diff options
Diffstat (limited to 'tools/src/h5repack')
| -rw-r--r-- | tools/src/h5repack/h5repack.c | 225 | ||||
| -rw-r--r-- | tools/src/h5repack/h5repack.h | 199 | ||||
| -rw-r--r-- | tools/src/h5repack/h5repack_copy.c | 1485 | ||||
| -rw-r--r-- | tools/src/h5repack/h5repack_filters.c | 311 | ||||
| -rw-r--r-- | tools/src/h5repack/h5repack_main.c | 410 | ||||
| -rw-r--r-- | tools/src/h5repack/h5repack_opttable.c | 106 | ||||
| -rw-r--r-- | tools/src/h5repack/h5repack_parse.c | 314 | ||||
| -rw-r--r-- | tools/src/h5repack/h5repack_refs.c | 546 | ||||
| -rw-r--r-- | tools/src/h5repack/h5repack_verify.c | 366 |
9 files changed, 2015 insertions, 1947 deletions
diff --git a/tools/src/h5repack/h5repack.c b/tools/src/h5repack/h5repack.c index 4fd163c..a1764df 100644 --- a/tools/src/h5repack/h5repack.c +++ b/tools/src/h5repack/h5repack.c @@ -22,10 +22,10 @@ *------------------------------------------------------------------------- */ -static int check_options(pack_opt_t *options); -static int check_objects(const char* fname, pack_opt_t *options); -static const char* get_sfilter(H5Z_filter_t filtn); -static int have_request(pack_opt_t *options); +static int check_options(pack_opt_t *options); +static int check_objects(const char *fname, pack_opt_t *options); +static const char *get_sfilter(H5Z_filter_t filtn); +static int have_request(pack_opt_t *options); /*------------------------------------------------------------------------- * Function: h5repack @@ -42,7 +42,7 @@ static int have_request(pack_opt_t *options); *------------------------------------------------------------------------- */ int -h5repack(const char* infile, const char* outfile, pack_opt_t *options) +h5repack(const char *infile, const char *outfile, pack_opt_t *options) { /* check input */ if (check_options(options) < 0) @@ -73,17 +73,17 @@ h5repack_init(pack_opt_t *options, int verbose, hbool_t latest) int k, n; HDmemset(options, 0, sizeof(pack_opt_t)); - options->min_comp = 0; - options->verbose = verbose; - options->latest = latest; - options->layout_g = H5D_LAYOUT_ERROR; - options->low_bound = H5F_LIBVER_EARLIEST; + options->min_comp = 0; + options->verbose = verbose; + options->latest = latest; + options->layout_g = H5D_LAYOUT_ERROR; + options->low_bound = H5F_LIBVER_EARLIEST; options->high_bound = H5F_LIBVER_LATEST; - options->fin_fapl = H5P_DEFAULT; - options->fout_fapl = H5P_DEFAULT; + options->fin_fapl = H5P_DEFAULT; + options->fout_fapl = H5P_DEFAULT; for (n = 0; n < H5_REPACK_MAX_NFILTERS; n++) { - options->filter_g[n].filtn = -1; + options->filter_g[n].filtn = -1; options->filter_g[n].cd_nelmts = 0; for (k = 0; k < CD_VALUES; k++) options->filter_g[n].cd_values[k] = 0; @@ -117,7 +117,7 @@ h5repack_end(pack_opt_t *options) int h5repack_addfilter(const char *str, pack_opt_t *options) { - obj_list_t *obj_list = NULL; /* one object list for the -f and -l option entry */ + 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 */ @@ -166,7 +166,7 @@ h5repack_addlayout(const char *str, pack_opt_t *options) init_packobject(&pack); if (options->all_layout == 1) { - error_msg( "invalid layout input: 'all' option is present with other objects <%s>\n", str); + error_msg("invalid layout input: 'all' option is present with other objects <%s>\n", str); return ret_value; } @@ -222,13 +222,14 @@ h5repack_addlayout(const char *str, pack_opt_t *options) *------------------------------------------------------------------------- */ hid_t -copy_named_datatype(hid_t type_in, hid_t fidout, named_dt_t **named_dt_head_p, trav_table_t *travt, pack_opt_t *options) +copy_named_datatype(hid_t type_in, hid_t fidout, named_dt_t **named_dt_head_p, trav_table_t *travt, + pack_opt_t *options) { - named_dt_t *dt = *named_dt_head_p; /* Stack pointer */ - named_dt_t *dt_ret = NULL; /* Datatype to return */ - H5O_info2_t oinfo; /* Object info of input dtype */ - int token_cmp; - hid_t ret_value = H5I_INVALID_HID; + named_dt_t *dt = *named_dt_head_p; /* Stack pointer */ + named_dt_t *dt_ret = NULL; /* Datatype to return */ + H5O_info2_t oinfo; /* Object info of input dtype */ + int token_cmp; + hid_t ret_value = H5I_INVALID_HID; if (H5Oget_info3(type_in, &oinfo, H5O_INFO_BASIC) < 0) H5TOOLS_GOTO_ERROR(H5I_INVALID_HID, "H5Oget_info failed"); @@ -256,7 +257,7 @@ copy_named_datatype(hid_t type_in, hid_t fidout, named_dt_t **named_dt_head_p, t /* Push onto the stack */ if (NULL == (dt = (named_dt_t *)HDmalloc(sizeof(named_dt_t)))) H5TOOLS_GOTO_ERROR(H5I_INVALID_HID, "buffer allocation failed failed"); - dt->next = *named_dt_head_p; + dt->next = *named_dt_head_p; *named_dt_head_p = dt; /* Update the token/address and id */ @@ -269,8 +270,8 @@ copy_named_datatype(hid_t type_in, hid_t fidout, named_dt_t **named_dt_head_p, t if (!token_cmp) dt_ret = dt; } /* end if named datatype */ - } /* end for each object in traversal table */ - } /* end else (create the stack) */ + } /* end for each object in traversal table */ + } /* end else (create the stack) */ /* Handle the case that the requested datatype was not found. This is * possible if the datatype was committed anonymously in the input file. @@ -279,7 +280,7 @@ copy_named_datatype(hid_t type_in, hid_t fidout, named_dt_t **named_dt_head_p, t /* Push the new datatype onto the stack */ if (NULL == (dt_ret = (named_dt_t *)HDmalloc(sizeof(named_dt_t)))) H5TOOLS_GOTO_ERROR(H5I_INVALID_HID, "buffer allocation failed failed"); - dt_ret->next = *named_dt_head_p; + dt_ret->next = *named_dt_head_p; *named_dt_head_p = dt_ret; /* Update the token/address and id */ @@ -323,8 +324,8 @@ done: int named_datatype_free(named_dt_t **named_dt_head_p, int ignore_err) { - named_dt_t *dt = *named_dt_head_p; - int ret_value = -1; + named_dt_t *dt = *named_dt_head_p; + int ret_value = -1; while (dt) { /* Pop the datatype off the stack and free it */ @@ -355,24 +356,24 @@ done: int copy_attr(hid_t loc_in, hid_t loc_out, named_dt_t **named_dt_head_p, trav_table_t *travt, pack_opt_t *options) { - hid_t attr_id = H5I_INVALID_HID; /* attr ID */ + hid_t attr_id = H5I_INVALID_HID; /* attr ID */ hid_t attr_out = H5I_INVALID_HID; /* attr ID */ hid_t space_id = H5I_INVALID_HID; /* space ID */ hid_t ftype_id = H5I_INVALID_HID; /* file type ID */ hid_t wtype_id = H5I_INVALID_HID; /* read/write type ID */ - size_t msize; /* size of type */ - void *buf = NULL; /* data buffer */ - hsize_t nelmts; /* number of elements in dataset */ - int rank; /* rank of dataset */ - htri_t is_named; /* Whether the datatype is named */ - hsize_t dims[H5S_MAX_RANK];/* dimensions of dataset */ + size_t msize; /* size of type */ + void * buf = NULL; /* data buffer */ + hsize_t nelmts; /* number of elements in dataset */ + int rank; /* rank of dataset */ + htri_t is_named; /* Whether the datatype is named */ + hsize_t dims[H5S_MAX_RANK]; /* dimensions of dataset */ char name[255]; - H5O_info2_t oinfo; /* object info */ + H5O_info2_t oinfo; /* object info */ int j; unsigned u; - hbool_t is_ref = 0; + hbool_t is_ref = 0; H5T_class_t type_class = -1; - int ret_value = 0; + int ret_value = 0; if (H5Oget_info3(loc_in, &oinfo, H5O_INFO_NUM_ATTRS) < 0) H5TOOLS_GOTO_ERROR((-1), "H5Oget_info failed"); @@ -381,12 +382,13 @@ copy_attr(hid_t loc_in, hid_t loc_out, named_dt_t **named_dt_head_p, trav_table_ * copy all attributes *------------------------------------------------------------------------- */ - for (u = 0; u < (unsigned) oinfo.num_attrs; u++) { + for (u = 0; u < (unsigned)oinfo.num_attrs; u++) { /* open attribute */ - if ((attr_id = H5Aopen_by_idx(loc_in, ".", H5_INDEX_CRT_ORDER, H5_ITER_INC, (hsize_t) u, H5P_DEFAULT, H5P_DEFAULT)) < 0) + if ((attr_id = H5Aopen_by_idx(loc_in, ".", H5_INDEX_CRT_ORDER, H5_ITER_INC, (hsize_t)u, H5P_DEFAULT, + H5P_DEFAULT)) < 0) H5TOOLS_GOTO_ERROR((-1), "H5Aopen_by_idx failed"); - if (H5Aget_name(attr_id, (size_t) 255, name) < 0) + if (H5Aget_name(attr_id, (size_t)255, name) < 0) H5TOOLS_GOTO_ERROR((-1), "H5Pclose failed"); /* get the file datatype */ @@ -442,12 +444,12 @@ copy_attr(hid_t loc_in, hid_t loc_out, named_dt_t **named_dt_head_p, trav_table_ *--------------------------------------------------------------------- */ type_class = H5Tget_class(wtype_id); - is_ref = (type_class == H5T_REFERENCE); + is_ref = (type_class == H5T_REFERENCE); if (type_class == H5T_VLEN || type_class == H5T_ARRAY) { hid_t base_type = H5I_INVALID_HID; base_type = H5Tget_super(ftype_id); - is_ref = (is_ref || (H5Tget_class(base_type) == H5T_REFERENCE)); + is_ref = (is_ref || (H5Tget_class(base_type) == H5T_REFERENCE)); if (H5Tclose(base_type) < 0) H5TOOLS_ERROR((-1), "H5Tclose base_type failed"); } /* end if type_class is variable length or array */ @@ -456,7 +458,7 @@ copy_attr(hid_t loc_in, hid_t loc_out, named_dt_t **named_dt_head_p, trav_table_ int nmembers = H5Tget_nmembers(wtype_id); for (j = 0; j < nmembers; j++) { - hid_t mtid = H5Tget_member_type(wtype_id, (unsigned)j); + hid_t mtid = H5Tget_member_type(wtype_id, (unsigned)j); H5T_class_t mtclass = H5Tget_class(mtid); if (H5Tclose(mtid) < 0) H5TOOLS_ERROR((-1), "H5Tclose mtid failed"); @@ -466,7 +468,7 @@ copy_attr(hid_t loc_in, hid_t loc_out, named_dt_t **named_dt_head_p, trav_table_ break; } } /* end for each member */ - } /* end if type_class is H5T_COMPOUND */ + } /* end if type_class is H5T_COMPOUND */ if (!is_ref) { /*----------------------------------------------------------------- @@ -525,7 +527,8 @@ copy_attr(hid_t loc_in, hid_t loc_out, named_dt_t **named_dt_head_p, trav_table_ } /* for u (each attribute) */ done: - H5E_BEGIN_TRY { + H5E_BEGIN_TRY + { if (buf) { /* Check if we have VL data and string in the attribute's * datatype that must be reclaimed @@ -542,7 +545,8 @@ done: H5Tclose(wtype_id); H5Tclose(ftype_id); H5Aclose(attr_id); - } H5E_END_TRY; + } + H5E_END_TRY; return ret_value; } /* end copy_attr() */ @@ -571,31 +575,31 @@ check_options(pack_opt_t *options) if (options->all_layout == 1) { HDprintf("All objects to modify layout are...\n"); switch (options->layout_g) { - case H5D_COMPACT: - strcpy(slayout, "compact"); - break; - case H5D_CONTIGUOUS: - strcpy(slayout, "contiguous"); - break; - case H5D_CHUNKED: - strcpy(slayout, "chunked"); - break; - case H5D_VIRTUAL: - strcpy(slayout, "virtual"); - break; - case H5D_LAYOUT_ERROR: - case H5D_NLAYOUTS: - H5TOOLS_GOTO_ERROR((-1), "invalid layout"); - break; - default: - strcpy(slayout, "invalid layout\n"); - H5TOOLS_GOTO_DONE((-1)); + case H5D_COMPACT: + strcpy(slayout, "compact"); + break; + case H5D_CONTIGUOUS: + strcpy(slayout, "contiguous"); + break; + case H5D_CHUNKED: + strcpy(slayout, "chunked"); + break; + case H5D_VIRTUAL: + strcpy(slayout, "virtual"); + break; + case H5D_LAYOUT_ERROR: + case H5D_NLAYOUTS: + H5TOOLS_GOTO_ERROR((-1), "invalid layout"); + break; + default: + strcpy(slayout, "invalid layout\n"); + H5TOOLS_GOTO_DONE((-1)); } HDprintf(" Apply %s layout to all", slayout); if (H5D_CHUNKED == options->layout_g) { HDprintf("with dimension [ "); for (j = 0; j < options->chunk_g.rank; j++) - HDprintf("%d ", (int) options->chunk_g.chunk_lengths[j]); + HDprintf("%d ", (int)options->chunk_g.chunk_lengths[j]); HDprintf("]"); } HDprintf("\n"); @@ -605,13 +609,13 @@ check_options(pack_opt_t *options) } /* end if verbose */ for (i = 0; i < options->op_tbl->nelems; i++) { - char* name = options->op_tbl->objs[i].path; + char *name = options->op_tbl->objs[i].path; if (options->op_tbl->objs[i].chunk.rank > 0) { if (options->verbose) { HDprintf(" <%s> with chunk size ", name); for (k = 0; k < options->op_tbl->objs[i].chunk.rank; k++) - HDprintf("%d ", (int) options->op_tbl->objs[i].chunk.chunk_lengths[k]); + HDprintf("%d ", (int)options->op_tbl->objs[i].chunk.chunk_lengths[k]); HDprintf("\n"); } has_ck = 1; @@ -641,36 +645,38 @@ check_options(pack_opt_t *options) continue; } switch (filtn) { - case H5Z_FILTER_NONE: - HDprintf(" Uncompress all\n"); - break; - case H5Z_FILTER_SHUFFLE: - case H5Z_FILTER_FLETCHER32: - HDprintf(" All with %s\n", get_sfilter(filtn)); - break; - case H5Z_FILTER_SZIP: - case H5Z_FILTER_DEFLATE: - HDprintf(" All with %s, parameter %d\n", get_sfilter(filtn), options->filter_g[k].cd_values[0]); - break; - default: - HDprintf(" User Defined %d\n", filtn); - break; + case H5Z_FILTER_NONE: + HDprintf(" Uncompress all\n"); + break; + case H5Z_FILTER_SHUFFLE: + case H5Z_FILTER_FLETCHER32: + HDprintf(" All with %s\n", get_sfilter(filtn)); + break; + case H5Z_FILTER_SZIP: + case H5Z_FILTER_DEFLATE: + HDprintf(" All with %s, parameter %d\n", get_sfilter(filtn), + options->filter_g[k].cd_values[0]); + break; + default: + HDprintf(" User Defined %d\n", filtn); + break; } /* end switch */ - } /* end for each filter */ - } /* end if options->all_filter == 1 (TODO: meaning) */ + } /* end for each filter */ + } /* end if options->all_filter == 1 (TODO: meaning) */ else HDprintf("No all objects to apply filter\n"); } /* end if verbose */ for (i = 0; i < options->op_tbl->nelems; i++) { pack_info_t pack = options->op_tbl->objs[i]; - char* name = pack.path; + char * name = pack.path; for (j = 0; j < pack.nfilters; j++) { if (options->verbose) { if (pack.filter[j].filtn >= 0) { if (pack.filter[j].filtn > H5Z_FILTER_SCALEOFFSET) { - HDprintf(" <%s> with %s filter %d\n", name, get_sfilter(pack.filter[j].filtn), pack.filter[j].filtn); + HDprintf(" <%s> with %s filter %d\n", name, get_sfilter(pack.filter[j].filtn), + pack.filter[j].filtn); } else { HDprintf(" <%s> with %s filter\n", name, get_sfilter(pack.filter[j].filtn)); @@ -679,7 +685,7 @@ check_options(pack_opt_t *options) } has_cp = 1; } /* end for each filter */ - } /* end for each object in options table */ + } /* end for each object in options table */ if (options->all_filter == 1 && has_cp) H5TOOLS_GOTO_ERROR((-1), "invalid compression input: 'all' option is present with other objects"); @@ -705,7 +711,8 @@ check_options(pack_opt_t *options) */ if (options->ublock_filename != NULL && options->ublock_size == 0) { if (options->verbose) { - HDprintf("Warning: user block size missing for file %s. Assigning a default size of 1024...\n", options->ublock_filename); + HDprintf("Warning: user block size missing for file %s. Assigning a default size of 1024...\n", + options->ublock_filename); options->ublock_size = 1024; } } @@ -735,14 +742,14 @@ done: *------------------------------------------------------------------------- */ static int -check_objects(const char* fname, pack_opt_t *options) +check_objects(const char *fname, pack_opt_t *options) { hid_t fid = H5I_INVALID_HID; hid_t did = H5I_INVALID_HID; hid_t sid = H5I_INVALID_HID; unsigned int i; int ifil; - trav_table_t *travt = NULL; + trav_table_t *travt = NULL; int ret_value = 0; /* nothing to do */ @@ -754,7 +761,7 @@ check_objects(const char* fname, pack_opt_t *options) *------------------------------------------------------------------------- */ if ((fid = h5tools_fopen(fname, H5F_ACC_RDONLY, options->fin_fapl, - (options->fin_fapl == H5P_DEFAULT) ? FALSE : TRUE, NULL, 0)) < 0) + (options->fin_fapl == H5P_DEFAULT) ? FALSE : TRUE, NULL, 0)) < 0) H5TOOLS_GOTO_ERROR((-1), "h5tools_fopen failed <%s>: %s", fname, H5FOPENERROR); /*------------------------------------------------------------------------- @@ -780,8 +787,8 @@ check_objects(const char* fname, pack_opt_t *options) HDprintf("Opening file. Searching %zu objects to modify ...\n", travt->nobjs); for (i = 0; i < options->op_tbl->nelems; i++) { - pack_info_t obj = options->op_tbl->objs[i]; - char* name = obj.path; + pack_info_t obj = options->op_tbl->objs[i]; + char * name = obj.path; if (options->verbose) HDprintf(" <%s>", name); @@ -789,7 +796,7 @@ check_objects(const char* fname, pack_opt_t *options) /* the input object names are present in the file and are valid */ if (h5trav_getindext(name, travt) < 0) H5TOOLS_GOTO_ERROR((-1), "%s Could not find <%s> in file <%s>. Exiting...