diff options
Diffstat (limited to 'tools/src')
| -rw-r--r-- | tools/src/h5repack/h5repack.c | 334 | ||||
| -rw-r--r-- | tools/src/h5repack/h5repack.h | 106 | ||||
| -rw-r--r-- | tools/src/h5repack/h5repack_copy.c | 292 | ||||
| -rw-r--r-- | tools/src/h5repack/h5repack_filters.c | 316 | ||||
| -rw-r--r-- | tools/src/h5repack/h5repack_main.c | 27 | ||||
| -rw-r--r-- | tools/src/h5repack/h5repack_opttable.c | 194 | ||||
| -rw-r--r-- | tools/src/h5repack/h5repack_parse.c | 13 | ||||
| -rw-r--r-- | tools/src/h5repack/h5repack_refs.c | 259 | ||||
| -rw-r--r-- | tools/src/h5repack/h5repack_verify.c | 372 |
9 files changed, 840 insertions, 1073 deletions
diff --git a/tools/src/h5repack/h5repack.c b/tools/src/h5repack/h5repack.c index 76ca117..6b8cf8a 100644 --- a/tools/src/h5repack/h5repack.c +++ b/tools/src/h5repack/h5repack.c @@ -39,11 +39,6 @@ static int have_request(pack_opt_t *options); * 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) { @@ -68,7 +63,6 @@ int h5repack(const char* infile, const char* outfile, pack_opt_t *options) { * Purpose: initialize options * * Return: 0, ok, -1, fail - * *------------------------------------------------------------------------- */ int @@ -96,7 +90,6 @@ h5repack_init(pack_opt_t *options, int verbose, hbool_t latest) * Function: h5repack_end * * Purpose: free options table - * *------------------------------------------------------------------------- */ @@ -111,18 +104,17 @@ int h5repack_end(pack_opt_t *options) { * Example: -f dset:GZIP=6 * * Return: 0, ok, -1, fail - * *------------------------------------------------------------------------- */ int -h5repack_addfilter(const char* str, pack_opt_t *options) +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 */ - /* parse the -f option */ + /* parse the -f (--filter) option */ if (NULL == (obj_list = parse_filter(str, &n_objs, &filter, options, &is_glb))) return -1; @@ -152,11 +144,10 @@ h5repack_addfilter(const char* str, pack_opt_t *options) * Purpose: add a layout option * * Return: 0, ok, -1, fail - * *------------------------------------------------------------------------- */ int -h5repack_addlayout(const char* str, pack_opt_t *options) +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 */ @@ -220,11 +211,6 @@ h5repack_addlayout(const char* str, pack_opt_t *options) * 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, @@ -298,24 +284,18 @@ hid_t copy_named_datatype(hid_t type_in, hid_t fidout, /* 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 */ + /* 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 */ /*------------------------------------------------------------------------- * 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) { @@ -346,11 +326,6 @@ done: * loc_id = H5Topen2( fid, name); * * Return: 0, ok, -1 no - * - * Programmer: Pedro Vicente, pvn@ncsa.uiuc.edu - * - * Date: October, 28, 2003 - * *------------------------------------------------------------------------- */ int @@ -477,7 +452,6 @@ copy_attr(hid_t loc_in, hid_t loc_out, named_dt_t **named_dt_head_p, 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"); } /* end if */ if (H5Aread(attr_id, wtype_id, buf) < 0) @@ -489,7 +463,7 @@ copy_attr(hid_t loc_in, hid_t loc_out, named_dt_t **named_dt_head_p, */ if ((attr_out = H5Acreate2(loc_out, name, wtype_id, space_id, H5P_DEFAULT, H5P_DEFAULT)) < 0) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Acreate2 failed"); + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Acreate2 failed on ,%s>", name); if (H5Awrite(attr_out, wtype_id, buf) < 0) HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Awrite failed"); @@ -507,24 +481,8 @@ copy_attr(hid_t loc_in, hid_t loc_out, named_dt_t **named_dt_head_p, if (options->verbose) printf(FORMAT_OBJ_ATTR, "attr", name); - - /*------------------------------------------------------------------------- - * close - *------------------------------------------------------------------------- - */ - - if (H5Tclose(ftype_id) < 0) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Tclose failed"); - if (H5Tclose(wtype_id) < 0) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Tclose failed"); - if (H5Sclose(space_id) < 0) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Sclose failed"); - if (H5Aclose(attr_id) < 0) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Aclose failed"); } /* u */ - return 0; - done: H5E_BEGIN_TRY { if (buf) { @@ -553,13 +511,10 @@ done: * Purpose: print options, checks for invalid options * * Return: void, return -1 on error - * - * Programmer: pvn@ncsa.uiuc.edu - * - * Date: September, 22, 2003 *------------------------------------------------------------------------- */ static int check_options(pack_opt_t *options) { + int ret_value = 0; /*no need to LEAVE() on ERROR: HERR_INIT(int, SUCCEED) */ unsigned int i; int k, j, has_cp = 0, has_ck = 0; char slayout[30]; @@ -569,8 +524,8 @@ static int check_options(pack_opt_t *options) { *------------------------------------------------------------------------- */ if (options->verbose && have_request(options) /* only print if requested */) { - printf("Objects to modify layout are...\n"); if (options->all_layout == 1) { + printf("All objects to modify layout are...\n"); switch (options->layout_g) { case H5D_COMPACT: strcpy(slayout, "compact"); @@ -586,20 +541,22 @@ static int check_options(pack_opt_t *options) { break; case H5D_LAYOUT_ERROR: case H5D_NLAYOUTS: - error_msg("invalid layout\n"); - return -1; + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "invalid layout"); default: strcpy(slayout, "invalid layout\n"); - return -1; + HGOTO_DONE(FAIL); } - printf(" Apply %s layout to all\n", slayout); + printf(" Apply %s layout to all", slayout); if (H5D_CHUNKED == options->layout_g) { - printf("with dimension ["); + printf("with dimension [ "); for (j = 0; j < options->chunk_g.rank; j++) printf("%d ", (int) options->chunk_g.chunk_lengths[j]); - printf("]\n"); + printf("]"); } + printf("\n"); } + else + printf("No all objects to modify layout\n"); }/* verbose */ for (i = 0; i < options->op_tbl->nelems; i++) { @@ -609,25 +566,20 @@ static int check_options(pack_opt_t *options) { 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("%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)"); + printf(" <%s> %s\n", name, "NONE (contiguous)"); 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; - } + if (options->all_layout == 1 && has_ck) + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "invalid chunking input: 'all' option is present with other objects"); /*------------------------------------------------------------------------- * objects to filter @@ -635,10 +587,14 @@ static int check_options(pack_opt_t *options) { */ if (options->verbose && have_request(options) /* only print if requested */) { - printf("Objects to apply filter are...\n"); if (options->all_filter == 1) { + printf("All objects to apply filter are...\n"); for (k = 0; k < options->n_filter_g; k++) { H5Z_filter_t filtn = options->filter_g[k].filtn; + if (filtn < 0) { + printf(" Unknown\n"); + continue; + } switch (filtn) { case H5Z_FILTER_NONE: printf(" Uncompress all\n"); @@ -649,8 +605,7 @@ static int check_options(pack_opt_t *options) { 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]); + 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); @@ -658,6 +613,8 @@ static int check_options(pack_opt_t *options) { } /* k */ }; } + else + printf("No all objects to apply filter\n"); } /* verbose */ for (i = 0; i < options->op_tbl->nelems; i++) { @@ -666,48 +623,34 @@ static int check_options(pack_opt_t *options) { for (j = 0; j < pack.nfilters; j++) { if (options->verbose) { - printf(" <%s> with %s filter\n", name, - get_sfilter(pack.filter[j].filtn)); + if(pack.filter[j].filtn >= 0) { + if(pack.filter[j].filtn > H5Z_FILTER_SCALEOFFSET) + printf(" <%s> with %s filter %d\n", name, get_sfilter(pack.filter[j].filtn), pack.filter[j].filtn); + else + 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; - } + if (options->all_filter == 1 && has_cp) + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "invalid compression input: 'all' option is present with other objects"); /*------------------------------------------------------------------------- * 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; - } - } + if (options->grp_compact < 0) + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "invalid maximum number of links to store as header messages"); + if (options->grp_indexed < 0) + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "invalid minimum number of links to store in the indexed format"); + if (options->grp_indexed > options->grp_compact) + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "minimum indexed size is greater than the maximum compact size"); + for (i = 0; i < 8; i++) + if (options->msg_size[i] < 0) + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "invalid shared message size"); /*-------------------------------------------------------------------------------- * verify new user userblock options; file name must be present @@ -715,30 +658,24 @@ static int check_options(pack_opt_t *options) { */ 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); + 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; - } + if (options->ublock_filename == NULL && options->ublock_size != 0) + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "file name missing for user block", options->ublock_filename); /*-------------------------------------------------------------------------------- * 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; - } + if (options->alignment == 0 && options->threshold != 0) + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "alignment for H5Pset_alignment missing"); - return 0; +done: + return ret_value; } /*------------------------------------------------------------------------- @@ -748,36 +685,32 @@ static int check_options(pack_opt_t *options) { * 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) { + int ret_value = 0; /*no need to LEAVE() on ERROR: HERR_INIT(int, SUCCEED) */ hid_t fid; + hid_t did; + hid_t sid; unsigned int i; + unsigned int uf; trav_table_t *travt = NULL; /* nothing to do */ if (options->op_tbl->nelems == 0) - return 0; + HGOTO_DONE(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; - } + * open the file + *------------------------------------------------------------------------- + */ + if ((fid = h5tools_fopen(fname, H5F_ACC_RDONLY, H5P_DEFAULT, NULL, NULL, 0)) < 0) + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "h5tools_fopen failed <%s>: %s", fname, H5FOPENERROR); /*------------------------------------------------------------------------- - * get the list of objects in the file - *------------------------------------------------------------------------- - */ + * get the list of objects in the file + *------------------------------------------------------------------------- + */ /* Initialize indexing options */ h5trav_set_index(sort_by, sort_order); @@ -786,16 +719,15 @@ static int check_objects(const char* fname, pack_opt_t *options) { /* get the list of objects in the file */ if (h5trav_gettable(fid, travt) < 0) - goto out; + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "h5trav_gettable failed"); /*------------------------------------------------------------------------- - * compare with user supplied list - *------------------------------------------------------------------------- - */ + * compare with user supplied list + *------------------------------------------------------------------------- + */ if (options->verbose) - printf("Opening file <%s>. Searching for objects to modify...\n", - fname); + printf("Opening file. Searching %d objects to modify ...\n", travt->nobjs); for (i = 0; i < options->op_tbl->nelems; i++) { char* name = options->op_tbl->objs[i].path; @@ -803,74 +735,70 @@ static int check_objects(const char* fname, pack_opt_t *options) { 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", + if (h5trav_getindext(name, travt) < 0) + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "%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; + for (uf = 0; uf < options->op_tbl->objs[i].nfilters; uf++) { + if (options->op_tbl->objs[i].filter[uf].filtn < 0) + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "invalid filter"); + /* check for extra filter conditions */ + switch (options->op_tbl->objs[i].filter[uf].