diff options
Diffstat (limited to 'tools/h5repack/h5repack.c')
| -rw-r--r-- | tools/h5repack/h5repack.c | 920 |
1 files changed, 455 insertions, 465 deletions
diff --git a/tools/h5repack/h5repack.c b/tools/h5repack/h5repack.c index 3f99374..0ab5404 100644 --- a/tools/h5repack/h5repack.c +++ b/tools/h5repack/h5repack.c @@ -5,12 +5,10 @@ * * * 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. * + * the COPYING file, which can be found at the root of the source code * + * distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases. * + * If you do not have access to either file, you may request a copy from * + * help@hdfgroup.org. * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ #include <stdlib.h> @@ -53,19 +51,19 @@ static int have_request(pack_opt_t *options); *------------------------------------------------------------------------- */ int h5repack(const char* infile, const char* outfile, pack_opt_t *options) { - /* check input */ - if (check_options(options) < 0) - return -1; + /* 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; + /* 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; + /* copy the objects */ + if (copy_objects(infile, outfile, options) < 0) + return -1; - return 0; + return 0; } /*------------------------------------------------------------------------- @@ -78,22 +76,23 @@ int h5repack(const char* infile, const char* outfile, pack_opt_t *options) { *------------------------------------------------------------------------- */ -int h5repack_init(pack_opt_t *options, int verbose) { - 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; - } +h5repack_init(pack_opt_t *options, int verbose) +{ + 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; + } - return (options_table_init(&(options->op_tbl))); + return (options_table_init(&(options->op_tbl))); } /*------------------------------------------------------------------------- @@ -105,7 +104,7 @@ int h5repack_init(pack_opt_t *options, int verbose) { */ int h5repack_end(pack_opt_t *options) { - return options_table_free(options->op_tbl); + return options_table_free(options->op_tbl); } /*------------------------------------------------------------------------- @@ -121,10 +120,10 @@ int h5repack_end(pack_opt_t *options) { 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 */ - unsigned n_objs; /* number of objects in the current -f or -l option entry */ - int is_glb; /* is the filter global */ + 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 */ + unsigned 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))) @@ -163,10 +162,10 @@ 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 */ - unsigned 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; + unsigned 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); @@ -232,87 +231,84 @@ h5repack_addlayout(const char* str, pack_opt_t *options) *------------------------------------------------------------------------- */ 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; - } + 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 = H5Tget_native_type(type_in, H5T_DIR_DEFAULT); + 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); + return (ret_value); } /* end copy_named_datatype */ /*------------------------------------------------------------------------- @@ -327,22 +323,22 @@ done: *------------------------------------------------------------------------- */ int named_datatype_free(named_dt_t **named_dt_head_p, int ignore_err) { - named_dt_t *dt = *named_dt_head_p; - int ret_value = -1; + named_dt_t *dt = *named_dt_head_p; + int 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 */ + 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; + ret_value = 0; done: - return (ret_value); + return (ret_value); } /* end named_datatype_free */ /*------------------------------------------------------------------------- @@ -363,25 +359,25 @@ done: */ 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) + trav_table_t *travt, pack_opt_t *options) { - int ret_value = 0; /*no need to LEAVE() on ERROR: HERR_INIT(int, SUCCEED) */ - 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; + int ret_value = 0; /*no need to LEAVE() on ERROR: HERR_INIT(int, SUCCEED) */ + 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) @@ -425,7 +421,7 @@ copy_attr(hid_t loc_in, hid_t loc_out, named_dt_t **named_dt_head_p, } /* end if */ else { if (options->use_native == 1) - wtype_id = h5tools_get_native_type(ftype_id); + wtype_id = H5Tget_native_type(ftype_id, H5T_DIR_DEFAULT); else wtype_id = H5Tcopy(ftype_id); } /* end else */ @@ -466,7 +462,7 @@ copy_attr(hid_t loc_in, hid_t loc_out, named_dt_t **named_dt_head_p, int nmembers = H5Tget_nmembers(wtype_id); for (j = 0; j < nmembers; j++) { - hid_t mtid = H5Tget_member_type(wtype_id, (unsigned) j); + hid_t mtid = H5Tget_member_type(wtype_id, (unsigned)j); H5T_class_t mtclass = H5Tget_class(mtid); H5Tclose(mtid); @@ -477,16 +473,13 @@ copy_attr(hid_t loc_in, hid_t loc_out, named_dt_t **named_dt_head_p, } /* for (j=0; i<nmembers; j++) */ } /* if (type_class == H5T_COMPOUND) */ - if (is_ref) { - ; /* handled by copy_refs_attr() */ - } - else { + if (!is_ref) { /*------------------------------------------------------------------------- * read to memory *------------------------------------------------------------------------- */ - buf = (void *) HDmalloc((size_t)(nelmts * msize)); + buf = (void *)HDmalloc((size_t)(nelmts * msize)); if (buf == NULL) { error_msg("h5repack", "cannot read into memory\n"); HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "HDmalloc failed"); @@ -568,190 +561,185 @@ done: * 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\ + 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; 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; } /*------------------------------------------------------------------------- @@ -769,119 +757,121 @@ static int check_options(pack_opt_t *options) { *------------------------------------------------------------------------- */ 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; + 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 + *------------------------------------------------------------------------- + */ + + /* Initialize indexing options */ + h5trav_set_index(sort_by, sort_order); + /* 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; } /*------------------------------------------------------------------------- @@ -897,10 +887,10 @@ out: */ static int have_request(pack_opt_t *options) { - if (options->all_filter || options->all_layout || options->op_tbl->nelems) - return 1; + if (options->all_filter || options->all_layout || options->op_tbl->nelems) + return 1; - return 0; + return 0; } @@ -915,21 +905,21 @@ static int have_request(pack_opt_t *options) { */ 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"; + 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"; } |