ + hsize_t hslab_nbytes; /* size of hyperslab in byte */ + + /* init to set as size of a data element */ + hslab_nbytes = size_datum; + + /* get layout of dataset */ + dset_layout = H5Pget_layout(dcpl_id); + + /* if dataset is chunked */ + if (dset_layout == H5D_CHUNKED) { + /* get chunk dims */ + rank_chunk = H5Pget_chunk(dcpl_id, rank_dset, dims_chunk); + if (rank_chunk < 0) { + status = -1; + goto out; + } + + for (k = rank_dset; k > 0; --k) + size_chunk *= dims_chunk[k - 1]; + + /* figure out how many chunks can fit in the hyperslab buffer */ + nchunk_fit = (H5TOOLS_BUFSIZE / size_datum) / size_chunk; + + /* 1. if a chunk fit in hyperslab buffer */ + if (nchunk_fit >= 1) { + /* Calulate a hyperslab that contains as many chunks that can fit + * in hyperslab buffer. Hyperslab will be increased starting from + * the last dimention of the dataset (see h5dump's dims output). + * The calculation boundary is dataset dims. + * In the loop, used mapping from a datum to a chunk to figure out + * chunk based hyperslab. + */ + for (k = rank_dset; k > 0; --k) { + /* map dataset dimentions with a chunk dims */ + chunk_dims_map[k - 1] = dims_dset[k - 1] / dims_chunk[k - 1]; + + /* if reminder exist, increse by 1 to cover partial edge chunks */ + if (dims_dset[k - 1] % dims_chunk[k - 1] > 0) + chunk_dims_map[k - 1]++; + + /* get mapped hyperslab dims */ + hs_dims_map[k - 1] = MIN (nchunk_fit, chunk_dims_map[k-1]); + + /* prepare next round */ + nchunk_fit = nchunk_fit / chunk_dims_map[k - 1]; + /* if a chunk is bigger than the rest of buffer */ + if (nchunk_fit == 0) + nchunk_fit = 1; + + /* get hyperslab dimentions as unmapping to actual size */ + dims_hslab[k - 1] = + MIN( (hs_dims_map[k-1] * dims_chunk[k-1]), dims_dset[k-1]); + + /* calculate total size for the hyperslab */ + hslab_nbytes *= dims_hslab[k - 1]; + } + } + /* 2. if a chunk is bigger than hyperslab buffer */ + else { + /* Calulate a hyperslab that contains as many data elements that + * can fit in hyperslab buffer. Hyperslab will be increased + * starting from the last dimention of the chunk (see h5dump's dims + * output). + * The calculation boundary is a chunk dims. + */ + for (k = rank_dset; k > 0; --k) { + ndatum_fit = H5TOOLS_BUFSIZE / hslab_nbytes; + + /* if a datum is bigger than rest of buffer */ + if (ndatum_fit == 0) + ndatum_fit = 1; + /* get hyperslab dimentions within a chunk boundary */ + dims_hslab[k - 1] = MIN (dims_chunk[k-1], ndatum_fit); + + /* calculate total size for the hyperslab */ + hslab_nbytes *= dims_hslab[k - 1]; + + if (hslab_nbytes <= 0) { + status = -1; + goto out; + } + } + } + } + /* 3. if dataset is not chunked */ + else { + /* Calulate a hyperslab that contains as many data elements that can + * fit in hyperslab buffer. Hyperslab will be increased starting from + * the last dimention of the dataset (see h5dump's dims output). + * The calculation boundary is dataset dims. + */ + for (k = rank_dset; k > 0; --k) { + ndatum_fit = H5TOOLS_BUFSIZE / hslab_nbytes; + + /* if a datum is bigger than rest of buffer */ + if (ndatum_fit == 0) + ndatum_fit = 1; + /* get hyperslab dimentions within dataset boundary */ + dims_hslab[k - 1] = MIN(dims_dset[k - 1], ndatum_fit); + + /* calculate total size for the hyperslab */ + hslab_nbytes *= dims_hslab[k - 1]; + + if (hslab_nbytes <= 0) { + status = -1; + goto out; + } + } + } + + /* pass out the hyperslab size*/ + *hslab_nbytes_p = hslab_nbytes; out: - return status; + return status; } /*------------------------------------------------------------------------- -* Function: do_copy_objects -* -* Purpose: duplicate all HDF5 objects in the file -* -* Return: 0, ok, -1 no -* -* Programmer: Pedro Vicente, pvn@ncsa.uiuc.edu -* -* Date: October, 23, 2003 -* -* Modifications: -* -* July 2004: Introduced the extra EC or NN option for SZIP -* -* December 2004: Added a check for H5Dcreate; if the dataset cannot be created -* with the requested filter, use the input one -* -* October 2006: Read/write using the file type by default. -* -* October 2006: Read by hyperslabs for big datasets. -* -* A threshold of H5TOOLS_MALLOCSIZE (128 MB) is the limit upon which I/O hyperslab is done -* i.e., if the memory needed to read a dataset is greater than this limit, -* then hyperslab I/O is done instead of one operation I/O -* For each dataset, the memory needed is calculated according to -* -* memory needed = number of elements * size of each element -* -* if the memory needed is lower than H5TOOLS_MALLOCSIZE, then the following operations -* are done -* -* H5Dread( input_dataset1 ) -* H5Dread( input_dataset2 ) -* -* with all elements in the datasets selected. If the memory needed is greater than -* H5TOOLS_MALLOCSIZE, then the following operations are done instead: -* -* a strip mine is defined for each dimension k (a strip mine is defined as a -* hyperslab whose size is memory manageable) according to the formula -* -* (1) strip_mine_size[k ] = MIN(dimension[k ], H5TOOLS_BUFSIZE / size of memory type) -* -* where H5TOOLS_BUFSIZE is a constant currently defined as 1MB. This formula assures -* that for small datasets (small relative to the H5TOOLS_BUFSIZE constant), the strip -* mine size k is simply defined as its dimension k, but for larger datasets the -* hyperslab size is still memory manageable. -* a cycle is done until the number of elements in the dataset is reached. In each -* iteration, two parameters are defined for the function H5Sselect_hyperslab, -* the start and size of each hyperslab, according to -* -* (2) hyperslab_size [k] = MIN(dimension[k] - hyperslab_offset[k], strip_mine_size [k]) -* -* where hyperslab_offset [k] is initially set to zero, and later incremented in -* hyperslab_size[k] offsets. The reason for the operation -* -* dimension[k] - hyperslab_offset[k] -* -* in (2) is that, when using the strip mine size, it assures that the "remaining" part -* of the dataset that does not fill an entire strip mine is processed. -* -* November 2006: Use H5Ocopy in the copy of objects. The logic for using -* H5Ocopy or not is if a change of filters or layout is requested by the user -* then use read/write else use H5Ocopy. -* -* May, 1, 2008: Add a printing of the compression ratio of old size / new size -* -* Feburary 2012: improve Read/Write by hyperslabs for big datasets. -* Programmer: Jonathan Kim -* -* A threshold of H5TOOLS_MALLOCSIZE is the limit upon which I/O hyperslab is done -* i.e., if the memory needed to read a dataset is greater than this limit, -* then hyperslab I/O is done instead of one operation I/O -* For each dataset, the memory needed is calculated according to -* -* memory needed = number of elements * size of each element -* -* if the memory needed is lower than H5TOOLS_MALLOCSIZE, then the following operations -* are done -* -* H5Dread( input_dataset ) -* H5Dwrite( output_dataset ) -* -* with all elements in the datasets selected. If the memory needed is greater than -* H5TOOLS_MALLOCSIZE, then the following operations are done instead: -* -* 1. figure out a hyperslab (dimentions) and size (refer to Get_hyperslab()). -* 2. Calculate the hyperslab selections as the selection is moving forward. -* Selection would be same as the hyperslab except for the remaining edge portion -* of the dataset. The code take care of the remaining portion if exist. -* -*------------------------------------------------------------------------- -*/ - -int do_copy_objects(hid_t fidin, - hid_t fidout, - trav_table_t *travt, - pack_opt_t *options) /* repack options */ + * Function: do_copy_objects + * + * Purpose: duplicate all HDF5 objects in the file + * + * Return: 0, ok, -1 no + * + * Programmer: Pedro Vicente, pvn@ncsa.uiuc.edu + * + * Date: October, 23, 2003 + * + * Modifications: + * + * July 2004: Introduced the extra EC or NN option for SZIP + * + * December 2004: Added a check for H5Dcreate; if the dataset cannot be created + * with the requested filter, use the input one + * + * October 2006: Read/write using the file type by default. + * + * October 2006: Read by hyperslabs for big datasets. + * + * A threshold of H5TOOLS_MALLOCSIZE (128 MB) is the limit upon which I/O hyperslab is done + * i.e., if the memory needed to read a dataset is greater than this limit, + * then hyperslab I/O is done instead of one operation I/O + * For each dataset, the memory needed is calculated according to + * + * memory needed = number of elements * size of each element + * + * if the memory needed is lower than H5TOOLS_MALLOCSIZE, then the following operations + * are done + * + * H5Dread( input_dataset1 ) + * H5Dread( input_dataset2 ) + * + * with all elements in the datasets selected. If the memory needed is greater than + * H5TOOLS_MALLOCSIZE, then the following operations are done instead: + * + * a strip mine is defined for each dimension k (a strip mine is defined as a + * hyperslab whose size is memory manageable) according to the formula + * + * (1) strip_mine_size[k ] = MIN(dimension[k ], H5TOOLS_BUFSIZE / size of memory type) + * + * where H5TOOLS_BUFSIZE is a constant currently defined as 1MB. This formula assures + * that for small datasets (small relative to the H5TOOLS_BUFSIZE constant), the strip + * mine size k is simply defined as its dimension k, but for larger datasets the + * hyperslab size is still memory manageable. + * a cycle is done until the number of elements in the dataset is reached. In each + * iteration, two parameters are defined for the function H5Sselect_hyperslab, + * the start and size of each hyperslab, according to + * + * (2) hyperslab_size [k] = MIN(dimension[k] - hyperslab_offset[k], strip_mine_size [k]) + * + * where hyperslab_offset [k] is initially set to zero, and later incremented in + * hyperslab_size[k] offsets. The reason for the operation + * + * dimension[k] - hyperslab_offset[k] + * + * in (2) is that, when using the strip mine size, it assures that the "remaining" part + * of the dataset that does not fill an entire strip mine is processed. + * + * November 2006: Use H5Ocopy in the copy of objects. The logic for using + * H5Ocopy or not is if a change of filters or layout is requested by the user + * then use read/write else use H5Ocopy. + * + * May, 1, 2008: Add a printing of the compression ratio of old size / new size + * + * Feburary 2012: improve Read/Write by hyperslabs for big datasets. + * Programmer: Jonathan Kim + * + * A threshold of H5TOOLS_MALLOCSIZE is the limit upon which I/O hyperslab is done + * i.e., if the memory needed to read a dataset is greater than this limit, + * then hyperslab I/O is done instead of one operation I/O + * For each dataset, the memory needed is calculated according to + * + * memory needed = number of elements * size of each element + * + * if the memory needed is lower than H5TOOLS_MALLOCSIZE, then the following operations + * are done + * + * H5Dread( input_dataset ) + * H5Dwrite( output_dataset ) + * + * with all elements in the datasets selected. If the memory needed is greater than + * H5TOOLS_MALLOCSIZE, then the following operations are done instead: + * + * 1. figure out a hyperslab (dimentions) and size (refer to Get_hyperslab()). + * 2. Calculate the hyperslab selections as the selection is moving forward. + * Selection would be same as the hyperslab except for the remaining edge portion + * of the dataset. The code take care of the remaining portion if exist. + * + *------------------------------------------------------------------------- + */ + +int