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[uf].cd_values[0]; + hsize_t dims[H5S_MAX_RANK]; + int rank; + + 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) + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dopen2 failed"); + if ((sid = H5Dget_space(did)) < 0) + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dget_space failed"); + if ((rank = H5Sget_simple_extent_ndims(sid)) < 0) + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Sget_simple_extent_ndims failed"); + HDmemset(dims, 0, sizeof dims); + if (H5Sget_simple_extent_dims(sid, dims, NULL) < 0) + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Sget_simple_extent_dims failed"); + for (j = 0; j < rank; j++) + csize *= dims[j]; + if (H5Sclose(sid) < 0) + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Sclose failed"); + if (H5Dclose(did) < 0) + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dclose failed"); + } + + if (csize < ppb) { + printf(" <warning: SZIP settings, chunk size is smaller than pixels per block>\n"); + HGOTO_DONE(0); + } } + break; + default: + break; } - break; - default: - break; - } - } /* i */ + } /* for uf */ + } /* for i */ - /*------------------------------------------------------------------------- - * close - *------------------------------------------------------------------------- - */ - H5Fclose(fid); - trav_table_free(travt); - return 0; - -out: - H5Fclose(fid); - trav_table_free(travt); - return -1; +done: + H5E_BEGIN_TRY { + H5Fclose(fid); + H5Sclose(sid); + H5Dclose(did); + } H5E_END_TRY; + if (travt) + trav_table_free(travt); + return ret_value; } /*------------------------------------------------------------------------- @@ -879,9 +807,6 @@ out: * 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) { @@ -899,12 +824,13 @@ static int have_request(pack_opt_t *options) { * 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) + if (filtn < 0) + return NULL; + else if (filtn == H5Z_FILTER_NONE) return "NONE"; else if (filtn == H5Z_FILTER_DEFLATE) return "GZIP"; diff --git a/tools/src/h5repack/h5repack.h b/tools/src/h5repack/h5repack.h index c8c6a0e..0252768 100644 --- a/tools/src/h5repack/h5repack.h +++ b/tools/src/h5repack/h5repack.h @@ -29,7 +29,7 @@ #define MAX_COMPACT_DSIZE 64512 /* max data size for compact layout. -1k for header size */ /* File space default information */ -#define FS_PAGESIZE_DEF 4096 +#define FS_PAGESIZE_DEF 4096 #define FS_STRATEGY_DEF H5F_FSPACE_STRATEGY_FSM_AGGR #define FS_PERSIST_DEF FALSE #define FS_THRESHOLD_DEF 1 @@ -42,7 +42,7 @@ /* a list of names */ typedef struct { - char obj[MAX_NC_NAME]; + char obj[MAX_NC_NAME]; } obj_list_t; /* @@ -60,16 +60,16 @@ typedef struct { #define CD_VALUES 20 typedef struct { - H5Z_filter_t filtn; /* filter identification number */ - unsigned filt_flag; /* filter definition flag */ - unsigned cd_values[CD_VALUES]; /* filter client data values */ - size_t cd_nelmts; /* filter client number of values */ + H5Z_filter_t filtn; /* filter identification number */ + unsigned filt_flag; /* filter definition flag */ + unsigned cd_values[CD_VALUES]; /* filter client data values */ + size_t cd_nelmts; /* filter client number of values */ } filter_info_t; /* chunk lengths along each dimension and rank */ typedef struct { - hsize_t chunk_lengths[MAX_VAR_DIMS]; - int rank; + hsize_t chunk_lengths[MAX_VAR_DIMS]; + int rank; } chunk_info_t; /* we currently define a maximum value for the filters array, @@ -78,19 +78,19 @@ typedef struct { /* information for one object, contains PATH, CHUNK info and FILTER info */ typedef struct { - char path[MAX_NC_NAME]; /* name of object */ - filter_info_t filter[H5_REPACK_MAX_NFILTERS]; /* filter array */ - int nfilters; /* current number of filters */ - H5D_layout_t layout; /* layout information */ - chunk_info_t chunk; /* chunk information */ - hid_t refobj_id; /* object ID, references */ + char path[MAX_NC_NAME]; /* name of object */ + filter_info_t filter[H5_REPACK_MAX_NFILTERS]; /* filter array */ + int nfilters; /* current number of filters */ + H5D_layout_t layout; /* layout information */ + chunk_info_t chunk; /* chunk information */ + hid_t refobj_id; /* object ID, references */ } pack_info_t; /* store a table of all objects */ typedef struct { - unsigned int size; - unsigned int nelems; - pack_info_t *objs; + unsigned int size; + unsigned int nelems; + pack_info_t *objs; } pack_opttbl_t; @@ -101,30 +101,30 @@ typedef struct { /* all the above, ready to go to the hrepack call */ typedef struct { - pack_opttbl_t *op_tbl; /*table with all -c and -f options */ - int all_layout; /*apply the layout to all objects */ - int all_filter; /*apply the filter to all objects */ - filter_info_t filter_g[H5_REPACK_MAX_NFILTERS]; /*global filter array for the ALL case */ - int n_filter_g; /*number of global filters */ - chunk_info_t chunk_g; /*global chunk INFO for the ALL case */ - H5D_layout_t layout_g; /*global layout information for the ALL case */ - int verbose; /*verbose mode */ - hsize_t min_comp; /*minimum size to compress, in bytes */ - int use_native; /*use a native type in write */ - hbool_t latest; /*pack file with the latest file format */ - int grp_compact; /* Set the maximum number of links to store as header messages in the group */ - int grp_indexed; /* Set the minimum number of links to store in the indexed format */ - int msg_size[8]; /* Minimum size of shared messages: dataspace, - datatype, fill value, filter pipleline, attribute */ - const char *ublock_filename; /* user block file name */ - hsize_t ublock_size; /* user block size */ - hsize_t meta_block_size; /* metadata aggregation block size (for H5Pset_meta_block_size) */ - hsize_t threshold; /* alignment threshold for H5Pset_alignment */ - hsize_t alignment; /* alignment for H5Pset_alignment */ - H5F_fspace_strategy_t fs_strategy; /* File space handling strategy */ - int fs_persist; /* Free space section threshold */ - long fs_threshold; /* Free space section threshold */ - long long fs_pagesize; /* File space page size */ + pack_opttbl_t *op_tbl; /*table with all -c and -f options */ + int all_layout; /*apply the layout to all objects */ + int all_filter; /*apply the filter to all objects */ + filter_info_t filter_g[H5_REPACK_MAX_NFILTERS]; /*global filter array for the ALL case */ + int n_filter_g; /*number of global filters */ + chunk_info_t chunk_g; /*global chunk INFO for the ALL case */ + H5D_layout_t layout_g; /*global layout information for the ALL case */ + int verbose; /*verbose mode */ + hsize_t min_comp; /*minimum size to compress, in bytes */ + int use_native; /*use a native type in write */ + hbool_t latest; /*pack file with the latest file format */ + int grp_compact; /* Set the maximum number of links to store as header messages in the group */ + int grp_indexed; /* Set the minimum number of links to store in the indexed format */ + int msg_size[8]; /* Minimum size of shared messages: dataspace, + datatype, fill value, filter pipleline, attribute */ + const char *ublock_filename; /* user block file name */ + hsize_t ublock_size; /* user block size */ + hsize_t meta_block_size; /* metadata aggregation block size (for H5Pset_meta_block_size) */ + hsize_t threshold; /* alignment threshold for H5Pset_alignment */ + hsize_t alignment; /* alignment for H5Pset_alignment */ + H5F_fspace_strategy_t fs_strategy; /* File space handling strategy */ + int fs_persist; /* Free space section threshold */ + long fs_threshold; /* Free space section threshold */ + long long fs_pagesize; /* File space page size */ } pack_opt_t; @@ -214,18 +214,18 @@ int apply_filters(const char* name, /* object name from traverse list */ * options table *------------------------------------------------------------------------- */ -int options_table_init( pack_opttbl_t **tbl ); -int options_table_free( pack_opttbl_t *table ); -int options_add_layout( obj_list_t *obj_list, - unsigned n_objs, - pack_info_t *pack, - pack_opttbl_t *table ); -int options_add_filter ( obj_list_t *obj_list, - unsigned n_objs, - filter_info_t filt, - pack_opttbl_t *table ); -pack_info_t* options_get_object( const char *path, - pack_opttbl_t *table); +int options_table_init(pack_opttbl_t **tbl); +int options_table_free(pack_opttbl_t *table); +int options_add_layout(obj_list_t *obj_list, + unsigned n_objs, + pack_info_t *pack, + pack_opttbl_t *table); +int options_add_filter(obj_list_t *obj_list, + unsigned n_objs, + filter_info_t filt, + pack_opttbl_t *table); +pack_info_t* options_get_object(const char *path, + pack_opttbl_t *table); /*------------------------------------------------------------------------- * parse functions diff --git a/tools/src/h5repack/h5repack_copy.c b/tools/src/h5repack/h5repack_copy.c index 501f084..9fcf218 100644 --- a/tools/src/h5repack/h5repack_copy.c +++ b/tools/src/h5repack/h5repack_copy.c @@ -109,10 +109,8 @@ int copy_objects(const char* fnamein, const char* fnameout, pack_opt_t *options) * 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); - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed"); - } + if ((fidin = h5tools_fopen(fnamein, H5F_ACC_RDONLY, H5P_DEFAULT, NULL, NULL, (size_t) 0)) < 0) + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "h5tools_fopen failed <%s>: %s", fnamein, H5FOPENERROR); /* get user block size and file space strategy/persist/threshold */ { @@ -120,27 +118,20 @@ int copy_objects(const char* fnamein, const char* fnameout, pack_opt_t *options) hid_t grp_in = -1; /* group ID */ hid_t gcpl_in = -1; /* group creation property list */ - if ((fcpl_in = H5Fget_create_plist(fidin)) < 0) { - error_msg("failed to retrieve file creation property list\n"); - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed"); - } + if ((fcpl_in = H5Fget_create_plist(fidin)) < 0) + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Fget_create_plist failed to retrieve file creation property list"); - if (H5Pget_userblock(fcpl_in, &ub_size) < 0) { - error_msg("failed to retrieve userblock size\n"); - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed"); - } + if (H5Pget_userblock(fcpl_in, &ub_size) < 0) + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pget_userblock failed to retrieve userblock size"); /* If the -S option is not set, get "strategy" from the input file */ - if(H5Pget_file_space_strategy(fcpl_in, &in_strategy, &in_persist, &in_threshold) < 0) { - error_msg("failed to retrieve file space strategy\n"); - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed"); - } + if(H5Pget_file_space_strategy(fcpl_in, &in_strategy, &in_persist, &in_threshold) < 0) + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pget_file_space_strategy failed to retrieve file space strategy"); /* If the -G option is not set, get "pagesize" from the input file */ - if(H5Pget_file_space_page_size(fcpl_in, &in_pagesize) < 0) { - error_msg("failed to retrieve file space threshold\n"); - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed"); - } + if(H5Pget_file_space_page_size(fcpl_in, &in_pagesize) < 0) + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pget_file_space_page_size failed to retrieve file space threshold"); + /* open root group */ if ((grp_in = H5Gopen2(fidin, "/", H5P_DEFAULT)) < 0) HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Gopen2 failed"); @@ -153,26 +144,19 @@ int copy_objects(const char* fnamein, const char* fnameout, pack_opt_t *options) if (H5Pget_link_creation_order(gcpl_in, &crt_order_flags) < 0) HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pget_link_creation_order failed"); - if (H5Pclose(fcpl_in) < 0) { - error_msg("failed to close property list\n"); - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed"); - } + if (H5Pclose(fcpl_in) < 0) + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed to close property list"); } /* 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"); - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed"); - } + if ((fcpl = H5Pcreate(H5P_FILE_CREATE)) < 0) + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pcreate failed to create a file creation property list"); - if (ub_size > 0) { - if (H5Pset_userblock(fcpl, ub_size) < 0) { - error_msg("failed to set non-default userblock size\n"); - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed"); - } - } + if (ub_size > 0) + if (H5Pset_userblock(fcpl, ub_size) < 0) + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pset_userblock failed to set non-default userblock size"); if (options->latest) { unsigned i = 0, nindex = 0, mesg_type_flags[5], min_mesg_sizes[5]; @@ -180,10 +164,8 @@ int copy_objects(const char* fnamein, const char* fnameout, pack_opt_t *options) /* 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"); - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed"); - } + (unsigned) options->grp_indexed) < 0) + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pset_link_phase_change failed to adjust group creation parameters for root group"); for (i = 0; i < 5; i++) { if (options->msg_size[i] > 0) { @@ -218,30 +200,21 @@ int copy_objects(const char* fnamein, const char* fnameout, pack_opt_t *options) } /* 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"); - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed"); - } + if (H5Pset_shared_mesg_nindexes(fcpl, nindex) < 0) + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pset_shared_mesg_nindexes failed to set the number of shared object header message indexes"); /* 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"); - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed"); - } /* end if */ - } /* end for */ + for (i = 0; i < (nindex - 1); i++) + if (H5Pset_shared_mesg_index(fcpl, i, mesg_type_flags[i], min_mesg_sizes[i]) < 0) + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pset_shared_mesg_index failed to configure the specified shared object header message index"); } /* 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"); - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed"); - } /* 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"); - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed"); - } /* end if */ + if ((fapl = H5Pcreate(H5P_FILE_ACCESS)) < 0) + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pcreate failed to create file access property list"); + + if (H5Pset_libver_bounds(fapl, H5F_LIBVER_LATEST, H5F_LIBVER_LATEST) < 0) + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pset_libver_bounds failed to set property for using latest version of the format"); } /* end if */ } /* end if */ #if defined (H5REPACK_DEBUG_USER_BLOCK) @@ -254,19 +227,14 @@ print_user_block(fnamein, fidin); */ if (options->ublock_size > 0) { /* either use the FCPL already created or create a new one */ - if (fcpl == H5P_DEFAULT) { + 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"); - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed"); - } - } + if ((fcpl = H5Pcreate(H5P_FILE_CREATE)) < 0) + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pcreate failed to create a file creation property list"); /* set user block size */ - if (H5Pset_userblock(fcpl, options->ublock_size) < 0) { - error_msg("failed to set userblock size\n"); - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed"); - } + if (H5Pset_userblock(fcpl, options->ublock_size) < 0) + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pset_userblock failed to set userblock size"); } /*------------------------------------------------------------------------- @@ -275,18 +243,13 @@ print_user_block(fnamein, fidin); */ if (options->alignment > 0) { /* either use the FAPL already created or create a new one */ - if (fapl == H5P_DEFAULT) { + 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"); - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed"); - } - } + if ((fapl = H5Pcreate(H5P_FILE_ACCESS)) < 0) + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pcreate failed to create file access property list"); - if (H5Pset_alignment(fapl, options->threshold, options->alignment) < 0) { - error_msg("failed to set alignment\n"); - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed"); - } + if (H5Pset_alignment(fapl, options->threshold, options->alignment) < 0) + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pset_alignment failed to set alignment"); } /*------------------------------------------------------------------------- @@ -295,18 +258,13 @@ print_user_block(fnamein, fidin); */ if (options->meta_block_size > 0) { /* either use the FAPL already created or create a