\n", - (options->verbose ? "\n" : ""), name, fname); + (options->verbose ? "\n" : ""), name, fname); if (options->verbose) HDprintf("...Found\n"); @@ -798,14 +805,13 @@ check_objects(const char* fname, pack_opt_t *options) H5TOOLS_GOTO_ERROR((-1), "invalid filter"); /* check for extra filter conditions */ switch (obj.filter[ifil].filtn) { - /* chunk size must be smaller than pixels per block */ - case H5Z_FILTER_SZIP: - { - int j; - hsize_t csize = 1; - unsigned ppb = obj.filter[ifil].cd_values[0]; - hsize_t dims[H5S_MAX_RANK]; - int rank; + /* chunk size must be smaller than pixels per block */ + case H5Z_FILTER_SZIP: { + int j; + hsize_t csize = 1; + unsigned ppb = obj.filter[ifil].cd_values[0]; + hsize_t dims[H5S_MAX_RANK]; + int rank; if (obj.chunk.rank > 0) { rank = obj.chunk.rank; @@ -836,18 +842,20 @@ check_objects(const char* fname, pack_opt_t *options) } } /* end case SZIP */ break; - default: - break; + default: + break; } /* end switch */ - } /* for ifil (each user-defined filter) */ - } /* for i (each object in options traversal table) */ + } /* for ifil (each user-defined filter) */ + } /* for i (each object in options traversal table) */ done: - H5E_BEGIN_TRY { + H5E_BEGIN_TRY + { H5Sclose(sid); H5Dclose(did); H5Fclose(fid); - } H5E_END_TRY; + } + H5E_END_TRY; if (travt) trav_table_free(travt); return ret_value; @@ -901,4 +909,3 @@ get_sfilter(H5Z_filter_t filtn) else return "UD"; } /* end get_sfilter() */ - diff --git a/tools/src/h5repack/h5repack.h b/tools/src/h5repack/h5repack.h index b124fdb..bcab1be 100644 --- a/tools/src/h5repack/h5repack.h +++ b/tools/src/h5repack/h5repack.h @@ -11,7 +11,6 @@ * help@hdfgroup.org. * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ - #ifndef H5REPACK_H__ #define H5REPACK_H__ @@ -19,21 +18,20 @@ #include "hdf5.h" #include "h5trav.h" -#define H5FOPENERROR "unable to open file" -#define PFORMAT "%-7s %-7s %-7s\n" /* chunk info, compression info, name*/ -#define PFORMAT1 "%-7s %-7s %-7s" /* chunk info, compression info, name*/ -#define MAX_NC_NAME 256 /* max length of a name */ -#define MAX_VAR_DIMS 32 /* max per variable dimensions */ -#define FORMAT_OBJ " %-27s %s\n" /* obj type, name */ -#define FORMAT_OBJ_ATTR " %-27s %s\n" /* obj type, name */ -#define MAX_COMPACT_DSIZE 64512 /* max data size for compact layout. -1k for header size */ +#define H5FOPENERROR "unable to open file" +#define PFORMAT "%-7s %-7s %-7s\n" /* chunk info, compression info, name*/ +#define PFORMAT1 "%-7s %-7s %-7s" /* chunk info, compression info, name*/ +#define MAX_NC_NAME 256 /* max length of a name */ +#define MAX_VAR_DIMS 32 /* max per variable dimensions */ +#define FORMAT_OBJ " %-27s %s\n" /* obj type, name */ +#define FORMAT_OBJ_ATTR " %-27s %s\n" /* obj type, name */ +#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_STRATEGY_DEF H5F_FSPACE_STRATEGY_FSM_AGGR -#define FS_PERSIST_DEF FALSE -#define FS_THRESHOLD_DEF 1 - +#define FS_PAGESIZE_DEF 4096 +#define FS_STRATEGY_DEF H5F_FSPACE_STRATEGY_FSM_AGGR +#define FS_PERSIST_DEF FALSE +#define FS_THRESHOLD_DEF 1 /*------------------------------------------------------------------------- * data structures for command line options @@ -42,7 +40,7 @@ /* a list of names */ typedef struct { - char obj[MAX_NC_NAME]; + char obj[MAX_NC_NAME]; } obj_list_t; /* @@ -60,16 +58,16 @@ 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, @@ -78,22 +76,21 @@ 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; - /*------------------------------------------------------------------------- * command line options *------------------------------------------------------------------------- @@ -101,43 +98,42 @@ 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 */ - hbool_t merge; /* Merge external file. */ - hbool_t prune; /* Don't follow external file. */ - 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 */ - H5F_libver_t low_bound; /* The file's low bound as in H5Fset_libver_bounds() */ - H5F_libver_t high_bound; /* The file's high bound as in H5Fset_libver_bounds() */ - hid_t fin_fapl; /* FAPL to use for opening the input file */ - hid_t fout_fapl; /* FAPL to use for opening/creating the output file */ - 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 */ + hbool_t merge; /* Merge external file. */ + hbool_t prune; /* Don't follow external file. */ + 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 */ + H5F_libver_t low_bound; /* The file's low bound as in H5Fset_libver_bounds() */ + H5F_libver_t high_bound; /* The file's high bound as in H5Fset_libver_bounds() */ + hid_t fin_fapl; /* FAPL to use for opening the input file */ + hid_t fout_fapl; /* FAPL to use for opening/creating the output file */ + 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; - typedef struct named_dt_t { - H5O_token_t obj_token; /* Object token for the named dtype in the in file */ - hid_t id_out; /* Open identifier for the dtype in the out file */ - struct named_dt_t *next; /* Next dtype */ + H5O_token_t obj_token; /* Object token for the named dtype in the in file */ + hid_t id_out; /* Open identifier for the dtype in the out file */ + struct named_dt_t *next; /* Next dtype */ } named_dt_t; /*------------------------------------------------------------------------- @@ -149,9 +145,9 @@ typedef struct named_dt_t { extern "C" { #endif -int h5repack(const char* infile, const char* outfile, pack_opt_t *options); -int h5repack_addfilter(const char* str, pack_opt_t *options); -int h5repack_addlayout(const char* str, pack_opt_t *options); +int h5repack(const char *infile, const char *outfile, pack_opt_t *options); +int h5repack_addfilter(const char *str, pack_opt_t *options); +int h5repack_addlayout(const char *str, pack_opt_t *options); int h5repack_init(pack_opt_t *options, int verbose, hbool_t latest); int h5repack_end(pack_opt_t *options); int h5repack_verify(const char *in_fname, const char *out_fname, pack_opt_t *options); @@ -164,36 +160,29 @@ int h5repack_cmp_pl(const char *fname1, hid_t fname1_fapl, const char *fname2, h * However copy_attr() may be obsoleted when H5Acopy is available and put back * others to static in h5repack_copy.c. */ -hid_t copy_named_datatype(hid_t type_in, hid_t fidout, named_dt_t **named_dt_head_p, trav_table_t *travt, pack_opt_t *options); -int named_datatype_free(named_dt_t **named_dt_head_p, int ignore_err); -int copy_attr(hid_t loc_in, hid_t loc_out, named_dt_t **named_dt_head_p, - trav_table_t *travt, pack_opt_t *options); +hid_t copy_named_datatype(hid_t type_in, hid_t fidout, named_dt_t **named_dt_head_p, trav_table_t *travt, + pack_opt_t *options); +int named_datatype_free(named_dt_t **named_dt_head_p, int ignore_err); +int copy_attr(hid_t loc_in, hid_t loc_out, named_dt_t **named_dt_head_p, trav_table_t *travt, + pack_opt_t *options); #ifdef __cplusplus } #endif - - /*------------------------------------------------------------------------- * private functions *------------------------------------------------------------------------- */ - /*------------------------------------------------------------------------- * copy module *------------------------------------------------------------------------- */ -int copy_objects (const char* fnamein, - const char* fnameout, - pack_opt_t *options); +int copy_objects(const char *fnamein, const char *fnameout, pack_opt_t *options); -int do_copy_refobjs(hid_t fidin, - hid_t fidout, - trav_table_t *travt, - pack_opt_t *options); +int do_copy_refobjs(hid_t fidin, hid_t fidout, trav_table_t *travt, pack_opt_t *options); /*------------------------------------------------------------------------- * filters and verify module @@ -201,56 +190,38 @@ int do_copy_refobjs(hid_t fidin, */ void init_packobject(pack_info_t *obj); - /*------------------------------------------------------------------------- * filters and copy module *------------------------------------------------------------------------- */ -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 */ +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 * has_filter); /* (OUT) object NAME has a filter */ /*------------------------------------------------------------------------- * 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 *------------------------------------------------------------------------- */ -obj_list_t* parse_filter(const char *str, - unsigned *n_objs, - filter_info_t *filt, - pack_opt_t *options, +obj_list_t *parse_filter(const char *str, unsigned *n_objs, filter_info_t *filt, pack_opt_t *options, int *is_glb); -obj_list_t* parse_layout(const char *str, - unsigned *n_objs, - pack_info_t *pack, /* info about object */ +obj_list_t *parse_layout(const char *str, unsigned *n_objs, pack_info_t *pack, /* info about object */ pack_opt_t *options); - - - -#endif /* H5REPACK_H__ */ - +#endif /* H5REPACK_H__ */ diff --git a/tools/src/h5repack/h5repack_copy.c b/tools/src/h5repack/h5repack_copy.c index 8f3496f..d2b0097 100644 --- a/tools/src/h5repack/h5repack_copy.c +++ b/tools/src/h5repack/h5repack_copy.c @@ -31,24 +31,21 @@ */ /* size of buffer/# of bytes to xfer at a time when copying userblock */ -#define USERBLOCK_XFER_SIZE 512 +#define USERBLOCK_XFER_SIZE 512 /*------------------------------------------------------------------------- * local functions *------------------------------------------------------------------------- */ -static int get_hyperslab(hid_t dcpl_id, int rank_dset, hsize_t dims_dset[], - size_t size_datum, hsize_t dims_hslab[], hsize_t * hslab_nbytes_p); +static int get_hyperslab(hid_t dcpl_id, int rank_dset, hsize_t dims_dset[], size_t size_datum, + hsize_t dims_hslab[], hsize_t *hslab_nbytes_p); static void print_dataset_info(hid_t dcpl_id, char *objname, double per, int pr); -static int do_copy_objects(hid_t fidin, hid_t fidout, trav_table_t *travt, - pack_opt_t *options); -static int copy_user_block(const char *infile, const char *outfile, - hsize_t size); -#if defined (H5REPACK_DEBUG_USER_BLOCK) +static int do_copy_objects(hid_t fidin, hid_t fidout, trav_table_t *travt, pack_opt_t *options); +static int copy_user_block(const char *infile, const char *outfile, hsize_t size); +#if defined(H5REPACK_DEBUG_USER_BLOCK) static void print_user_block(const char *filename, hid_t fid); #endif - /*------------------------------------------------------------------------- * Function: copy_objects * @@ -59,33 +56,33 @@ static void print_user_block(const char *filename, hid_t fid); *------------------------------------------------------------------------- */ int -copy_objects(const char* fnamein, const char* fnameout, pack_opt_t *options) +copy_objects(const char *fnamein, const char *fnameout, pack_opt_t *options) { - hid_t fidin = H5I_INVALID_HID; - hid_t fidout = H5I_INVALID_HID; - hid_t fcpl_in = H5I_INVALID_HID; /* file creation property list ID for input file */ - hid_t grp_in = H5I_INVALID_HID; /* group ID */ - hid_t gcpl_in = H5I_INVALID_HID; /* group creation property list */ - hid_t fcpl = H5P_DEFAULT; /* file creation property list ID */ - trav_table_t *travt = NULL; - hsize_t ub_size = 0; /* size of user block */ - H5F_fspace_strategy_t set_strategy; /* Strategy to be set in outupt file */ - hbool_t set_persist; /* Persist free-space status to be set in output file */ - hsize_t set_threshold; /* Free-space section threshold to be set in output file */ - hsize_t set_pagesize; /* File space page size to be set in output file */ - H5F_fspace_strategy_t in_strategy; /* Strategy from input file */ - hbool_t in_persist; /* Persist free-space status from input file */ - hsize_t in_threshold; /* Free-space section threshold from input file */ - hsize_t in_pagesize; /* File space page size from input file */ - unsigned crt_order_flags; /* group creation order flag */ - int ret_value = 0; + hid_t fidin = H5I_INVALID_HID; + hid_t fidout = H5I_INVALID_HID; + hid_t fcpl_in = H5I_INVALID_HID; /* file creation property list ID for input file */ + hid_t grp_in = H5I_INVALID_HID; /* group ID */ + hid_t gcpl_in = H5I_INVALID_HID; /* group creation property list */ + hid_t fcpl = H5P_DEFAULT; /* file creation property list ID */ + trav_table_t * travt = NULL; + hsize_t ub_size = 0; /* size of user block */ + H5F_fspace_strategy_t set_strategy; /* Strategy to be set in outupt file */ + hbool_t set_persist; /* Persist free-space status to be set in output file */ + hsize_t set_threshold; /* Free-space section threshold to be set in output file */ + hsize_t set_pagesize; /* File space page size to be set in output file */ + H5F_fspace_strategy_t in_strategy; /* Strategy from input file */ + hbool_t in_persist; /* Persist free-space status from input file */ + hsize_t in_threshold; /* Free-space section threshold from input file */ + hsize_t in_pagesize; /* File space page size from input file */ + unsigned crt_order_flags; /* group creation order flag */ + int ret_value = 0; /*------------------------------------------------------------------------- * open input file *------------------------------------------------------------------------- */ if ((fidin = h5tools_fopen(fnamein, H5F_ACC_RDONLY, options->fin_fapl, - (options->fin_fapl == H5P_DEFAULT) ? FALSE : TRUE, NULL, (size_t) 0)) < 0) + (options->fin_fapl == H5P_DEFAULT) ? FALSE : TRUE, NULL, (size_t)0)) < 0) H5TOOLS_GOTO_ERROR((-1), "h5tools_fopen failed <%s>: %s", fnamein, H5FOPENERROR); /* get user block size and file space strategy/persist/threshold */ @@ -97,11 +94,11 @@ copy_objects(const char* fnamein, const char* fnameout, pack_opt_t *options) H5TOOLS_GOTO_ERROR((-1), "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) + if (H5Pget_file_space_strategy(fcpl_in, &in_strategy, &in_persist, &in_threshold) < 0) H5TOOLS_GOTO_ERROR((-1), "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) + if (H5Pget_file_space_page_size(fcpl_in, &in_pagesize) < 0) H5TOOLS_GOTO_ERROR((-1), "H5Pget_file_space_page_size failed to retrieve file space threshold"); /* open root group */ @@ -120,7 +117,7 @@ copy_objects(const char* fnamein, const char* fnameout, pack_opt_t *options) H5TOOLS_GOTO_ERROR((-1), "H5Pclose failed to close property list"); } - if(options->latest) + if (options->latest) options->low_bound = options->high_bound = H5F_LIBVER_LATEST; /* Create file access property list */ @@ -129,7 +126,7 @@ copy_objects(const char* fnamein, const char* fnameout, pack_opt_t *options) H5TOOLS_GOTO_ERROR((-1), "H5Pcreate failed to create file access property list"); /* It can be default, latest or other settings by users */ - if(H5Pset_libver_bounds(options->fout_fapl, options->low_bound, options->high_bound) < 0) + if (H5Pset_libver_bounds(options->fout_fapl, options->low_bound, options->high_bound) < 0) H5TOOLS_GOTO_ERROR((-1), "H5Pset_libver_bounds failed to set format version bounds"); /* Check if we need to create a non-default file creation property list */ @@ -147,8 +144,11 @@ 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) - H5TOOLS_GOTO_ERROR((-1), "H5Pset_link_phase_change failed to adjust group creation parameters for root group"); + if (H5Pset_link_phase_change(fcpl, (unsigned)options->grp_compact, + (unsigned)options->grp_indexed) < 0) + H5TOOLS_GOTO_ERROR( + (-1), + "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) { @@ -176,26 +176,28 @@ copy_objects(const char* fnamein, const char* fnameout, pack_opt_t *options) default: break; } /* end switch */ - min_mesg_sizes[nindex] = (unsigned) options->msg_size[i]; + min_mesg_sizes[nindex] = (unsigned)options->msg_size[i]; nindex++; } /* end if */ - } /* end for */ + } /* end for */ if (nindex > 0) { if (H5Pset_shared_mesg_nindexes(fcpl, nindex) < 0) - H5TOOLS_GOTO_ERROR((-1), "H5Pset_shared_mesg_nindexes failed to set the number of shared object header message indexes"); + H5TOOLS_GOTO_ERROR((-1), "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) - H5TOOLS_GOTO_ERROR((-1), "H5Pset_shared_mesg_index failed to configure the specified shared object header message index"); + H5TOOLS_GOTO_ERROR((-1), "H5Pset_shared_mesg_index failed to configure the specified " + "shared object header message index"); } /* if (nindex>0) */ } /* end if */ - } /* end if */ -#if defined (H5REPACK_DEBUG_USER_BLOCK) -print_user_block(fnamein, fidin); + } /* end if */ +#if defined(H5REPACK_DEBUG_USER_BLOCK) + print_user_block(fnamein, fidin); #endif /*------------------------------------------------------------------------- @@ -255,41 +257,41 @@ print_user_block(fnamein, fidin); if ((fcpl = H5Pcreate(H5P_FILE_CREATE)) < 0) H5TOOLS_GOTO_ERROR((-1), "H5Pcreate failed to create a file creation property list"); - if(H5Pset_link_creation_order(fcpl, crt_order_flags ) < 0) + if (H5Pset_link_creation_order(fcpl, crt_order_flags) < 0) H5TOOLS_GOTO_ERROR((-1), "H5Pset_link_creation_order failed"); /* Set file space info to those from input file */ - set_strategy = in_strategy; - set_persist = in_persist; + set_strategy = in_strategy; + set_persist = in_persist; set_threshold = in_threshold; - set_pagesize = in_pagesize; + set_pagesize = in_pagesize; - if(options->fs_strategy == (H5F_fspace_strategy_t)-1) /* A default strategy is specified by user */ + if (options->fs_strategy == (H5F_fspace_strategy_t)-1) /* A default strategy is specified by user */ set_strategy = FS_STRATEGY_DEF; - else if(options->fs_strategy != (H5F_fspace_strategy_t)0) /* Set strategy as specified by user */ + else if (options->fs_strategy != (H5F_fspace_strategy_t)0) /* Set strategy as specified by user */ set_strategy = options->fs_strategy; - if(options->fs_persist == -1) /* A default "persist" is specified by user */ + if (options->fs_persist == -1) /* A default "persist" is specified by user */ set_persist = FS_PERSIST_DEF; - else if(options->fs_persist != 0) /* Set "persist" as specified by user */ + else if (options->fs_persist != 0) /* Set "persist" as specified by user */ set_persist = (hbool_t)options->fs_persist; - if(options->fs_threshold == -1) /* A "0" threshold is specified by user */ + if (options->fs_threshold == -1) /* A "0" threshold is specified by user */ set_threshold = (hsize_t)0; - else if(options->fs_threshold != 0) /* Set threshold as specified by user */ + else if (options->fs_threshold != 0) /* Set threshold as specified by user */ 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) + if (H5Pset_file_space_strategy(fcpl, set_strategy, set_persist, set_threshold) < 0) H5TOOLS_GOTO_ERROR((-1), "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 */ + if (options->fs_pagesize == -1) /* A "0" file space page size is specified by user */ set_pagesize = (hsize_t)0; - else if(options->fs_pagesize != 0) /* Set file space page size as specified by user */ + else if (options->fs_pagesize != 0) /* Set file space page size as specified by user */ 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) + 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) H5TOOLS_GOTO_ERROR((-1), "H5Pset_file_space_page_size failed to set file space page size"); /*------------------------------------------------------------------------- @@ -326,19 +328,21 @@ print_user_block(fnamein, fidin); H5TOOLS_GOTO_ERROR((-1), "h5trav_gettable failed"); /*------------------------------------------------------------------------- - * do the copy - *------------------------------------------------------------------------- - */ + * do the copy + *------------------------------------------------------------------------- + */ if (do_copy_objects(fidin, fidout, travt, options) < 0) - H5TOOLS_GOTO_ERROR((-1), "do_copy_objects from <%s> could not copy data to <%s>", fnamein, fnameout); + H5TOOLS_GOTO_ERROR((-1), "do_copy_objects from <%s> could not copy data to <%s>", fnamein, + fnameout); /*------------------------------------------------------------------------- - * do the copy of referenced objects - * and create hard links - *------------------------------------------------------------------------- - */ + * do the copy of referenced objects + * and create hard links + *------------------------------------------------------------------------- + */ if (do_copy_refobjs(fidin, fidout, travt, options) < 0) - H5TOOLS_GOTO_ERROR((-1), "do_copy_refobjs from <%s> could not copy data to <%s>", fnamein, fnameout); + H5TOOLS_GOTO_ERROR((-1), "do_copy_refobjs from <%s> could not copy data to <%s>", fnamein, + fnameout); } /*------------------------------------------------------------------------- @@ -351,7 +355,8 @@ print_user_block(fnamein, fidin); H5TOOLS_GOTO_ERROR((-1), "Could not copy user block. Exiting..."); done: - H5E_BEGIN_TRY { + H5E_BEGIN_TRY + { H5Pclose(fcpl_in); H5Pclose(gcpl_in); H5Pclose(fcpl); @@ -360,7 +365,8 @@ done: H5Fclose(fidout); H5Fclose(fidin); H5Fclose(fidout); - } H5E_END_TRY; + } + H5E_END_TRY; if (travt) trav_table_free(travt); @@ -400,20 +406,20 @@ done: *-----------------------------------------*/ int -get_hyperslab(hid_t dcpl_id, int rank_dset, hsize_t dims_dset[], - size_t size_datum, hsize_t dims_hslab[], hsize_t * hslab_nbytes_p) +get_hyperslab(hid_t dcpl_id, int rank_dset, hsize_t dims_dset[], size_t size_datum, hsize_t dims_hslab[], + hsize_t *hslab_nbytes_p) { - int k; + int k; H5D_layout_t dset_layout; - int rank_chunk; - hsize_t dims_chunk[H5S_MAX_RANK]; - hsize_t size_chunk = 1; - hsize_t nchunk_fit; /* number of chunks that fits in hyperslab buffer (H5TOOLS_BUFSIZE) */ - hsize_t ndatum_fit; /* number of dataum that fits in hyperslab buffer (H5TOOLS_BUFSIZE) */ - hsize_t chunk_dims_map[H5S_MAX_RANK]; /* mapped chunk dimentions */ - hsize_t hs_dims_map[H5S_MAX_RANK]; /* mapped hyperslab dimentions */ - hsize_t hslab_nbytes; /* size of hyperslab in byte */ - int ret_value = 0; + int rank_chunk; + hsize_t dims_chunk[H5S_MAX_RANK]; + hsize_t size_chunk = 1; + hsize_t nchunk_fit; /* number of chunks that fits in hyperslab buffer (H5TOOLS_BUFSIZE) */ + hsize_t ndatum_fit; /* number of dataum that fits in hyperslab buffer (H5TOOLS_BUFSIZE) */ + hsize_t chunk_dims_map[H5S_MAX_RANK]; /* mapped chunk dimentions */ + hsize_t hs_dims_map[H5S_MAX_RANK]; /* mapped hyperslab dimentions */ + hsize_t hslab_nbytes; /* size of hyperslab in byte */ + int ret_value = 0; /* init to set as size of a data element */ hslab_nbytes = size_datum; @@ -452,7 +458,7 @@ get_hyperslab(hid_t dcpl_id, int rank_dset, hsize_t dims_dset[], chunk_dims_map[k - 1]++; /* get mapped hyperslab dims */ - hs_dims_map[k - 1] = MIN (nchunk_fit, chunk_dims_map[k-1]); + hs_dims_map[k - 1] = MIN(nchunk_fit, chunk_dims_map[k - 1]); /* prepare next round */ nchunk_fit = nchunk_fit / chunk_dims_map[k - 1]; @@ -461,7 +467,7 @@ get_hyperslab(hid_t dcpl_id, int rank_dset, hsize_t dims_dset[], nchunk_fit = 1; /* get hyperslab dimentions as unmapping to actual size */ - dims_hslab[k - 1] = MIN( (hs_dims_map[k-1] * dims_chunk[k-1]), dims_dset[k-1]); + dims_hslab[k - 1] = MIN((hs_dims_map[k - 1] * dims_chunk[k - 1]), dims_dset[k - 1]); /* calculate total size for the hyperslab */ hslab_nbytes *= dims_hslab[k - 1]; @@ -482,7 +488,7 @@ get_hyperslab(hid_t dcpl_id, int rank_dset, hsize_t dims_dset[], if (ndatum_fit == 0) ndatum_fit = 1; /* get hyperslab dimentions within a chunk boundary */ - dims_hslab[k - 1] = MIN (dims_chunk[k-1], ndatum_fit); + dims_hslab[k - 1] = MIN(dims_chunk[k - 1], ndatum_fit); /* calculate total size for the hyperslab */ hslab_nbytes *= dims_hslab[k - 1]; @@ -578,49 +584,48 @@ done: */ int -do_copy_objects(hid_t fidin, hid_t fidout, trav_table_t *travt, - pack_opt_t *options) /* repack options */ +do_copy_objects(hid_t fidin, hid_t fidout, trav_table_t *travt, pack_opt_t *options) /* repack options */ { - hid_t grp_in = H5I_INVALID_HID; /* group ID */ - hid_t grp_out = H5I_INVALID_HID; /* group ID */ - hid_t dset_in = H5I_INVALID_HID; /* read dataset ID */ - hid_t dset_out = H5I_INVALID_HID; /* write dataset ID */ - hid_t gcpl_in = H5I_INVALID_HID; /* group creation property list */ - hid_t gcpl_out = H5I_INVALID_HID; /* group creation property list */ - hid_t type_in = H5I_INVALID_HID; /* named type ID */ - hid_t type_out = H5I_INVALID_HID; /* named type ID */ - hid_t dcpl_in = H5I_INVALID_HID; /* dataset creation property list ID */ - hid_t dcpl_out = H5I_INVALID_HID; /* dataset creation property list ID */ - hid_t f_space_id = H5I_INVALID_HID; /* file space ID */ - hid_t ftype_id = H5I_INVALID_HID; /* file type ID */ - hid_t wtype_id = H5I_INVALID_HID; /* read/write type ID */ - hid_t ocpl_id = H5I_INVALID_HID; /* property to pass copy options */ - hid_t lcpl_id = H5I_INVALID_HID; /* link creation property list */ - named_dt_t *named_dt_head = NULL; /* Pointer to the stack of named datatypes copied */ - size_t msize; /* size of type */ - hsize_t nelmts; /* number of elements in dataset */ - H5D_space_status_t space_status; /* determines whether space has been allocated for the dataset */ - int rank; /* rank of dataset */ - hsize_t dims[H5S_MAX_RANK];/* dimensions of dataset */ - hsize_t dsize_in; /* input dataset size before filter */ - hsize_t dsize_out; /* output dataset size after filter */ - int apply_s; /* flag for apply filter to small dataset sizes */ - int apply_f; /* flag for apply filter to return error on H5Dcreate */ - void *buf = NULL; /* buffer for raw data */ - void *hslab_buf = NULL; /* hyperslab buffer for raw data */ - int has_filter; /* current object has a filter */ - int req_filter; /* there was a request for a filter */ - int req_obj_layout = 0; /* request layout to current object */ - unsigned crt_order_flags; /* group creation order flag */ + hid_t grp_in = H5I_INVALID_HID; /* group ID */ + hid_t grp_out = H5I_INVALID_HID; /* group ID */ + hid_t dset_in = H5I_INVALID_HID; /* read dataset ID */ + hid_t dset_out = H5I_INVALID_HID; /* write dataset ID */ + hid_t gcpl_in = H5I_INVALID_HID; /* group creation property list */ + hid_t gcpl_out = H5I_INVALID_HID; /* group creation property list */ + hid_t type_in = H5I_INVALID_HID; /* named type ID */ + hid_t type_out = H5I_INVALID_HID; /* named type ID */ + hid_t dcpl_in = H5I_INVALID_HID; /* dataset creation property list ID */ + hid_t dcpl_out = H5I_INVALID_HID; /* dataset creation property list ID */ + hid_t f_space_id = H5I_INVALID_HID; /* file space ID */ + hid_t ftype_id = H5I_INVALID_HID; /* file type ID */ + hid_t wtype_id = H5I_INVALID_HID; /* read/write type ID */ + hid_t ocpl_id = H5I_INVALID_HID; /* property to pass copy options */ + hid_t lcpl_id = H5I_INVALID_HID; /* link creation property list */ + named_dt_t * named_dt_head = NULL; /* Pointer to the stack of named datatypes copied */ + size_t msize; /* size of type */ + hsize_t nelmts; /* number of elements in dataset */ + H5D_space_status_t space_status; /* determines whether space has been allocated for the dataset */ + int rank; /* rank of dataset */ + hsize_t dims[H5S_MAX_RANK]; /* dimensions of dataset */ + hsize_t dsize_in; /* input dataset size before filter */ + hsize_t dsize_out; /* output dataset size after filter */ + int apply_s; /* flag for apply filter to small dataset sizes */ + int apply_f; /* flag for apply filter to return error on H5Dcreate */ + void * buf = NULL; /* buffer for raw data */ + void * hslab_buf = NULL; /* hyperslab buffer for raw data */ + int has_filter; /* current object has a filter */ + int req_filter; /* there was a request for a filter */ + int req_obj_layout = 0; /* request layout to current object */ + unsigned crt_order_flags; /* group creation order flag */ h5tool_link_info_t linkinfo; - unsigned i; - unsigned u; - int ifil; - int is_ref = 0; - htri_t is_named; - hbool_t limit_maxdims; - hsize_t size_dset; - int ret_value = 0; + unsigned i; + unsigned u; + int ifil; + int is_ref = 0; + htri_t is_named; + hbool_t limit_maxdims; + hsize_t size_dset; + int ret_value = 0; /* init linkinfo struct */ HDmemset(&linkinfo, 0, sizeof(h5tool_link_info_t)); @@ -639,662 +644,689 @@ do_copy_objects(hid_t fidin, hid_t fidout, trav_table_t *travt, if (travt->objs) { for (i = 0; i < travt->nobjs; i++) { /* init variables per obj */ - buf = NULL; + buf = NULL; limit_maxdims = FALSE; switch (travt->objs[i].type) { - case H5TRAV_TYPE_UNKNOWN: - break; + case H5TRAV_TYPE_UNKNOWN: + break; - /*------------------------------------------------------------------------- - * H5TRAV_TYPE_GROUP - *------------------------------------------------------------------------- - */ - case H5TRAV_TYPE_GROUP: - if (options->verbose) - HDprintf(FORMAT_OBJ, "group", travt->objs[i].name); + /*------------------------------------------------------------------------- + * H5TRAV_TYPE_GROUP + *------------------------------------------------------------------------- + */ + case H5TRAV_TYPE_GROUP: + if (options->verbose) + HDprintf(FORMAT_OBJ, "group", travt->objs[i].name); - /* open input group */ - if ((grp_in = H5Gopen2(fidin, travt->objs[i].name, H5P_DEFAULT)) < 0) - H5TOOLS_GOTO_ERROR((-1), "H5Gopen2 failed"); + /* open input group */ + if ((grp_in = H5Gopen2(fidin, travt->objs[i].name, H5P_DEFAULT)) < 0) + H5TOOLS_GOTO_ERROR((-1), "H5Gopen2 failed"); - /* get input group creation property list */ - if ((gcpl_in = H5Gget_create_plist(grp_in)) < 0) - H5TOOLS_GOTO_ERROR((-1), "H5Gget_create_plist failed"); + /* get input group creation property list */ + if ((gcpl_in = H5Gget_create_plist(grp_in)) < 0) + H5TOOLS_GOTO_ERROR((-1), "H5Gget_create_plist failed"); - /* query and set the group creation properties */ - if (H5Pget_link_creation_order(gcpl_in, &crt_order_flags) < 0) - H5TOOLS_GOTO_ERROR((-1), "H5Pget_link_creation_order failed"); + /* query and set the group creation properties */ + if (H5Pget_link_creation_order(gcpl_in, &crt_order_flags) < 0) + H5TOOLS_GOTO_ERROR((-1), "H5Pget_link_creation_order failed"); - /* set up group creation property list */ - if ((gcpl_out = H5Pcreate(H5P_GROUP_CREATE)) < 0) - H5TOOLS_GOTO_ERROR((-1), "H5Pcreate failed"); + /* set up group creation property list */ + if ((gcpl_out = H5Pcreate(H5P_GROUP_CREATE)) < 0) + H5TOOLS_GOTO_ERROR((-1), "H5Pcreate failed"); - if (H5Pset_link_creation_order(gcpl_out, crt_order_flags) < 0) - H5TOOLS_GOTO_ERROR((-1), "H5Pset_link_creation_order failed"); + if (H5Pset_link_creation_order(gcpl_out, crt_order_flags) < 0) + H5TOOLS_GOTO_ERROR((-1), "H5Pset_link_creation_order failed"); - /*------------------------------------------------------------------------- - * the root is a special case, we get an ID for the root group - * and copy its attributes using that ID - *------------------------------------------------------------------------- - */ - if (HDstrcmp(travt->objs[i].name, "/") == 0) { - if ((grp_out = H5Gopen2(fidout, "/", H5P_DEFAULT)) < 0) - H5TOOLS_GOTO_ERROR((-1), "H5Gopen2 failed"); - } - else { - if (options->grp_compact > 0 || options->grp_indexed > 0) - if (H5Pset_link_phase_change(gcpl_out, (unsigned) options->grp_compact, (unsigned) options->grp_indexed) < 0) - H5TOOLS_GOTO_ERROR((-1), "H5Pset_link_phase_change failed"); + /*------------------------------------------------------------------------- + * the root is a special case, we get an ID for the root group + * and copy its attributes using that ID + *------------------------------------------------------------------------- + */ + if (HDstrcmp(travt->objs[i].name, "/") == 0) { + if ((grp_out = H5Gopen2(fidout, "/", H5P_DEFAULT)) < 0) + H5TOOLS_GOTO_ERROR((-1), "H5Gopen2 failed"); + } + else { + if (options->grp_compact > 0 || options->grp_indexed > 0) + if (H5Pset_link_phase_change(gcpl_out, (unsigned)options->grp_compact, + (unsigned)options->grp_indexed) < 0) + H5TOOLS_GOTO_ERROR((-1), "H5Pset_link_phase_change failed"); + + if ((grp_out = H5Gcreate2(fidout, travt->objs[i].name, H5P_DEFAULT, gcpl_out, + H5P_DEFAULT)) < 0) + H5TOOLS_GOTO_ERROR((-1), "H5Gcreate2 failed"); + } - if ((grp_out = H5Gcreate2(fidout, travt->objs[i].name, H5P_DEFAULT, gcpl_out, H5P_DEFAULT)) < 0) - H5TOOLS_GOTO_ERROR((-1), "H5Gcreate2 failed"); - } + /*------------------------------------------------------------------------- + * copy attrs + *------------------------------------------------------------------------- + */ + if (copy_attr(grp_in, grp_out, &named_dt_head, travt, options) < 0) + H5TOOLS_GOTO_ERROR((-1), "copy_attr failed"); + + if (H5Pclose(gcpl_out) < 0) + H5TOOLS_GOTO_ERROR((-1), "H5Pclose failed"); + if (H5Pclose(gcpl_in) < 0) + H5TOOLS_GOTO_ERROR((-1), "H5Pclose failed"); + if (H5Gclose(grp_out) < 0) + H5TOOLS_GOTO_ERROR((-1), "H5Gclose failed"); + if (H5Gclose(grp_in) < 0) + H5TOOLS_GOTO_ERROR((-1), "H5Gclose failed"); + + break; /*------------------------------------------------------------------------- - * copy attrs + * H5TRAV_TYPE_DATASET *------------------------------------------------------------------------- */ - if (copy_attr(grp_in, grp_out, &named_dt_head, travt, options) < 0) - H5TOOLS_GOTO_ERROR((-1), "copy_attr failed"); - - if (H5Pclose(gcpl_out) < 0) - H5TOOLS_GOTO_ERROR((-1), "H5Pclose failed"); - if (H5Pclose(gcpl_in) < 0) - H5TOOLS_GOTO_ERROR((-1), "H5Pclose failed"); - if (H5Gclose(grp_out) < 0) - H5TOOLS_GOTO_ERROR((-1), "H5Gclose failed"); - if (H5Gclose(grp_in) < 0) - H5TOOLS_GOTO_ERROR((-1), "H5Gclose failed"); + case H5TRAV_TYPE_DATASET: { + hbool_t use_h5ocopy; + + has_filter = 0; + req_filter = 0; + + /* check if global filters were requested */ + if (options->n_filter_g) + req_filter = 