diff options
Diffstat (limited to 'tools/h5repack/h5repack.c')
| -rw-r--r-- | tools/h5repack/h5repack.c | 1822 |
1 files changed, 875 insertions, 947 deletions
diff --git a/tools/h5repack/h5repack.c b/tools/h5repack/h5repack.c index 5d30bf2..c79fea7 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 <stdlib.h> #include <string.h> @@ -23,224 +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; - - /* copy the objects */ - if (copy_objects(infile,outfile,options) < 0) - return -1; - - - return 0; -} + * 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; -/*------------------------------------------------------------------------- -* Function: h5repack_init -* -* Purpose: initialize options -* -* Return: 0, ok, -1, fail -* -*------------------------------------------------------------------------- -*/ - -int -h5repack_init(pack_opt_t *options, int verbose, hbool_t latest, - 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->latest = latest; - 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))); + 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_init + * + * Purpose: initialize options + * + * Return: 0, ok, -1, fail + * + *------------------------------------------------------------------------- + */ +int h5repack_init(pack_opt_t *options, int verbose, hbool_t latest, + 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->latest = latest; + 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))); } - /*------------------------------------------------------------------------- -* 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() @@ -250,766 +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; 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 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; 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; i<nmembers; j++) */ - } /* if (type_class == H5T_COMPOUND) */ - - if(is_ref) { - ; /* handled by copy_refs_attr() */ - } - else { - /*------------------------------------------------------------------------- - * read to memory - *------------------------------------------------------------------------- - */ - - buf = (void *)HDmalloc((size_t)(nelmts * msize)); - if(buf == NULL) { - error_msg("h5repack", "cannot read into memory\n" ); - goto error; - } /* end if */ - if(H5Aread(attr_id, wtype_id, buf) < 0) - goto error; - - /*------------------------------------------------------------------------- - * copy - *------------------------------------------------------------------------- - */ - - if((attr_out = H5Acreate2(loc_out, name, wtype_id, space_id, H5P_DEFAULT, H5P_DEFAULT)) < 0) - goto error; - if(H5Awrite(attr_out, wtype_id, buf) < 0) - goto error; - - /*close*/ - if(H5Aclose(attr_out) < 0) - goto error; - - /* 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); - HDfree(buf); - buf = NULL; - } /*H5T_REFERENCE*/ - - - if(options->verbose) - printf(FORMAT_OBJ_ATTR, "attr", name); - - /*------------------------------------------------------------------------- - * close - *------------------------------------------------------------------------- - */ - - if(H5Tclose(ftype_id) < 0) - goto error; - if(H5Tclose(wtype_id) < 0) - goto error; - if(H5Sclose(space_id) < 0) - goto error; - if(H5Aclose(attr_id) < 0) - goto error; - } /* u */ - - return 0; + * 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; i<nmembers; j++) */ + } /* if (type_class == H5T_COMPOUND) */ + + if (is_ref) { + ; /* handled by copy_refs_attr() */ + } + else { + /*------------------------------------------------------------------------- + * read to memory + *------------------------------------------------------------------------- + */ + + buf = (void *) HDmalloc((size_t)(nelmts * msize)); + if (buf == NULL) { + error_msg("h5repack", "cannot read into memory\n"); + goto error; + } /* end if */ + if (H5Aread(attr_id, wtype_id, buf) < 0) + goto error; + + /*------------------------------------------------------------------------- + * copy + *------------------------------------------------------------------------- + */ + + if ((attr_out = H5Acreate2(loc_out, name, wtype_id, space_id, + H5P_DEFAULT, H5P_DEFAULT)) < 0) + goto error; + if (H5Awrite(attr_out, wtype_id, buf) < 0) + goto error; + + /*close*/ + if (H5Aclose(attr_out) < 0) + goto error; + + /* 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); + HDfree(buf); + buf = NULL; + } /*H5T_REFERENCE*/ + + if (options->verbose) + printf(FORMAT_OBJ_ATTR, "attr", name); + + /*------------------------------------------------------------------------- + * close + *------------------------------------------------------------------------- + */ + + if (H5Tclose(ftype_id) < 0) + goto error; + if (H5Tclose(wtype_id) < 0) + goto error; + if (H5Sclose(space_id) < 0) + goto error; + if (H5Aclose(attr_id) < 0) + goto error; + } /* u */ + + return 0; error: - H5E_BEGIN_TRY { - 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: - 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\ + 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(" <warning: SZIP settins, chunk size is smaller than pixels per block>\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( + " <warning: SZIP settins, chunk size is smaller than pixels per block>\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 { - error_msg("input error in filter type\n"); - HDexit(EXIT_FAILURE); - } + * 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"; } |