new one */ - if (fapl == H5P_DEFAULT) { + 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"); - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed"); - } - } + if ((fapl = H5Pcreate(H5P_FILE_ACCESS)) < 0) + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pcreate failed to create file access property list"); - if (H5Pset_meta_block_size(fapl, options->meta_block_size) < 0) { - error_msg("failed to set metadata block size\n"); - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed"); - } + if (H5Pset_meta_block_size(fapl, options->meta_block_size) < 0) + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pset_meta_block_size failed to set metadata block size"); } /*------------------------------------------------------------------------- @@ -315,13 +273,10 @@ print_user_block(fnamein, fidin); */ /* either use the FCPL already created or create a new one */ - if (fcpl == H5P_DEFAULT) { + 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"); - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed"); - } - } + if ((fcpl = H5Pcreate(H5P_FILE_CREATE)) < 0) + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pcreate failed to create a file creation property list"); if(H5Pset_link_creation_order(fcpl, crt_order_flags ) < 0) HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pset_link_creation_order failed"); @@ -348,10 +303,8 @@ print_user_block(fnamein, fidin); set_threshold = (hsize_t)options->fs_threshold; /* Set file space information as specified */ - if(H5Pset_file_space_strategy(fcpl, set_strategy, set_persist, set_threshold) < 0) { - error_msg("failed to set file space strategy\n"); - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed"); - } + if(H5Pset_file_space_strategy(fcpl, set_strategy, set_persist, set_threshold) < 0) + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pset_file_space_strategy failed to set file space strategy"); if(options->fs_pagesize == -1) /* A "0" file space page size is specified by user */ set_pagesize = (hsize_t)0; @@ -359,33 +312,26 @@ print_user_block(fnamein, fidin); set_pagesize = (hsize_t)options->fs_pagesize; if(set_pagesize != FS_PAGESIZE_DEF) /* Set non-default file space page size as specified */ - if(H5Pset_file_space_page_size(fcpl, set_pagesize) < 0) { - error_msg("failed to set file space page size\n"); - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed"); - } + if(H5Pset_file_space_page_size(fcpl, set_pagesize) < 0) + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pset_file_space_page_size failed to set file space page size"); /*------------------------------------------------------------------------- * create the output file *------------------------------------------------------------------------- */ if (options->verbose) - printf("Making file <%s>...\n", fnameout); + printf("Making new file ...\n"); - if ((fidout = H5Fcreate(fnameout, H5F_ACC_TRUNC, fcpl, fapl)) < 0) { - error_msg("<%s>: Could not create file\n", fnameout); - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed"); - } + if ((fidout = H5Fcreate(fnameout, H5F_ACC_TRUNC, fcpl, fapl)) < 0) + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Fcreate could not create file <%s>:", fnameout); /*------------------------------------------------------------------------- * 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"); - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed"); - } - } + if (options->ublock_size > 0) + if (copy_user_block(options->ublock_filename, fnameout, options->ublock_size) < 0) + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "Could not copy user block. Exiting..."); /*------------------------------------------------------------------------- * get list of objects @@ -399,26 +345,22 @@ print_user_block(fnamein, fidin); /* get the list of objects in the file */ if (h5trav_gettable(fidin, travt) < 0) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed"); + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "h5trav_gettable failed"); /*------------------------------------------------------------------------- * do the copy *------------------------------------------------------------------------- */ - if (do_copy_objects(fidin, fidout, travt, options) < 0) { - error_msg("<%s>: Could not copy data to: %s\n", fnamein, fnameout); - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed"); - } /* end if */ + if (do_copy_objects(fidin, fidout, travt, options) < 0) + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "do_copy_objects from <%s> could not copy data to <%s>", fnamein, fnameout); /*------------------------------------------------------------------------- * 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); - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed"); - } + if (do_copy_refobjs(fidin, fidout, travt, options) < 0) + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "do_copy_refobjs from <%s> could not copy data to <%s>", fnamein, fnameout); /*------------------------------------------------------------------------- * close @@ -443,12 +385,9 @@ print_user_block(fnamein, fidin); *------------------------------------------------------------------------- */ - 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"); - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed"); - } - } + if (ub_size > 0 && options->ublock_size == 0) + if (copy_user_block(fnamein, fnameout, ub_size) < 0) + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "Could not copy user block. Exiting..."); return 0; @@ -533,7 +472,7 @@ int Get_hyperslab(hid_t dcpl_id, int rank_dset, hsize_t dims_dset[], /* get chunk dims */ rank_chunk = H5Pget_chunk(dcpl_id, rank_dset, dims_chunk); if (rank_chunk < 0) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed"); + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pget_chunk failed"); for (k = rank_dset; k > 0; --k) size_chunk *= dims_chunk[k - 1]; @@ -595,7 +534,7 @@ int Get_hyperslab(hid_t dcpl_id, int rank_dset, hsize_t dims_dset[], hslab_nbytes *= dims_hslab[k - 1]; if (hslab_nbytes <= 0) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed"); + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "calculate total size for the hyperslab failed"); } } } @@ -619,7 +558,7 @@ int Get_hyperslab(hid_t dcpl_id, int rank_dset, hsize_t dims_dset[], hslab_nbytes *= dims_hslab[k - 1]; if (hslab_nbytes <= 0) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed"); + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "calculate total size for the hyperslab failed"); } } @@ -759,13 +698,14 @@ int do_copy_objects(hid_t fidin, hid_t fidout, trav_table_t *travt, unsigned crt_order_flags; /* group creation order flag */ unsigned i; unsigned u; + unsigned uf; int is_ref = 0; htri_t is_named; hbool_t limit_maxdims; hsize_t size_dset; /*------------------------------------------------------------------------- - * copy the suppplied object list + * copy the supplied object list *------------------------------------------------------------------------- */ @@ -775,12 +715,13 @@ int do_copy_objects(hid_t fidin, hid_t fidout, trav_table_t *travt, printf("-----------------------------------------\n"); } - for (i = 0; i < travt->nobjs; i++) { - /* init variables per obj */ - buf = NULL; - limit_maxdims = FALSE; + if (travt->objs) { + for (i = 0; i < travt->nobjs; i++) { + /* init variables per obj */ + buf = NULL; + limit_maxdims = FALSE; - switch (travt->objs[i].type) { + switch (travt->objs[i].type) { case H5TRAV_TYPE_UNKNOWN: break; @@ -860,10 +801,15 @@ int do_copy_objects(hid_t fidin, hid_t fidout, trav_table_t *travt, 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; + if (options->op_tbl->objs) { + for (u = 0; u < options->op_tbl->nelems; u++) { + if (HDstrcmp(travt->objs[i].name, options->op_tbl->objs[u].path) == 0) + for (uf = 0; uf < options->op_tbl->objs[uf].nfilters; uf++) { + if (options->op_tbl->objs[u].filter[uf].filtn > 0) + req_filter = 1; + } + } + } /* check if layout change requested individual object */ if (options->layout_g != H5D_LAYOUT_ERROR) { @@ -1039,9 +985,10 @@ int do_copy_objects(hid_t fidin, hid_t fidout, trav_table_t *travt, 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, FAIL, dset_in, wtype_id, H5S_ALL, H5S_ALL, H5P_DEFAULT, buf); - CHECK_H5DRW_ERROR(H5Dwrite, FAIL, dset_out, wtype_id, H5S_ALL, H5S_ALL, H5P_DEFAULT, buf); + if(H5Dread(dset_in, wtype_id, H5S_ALL, H5S_ALL, H5P_DEFAULT, buf) < 0) + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dread failed"); + if(H5Dwrite(dset_out, wtype_id, H5S_ALL, H5S_ALL, H5P_DEFAULT, buf) < 0) + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dread failed"); /* Check if we have VL data in the dataset's * datatype that must be reclaimed */ @@ -1124,9 +1071,10 @@ int do_copy_objects(hid_t fidin, hid_t fidout, trav_table_t *travt, 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, FAIL, dset_in, wtype_id, hslab_space, f_space_id, H5P_DEFAULT, hslab_buf); - CHECK_H5DRW_ERROR(H5Dwrite, FAIL, dset_out, wtype_id, hslab_space, f_space_id, H5P_DEFAULT, hslab_buf); + if(H5Dread(dset_in, wtype_id, hslab_space, f_space_id, H5P_DEFAULT, hslab_buf) < 0) + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dread failed"); + if(H5Dwrite(dset_out, wtype_id, hslab_space, f_space_id, H5P_DEFAULT, hslab_buf) < 0) + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dread failed"); /* reclaim any VL memory, if necessary */ if (vl_data) @@ -1320,19 +1268,9 @@ int do_copy_objects(hid_t fidin, hid_t fidout, trav_table_t *travt, default: HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "Object type not found"); - } /* 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 ret_value; + } /* switch */ + } /* end for */ + } /* end if */ done: H5E_BEGIN_TRY @@ -1349,8 +1287,7 @@ done: H5Tclose(wtype_id); H5Tclose(type_in); H5Tclose(type_out); - named_datatype_free(&named_dt_head, 1); - }H5E_END_TRY; + } H5E_END_TRY; /* free */ if (buf != NULL) @@ -1358,6 +1295,14 @@ done: if (hslab_buf != NULL) HDfree(hslab_buf); + /* Finalize (link) the stack of named datatypes (if any) */ + if (0 == ret_value && named_dt_head != NULL) + named_datatype_free(&named_dt_head, 0); + else + H5E_BEGIN_TRY { + named_datatype_free(&named_dt_head, 1); + } H5E_END_TRY; + return ret_value; } @@ -1391,8 +1336,11 @@ static void print_dataset_info(hid_t dcpl_id, char *objname, double ratio, int p 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); + if ((filtn = H5Pget_filter2(dcpl_id, (unsigned) i, &filt_flags, &cd_nelmts, + cd_values, sizeof(f_objname), f_objname, NULL)) < 0) { + HDstrcat(strfilter, "ERROR "); + continue; + } switch (filtn) { case H5Z_FILTER_NONE: @@ -1488,9 +1436,9 @@ static int copy_user_block(const char *infile, const char *outfile, hsize_t size /* Open files */ if ((infid = HDopen(infile, O_RDONLY)) < 0) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "HDopen failed"); + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "HDopen failed input file <%s>", infile); if ((outfid = HDopen(outfile, O_WRONLY)) < 0) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "HDopen failed"); + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "HDopen failed output file <%s>", outfile); /* Copy the userblock from the input file to the output file */ while (size > 0) { @@ -1504,7 +1452,7 @@ static int copy_user_block(const char *infile, const char *outfile, hsize_t size else nread = HDread(infid, rbuf, (size_t)size); if (nread < 0) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "HDread failed"); + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "HDread failed to read userblock"); /* Write buffer to destination file */ /* (compensating for interrupted writes & checking for errors, etc.) */ @@ -1566,24 +1514,20 @@ void print_user_block(const char *filename, hid_t fid) /* get user block size */ if(( fcpl = H5Fget_create_plist(fid)) < 0) { - error_msg("failed to retrieve file creation property list\n"); - HGOTO_ERROR(H5E_tools_g, H5E_tools_min_id_g, "H5Fget_create_plist failed"); + HGOTO_ERROR(H5E_tools_g, H5E_tools_min_id_g, "H5Fget_create_plist failed to retrieve file creation property list"); } if(H5Pget_userblock(fcpl, &ub_size) < 0) { - error_msg("failed to retrieve userblock size\n"); - HGOTO_ERROR(H5E_tools_g, H5E_tools_min_id_g, "H5Pget_userblock failed"); + HGOTO_ERROR(H5E_tools_g, H5E_tools_min_id_g, "H5Pget_userblock failed to retrieve userblock size"); } if(H5Pclose(fcpl) < 0) { - error_msg("failed to close property list\n"); - HGOTO_ERROR(H5E_tools_g, H5E_tools_min_id_g, "H5Pclose failed"); + HGOTO_ERROR(H5E_tools_g, H5E_tools_min_id_g, "H5Pclose failed to close property list"); } /* open file */ if((fh = HDopen(filename, O_RDONLY)) < 0) { - error_msg("failed to open file\n"); - HGOTO_ERROR(H5E_tools_g, H5E_tools_min_id_g, "HDopen failed"); + HGOTO_ERROR(H5E_tools_g, H5E_tools_min_id_g, "HDopen failed to open file <%s>", filename); } size = ub_size; diff --git a/tools/src/h5repack/h5repack_filters.c b/tools/src/h5repack/h5repack_filters.c index 5ccb2ef..e968b3c 100644 --- a/tools/src/h5repack/h5repack_filters.c +++ b/tools/src/h5repack/h5repack_filters.c @@ -25,23 +25,71 @@ #define MIN(a,b) (((a)<(b)) ? (a) : (b)) /*------------------------------------------------------------------------- + * Function: aux_copy_obj + * + * Purpose: copy the object filters for object copy + * + * Return: 0 success, -1 failure + *------------------------------------------------------------------------- + */ +static int aux_copy_obj(hid_t dcpl_id, /* dataset creation property list */ + const char* name, /* object name from traverse list */ + pack_info_t *objout /*OUT*/) /* info about object to filter */ +{ + int ret_value = 0; /*no need to LEAVE() on ERROR: HERR_INIT(int, SUCCEED) */ + int nfilters; /* number of filters in DCPL */ + char f_objname[256]; /* filter objname */ + H5D_layout_t layout; + int rank; /* rank of dataset */ + hsize_t chsize[64]; /* chunk size in elements */ + unsigned int i, j; + + /* get information about input filters */ + if ((nfilters = H5Pget_nfilters(dcpl_id)) < 0) + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pget_nfilters failed"); + /* copy filter_info_t structure */ + for (i = 0; i < nfilters; i++) { + if ((objout->filter[i].filtn = H5Pget_filter2(dcpl_id, (unsigned) i, &objout->filter[i].filt_flag, &objout->filter[i].cd_nelmts, + objout->filter[i].cd_values, sizeof(f_objname), f_objname, NULL)) < 0) + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pget_filter2 