do_copy_objects(hid_t fidin, hid_t fidout, trav_table_t *travt, + pack_opt_t *options) /* repack options */ { - hid_t grp_in = -1; /* group ID */ - hid_t grp_out = -1; /* group ID */ - hid_t dset_in = -1; /* read dataset ID */ - hid_t dset_out = -1; /* write dataset ID */ - hid_t gcpl_in = -1; /* group creation property list */ - hid_t gcpl_out = -1; /* group creation property list */ - hid_t type_in = -1; /* named type ID */ - hid_t type_out = -1; /* named type ID */ - hid_t dcpl_in = -1; /* dataset creation property list ID */ - hid_t dcpl_out = -1; /* dataset creation property list ID */ - hid_t f_space_id = -1; /* file space ID */ - hid_t ftype_id = -1; /* file type ID */ - hid_t wtype_id = -1; /* read/write type ID */ - named_dt_t *named_dt_head = NULL; /* Pointer to the stack of named datatypes copied */ - size_t msize; /* size of type */ - hsize_t nelmts; /* number of elements in dataset */ - H5D_space_status_t space_status; /* determines whether space has been allocated for the dataset */ - int rank; /* rank of dataset */ - hsize_t dims[H5S_MAX_RANK];/* dimensions of dataset */ - hsize_t dsize_in; /* input dataset size before filter */ - hsize_t dsize_out; /* output dataset size after filter */ - int apply_s; /* flag for apply filter to small dataset sizes */ - int apply_f; /* flag for apply filter to return error on H5Dcreate */ - void *buf=NULL; /* buffer for raw data */ - void *hslab_buf=NULL; /* hyperslab buffer for raw data */ - int has_filter; /* current object has a filter */ - int req_filter; /* there was a request for a filter */ - int req_obj_layout=0; /* request layout to current object */ - unsigned crt_order_flags; /* group creation order flag */ - unsigned i; - unsigned u; - int is_ref=0; - htri_t is_named; - hbool_t limit_maxdims; - hsize_t size_dset; - - - /*------------------------------------------------------------------------- - * copy the suppplied object list - *------------------------------------------------------------------------- - */ - - if (options->verbose) - { - printf("-----------------------------------------\n"); - printf(" Type Filter (Compression) Name\n"); - printf("-----------------------------------------\n"); - } - - for ( i = 0; i < travt->nobjs; i++) - { - /* init variables per obj */ - buf = NULL; - limit_maxdims = FALSE; - - switch ( travt->objs[i].type ) - { - - case H5TRAV_TYPE_UNKNOWN: - HDassert(0); - break; - /*------------------------------------------------------------------------- - * H5TRAV_TYPE_GROUP - *------------------------------------------------------------------------- - */ - case H5TRAV_TYPE_GROUP: - - if (options->verbose) - { - printf(FORMAT_OBJ,"group",travt->objs[i].name ); - } - - /* open input group */ - if ((grp_in = H5Gopen2(fidin, travt->objs[i].name, H5P_DEFAULT)) < 0) - goto error; - - /* get input group creation property list */ - if ((gcpl_in = H5Gget_create_plist(grp_in)) < 0) - goto error; - - /* query and set the group creation properties */ - if (H5Pget_link_creation_order(gcpl_in, &crt_order_flags) < 0) - goto error; - - /* set up group creation property list */ - if ((gcpl_out = H5Pcreate(H5P_GROUP_CREATE)) < 0) - goto error; - - if (H5Pset_link_creation_order(gcpl_out, crt_order_flags) < 0) - goto error; - - - /*------------------------------------------------------------------------- - * the root is a special case, we get an ID for the root group - * and copy its attributes using that ID - *------------------------------------------------------------------------- - */ - if(HDstrcmp(travt->objs[i].name, "/") == 0) - { - if ((grp_out = H5Gopen2(fidout, "/", H5P_DEFAULT)) < 0) - goto error; - } - - else - { - - if (options->grp_compact>0 || options->grp_indexed>0) - { - if(H5Pset_link_phase_change(gcpl_out, (unsigned)options->grp_compact, (unsigned)options->grp_indexed) < 0) - goto error; - } - - if((grp_out = H5Gcreate2(fidout, travt->objs[i].name, H5P_DEFAULT, gcpl_out, H5P_DEFAULT)) < 0) - goto error; - - } - - /*------------------------------------------------------------------------- - * copy attrs - *------------------------------------------------------------------------- - */ - if(copy_attr(grp_in, grp_out, &named_dt_head, travt, options) < 0) - goto error; - - - if(H5Pclose(gcpl_out) < 0) - goto error; - if(H5Pclose(gcpl_in) < 0) - goto error; - if(H5Gclose(grp_out) < 0) - goto error; - if(H5Gclose(grp_in) < 0) - goto error; - - break; - - /*------------------------------------------------------------------------- - * H5TRAV_TYPE_DATASET - *------------------------------------------------------------------------- - */ - case H5TRAV_TYPE_DATASET: - - has_filter = 0; - req_filter = 0; - - /* check if global filters were requested */ - if ( options->n_filter_g ) - req_filter = 1; - - /* check if filters were requested for individual objects */ - for (u = 0; u < options->op_tbl->nelems; u++) { - - if (HDstrcmp(travt->objs[i].name, options->op_tbl->objs[u].path) == 0) { - if (options->op_tbl->objs[u].filter->filtn > 0) { - req_filter = 1; - } - } - } - - /* check if layout change requested individual object */ - if (options->layout_g != H5D_LAYOUT_ERROR) - { - pack_info_t *pckinfo; - /* any dataset is specified */ - if (options->op_tbl->nelems > 0) - { - /* check if object exist */ - pckinfo = options_get_object (travt->objs[i].name, options->op_tbl); - if (pckinfo) - { - req_obj_layout = 1; - } - } - } - - /* early detection of references */ - if((dset_in = H5Dopen2(fidin, travt->objs[i].name, H5P_DEFAULT)) < 0) - goto error; - if((ftype_id = H5Dget_type(dset_in)) < 0) - goto error; - if(H5T_REFERENCE == H5Tget_class(ftype_id)) - is_ref = 1; - - /* Check if the datatype is committed */ - if((is_named = H5Tcommitted(ftype_id)) < 0) - goto error; - if(is_named) - if((wtype_id = copy_named_datatype(ftype_id, fidout, &named_dt_head, travt, options)) < 0) - goto error; - - if(H5Tclose(ftype_id) < 0) - goto error; - if(H5Dclose(dset_in) < 0) - goto error; - - - /*------------------------------------------------------------------------- - * check if we should use H5Ocopy or not - * if there is a request for filters/layout, we read/write the object - * otherwise we do a copy using H5Ocopy - *------------------------------------------------------------------------- - */ - if ( options->op_tbl->nelems || - options->all_filter == 1 || - options->all_layout == 1 || - is_ref || - is_named) - { - - int j; - - if((dset_in = H5Dopen2(fidin, travt->objs[i].name, H5P_DEFAULT)) < 0) - goto error; - if((f_space_id = H5Dget_space(dset_in)) < 0) - goto error; - if((ftype_id = H5Dget_type(dset_in)) < 0) - goto error; - if((dcpl_in = H5Dget_create_plist(dset_in)) < 0) - goto error; - if((dcpl_out = H5Pcopy(dcpl_in)) < 0) - goto error; - if((rank = H5Sget_simple_extent_ndims(f_space_id)) < 0) - goto error; - HDmemset(dims, 0, sizeof dims); - if(H5Sget_simple_extent_dims(f_space_id, dims, NULL) < 0) - goto error; - - if(H5Dget_space_status(dset_in, &space_status) < 0) - goto error; - - nelmts = 1; - for(j = 0; j < rank; j++) - nelmts *= dims[j]; - - /* wtype_id will have already been set if using a named dtype */ - if(!is_named) { - if(options->use_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; - - /* size of current dset */ - size_dset = nelmts * msize; - - /*------------------------------------------------------------------------- - * check if the dataset creation property list has filters that - * are not registered in the current configuration - * 1) the external filters GZIP and SZIP might not be available - * 2) the internal filters might be turned off - *------------------------------------------------------------------------- - */ - if (h5tools_canreadf((travt->objs[i].name),dcpl_in)==1) - { - apply_s=1; - apply_f=1; - - /*------------------------------------------------------------------------- - * references are a special case - * we cannot just copy the buffers, but instead we recreate the reference - * in a second traversal of the output file - *------------------------------------------------------------------------- - */ - if (H5T_REFERENCE!=H5Tget_class(wtype_id)) - { - /* get the storage size of the input dataset */ - dsize_in=H5Dget_storage_size(dset_in); - - /* check for small size datasets (less than 1k) except - * changing to COMPACT. For the reference, COMPACT is limited - * by size 64K by library. - */ - if (options->layout_g != H5D_COMPACT) - { - if ( size_dset < options->min_comp ) - apply_s=0; - } - - /* apply the filter */ - if (apply_s) - { - if (apply_filters(travt->objs[i].name, - rank, - dims, - msize, - dcpl_out, - options, - &has_filter) < 0) - goto error; - } - - /* only if layout change requested for entire file or - * individual obj */ - if (options->all_layout > 0 || req_obj_layout == 1) - /*------------------------------------------------- - * Unset the unlimited max dims if convert to other - * than chunk layouts, because unlimited max dims - * only can be applied to chunk layout. - * Also perform only for targeted dataset - * Also check for size limit to convert to compact - *-------------------------------------------------*/ - if (options->layout_g != H5D_CHUNKED) - { - /* any dataset is specified */ - if (options->op_tbl->nelems > 0) - { - /* if current obj match specified obj */ - if (options_get_object (travt->objs[i].name, options->op_tbl)) - limit_maxdims = TRUE; - } - else /* no dataset is specified */ - { - limit_maxdims = TRUE; - } - - /* if convert to COMPACT */ - if (options->layout_g == H5D_COMPACT) - { - /* should be smaller than 64K */ - if ( size_dset > MAX_COMPACT_DSIZE ) - limit_maxdims = FALSE; - } - - /* unset unlimited max dims */ - if (limit_maxdims) - H5Sset_extent_simple( f_space_id, rank, dims, NULL ); - } - - /*------------------------------------------------------------------------- - * create the output dataset; - * disable error checking in case the dataset cannot be created with the - * modified dcpl; in that case use the original instead - *------------------------------------------------------------------------- - */ - H5E_BEGIN_TRY { - dset_out = H5Dcreate2(fidout, travt->objs[i].name, wtype_id, f_space_id, H5P_DEFAULT, dcpl_out, H5P_DEFAULT); - } H5E_END_TRY; - - if(dset_out == FAIL) - { - if(options->verbose) - printf(" warning: could not create dataset <%s>. Applying original settings\n", - travt->objs[i].name); - - if((dset_out = H5Dcreate2(fidout, travt->objs[i].name, wtype_id, f_space_id, H5P_DEFAULT, dcpl_in, H5P_DEFAULT)) < 0) - goto error; - apply_f = 0; - } - - /*------------------------------------------------------------------------- - * read/write - *------------------------------------------------------------------------- - */ - if(nelmts > 0 && space_status != H5D_SPACE_STATUS_NOT_ALLOCATED) - { - size_t need = (size_t)(nelmts * msize); /* bytes needed */ - - /* have to read the whole dataset if there is only one element in the dataset */ - if(need < H5TOOLS_MALLOCSIZE) - buf = HDmalloc(need); - - if(buf != NULL) { - /* read/write: use the macro to check error, e.g. memory allocation error inside the library. */ - CHECK_H5DRW_ERROR(H5Dread, dset_in, wtype_id, H5S_ALL, H5S_ALL, H5P_DEFAULT, buf); - CHECK_H5DRW_ERROR(H5Dwrite, dset_out, wtype_id, H5S_ALL, H5S_ALL, H5P_DEFAULT, buf); - - /* Check if we have VL data in the dataset's - * datatype that must be reclaimed */ - if(TRUE == H5Tdetect_class(wtype_id, H5T_VLEN)) - if(H5Dvlen_reclaim(wtype_id, f_space_id, H5P_DEFAULT, buf) < 0) - goto error; - } - else /* possibly not enough memory, read/write by hyperslabs */ - { - size_t p_type_nbytes = msize; /*size of memory type */ - hsize_t p_nelmts = nelmts; /*total elements */ - hsize_t elmtno; /*counter */ - int carry; /*counter carry value */ - unsigned int vl_data = 0; /*contains VL datatypes */ - - /* hyperslab info */ - hsize_t hslab_dims[H5S_MAX_RANK]; /*hyperslab dims */ - hsize_t hslab_nbytes; /*bytes per hyperslab */ - hsize_t hslab_nelmts; /*elements per hyperslab*/ - hid_t hslab_space; /*hyperslab data space */ - - /* hyperslab selection info */ - hsize_t hs_sel_offset[H5S_MAX_RANK];/* selection offset */ - hsize_t hs_sel_count[H5S_MAX_RANK]; /* selection count */ - hsize_t hs_select_nelmts; /* selected elements */ - hsize_t zero[8]; /*vector of zeros */ - int k; - H5D_layout_t dset_layout; - hid_t dcpl_tmp = -1; /* dataset creation property list ID */ - - /* check if we have VL data in the dataset's datatype */ - if (H5Tdetect_class(wtype_id, H5T_VLEN) == TRUE) - vl_data = TRUE; - - - /* check first if writing dataset is chunked, - * if so use its chunk layout for better performance. */ - dset_layout = H5Pget_layout(dcpl_out); - if (dset_layout == H5D_CHUNKED) - dcpl_tmp = dcpl_out; /* writing dataset */ - else /* if reading dataset is chunked */ - { - dset_layout = H5Pget_layout(dcpl_in); - if (dset_layout == H5D_CHUNKED) - dcpl_tmp = dcpl_in; /* reading dataset */ - } - - /* get hyperslab dims and size in byte */ - if(Get_hyperslab(dcpl_tmp, rank, dims, p_type_nbytes, hslab_dims, &hslab_nbytes) < 0) - goto error; - - hslab_buf = HDmalloc((size_t)hslab_nbytes); - - hslab_nelmts = hslab_nbytes / p_type_nbytes; - hslab_space = H5Screate_simple(1, &hslab_nelmts, NULL); - - /* the hyperslab selection loop */ - HDmemset(hs_sel_offset, 0, sizeof hs_sel_offset); - HDmemset(zero, 0, sizeof zero); - - for (elmtno = 0; elmtno < p_nelmts; elmtno += hs_select_nelmts) - { - if (rank > 0) - { - /* calculate the hyperslab selections. The selection would be same as the hyperslab except for remaining edge portion of the dataset which is smaller then the hyperslab. - */ - for (k = 0, hs_select_nelmts = 1; k < rank; k++) - { - /* MIN() is used to get the remaining edge portion if exist. - * "dims[k] - hs_sel_offset[k]" is remaining edge portion that is smaller then the hyperslab.*/ - hs_sel_count[k] = MIN(dims[k] - hs_sel_offset[k], hslab_dims[k]); - hs_select_nelmts *= hs_sel_count[k]; - } - - if (H5Sselect_hyperslab(f_space_id, H5S_SELECT_SET, hs_sel_offset, NULL, hs_sel_count, NULL) < 0) - goto error; - if (H5Sselect_hyperslab(hslab_space, H5S_SELECT_SET, zero, NULL, &hs_select_nelmts, NULL) < 0) - goto error; - } - else - { - H5Sselect_all(f_space_id); - H5Sselect_all(hslab_space); - hs_select_nelmts = 1; - } /* rank */ - - /* read/write: use the macro to check error, e.g. memory allocation error inside the library. */ - CHECK_H5DRW_ERROR(H5Dread, dset_in, wtype_id, hslab_space, f_space_id, H5P_DEFAULT, hslab_buf); - CHECK_H5DRW_ERROR(H5Dwrite, dset_out, wtype_id, hslab_space, f_space_id, H5P_DEFAULT, hslab_buf); - - /* reclaim any VL memory, if necessary */ - if(vl_data) - H5Dvlen_reclaim(wtype_id, hslab_space, H5P_DEFAULT, hslab_buf); - - /* calculate the next hyperslab offset */ - for (k = rank, carry = 1; k > 0 && carry; --k) - { - hs_sel_offset[k - 1] += hs_sel_count[k - 1]; - /* if reached the end of a dim */ - if (hs_sel_offset[k - 1] == dims[k - 1]) - hs_sel_offset[k - 1] = 0; - else - carry = 0; - } /* k */ - } /* elmtno */ - - H5Sclose(hslab_space); - /* free */ - if (hslab_buf!=NULL) - { - HDfree(hslab_buf); - hslab_buf=NULL; - } - } /* hyperslab read */ - } /* if (nelmts>0 && space_status==H5D_SPACE_STATUS_NOT_ALLOCATED) */ - - /*------------------------------------------------------------------------- - * amount of compression used - *------------------------------------------------------------------------- - */ - if (options->verbose) - { - double ratio=0; - - /* only print the compression ration if there was a filter request */ - if (apply_s && apply_f && req_filter) - { - /* get the storage size of the output dataset */ - dsize_out=H5Dget_storage_size(dset_out); - - /* compression ratio = uncompressed size / compressed size */ - if (dsize_out!=0) - ratio = (double) dsize_in / (double) dsize_out; - - print_dataset_info(dcpl_out,travt->objs[i].name,ratio,1); - } - else - print_dataset_info(dcpl_in,travt->objs[i].name,ratio,0); - - /* print a message that the filter was not applied - (in case there was a filter) - */ - if ( has_filter && apply_s == 0 ) - printf(" \n", - travt->objs[i].name, - (int)options->min_comp); - - if ( has_filter && apply_f == 0 ) - printf(" \n", - travt->objs[i].name); - - } /* verbose */ - - /*------------------------------------------------------------------------- - * copy attrs - *------------------------------------------------------------------------- - */ - if (copy_attr(dset_in, dset_out, &named_dt_head, travt, options) < 0) - goto error; - /*close */ - if (H5Dclose(dset_out) < 0) - goto error; - - }/*!H5T_REFERENCE*/ - }/*h5tools_canreadf*/ - - - /*------------------------------------------------------------------------- - * close - *------------------------------------------------------------------------- - */ - if (H5Tclose(ftype_id) < 0) - goto error; - if (H5Tclose(wtype_id) < 0) - goto error; - if (H5Pclose(dcpl_in) < 0) - goto error; - if (H5Pclose(dcpl_out) < 0) - goto error; - if (H5Sclose(f_space_id) < 0) - goto error; - if (H5Dclose(dset_in) < 0) - goto error; - - } - /*------------------------------------------------------------------------- - * we do not have request for filter/chunking use H5Ocopy instead - *------------------------------------------------------------------------- - */ - else - { - hid_t pid; - - /* create property to pass copy options */ - if ( (pid = H5Pcreate(H5P_OBJECT_COPY)) < 0) - goto error; - - /* set options for object copy */ - if(H5Pset_copy_object(pid, H5O_COPY_WITHOUT_ATTR_FLAG) < 0) - goto error; - - /*------------------------------------------------------------------------- - * do the copy - *------------------------------------------------------------------------- - */ - - if(H5Ocopy(fidin, /* Source file or group identifier */ - travt->objs[i].name, /* Name of the source object to be copied */ - fidout, /* Destination file or group identifier */ - travt->objs[i].name, /* Name of the destination object */ - pid, /* Properties which apply to the copy */ - H5P_DEFAULT) < 0) /* Properties which apply to the new hard link */ - goto error; - - /* close property */ - if(H5Pclose(pid) < 0) - goto error; - - - /*------------------------------------------------------------------------- - * copy attrs manually - *------------------------------------------------------------------------- - */ - if((dset_in = H5Dopen2(fidin, travt->objs[i].name, H5P_DEFAULT)) < 0) - goto error; - if((dset_out = H5Dopen2(fidout, travt->objs[i].name, H5P_DEFAULT)) < 0) - goto error; - if(copy_attr(dset_in, dset_out, &named_dt_head, travt, options) < 0) - goto error; - if(H5Dclose(dset_in) < 0) - goto error; - if(H5Dclose(dset_out) < 0) - goto error; - - - if (options->verbose) - printf(FORMAT_OBJ,"dset",travt->objs[i].name ); - - - } /* end do we have request for filter/chunking */ - - break; - - /*------------------------------------------------------------------------- - * H5TRAV_TYPE_NAMED_DATATYPE - *------------------------------------------------------------------------- - */ - case H5TRAV_TYPE_NAMED_DATATYPE: - - if(options->verbose) - printf(FORMAT_OBJ, "type", travt->objs[i].name); - - if((type_in = H5Topen2(fidin, travt->objs[i].name, H5P_DEFAULT)) < 0) - goto error; - - /* Copy the datatype anonymously */ - if((type_out = copy_named_datatype(type_in, fidout, &named_dt_head, - travt, options)) < 0) - goto error; - - /* Link in to group structure */ - if(H5Lcreate_hard(type_out, ".", fidout, travt->objs[i].name, - H5P_DEFAULT, H5P_DEFAULT) < 0) - goto error; - - /*------------------------------------------------------------------------- - * copy attrs - *------------------------------------------------------------------------- - */ - if(copy_attr(type_in, type_out, &named_dt_head, travt, options) < 0) - goto error; - - if(H5Tclose(type_in) < 0) - goto error; - if(H5Tclose(type_out) < 0) - goto error; - - - - break; - - - /*------------------------------------------------------------------------- - * H5TRAV_TYPE_LINK - * H5TRAV_TYPE_UDLINK - * - * Only handles external links; H5Lcopy will fail for other UD link types - * since we don't have creation or copy callbacks for them. - *------------------------------------------------------------------------- - */ - - case H5TRAV_TYPE_LINK: - case H5TRAV_TYPE_UDLINK: - { - - if(options->verbose) - printf(FORMAT_OBJ, "link", travt->objs[i].name); - - if(H5Lcopy(fidin, travt->objs[i].name,fidout, travt->objs[i].name, H5P_DEFAULT, H5P_DEFAULT) < 0) - goto error; - - if (options->verbose) - printf(FORMAT_OBJ,"link",travt->objs[i].name ); - - } - break; - - default: - goto error; - } /* switch */ - - /* free */ - if (buf!=NULL) - { - HDfree(buf); - buf=NULL; - } - - } /* i */ - - /* Finalize (link) the stack of named datatypes (if any) */ - named_datatype_free(&named_dt_head, 0); - - return 0; + hid_t grp_in = -1; /* group ID */ + hid_t grp_out = -1; /* group ID */ + hid_t dset_in = -1; /* read dataset ID */ + hid_t dset_out = -1; /* write dataset ID */ + hid_t gcpl_in = -1; /* group creation property list */ + hid_t gcpl_out = -1; /* group creation property list */ + hid_t type_in = -1; /* named type ID */ + hid_t type_out = -1; /* named type ID */ + hid_t dcpl_in = -1; /* dataset creation property list ID */ + hid_t dcpl_out = -1; /* dataset creation property list ID */ + hid_t f_space_id = -1; /* file space ID */ + hid_t ftype_id = -1; /* file type ID */ + hid_t wtype_id = -1; /* read/write type ID */ + named_dt_t *named_dt_head = NULL; /* Pointer to the stack of named datatypes copied */ + size_t msize; /* size of type */ + hsize_t nelmts; /* number of elements in dataset */ + H5D_space_status_t space_status; /* determines whether space has been allocated for the dataset */ + int rank; /* rank of dataset */ + hsize_t dims[H5S_MAX_RANK];/* dimensions of dataset */ + hsize_t dsize_in; /* input dataset size before filter */ + hsize_t dsize_out; /* output dataset size after filter */ + int apply_s; /* flag for apply filter to small dataset sizes */ + int apply_f; /* flag for apply filter to return error on H5Dcreate */ + void *buf = NULL; /* buffer for raw data */ + void *hslab_buf = NULL; /* hyperslab buffer for raw data */ + int has_filter; /* current object has a filter */ + int req_filter; /* there was a request for a filter */ + int req_obj_layout = 0; /* request layout to current object */ + unsigned crt_order_flags; /* group creation order flag */ + unsigned i; + unsigned u; + int is_ref = 0; + htri_t is_named; + hbool_t limit_maxdims; + hsize_t size_dset; + + /*------------------------------------------------------------------------- + * copy the suppplied object list + *------------------------------------------------------------------------- + */ + + if (options->verbose) { + printf("-----------------------------------------\n"); + printf(" Type Filter (Compression) Name\n"); + printf("-----------------------------------------\n"); + } + + for (i = 0; i < travt->nobjs; i++) { + /* init variables per obj */ + buf = NULL; + limit_maxdims = FALSE; + + switch (travt->objs[i].type) { + + case H5TRAV_TYPE_UNKNOWN: + HDassert(0); + break; + /*------------------------------------------------------------------------- + * H5TRAV_TYPE_GROUP + *------------------------------------------------------------------------- + */ + case H5TRAV_TYPE_GROUP: + + if (options->verbose) { + printf(FORMAT_OBJ, "group", travt->objs[i].name); + } + + /* open input group */ + if ((grp_in = H5Gopen2(fidin, travt->objs[i].name, H5P_DEFAULT)) + < 0) + goto error; + + /* get input group creation property list */ + if ((gcpl_in = H5Gget_create_plist(grp_in)) < 0) + goto error; + + /* query and set the group creation properties */ + if (H5Pget_link_creation_order(gcpl_in, &crt_order_flags) < 0) + goto error; + + /* set up group creation property list */ + if ((gcpl_out = H5Pcreate(H5P_GROUP_CREATE)) < 0) + goto error; + + if (H5Pset_link_creation_order(gcpl_out, crt_order_flags) < 0) + goto error; + + /*------------------------------------------------------------------------- + * the root is a special case, we get an ID for the root group + * and copy its attributes using that ID + *------------------------------------------------------------------------- + */ + if (HDstrcmp(travt->objs[i].name, "/") == 0) { + if ((grp_out = H5Gopen2(fidout, "/", H5P_DEFAULT)) < 0) + goto error; + } + else { + + if (options->grp_compact > 0 || options->grp_indexed > 0) { + if (H5Pset_link_phase_change(gcpl_out, + (unsigned) options->grp_compact, + (unsigned) options->grp_indexed) < 0) + goto error; + } + + if ((grp_out = H5Gcreate2(fidout, travt->objs[i].name, + H5P_DEFAULT, gcpl_out, H5P_DEFAULT)) < 0) + goto error; + + } + + /*------------------------------------------------------------------------- + * copy attrs + *------------------------------------------------------------------------- + */ + if (copy_attr(grp_in, grp_out, &named_dt_head, travt, options) < 0) + goto error; + + if (H5Pclose(gcpl_out) < 0) + goto error; + if (H5Pclose(gcpl_in) < 0) + goto error; + if (H5Gclose(grp_out) < 0) + goto error; + if (H5Gclose(grp_in) < 0) + goto error; + + break; + + /*------------------------------------------------------------------------- + * H5TRAV_TYPE_DATASET + *------------------------------------------------------------------------- + */ + case H5TRAV_TYPE_DATASET: + + has_filter = 0; + req_filter = 0; + + /* check if global filters were requested */ + if (options->n_filter_g) + req_filter = 1; + + /* check if filters were requested for individual objects */ + for (u = 0; u < options->op_tbl->nelems; u++) { + + if (HDstrcmp(travt->objs[i].name, options->op_tbl->objs[u].path) == 0) { + if (options->op_tbl->objs[u].filter->filtn > 0) { + req_filter = 1; + } + } + } + + /* check if layout change requested individual object */ + if (options->layout_g != H5D_LAYOUT_ERROR) { + pack_info_t *pckinfo; + /* any dataset is specified */ + if (options->op_tbl->nelems > 0) { + /* check if object exist */ + pckinfo = options_get_object(travt->objs[i].name, + options->op_tbl); + if (pckinfo) { + req_obj_layout = 1; + } + } + } + + /* early detection of references */ + if ((dset_in = H5Dopen2(fidin, travt->objs[i].name, H5P_DEFAULT)) + < 0) + goto error; + if ((ftype_id = H5Dget_type(dset_in)) < 0) + goto error; + if (H5T_REFERENCE == H5Tget_class(ftype_id)) + is_ref = 1; + + /* Check if the datatype is committed */ + if ((is_named = H5Tcommitted(ftype_id)) < 0) + goto error; + if (is_named) + if ((wtype_id = copy_named_datatype(ftype_id, fidout, + &named_dt_head, travt, options)) < 0) + goto error; + + if (H5Tclose(ftype_id) < 0) + goto error; + if (H5Dclose(dset_in) < 0) + goto error; + + /*------------------------------------------------------------------------- + * check if we should use H5Ocopy or not + * if there is a request for filters/layout, we read/write the object + * otherwise we do a copy using H5Ocopy + *------------------------------------------------------------------------- + */ + if (options->op_tbl->nelems || options->all_filter == 1 + || options->all_layout == 1 || is_ref || is_named) { + + int j; + + if ((dset_in = H5Dopen2(fidin, travt->objs[i].name, H5P_DEFAULT)) < 0) + goto error; + if ((f_space_id = H5Dget_space(dset_in)) < 0) + goto error; + if ((ftype_id = H5Dget_type(dset_in)) < 0) + goto error; + if ((dcpl_in = H5Dget_create_plist(dset_in)) < 0) + goto error; + if ((dcpl_out = H5Pcopy(dcpl_in)) < 0) + goto error; + if ((rank = H5Sget_simple_extent_ndims(f_space_id)) < 0) + goto error; + HDmemset(dims, 0, sizeof dims); + if (H5Sget_simple_extent_dims(f_space_id, dims, NULL) < 0) + goto error; + + if (H5Dget_space_status(dset_in, &space_status) < 0) + goto error; + + nelmts = 1; + for (j = 0; j < rank; j++) + nelmts *= dims[j]; + + /* wtype_id will have already been set if using a named dtype */ + if (!is_named) { + if (options->use_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; + + /* size of current dset */ + size_dset = nelmts * msize; + + /*------------------------------------------------------------------------- + * check if the dataset creation property list has filters that + * are not registered in the current configuration + * 1) the external filters GZIP and SZIP might not be available + * 2) the internal filters might be turned off + *------------------------------------------------------------------------- + */ + if (h5tools_canreadf((travt->objs[i].name), dcpl_in) == 1) { + apply_s = 1; + apply_f = 1; + + /*------------------------------------------------------------------------- + * references are a special case + * we cannot just copy the buffers, but instead we recreate the reference + * in a second traversal of the output file + *------------------------------------------------------------------------- + */ + if (H5T_REFERENCE != H5Tget_class(wtype_id)) { + /* get the storage size of the input dataset */ + dsize_in = H5Dget_storage_size(dset_in); + + /* check for small size datasets (less than 1k) except + * changing to COMPACT. For the reference, COMPACT is limited + * by size 64K by library. + */ + if (options->layout_g != H5D_COMPACT) { + if (size_dset < options->min_comp) + apply_s = 0; + } + + /* apply the filter */ + if (apply_s) { + if (apply_filters(travt->objs[i].name, rank, dims, + msize, dcpl_out, options, &has_filter) < 0) + goto error; + } + + /* only if layout change requested for entire file or + * individual obj */ + if (options->all_layout > 0 || req_obj_layout == 1) + /*------------------------------------------------- + * Unset the unlimited max dims if convert to other + * than chunk layouts, because unlimited max dims + * only can be applied to chunk layout. + * Also perform only for targeted dataset + * Also check for size limit to convert to compact + *-------------------------------------------------*/ + if (options->layout_g != H5D_CHUNKED) { + /* any dataset is specified */ + if (options->op_tbl->nelems > 0) { + /* if current obj match specified obj */ + if (options_get_object(travt->objs[i].name, + options->op_tbl)) + limit_maxdims = TRUE; + } + else { /* no dataset is specified */ + limit_maxdims = TRUE; + } + + /* if convert to COMPACT */ + if (options->layout_g == H5D_COMPACT) { + /* should be smaller than 64K */ + if (size_dset > MAX_COMPACT_DSIZE) + limit_maxdims = FALSE; + } + + /* unset unlimited max dims */ + if (limit_maxdims) + H5Sset_extent_simple(f_space_id, rank, dims, + NULL); + } + + /*------------------------------------------------------------------------- + * create the output dataset; + * disable error checking in case the dataset cannot be created with the + * modified dcpl; in that case use the original instead + *------------------------------------------------------------------------- + */ + H5E_BEGIN_TRY + { + dset_out = H5Dcreate2(fidout, + travt->objs[i].name, wtype_id, + f_space_id, H5P_DEFAULT, dcpl_out, + H5P_DEFAULT); + }H5E_END_TRY; + + if (dset_out == FAIL) { + if (options->verbose) + printf( + " warning: could not create dataset <%s>. Applying original settings\n", + travt->objs[i].name); + + if ((dset_out = H5Dcreate2(fidout, + travt->objs[i].name, wtype_id, f_space_id, + H5P_DEFAULT, dcpl_in, H5P_DEFAULT)) < 0) + goto error; + apply_f = 0; + } + + /*------------------------------------------------------------------------- + * read/write + *------------------------------------------------------------------------- + */ + if (nelmts > 0 && space_status != H5D_SPACE_STATUS_NOT_ALLOCATED) { + size_t need = (size_t)(nelmts * msize); /* bytes needed */ + + /* have to read the whole dataset if there is only one element in the dataset */ + if (need < H5TOOLS_MALLOCSIZE) + buf = HDmalloc(need); + + if (buf != NULL) { + /* read/write: use the macro to check error, e.g. memory allocation error inside the library. */ + CHECK_H5DRW_ERROR(H5Dread, dset_in, wtype_id, + H5S_ALL, H5S_ALL, H5P_DEFAULT, buf); + CHECK_H5DRW_ERROR(H5Dwrite, dset_out, wtype_id, + H5S_ALL, H5S_ALL, H5P_DEFAULT, buf); + + /* Check if we have VL data in the dataset's + * datatype that must be reclaimed */ + if (TRUE == H5Tdetect_class(wtype_id, H5T_VLEN)) + if (H5Dvlen_reclaim(wtype_id, f_space_id, + H5P_DEFAULT, buf) < 0) + goto error; + } + else { /* possibly not enough memory, read/write by hyperslabs */ + size_t p_type_nbytes = msize; /*size of memory type */ + hsize_t p_nelmts = nelmts; /*total elements */ + hsize_t elmtno; /*counter */ + int carry; /*counter carry value */ + unsigned int vl_data = 0; /*contains VL datatypes */ + + /* hyperslab info */ + hsize_t hslab_dims[H5S_MAX_RANK]; /*hyperslab dims */ + hsize_t hslab_nbytes; /*bytes per hyperslab */ + hsize_t hslab_nelmts; /*elements per hyperslab*/ + hid_t hslab_space; /*hyperslab data space */ + + /* hyperslab selection info */ + hsize_t hs_sel_offset[H5S_MAX_RANK];/* selection offset */ + hsize_t hs_sel_count[H5S_MAX_RANK]; /* selection count */ + hsize_t hs_select_nelmts; /* selected elements */ + hsize_t zero[8]; /*vector of zeros */ + int k; + H5D_layout_t dset_layout; + hid_t dcpl_tmp = -1; /* dataset creation property list ID */ + + /* check if we have VL data in the dataset's datatype */ + if (H5Tdetect_class(wtype_id, H5T_VLEN) == TRUE) + vl_data = TRUE; + + /* check first if writing dataset is chunked, + * if so use its chunk layout for better performance. */ + dset_layout = H5Pget_layout(dcpl_out); + if (dset_layout == H5D_CHUNKED) + dcpl_tmp = dcpl_out; /* writing dataset */ + else { /* if reading dataset is chunked */ + dset_layout = H5Pget_layout(dcpl_in); + if (dset_layout == H5D_CHUNKED) + dcpl_tmp = dcpl_in; /* reading dataset */ + } + + /* get hyperslab dims and size in byte */ + if (Get_hyperslab(dcpl_tmp, rank, dims, + p_type_nbytes, hslab_dims, + &hslab_nbytes) < 0) + goto error; + + hslab_buf = HDmalloc((size_t)hslab_nbytes); + + hslab_nelmts = hslab_nbytes / p_type_nbytes; + hslab_space = H5Screate_simple(1, &hslab_nelmts, + NULL); + + /* the hyperslab selection loop */ + HDmemset(hs_sel_offset, 0, + sizeof hs_sel_offset); + HDmemset(zero, 0, sizeof zero); + + for (elmtno = 0; elmtno < p_nelmts; elmtno += + hs_select_nelmts) { + if (rank > 0) { + /* calculate the hyperslab selections. The selection would be same as the hyperslab except for remaining edge portion of the dataset which is smaller then the hyperslab. + */ + for (k = 0, hs_select_nelmts = 1; + k < rank; k++) { + /* MIN() is used to get the remaining edge portion if exist. + * "dims[k] - hs_sel_offset[k]" is remaining edge portion that is smaller then the hyperslab.