1; + + /* check if filters were requested for individual objects */ + 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 (ifil = 0; ifil < options->op_tbl->objs[ifil].nfilters; ifil++) { + if (options->op_tbl->objs[u].filter[ifil].filtn > 0) + req_filter = 1; + } + } + } - break; + /* check if layout change requested individual object */ + if (options->layout_g != H5D_LAYOUT_ERROR) { + pack_info_t *pckinfo; - /*------------------------------------------------------------------------- - * H5TRAV_TYPE_DATASET - *------------------------------------------------------------------------- - */ - case H5TRAV_TYPE_DATASET: - { - hbool_t use_h5ocopy; - - has_filter = 0; - req_filter = 0; - - /* check if global filters were requested */ - if (options->n_filter_g) - req_filter = 1; - - /* check if filters were requested for individual objects */ - 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 (ifil = 0; ifil < options->op_tbl->objs[ifil].nfilters; ifil++) { - if (options->op_tbl->objs[u].filter[ifil].filtn > 0) - req_filter = 1; - } + /* any dataset is specified */ + if (options->op_tbl->nelems > 0) { + /* check if object exist */ + pckinfo = options_get_object(travt->objs[i].name, options->op_tbl); + if (pckinfo) + req_obj_layout = 1; + } } - } - /* check if layout change requested individual object */ - if (options->layout_g != H5D_LAYOUT_ERROR) { - pack_info_t *pckinfo; + /* early detection of references */ + if ((dset_in = H5Dopen2(fidin, travt->objs[i].name, H5P_DEFAULT)) < 0) + H5TOOLS_GOTO_ERROR((-1), "H5Dopen2 failed"); + if ((ftype_id = H5Dget_type(dset_in)) < 0) + H5TOOLS_GOTO_ERROR((-1), "H5Dget_type failed"); + if (H5T_REFERENCE == H5Tget_class(ftype_id)) + is_ref = 1; - /* any dataset is specified */ - if (options->op_tbl->nelems > 0) { - /* check if object exist */ - pckinfo = options_get_object(travt->objs[i].name, options->op_tbl); - if (pckinfo) - req_obj_layout = 1; - } - } + /* Check if the datatype is committed */ + if ((is_named = H5Tcommitted(ftype_id)) < 0) + H5TOOLS_GOTO_ERROR((-1), "H5Tcommitted failed"); + if (is_named) + if ((wtype_id = + copy_named_datatype(ftype_id, fidout, &named_dt_head, travt, options)) < 0) + H5TOOLS_GOTO_ERROR((-1), "copy_named_datatype failed"); - /* early detection of references */ - if ((dset_in = H5Dopen2(fidin, travt->objs[i].name, H5P_DEFAULT)) < 0) - H5TOOLS_GOTO_ERROR((-1), "H5Dopen2 failed"); - if ((ftype_id = H5Dget_type(dset_in)) < 0) - H5TOOLS_GOTO_ERROR((-1), "H5Dget_type failed"); - if (H5T_REFERENCE == H5Tget_class(ftype_id)) - is_ref = 1; - - /* Check if the datatype is committed */ - if ((is_named = H5Tcommitted(ftype_id)) < 0) - H5TOOLS_GOTO_ERROR((-1), "H5Tcommitted failed"); - if (is_named) - if ((wtype_id = copy_named_datatype(ftype_id, fidout, &named_dt_head, travt, options)) < 0) - H5TOOLS_GOTO_ERROR((-1), "copy_named_datatype failed"); + if (H5Tclose(ftype_id) < 0) + H5TOOLS_GOTO_ERROR((-1), "H5Tclose failed"); + if (H5Dclose(dset_in) < 0) + H5TOOLS_GOTO_ERROR((-1), "H5Dclose failed"); - if (H5Tclose(ftype_id) < 0) - H5TOOLS_GOTO_ERROR((-1), "H5Tclose failed"); - if (H5Dclose(dset_in) < 0) - H5TOOLS_GOTO_ERROR((-1), "H5Dclose failed"); + /*------------------------------------------------------------------------- + * check if we should use H5Ocopy or not + * if there is a request for filters/layout, we read/write the object + * otherwise we do a copy using H5Ocopy + *------------------------------------------------------------------------- + */ + use_h5ocopy = !(options->op_tbl->nelems || options->all_filter == 1 || + options->all_layout == 1 || is_ref || is_named); - /*------------------------------------------------------------------------- - * check if we should use H5Ocopy or not - * if there is a request for filters/layout, we read/write the object - * otherwise we do a copy using H5Ocopy - *------------------------------------------------------------------------- - */ - use_h5ocopy = !(options->op_tbl->nelems || options->all_filter == 1 - || options->all_layout == 1 || is_ref || is_named); + /* + * Check if we are using different source and destination VOL connectors. + * In this case, we currently have to avoid usage of H5Ocopy since it + * doesn't support this. + */ + if (use_h5ocopy && + (options->fin_fapl != H5P_DEFAULT || options->fout_fapl != H5P_DEFAULT)) { + hid_t in_vol_id; + hid_t out_vol_id; + hid_t default_vol_id; - /* - * Check if we are using different source and destination VOL connectors. - * In this case, we currently have to avoid usage of H5Ocopy since it - * doesn't support this. - */ - if (use_h5ocopy && (options->fin_fapl != H5P_DEFAULT || options->fout_fapl != H5P_DEFAULT)) { - hid_t in_vol_id; - hid_t out_vol_id; - hid_t default_vol_id; - - if (H5Pget_vol_id(H5P_FILE_ACCESS_DEFAULT, &default_vol_id) < 0) - H5TOOLS_GOTO_ERROR((-1), "H5Pget_vol_id failed"); - - if (options->fin_fapl == H5P_DEFAULT) - in_vol_id = default_vol_id; - else - if (H5Pget_vol_id(options->fin_fapl, &in_vol_id) < 0) + if (H5Pget_vol_id(H5P_FILE_ACCESS_DEFAULT, &default_vol_id) < 0) H5TOOLS_GOTO_ERROR((-1), "H5Pget_vol_id failed"); - if (options->fout_fapl == H5P_DEFAULT) - out_vol_id = default_vol_id; - else - if (H5Pget_vol_id(options->fout_fapl, &out_vol_id) < 0) + + if (options->fin_fapl == H5P_DEFAULT) + in_vol_id = default_vol_id; + else if (H5Pget_vol_id(options->fin_fapl, &in_vol_id) < 0) + H5TOOLS_GOTO_ERROR((-1), "H5Pget_vol_id failed"); + if (options->fout_fapl == H5P_DEFAULT) + out_vol_id = default_vol_id; + else if (H5Pget_vol_id(options->fout_fapl, &out_vol_id) < 0) H5TOOLS_GOTO_ERROR((-1), "H5Pget_vol_id failed"); - if (in_vol_id != out_vol_id) - use_h5ocopy = FALSE; + if (in_vol_id != out_vol_id) + use_h5ocopy = FALSE; - if (in_vol_id != default_vol_id) - if (H5VLclose(in_vol_id) < 0) - H5TOOLS_GOTO_ERROR((-1), "H5VLclose failed"); - if (out_vol_id != default_vol_id) - if (H5VLclose(out_vol_id) < 0) + if (in_vol_id != default_vol_id) + if (H5VLclose(in_vol_id) < 0) + H5TOOLS_GOTO_ERROR((-1), "H5VLclose failed"); + if (out_vol_id != default_vol_id) + if (H5VLclose(out_vol_id) < 0) + H5TOOLS_GOTO_ERROR((-1), "H5VLclose failed"); + if (H5VLclose(default_vol_id) < 0) H5TOOLS_GOTO_ERROR((-1), "H5VLclose failed"); - if (H5VLclose(default_vol_id) < 0) - H5TOOLS_GOTO_ERROR((-1), "H5VLclose failed"); - } - - if (!use_h5ocopy) { - int j; - - if ((dset_in = H5Dopen2(fidin, travt->objs[i].name, H5P_DEFAULT)) < 0) - H5TOOLS_GOTO_ERROR((-1), "H5Dopen2 failed"); - if ((f_space_id = H5Dget_space(dset_in)) < 0) - H5TOOLS_GOTO_ERROR((-1), "H5Dget_space failed"); - if ((ftype_id = H5Dget_type(dset_in)) < 0) - H5TOOLS_GOTO_ERROR((-1), "H5Dget_type failed"); - if ((dcpl_in = H5Dget_create_plist(dset_in)) < 0) - H5TOOLS_GOTO_ERROR((-1), "H5Dget_create_plist failed"); - if ((rank = H5Sget_simple_extent_ndims(f_space_id)) < 0) - H5TOOLS_GOTO_ERROR((-1), "H5Sget_simple_extent_ndims failed"); - HDmemset(dims, 0, sizeof dims); - if (H5Sget_simple_extent_dims(f_space_id, dims, NULL) < 0) - H5TOOLS_GOTO_ERROR((-1), "H5Sget_simple_extent_dims failed"); - if (H5Dget_space_status(dset_in, &space_status) < 0) - H5TOOLS_GOTO_ERROR((-1), "H5Dget_space_status failed"); - - /* If the input dataset has external storage, it must be contiguous. - * Accordingly, there would be no filter or chunk properties to preserve, - * so create a new DCPL. - * Otherwise, copy dcpl_in. - */ - if (H5Pget_external_count(dcpl_in)) { - if ((dcpl_out = H5Pcreate(H5P_DATASET_CREATE)) < 0) - H5TOOLS_GOTO_ERROR((-1), "H5Pcreate failed"); - } - else if ((dcpl_out = H5Pcopy(dcpl_in)) < 0) { - H5TOOLS_GOTO_ERROR((-1), "H5Pcopy failed"); } - nelmts = 1; - for (j = 0; j < rank; j++) - nelmts *= dims[j]; + if (!use_h5ocopy) { + int j; + + if ((dset_in = H5Dopen2(fidin, travt->objs[i].name, H5P_DEFAULT)) < 0) + H5TOOLS_GOTO_ERROR((-1), "H5Dopen2 failed"); + if ((f_space_id = H5Dget_space(dset_in)) < 0) + H5TOOLS_GOTO_ERROR((-1), "H5Dget_space failed"); + if ((ftype_id = H5Dget_type(dset_in)) < 0) + H5TOOLS_GOTO_ERROR((-1), "H5Dget_type failed"); + if ((dcpl_in = H5Dget_create_plist(dset_in)) < 0) + H5TOOLS_GOTO_ERROR((-1), "H5Dget_create_plist failed"); + if ((rank = H5Sget_simple_extent_ndims(f_space_id)) < 0) + H5TOOLS_GOTO_ERROR((-1), "H5Sget_simple_extent_ndims failed"); + HDmemset(dims, 0, sizeof dims); + if (H5Sget_simple_extent_dims(f_space_id, dims, NULL) < 0) + H5TOOLS_GOTO_ERROR((-1), "H5Sget_simple_extent_dims failed"); + if (H5Dget_space_status(dset_in, &space_status) < 0) + H5TOOLS_GOTO_ERROR((-1), "H5Dget_space_status failed"); + + /* If the input dataset has external storage, it must be contiguous. + * Accordingly, there would be no filter or chunk properties to preserve, + * so create a new DCPL. + * Otherwise, copy dcpl_in. + */ + if (H5Pget_external_count(dcpl_in)) { + if ((dcpl_out = H5Pcreate(H5P_DATASET_CREATE)) < 0) + H5TOOLS_GOTO_ERROR((-1), "H5Pcreate failed"); + } + else if ((dcpl_out = H5Pcopy(dcpl_in)) < 0) { + H5TOOLS_GOTO_ERROR((-1), "H5Pcopy failed"); + } - /* wtype_id will have already been set if using a named dtype */ - if (!is_named) { - if (options->use_native == 1) - wtype_id = H5Tget_native_type(ftype_id, H5T_DIR_DEFAULT); - else - wtype_id = H5Tcopy(ftype_id); - } + nelmts = 1; + for (j = 0; j < rank; j++) + nelmts *= dims[j]; - if ((msize = H5Tget_size(wtype_id)) == 0) - H5TOOLS_GOTO_ERROR((-1), "H5Tget_size failed"); + /* wtype_id will have already been set if using a named dtype */ + if (!is_named) { + if (options->use_native == 1) + wtype_id = H5Tget_native_type(ftype_id, H5T_DIR_DEFAULT); + else + wtype_id = H5Tcopy(ftype_id); + } - /* size of current dset */ - size_dset = nelmts * msize; + if ((msize = H5Tget_size(wtype_id)) == 0) + H5TOOLS_GOTO_ERROR((-1), "H5Tget_size failed"); - /*------------------------------------------------------------------------- - * check if the dataset creation property list has filters that - * are not registered in the current configuration - * 1) the external filters GZIP and SZIP might not be available - * 2) the internal filters might be turned off - *------------------------------------------------------------------------- - */ - if (h5tools_canreadf((travt->objs[i].name), dcpl_in) == 1) { - apply_s = 1; - apply_f = 1; + /* size of current dset */ + size_dset = nelmts * msize; /*------------------------------------------------------------------------- - * references are a special case - * we cannot just copy the buffers, but instead we recreate the reference - * in a second traversal of the output file + * check if the dataset creation property list has filters that + * are not registered in the current configuration + * 1) the external filters GZIP and SZIP might not be available + * 2) the internal filters might be turned off *------------------------------------------------------------------------- */ - if (H5T_REFERENCE != H5Tget_class(wtype_id)) { - /* get the storage size of the input dataset */ - dsize_in = H5Dget_storage_size(dset_in); + if (h5tools_canreadf((travt->objs[i].name), dcpl_in) == 1) { + apply_s = 1; + apply_f = 1; - /* check for small size datasets (less than 1k) except - * changing to COMPACT. For the reference, COMPACT is limited - * by size 64K by library. + /*------------------------------------------------------------------------- + * references are a special case + * we cannot just copy the buffers, but instead we recreate the reference + * in a second traversal of the output file + *------------------------------------------------------------------------- */ - if (options->layout_g != H5D_COMPACT) - if (size_dset < options->min_comp) - apply_s = 0; - - /* apply the filter */ - if (apply_s) - if (apply_filters(travt->objs[i].name, rank, dims, msize, dcpl_out, options, &has_filter) < 0) - H5TOOLS_GOTO_ERROR((-1), "apply_filters failed"); - - /* only if layout change requested for entire file or - * individual obj */ - if (options->all_layout > 0 || req_obj_layout == 1) { - /*------------------------------------------------- - * Unset the unlimited max dims if convert to other - * than chunk layouts, because unlimited max dims - * only can be applied to chunk layout. - * Also perform only for targeted dataset - * Also check for size limit to convert to compact - *-------------------------------------------------*/ - if (options->layout_g != H5D_CHUNKED) { - /* any dataset is specified */ - if (options->op_tbl->nelems > 0) { - /* if current obj match specified obj */ - if (options_get_object(travt->objs[i].name, options->op_tbl)) + if (H5T_REFERENCE != H5Tget_class(wtype_id)) { + /* get the storage size of the input dataset */ + dsize_in = H5Dget_storage_size(dset_in); + + /* check for small size datasets (less than 1k) except + * changing to COMPACT. For the reference, COMPACT is limited + * by size 64K by library. + */ + if (options->layout_g != H5D_COMPACT) + if (size_dset < options->min_comp) + apply_s = 0; + + /* apply the filter */ + if (apply_s) + if (apply_filters(travt->objs[i].name, rank, dims, msize, dcpl_out, + options, &has_filter) < 0) + H5TOOLS_GOTO_ERROR((-1), "apply_filters failed"); + + /* only if layout change requested for entire file or + * individual obj */ + if (options->all_layout > 0 || req_obj_layout == 1) { + /*------------------------------------------------- + * Unset the unlimited max dims if convert to other + * than chunk layouts, because unlimited max dims + * only can be applied to chunk layout. + * Also perform only for targeted dataset + * Also check for size limit to convert to compact + *-------------------------------------------------*/ + if (options->layout_g != H5D_CHUNKED) { + /* any dataset is specified */ + if (options->op_tbl->nelems > 0) { + /* if current obj match specified obj */ + if (options_get_object(travt->objs[i].name, options->op_tbl)) + limit_maxdims = TRUE; + } + else /* no dataset is specified */ limit_maxdims = TRUE; - } - else /* no dataset is specified */ - limit_maxdims = TRUE; - /* if convert to COMPACT */ - if (options->layout_g == H5D_COMPACT) - if (size_dset > MAX_COMPACT_DSIZE) - limit_maxdims = FALSE; + /* if convert to COMPACT */ + if (options->layout_g == H5D_COMPACT) + if (size_dset > MAX_COMPACT_DSIZE) + limit_maxdims = FALSE; + + /* unset unlimited max dims */ + if (limit_maxdims) + H5Sset_extent_simple(f_space_id, rank, dims, NULL); + } /* end if not chunked */ + } /* end if layout change requested for entire file or individual object */ + + /*------------------------------------------------------------------------- + * create the output dataset; + * disable error checking in case the dataset cannot be created with the + * modified dcpl; in that case use the original instead + *------------------------------------------------------------------------- + */ + dset_out = H5Dcreate2(fidout, travt->objs[i].name, wtype_id, f_space_id, + H5P_DEFAULT, dcpl_out, H5P_DEFAULT); + if (dset_out == H5I_INVALID_HID) { + H5TOOLS_INFO("H5Dcreate2 failed"); + if (options->verbose) + HDprintf(" warning: could not create dataset <%s>. Applying original " + "settings\n", + travt->objs[i].name); + + if ((dset_out = + H5Dcreate2(fidout, travt->objs[i].name, wtype_id, f_space_id, + H5P_DEFAULT, dcpl_in, H5P_DEFAULT)) < 0) + H5TOOLS_GOTO_ERROR((-1), "H5Dcreate2 failed"); + apply_f = 0; + } /* end if retry dataset create */ + + /*------------------------------------------------------------------------- + * read/write + *------------------------------------------------------------------------- + */ + if (nelmts > 0 && space_status != H5D_SPACE_STATUS_NOT_ALLOCATED) { + size_t need = (size_t)(nelmts * msize); /* bytes needed */ - /* unset unlimited max dims */ - if (limit_maxdims) - H5Sset_extent_simple(f_space_id, rank, dims, NULL); - } /* end if not chunked */ - } /* end if layout change requested for entire file or individual object */ + /* have to read the whole dataset if there is only one element in the + * dataset */ + if (need < H5TOOLS_MALLOCSIZE) + buf = HDmalloc(need); - /*------------------------------------------------------------------------- - * create the output dataset; - * disable error checking in case the dataset cannot be created with the - * modified dcpl; in that case use the original instead - *------------------------------------------------------------------------- - */ - dset_out = H5Dcreate2(fidout, travt->objs[i].name, wtype_id, f_space_id, H5P_DEFAULT, dcpl_out, H5P_DEFAULT); - if (dset_out == H5I_INVALID_HID) { - H5TOOLS_INFO("H5Dcreate2 failed"); - if (options->verbose) - HDprintf(" warning: could not create dataset <%s>. Applying original settings\n", travt->objs[i].name); + if (buf != NULL) { + if (H5Dread(dset_in, wtype_id, H5S_ALL, H5S_ALL, H5P_DEFAULT, buf) < + 0) + H5TOOLS_GOTO_ERROR((-1), "H5Dread failed"); + if (H5Dwrite(dset_out, wtype_id, H5S_ALL, H5S_ALL, H5P_DEFAULT, buf) < + 0) + H5TOOLS_GOTO_ERROR((-1), "H5Dwrite failed"); - if ((dset_out = H5Dcreate2(fidout, travt->objs[i].name, wtype_id, f_space_id, H5P_DEFAULT, dcpl_in, H5P_DEFAULT)) < 0) - H5TOOLS_GOTO_ERROR((-1), "H5Dcreate2 failed"); - apply_f = 0; - } /* end if retry dataset create */ + /* Check if we have VL data in the dataset's + * datatype that must be reclaimed */ + if (TRUE == H5Tdetect_class(wtype_id, H5T_VLEN)) + if (H5Treclaim(wtype_id, f_space_id, H5P_DEFAULT, buf) < 0) + H5TOOLS_GOTO_ERROR((-1), "H5Treclaim failed"); - /*------------------------------------------------------------------------- - * read/write - *------------------------------------------------------------------------- - */ - if (nelmts > 0 && space_status != H5D_SPACE_STATUS_NOT_ALLOCATED) { - size_t need = (size_t)(nelmts * msize); /* bytes needed */ - - /* have to read the whole dataset if there is only one element in the dataset */ - if (need < H5TOOLS_MALLOCSIZE) - buf = HDmalloc(need); - - if (buf != NULL) { - if(H5Dread(dset_in, wtype_id, H5S_ALL, H5S_ALL, H5P_DEFAULT, buf) < 0) - H5TOOLS_GOTO_ERROR((-1), "H5Dread failed"); - if(H5Dwrite(dset_out, wtype_id, H5S_ALL, H5S_ALL, H5P_DEFAULT, buf) < 0) - H5TOOLS_GOTO_ERROR((-1), "H5Dwrite failed"); - - /* Check if we have VL data in the dataset's - * datatype that must be reclaimed */ - if (TRUE == H5Tdetect_class(wtype_id, H5T_VLEN)) - if (H5Treclaim(wtype_id, f_space_id, H5P_DEFAULT, buf) < 0) - H5TOOLS_GOTO_ERROR((-1), "H5Treclaim failed"); - - if (buf != NULL) { /* TODO: is buf potentially released by H5Dvlen_reclaim()? */ - HDfree(buf); - buf = NULL; + if (buf != NULL) { /* TODO: is buf potentially released by + H5Dvlen_reclaim()? */ + HDfree(buf); + buf = NULL; + } } - } - else { /* possibly not enough memory, read/write by hyperslabs */ - size_t p_type_nbytes = msize; /*size of memory type */ - hsize_t p_nelmts = nelmts; /*total elements */ - hsize_t elmtno; /*counter */ - int carry; /*counter carry value */ - unsigned int vl_data = 0; /*contains VL datatypes */ - - /* hyperslab info */ - hsize_t hslab_dims[H5S_MAX_RANK]; /*hyperslab dims */ - hsize_t hslab_nbytes; /*bytes per hyperslab */ - hsize_t hslab_nelmts; /*elements per hyperslab*/ - hid_t hslab_space; /*hyperslab data space */ - - /* hyperslab selection info */ - hsize_t hs_sel_offset[H5S_MAX_RANK];/* selection offset */ - hsize_t hs_sel_count[H5S_MAX_RANK]; /* selection count */ - hsize_t hs_select_nelmts; /* selected elements */ - hsize_t zero[8]; /*vector of zeros */ - int k; - H5D_layout_t dset_layout; - hid_t dcpl_tmp = H5I_INVALID_HID; /* dataset creation property list ID */ - - /* check if we have VL data in the dataset's datatype */ - if (H5Tdetect_class(wtype_id, H5T_VLEN) == TRUE) - vl_data = TRUE; - - /* check first if writing dataset is chunked, - * if so use its chunk layout for better performance. */ - dset_layout = H5Pget_layout(dcpl_out); - if (dset_layout == H5D_CHUNKED) - dcpl_tmp = dcpl_out; /* writing dataset */ - else { - dset_layout = H5Pget_layout(dcpl_in); + else { /* possibly not enough memory, read/write by hyperslabs */ + size_t p_type_nbytes = msize; /*size of memory type */ + hsize_t p_nelmts = nelmts; /*total elements */ + hsize_t elmtno; /*counter */ + int carry; /*counter carry value */ + unsigned int vl_data = 0; /*contains VL datatypes */ + + /* hyperslab info */ + hsize_t hslab_dims[H5S_MAX_RANK]; /*hyperslab dims */ + hsize_t hslab_nbytes; /*bytes per hyperslab */ + hsize_t hslab_nelmts; /*elements per hyperslab*/ + hid_t hslab_space; /*hyperslab data space */ + + /* hyperslab selection info */ + hsize_t hs_sel_offset[H5S_MAX_RANK]; /* selection offset */ + hsize_t hs_sel_count[H5S_MAX_RANK]; /* selection count */ + hsize_t hs_select_nelmts; /* selected elements */ + hsize_t zero[8]; /*vector of zeros */ + int k; + H5D_layout_t dset_layout; + hid_t dcpl_tmp = + H5I_INVALID_HID; /* dataset creation property list ID */ + + /* check if we have VL data in the dataset's datatype */ + if (H5Tdetect_class(wtype_id, H5T_VLEN) == TRUE) + vl_data = TRUE; + + /* check first if writing dataset is chunked, + * if so use its chunk layout for better performance. */ + dset_layout = H5Pget_layout(dcpl_out); if (dset_layout == H5D_CHUNKED) - dcpl_tmp = dcpl_in; /* reading dataset */ - } - - /* get hyperslab dims and size in byte */ - if (get_hyperslab(dcpl_tmp, rank, dims, p_type_nbytes, hslab_dims, &hslab_nbytes) < 0) - H5TOOLS_GOTO_ERROR((-1), "get_hyperslab failed"); - - hslab_buf = HDmalloc((size_t)hslab_nbytes); - if (hslab_buf == NULL) - H5TOOLS_GOTO_ERROR((-1), "can't allocate space for hyperslab"); - - hslab_nelmts = hslab_nbytes / p_type_nbytes; - hslab_space = H5Screate_simple(1, &hslab_nelmts, NULL); - - /* the hyperslab selection loop */ - HDmemset(hs_sel_offset, 0, sizeof hs_sel_offset); - HDmemset(zero, 0, sizeof zero); - - for (elmtno = 0; elmtno < p_nelmts; elmtno += hs_select_nelmts) { - if (rank > 0) { - /* calculate the hyperslab selections. - * The selection would be same as the hyperslab - * except for remaining edge portion of the dataset - * which is smaller then the hyperslab. - */ - for (k = 0, hs_select_nelmts = 1; k < rank; k++) { - /* MIN() is used to get the remaining edge portion if exist. - * "dims[k] - hs_sel_offset[k]" is remaining edge portion that is smaller then the hyperslab.*/ - hs_sel_count[k] = MIN(dims[k] - hs_sel_offset[k], hslab_dims[k]); - hs_select_nelmts *= hs_sel_count[k]; - } - - if (H5Sselect_hyperslab(f_space_id, H5S_SELECT_SET, hs_sel_offset, NULL, hs_sel_count, NULL) < 0) - H5TOOLS_GOTO_ERROR((-1), "H5Sselect_hyperslab failed"); - if (H5Sselect_hyperslab(hslab_space, H5S_SELECT_SET, zero, NULL, &hs_select_nelmts, NULL) < 0) - H5TOOLS_GOTO_ERROR((-1), "H5Sselect_hyperslab failed"); - } /* end if rank > 0 */ + dcpl_tmp = dcpl_out; /* writing dataset */ else { - H5Sselect_all(f_space_id); - H5Sselect_all(hslab_space); - hs_select_nelmts = 1; - } /* end (else) rank == 0 */ + dset_layout = H5Pget_layout(dcpl_in); + if (dset_layout == H5D_CHUNKED) + dcpl_tmp = dcpl_in; /* reading dataset */ + } - if(H5Dread(dset_in, wtype_id, hslab_space, f_space_id, H5P_DEFAULT, hslab_buf) < 0) - H5TOOLS_GOTO_ERROR((-1), "H5Dread failed"); - if(H5Dwrite(dset_out, wtype_id, hslab_space, f_space_id, H5P_DEFAULT, hslab_buf) < 0) - H5TOOLS_GOTO_ERROR((-1), "H5Dwrite failed"); + /* get hyperslab dims and size in byte */ + if (get_hyperslab(dcpl_tmp, rank, dims, p_type_nbytes, hslab_dims, + &hslab_nbytes) < 0) + H5TOOLS_GOTO_ERROR((-1), "get_hyperslab failed"); + + hslab_buf = HDmalloc((size_t)hslab_nbytes); + if (hslab_buf == NULL) + H5TOOLS_GOTO_ERROR((-1), "can't allocate space for hyperslab"); + + hslab_nelmts = hslab_nbytes / p_type_nbytes; + hslab_space = H5Screate_simple(1, &hslab_nelmts, NULL); + + /* the hyperslab selection loop */ + HDmemset(hs_sel_offset, 0, sizeof hs_sel_offset); + HDmemset(zero, 0, sizeof zero); + + for (elmtno = 0; elmtno < p_nelmts; elmtno += hs_select_nelmts) { + if (rank > 0) { + /* calculate the hyperslab selections. + * The selection would be same as the hyperslab + * except for remaining edge portion of the dataset + * which is smaller then the hyperslab. + */ + for (k = 0, hs_select_nelmts = 1; k < rank; k++) { + /* MIN() is used to get the remaining edge portion if + * exist. "dims[k] - hs_sel_offset[k]" is remaining edge + * portion that is smaller then the hyperslab.*/ + hs_sel_count[k] = + MIN(dims[k] - hs_sel_offset[k], hslab_dims[k]); + hs_select_nelmts *= hs_sel_count[k]; + } + + if (H5Sselect_hyperslab(f_space_id, H5S_SELECT_SET, + hs_sel_offset, NULL, hs_sel_count, + NULL) < 0) + H5TOOLS_GOTO_ERROR((-1), "H5Sselect_hyperslab failed"); + if (H5Sselect_hyperslab(hslab_space, H5S_SELECT_SET, zero, + NULL, &hs_select_nelmts, NULL) < 0) + H5TOOLS_GOTO_ERROR((-1), "H5Sselect_hyperslab failed"); + } /* end if rank > 0 */ + else { + H5Sselect_all(f_space_id); + H5Sselect_all(hslab_space); + hs_select_nelmts = 1; + } /* end (else) rank == 0 */ + + if (H5Dread(dset_in, wtype_id, hslab_space, f_space_id, + H5P_DEFAULT, hslab_buf) < 0) + H5TOOLS_GOTO_ERROR((-1), "H5Dread failed"); + if (H5Dwrite(dset_out, wtype_id, hslab_space, f_space_id, + H5P_DEFAULT, hslab_buf) < 0) + H5TOOLS_GOTO_ERROR((-1), "H5Dwrite failed"); + + /* reclaim any VL memory, if necessary */ + if (vl_data) + H5Treclaim(wtype_id, hslab_space, H5P_DEFAULT, hslab_buf); + + /* calculate the next hyperslab offset */ + for (k = rank, carry = 1; k > 0 && carry; --k) { + hs_sel_offset[k - 1] += hs_sel_count[k - 1]; + /* if reached the end of a dim */ + if (hs_sel_offset[k - 1] == dims[k - 1]) + hs_sel_offset[k - 1] = 0; + else + carry = 0; + } + } /* end for (hyperslab selection loop) */ - /* reclaim any VL memory, if necessary */ - if (vl_data) - H5Treclaim(wtype_id, hslab_space, H5P_DEFAULT, hslab_buf); - - /* calculate the next hyperslab offset */ - for (k = rank, carry = 1; k > 0 && carry; --k) { - hs_sel_offset[k - 1] += hs_sel_count[k - 1]; - /* if reached the end of a dim */ - if (hs_sel_offset[k - 1] == dims[k - 1]) - hs_sel_offset[k - 1] = 0; - else - carry = 0; + H5Sclose(hslab_space); + if (hslab_buf != NULL) { + HDfree(hslab_buf); + hslab_buf = NULL; } - } /* end for (hyperslab selection loop) */ + } /* end if reading/writing by hyperslab */ + } /* end if (nelmts > 0 && space_status != H5D_SPACE_STATUS_NOT_ALLOCATED) */ - H5Sclose(hslab_space); - if (hslab_buf != NULL) { - HDfree(hslab_buf); - hslab_buf = NULL; + /*------------------------------------------------------------------------- + * print amount of compression used + *------------------------------------------------------------------------- + */ + if (options->verbose) { + double ratio = 0; + + /* only print the compression ration if there was a filter request */ + if (apply_s && apply_f && req_filter) { + /* get the storage size of the output dataset */ + dsize_out = H5Dget_storage_size(dset_out); + + /* compression ratio = uncompressed size / compressed size */ + if (dsize_out != 0) + ratio = (double)dsize_in / (double)dsize_out; + print_dataset_info(dcpl_out, travt->objs[i].name, ratio, 1); } - } /* end if reading/writing by hyperslab */ - } /* end if (nelmts > 0 && space_status != H5D_SPACE_STATUS_NOT_ALLOCATED) */ - - /*------------------------------------------------------------------------- - * print amount of compression used - *------------------------------------------------------------------------- - */ - if (options->verbose) { - double ratio = 0; - - /* only print the compression ration if there was a filter request */ - if (apply_s && apply_f && req_filter) { - /* get the storage size of the output dataset */ - dsize_out = H5Dget_storage_size(dset_out); - - /* compression ratio = uncompressed size / compressed size */ - if (dsize_out != 0) - ratio = (double) dsize_in / (double) dsize_out; - print_dataset_info(dcpl_out, travt->objs[i].name, ratio, 1); - } - else - print_dataset_info(dcpl_in, travt->objs[i].name, ratio, 0); - - /* print a message that the filter was not applied - * (in case there was a filter) + else + print_dataset_info(dcpl_in, travt->objs[i].name, ratio, 0); + + /* print a message that the filter was not applied + * (in case there was a filter) + */ + if (has_filter && apply_s == 0) + HDprintf(" <warning: filter not applied to %s. dataset smaller than " + "%d bytes>\n", + travt->objs[i].name, (int)options->min_comp); + + if (has_filter && apply_f == 0) + HDprintf(" <warning: could not apply the filter to %s>\n", + travt->objs[i].name); + } /* end if verbose (print compression) */ + + /*------------------------------------------------------------------------- + * copy attrs + *------------------------------------------------------------------------- */ - if (has_filter && apply_s == 0) - HDprintf(" <warning: filter not applied to %s. dataset smaller than %d bytes>\n", travt->objs[i].name, (int) options->min_comp); - - if (has_filter && apply_f == 0) - HDprintf(" <warning: could not apply the filter to %s>\n", travt->objs[i].name); - } /* end if verbose (print compression) */ - - /*------------------------------------------------------------------------- - * copy attrs - *------------------------------------------------------------------------- - */ - if (copy_attr(dset_in, dset_out, &named_dt_head, travt, options) < 0) - H5TOOLS_GOTO_ERROR((-1), "copy_attr failed"); + if (copy_attr(dset_in, dset_out, &named_dt_head, travt, options) < 0) + H5TOOLS_GOTO_ERROR((-1), "copy_attr failed"); - if (H5Dclose(dset_out) < 0) - H5TOOLS_GOTO_ERROR((-1), "H5Dclose failed"); - } /* end if not a reference */ - } /* end if h5tools_canreadf (filter availability check) */ + if (H5Dclose(dset_out) < 0) + H5TOOLS_GOTO_ERROR((-1), "H5Dclose failed"); + } /* end if not a reference */ + } /* end if h5tools_canreadf (filter availability check) */ + /*------------------------------------------------------------------------- + * Close + *------------------------------------------------------------------------- + */ + if (H5Tclose(ftype_id) < 0) + H5TOOLS_GOTO_ERROR((-1), "H5Tclose failed"); + if (H5Tclose(wtype_id) < 0) + H5TOOLS_GOTO_ERROR((-1), "H5Tclose failed"); + if (H5Pclose(dcpl_in) < 0) + H5TOOLS_GOTO_ERROR((-1), "H5Pclose failed"); + if (H5Pclose(dcpl_out) < 0) + H5TOOLS_GOTO_ERROR((-1), "H5Pclose failed"); + if (H5Sclose(f_space_id) < 0) + H5TOOLS_GOTO_ERROR((-1), "H5Sclose failed"); + if (H5Dclose(dset_in) < 0) + H5TOOLS_GOTO_ERROR((-1), "H5Dclose failed"); + } /*------------------------------------------------------------------------- - * Close + * We do not have request for filter/chunking; use H5Ocopy instead *------------------------------------------------------------------------- */ - if (H5Tclose(ftype_id) < 0) - H5TOOLS_GOTO_ERROR((-1), "H5Tclose failed"); - if (H5Tclose(wtype_id) < 0) - H5TOOLS_GOTO_ERROR((-1), "H5Tclose failed"); - if (H5Pclose(dcpl_in) < 0) - H5TOOLS_GOTO_ERROR((-1), "H5Pclose failed"); - if (H5Pclose(dcpl_out) < 0) - H5TOOLS_GOTO_ERROR((-1), "H5Pclose failed"); - if (H5Sclose(f_space_id) < 0) - H5TOOLS_GOTO_ERROR((-1), "H5Sclose failed"); - if (H5Dclose(dset_in) < 0) - H5TOOLS_GOTO_ERROR((-1), "H5Dclose failed"); - } + else { + /* create property to pass copy options */ + if ((ocpl_id = H5Pcreate(H5P_OBJECT_COPY)) < 0) + H5TOOLS_GOTO_ERROR((-1), "H5Pcreate failed"); + + /* set options for object copy */ + if (H5Pset_copy_object(ocpl_id, H5O_COPY_WITHOUT_ATTR_FLAG) < 0) + H5TOOLS_GOTO_ERROR((-1), "H5Pset_copy_object failed"); + + if (H5Ocopy(fidin, /* Source file or group identifier */ + travt->objs[i].name, /* Name of the source object to be copied */ + fidout, /* Destination file or group identifier */ + travt->objs[i].name, /* Name of the destination object */ + ocpl_id, /* Properties which apply to the copy */ + H5P_DEFAULT) < 0) /* Properties which apply to the new hard link */ + H5TOOLS_GOTO_ERROR((-1), "H5Ocopy failed"); + + if (H5Pclose(ocpl_id) < 0) + H5TOOLS_GOTO_ERROR((-1), "H5Pclose failed"); + ocpl_id = H5I_INVALID_HID; + + /*------------------------------------------------------------------------- + * Copy attrs manually + *------------------------------------------------------------------------- + */ + if ((dset_in = H5Dopen2(fidin, travt->objs[i].name, H5P_DEFAULT)) < 0) + H5TOOLS_GOTO_ERROR((-1), "H5Dopen2 failed"); + if ((dset_out = H5Dopen2(fidout, travt->objs[i].name, H5P_DEFAULT)) < 0) + H5TOOLS_GOTO_ERROR((-1), "H5Dopen2 failed"); + if (copy_attr(dset_in, dset_out, &named_dt_head, travt, options) < 0) + H5TOOLS_GOTO_ERROR((-1), "copy_attr failed"); + if (H5Dclose(dset_in) < 0) + H5TOOLS_GOTO_ERROR((-1), "H5Dclose failed"); + if (H5Dclose(dset_out) < 0) + H5TOOLS_GOTO_ERROR((-1), "H5Dclose failed"); + + if (options->verbose) + HDprintf(FORMAT_OBJ, "dset", travt->objs[i].name); + + } /* end whether we have request for filter/chunking */ + + break; + } /* H5TRAV_TYPE_DATASET */ + /*------------------------------------------------------------------------- - * We do not have request for filter/chunking; use H5Ocopy instead + * H5TRAV_TYPE_NAMED_DATATYPE *------------------------------------------------------------------------- */ - else { - /* create property to pass copy options */ - if ((ocpl_id = H5Pcreate(H5P_OBJECT_COPY)) < 0) - H5TOOLS_GOTO_ERROR((-1), "H5Pcreate failed"); + case H5TRAV_TYPE_NAMED_DATATYPE: + if (options->verbose) + HDprintf(FORMAT_OBJ, "type", travt->objs[i].name); - /* set options for object copy */ - if (H5Pset_copy_object(ocpl_id, H5O_COPY_WITHOUT_ATTR_FLAG) < 0) - H5TOOLS_GOTO_ERROR((-1), "H5Pset_copy_object failed"); + if ((type_in = H5Topen2(fidin, travt->objs[i].name, H5P_DEFAULT)) < 0) + H5TOOLS_GOTO_ERROR((-1), "H5Topen2 failed"); - if (H5Ocopy(fidin, /* Source file or group identifier */ - travt->objs[i].name, /* Name of the source object to be copied */ - fidout, /* Destination file or group identifier */ - travt->objs[i].name, /* Name of the destination object */ - ocpl_id, /* Properties which apply to the copy */ - H5P_DEFAULT) < 0) /* Properties which apply to the new hard link */ - H5TOOLS_GOTO_ERROR((-1), "H5Ocopy failed"); + /* Copy the datatype anonymously */ + if ((type_out = copy_named_datatype(type_in, fidout, &named_dt_head, travt, options)) < 0) + H5TOOLS_GOTO_ERROR((-1), "copy_named_datatype failed"); - if (H5Pclose(ocpl_id) < 0) - H5TOOLS_GOTO_ERROR((-1), "H5Pclose failed"); - ocpl_id = H5I_INVALID_HID; + /* Link in to group structure */ + if (H5Lcreate_hard(type_out, ".", fidout, travt->objs[i].name, H5P_DEFAULT, H5P_DEFAULT) < + 0) + H5TOOLS_GOTO_ERROR((-1), "H5Lcreate_hard failed"); /*------------------------------------------------------------------------- - * Copy attrs manually + * copy attrs *------------------------------------------------------------------------- */ - if ((dset_in = H5Dopen2(fidin, travt->objs[i].name, H5P_DEFAULT)) < 0) - H5TOOLS_GOTO_ERROR((-1), "H5Dopen2 failed"); - if ((dset_out = H5Dopen2(fidout, travt->objs[i].name, H5P_DEFAULT)) < 0) - H5TOOLS_GOTO_ERROR((-1), "H5Dopen2 failed"); - if (copy_attr(dset_in, dset_out, &named_dt_head, travt, options) < 0) + if (copy_attr(type_in, type_out, &named_dt_head, travt, options) < 0) H5TOOLS_GOTO_ERROR((-1), "copy_attr failed"); - if (H5Dclose(dset_in) < 0) - H5TOOLS_GOTO_ERROR((-1), "H5Dclose failed"); - if (H5Dclose(dset_out) < 0) - H5TOOLS_GOTO_ERROR((-1), "H5Dclose failed"); - - if (options->verbose) - HDprintf(FORMAT_OBJ, "dset", travt->objs[i].name); - - } /* end whether we have request for filter/chunking */ - break; - } /* H5TRAV_TYPE_DATASET */ - - /*------------------------------------------------------------------------- - * H5TRAV_TYPE_NAMED_DATATYPE - *------------------------------------------------------------------------- - */ - case H5TRAV_TYPE_NAMED_DATATYPE: - if (options->verbose) - HDprintf(FORMAT_OBJ, "type", travt->objs[i].name); - - if ((type_in = H5Topen2(fidin, travt->objs[i].name, H5P_DEFAULT)) < 0) - H5TOOLS_GOTO_ERROR((-1), "H5Topen2 failed"); - - /* Copy the datatype anonymously */ - if ((type_out = copy_named_datatype(type_in, fidout, &named_dt_head, travt, options)) < 0) - H5TOOLS_GOTO_ERROR((-1), "copy_named_datatype failed"); + if (H5Tclose(type_in) < 0) + H5TOOLS_GOTO_ERROR((-1), "H5Tclose failed"); + if (H5Tclose(type_out) < 0) + H5TOOLS_GOTO_ERROR((-1), "H5Tclose failed"); + type_out = H5I_INVALID_HID; /* named datatypes stack, named_dt_head, manages allocation */ - /* Link in to group structure */ - if (H5Lcreate_hard(type_out, ".", fidout, travt->objs[i].name, H5P_DEFAULT, H5P_DEFAULT) < 0) - H5TOOLS_GOTO_ERROR((-1), "H5Lcreate_hard failed"); + break; /*------------------------------------------------------------------------- - * copy attrs + * H5TRAV_TYPE_LINK + * H5TRAV_TYPE_UDLINK + * + * Only handles external links; H5Lcopy will fail for other UD link types + * since we don't have creation or copy callbacks for them. *------------------------------------------------------------------------- */ - if (copy_attr(type_in, type_out, &named_dt_head, travt, options) < 0) - H5TOOLS_GOTO_ERROR((-1), "copy_attr failed"); + case H5TRAV_TYPE_LINK: + case H5TRAV_TYPE_UDLINK: + if (options->verbose) + HDprintf(FORMAT_OBJ, "link", travt->objs[i].name); + + /* Check -X option. */ + if (options->merge) { + if (H5tools_get_symlink_info(fidin, travt->objs[i].name, &linkinfo, 1) == 0) { + /* dangling link */ + if (options->prune) { + HDprintf("Pruned %s.\n", travt->objs[i].name); + } + else { + if (H5Lcopy(fidin, travt->objs[i].name, fidout, travt->objs[i].name, + H5P_DEFAULT, H5P_DEFAULT) < 0) + H5TOOLS_GOTO_ERROR((-1), "H5Lcopy failed"); + } + } + else { + /* valid link */ + /* create property to pass copy options */ + if ((ocpl_id = H5Pcreate(H5P_OBJECT_COPY)) < 0) + H5TOOLS_GOTO_ERROR((-1), "H5Pcreate create property failed"); + + /* set options for object copy */ + if (H5Pset_copy_object(ocpl_id, H5O_COPY_EXPAND_EXT_LINK_FLAG) < 0) + H5TOOLS_GOTO_ERROR((-1), "H5Pset_copy_object failed"); + + /* Create link creation property list */ + if ((lcpl_id = H5Pcreate(H5P_LINK_CREATE)) < 0) { + H5TOOLS_GOTO_ERROR((-1), "H5Pcreate link creation property failed"); + } - if (H5Tclose(type_in) < 0) - H5TOOLS_GOTO_ERROR((-1), "H5Tclose failed"); - if (H5Tclose(type_out) < 0) - H5TOOLS_GOTO_ERROR((-1), "H5Tclose failed"); - type_out = H5I_INVALID_HID; /* named datatypes stack, named_dt_head, manages allocation */ + /* Set flag for intermediate group creation */ + if (H5Pset_create_intermediate_group(lcpl_id, TRUE) < 0) + H5TOOLS_GOTO_ERROR((-1), "H5Pset_create_intermediate_group failed"); - break; + if (H5Ocopy(fidin, travt->objs[i].name, fidout, travt->objs[i].name, ocpl_id, + lcpl_id) < 0) + H5TOOLS_GOTO_ERROR((-1), "H5Ocopy failed"); - /*------------------------------------------------------------------------- - * H5TRAV_TYPE_LINK - * H5TRAV_TYPE_UDLINK - * - * Only handles external links; H5Lcopy will fail for other UD link types - * since we don't have creation or copy callbacks for them. - *------------------------------------------------------------------------- - */ - case H5TRAV_TYPE_LINK: - case H5TRAV_TYPE_UDLINK: - if (options->verbose) - HDprintf(FORMAT_OBJ, "link", travt->objs[i].name); - - /* Check -X option. */ - if (options->merge) { - if (H5tools_get_symlink_info(fidin, travt->objs[i].name, &linkinfo, 1) == 0) { - /* dangling link */ + if (H5Pclose(lcpl_id) < 0) + H5TOOLS_GOTO_ERROR((-1), "H5Pclose failed"); + + if (H5Pclose(ocpl_id) < 0) + H5TOOLS_GOTO_ERROR((-1), "H5Pclose failed"); + } + + /* free link info path */ + if (linkinfo.trg_path) + HDfree(linkinfo.trg_path); + linkinfo.trg_path = NULL; + } /* options->merge */ + else { if (options->prune) { HDprintf("Pruned %s.\n", travt->objs[i].name); } else { - if (H5Lcopy(fidin, travt->objs[i].name, fidout, travt->objs[i].name, H5P_DEFAULT, H5P_DEFAULT) < 0) + if (H5Lcopy(fidin, travt->objs[i].name, fidout, travt->objs[i].name, H5P_DEFAULT, + H5P_DEFAULT) < 0) H5TOOLS_GOTO_ERROR((-1), "H5Lcopy failed"); } } - else { - /* valid link */ - /* create property to pass copy options */ - if ((ocpl_id = H5Pcreate(H5P_OBJECT_COPY)) < 0) - H5TOOLS_GOTO_ERROR((-1), "H5Pcreate create property failed"); - - /* set options for object copy */ - if (H5Pset_copy_object(ocpl_id, H5O_COPY_EXPAND_EXT_LINK_FLAG) < 0) - H5TOOLS_GOTO_ERROR((-1), "H5Pset_copy_object failed"); - - /* Create link creation property list */ - if((lcpl_id = H5Pcreate(H5P_LINK_CREATE)) < 0) { - H5TOOLS_GOTO_ERROR((-1), "H5Pcreate link creation property failed"); - } - - /* Set flag for intermediate group creation */ - if (H5Pset_create_intermediate_group(lcpl_id, TRUE) < 0) - H5TOOLS_GOTO_ERROR((-1), "H5Pset_create_intermediate_group failed"); - - if (H5Ocopy(fidin, travt->objs[i].name, fidout, travt->objs[i].name, ocpl_id, lcpl_id) < 0) - H5TOOLS_GOTO_ERROR((-1), "H5Ocopy failed"); - - if (H5Pclose(lcpl_id) < 0) - H5TOOLS_GOTO_ERROR((-1), "H5Pclose failed"); - - if (H5Pclose(ocpl_id) < 0) - H5TOOLS_GOTO_ERROR((-1), "H5Pclose failed"); - } + break; - /* free link info path */ - if (linkinfo.trg_path) - HDfree(linkinfo.trg_path); - linkinfo.trg_path = NULL; - } /* options->merge */ - else { - if (options->prune) { - HDprintf("Pruned %s.\n", travt->objs[i].name); - } - else { - if (H5Lcopy(fidin, travt->objs[i].name, fidout, travt->objs[i].name, H5P_DEFAULT, H5P_DEFAULT) < 0) - H5TOOLS_GOTO_ERROR((-1), "H5Lcopy failed"); - } - } - break; - - default: - H5TOOLS_GOTO_ERROR((-1), "Object type not found"); + default: + H5TOOLS_GOTO_ERROR((-1), "Object type not found"); } /* switch */ - } /* end for each object to traverse */ - } /* end if there are objects */ + } /* end for each object to traverse */ + } /* end if there are objects */ done: @@ -1305,9 +1337,8 @@ done: H5TOOLS_ERROR((-1), "named_datatype_free failed"); } else { - H5E_BEGIN_TRY { - named_datatype_free(&named_dt_head, 1); - } H5E_END_TRY; + H5E_BEGIN_TRY { named_datatype_free(&named_dt_head, 1); } + H5E_END_TRY; } /* free link info path */ @@ -1330,7 +1361,8 @@ done: H5Tclose(wtype_id); H5Tclose(type_in); H5Tclose(type_out); - } H5E_END_TRY; + } + H5E_END_TRY; /* free */ if (buf != NULL) @@ -1350,17 +1382,17 @@ done: static void print_dataset_info(hid_t dcpl_id, char *objname, double ratio, int pr) { - char strfilter[255]; -#if defined (PRINT_DEBUG ) - char temp[255]; + char strfilter[255]; +#if defined(PRINT_DEBUG) + char temp[255]; #endif - int nfilters; /* number of filters */ - unsigned filt_flags; /* filter flags */ - H5Z_filter_t filtn; /* filter identification number */ - unsigned cd_values[20]; /* filter client data values */ - size_t cd_nelmts; /* filter client number of values */ - char f_objname[256]; /* filter objname */ - int i; + int nfilters; /* number of filters */ + unsigned filt_flags; /* filter flags */ + H5Z_filter_t filtn; /* filter identification number */ + unsigned cd_values[20]; /* filter client data values */ + size_t cd_nelmts; /* filter client number of values */ + char f_objname[256]; /* filter objname */ + int i; HDstrcpy(strfilter, "\0"); @@ -1371,8 +1403,8 @@ print_dataset_info(hid_t dcpl_id, char *objname, double ratio, int pr) for (i = 0; i < nfilters; i++) { cd_nelmts = NELMTS(cd_values); - if ((filtn = H5Pget_filter2(dcpl_id, (unsigned) i, &filt_flags, &cd_nelmts, - cd_values, sizeof(f_objname), f_objname, NULL)) < 0) { + 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; } @@ -1385,11 +1417,11 @@ print_dataset_info(hid_t dcpl_id, char *objname, double ratio, int pr) case H5Z_FILTER_DEFLATE: HDstrcat(strfilter, "GZIP "); -#if defined (PRINT_DEBUG) +#if defined(PRINT_DEBUG) { unsigned level = cd_values[0]; - HDsprintf(temp,"(%d)", level); + HDsprintf(temp, "(%d)", level); HDstrcat(strfilter, temp); } #endif @@ -1398,12 +1430,12 @@ print_dataset_info(hid_t dcpl_id, char *objname, double ratio, int pr) case H5Z_FILTER_SZIP: HDstrcat(strfilter, "SZIP "); -#if defined (PRINT_DEBUG) +#if defined(PRINT_DEBUG) { unsigned options_mask = cd_values[0]; /* from dcpl, not filt*/ - unsigned ppb = cd_values[1]; + unsigned ppb = cd_values[1]; - HDsprintf(temp,"(%d,", ppb); + HDsprintf(temp, "(%d,", ppb); HDstrcat(strfilter, temp); if (options_mask & H5_SZIP_EC_OPTION_MASK) HDstrcpy(temp, "EC) "); @@ -1434,7 +1466,7 @@ print_dataset_info(hid_t dcpl_id, char *objname, double ratio, int pr) HDstrcat(strfilter, "UD "); break; } /* end switch */ - } /* end for each filter */ + } /* end for each filter */ if (!pr) HDprintf(FORMAT_OBJ, "dset", objname); @@ -1473,9 +1505,9 @@ copy_user_block(const char *infile, const char *outfile, hsize_t size) /* Copy the userblock from the input file to the output file */ while (size > 0) { - ssize_t nread, nbytes; /* # of bytes transfered, etc. */ - char rbuf[USERBLOCK_XFER_SIZE]; /* Buffer for reading */ - const char *wbuf; /* Pointer into buffer, for writing */ + ssize_t nread, nbytes; /* # of bytes transfered, etc. */ + char rbuf[USERBLOCK_XFER_SIZE]; /* Buffer for reading */ + const char *wbuf; /* Pointer into buffer, for writing */ /* Read buffer from source file */ if (size > USERBLOCK_XFER_SIZE) @@ -1488,14 +1520,14 @@ copy_user_block(const char *infile, const char *outfile, hsize_t size) /* Write buffer to destination file */ /* (compensating for interrupted writes & checking for errors, etc.) */ nbytes = nread; - wbuf = rbuf; + wbuf = rbuf; while (nbytes > 0) { ssize_t nwritten; /* # of bytes written */ do { nwritten = HDwrite(outfid, wbuf, (size_t)nbytes); } while (-1 == nwritten && EINTR == errno); - if (-1 == nwritten) /* error */ + if (-1 == nwritten) /* error */ H5TOOLS_GOTO_ERROR((-1), "HDwrite failed"); HDassert(nwritten > 0); HDassert(nwritten <= nbytes); @@ -1507,7 +1539,7 @@ copy_user_block(const char *infile, const char *outfile, hsize_t size) } /* end while */ /* Update size of userblock left to transfer */ - size = size - (hsize_t) nread; + size = size - (hsize_t)nread; } /* end while */ done: @@ -1527,14 +1559,13 @@ done: * Return: 0, ok, -1 no *------------------------------------------------------------------------- */ -#if defined (H5REPACK_DEBUG_USER_BLOCK) -static -void +#if defined(H5REPACK_DEBUG_USER_BLOCK) +static void print_user_block(const char *filename, hid_t fid) { - int fh = -1; /* file handle */ - hsize_t ub_size; /* user block size */ - hsize_t size; /* size read */ + int fh = -1; /* file handle */ + hsize_t ub_size; /* user block size */ + hsize_t size; /* size read */ hid_t fcpl = H5I_INVALID_HID; /* file creation property list ID for HDF5 file */ int i; int ret_value = 0; @@ -1561,8 +1592,8 @@ print_user_block(const char *filename, hid_t fid) /* read file */ while (size > 0) { - ssize_t nread; /* # of bytes read */ - char rbuf[USERBLOCK_XFER_SIZE]; /* buffer for reading */ + ssize_t nread; /* # of bytes read */ + char rbuf[USERBLOCK_XFER_SIZE]; /* buffer for reading */ /* read buffer */ if (size > USERBLOCK_XFER_SIZE) @@ -1573,7 +1604,6 @@ print_user_block(const char *filename, hid_t fid) for (i = 0; i < nread; i++) { HDprintf("%c ", rbuf[i]); - } HDprintf("\n"); @@ -1592,4 +1622,3 @@ done: return; } /* end print_user_block() */ #endif - diff --git a/tools/src/h5repack/h5repack_filters.c b/tools/src/h5repack/h5repack_filters.c index d1179fb..0570c0f 100644 --- a/tools/src/h5repack/h5repack_filters.c +++ b/tools/src/h5repack/h5repack_filters.c @@ -17,12 +17,12 @@ /* number of members in an array */ #ifndef NELMTS -# define NELMTS(X) (sizeof(X)/sizeof(X[0])) +#define NELMTS(X) (sizeof(X) / sizeof(X[0])) #endif /* minimum of two values */ #undef MIN -#define MIN(a,b) (((a)<(b)) ? (a) : (b)) +#define MIN(a, b) (((a) < (b)) ? (a) : (b)) /*------------------------------------------------------------------------- * Function: aux_copy_obj @@ -32,15 +32,16 @@ * 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 */ +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 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 */ + int rank; /* rank of dataset */ + hsize_t chsize[64]; /* chunk size in elements */ int i; unsigned u; int ret_value = 0; @@ -50,8 +51,9 @@ static int aux_copy_obj(hid_t dcpl_id, /* dataset creation property list */ H5TOOLS_GOTO_ERROR((-1), "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) + 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) H5TOOLS_GOTO_ERROR((-1), "H5Pget_filter2 failed"); } @@ -63,7 +65,7 @@ static int aux_copy_obj(hid_t dcpl_id, /* dataset creation property list */ objout->layout = layout; if (layout == H5D_CHUNKED) { - if ((rank = H5Pget_chunk(dcpl_id, NELMTS(chsize), chsize/*out*/)) < 0) + if ((rank = H5Pget_chunk(dcpl_id, NELMTS(chsize), chsize /*out*/)) < 0) H5TOOLS_GOTO_ERROR((-1), "H5Pget_chunk failed"); objout->chunk.rank = rank; for (u = 0; u < (unsigned)rank; u++) @@ -81,30 +83,33 @@ done: * 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 */ +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 */ { - char *pdest = NULL; - const char *pname = NULL; + char * pdest = NULL; + const char * pname = NULL; unsigned int i; for (i = 0; i < options->op_tbl->nelems; i++) { if (HDstrcmp(options->op_tbl->objs[i].path, name) == 0) { *obj = options->op_tbl->objs[i]; - return (int) i; + return (int)i; } pdest = options->op_tbl->objs[i].path; - if (pdest[0] == '/') pdest++; + if (pdest[0] == '/') + pdest++; pname = name; - if (pname[0] == '/') pname++; + if (pname[0] == '/') + pname++; if (HDstrcmp(pdest, pname) == 0) { *obj = options->op_tbl->objs[i]; - return (int) i; + return (int)i; } - }/*i*/ + } /*i*/ return -1; } @@ -118,9 +123,10 @@ static int aux_find_obj(const char* name, /* object name from traverse list */ * 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 */ +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 */ { int idx, i; pack_info_t tmp; @@ -136,44 +142,44 @@ static int aux_assign_obj(const char* name, /* object name from traverse list */ /* assign the global layout info to the OBJ info */ tmp.layout = options->layout_g; switch (options->layout_g) { - 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]; - break; - case H5D_LAYOUT_ERROR: - case H5D_COMPACT: - case H5D_CONTIGUOUS: - case H5D_VIRTUAL: - case H5D_NLAYOUTS: - break; - default: - break; - }/*switch*/ + 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]; + break; + case H5D_LAYOUT_ERROR: + case H5D_COMPACT: + case H5D_CONTIGUOUS: + case H5D_VIRTUAL: + case H5D_NLAYOUTS: + break; + default: + break; + } /*switch*/ } else { tmp.layout = options->op_tbl->objs[idx].layout; switch (tmp.layout) { - 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]; - break; - case H5D_LAYOUT_ERROR: - case H5D_COMPACT: - case H5D_CONTIGUOUS: - case H5D_VIRTUAL: - case H5D_NLAYOUTS: - break; - default: - break; - }/*switch*/ + 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]; + break; + case H5D_LAYOUT_ERROR: + case H5D_COMPACT: + case H5D_CONTIGUOUS: + case H5D_VIRTUAL: + case H5D_NLAYOUTS: + break; + default: + break; + } /*switch*/ } /* applying to all objects */ if (options->all_filter) { /* assign the global filter */ - tmp.nfilters = 1; + tmp.nfilters = 1; tmp.filter[0] = options->filter_g[0]; } /* if all */ else { @@ -197,21 +203,20 @@ static int aux_assign_obj(const char* name, /* object name from traverse list */ /* assign the global layout info to the OBJ info */ tmp.layout = options->layout_g; switch (options->layout_g) { - 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]; - break; - case H5D_LAYOUT_ERROR: - case H5D_COMPACT: - case H5D_CONTIGUOUS: - case H5D_VIRTUAL: - case H5D_NLAYOUTS: - break; - default: - break; - }/*switch*/ + 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]; + break; + case H5D_LAYOUT_ERROR: + case H5D_COMPACT: + case H5D_CONTIGUOUS: + case H5D_VIRTUAL: + case H5D_NLAYOUTS: + break; + default: + break; + } /*switch*/ } } @@ -230,16 +235,17 @@ static int aux_assign_obj(const char* name, /* object name from traverse list */ *------------------------------------------------------------------------- */ -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 +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 nfilters; /* number of filters in DCPL */ - hsize_t chsize[64]; /* chunk size in elements */ + int nfilters; /* number of filters in DCPL */ + hsize_t chsize[64]; /* chunk size in elements */ H5D_layout_t layout; int i; pack_info_t obj; @@ -269,7 +275,6 @@ int apply_filters(const char* name, /* object name from traverse list */ if ((nfilters = H5Pget_nfilters(dcpl_id)) < 0) H5TOOLS_GOTO_ERROR((-1), "H5Pget_nfilters failed"); - /*------------------------------------------------------------------------- * check if we have filters in the pipeline * we want to replace them with the input filters @@ -281,7 +286,7 @@ int apply_filters(const char* name, /* object name from traverse list */ if (H5Premove_filter(dcpl_id, H5Z_FILTER_ALL) < 0) H5TOOLS_GOTO_ERROR((-1), "H5Premove_filter failed"); } - else if(nfilters) { + else if (nfilters) { *has_filter = 1; if (aux_copy_obj(dcpl_id, name, &filtobj) < 0) H5TOOLS_GOTO_ERROR((-1), "aux_copy_obj failed"); @@ -297,9 +302,9 @@ int apply_filters(const char* name, /* object name from traverse list */ H5TOOLS_GOTO_ERROR((-1), "H5Pget_layout failed"); if (layout == H5D_CHUNKED) { - if ((rank = H5Pget_chunk(dcpl_id, NELMTS(chsize), chsize/*out*/)) < 0) + if ((rank = H5Pget_chunk(dcpl_id, NELMTS(chsize), chsize /*out*/)) < 0) H5TOOLS_GOTO_ERROR((-1), "H5Pget_chunk failed"); - obj.layout = H5D_CHUNKED; + obj.layout = H5D_CHUNKED; obj.chunk.rank = rank; for (i = 0; i < rank; i++) obj.chunk.chunk_lengths[i] = chsize[i]; @@ -327,7 +332,7 @@ int apply_filters(const char* name, /* object name from traverse list */ if (obj.layout == -1) { /* stripmine info */ hsize_t sm_size[H5S_MAX_RANK]; /*stripmine size */ - hsize_t sm_nbytes; /*bytes per stripmine */ + hsize_t sm_nbytes; /*bytes per stripmine */ obj.chunk.rank = rank; @@ -339,7 +344,7 @@ int apply_filters(const char* name, /* object name from traverse list */ sm_nbytes = msize; for (i = rank; i > 0; --i) { hsize_t size = 0; - if(sm_nbytes == 0) + if (sm_nbytes == 0) H5TOOLS_GOTO_ERROR((-1), "number of bytes per stripmine must be > 0"); size = H5TOOLS_BUFSIZE / sm_nbytes; if (size == 0) /* datum size > H5TOOLS_BUFSIZE */ @@ -358,19 +363,18 @@ int apply_filters(const char* name, /* object name from traverse list */ H5TOOLS_GOTO_ERROR((-1), "invalid filter"); switch (obj.filter[i].filtn) { - /*------------------------------------------------------------------------- - * H5Z_FILTER_NONE 0 , uncompress if compressed - *------------------------------------------------------------------------- - */ - case H5Z_FILTER_NONE: - break; - - /*------------------------------------------------------------------------- - * H5Z_FILTER_DEFLATE 1 , deflation like gzip - *------------------------------------------------------------------------- - */ - case H5Z_FILTER_DEFLATE: - { + /*------------------------------------------------------------------------- + * H5Z_FILTER_NONE 0 , uncompress if compressed + *------------------------------------------------------------------------- + */ + case H5Z_FILTER_NONE: + break; + + /*------------------------------------------------------------------------- + * H5Z_FILTER_DEFLATE 1 , deflation like gzip + *------------------------------------------------------------------------- + */ + case H5Z_FILTER_DEFLATE: { unsigned aggression; /* the deflate level */ aggression = obj.filter[i].cd_values[0]; @@ -379,19 +383,17 @@ int apply_filters(const char* name, /* object name from traverse list */ H5TOOLS_GOTO_ERROR((-1), "H5Pset_chunk failed"); if (H5Pset_deflate(dcpl_id, aggression) < 0) H5TOOLS_GOTO_ERROR((-1), "H5Pset_deflate failed"); - } - break; + } break; - /*------------------------------------------------------------------------- - * H5Z_FILTER_SZIP 4 , szip compression - *------------------------------------------------------------------------- - */ - case H5Z_FILTER_SZIP: - { + /*------------------------------------------------------------------------- + * H5Z_FILTER_SZIP 4 , szip compression + *------------------------------------------------------------------------- + */ + case H5Z_FILTER_SZIP: { unsigned options_mask; unsigned pixels_per_block; - options_mask = obj.filter[i].cd_values[0]; + options_mask = obj.filter[i].cd_values[0]; pixels_per_block = obj.filter[i].cd_values[1]; /* set up for szip data */ @@ -399,70 +401,64 @@ int apply_filters(const char* name, /* object name from traverse list */ H5TOOLS_GOTO_ERROR((-1), "H5Pset_chunk failed"); if (H5Pset_szip(dcpl_id, options_mask, pixels_per_block) < 0) H5TOOLS_GOTO_ERROR((-1), "H5Pset_szip failed"); - } - break; + } break; - /*------------------------------------------------------------------------- - * H5Z_FILTER_SHUFFLE 2 , shuffle the data - *------------------------------------------------------------------------- - */ - case H5Z_FILTER_SHUFFLE: - if (H5Pset_chunk(dcpl_id, obj.chunk.rank, obj.chunk.chunk_lengths) < 0) - H5TOOLS_GOTO_ERROR((-1), "H5Pset_chunk failed"); - if (H5Pset_shuffle(dcpl_id) < 0) - H5TOOLS_GOTO_ERROR((-1), "H5Pset_shuffle failed"); - break; - - /*------------------------------------------------------------------------- - * 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) - H5TOOLS_GOTO_ERROR((-1), "H5Pset_chunk failed"); - if (H5Pset_fletcher32(dcpl_id) < 0) - H5TOOLS_GOTO_ERROR((-1), "H5Pset_fletcher32 failed"); - break; - /*----------- ------------------------------------------------------------- - * H5Z_FILTER_NBIT , NBIT compression - *------------------------------------------------------------------------- - */ - case H5Z_FILTER_NBIT: - if (H5Pset_chunk(dcpl_id, obj.chunk.rank, obj.chunk.chunk_lengths) < 0) - H5TOOLS_GOTO_ERROR((-1), "H5Pset_chunk failed"); - if (H5Pset_nbit(dcpl_id) < 0) - H5TOOLS_GOTO_ERROR((-1), "H5Pset_nbit failed"); - break; - /*----------- ------------------------------------------------------------- - * H5Z_FILTER_SCALEOFFSET , scale+offset compression - *------------------------------------------------------------------------- - */ - case H5Z_FILTER_SCALEOFFSET: - { + /*------------------------------------------------------------------------- + * H5Z_FILTER_SHUFFLE 2 , shuffle the data + *------------------------------------------------------------------------- + */ + case H5Z_FILTER_SHUFFLE: + if (H5Pset_chunk(dcpl_id, obj.chunk.rank, obj.chunk.chunk_lengths) < 0) + H5TOOLS_GOTO_ERROR((-1), "H5Pset_chunk failed"); + if (H5Pset_shuffle(dcpl_id) < 0) + H5TOOLS_GOTO_ERROR((-1), "H5Pset_shuffle failed"); + break; + + /*------------------------------------------------------------------------- + * 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) + H5TOOLS_GOTO_ERROR((-1), "H5Pset_chunk failed"); + if (H5Pset_fletcher32(dcpl_id) < 0) + H5TOOLS_GOTO_ERROR((-1), "H5Pset_fletcher32 failed"); + break; + /*----------- ------------------------------------------------------------- + * H5Z_FILTER_NBIT , NBIT compression + *------------------------------------------------------------------------- + */ + case H5Z_FILTER_NBIT: + if (H5Pset_chunk(dcpl_id, obj.chunk.rank, obj.chunk.chunk_lengths) < 0) + H5TOOLS_GOTO_ERROR((-1), "H5Pset_chunk failed"); + if (H5Pset_nbit(dcpl_id) < 0) + H5TOOLS_GOTO_ERROR((-1), "H5Pset_nbit failed"); + break; + /*----------- ------------------------------------------------------------- + * H5Z_FILTER_SCALEOFFSET , scale+offset compression + *------------------------------------------------------------------------- + */ + case H5Z_FILTER_SCALEOFFSET: { H5Z_SO_scale_type_t scale_type; - int scale_factor; + int scale_factor; - scale_type = (H5Z_SO_scale_type_t) obj.filter[i].cd_values[0]; - scale_factor = (int) obj.filter[i].cd_values[1]; + scale_type = (H5Z_SO_scale_type_t)obj.filter[i].cd_values[0]; + scale_factor = (int)obj.filter[i].cd_values[1]; if (H5Pset_chunk(dcpl_id, obj.chunk.rank, obj.chunk.chunk_lengths) < 0) H5TOOLS_GOTO_ERROR((-1), "H5Pset_chunk failed"); if (H5Pset_scaleoffset(dcpl_id, scale_type, scale_factor) < 0) H5TOOLS_GOTO_ERROR((-1), "H5Pset_scaleoffset failed"); - } - break; - default: - { + } break; + default: { if (H5Pset_chunk(dcpl_id, obj.chunk.rank, obj.chunk.chunk_lengths) < 0) H5TOOLS_GOTO_ERROR((-1), "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) + 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) H5TOOLS_GOTO_ERROR((-1), "H5Pset_filter failed"); - } - break; + } break; } /* switch */ - }/*i*/ + } /*i*/ } /*obj.nfilters*/ @@ -474,7 +470,7 @@ int apply_filters(const char* name, /* object name from traverse list */ if (H5Zfilter_avail(filtobj.filter[i].filtn) <= 0) H5TOOLS_GOTO_ERROR((-1), "%d filter unavailable", filtobj.filter[i].filtn); } /* for */ - } /* nfilters */ + } /* nfilters */ /*------------------------------------------------------------------------- * layout @@ -504,4 +500,3 @@ int apply_filters(const char* name, /* object name from traverse list */ done: return ret_value; } - diff --git a/tools/src/h5repack/h5repack_main.c b/tools/src/h5repack/h5repack_main.c index cf0c611..c38dd66 100644 --- a/tools/src/h5repack/h5repack_main.c +++ b/tools/src/h5repack/h5repack_main.c @@ -18,60 +18,57 @@ /* Name of tool */ #define PROGRAMNAME "h5repack" -static int parse_command_line(int argc, const char **argv, pack_opt_t* options); +static int parse_command_line(int argc, const char **argv, pack_opt_t *options); static void leave(int ret) H5_ATTR_NORETURN; - /* module-scoped variables */ -static int has_i = 0; -static int has_o = 0; -const char *infile = NULL; +static int has_i = 0; +static int has_o = 0; +const char *infile = NULL; const char *outfile = NULL; /* * Command-line options: The user can specify short or long-named * parameters. */ -static const char *s_opts = "a:b:c:d:e:f:hi:j:k:l:m:no:q:s:t:u:vz:EG:LM:P:S:T:VXW1:2:3:4:5:6:"; -static struct long_options l_opts[] = { - { "alignment", require_arg, 'a' }, - { "block", require_arg, 'b' }, - { "compact", require_arg, 'c' }, - { "indexed", require_arg, 'd' }, - { "file", require_arg, 'e' }, - { "filter", require_arg, 'f' }, - { "help", no_arg, 'h' }, - { "infile", require_arg, 'i' }, /* for backward compability */ - { "low", require_arg, 'j' }, - { "high", require_arg, 'k' }, - { "layout", require_arg, 'l' }, - { "minimum", require_arg, 'm' }, - { "native", no_arg, 'n' }, - { "outfile", require_arg, 'o' }, /* for backward compability */ - { "sort_by", require_arg, 'q' }, - { "ssize", require_arg, 's' }, - { "threshold", require_arg, 't' }, - { "ublock", require_arg, 'u' }, - { "verbose", no_arg, 'v' }, - { "sort_order", require_arg, 'z' }, - { "enable-error-stack", no_arg, 'E' }, - { "fs_pagesize", require_arg, 'G' }, - { "latest", no_arg, 'L' }, - { "metadata_block_size", require_arg, 'M' }, - { "fs_persist", require_arg, 'P' }, - { "fs_strategy", require_arg, 'S' }, - { "fs_threshold", require_arg, 'T' }, - { "version", no_arg, 'V' }, - { "merge", no_arg, 'X' }, - { "prune", no_arg, 'W' }, - { "src-vol-value", require_arg, '1' }, - { "src-vol-name", require_arg, '2' }, - { "src-vol-info", require_arg, '3' }, - { "dst-vol-value", require_arg, '4' }, - { "dst-vol-name", require_arg, '5' }, - { "dst-vol-info", require_arg, '6' }, - { NULL, 0, '\0' } -}; +static const char * s_opts = "a:b:c:d:e:f:hi:j:k:l:m:no:q:s:t:u:vz:EG:LM:P:S:T:VXW1:2:3:4:5:6:"; +static struct long_options l_opts[] = {{"alignment", require_arg, 'a'}, + {"block", require_arg, 'b'}, + {"compact", require_arg, 'c'}, + {"indexed", require_arg, 'd'}, + {"file", require_arg, 'e'}, + {"filter", require_arg, 'f'}, + {"help", no_arg, 'h'}, + {"infile", require_arg, 'i'}, /* for backward compability */ + {"low", require_arg, 'j'}, + {"high", require_arg, 'k'}, + {"layout", require_arg, 'l'}, + {"minimum", require_arg, 'm'}, + {"native", no_arg, 'n'}, + {"outfile", require_arg, 'o'}, /* for backward compability */ + {"sort_by", require_arg, 'q'}, + {"ssize", require_arg, 's'}, + {"threshold", require_arg, 't'}, + {"ublock", require_arg, 'u'}, + {"verbose", no_arg, 'v'}, + {"sort_order", require_arg, 'z'}, + {"enable-error-stack", no_arg, 'E'}, + {"fs_pagesize", require_arg, 'G'}, + {"latest", no_arg, 'L'}, + {"metadata_block_size", require_arg, 'M'}, + {"fs_persist", require_arg, 'P'}, + {"fs_strategy", require_arg, 'S'}, + {"fs_threshold", require_arg, 'T'}, + {"version", no_arg, 'V'}, + {"merge", no_arg, 'X'}, + {"prune", no_arg, 'W'}, + {"src-vol-value", require_arg, '1'}, + {"src-vol-name", require_arg, '2'}, + {"src-vol-info", require_arg, '3'}, + {"dst-vol-value", require_arg, '4'}, + {"dst-vol-name", require_arg, '5'}, + {"dst-vol-info", require_arg, '6'}, + {NULL, 0, '\0'}}; /*------------------------------------------------------------------------- * Function: usage @@ -82,7 +79,9 @@ static struct long_options l_opts[] = { * *------------------------------------------------------------------------- */ -static void usage(const char *prog) { +static void +usage(const char *prog) +{ FLUSHSTREAM(rawoutstream); PRINTSTREAM(rawoutstream, "usage: %s [OPTIONS] file1 file2\n", prog); PRINTVALSTREAM(rawoutstream, " file1 Input HDF5 File\n"); @@ -92,105 +91,140 @@ static void usage(const char *prog) { PRINTVALSTREAM(rawoutstream, " -v, --verbose Verbose mode, print object information\n"); PRINTVALSTREAM(rawoutstream, " -V, --version Print version number and exit\n"); PRINTVALSTREAM(rawoutstream, " -n, --native Use a native HDF5 type when repacking\n"); - PRINTVALSTREAM(rawoutstream, " --enable-error-stack Prints messages from the HDF5 error stack as they\n"); + PRINTVALSTREAM(rawoutstream, + " --enable-error-stack Prints messages from the HDF5 error stack as they\n"); PRINTVALSTREAM(rawoutstream, " occur\n"); - PRINTVALSTREAM(rawoutstream, " --src-vol-value