failed"); + } + + objout->nfilters = nfilters; + HDstrcpy(objout->path, name); + + if ((layout = H5Pget_layout(dcpl_id)) < 0) + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pget_layout failed"); + objout->layout = layout; + + if (layout == H5D_CHUNKED) { + if ((rank = H5Pget_chunk(dcpl_id, NELMTS(chsize), chsize/*out*/)) < 0) + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pget_chunk failed"); + objout->chunk.rank = rank; + for (i = 0; i < rank; i++) + objout->chunk.chunk_lengths[i] = chsize[i]; + } + +done: + return ret_value; +} + +/*------------------------------------------------------------------------- * Function: aux_find_obj * * Purpose: find the object name NAME (got from the traverse list) * in the repack options list - * *------------------------------------------------------------------------- */ static int aux_find_obj(const char* name, /* object name from traverse list */ - pack_opt_t *options, /* repack options */ - pack_info_t *obj /*OUT*/) /* info about object to filter */ + pack_opt_t *options, /* repack options */ + pack_info_t *obj /*OUT*/) /* info about object to filter */ { char *pdest; int result; unsigned int i; for (i = 0; i < options->op_tbl->nelems; i++) { - if (HDstrcmp(options->op_tbl->objs[i].path,name) == 0) { + if (HDstrcmp(options->op_tbl->objs[i].path, name) == 0) { *obj = options->op_tbl->objs[i]; return (int) i; } @@ -66,14 +114,12 @@ static int aux_find_obj(const char* name, /* object name from traverse list */ * in the repack options list; assign the filter information OBJ * * Return: 0 not found, 1 found - * *------------------------------------------------------------------------- */ static int aux_assign_obj(const char* name, /* object name from traverse list */ - pack_opt_t *options, /* repack options */ - pack_info_t *obj /*OUT*/) /* info about object to filter */ + pack_opt_t *options, /* repack options */ + pack_info_t *obj /*OUT*/) /* info about object to filter */ { - int idx, i; pack_info_t tmp; @@ -83,7 +129,6 @@ static int aux_assign_obj(const char* name, /* object name from traverse list */ /* name was on input */ if (idx >= 0) { - /* applying to all objects */ if (options->all_layout) { /* assign the global layout info to the OBJ info */ @@ -92,8 +137,7 @@ static int aux_assign_obj(const char* name, /* object name from traverse list */ case H5D_CHUNKED: tmp.chunk.rank = options->chunk_g.rank; for (i = 0; i < tmp.chunk.rank; i++) - tmp.chunk.chunk_lengths[i] = - options->chunk_g.chunk_lengths[i]; + tmp.chunk.chunk_lengths[i] = options->chunk_g.chunk_lengths[i]; break; case H5D_LAYOUT_ERROR: case H5D_COMPACT: @@ -111,8 +155,7 @@ static int aux_assign_obj(const char* name, /* object name from traverse list */ case H5D_CHUNKED: tmp.chunk.rank = options->op_tbl->objs[idx].chunk.rank; for (i = 0; i < tmp.chunk.rank; i++) - tmp.chunk.chunk_lengths[i] = - options->op_tbl->objs[idx].chunk.chunk_lengths[i]; + tmp.chunk.chunk_lengths[i] = options->op_tbl->objs[idx].chunk.chunk_lengths[i]; break; case H5D_LAYOUT_ERROR: case H5D_COMPACT: @@ -123,7 +166,6 @@ static int aux_assign_obj(const char* name, /* object name from traverse list */ default: break; }/*switch*/ - } /* applying to all objects */ @@ -183,99 +225,103 @@ static int aux_assign_obj(const char* name, /* object name from traverse list */ * of H5Z_FILTER_NONE present in the PACK_INFO_T filter array * * Return: 0 success, -1 an error occured - * - * Programmer: Pedro Vicente, pvn@ncsa.uiuc.edu - * - * Date: December 19, 2003 - * *------------------------------------------------------------------------- */ int apply_filters(const char* name, /* object name from traverse list */ - int rank, /* rank of dataset */ - hsize_t *dims, /* dimensions of dataset */ - size_t msize, /* size of type */ - hid_t dcpl_id, /* dataset creation property list */ - pack_opt_t *options, /* repack options */ - int *has_filter) /* (OUT) object NAME has a filter */ + int rank, /* rank of dataset */ + hsize_t *dims, /* dimensions of dataset */ + size_t msize, /* size of type */ + hid_t dcpl_id, /* dataset creation property list */ + pack_opt_t *options, /* repack options */ + int *has_filter) /* (OUT) object NAME has a filter */ { - int nfilters; /* number of filters in DCPL */ - hsize_t chsize[64]; /* chunk size in elements */ + int ret_value = 0; /*no need to LEAVE() on ERROR: HERR_INIT(int, SUCCEED) */ + int nfilters; /* number of filters in DCPL */ + hsize_t chsize[64]; /* chunk size in elements */ H5D_layout_t layout; - int i; + int i, j; pack_info_t obj; + pack_info_t filtobj; *has_filter = 0; if (rank == 0) /* scalar dataset, do not apply */ - return 0; + HGOTO_DONE(0); /*------------------------------------------------------------------------- - * initialize the assigment object - *------------------------------------------------------------------------- - */ + * initialize the assigment object + *------------------------------------------------------------------------- + */ init_packobject(&obj); + init_packobject(&filtobj); /*------------------------------------------------------------------------- - * find options - *------------------------------------------------------------------------- - */ + * find options + *------------------------------------------------------------------------- + */ if (aux_assign_obj(name, options, &obj) == 0) - return 0; + HGOTO_DONE(0); /* get information about input filters */ if ((nfilters = H5Pget_nfilters(dcpl_id)) < 0) - return -1; + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pget_nfilters failed"); + /*------------------------------------------------------------------------- - * check if we have filters in the pipeline - * we want to replace them with the input filters - * only remove if we are inserting new ones - *------------------------------------------------------------------------- - */ + * check if we have filters in the pipeline + * we want to replace them with the input filters + * only remove if we are inserting new ones + *------------------------------------------------------------------------- + */ if (nfilters && obj.nfilters) { *has_filter = 1; if (H5Premove_filter(dcpl_id, H5Z_FILTER_ALL) < 0) - return -1; - } + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Premove_filter failed"); - /*------------------------------------------------------------------------- - * check if there is an existent chunk - * read it only if there is not a requested layout - *------------------------------------------------------------------------- - */ - if (obj.layout == -1) { - if ((layout = H5Pget_layout(dcpl_id)) < 0) - return -1; - - if (layout == H5D_CHUNKED) { - if ((rank = H5Pget_chunk(dcpl_id, NELMTS(chsize), chsize/*out*/)) < 0) - return -1; - obj.layout = H5D_CHUNKED; - obj.chunk.rank = rank; - for (i = 0; i < rank; i++) - obj.chunk.chunk_lengths[i] = chsize[i]; + /*------------------------------------------------------------------------- + * check if there is an existent chunk + * read it only if there is not a requested layout + *------------------------------------------------------------------------- + */ + if (obj.layout == -1) { + if ((layout = H5Pget_layout(dcpl_id)) < 0) + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pget_layout failed"); + + if (layout == H5D_CHUNKED) { + if ((rank = H5Pget_chunk(dcpl_id, NELMTS(chsize), chsize/*out*/)) < 0) + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pget_chunk failed"); + obj.layout = H5D_CHUNKED; + obj.chunk.rank = rank; + for (i = 0; i < rank; i++) + obj.chunk.chunk_lengths[i] = chsize[i]; + } } } + else if(nfilters) { + *has_filter = 1; + if (aux_copy_obj(dcpl_id, name, &filtobj) < 0) + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "aux_copy_obj failed"); + } /*------------------------------------------------------------------------- - * the type of filter and additional parameter - * type can be one of the filters - * H5Z_FILTER_NONE 0 , uncompress if compressed - * H5Z_FILTER_DEFLATE 1 , deflation like gzip - * H5Z_FILTER_SHUFFLE 2 , shuffle the data - * H5Z_FILTER_FLETCHER32 3 , fletcher32 checksum of EDC - * H5Z_FILTER_SZIP 4 , szip compression - * H5Z_FILTER_NBIT 5 , nbit compression - * H5Z_FILTER_SCALEOFFSET 6 , scaleoffset compression - *------------------------------------------------------------------------- - */ + * the type of filter and additional parameter + * type can be one of the filters + * H5Z_FILTER_NONE 0 , uncompress if compressed + * H5Z_FILTER_DEFLATE 1 , deflation like gzip + * H5Z_FILTER_SHUFFLE 2 , shuffle the data + * H5Z_FILTER_FLETCHER32 3 , fletcher32 checksum of EDC + * H5Z_FILTER_SZIP 4 , szip compression + * H5Z_FILTER_NBIT 5 , nbit compression + * H5Z_FILTER_SCALEOFFSET 6 , scaleoffset compression + *------------------------------------------------------------------------- + */ if (obj.nfilters) { /*------------------------------------------------------------------------- - * filters require CHUNK layout; if we do not have one define a default - *------------------------------------------------------------------------- - */ + * filters require CHUNK layout; if we do not have one define a default + *------------------------------------------------------------------------- + */ if (obj.layout == -1) { /* stripmine info */ hsize_t sm_size[H5S_MAX_RANK]; /*stripmine size */ @@ -284,9 +330,9 @@ int apply_filters(const char* name, /* object name from traverse list */ obj.chunk.rank = rank; /* - * determine the strip mine size. The strip mine is - * a hyperslab whose size is manageable. - */ + * determine the strip mine size. The strip mine is + * a hyperslab whose size is manageable. + */ sm_nbytes = msize; for (i = rank; i > 0; --i) { @@ -304,18 +350,21 @@ int apply_filters(const char* name, /* object name from traverse list */ } for (i = 0; i < obj.nfilters; i++) { + if (obj.filter[i].filtn < 0) + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "invalid filter"); + switch (obj.filter[i].filtn) { /*------------------------------------------------------------------------- - * H5Z_FILTER_NONE 0 , uncompress if compressed - *------------------------------------------------------------------------- - */ + * H5Z_FILTER_NONE 0 , uncompress if compressed + *------------------------------------------------------------------------- + */ case H5Z_FILTER_NONE: break; - /*------------------------------------------------------------------------- - * H5Z_FILTER_DEFLATE 1 , deflation like gzip - *------------------------------------------------------------------------- - */ + /*------------------------------------------------------------------------- + * H5Z_FILTER_DEFLATE 1 , deflation like gzip + *------------------------------------------------------------------------- + */ case H5Z_FILTER_DEFLATE: { unsigned aggression; /* the deflate level */ @@ -323,16 +372,16 @@ int apply_filters(const char* name, /* object name from traverse list */ aggression = obj.filter[i].cd_values[0]; /* set up for deflated data */ if (H5Pset_chunk(dcpl_id, obj.chunk.rank, obj.chunk.chunk_lengths) < 0) - return -1; + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pset_chunk failed"); if (H5Pset_deflate(dcpl_id, aggression) < 0) - return -1; + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pset_deflate failed"); } break; - /*------------------------------------------------------------------------- - * H5Z_FILTER_SZIP 4 , szip compression - *------------------------------------------------------------------------- - */ + /*------------------------------------------------------------------------- + * H5Z_FILTER_SZIP 4 , szip compression + *------------------------------------------------------------------------- + */ case H5Z_FILTER_SZIP: { unsigned options_mask; @@ -343,48 +392,47 @@ int apply_filters(const char* name, /* object name from traverse list */ /* set up for szip data */ if (H5Pset_chunk(dcpl_id, obj.chunk.rank, obj.chunk.chunk_lengths) < 0) - return -1; + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pset_chunk failed"); if (H5Pset_szip(dcpl_id, options_mask, pixels_per_block) < 0) - return -1; + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pset_szip failed"); } break; - /*------------------------------------------------------------------------- - * H5Z_FILTER_SHUFFLE 2 , shuffle the data - *------------------------------------------------------------------------- - */ + /*------------------------------------------------------------------------- + * H5Z_FILTER_SHUFFLE 2 , shuffle the data + *------------------------------------------------------------------------- + */ case H5Z_FILTER_SHUFFLE: if (H5Pset_chunk(dcpl_id, obj.chunk.rank, obj.chunk.chunk_lengths) < 0) - return -1; + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pset_chunk failed"); if (H5Pset_shuffle(dcpl_id) < 0) - return -1; + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pset_shuffle failed"); break; - /*------------------------------------------------------------------------- - * H5Z_FILTER_FLETCHER32 3 , fletcher32 checksum of EDC - *------------------------------------------------------------------------- - */ + /*------------------------------------------------------------------------- + * H5Z_FILTER_FLETCHER32 3 , fletcher32 checksum of EDC + *------------------------------------------------------------------------- + */ case H5Z_FILTER_FLETCHER32: if (H5Pset_chunk(dcpl_id, obj.chunk.rank, obj.chunk.chunk_lengths) < 0) - return -1; + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pset_chunk failed"); if (H5Pset_fletcher32(dcpl_id) < 0) - return -1; + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pset_fletcher32 failed"); break; - /*----------- ------------------------------------------------------------- - * H5Z_FILTER_NBIT , NBIT compression - *------------------------------------------------------------------------- - */ + /*----------- ------------------------------------------------------------- + * H5Z_FILTER_NBIT , NBIT compression + *------------------------------------------------------------------------- + */ case H5Z_FILTER_NBIT: if (H5Pset_chunk(dcpl_id, obj.chunk.rank, obj.chunk.chunk_lengths) < 0) - return -1; + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pset_chunk failed"); if (H5Pset_nbit(dcpl_id) < 0) - return -1; + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pset_nbit failed"); break; - /*----------- ------------------------------------------------------------- - * H5Z_FILTER_SCALEOFFSET , scale+offset compression - *------------------------------------------------------------------------- - */ - + /*----------- ------------------------------------------------------------- + * H5Z_FILTER_SCALEOFFSET , scale+offset compression + *------------------------------------------------------------------------- + */ case H5Z_FILTER_SCALEOFFSET: { H5Z_SO_scale_type_t scale_type; @@ -394,19 +442,19 @@ int apply_filters(const char* name, /* object name from traverse list */ scale_factor = (int) obj.filter[i].cd_values[1]; if (H5Pset_chunk(dcpl_id, obj.chunk.rank, obj.chunk.chunk_lengths) < 0) - return -1; + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pset_chunk failed"); if (H5Pset_scaleoffset(dcpl_id, scale_type, scale_factor) < 0) - return -1; + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pset_scaleoffset failed"); } break; default: { + if (H5Pset_chunk(dcpl_id, obj.chunk.rank, obj.chunk.chunk_lengths) < 0) + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pset_chunk failed"); if (H5Pset_filter(dcpl_id, obj.filter[i].filtn, obj.filter[i].filt_flag, obj.filter[i].cd_nelmts, obj.filter[i].cd_values) < 0) - return -1; - if (H5Pset_chunk(dcpl_id, obj.chunk.rank, obj.chunk.chunk_lengths) < 0) - return -1; + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pset_filter failed"); } break; } /* switch */ @@ -414,32 +462,42 @@ int apply_filters(const char* name, /* object name from traverse list */ } /*obj.nfilters*/ + if (filtobj.nfilters) { + for (i = 0; i < filtobj.nfilters; i++) { + if (filtobj.filter[i].filtn < 0) + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "invalid filter"); + + if (H5Zfilter_avail(filtobj.filter[i].filtn) <= 0) + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "%d filter unavailable", filtobj.filter[i].filtn); + } /* for */ + } /* nfilters */ + /*------------------------------------------------------------------------- - * layout - *------------------------------------------------------------------------- - */ + * layout + *------------------------------------------------------------------------- + */ if (obj.layout >= 0) { /* a layout was defined */ if (H5Pset_layout(dcpl_id, obj.layout) < 0) - return -1; + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pset_layout failed"); if (H5D_CHUNKED == obj.layout) { if (H5Pset_chunk(dcpl_id, obj.chunk.rank, obj.chunk.chunk_lengths) < 0) - return -1; + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pset_chunk failed"); } else if (H5D_COMPACT == obj.layout) { if (H5Pset_alloc_time(dcpl_id, H5D_ALLOC_TIME_EARLY) < 0) - return -1; + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pset_alloc_time failed"); } /* remove filters for the H5D_CONTIGUOUS case */ else if (H5D_CONTIGUOUS == obj.layout) { if (H5Premove_filter(dcpl_id, H5Z_FILTER_ALL) < 0) - return -1; + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Premove_filter failed"); } - } - return 0; +done: + return ret_value; } diff --git a/tools/src/h5repack/h5repack_main.c b/tools/src/h5repack/h5repack_main.c index a3f5678..d34c394 100644 --- a/tools/src/h5repack/h5repack_main.c +++ b/tools/src/h5repack/h5repack_main.c @@ -221,10 +221,6 @@ static void usage(const char *prog) { * Purpose: Shutdown MPI & HDF5 and call exit() * * Return: Does not return - * - * Programmer: Quincey Koziol - * Saturday, 31. January 2004 - * *------------------------------------------------------------------------- */ static void leave(int ret) @@ -239,11 +235,6 @@ static void leave(int ret) * Purpose: read comp and chunk options from a file * * Return: void, exit on error - * - * Programmer: pvn@ncsa.uiuc.edu - * - * Date: September, 22, 2003 - * *------------------------------------------------------------------------- */ static @@ -425,7 +416,6 @@ set_sort_order(const char *form) * Function: parse_command_line * * Purpose: parse command line input - * *------------------------------------------------------------------------- */ static @@ -438,13 +428,13 @@ int parse_command_line(int argc, const char **argv, pack_opt_t* options) while ((opt = get_option(argc, argv, s_opts, l_opts)) != EOF) { switch ((char) opt) { - /* -i for backward compability */ + /* -i for backward compatibility */ case 'i': infile = opt_arg; has_i_o = 1; break; - /* -o for backward compability */ + /* -o for backward compatibility */ case 'o': outfile = opt_arg; has_i_o = 1; @@ -674,13 +664,6 @@ done: * Return: Success: EXIT_SUCCESS(0) * * Failure: EXIT_FAILURE(1) - * - * Programmer: Pedro Vicente, pvn@ncsa.uiuc.edu - * - * Date: May 9, 2003 - * - * Comments: - * *------------------------------------------------------------------------- */ int main(int argc, const char **argv) @@ -712,8 +695,10 @@ int main(int argc, const char **argv) } /* initialize options */ - h5repack_init(&options, 0, FALSE); - + if (h5repack_init(&options, 0, FALSE) < 0) { + h5tools_setstatus(EXIT_FAILURE); + goto done; + } /* Initialize default indexing options */ sort_by = H5_INDEX_CRT_ORDER; diff --git a/tools/src/h5repack/h5repack_opttable.c b/tools/src/h5repack/h5repack_opttable.c index 93e34b3..7ab8c6e 100644 --- a/tools/src/h5repack/h5repack_opttable.c +++ b/tools/src/h5repack/h5repack_opttable.c @@ -21,23 +21,23 @@ * Purpose: initialize a pack_info_t structure * * Return: void - * - *------------------------------------------------------------------------- + *------------------------------------------------------------------------- */ 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; + int j, k; + + HDstrcpy(obj->path, "\0"); + for (j = 0; j < H5_REPACK_MAX_NFILTERS; j++) { + obj->filter[j].filtn = -1; + obj->filter[j].cd_nelmts = CD_VALUES; + 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; } /*------------------------------------------------------------------------- @@ -46,20 +46,14 @@ void init_packobject(pack_info_t *obj) { * Purpose: auxiliary function, inserts the filter in object OBJS[ I ] * * Return: void - * *------------------------------------------------------------------------- */ -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"); - } +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 + H5TOOLS_INFO(H5E_tools_min_id_g, "cannot insert the filter in this object. Maximum capacity exceeded"); } /*------------------------------------------------------------------------- @@ -68,30 +62,27 @@ static void aux_tblinsert_filter(pack_opttbl_t *table, unsigned int I, * Purpose: auxiliary function, inserts the layout in object OBJS[ I ] * * Return: void - * *------------------------------------------------------------------------- */ - -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]; + } + } } /*------------------------------------------------------------------------- @@ -100,7 +91,6 @@ static void aux_tblinsert_layout(pack_opttbl_t *table, unsigned int I, * Purpose: auxiliary function, increases the size of the collection by N_OBJS * * Return: 0, ok, -1, fail - * *------------------------------------------------------------------------- */ static int @@ -111,7 +101,7 @@ aux_inctable(pack_opttbl_t *table, unsigned n_objs) 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"); + H5TOOLS_INFO(H5E_tools_min_id_g, "not enough memory for options table"); return -1; } @@ -128,32 +118,30 @@ aux_inctable(pack_opttbl_t *table, unsigned n_objs) * Purpose: init options table * * Return: 0, ok, -1, fail - * - *------------------------------------------------------------------------- + *------------------------------------------------------------------------- */ 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; + unsigned int i; + pack_opttbl_t *table; + + if (NULL == (table = (pack_opttbl_t *) HDmalloc(sizeof(pack_opttbl_t)))) { + H5TOOLS_INFO(H5E_tools_min_id_g, "not enough memory for options table"); + return -1; + } + + table->size = 30; + table->nelems = 0; + if (NULL == (table->objs = (pack_info_t*) HDmalloc(table->size * sizeof(pack_info_t)))) { + H5TOOLS_INFO(H5E_tools_min_id_g, "not enough memory for options table"); + HDfree(table); + return -1; + } + + for (i = 0; i < table->size; i++) + init_packobject(&table->objs[i]); + + *tbl = table; + return 0; } @@ -163,14 +151,13 @@ int options_table_init(pack_opttbl_t **tbl) { * Purpose: free table memory * * Return: 0 - * *------------------------------------------------------------------------- */ int options_table_free(pack_opttbl_t *table) { - HDfree(table->objs); - HDfree(table); - return 0; + HDfree(table->objs); + HDfree(table); + return 0; } /*------------------------------------------------------------------------- @@ -179,12 +166,10 @@ int options_table_free(pack_opttbl_t *table) { * Purpose: add a layout option to the option list * * Return: 0, ok, -1, fail - * - *------------------------------------------------------------------------- + *------------------------------------------------------------------------- */ int -options_add_layout(obj_list_t *obj_list, unsigned n_objs, pack_info_t *pack, - pack_opttbl_t *table) +options_add_layout(obj_list_t *obj_list, unsigned n_objs, pack_info_t *pack, pack_opttbl_t *table) { unsigned i, j, I; unsigned added = 0; @@ -205,7 +190,7 @@ options_add_layout(obj_list_t *obj_list, unsigned n_objs, pack_info_t *pack, 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); + H5TOOLS_INFO(H5E_tools_min_id_g, "chunk information already inserted for <%s>\n", obj_list[j].obj); HDexit(EXIT_FAILURE); } /* insert the layout info */ @@ -261,12 +246,10 @@ options_add_layout(obj_list_t *obj_list, unsigned n_objs, pack_info_t *pack, * Purpose: add a compression -f option to the option list * * Return: 0, ok, -1, fail - * *------------------------------------------------------------------------- */ int -options_add_filter(obj_list_t *obj_list, unsigned n_objs, filter_info_t filt, - pack_opttbl_t *table) +options_add_filter(obj_list_t *obj_list, unsigned n_objs, filter_info_t filt, pack_opttbl_t *table) { unsigned int i, j, I; unsigned added = 0; @@ -279,7 +262,7 @@ options_add_filter(obj_list_t *obj_list, unsigned n_objs, filter_info_t filt, /* search if this object is already in the table; "path" is the key */ if (table->nelems > 0) { - /* go tru the supplied list of names */ + /* go through the supplied list of names */ for (j = 0; j < n_objs; j++) { /* linear table search */ for (i = 0; i < table->nelems; i++) { @@ -337,29 +320,26 @@ options_add_filter(obj_list_t *obj_list, unsigned n_objs, filter_info_t filt, * Purpose: get object from table; "path" is the key * * Return: pack_info_t* OBJECT or NULL if not found; PATH is the key - * *------------------------------------------------------------------------- */ 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; -} + 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; +} diff --git a/tools/src/h5repack/h5repack_parse.c b/tools/src/h5repack/h5repack_parse.c index 4d62723..05af197 100644 --- a/tools/src/h5repack/h5repack_parse.c +++ b/tools/src/h5repack/h5repack_parse.c @@ -58,26 +58,30 @@ obj_list_t* parse_filter(const char *str, unsigned *n_objs, filter_info_t *filt, /* check for the end of object list and number of objects */ for (i = 0, n = 0; i < len; i++) { c = str[i]; - if (c == ':') + if (c == ':') { end_obj = (int) i; + break; + } if (c == ',') n++; } + n++; /* Check for missing : */ if (end_obj == -1) { /* apply to all objects */ options->all_filter = 1; *is_glb = 1; + *n_objs = 1; } + else + *n_objs = n; - n++; obj_list = (obj_list_t *) HDmalloc(n * sizeof(obj_list_t)); if (obj_list == NULL) { error_msg("could not allocate object list\n"); return NULL; } - *n_objs = n; /* get object list */ if (end_obj > 0) @@ -89,6 +93,7 @@ obj_list_t* parse_filter(const char *str, unsigned *n_objs, filter_info_t *filt, sobj[k] = '\0'; else sobj[k + 1] = '\0'; + HDstrcpy(obj_list[n].obj, sobj); HDmemset(sobj, 0, sizeof(sobj)); n++; @@ -142,7 +147,6 @@ obj_list_t* parse_filter(const char *str, unsigned *n_objs, filter_info_t *filt, if (l == 2) { smask[l] = '\0'; i = len - 1; /* end */ - (*n_objs)--; /* we counted an extra ',' */ if (HDstrcmp(smask,"NN") == 0) filt->cd_values[j++] = H5_SZIP_NN_OPTION_MASK; else if (HDstrcmp(smask,"EC") == 0) @@ -193,7 +197,6 @@ obj_list_t* parse_filter(const char *str, unsigned *n_objs, filter_info_t *filt, if (l == 2) { smask[l] = '\0'; i = len - 1; /* end */ - (*n_objs)--; /* we counted an extra ',' */ if (HDstrcmp(smask,"IN") == 0) filt->cd_values[j++] = H5Z_SO_INT; else if (HDstrcmp(smask, "DS") == H5Z_SO_FLOAT_DSCALE) diff --git a/tools/src/h5repack/h5repack_refs.c b/tools/src/h5repack/h5repack_refs.c index 36038b5..376ab92 100644 --- a/tools/src/h5repack/h5repack_refs.c +++ b/tools/src/h5repack/h5repack_refs.c @@ -30,15 +30,10 @@ static herr_t update_ref_value(hid_t obj_id, H5R_type_t ref_type, void *ref_in, /*------------------------------------------------------------------------- * Function: do_copy_refobjs * - * Purpose: duplicate all referenced HDF5 objects in the file - * and create hard links - * - * Return: 0, ok, -1 no - * - * Programmer: Pedro Vicente, pvn@ncsa.uiuc.edu - * - * Date: December, 10, 2003 + * Purpose: duplicate all referenced HDF5 objects in the file + * and create hard links * + * Return: 0, ok, -1 no *------------------------------------------------------------------------- */ @@ -47,41 +42,39 @@ int do_copy_refobjs(hid_t fidin, trav_table_t *travt, pack_opt_t *options) /* repack options */ { - int ret_value = 0; /*no need to LEAVE() on ERROR: HERR_INIT(int, SUCCEED) */ - hid_t grp_in = (-1); /* read group ID */ - hid_t grp_out = (-1); /* write group ID */ - hid_t dset_in = (-1); /* read dataset ID */ - hid_t dset_out = (-1); /* write dataset ID */ - hid_t type_in = (-1); /* named type ID */ - hid_t dcpl_id = (-1); /* dataset creation property list ID */ - hid_t space_id = (-1); /* space ID */ - hid_t ftype_id = (-1); /* file data type ID */ - hid_t mtype_id = (-1); /* memory data type ID */ + int ret_value = 0; /*no need to LEAVE() on ERROR: HERR_INIT(int, SUCCEED) */ + hid_t grp_in = -1; /* read group ID */ + hid_t grp_out = -1; /* write group ID */ + hid_t dset_in = -1; /* read dataset ID */ + hid_t dset_out = -1; /* write dataset ID */ + hid_t type_in = -1; /* named type ID */ + hid_t dcpl_id = -1; /* dataset creation property list ID */ + hid_t space_id = -1; /* space ID */ + hid_t ftype_id = -1; /* file data type ID */ + hid_t mtype_id = -1; /* memory data type ID */ size_t msize; /* memory size of memory type */ hsize_t nelmts; /* number of elements in dataset */ int rank; /* rank of dataset */ hsize_t dims[H5S_MAX_RANK]; /* dimensions of dataset */ unsigned int i, j; int k; - named_dt_t *named_dt_head=NULL; /* Pointer to the stack of named datatypes - copied */ + named_dt_t *named_dt_head = NULL; /* Pointer to the stack of named datatypes copied */ /*------------------------------------------------------------------------- * browse *------------------------------------------------------------------------- */ for(i = 0; i < travt->nobjs; i++) { - switch(travt->objs[i].type) - { + switch(travt->objs[i].type) { /*------------------------------------------------------------------------- - * H5TRAV_TYPE_GROUP - *------------------------------------------------------------------------- - */ + * H5TRAV_TYPE_GROUP + *------------------------------------------------------------------------- + */ case H5TRAV_TYPE_GROUP: /*------------------------------------------------------------------------- - * copy referenced objects in attributes - *------------------------------------------------------------------------- - */ + * copy referenced objects in attributes + *------------------------------------------------------------------------- + */ if((grp_out = H5Gopen2(fidout, travt->objs[i].name, H5P_DEFAULT)) < 0) HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Gopen2 failed"); @@ -97,18 +90,18 @@ int do_copy_refobjs(hid_t fidin, HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Gclose failed"); /*------------------------------------------------------------------------- - * check for hard links - *------------------------------------------------------------------------- - */ + * check for hard links + *------------------------------------------------------------------------- + */ if(travt->objs[i].nlinks) for(j = 0; j < travt->objs[i].nlinks; j++) H5Lcreate_hard(fidout, travt->objs[i].name, H5L_SAME_LOC, travt->objs[i].links[j].new_name, H5P_DEFAULT, H5P_DEFAULT); break; /*------------------------------------------------------------------------- - * H5TRAV_TYPE_DATASET - *------------------------------------------------------------------------- - */ + * H5TRAV_TYPE_DATASET + *------------------------------------------------------------------------- + */ case H5TRAV_TYPE_DATASET: if((dset_in = H5Dopen2(fidin, travt->objs[i].name, H5P_DEFAULT)) < 0) HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dopen2 failed"); @@ -141,16 +134,16 @@ int do_copy_refobjs(hid_t fidin, */ if(h5tools_canreadf(NULL, dcpl_id) == 1) { /*------------------------------------------------------------------------- - * test for a valid output dataset - *------------------------------------------------------------------------- - */ + * test for a valid output dataset + *------------------------------------------------------------------------- + */ dset_out = FAIL; /*------------------------------------------------------------------------- - * object references are a special case - * we cannot just copy the buffers, but instead we recreate the reference - *------------------------------------------------------------------------- - */ + * object references are a special case + * we cannot just copy the buffers, but instead we recreate the reference + *------------------------------------------------------------------------- + */ if(H5Tequal(mtype_id, H5T_STD_REF_OBJ)) { hid_t refobj_id; hobj_ref_t *refbuf = NULL; /* buffer for object references */ @@ -159,9 +152,9 @@ int do_copy_refobjs(hid_t fidin, unsigned u; /*------------------------------------------------------------------------- - * read to memory - *------------------------------------------------------------------------- - */ + * read to memory + *------------------------------------------------------------------------- + */ if(nelmts) { buf = (hobj_ref_t *)HDmalloc((unsigned)(nelmts * msize)); if(buf==NULL) { @@ -201,9 +194,9 @@ int do_copy_refobjs(hid_t fidin, } /*nelmts*/ /*------------------------------------------------------------------------- - * create/write dataset/close - *------------------------------------------------------------------------- - */ + * create/write dataset/close + *------------------------------------------------------------------------- + */ if((dset_out = H5Dcreate2(fidout, travt->objs[i].name, mtype_id, space_id, H5P_DEFAULT, dcpl_id, H5P_DEFAULT)) < 0) HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dcreate2 failed"); if(nelmts) @@ -223,11 +216,10 @@ int do_copy_refobjs(hid_t fidin, } /*H5T_STD_REF_OBJ*/ /*------------------------------------------------------------------------- - * dataset region references - *------------------------------------------------------------------------- - */ - else if(H5Tequal(mtype_id, H5T_STD_REF_DSETREG)) - { + * dataset region references + *------------------------------------------------------------------------- + */ + else if(H5Tequal(mtype_id, H5T_STD_REF_DSETREG)) { hid_t refobj_id; hdset_reg_ref_t *refbuf = NULL; /* input buffer for region references */ hdset_reg_ref_t *buf = NULL; /* output buffer */ @@ -235,9 +227,9 @@ int do_copy_refobjs(hid_t fidin, unsigned u; /*------------------------------------------------------------------------- - * read input to memory - *------------------------------------------------------------------------- - */ + * read input to memory + *------------------------------------------------------------------------- + */ if(nelmts) { buf = (hdset_reg_ref_t *)HDmalloc((unsigned)(nelmts * msize)); if(buf == NULL) { @@ -248,9 +240,9 @@ int do_copy_refobjs(hid_t fidin, HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dread failed"); /*------------------------------------------------------------------------- - * create output - *------------------------------------------------------------------------- - */ + * create output + *------------------------------------------------------------------------- + */ refbuf = (hdset_reg_ref_t *)HDcalloc(sizeof(hdset_reg_ref_t), (size_t)nelmts); /*init to zero */ if(refbuf == NULL) { printf("cannot allocate memory\n"); @@ -289,9 +281,9 @@ int do_copy_refobjs(hid_t fidin, } /*nelmts*/ /*------------------------------------------------------------------------- - * create/write dataset/close - *------------------------------------------------------------------------- - */ + * create/write dataset/close + *------------------------------------------------------------------------- + */ if((dset_out = H5Dcreate2(fidout, travt->objs[i].name, mtype_id, space_id, H5P_DEFAULT, dcpl_id, H5P_DEFAULT)) < 0) HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dcreate2 failed"); if(nelmts) @@ -310,25 +302,25 @@ int do_copy_refobjs(hid_t fidin, HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "copy_attr failed"); } /* H5T_STD_REF_DSETREG */ /*------------------------------------------------------------------------- - * not references, open previously created object in 1st traversal - *------------------------------------------------------------------------- - */ + * not references, open previously created object in 1st traversal + *------------------------------------------------------------------------- + */ else { if((dset_out = H5Dopen2(fidout, travt->objs[i].name, H5P_DEFAULT)) < 0) HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dopen2 failed"); } /* end else */ /*------------------------------------------------------------------------- - * copy referenced objects in attributes - *------------------------------------------------------------------------- - */ + * copy referenced objects in attributes + *------------------------------------------------------------------------- + */ if(copy_refs_attr(dset_in, dset_out, options, travt, fidout) < 0) HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "copy_refs_attr failed"); /*------------------------------------------------------------------------- - * check for hard links - *------------------------------------------------------------------------- - */ + * check for hard links + *------------------------------------------------------------------------- + */ if(travt->objs[i].nlinks) for(j = 0; j < travt->objs[i].nlinks; j++) H5Lcreate_hard(fidout, travt->objs[i].name, H5L_SAME_LOC, travt->objs[i].links[j].new_name, H5P_DEFAULT, H5P_DEFAULT); @@ -338,9 +330,9 @@ int do_copy_refobjs(hid_t fidin, } /*can_read*/ /*------------------------------------------------------------------------- - * close - *------------------------------------------------------------------------- - */ + * close + *------------------------------------------------------------------------- + */ if(H5Tclose(ftype_id) < 0) HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Tclose failed"); if(H5Tclose(mtype_id) < 0) @@ -354,9 +346,9 @@ int do_copy_refobjs(hid_t fidin, break; /*------------------------------------------------------------------------- - * H5TRAV_TYPE_NAMED_DATATYPE - *------------------------------------------------------------------------- - */ + * H5TRAV_TYPE_NAMED_DATATYPE + *------------------------------------------------------------------------- + */ case H5TRAV_TYPE_NAMED_DATATYPE: if((type_in = H5Topen2(fidin, travt->objs[i].name, H5P_DEFAULT)) < 0) HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Topen2 failed"); @@ -365,9 +357,9 @@ int do_copy_refobjs(hid_t fidin, break; /*------------------------------------------------------------------------- - * H5TRAV_TYPE_LINK - *------------------------------------------------------------------------- - */ + * H5TRAV_TYPE_LINK + *------------------------------------------------------------------------- + */ case H5TRAV_TYPE_LINK: /*nothing to do */ break; @@ -410,27 +402,22 @@ done: /*------------------------------------------------------------------------- * Function: copy_refs_attr * - * Purpose: duplicate all referenced HDF5 located in attributes - * relative to LOC_IN, which is obtained either from - * loc_id = H5Gopen2(fid, name, H5P_DEFAULT); - * loc_id = H5Dopen2(fid, name, H5P_DEFAULT); - * loc_id = H5Topen2(fid, name, H5P_DEFAULT); - * - * Return: 0, ok, -1 no + * Purpose: duplicate all referenced HDF5 located in attributes + * relative to LOC_IN, which is obtained either from + * loc_id = H5Gopen2(fid, name, H5P_DEFAULT); + * loc_id = H5Dopen2(fid, name, H5P_DEFAULT); + * loc_id = H5Topen2(fid, name, H5P_DEFAULT); * - * Programmer: Pedro Vicente, pvn@ncsa.uiuc.edu + * Return: 0, ok, -1 no * - * Modifier: xcao@hdfgroup.org, 9/12/2011 - * Update values of references(object and region) for the following types: + * Modified: + * Update values of references(object and region) for the following types: * 1) References, * 2) ARRAY of reference, * 3) VLEN of references. * 4) COMPOUND of references. - * This function does not handle references in other complicated structures, - * such as references in nested compound datatypes. - * - * Date: October, 28, 2003 - * + * This function does not handle references in other complicated structures, + * such as references in nested compound datatypes. *------------------------------------------------------------------------- */ @@ -438,30 +425,32 @@ static int copy_refs_attr(hid_t loc_in, hid_t loc_out, pack_opt_t *options, trav_table_t *travt, - hid_t fidout /* for saving references */ - ) + hid_t fidout) /* for saving references */ { - 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 data type ID */ - hid_t mtype_id = -1; /* memory data type ID */ - size_t msize; /* memory size of type */ - hsize_t nelmts; /* number of elements in dataset */ - hsize_t dims[H5S_MAX_RANK];/* dimensions of dataset */ - char name[255]; - H5O_info_t oinfo; /* Object info */ - unsigned u, i, j; - int rank; + 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 data type ID */ + hid_t mtype_id = -1; /* memory data type ID */ + size_t msize; /* memory size of type */ + hsize_t nelmts; /* number of elements in dataset */ + hsize_t dims[H5S_MAX_RANK];/* dimensions of dataset */ + char name[255]; + H5O_info_t oinfo; /* Object info */ + unsigned u, i, j; + int rank; H5T_class_t type_class = -1; - hbool_t is_ref=0, is_ref_vlen=0, is_ref_array=0, is_ref_comp=0; - void *refbuf = NULL; - void *buf = NULL; - const char* refname = NULL; - unsigned *ref_comp_index = NULL; - size_t *ref_comp_size = NULL; - int ref_comp_field_n = 0; + hbool_t is_ref = 0, + is_ref_vlen = 0, + is_ref_array = 0, + is_ref_comp = 0; + void *refbuf = NULL; + void *buf = NULL; + const char *refname = NULL; + unsigned *ref_comp_index = NULL; + size_t *ref_comp_size = NULL; + int ref_comp_field_n = 0; if(H5Oget_info(loc_in, &oinfo) < 0) @@ -492,7 +481,7 @@ static int copy_refs_attr(hid_t loc_in, hid_t base_type; base_type = H5Tget_super(ftype_id); - is_ref_vlen = (H5Tget_class(base_type)==H5T_REFERENCE); + is_ref_vlen = (H5Tget_class(base_type) == H5T_REFERENCE); msize = H5Tget_size(base_type); H5Tclose(base_type); } @@ -500,7 +489,7 @@ static int copy_refs_attr(hid_t loc_in, hid_t base_type; base_type = H5Tget_super(ftype_id); - is_ref_array = (H5Tget_class(base_type)==H5T_REFERENCE); + is_ref_array = (H5Tget_class(base_type) == H5T_REFERENCE); msize = H5Tget_size(base_type); H5Tclose(base_type); } @@ -515,9 +504,9 @@ static int copy_refs_attr(hid_t loc_in, ref_comp_field_n = 0; for (i=0; i<(unsigned)nmembers; i++) { - hid_t mtid = H5Tget_member_type( ftype_id, i ); + hid_t mtid = H5Tget_member_type(ftype_id, i); - if ((H5Tget_class(mtid)==H5T_REFERENCE)) { + if ((H5Tget_class(mtid) == H5T_REFERENCE)) { ref_comp_index[ref_comp_field_n] = i; ref_comp_size[ref_comp_field_n] = H5Tget_size(mtid); ref_comp_field_n++; @@ -627,9 +616,9 @@ static int copy_refs_attr(hid_t loc_in, HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Aread failed"); /*------------------------------------------------------------------------- - * create output - *------------------------------------------------------------------------- - */ + * create output + *------------------------------------------------------------------------- + */ refbuf = (hdset_reg_ref_t *)HDcalloc(sizeof(hdset_reg_ref_t), (size_t)nelmts); /*init to zero */ if(refbuf == NULL) { printf( "cannot allocate memory\n" ); @@ -669,7 +658,8 @@ static int copy_refs_attr(hid_t loc_in, HDmemcpy(&(ptr[j]), &ref_out, msize); } } /* for (i=0; i<nelems; i++) */ - } else if (H5R_DSET_REG_REF_BUF_SIZE == msize) { + } + else if (H5R_DSET_REG_REF_BUF_SIZE == msize) { hdset_reg_ref_t ref_out; for (i=0; i<(unsigned)nelmts; i++) { @@ -689,8 +679,7 @@ static int copy_refs_attr(hid_t loc_in, buf = HDmalloc((unsigned)(nelmts * msize)); refbuf = buf; /* reuse the read buffer for write */ - if(buf == NULL) - { + if(buf == NULL) { printf( "cannot read into memory\n" ); HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "HDmalloc failed"); } /* end if */ @@ -767,8 +756,6 @@ static int copy_refs_attr(hid_t loc_in, HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Aclose failed"); } /* for(u = 0; u < (unsigned)oinfo.num_attrs; u++) */ - return ret_value; - done: if(refbuf) HDfree(refbuf); @@ -795,7 +782,7 @@ done: /*------------------------------------------------------------------------- * Function: MapIdToName * - * Purpose: map a ID from a reference to a dataset name + * Purpose: map a ID from a reference to a dataset name * *------------------------------------------------------------------------- */ @@ -803,7 +790,7 @@ static const char* MapIdToName(hid_t refobj_id, trav_table_t *travt) { unsigned int u; - const char* ret = NULL; + const char *ret = NULL; /* linear search */ for(u = 0; u < travt->nobjs; u++) { @@ -830,18 +817,16 @@ out: /*------------------------------------------------------------------------- * Function: Update_Ref_value * - * Purpose: Update a reference value - * - * Programmer: xcao@hdfgroup.org 9/12/2011 - * + * Purpose: Update a reference value *------------------------------------------------------------------------- */ static herr_t update_ref_value(hid_t obj_id, H5R_type_t ref_type, void *ref_in, hid_t fid_out, void *ref_out, trav_table_t *travt) { - int ret_value = 0; /*no need to LEAVE() on ERROR: HERR_INIT(int, SUCCEED) */ - const char* ref_obj_name; - hid_t space_id=-1, ref_obj_id=-1; + int ret_value = 0; /*no need to LEAVE() on ERROR: HERR_INIT(int, SUCCEED) */ + const char *ref_obj_name; + hid_t space_id = -1; + hid_t ref_obj_id = -1; ref_obj_id = H5Rdereference2(obj_id, H5P_DEFAULT, ref_type, ref_in); if (ref_obj_id < 0) diff --git a/tools/src/h5repack/h5repack_verify.c b/tools/src/h5repack/h5repack_verify.c index 1a0dab7..dbe8e1a 100644 --- a/tools/src/h5repack/h5repack_verify.c +++ b/tools/src/h5repack/h5repack_verify.c @@ -33,41 +33,35 @@ static int verify_filters(hid_t pid, hid_t tid, int nfilters, filter_info_t *fil * 1 match * 0 do not match * -1 error - * - * Programmer: Pedro Vicente, pvn@hdfgroup.org - * - * Date: December 19, 2003 - * *------------------------------------------------------------------------- */ int h5repack_verify(const char *in_fname, const char *out_fname, pack_opt_t *options) { - int ret_value = 0; /*no need to LEAVE() on ERROR: HERR_INIT(int, SUCCEED) */ + int ret_value = 0; /*no need to LEAVE() on ERROR: HERR_INIT(int, SUCCEED) */ hid_t fidin = -1; /* file ID for input file*/ hid_t fidout = -1; /* file ID for output file*/ hid_t did = -1; /* dataset ID */ hid_t pid = -1; /* dataset creation property list ID */ hid_t sid = -1; /* space ID */ hid_t tid = -1; /* type ID */ + int ok = 1; /* step results */ unsigned int i; trav_table_t *travt = NULL; - int ok = 1; - hid_t fcpl_in = -1; /* file creation property for input file */ - hid_t fcpl_out = -1; /* file creation property for output file */ + hid_t fcpl_in = -1; /* file creation property for input file */ + hid_t fcpl_out = -1; /* file creation property for output file */ H5F_fspace_strategy_t in_strategy, out_strategy; /* file space handling strategy for in/output file */ - hbool_t in_persist, out_persist; /* free-space persist status for in/output file */ - hsize_t in_threshold, out_threshold; /* free-space section threshold for in/output file */ - hsize_t in_pagesize, out_pagesize; /* file space page size for input/output file */ + hbool_t in_persist, out_persist; /* free-space persist status for in/output file */ + hsize_t in_threshold, out_threshold; /* free-space section threshold for in/output file */ + hsize_t in_pagesize, out_pagesize; /* file space page size for input/output file */ /* open the output file */ if((fidout = H5Fopen(out_fname, H5F_ACC_RDONLY, H5P_DEFAULT)) < 0 ) - return -1; + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Fopen failed on <%s>", out_fname); - for(i = 0; i < options->op_tbl->nelems; i++) - { - char* name = options->op_tbl->objs[i].path; + for(i = 0; i < options->op_tbl->nelems; i++) { + char *name = options->op_tbl->objs[i].path; pack_info_t *obj = &options->op_tbl->objs[i]; /*------------------------------------------------------------------------- @@ -75,7 +69,7 @@ h5repack_verify(const char *in_fname, const char *out_fname, pack_opt_t *options *------------------------------------------------------------------------- */ if((did = H5Dopen2(fidout, name, H5P_DEFAULT)) < 0) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dopen2 failed"); + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dopen2 failed on <%s>", name); if((sid = H5Dget_space(did)) < 0) HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dget_space failed"); if((pid = H5Dget_create_plist(did)) < 0) @@ -90,7 +84,6 @@ h5repack_verify(const char *in_fname, const char *out_fname, pack_opt_t *options if(verify_filters(pid, tid, obj->nfilters, obj->filter) <= 0) ok = 0; - /*------------------------------------------------------------------------- * layout check *------------------------------------------------------------------------- @@ -110,18 +103,14 @@ h5repack_verify(const char *in_fname, const char *out_fname, pack_opt_t *options HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dclose failed"); if (H5Tclose(tid) < 0) HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Tclose failed"); - } - /*------------------------------------------------------------------------- * check for the "all" objects option *------------------------------------------------------------------------- */ - if(options->all_filter == 1 || options->all_layout == 1) - { - + if(options->all_filter == 1 || options->all_layout == 1) { /* Initialize indexing options */ h5trav_set_index(sort_by, sort_order); /* init table */ @@ -131,19 +120,16 @@ h5repack_verify(const char *in_fname, const char *out_fname, pack_opt_t *options if(h5trav_gettable(fidout, travt) < 0) HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "h5trav_gettable failed"); - for(i = 0; i < travt->nobjs; i++) - { + for(i = 0; i < travt->nobjs; i++) { char *name = travt->objs[i].name; - if(travt->objs[i].type == H5TRAV_TYPE_DATASET) - { - + if(travt->objs[i].type == H5TRAV_TYPE_DATASET) { /*------------------------------------------------------------------------- * open *------------------------------------------------------------------------- */ if((did = H5Dopen2(fidout, name, H5P_DEFAULT)) < 0) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dopen2 failed"); + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dopen2 failed on <%s>", name); if((sid = H5Dget_space(did)) < 0) HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dget_space failed"); if((pid = H5Dget_create_plist(did)) < 0) @@ -155,8 +141,7 @@ h5repack_verify(const char *in_fname, const char *out_fname, pack_opt_t *options * filter check *------------------------------------------------------------------------- */ - if(options->all_filter == 1) - { + if(options->all_filter == 1) { if(verify_filters(pid, tid, options->n_filter_g, options->filter_g) <= 0) ok = 0; } @@ -165,8 +150,7 @@ h5repack_verify(const char *in_fname, const char *out_fname, pack_opt_t *options * layout check *------------------------------------------------------------------------- */ - if(options->all_layout == 1) - { + if(options->all_layout == 1) { pack_info_t pack; init_packobject(&pack); @@ -176,7 +160,6 @@ h5repack_verify(const char *in_fname, const char *out_fname, pack_opt_t *options ok = 0; } - /*------------------------------------------------------------------------- * close *------------------------------------------------------------------------- @@ -190,11 +173,11 @@ h5repack_verify(const char *in_fname, const char *out_fname, pack_opt_t *options if (H5Tclose(tid) < 0) HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Tclose failed"); } /* if */ - } /* i */ /* free table */ trav_table_free(travt); + travt = NULL; } /*------------------------------------------------------------------------- @@ -203,45 +186,33 @@ h5repack_verify(const char *in_fname, const char *out_fname, pack_opt_t *options */ /* open the input file */ - if((fidin = H5Fopen(in_fname, H5F_ACC_RDONLY, H5P_DEFAULT)) < 0 ) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Fopen failed"); + if((fidin = H5Fopen(in_fname, H5F_ACC_RDONLY, H5P_DEFAULT)) < 0) + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Fopen failed on file <%s>", in_fname); /* Get file creation property list for input file */ - if((fcpl_in = H5Fget_create_plist(fidin)) < 0) { - error_msg("failed to retrieve file creation property list\n"); - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Fget_create_plist failed"); - } + if((fcpl_in = H5Fget_create_plist(fidin)) < 0) + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Fget_create_plist failed to retrieve file creation property list"); /* Get file space info for input file */ - if(H5Pget_file_space_strategy(fcpl_in, &in_strategy, &in_persist, &in_threshold) < 0) { - error_msg("failed to retrieve file space strategy & threshold\n"); - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pget_file_space failed"); - } + if(H5Pget_file_space_strategy(fcpl_in, &in_strategy, &in_persist, &in_threshold) < 0) + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pget_file_space_strategy failed to retrieve file space strategy & threshold"); /* Get file space page size for input file */ - if(H5Pget_file_space_page_size(fcpl_in, &in_pagesize) < 0) { - error_msg("failed to retrieve file space page size\n"); - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Fget_create_plist failed"); - } + if(H5Pget_file_space_page_size(fcpl_in, &in_pagesize) < 0) + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pget_file_space_page_size failed to retrieve file space page size"); /* Output file is already opened */ /* Get file creation property list for output file */ - if((fcpl_out = H5Fget_create_plist(fidout)) < 0) { - error_msg("failed to retrieve file creation property list\n"); - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Fget_create_plist failed"); - } + if((fcpl_out = H5Fget_create_plist(fidout)) < 0) + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Fget_create_plist failed to retrieve file creation property list"); /* Get file space info for output file */ - if(H5Pget_file_space_strategy(fcpl_out, &out_strategy, &out_persist, &out_threshold) < 0) { - error_msg("failed to retrieve file space strategy & threshold\n"); - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pget_file_space failed"); - } + if(H5Pget_file_space_strategy(fcpl_out, &out_strategy, &out_persist, &out_threshold) < 0) + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pget_file_space_strategy failed to retrieve file space strategy & threshold"); /* Get file space page size for output file */ - if(H5Pget_file_space_page_size(fcpl_out, &out_pagesize) < 0) { - error_msg("failed to retrieve file space page size\n"); - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Fget_create_plist failed"); - } + if(H5Pget_file_space_page_size(fcpl_out, &out_pagesize) < 0) + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pget_file_space_page_size failed to retrieve file space page size"); /* * If -S option is set, the file space handling strategy should be set as specified. @@ -249,15 +220,12 @@ h5repack_verify(const char *in_fname, const char *out_fname, pack_opt_t *options * the same as the input file's strategy. */ if(options->fs_strategy) { - if(out_strategy != (options->fs_strategy == (H5F_fspace_strategy_t)-1 ? 0 : options->fs_strategy)) { - error_msg("file space strategy not set as unexpected\n"); + if(out_strategy != (options->fs_strategy == (H5F_fspace_strategy_t)-1 ? 0 : options->fs_strategy)) HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "file space strategy not set as unexpected"); - } - } else { - if(out_strategy != in_strategy) { - error_msg("file space strategy not set as unexpected\n"); + } + else { + if(out_strategy != in_strategy) HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "file space strategy not set as unexpected"); - } } /* @@ -266,15 +234,12 @@ h5repack_verify(const char *in_fname, const char *out_fname, pack_opt_t *options * the same as the input file's free-space persist status */ if(options->fs_persist) { - if(out_persist != (hbool_t)(options->fs_persist == (-1) ? FALSE : options->fs_persist)) { - error_msg("free-space persist status is not set as unexpected\n"); - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "file space strategy not set as unexpected"); - } - } else { - if(out_persist != in_persist) { - error_msg("free-space persist status is not set as unexpected\n"); - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "file space strategy not set as unexpected"); - } + if(out_persist != (hbool_t)(options->fs_persist == (-1) ? FALSE : options->fs_persist)) + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "free-space persist status not set as unexpected"); + } + else { + if(out_persist != in_persist) + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "free-space persist status not set as unexpected"); } /* @@ -283,15 +248,12 @@ h5repack_verify(const char *in_fname, const char *out_fname, pack_opt_t *options * input file's threshold size. */ if(options->fs_threshold) { - if(out_threshold != (hsize_t)(options->fs_threshold == (-1) ? 0 : options->fs_threshold)) { - error_msg("threshold is not set as unexpectec\n"); - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "file space strategy not set as unexpected"); - } - } else { - if(out_threshold != in_threshold) { - error_msg("threshold is not set as unexpected\n"); - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "file space strategy not set as unexpected"); - } + if(out_threshold != (hsize_t)(options->fs_threshold == (-1) ? 0 : options->fs_threshold)) + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "threshold not set as unexpected"); + } + else { + if(out_threshold != in_threshold) + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "threshold not set as unexpected"); } /* @@ -300,28 +262,16 @@ h5repack_verify(const char *in_fname, const char *out_fname, pack_opt_t *options * the same as the input file's file space page size. */ if(options->fs_pagesize) { - if(out_pagesize != (hsize_t)(options->fs_pagesize == (-1) ? 