*/ + hs_sel_count[k] = + MIN(dims[k] - hs_sel_offset[k], hslab_dims[k]); + hs_select_nelmts *= hs_sel_count[k]; + } + + if (H5Sselect_hyperslab(f_space_id, + H5S_SELECT_SET, hs_sel_offset, + NULL, hs_sel_count, NULL) < 0) + goto error; + if (H5Sselect_hyperslab(hslab_space, + H5S_SELECT_SET, zero, NULL, + &hs_select_nelmts, NULL) < 0) + goto error; + } + else { + H5Sselect_all(f_space_id); + H5Sselect_all(hslab_space); + hs_select_nelmts = 1; + } /* rank */ + + /* read/write: use the macro to check error, e.g. memory allocation error inside the library. */ + CHECK_H5DRW_ERROR(H5Dread, dset_in, + wtype_id, hslab_space, f_space_id, + H5P_DEFAULT, hslab_buf); + CHECK_H5DRW_ERROR(H5Dwrite, dset_out, + wtype_id, hslab_space, f_space_id, + H5P_DEFAULT, hslab_buf); + + /* reclaim any VL memory, if necessary */ + if (vl_data) + H5Dvlen_reclaim(wtype_id, hslab_space, + H5P_DEFAULT, hslab_buf); + + /* calculate the next hyperslab offset */ + for (k = rank, carry = 1; k > 0 && carry; + --k) { + hs_sel_offset[k - 1] += hs_sel_count[k + - 1]; + /* if reached the end of a dim */ + if (hs_sel_offset[k - 1] == dims[k - 1]) + hs_sel_offset[k - 1] = 0; + else + carry = 0; + } /* k */ + } /* elmtno */ + + H5Sclose(hslab_space); + /* free */ + if (hslab_buf != NULL) { + HDfree(hslab_buf); + hslab_buf = NULL; + } + } /* hyperslab read */ + } /* if (nelmts>0 && space_status==H5D_SPACE_STATUS_NOT_ALLOCATED) */ + + /*------------------------------------------------------------------------- + * amount of compression used + *------------------------------------------------------------------------- + */ + if (options->verbose) { + double ratio = 0; + + /* only print the compression ration if there was a filter request */ + if (apply_s && apply_f && req_filter) { + /* get the storage size of the output dataset */ + dsize_out = H5Dget_storage_size(dset_out); + + /* compression ratio = uncompressed size / compressed size */ + if (dsize_out != 0) + ratio = (double) dsize_in + / (double) dsize_out; + + print_dataset_info(dcpl_out, + travt->objs[i].name, ratio, 1); + } + else + print_dataset_info(dcpl_in, travt->objs[i].name, + ratio, 0); + + /* print a message that the filter was not applied + (in case there was a filter) + */ + if (has_filter && apply_s == 0) + printf( + " \n", + travt->objs[i].name, + (int) options->min_comp); + + if (has_filter && apply_f == 0) + printf( + " \n", + travt->objs[i].name); + + } /* verbose */ + + /*------------------------------------------------------------------------- + * copy attrs + *------------------------------------------------------------------------- + */ + if (copy_attr(dset_in, dset_out, &named_dt_head, travt, + options) < 0) + goto error; + /*close */ + if (H5Dclose(dset_out) < 0) + goto error; + + }/*!H5T_REFERENCE*/ + }/*h5tools_canreadf*/ + + /*------------------------------------------------------------------------- + * close + *------------------------------------------------------------------------- + */ + if (H5Tclose(ftype_id) < 0) + goto error; + if (H5Tclose(wtype_id) < 0) + goto error; + if (H5Pclose(dcpl_in) < 0) + goto error; + if (H5Pclose(dcpl_out) < 0) + goto error; + if (H5Sclose(f_space_id) < 0) + goto error; + if (H5Dclose(dset_in) < 0) + goto error; + + } + /*------------------------------------------------------------------------- + * we do not have request for filter/chunking use H5Ocopy instead + *------------------------------------------------------------------------- + */ + else { + hid_t pid; + + /* create property to pass copy options */ + if ((pid = H5Pcreate(H5P_OBJECT_COPY)) < 0) + goto error; + + /* set options for object copy */ + if (H5Pset_copy_object(pid, H5O_COPY_WITHOUT_ATTR_FLAG) < 0) + goto error; + + /*------------------------------------------------------------------------- + * do the copy + *------------------------------------------------------------------------- + */ + + if (H5Ocopy(fidin, /* Source file or group identifier */ + travt->objs[i].name, /* Name of the source object to be copied */ + fidout, /* Destination file or group identifier */ + travt->objs[i].name, /* Name of the destination object */ + pid, /* Properties which apply to the copy */ + H5P_DEFAULT) < 0) /* Properties which apply to the new hard link */ + goto error; + + /* close property */ + if (H5Pclose(pid) < 0) + goto error; + + /*------------------------------------------------------------------------- + * copy attrs manually + *------------------------------------------------------------------------- + */ + if ((dset_in = H5Dopen2(fidin, travt->objs[i].name, H5P_DEFAULT)) + < 0) + goto error; + if ((dset_out = H5Dopen2(fidout, travt->objs[i].name, + H5P_DEFAULT)) < 0) + goto error; + if (copy_attr(dset_in, dset_out, &named_dt_head, travt, options) + < 0) + goto error; + if (H5Dclose(dset_in) < 0) + goto error; + if (H5Dclose(dset_out) < 0) + goto error; + + if (options->verbose) + printf(FORMAT_OBJ, "dset", travt->objs[i].name); + + } /* end do we have request for filter/chunking */ + + break; + + /*------------------------------------------------------------------------- + * H5TRAV_TYPE_NAMED_DATATYPE + *------------------------------------------------------------------------- + */ + case H5TRAV_TYPE_NAMED_DATATYPE: + + if (options->verbose) + printf(FORMAT_OBJ, "type", travt->objs[i].name); + + if ((type_in = H5Topen2(fidin, travt->objs[i].name, H5P_DEFAULT)) + < 0) + goto error; + + /* Copy the datatype anonymously */ + if ((type_out = copy_named_datatype(type_in, fidout, &named_dt_head, + travt, options)) < 0) + goto error; + + /* Link in to group structure */ + if (H5Lcreate_hard(type_out, ".", fidout, travt->objs[i].name, + H5P_DEFAULT, H5P_DEFAULT) < 0) + goto error; + + /*------------------------------------------------------------------------- + * copy attrs + *------------------------------------------------------------------------- + */ + if (copy_attr(type_in, type_out, &named_dt_head, travt, options) + < 0) + goto error; + + if (H5Tclose(type_in) < 0) + goto error; + if (H5Tclose(type_out) < 0) + goto error; + + break; + + /*------------------------------------------------------------------------- + * H5TRAV_TYPE_LINK + * H5TRAV_TYPE_UDLINK + * + * Only handles external links; H5Lcopy will fail for other UD link types + * since we don't have creation or copy callbacks for them. + *------------------------------------------------------------------------- + */ + + case H5TRAV_TYPE_LINK: + case H5TRAV_TYPE_UDLINK: { + + if (options->verbose) + printf(FORMAT_OBJ, "link", travt->objs[i].name); + + if (H5Lcopy(fidin, travt->objs[i].name, fidout, travt->objs[i].name, + H5P_DEFAULT, H5P_DEFAULT) < 0) + goto error; + + if (options->verbose) + printf(FORMAT_OBJ, "link", travt->objs[i].name); + + } + break; + + default: + goto error; + } /* switch */ + + /* free */ + if (buf != NULL) { + HDfree(buf); + buf = NULL; + } + + } /* i */ + + /* Finalize (link) the stack of named datatypes (if any) */ + named_datatype_free(&named_dt_head, 0); + + return 0; error: - H5E_BEGIN_TRY { - H5Gclose(grp_in); - H5Gclose(grp_out); - H5Pclose(dcpl_in); - H5Pclose(gcpl_in); - H5Pclose(gcpl_out); - H5Sclose(f_space_id); - H5Dclose(dset_in); - H5Dclose(dset_out); - H5Tclose(ftype_id); - H5Tclose(wtype_id); - H5Tclose(type_in); - H5Tclose(type_out); - named_datatype_free(&named_dt_head, 1); - } H5E_END_TRY; - /* free */ - if (buf!=NULL) - HDfree(buf); - if (hslab_buf!=NULL) - HDfree(hslab_buf); - return -1; + H5E_BEGIN_TRY + { + H5Gclose(grp_in); + H5Gclose(grp_out); + H5Pclose(dcpl_in); + H5Pclose(gcpl_in); + H5Pclose(gcpl_out); + H5Sclose(f_space_id); + H5Dclose(dset_in); + H5Dclose(dset_out); + H5Tclose(ftype_id); + H5Tclose(wtype_id); + H5Tclose(type_in); + H5Tclose(type_out); + named_datatype_free(&named_dt_head, 1); + }H5E_END_TRY; + /* free */ + if (buf != NULL) + HDfree(buf); + if (hslab_buf != NULL) + HDfree(hslab_buf); + return -1; } - /*------------------------------------------------------------------------- -* Function: print_dataset_info -* -* Purpose: print name, filters, percentage compression of a dataset -* -*------------------------------------------------------------------------- -*/ -static void print_dataset_info(hid_t dcpl_id, - char *objname, - double ratio, - int pr) -{ - char strfilter[255]; + * Function: print_dataset_info + * + * Purpose: print name, filters, percentage compression of a dataset + * + *------------------------------------------------------------------------- + */ +static void print_dataset_info(hid_t dcpl_id, char *objname, double ratio, + int pr) { + char strfilter[255]; #if defined (PRINT_DEBUG ) - char temp[255]; + char temp[255]; #endif - int nfilters; /* number of filters */ - unsigned filt_flags; /* filter flags */ - H5Z_filter_t filtn; /* filter identification number */ - unsigned cd_values[20]; /* filter client data values */ - size_t cd_nelmts; /* filter client number of values */ - char f_objname[256]; /* filter objname */ - int i; - + int nfilters; /* number of filters */ + unsigned filt_flags; /* filter flags */ + H5Z_filter_t filtn; /* filter identification number */ + unsigned cd_values[20]; /* filter client data values */ + size_t cd_nelmts; /* filter client number of values */ + char f_objname[256]; /* filter objname */ + int i; - HDstrcpy(strfilter,"\0"); + HDstrcpy(strfilter, "\0"); - /* get information about input filters */ - if((nfilters = H5Pget_nfilters(dcpl_id)) < 0) - return; + /* get information about input filters */ + if ((nfilters = H5Pget_nfilters(dcpl_id)) < 0) + return; - for(i = 0; i < nfilters; i++) { - cd_nelmts = NELMTS(cd_values); + for (i = 0; i < nfilters; i++) { + cd_nelmts = NELMTS(cd_values); - filtn = H5Pget_filter2(dcpl_id, (unsigned)i, &filt_flags, &cd_nelmts, - cd_values, sizeof(f_objname), f_objname, NULL); + filtn = H5Pget_filter2(dcpl_id, (unsigned) i, &filt_flags, &cd_nelmts, + cd_values, sizeof(f_objname), f_objname, NULL); - switch(filtn) { + switch (filtn) { - case H5Z_FILTER_NONE: - HDstrcat(strfilter,"NONE "); - break; + case H5Z_FILTER_NONE: + HDstrcat(strfilter, "NONE "); + break; - case H5Z_FILTER_DEFLATE: - HDstrcat(strfilter,"GZIP "); + case H5Z_FILTER_DEFLATE: + HDstrcat(strfilter, "GZIP "); #if defined (PRINT_DEBUG) - { - unsigned level=cd_values[0]; - sprintf(temp,"(%d)",level); - HDstrcat(strfilter,temp); - } + { + unsigned level=cd_values[0]; + sprintf(temp,"(%d)",level); + HDstrcat(strfilter,temp); + } #endif - break; + break; - case H5Z_FILTER_SZIP: - HDstrcat(strfilter,"SZIP "); + case H5Z_FILTER_SZIP: + HDstrcat(strfilter, "SZIP "); #if defined (PRINT_DEBUG) - { - unsigned options_mask=cd_values[0]; /* from dcpl, not filt*/ - unsigned ppb=cd_values[1]; - sprintf(temp,"(%d,",ppb); - HDstrcat(strfilter,temp); - if (options_mask & H5_SZIP_EC_OPTION_MASK) - HDstrcpy(temp,"EC) "); - else if (options_mask & H5_SZIP_NN_OPTION_MASK) - HDstrcpy(temp,"NN) "); - } - HDstrcat(strfilter,temp); + { + unsigned options_mask=cd_values[0]; /* from dcpl, not filt*/ + unsigned ppb=cd_values[1]; + sprintf(temp,"(%d,",ppb); + HDstrcat(strfilter,temp); + if (options_mask & H5_SZIP_EC_OPTION_MASK) + HDstrcpy(temp,"EC) "); + else if (options_mask & H5_SZIP_NN_OPTION_MASK) + HDstrcpy(temp,"NN) "); + } + HDstrcat(strfilter,temp); #endif - break; - - case H5Z_FILTER_SHUFFLE: - HDstrcat(strfilter,"SHUF "); - break; - - case H5Z_FILTER_FLETCHER32: - HDstrcat(strfilter,"FLET "); - break; - - case H5Z_FILTER_NBIT: - HDstrcat(strfilter,"NBIT "); - break; - - case H5Z_FILTER_SCALEOFFSET: - HDstrcat(strfilter,"SCALEOFFSET "); - break; - - default: - HDstrcat(strfilter,"UD "); - break; - } /* switch */ - }/*i*/ - - if(!pr) - printf(FORMAT_OBJ,"dset",objname ); - else - { - char str[255], temp[28]; - HDstrcpy(str,"dset "); - HDstrcat(str,strfilter); - sprintf(temp," (%.3f:1)",ratio); - HDstrcat(str,temp); - printf(FORMAT_OBJ,str,objname); - } + break; + + case H5Z_FILTER_SHUFFLE: + HDstrcat(strfilter, "SHUF "); + break; + + case H5Z_FILTER_FLETCHER32: + HDstrcat(strfilter, "FLET "); + break; + + case H5Z_FILTER_NBIT: + HDstrcat(strfilter, "NBIT "); + break; + + case H5Z_FILTER_SCALEOFFSET: + HDstrcat(strfilter, "SCALEOFFSET "); + break; + + default: + HDstrcat(strfilter, "UD "); + break; + } /* switch */ + }/*i*/ + + if (!pr) + printf(FORMAT_OBJ, "dset", objname); + else { + char str[255], temp[28]; + HDstrcpy(str, "dset "); + HDstrcat(str, strfilter); + sprintf(temp, " (%.3f:1)", ratio); + HDstrcat(str, temp); + printf(FORMAT_OBJ, str, objname); + } } - /*------------------------------------------------------------------------- -* Function: copy_user_block -* -* Purpose: copy user block from one file to another -* -* Return: 0, ok, -1 no -* -* Programmer: Peter Cao -* -* Date: October, 25, 2007 -* -*------------------------------------------------------------------------- -*/ -static int -copy_user_block(const char *infile, const char *outfile, hsize_t size) -{ - int infid = -1, outfid = -1; /* File descriptors */ - int status = 0; /* Return value */ - - /* User block must be any power of 2 equal to 512 or greater (512, 1024, 2048, etc.) */ - HDassert(size > 0); - - /* Open files */ - if((infid = HDopen(infile, O_RDONLY, 0)) < 0) { - status = -1; - goto done; - } - if((outfid = HDopen(outfile, O_WRONLY, 0644)) < 0) { - status = -1; - goto done; - } - - /* Copy the userblock from the input file to the output file */ - while(size > 0) { - ssize_t nread, nbytes; /* # of bytes transfered, etc. */ - char rbuf[USERBLOCK_XFER_SIZE]; /* Buffer for reading */ - const char *wbuf; /* Pointer into buffer, for writing */ - - /* Read buffer from source file */ - if(size > USERBLOCK_XFER_SIZE) - nread = HDread(infid, rbuf, (size_t)USERBLOCK_XFER_SIZE); - else - nread = HDread(infid, rbuf, (size_t)size); - if(nread < 0) { - status = -1; - goto done; - } /* end if */ - - /* Write buffer to destination file */ - /* (compensating for interrupted writes & checking for errors, etc.) */ - nbytes = nread; - wbuf = rbuf; - while(nbytes > 0) { - ssize_t nwritten; /* # of bytes written */ - - do { - nwritten = HDwrite(outfid, wbuf, (size_t)nbytes); - } while(-1 == nwritten && EINTR == errno); - if(-1 == nwritten) { /* error */ - status = -1; - goto done; - } /* end if */ - HDassert(nwritten > 0); - HDassert(nwritten <= nbytes); - - /* Update # of bytes left & offset in buffer */ - nbytes -= nwritten; - wbuf += nwritten; - HDassert(nbytes == 0 || wbuf < (rbuf + USERBLOCK_XFER_SIZE)); - } /* end while */ - - /* Update size of userblock left to transfer */ - size = size - (hsize_t)nread; - } /* end while */ + * Function: copy_user_block + * + * Purpose: copy user block from one file to another + * + * Return: 0, ok, -1 no + * + * Programmer: Peter Cao + * + * Date: October, 25, 2007 + * + *------------------------------------------------------------------------- + */ +static int copy_user_block(const char *infile, const char *outfile, + hsize_t size) { + int infid = -1, outfid = -1; /* File descriptors */ + int status = 0; /* Return value */ + + /* User block must be any power of 2 equal to 512 or greater (512, 1024, 2048, etc.) */ + HDassert(size > 0); + + /* Open files */ + if ((infid = HDopen(infile, O_RDONLY, 0)) < 0) { + status = -1; + goto done; + } + if ((outfid = HDopen(outfile, O_WRONLY, 0644)) < 0) { + status = -1; + goto done; + } + + /* Copy the userblock from the input file to the output file */ + while (size > 0) { + ssize_t nread, nbytes; /* # of bytes transfered, etc. */ + char rbuf[USERBLOCK_XFER_SIZE]; /* Buffer for reading */ + const char *wbuf; /* Pointer into buffer, for writing */ + + /* Read buffer from source file */ + if (size > USERBLOCK_XFER_SIZE) + nread = HDread(infid, rbuf, (size_t)USERBLOCK_XFER_SIZE); + else + nread = HDread(infid, rbuf, (size_t)size); + if (nread < 0) { + status = -1; + goto done; + } /* end if */ + + /* Write buffer to destination file */ + /* (compensating for interrupted writes & checking for errors, etc.) */ + nbytes = nread; + wbuf = rbuf; + while (nbytes > 0) { + ssize_t nwritten; /* # of bytes written */ + + do { + nwritten = HDwrite(outfid, wbuf, (size_t)nbytes); + } while (-1 == nwritten && EINTR == errno); + if (-1 == nwritten) { /* error */ + status = -1; + goto done; + } /* end if */ + HDassert(nwritten > 0); + HDassert(nwritten <= nbytes); + + /* Update # of bytes left & offset in buffer */ + nbytes -= nwritten; + wbuf += nwritten; + HDassert(nbytes == 0 || wbuf < (rbuf + USERBLOCK_XFER_SIZE)); + } /* end while */ + + /* Update size of userblock left to transfer */ + size = size - (hsize_t) nread; + } /* end while */ done: - if(infid > 0) - HDclose(infid); - if(outfid > 0) - HDclose(outfid); + if (infid > 0) + HDclose(infid); + if (outfid > 0) + HDclose(outfid); - return status; + return status; } - - /*------------------------------------------------------------------------- -* Function: print_user_block -* -* Purpose: print user block -* -* Return: 0, ok, -1 no -* -* Programmer: Pedro Vicente -* -* Date: August, 20, 2008 -* -*------------------------------------------------------------------------- -*/ + * Function: print_user_block + * + * Purpose: print user block + * + * Return: 0, ok, -1 no + * + * Programmer: Pedro Vicente + * + * Date: August, 20, 2008 + * + *------------------------------------------------------------------------- + */ #if defined (H5REPACK_DEBUG_USER_BLOCK) static void print_user_block(const char *filename, hid_t fid) { - int fh; /* file handle */ - hsize_t ub_size; /* user block size */ - hsize_t size; /* size read */ - hid_t fcpl; /* file creation property list ID for HDF5 file */ - int i; - - /* get user block size */ - if(( fcpl = H5Fget_create_plist(fid)) < 0) - { - error_msg("failed to retrieve file creation property list\n"); - goto done; - } - - if(H5Pget_userblock(fcpl, &ub_size) < 0) - { - error_msg("failed to retrieve userblock size\n"); - goto done; - } - - if(H5Pclose(fcpl) < 0) - { - error_msg("failed to close property list\n"); - goto done; - } - - /* open file */ - if((fh = HDopen(filename, O_RDONLY, 0)) < 0) - { - goto done; - } - - size = ub_size; - - /* read file */ - while(size > 0) - { - ssize_t nread; /* # of bytes read */ - char rbuf[USERBLOCK_XFER_SIZE]; /* buffer for reading */ - - /* read buffer */ - if(size > USERBLOCK_XFER_SIZE) - nread = HDread(fh, rbuf, (size_t)USERBLOCK_XFER_SIZE); - else - nread = HDread(fh, rbuf, (size_t)size); - - for(i = 0; i < nread; i++) - { - - printf("%c ", rbuf[i]); - - } - printf("\n"); - - if(nread < 0) - { - goto done; - } - - - /* update size of userblock left to transfer */ - size -= nread; - } + int fh; /* file handle */ + hsize_t ub_size; /* user block size */ + hsize_t size; /* size read */ + hid_t fcpl; /* file creation property list ID for HDF5 file */ + int i; -done: - if(fh > 0) - HDclose(fh); + /* get user block size */ + if(( fcpl = H5Fget_create_plist(fid)) < 0) { + error_msg("failed to retrieve file creation property list\n"); + goto done; + } + + if(H5Pget_userblock(fcpl, &ub_size) < 0) { + error_msg("failed to retrieve userblock size\n"); + goto done; + } + + if(H5Pclose(fcpl) < 0) { + error_msg("failed to close property list\n"); + goto done; + } + + /* open file */ + if((fh = HDopen(filename, O_RDONLY, 0)) < 0) { + goto done; + } + size = ub_size; + + /* read file */ + while(size > 0) { + ssize_t nread; /* # of bytes read */ + char rbuf[USERBLOCK_XFER_SIZE]; /* buffer for reading */ + + /* read buffer */ + if(size > USERBLOCK_XFER_SIZE) + nread = HDread(fh, rbuf, (size_t)USERBLOCK_XFER_SIZE); + else + nread = HDread(fh, rbuf, (size_t)size); + + for(i = 0; i < nread; i++) { + + printf("%c ", rbuf[i]); + + } + printf("\n"); + + if(nread < 0) { + goto done; + } + + /* update size of userblock left to transfer */ + size -= nread; + } + +done: + if(fh > 0) + HDclose(fh); - return; + return; } #endif diff --git a/tools/h5repack/h5repack_main.c b/tools/h5repack/h5repack_main.c index b5f9d31..7af776d 100644 --- a/tools/h5repack/h5repack_main.c +++ b/tools/h5repack/h5repack_main.c @@ -20,267 +20,345 @@ /* Name of tool */ #define PROGRAMNAME "h5repack" -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); - +static int parse_command_line(int argc, const char **argv, pack_opt_t* options); /* module-scoped variables */ -static int has_i_o = 0; -const char *infile = NULL; -const char *outfile = NULL; - +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: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' }, - { "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 */ - { "fs_strategy", require_arg, 'S' }, - { "fs_threshold", require_arg, 'T' }, - { NULL, 0, '\0' } -}; - - - +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 */ + { "fs_strategy", require_arg, 'S' }, + { "fs_threshold", require_arg, 'T' }, { NULL, 0, '\0' } }; /*------------------------------------------------------------------------- - * Function: main + * Function: usage * - * Purpose: h5repack main program + * Purpose: print usage * - * Return: Success: EXIT_SUCCESS(0) + * Return: void * - * Failure: EXIT_FAILURE(1) + *------------------------------------------------------------------------- + */ +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( + " -M A, --metadata_block_size=A Metadata block size for H5Pset_meta_block_size\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 0) \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(" UD, to apply a user defined 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( + " UD=\n"); + printf( + " required values for filter_number,cd_value_count,value_1\n"); + printf(" optional values for value_2 to value_N\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 contiguous 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"); + printf("6) h5repack -f UD=307,1,9 file1 file2 \n"); + printf("\n"); + printf(" Add bzip2 filter to all datasets\n"); + printf("\n"); +} + +/*------------------------------------------------------------------------- + * Function: leave * - * Programmer: Pedro Vicente, pvn@ncsa.uiuc.edu + * Purpose: Shutdown MPI & HDF5 and call exit() * - * Date: May 9, 2003 + * Return: Does not return * - * Comments: + * Programmer: Quincey Koziol + * Saturday, 31. January 2004 + * + * Modifications: * *------------------------------------------------------------------------- */ -int main(int argc, const char **argv) -{ - - pack_opt_t options; /*the global options */ - int ret=-1; - - h5tools_setprogname(PROGRAMNAME); - h5tools_setstatus(EXIT_SUCCESS); - - /* Initialize h5tools lib */ - h5tools_init(); - - /* update hyperslab buffer size from H5TOOLS_BUFSIZE env if exist */ - if ( h5tools_getenv_update_hyperslab_bufsize() < 0) - HDexit(EXIT_FAILURE); - - /* initialize options */ - h5repack_init(&options, 0, H5F_FILE_SPACE_DEFAULT, (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 ( HDstrcmp( infile, outfile ) == 0 ) - { - error_msg("file names cannot be the same\n"); - usage(h5tools_getprogname()); - HDexit(EXIT_FAILURE); - - } - } - - else - { - error_msg("file