0 : options->fs_pagesize)) { - error_msg("file space page size is not set as unexpected\n"); - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "file space strategy not set as unexpected"); - } - } else { /* "-G" is not set */ - if(out_pagesize != in_pagesize) { - error_msg("file space page size is not set as unexpected\n"); - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "file space strategy not set as unexpected"); - } + if(out_pagesize != (hsize_t)(options->fs_pagesize == (-1) ? 0 : options->fs_pagesize)) + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "file space page size not set as unexpected"); } + else { /* "-G" is not set */ + if(out_pagesize != in_pagesize) + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "file space page size not set as unexpected"); - /* Closing */ - if (H5Pclose(fcpl_in) < 0) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed"); - if (H5Pclose(fcpl_out) < 0) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed"); - if (H5Fclose(fidin) < 0) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Fclose failed"); - if (H5Fclose(fidout) < 0) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Fclose failed"); + } - return ok; + ret_value = ok; done: H5E_BEGIN_TRY { @@ -330,6 +280,7 @@ done: H5Pclose(pid); H5Sclose(sid); H5Dclose(did); + H5Tclose(tid); H5Fclose(fidin); H5Fclose(fidout); if (travt) @@ -339,28 +290,22 @@ done: return ret_value; } /* h5repack_verify() */ - - /*------------------------------------------------------------------------- * Function: verify_layout * - * Purpose: verify which layout is present in the property list DCPL_ID - * - * H5D_COMPACT = 0 - * H5D_CONTIGUOUS = 1 - * H5D_CHUNKED = 2 - * - * Return: 1 has, 0 does not, -1 error - * - * Programmer: Pedro Vicente, pvn@ncsa.uiuc.edu - * - * Date: December 30, 2003 + * Purpose: verify which layout is present in the property list DCPL_ID + * H5D_COMPACT = 0 + * H5D_CONTIGUOUS = 1 + * H5D_CHUNKED = 2 * + * Return: + * 1 has, + * 0 does not, + * -1 error *------------------------------------------------------------------------- */ -int verify_layout(hid_t pid, - pack_info_t *obj) +int verify_layout(hid_t pid, pack_info_t *obj) { hsize_t chsize[64]; /* chunk size in elements */ H5D_layout_t layout; /* layout */ @@ -373,7 +318,7 @@ int verify_layout(hid_t pid, return -1; /* a non chunked layout was requested on a filtered object */ - if (nfilters && obj->layout!=H5D_CHUNKED) + if (nfilters && obj->layout != H5D_CHUNKED) return 0; /* get layout */ @@ -383,13 +328,12 @@ int verify_layout(hid_t pid, if (obj->layout != layout) return 0; - if (layout==H5D_CHUNKED) - { - if ((rank = H5Pget_chunk(pid,NELMTS(chsize),chsize/*out*/)) < 0) + if (layout==H5D_CHUNKED) { + if ((rank = H5Pget_chunk(pid, NELMTS(chsize), chsize/*out*/)) < 0) return -1; if (obj->chunk.rank != rank) return 0; - for ( i=0; i<rank; i++) + for (i = 0; i < rank; i++) if (chsize[i] != obj->chunk.chunk_lengths[i]) return 0; } @@ -400,58 +344,40 @@ int verify_layout(hid_t pid, /*------------------------------------------------------------------------- * Function: h5repack_cmp_pl * - * Purpose: compare 2 files for identical property lists of all objects - * - * Return: 1=identical, 0=not identical, -1=error - * - * Programmer: Pedro Vicente, pvn@ncsa.uiuc.edu - * - * Date: December 31, 2003 + * Purpose: compare 2 files for identical property lists of all objects * + * Return: + * 1 = identical, + * 0 = not identical, + * -1 = error *------------------------------------------------------------------------- */ -int h5repack_cmp_pl(const char *fname1, - const char *fname2) +int h5repack_cmp_pl(const char *fname1, const char *fname2) { - int ret_value = 0; /*no need to LEAVE() on ERROR: HERR_INIT(int, SUCCEED) */ - hid_t fid1=-1; /* file ID */ - hid_t fid2=-1; /* file ID */ - hid_t dset1=-1; /* dataset ID */ - hid_t dset2=-1; /* dataset ID */ - hid_t gid=-1; /* group ID */ - hid_t dcpl1=-1; /* dataset creation property list ID */ - hid_t dcpl2=-1; /* dataset creation property list ID */ - hid_t gcplid=-1; /* group creation property list */ - unsigned crt_order_flag1; /* group creation order flag */ - unsigned crt_order_flag2; /* group creation order flag */ - trav_table_t *trav=NULL; - int ret=1; + int ret_value = 1; /*no need to LEAVE() on ERROR: HERR_INIT(int, SUCCEED) */ + hid_t fid1 =-1; /* file ID */ + hid_t fid2 =-1; /* file ID */ + hid_t dset1 =-1; /* dataset ID */ + hid_t dset2 =-1; /* dataset ID */ + hid_t gid =-1; /* group ID */ + hid_t dcpl1 =-1; /* dataset creation property list ID */ + hid_t dcpl2 =-1; /* dataset creation property list ID */ + hid_t gcplid =-1; /* group creation property list */ + unsigned crt_order_flag1; /* group creation order flag */ + unsigned crt_order_flag2; /* group creation order flag */ + trav_table_t *trav = NULL; unsigned int i; /*------------------------------------------------------------------------- * open the files *------------------------------------------------------------------------- */ - - /* disable error reporting */ - H5E_BEGIN_TRY - { - - /* Open the files */ - if ((fid1 = H5Fopen(fname1,H5F_ACC_RDONLY,H5P_DEFAULT)) < 0 ) - { - error_msg("<%s>: %s\n", fname1, H5FOPENERROR ); - return -1; - } - if ((fid2 = H5Fopen(fname2,H5F_ACC_RDONLY,H5P_DEFAULT)) < 0 ) - { - error_msg("<%s>: %s\n", fname2, H5FOPENERROR ); - H5Fclose(fid1); - return -1; - } - /* enable error reporting */ - } H5E_END_TRY; + /* Open the files */ + if ((fid1 = H5Fopen(fname1, H5F_ACC_RDONLY, H5P_DEFAULT)) < 0) + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "h5tools_fopen failed <%s>: %s", fname1, H5FOPENERROR); + if ((fid2 = H5Fopen(fname2, H5F_ACC_RDONLY, H5P_DEFAULT)) < 0) + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "h5tools_fopen failed <%s>: %s", fname2, H5FOPENERROR); /*------------------------------------------------------------------------- * get file table list of objects @@ -468,14 +394,10 @@ int h5repack_cmp_pl(const char *fname1, * traverse the suppplied object list *------------------------------------------------------------------------- */ - for(i = 0; i < trav->nobjs; i++) - { - - if(trav->objs[i].type == H5TRAV_TYPE_GROUP) - { - + for(i = 0; i < trav->nobjs; i++) { + if(trav->objs[i].type == H5TRAV_TYPE_GROUP) { if ((gid = H5Gopen2(fid1, trav->objs[i].name, H5P_DEFAULT)) < 0) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Gopen2 failed"); + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Gopen2 failed on first <%s>", trav->objs[i].name); if ((gcplid = H5Gget_create_plist(gid)) < 0) HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Gget_create_plist failed"); if (H5Pget_link_creation_order(gcplid, &crt_order_flag1) < 0) @@ -486,7 +408,7 @@ int h5repack_cmp_pl(const char *fname1, HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Gclose failed"); if ((gid = H5Gopen2(fid2, trav->objs[i].name, H5P_DEFAULT)) < 0) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Gopen2 failed"); + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Gopen2 failed on second <%s>", trav->objs[i].name); if ((gcplid = H5Gget_create_plist(gid)) < 0) HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Gget_create_plist failed"); if (H5Pget_link_creation_order(gcplid, &crt_order_flag2) < 0) @@ -496,21 +418,14 @@ int h5repack_cmp_pl(const char *fname1, if (H5Gclose(gid) < 0) HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Gclose failed"); - if (crt_order_flag1 != crt_order_flag2) { - error_msg("property lists for <%s> are different\n",trav->objs[i].name); - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "property lists failed"); - } - + if (crt_order_flag1 != crt_order_flag2) + HGOTO_ERROR(0, H5E_tools_min_id_g, "property lists failed for <%s> are different", trav->objs[i].name); } - - - - else if(trav->objs[i].type == H5TRAV_TYPE_DATASET) - { + else if(trav->objs[i].type == H5TRAV_TYPE_DATASET) { if((dset1 = H5Dopen2(fid1, trav->objs[i].name, H5P_DEFAULT)) < 0) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dopen2 failed"); + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dopen2 failed on first <%s>", trav->objs[i].name); if((dset2 = H5Dopen2(fid2, trav->objs[i].name, H5P_DEFAULT)) < 0) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dopen2 failed"); + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dopen2 failed on second <%s>", trav->objs[i].name); if((dcpl1 = H5Dget_create_plist(dset1)) < 0) HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dget_create_plist failed"); if((dcpl2 = H5Dget_create_plist(dset2)) < 0) @@ -520,13 +435,11 @@ int h5repack_cmp_pl(const char *fname1, * compare the property lists *------------------------------------------------------------------------- */ - if((ret = H5Pequal(dcpl1, dcpl2)) < 0) + if((ret_value = H5Pequal(dcpl1, dcpl2)) < 0) HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pequal failed"); - if(ret == 0) { - error_msg("property lists for <%s> are different\n",trav->objs[i].name); - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "property lists failed"); - } + if(ret_value == 0) + HGOTO_ERROR(0, H5E_tools_min_id_g, "property lists failed for <%s> are different", trav->objs[i].name); /*------------------------------------------------------------------------- * close @@ -541,29 +454,8 @@ int h5repack_cmp_pl(const char *fname1, if(H5Dclose(dset2) < 0) HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dclose failed"); } /*if*/ - } /*i*/ + } /*for*/ - /*------------------------------------------------------------------------- - * free - *------------------------------------------------------------------------- - */ - - trav_table_free(trav); - - /*------------------------------------------------------------------------- - * close - *------------------------------------------------------------------------- - */ - - H5Fclose(fid1); - H5Fclose(fid2); - - return ret; - -/*------------------------------------------------------------------------- -* error -*------------------------------------------------------------------------- -*/ done: H5E_BEGIN_TRY { @@ -575,7 +467,8 @@ done: H5Fclose(fid2); H5Pclose(gcplid); H5Gclose(gid); - trav_table_free(trav); + if(trav) + trav_table_free(trav); } H5E_END_TRY; return ret_value; @@ -585,19 +478,14 @@ done: /*------------------------------------------------------------------------- * Function: verify_filters * - * Purpose: verify if all requested filters in the array FILTER obtained - * from user input are present in the property list PID obtained from - * the output file + * Purpose: verify if all requested filters in the array FILTER obtained + * from user input are present in the property list PID obtained from + * the output file * * Return: - * 1 match - * 0 do not match - * -1 error - * - * Programmer: Pedro Vicente, pvn@hdfgroup.org - * - * Date: December 21, 2007 - * + * 1 match + * 0 do not match + * -1 error *------------------------------------------------------------------------- */ @@ -621,11 +509,11 @@ int verify_filters(hid_t pid, hid_t tid, int nfilters, filter_info_t *filter) /* if we do not have filters and the requested filter is NONE, return 1 */ if(!nfilters_dcpl && nfilters == 1 && - filter[0].filtn == H5Z_FILTER_NONE ) + filter[0].filtn == H5Z_FILTER_NONE) return 1; /* else the numbers of filters must match */ - if (nfilters_dcpl != nfilters ) + if (nfilters_dcpl != nfilters) return 0; /*------------------------------------------------------------------------- @@ -633,26 +521,25 @@ int verify_filters(hid_t pid, hid_t tid, int nfilters, filter_info_t *filter) *------------------------------------------------------------------------- */ - for( i = 0; i < nfilters_dcpl; i++) - { + for (i = 0; i < nfilters_dcpl; i++) { cd_nelmts = NELMTS(cd_values); filtn = H5Pget_filter2(pid, (unsigned)i, &filt_flags, &cd_nelmts, cd_values, sizeof(f_name), f_name, NULL); /* filter ID */ + if (filtn < 0) + return -1; if (filtn != filter[i].filtn) return 0; /* compare client data values. some filters do return local values */ - switch (filtn) - { - + switch (filtn) { case H5Z_FILTER_NONE: break; case H5Z_FILTER_SHUFFLE: /* 1 private client value is returned by DCPL */ - if ( cd_nelmts != H5Z_SHUFFLE_TOTAL_NPARMS && filter[i].cd_nelmts != H5Z_SHUFFLE_USER_NPARMS ) + if (cd_nelmts != H5Z_SHUFFLE_TOTAL_NPARMS && filter[i].cd_nelmts != H5Z_SHUFFLE_USER_NPARMS) return 0; /* get dataset's type size */ @@ -660,31 +547,31 @@ int verify_filters(hid_t pid, hid_t tid, int nfilters, filter_info_t *filter) return -1; /* the private client value holds the dataset's type size */ - if ( size != cd_values[0] ) + if (size != cd_values[0]) return 0; break; case H5Z_FILTER_SZIP: /* 4 private client values are returned by DCPL */ - if ( cd_nelmts != H5Z_SZIP_TOTAL_NPARMS && filter[i].cd_nelmts != H5Z_SZIP_USER_NPARMS ) + if (cd_nelmts != H5Z_SZIP_TOTAL_NPARMS && filter[i].cd_nelmts != H5Z_SZIP_USER_NPARMS) return 0; /* "User" parameter for pixels-per-block (index 1) */ - if ( cd_values[H5Z_SZIP_PARM_PPB] != filter[i].cd_values[H5Z_SZIP_PARM_PPB] ) + if (cd_values[H5Z_SZIP_PARM_PPB] != filter[i].cd_values[H5Z_SZIP_PARM_PPB]) return 0; break; case H5Z_FILTER_NBIT: /* only client data values number of values checked */ - if ( H5Z_NBIT_USER_NPARMS != filter[i].cd_nelmts) + if (H5Z_NBIT_USER_NPARMS != filter[i].cd_nelmts) return 0; break; case H5Z_FILTER_SCALEOFFSET: /* only client data values checked */ - for( j = 0; j < H5Z_SCALEOFFSET_USER_NPARMS; j++) + for (j = 0; j < H5Z_SCALEOFFSET_USER_NPARMS; j++) if (cd_values[j] != filter[i].cd_values[j]) return 0; break; @@ -693,20 +580,20 @@ int verify_filters(hid_t pid, hid_t tid, int nfilters, filter_info_t *filter) case H5Z_FILTER_FLETCHER32: case H5Z_FILTER_DEFLATE: - if ( cd_nelmts != filter[i].cd_nelmts) + if (cd_nelmts != filter[i].cd_nelmts) return 0; - for( j = 0; j < cd_nelmts; j++) + for (j = 0; j < cd_nelmts; j++) if (cd_values[j] != filter[i].cd_values[j]) return 0; break; default: - if ( cd_nelmts != filter[i].cd_nelmts) + if (cd_nelmts != filter[i].cd_nelmts) return 0; - for( j = 0; j < cd_nelmts; j++) + for (j = 0; j < cd_nelmts; j++) if (cd_values[j] != filter[i].cd_values[j]) return 0; break; @@ -716,4 +603,3 @@ int verify_filters(hid_t pid, hid_t tid, int nfilters, filter_info_t *filter) return 1; } - |