names missing\n"); - usage(h5tools_getprogname()); - HDexit(EXIT_FAILURE); - } - } - - - /* pack it */ - ret=h5repack(infile,outfile,&options); +static void leave(int ret) { + h5tools_close(); - /* free tables */ - h5repack_end(&options); - - if (ret==-1) - return 1; - else - return 0; + HDexit(ret); } - - /*------------------------------------------------------------------------- - * Function: usage + * Function: read_info * - * Purpose: print usage + * Purpose: read comp and chunk options from a file * - * Return: void + * Return: void, exit on error + * + * Programmer: pvn@ncsa.uiuc.edu + * + * Date: September, 22, 2003 * *------------------------------------------------------------------------- */ -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(" -M A, --metadata_block_size=A Metadata block size for H5Pset_meta_block_size\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 0) \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(" UD, to apply a user defined 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(" UD=\n"); - printf(" required values for filter_number,cd_value_count,value_1\n"); - printf(" optional values for value_2 to value_N\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 contiguous 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"); - printf("6) h5repack -f UD=307,1,9 file1 file2 \n"); - printf("\n"); - printf(" Add bzip2 filter to all datasets\n"); - printf("\n"); -} +static +int read_info(const char *filename, pack_opt_t *options) { + + char stype[10]; + 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 != ' ') { + fscanf(fp, "%c", &c); + if (HDfeof(fp)) + break; + } + c = '0'; + /* go until end */ + while (c != ' ') { + fscanf(fp, "%c", &c); + 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 != ' ') { + fscanf(fp, "%c", &c); + if (HDfeof(fp)) + break; + } + c = '0'; + /* go until end */ + while (c != ' ') { + fscanf(fp, "%c", &c); + 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: parse_command_line @@ -291,316 +369,275 @@ static void usage(const char *prog) */ 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(h5tools_getprogname()); - HDexit(EXIT_SUCCESS); - case 'V': - print_version(h5tools_getprogname()); - HDexit(EXIT_SUCCESS); - 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"); - HDexit(EXIT_FAILURE); - } - break; - case 'l': - - /* parse the -l layout option */ - if (h5repack_addlayout( opt_arg, options)<0) - { - error_msg("in parsing layout\n"); - HDexit(EXIT_FAILURE); - } - break; - - - case 'm': - - options->min_comp = HDatoi( opt_arg ); - if ((int)options->min_comp<=0) - { - error_msg("invalid minimum compress size <%s>\n", opt_arg ); - HDexit(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 = HDatoi( opt_arg ); - if (options->grp_compact>0) - options->latest = 1; /* must use latest format */ - break; - - - case 'd': - - options->grp_indexed = HDatoi( 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 = HDstrchr( opt_arg, ':'); - options->latest = 1; /* 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 = HDatol( opt_arg ); - if ( options->alignment < 1 ) - { - error_msg("invalid alignment size\n", opt_arg ); - HDexit(EXIT_FAILURE); - } - break; - - case 'S': - { - char strategy[MAX_NC_NAME]; - - HDstrcpy(strategy, opt_arg); - if(!HDstrcmp(strategy, "ALL_PERSIST")) - options->fs_strategy = H5F_FILE_SPACE_ALL_PERSIST; - else if(!HDstrcmp(strategy, "ALL")) - options->fs_strategy = H5F_FILE_SPACE_ALL; - else if(!HDstrcmp(strategy, "AGGR_VFD")) - options->fs_strategy = H5F_FILE_SPACE_AGGR_VFD; - else if(!HDstrcmp(strategy, "VFD")) - options->fs_strategy = H5F_FILE_SPACE_VFD; - else { - error_msg("invalid file space management strategy\n", opt_arg ); - HDexit(EXIT_FAILURE); - } - break; - } - - case 'T': - - options->fs_threshold = (hsize_t)HDatol( opt_arg ); - 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()); - HDexit(EXIT_FAILURE); - } - } - +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 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(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 = HDatoi( opt_arg ); + 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 = 1; + break; + + case 'c': + options->grp_compact = HDatoi( opt_arg ); + if (options->grp_compact > 0) + options->latest = 1; /* must use latest format */ + break; + + case 'd': + options->grp_indexed = HDatoi( 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 = HDstrchr( opt_arg, ':'); + options->latest = 1; /* 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 = HDatol( opt_arg ); + if (options->alignment < 1) { + error_msg("invalid alignment size\n", opt_arg); + h5tools_setstatus(EXIT_FAILURE); + ret_value = -1; + goto done; + } + break; + + case 'S': + { + char strategy[MAX_NC_NAME]; + + HDstrcpy(strategy, opt_arg); + if (!HDstrcmp(strategy, "ALL_PERSIST")) + options->fs_strategy = H5F_FILE_SPACE_ALL_PERSIST; + else if (!HDstrcmp(strategy, "ALL")) + options->fs_strategy = H5F_FILE_SPACE_ALL; + else if (!HDstrcmp(strategy, "AGGR_VFD")) + options->fs_strategy = H5F_FILE_SPACE_AGGR_VFD; + else if (!HDstrcmp(strategy, "VFD")) + options->fs_strategy = H5F_FILE_SPACE_VFD; + else { + error_msg("invalid file space management strategy\n", opt_arg); + h5tools_setstatus(EXIT_FAILURE); + ret_value = -1; + goto done; + } + } + break; + + case 'T': + options->fs_threshold = (hsize_t) HDatol( opt_arg ); + 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: read_info + * Function: main * - * Purpose: read comp and chunk options from a file + * Purpose: h5repack main program * - * Return: void, exit on error + * Return: Success: EXIT_SUCCESS(0) * - * Programmer: pvn@ncsa.uiuc.edu + * Failure: EXIT_FAILURE(1) * - * Date: September, 22, 2003 + * Programmer: Pedro Vicente, pvn@ncsa.uiuc.edu + * + * Date: May 9, 2003 + * + * Comments: * *------------------------------------------------------------------------- */ - -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 = HDfopen(filename, "r")) == (FILE *)NULL) { - error_msg("cannot open options file %s\n", filename); - HDexit(EXIT_FAILURE); - } - - /* 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!=' ' ) - { - fscanf(fp, "%c", &c); - if (HDfeof(fp)) break; - } - c='0'; - /* go until end */ - while( c!=' ' ) - { - fscanf(fp, "%c", &c); - 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"); - HDexit(EXIT_FAILURE); - } - } - /*------------------------------------------------------------------------- - * layout - *------------------------------------------------------------------------- - */ - else if (HDstrcmp(stype,"-l") == 0) { - - /* find begining of info */ - i=0; c='0'; - while( c!=' ' ) - { - fscanf(fp, "%c", &c); - if (HDfeof(fp)) break; - } - c='0'; - /* go until end */ - while( c!=' ' ) - { - fscanf(fp, "%c", &c); - 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"); - HDexit(EXIT_FAILURE); - } - } - /*------------------------------------------------------------------------- - * not valid - *------------------------------------------------------------------------- - */ - else { - error_msg("bad file format for %s", filename); - HDexit(EXIT_FAILURE); - } - } - - HDfclose(fp); - return; +int main(int argc, const char **argv) { + + pack_opt_t options; /*the global options */ + int ret = -1; + + h5tools_setprogname(PROGRAMNAME); + h5tools_setstatus(EXIT_SUCCESS); + + /* Initialize h5tools lib */ + h5tools_init(); + + /* 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 */ + h5repack_init(&options, 0, H5F_FILE_SPACE_DEFAULT, (hsize_t) 0); + + 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; + } + } + + /* pack it */ + h5tools_setstatus(h5repack(infile, outfile, &options)); + +done: + /* free tables */ + h5repack_end(&options); + + leave(h5tools_getstatus()); } + diff --git a/tools/h5repack/h5repack_opttable.c b/tools/h5repack/h5repack_opttable.c index bcddbb9..b54e887 100644 --- a/tools/h5repack/h5repack_opttable.c +++ b/tools/h5repack/h5repack_opttable.c @@ -1,4 +1,4 @@ - /* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * +/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * Copyright by The HDF Group. * * Copyright by the Board of Trustees of the University of Illinois. * * All rights reserved. * @@ -27,21 +27,19 @@ *------------------------------------------------------------------------- */ -void init_packobject(pack_info_t *obj) -{ - int j, k; - - HDstrcpy(obj->path,"\0"); - for ( j=0; jfilter[j].filtn = -1; - for ( k=0; kfilter[j].cd_values[k] = 0; - } - obj->chunk.rank = -1; - obj->refobj_id = -1; - obj->layout = H5D_LAYOUT_ERROR; - obj->nfilters = 0; +void init_packobject(pack_info_t *obj) { + int j, k; + + HDstrcpy(obj->path, "\0"); + for (j = 0; j < H5_REPACK_MAX_NFILTERS; j++) { + obj->filter[j].filtn = -1; + for (k = 0; k < CD_VALUES; k++) + obj->filter[j].cd_values[k] = 0; + } + obj->chunk.rank = -1; + obj->refobj_id = -1; + obj->layout = H5D_LAYOUT_ERROR; + obj->nfilters = 0; } /*------------------------------------------------------------------------- @@ -54,19 +52,16 @@ void init_packobject(pack_info_t *obj) *------------------------------------------------------------------------- */ -static void aux_tblinsert_filter(pack_opttbl_t *table, - unsigned int I, - filter_info_t filt) -{ - if (table->objs[ I ].nfiltersobjs[ I ].filter[ table->objs[ I ].nfilters++ ] = filt; - } - else - { - error_msg("cannot insert the filter in this object.\ +static void aux_tblinsert_filter(pack_opttbl_t *table, unsigned int I, + filter_info_t filt) { + if (table->objs[I].nfilters < H5_REPACK_MAX_NFILTERS) { + table->objs[I].filter[table->objs[I].nfilters++] = filt; + } + else { + error_msg( + "cannot insert the filter in this object.\ Maximum capacity exceeded\n"); - } + } } /*------------------------------------------------------------------------- @@ -79,33 +74,28 @@ static void aux_tblinsert_filter(pack_opttbl_t *table, *------------------------------------------------------------------------- */ -static void aux_tblinsert_layout(pack_opttbl_t *table, - unsigned int I, - pack_info_t *pack) -{ - int k; - - table->objs[I].layout = pack->layout; - if (H5D_CHUNKED==pack->layout) - { - /* -2 means the NONE option, remove chunking - and set the layout to contiguous */ - if (pack->chunk.rank==-2) - { - table->objs[I].layout = H5D_CONTIGUOUS; - table->objs[I].chunk.rank = -2; - } - /* otherwise set the chunking type */ - else - { - table->objs[I].chunk.rank = pack->chunk.rank; - for (k = 0; k < pack->chunk.rank; k++) - table->objs[I].chunk.chunk_lengths[k] = pack->chunk.chunk_lengths[k]; - } - } +static void aux_tblinsert_layout(pack_opttbl_t *table, unsigned int I, + pack_info_t *pack) { + int k; + + table->objs[I].layout = pack->layout; + if (H5D_CHUNKED == pack->layout) { + /* -2 means the NONE option, remove chunking + and set the layout to contiguous */ + if (pack->chunk.rank == -2) { + table->objs[I].layout = H5D_CONTIGUOUS; + table->objs[I].chunk.rank = -2; + } + /* otherwise set the chunking type */ + else { + table->objs[I].chunk.rank = pack->chunk.rank; + for (k = 0; k < pack->chunk.rank; k++) + table->objs[I].chunk.chunk_lengths[k] = + pack->chunk.chunk_lengths[k]; + } + } } - /*------------------------------------------------------------------------- * Function: aux_inctable * @@ -116,21 +106,20 @@ static void aux_tblinsert_layout(pack_opttbl_t *table, *------------------------------------------------------------------------- */ -static int aux_inctable(pack_opttbl_t *table, int n_objs ) -{ - unsigned int i; - - table->size += n_objs; - table->objs = (pack_info_t*)HDrealloc(table->objs, table->size * sizeof(pack_info_t)); - if (table->objs==NULL) { - error_msg("not enough memory for options table\n"); - return -1; - } - for (i = table->nelems; i < table->size; i++) - { - init_packobject(&table->objs[i]); - } - return 0; +static int aux_inctable(pack_opttbl_t *table, int n_objs) { + unsigned int i; + + table->size += n_objs; + table->objs = + (pack_info_t*) HDrealloc(table->objs, table->size * sizeof(pack_info_t)); + if (table->objs == NULL) { + error_msg("not enough memory for options table\n"); + return -1; + } + for (i = table->nelems; i < table->size; i++) { + init_packobject(&table->objs[i]); + } + return 0; } @@ -143,31 +132,29 @@ static int aux_inctable(pack_opttbl_t *table, int n_objs ) * *------------------------------------------------------------------------- */ -int options_table_init( pack_opttbl_t **tbl ) -{ - unsigned int i; - pack_opttbl_t *table; - - if(NULL == (table = (pack_opttbl_t *)HDmalloc(sizeof(pack_opttbl_t)))) - { - error_msg("not enough memory for options table\n"); - return -1; - } - - table->size = 30; - table->nelems = 0; - if(NULL == (table->objs = (pack_info_t*)HDmalloc(table->size * sizeof(pack_info_t)))) - { - error_msg("not enough memory for options table\n"); - HDfree(table); - return -1; - } - - for(i = 0; i < table->size; i++) - init_packobject(&table->objs[i]); - - *tbl = table; - return 0; +int options_table_init(pack_opttbl_t **tbl) { + unsigned int i; + pack_opttbl_t *table; + + if (NULL == (table = (pack_opttbl_t *) HDmalloc(sizeof(pack_opttbl_t)))) { + error_msg("not enough memory for options table\n"); + return -1; + } + + table->size = 30; + table->nelems = 0; + if (NULL == (table->objs = + (pack_info_t*) HDmalloc(table->size * sizeof(pack_info_t)))) { + error_msg("not enough memory for options table\n"); + HDfree(table); + return -1; + } + + for (i = 0; i < table->size; i++) + init_packobject(&table->objs[i]); + + *tbl = table; + return 0; } @@ -181,11 +168,10 @@ int options_table_init( pack_opttbl_t **tbl ) *------------------------------------------------------------------------- */ -int options_table_free( pack_opttbl_t *table ) -{ - HDfree(table->objs); - HDfree(table); - return 0; +int options_table_free(pack_opttbl_t *table) { + HDfree(table->objs); + HDfree(table); + return 0; } /*------------------------------------------------------------------------- @@ -198,95 +184,81 @@ int options_table_free( pack_opttbl_t *table ) *------------------------------------------------------------------------- */ - -int options_add_layout( obj_list_t *obj_list, - int n_objs, - pack_info_t *pack, - pack_opttbl_t *table ) -{ - unsigned int i, I; - int j, added=0, found=0; - - /* increase the size of the collection by N_OBJS if necessary */ - if (table->nelems+n_objs >= table->size) - { - if (aux_inctable(table,n_objs)<0) - return -1; - } - - /* search if this object is already in the table; "path" is the key */ - if (table->nelems>0) - { - /* go tru the supplied list of names */ - for (j = 0; j < n_objs; j++) - { - /* linear table search */ - for (i = 0; i < table->nelems; i++) - { - /*already on the table */ - if (HDstrcmp(obj_list[j].obj,table->objs[i].path)==0) - { - /* already chunk info inserted for this one; exit */ - if (table->objs[i].chunk.rank>0) - { - error_msg("chunk information already inserted for <%s>\n",obj_list[j].obj); - HDexit(EXIT_FAILURE); - } - /* insert the layout info */ - else - { - aux_tblinsert_layout(table,i,pack); - found=1; - break; - } - } /* if */ - } /* i */ - - if (found==0) - { - /* keep the grow in a temp var */ - I = table->nelems + added; - added++; - HDstrcpy(table->objs[I].path,obj_list[j].obj); - aux_tblinsert_layout(table,I,pack); - } - /* cases where we have an already inserted name but there is a new name also - example: - -f dset1:GZIP=1 -l dset1,dset2:CHUNK=20x20 - dset1 is already inserted, but dset2 must also be - */ - else if (found==1 && HDstrcmp(obj_list[j].obj,table->objs[i].path)!=0) - { - /* keep the grow in a temp var */ - I = table->nelems + added; - added++; - HDstrcpy(table->objs[I].path,obj_list[j].obj); - aux_tblinsert_layout(table,I,pack); - } - } /* j */ - } - - /* first time insertion */ - else - { - /* go tru the supplied list of names */ - for (j = 0; j < n_objs; j++) - { - I = table->nelems + added; - added++; - HDstrcpy(table->objs[I].path,obj_list[j].obj); - aux_tblinsert_layout(table,I,pack); - - } - } - - table->nelems+= added; - - return 0; +int options_add_layout(obj_list_t *obj_list, int n_objs, pack_info_t *pack, + pack_opttbl_t *table) { + unsigned int i, I; + int j, added = 0, found = 0; + + /* increase the size of the collection by N_OBJS if necessary */ + if (table->nelems + n_objs >= table->size) { + if (aux_inctable(table, n_objs) < 0) + return -1; + } + + /* search if this object is already in the table; "path" is the key */ + if (table->nelems > 0) { + /* go tru the supplied list of names */ + for (j = 0; j < n_objs; j++) { + /* linear table search */ + for (i = 0; i < table->nelems; i++) { + /*already on the table */ + if (HDstrcmp(obj_list[j].obj,table->objs[i].path) == 0) { + /* already chunk info inserted for this one; exit */ + if (table->objs[i].chunk.rank > 0) { + error_msg( + "chunk information already inserted for <%s>\n", + obj_list[j].obj); + HDexit(EXIT_FAILURE); + } + /* insert the layout info */ + else { + aux_tblinsert_layout(table, i, pack); + found = 1; + break; + } + } /* if */ + } /* i */ + + if (found == 0) { + /* keep the grow in a temp var */ + I = table->nelems + added; + added++; + HDstrcpy(table->objs[I].path, obj_list[j].obj); + aux_tblinsert_layout(table, I, pack); + } + /* cases where we have an already inserted name but there is a new name also + example: + -f dset1:GZIP=1 -l dset1,dset2:CHUNK=20x20 + dset1 is already inserted, but dset2 must also be + */ + else if (found == 1 + && HDstrcmp(obj_list[j].obj,table->objs[i].path) != 0) { + /* keep the grow in a temp var */ + I = table->nelems + added; + added++; + HDstrcpy(table->objs[I].path, obj_list[j].obj); + aux_tblinsert_layout(table, I, pack); + } + } /* j */ + } + + /* first time insertion */ + else { + /* go tru the supplied list of names */ + for (j = 0; j < n_objs; j++) { + I = table->nelems + added; + added++; + HDstrcpy(table->objs[I].path, obj_list[j].obj); + aux_tblinsert_layout(table, I, pack); + + } + } + + table->nelems += added; + + return 0; } - - /*------------------------------------------------------------------------- * Function: options_add_filter * @@ -297,81 +269,70 @@ int options_add_layout( obj_list_t *obj_list, *------------------------------------------------------------------------- */ -int options_add_filter(obj_list_t *obj_list, - int n_objs, - filter_info_t filt, - pack_opttbl_t *table ) -{ - - unsigned int i, I; - int j, added=0, found=0; - - /* increase the size of the collection by N_OBJS if necessary */ - if (table->nelems+n_objs >= table->size) - { - if (aux_inctable(table,n_objs)<0) - return -1; - } - - /* search if this object is already in the table; "path" is the key */ - if (table->nelems>0) - { - /* go tru the supplied list of names */ - for (j = 0; j < n_objs; j++) - { - /* linear table search */ - for (i = 0; i < table->nelems; i++) - { - /*already on the table */ - if (HDstrcmp(obj_list[j].obj,table->objs[i].path)==0) - { - /* insert */ - aux_tblinsert_filter(table,i,filt); - found=1; - break; - } /* if */ - } /* i */ - - if (found==0) - { - /* keep the grow in a temp var */ - I = table->nelems + added; - added++; - HDstrcpy(table->objs[I].path,obj_list[j].obj); - aux_tblinsert_filter(table,I,filt); - } - /* cases where we have an already inserted name but there is a new name also - example: - -l dset1:CHUNK=20x20 -f dset1,dset2:GZIP=1 - dset1 is already inserted, but dset2 must also be - */ - else if (found==1 && HDstrcmp(obj_list[j].obj,table->objs[i].path)!=0) - { - /* keep the grow in a temp var */ - I = table->nelems + added; - added++; - HDstrcpy(table->objs[I].path,obj_list[j].obj); - aux_tblinsert_filter(table,I,filt); - } - } /* j */ - } - - /* first time insertion */ - else - { - /* go tru the supplied list of names */ - for (j = 0; j < n_objs; j++) - { - I = table->nelems + added; - added++; - HDstrcpy(table->objs[I].path,obj_list[j].obj); - aux_tblinsert_filter(table,I,filt); - } - } - - table->nelems+= added; - - return 0; +int options_add_filter(obj_list_t *obj_list, int n_objs, filter_info_t filt, + pack_opttbl_t *table) { + + unsigned int i, I; + int j, added = 0, found = 0; + + /* increase the size of the collection by N_OBJS if necessary */ + if (table->nelems + n_objs >= table->size) { + if (aux_inctable(table, n_objs) < 0) + return -1; + } + + /* search if this object is already in the table; "path" is the key */ + if (table->nelems > 0) { + /* go tru the supplied list of names */ + for (j = 0; j < n_objs; j++) { + /* linear table search */ + for (i = 0; i < table->nelems; i++) { + /*already on the table */ + if (HDstrcmp(obj_list[j].obj,table->objs[i].path) == 0) { + /* insert */ + aux_tblinsert_filter(table, i, filt); + found = 1; + break; + } /* if */ + } /* i */ + + if (found == 0) { + /* keep the grow in a temp var */ + I = table->nelems + added; + added++; + HDstrcpy(table->objs[I].path, obj_list[j].obj); + aux_tblinsert_filter(table, I, filt); + } + /* cases where we have an already inserted name but there is a new name also + example: + -l dset1:CHUNK=20x20 -f dset1,dset2:GZIP=1 + dset1 is already inserted, but dset2 must also be + */ + else if (found == 1 + && HDstrcmp(obj_list[j].obj,table->objs[i].path) != 0) { + /* keep the grow in a temp var */ + I = table->nelems + added; + added++; + HDstrcpy(table->objs[I].path, obj_list[j].obj); + aux_tblinsert_filter(table, I, filt); + } + } /* j */ + } + + /* first time insertion */ + else { + /* go tru the supplied list of names */ + for (j = 0; j < n_objs; j++) { + I = table->nelems + added; + added++; + HDstrcpy(table->objs[I].path, obj_list[j].obj); + aux_tblinsert_filter(table, I, filt); + } + } + + table->nelems += added; + + return 0; } /*------------------------------------------------------------------------- @@ -384,34 +345,25 @@ int options_add_filter(obj_list_t *obj_list, *------------------------------------------------------------------------- */ -pack_info_t* options_get_object( const char *path, - pack_opttbl_t *table ) -{ - unsigned int i; - char tbl_path[MAX_NC_NAME+1]; /* +1 for start with "/" case */ - - - for ( i = 0; i < table->nelems; i++) - { - /* make full path (start with "/") to compare correctly */ - if (HDstrncmp(table->objs[i].path, "/", 1)) - { - HDstrcpy(tbl_path, "/"); - HDstrcat(tbl_path, table->objs[i].path); - } - else - HDstrcpy(tbl_path, table->objs[i].path); - - /* found it */ - if (HDstrcmp(tbl_path, path)==0) - { - return (&table->objs[i]); - } - } - - return NULL; +pack_info_t* options_get_object(const char *path, pack_opttbl_t *table) { + unsigned int i; + char tbl_path[MAX_NC_NAME + 1]; /* +1 for start with "/" case */ + + for (i = 0; i < table->nelems; i++) { + /* make full path (start with "/") to compare correctly */ + if (HDstrncmp(table->objs[i].path, "/", 1)) { + HDstrcpy(tbl_path, "/"); + HDstrcat(tbl_path, table->objs[i].path); + } + else + HDstrcpy(tbl_path, table->objs[i].path); + + /* found it */ + if (HDstrcmp(tbl_path, path) == 0) { + return (&table->objs[i]); + } + } + + return NULL; } - - - -- cgit v0.12