Value (ID) of the VOL connector to use for opening the\n"); + PRINTVALSTREAM(rawoutstream, + " --src-vol-value Value (ID) of the VOL connector to use for opening the\n"); PRINTVALSTREAM(rawoutstream, " input HDF5 file specified\n"); - PRINTVALSTREAM(rawoutstream, " --src-vol-name Name of the VOL connector to use for opening the input\n"); + PRINTVALSTREAM(rawoutstream, + " --src-vol-name Name of the VOL connector to use for opening the input\n"); PRINTVALSTREAM(rawoutstream, " HDF5 file specified\n"); - PRINTVALSTREAM(rawoutstream, " --src-vol-info VOL-specific info to pass to the VOL connector used for\n"); + PRINTVALSTREAM(rawoutstream, + " --src-vol-info VOL-specific info to pass to the VOL connector used for\n"); PRINTVALSTREAM(rawoutstream, " opening the input HDF5 file specified\n"); - PRINTVALSTREAM(rawoutstream, " --dst-vol-value Value (ID) of the VOL connector to use for opening the\n"); + PRINTVALSTREAM(rawoutstream, + " --dst-vol-value Value (ID) of the VOL connector to use for opening the\n"); PRINTVALSTREAM(rawoutstream, " output HDF5 file specified\n"); - PRINTVALSTREAM(rawoutstream, " --dst-vol-name Name of the VOL connector to use for opening the output\n"); + PRINTVALSTREAM(rawoutstream, + " --dst-vol-name Name of the VOL connector to use for opening the output\n"); PRINTVALSTREAM(rawoutstream, " HDF5 file specified\n"); - PRINTVALSTREAM(rawoutstream, " --dst-vol-info VOL-specific info to pass to the VOL connector used for\n"); + PRINTVALSTREAM(rawoutstream, + " --dst-vol-info VOL-specific info to pass to the VOL connector used for\n"); PRINTVALSTREAM(rawoutstream, " opening the output HDF5 file specified\n"); PRINTVALSTREAM(rawoutstream, " -L, --latest Use latest version of file format\n"); - PRINTVALSTREAM(rawoutstream, " This option will take precedence over the options\n"); + PRINTVALSTREAM(rawoutstream, + " This option will take precedence over the options\n"); PRINTVALSTREAM(rawoutstream, " --low and --high\n"); - PRINTVALSTREAM(rawoutstream, " --low=BOUND The low bound for library release versions to use\n"); + PRINTVALSTREAM(rawoutstream, + " --low=BOUND The low bound for library release versions to use\n"); PRINTVALSTREAM(rawoutstream, " when creating objects in the file\n"); PRINTVALSTREAM(rawoutstream, " (default is H5F_LIBVER_EARLIEST)\n"); - PRINTVALSTREAM(rawoutstream, " --high=BOUND The high bound for library release versions to use\n"); + PRINTVALSTREAM(rawoutstream, + " --high=BOUND The high bound for library release versions to use\n"); PRINTVALSTREAM(rawoutstream, " when creating objects in the file\n"); PRINTVALSTREAM(rawoutstream, " (default is H5F_LIBVER_LATEST)\n"); - PRINTVALSTREAM(rawoutstream, " --merge Follow external soft link recursively and merge data\n"); - PRINTVALSTREAM(rawoutstream, " --prune Do not follow external soft links and remove link\n"); - PRINTVALSTREAM(rawoutstream, " --merge --prune Follow external link, merge data and remove dangling link\n"); + PRINTVALSTREAM(rawoutstream, + " --merge Follow external soft link recursively and merge data\n"); + PRINTVALSTREAM(rawoutstream, + " --prune Do not follow external soft links and remove link\n"); + PRINTVALSTREAM(rawoutstream, + " --merge --prune Follow external link, merge data and remove dangling link\n"); PRINTVALSTREAM(rawoutstream, " -c L1, --compact=L1 Maximum number of links in header messages\n"); - PRINTVALSTREAM(rawoutstream, " -d L2, --indexed=L2 Minimum number of links in the indexed format\n"); + PRINTVALSTREAM(rawoutstream, + " -d L2, --indexed=L2 Minimum number of links in the indexed format\n"); PRINTVALSTREAM(rawoutstream, " -s S[:F], --ssize=S[:F] Shared object header message minimum size\n"); - PRINTVALSTREAM(rawoutstream, " -m M, --minimum=M Do not apply the filter to datasets smaller than M\n"); + PRINTVALSTREAM(rawoutstream, + " -m M, --minimum=M Do not apply the filter to datasets smaller than M\n"); PRINTVALSTREAM(rawoutstream, " -e E, --file=E Name of file E with the -f and -l options\n"); - PRINTVALSTREAM(rawoutstream, " -u U, --ublock=U Name of file U with user block data to be added\n"); + PRINTVALSTREAM(rawoutstream, + " -u U, --ublock=U Name of file U with user block data to be added\n"); PRINTVALSTREAM(rawoutstream, " -b B, --block=B Size of user block to be added\n"); - PRINTVALSTREAM(rawoutstream, " -M A, --metadata_block_size=A Metadata block size for H5Pset_meta_block_size\n"); + PRINTVALSTREAM(rawoutstream, + " -M A, --metadata_block_size=A Metadata block size for H5Pset_meta_block_size\n"); PRINTVALSTREAM(rawoutstream, " -t T, --threshold=T Threshold value for H5Pset_alignment\n"); PRINTVALSTREAM(rawoutstream, " -a A, --alignment=A Alignment value for H5Pset_alignment\n"); PRINTVALSTREAM(rawoutstream, " -q Q, --sort_by=Q Sort groups and attributes by index Q\n"); PRINTVALSTREAM(rawoutstream, " -z Z, --sort_order=Z Sort groups and attributes by order Z\n"); PRINTVALSTREAM(rawoutstream, " -f FILT, --filter=FILT Filter type\n"); PRINTVALSTREAM(rawoutstream, " -l LAYT, --layout=LAYT Layout type\n"); - PRINTVALSTREAM(rawoutstream, " -S FS_STRATEGY, --fs_strategy=FS_STRATEGY File space management strategy for\n"); + PRINTVALSTREAM(rawoutstream, + " -S FS_STRATEGY, --fs_strategy=FS_STRATEGY File space management strategy for\n"); PRINTVALSTREAM(rawoutstream, " H5Pset_file_space_strategy\n"); - PRINTVALSTREAM(rawoutstream, " -P FS_PERSIST, --fs_persist=FS_PERSIST Persisting or not persisting free-\n"); + PRINTVALSTREAM(rawoutstream, + " -P FS_PERSIST, --fs_persist=FS_PERSIST Persisting or not persisting free-\n"); PRINTVALSTREAM(rawoutstream, " space for H5Pset_file_space_strategy\n"); - PRINTVALSTREAM(rawoutstream, " -T FS_THRESHOLD, --fs_threshold=FS_THRESHOLD Free-space section threshold\n"); + PRINTVALSTREAM(rawoutstream, + " -T FS_THRESHOLD, --fs_threshold=FS_THRESHOLD Free-space section threshold\n"); PRINTVALSTREAM(rawoutstream, " for H5Pset_file_space_strategy\n"); PRINTVALSTREAM(rawoutstream, " -G FS_PAGESIZE, --fs_pagesize=FS_PAGESIZE File space page size for\n"); PRINTVALSTREAM(rawoutstream, " H5Pset_file_space_page_size\n"); PRINTVALSTREAM(rawoutstream, "\n"); - PRINTVALSTREAM(rawoutstream, " M - is an integer greater than 1, size of dataset in bytes (default is 0)\n"); + PRINTVALSTREAM(rawoutstream, + " M - is an integer greater than 1, size of dataset in bytes (default is 0)\n"); PRINTVALSTREAM(rawoutstream, " E - is a filename.\n"); PRINTVALSTREAM(rawoutstream, " S - is an integer\n"); PRINTVALSTREAM(rawoutstream, " U - is a filename.\n"); PRINTVALSTREAM(rawoutstream, " T - is an integer\n"); PRINTVALSTREAM(rawoutstream, " A - is an integer greater than zero\n"); - PRINTVALSTREAM(rawoutstream, " Q - is the sort index type for the input file. It can be \"name\" or\n"); + PRINTVALSTREAM(rawoutstream, + " Q - is the sort index type for the input file. It can be \"name\" or\n"); PRINTVALSTREAM(rawoutstream, " \"creation_order\" (default)\n"); - PRINTVALSTREAM(rawoutstream, " Z - is the sort order type for the input file. It can be \"descending\" or\n"); + PRINTVALSTREAM(rawoutstream, + " Z - is the sort order type for the input file. It can be \"descending\" or\n"); PRINTVALSTREAM(rawoutstream, " \"ascending\" (default)\n"); PRINTVALSTREAM(rawoutstream, " B - is the user block size, any value that is 512 or greater and is\n"); PRINTVALSTREAM(rawoutstream, " a power of 2 (1024 default)\n"); - PRINTVALSTREAM(rawoutstream, " F - is the shared object header message type, any of <dspace|dtype|fill|\n"); + PRINTVALSTREAM(rawoutstream, + " F - is the shared object header message type, any of <dspace|dtype|fill|\n"); PRINTVALSTREAM(rawoutstream, " pline|attr>. If F is not specified, S applies to all messages\n"); PRINTVALSTREAM(rawoutstream, "\n"); - PRINTVALSTREAM(rawoutstream, " BOUND is an integer indicating the library release versions to use when\n"); + PRINTVALSTREAM(rawoutstream, + " BOUND is an integer indicating the library release versions to use when\n"); PRINTVALSTREAM(rawoutstream, " creating objects in the file (see H5Pset_libver_bounds()):\n"); PRINTVALSTREAM(rawoutstream, " 0: This is H5F_LIBVER_EARLIEST in H5F_libver_t struct\n"); PRINTVALSTREAM(rawoutstream, " 1: This is H5F_LIBVER_V18 in H5F_libver_t struct\n"); PRINTVALSTREAM(rawoutstream, " 2: This is H5F_LIBVER_V110 in H5F_libver_t struct\n"); PRINTVALSTREAM(rawoutstream, " 3: This is H5F_LIBVER_V112 in H5F_libver_t struct\n"); PRINTVALSTREAM(rawoutstream, " 4: This is H5F_LIBVER_V114 in H5F_libver_t struct\n"); - PRINTVALSTREAM(rawoutstream, " (H5F_LIBVER_LATEST is aliased to H5F_LIBVER_V114 for this release\n"); + PRINTVALSTREAM(rawoutstream, + " (H5F_LIBVER_LATEST is aliased to H5F_LIBVER_V114 for this release\n"); PRINTVALSTREAM(rawoutstream, "\n"); PRINTVALSTREAM(rawoutstream, " FS_STRATEGY is a string indicating the file space strategy used:\n"); PRINTVALSTREAM(rawoutstream, " FSM_AGGR:\n"); - PRINTVALSTREAM(rawoutstream, " The mechanisms used in managing file space are free-space\n"); + PRINTVALSTREAM(rawoutstream, + " The mechanisms used in managing file space are free-space\n"); PRINTVALSTREAM(rawoutstream, " managers, aggregators and virtual file driver.\n"); PRINTVALSTREAM(rawoutstream, " PAGE:\n"); - PRINTVALSTREAM(rawoutstream, " The mechanisms used in managing file space are free-space\n"); - PRINTVALSTREAM(rawoutstream, " managers with embedded paged aggregation and virtual file driver.\n"); + PRINTVALSTREAM(rawoutstream, + " The mechanisms used in managing file space are free-space\n"); + PRINTVALSTREAM(rawoutstream, + " managers with embedded paged aggregation and virtual file driver.\n"); PRINTVALSTREAM(rawoutstream, " AGGR:\n"); - PRINTVALSTREAM(rawoutstream, " The mechanisms used in managing file space are aggregators and\n"); + PRINTVALSTREAM(rawoutstream, + " The mechanisms used in managing file space are aggregators and\n"); PRINTVALSTREAM(rawoutstream, " virtual file driver.\n"); PRINTVALSTREAM(rawoutstream, " NONE:\n"); - PRINTVALSTREAM(rawoutstream, " The mechanisms used in managing file space are virtual file\n"); + PRINTVALSTREAM(rawoutstream, + " The mechanisms used in managing file space are virtual file\n"); PRINTVALSTREAM(rawoutstream, " driver.\n"); - PRINTVALSTREAM(rawoutstream, " The default strategy when not set is FSM_AGGR without persisting free-\n"); + PRINTVALSTREAM(rawoutstream, + " The default strategy when not set is FSM_AGGR without persisting free-\n"); PRINTVALSTREAM(rawoutstream, " space.\n"); PRINTVALSTREAM(rawoutstream, "\n"); - PRINTVALSTREAM(rawoutstream, " FS_PERSIST is 1 to persisting free-space or 0 to not persisting free-space.\n"); + PRINTVALSTREAM(rawoutstream, + " FS_PERSIST is 1 to persisting free-space or 0 to not persisting free-space.\n"); PRINTVALSTREAM(rawoutstream, " The default when not set is not persisting free-space.\n"); PRINTVALSTREAM(rawoutstream, " The value is ignored for AGGR and NONE strategies.\n"); PRINTVALSTREAM(rawoutstream, "\n"); - PRINTVALSTREAM(rawoutstream, " FS_THRESHOLD is the minimum size (in bytes) of free-space sections to be\n"); + PRINTVALSTREAM(rawoutstream, + " FS_THRESHOLD is the minimum size (in bytes) of free-space sections to be\n"); PRINTVALSTREAM(rawoutstream, " tracked by the library.\n"); PRINTVALSTREAM(rawoutstream, " The default when not set is 1.\n"); PRINTVALSTREAM(rawoutstream, " The value is ignored for AGGR and NONE strategies.\n"); PRINTVALSTREAM(rawoutstream, "\n"); - PRINTVALSTREAM(rawoutstream, " FS_PAGESIZE is the size (in bytes) >=512 that is used by the library when\n"); + PRINTVALSTREAM(rawoutstream, + " FS_PAGESIZE is the size (in bytes) >=512 that is used by the library when\n"); PRINTVALSTREAM(rawoutstream, " the file space strategy PAGE is used.\n"); PRINTVALSTREAM(rawoutstream, " The default when not set is 4096.\n"); PRINTVALSTREAM(rawoutstream, "\n"); @@ -198,8 +232,10 @@ static void usage(const char *prog) { PRINTVALSTREAM(rawoutstream, "\n"); PRINTVALSTREAM(rawoutstream, " <list of objects>:<name of filter>=<filter parameters>\n"); PRINTVALSTREAM(rawoutstream, "\n"); - PRINTVALSTREAM(rawoutstream, " <list of objects> is a comma separated list of object names, meaning apply\n"); - PRINTVALSTREAM(rawoutstream, " compression only to those objects. If no names are specified, the filter\n"); + PRINTVALSTREAM(rawoutstream, + " <list of objects> is a comma separated list of object names, meaning apply\n"); + PRINTVALSTREAM(rawoutstream, + " compression only to those objects. If no names are specified, the filter\n"); PRINTVALSTREAM(rawoutstream, " is applied to all objects\n"); PRINTVALSTREAM(rawoutstream, " <name of filter> can be:\n"); PRINTVALSTREAM(rawoutstream, " GZIP, to apply the HDF5 GZIP filter (GZIP compression)\n"); @@ -212,15 +248,19 @@ static void usage(const char *prog) { PRINTVALSTREAM(rawoutstream, " NONE, to remove all filters\n"); PRINTVALSTREAM(rawoutstream, " <filter parameters> is optional filter parameter information\n"); PRINTVALSTREAM(rawoutstream, " GZIP=<deflation level> from 1-9\n"); - PRINTVALSTREAM(rawoutstream, " SZIP=<pixels per block,coding> pixels per block is a even number in\n"); + PRINTVALSTREAM(rawoutstream, + " SZIP=<pixels per block,coding> pixels per block is a even number in\n"); PRINTVALSTREAM(rawoutstream, " 2-32 and coding method is either EC or NN\n"); PRINTVALSTREAM(rawoutstream, " SHUF (no parameter)\n"); PRINTVALSTREAM(rawoutstream, " FLET (no parameter)\n"); PRINTVALSTREAM(rawoutstream, " NBIT (no parameter)\n"); - PRINTVALSTREAM(rawoutstream, " SOFF=<scale_factor,scale_type> scale_factor is an integer and scale_type\n"); + PRINTVALSTREAM(rawoutstream, + " SOFF=<scale_factor,scale_type> scale_factor is an integer and scale_type\n"); PRINTVALSTREAM(rawoutstream, " is either IN or DS\n"); - PRINTVALSTREAM(rawoutstream, " UD=<filter_number,filter_flag,cd_value_count,value1[,value2,...,valueN]>\n"); - PRINTVALSTREAM(rawoutstream, " Required values: filter_number, filter_flag, cd_value_count, value1\n"); + PRINTVALSTREAM(rawoutstream, + " UD=<filter_number,filter_flag,cd_value_count,value1[,value2,...,valueN]>\n"); + PRINTVALSTREAM(rawoutstream, + " Required values: filter_number, filter_flag, cd_value_count, value1\n"); PRINTVALSTREAM(rawoutstream, " Optional values: value2 to valueN\n"); PRINTVALSTREAM(rawoutstream, " NONE (no parameter)\n"); PRINTVALSTREAM(rawoutstream, "\n"); @@ -228,8 +268,10 @@ static void usage(const char *prog) { PRINTVALSTREAM(rawoutstream, "\n"); PRINTVALSTREAM(rawoutstream, " <list of objects>:<layout type>=<layout parameters>\n"); PRINTVALSTREAM(rawoutstream, "\n"); - PRINTVALSTREAM(rawoutstream, " <list of objects> is a comma separated list of object names, meaning that\n"); - PRINTVALSTREAM(rawoutstream, " layout information is supplied for those objects. If no names are\n"); + PRINTVALSTREAM(rawoutstream, + " <list of objects> is a comma separated list of object names, meaning that\n"); + PRINTVALSTREAM(rawoutstream, + " layout information is supplied for those objects. If no names are\n"); PRINTVALSTREAM(rawoutstream, " specified, the layout type is applied to all objects\n"); PRINTVALSTREAM(rawoutstream, " <layout type> can be:\n"); PRINTVALSTREAM(rawoutstream, " CHUNK, to apply chunking layout\n"); @@ -248,11 +290,14 @@ static void usage(const char *prog) { PRINTVALSTREAM(rawoutstream, "\n"); PRINTVALSTREAM(rawoutstream, "2) h5repack -v -f dset1:SZIP=8,NN file1 file2\n"); PRINTVALSTREAM(rawoutstream, "\n"); - PRINTVALSTREAM(rawoutstream, " SZIP compression with 8 pixels per block and NN coding method to object dset1\n"); + PRINTVALSTREAM(rawoutstream, + " SZIP compression with 8 pixels per block and NN coding method to object dset1\n"); PRINTVALSTREAM(rawoutstream, "\n"); - PRINTVALSTREAM(rawoutstream, "3) h5repack -v -l dset1,dset2:CHUNK=20x10 -f dset3,dset4,dset5:NONE file1 file2\n"); + PRINTVALSTREAM(rawoutstream, + "3) h5repack -v -l dset1,dset2:CHUNK=20x10 -f dset3,dset4,dset5:NONE file1 file2\n"); PRINTVALSTREAM(rawoutstream, "\n"); - PRINTVALSTREAM(rawoutstream, " Chunked layout, with a layout size of 20x10, to objects dset1 and dset2\n"); + PRINTVALSTREAM(rawoutstream, + " Chunked layout, with a layout size of 20x10, to objects dset1 and dset2\n"); PRINTVALSTREAM(rawoutstream, " and remove filters to objects dset3, dset4, dset5\n"); PRINTVALSTREAM(rawoutstream, "\n"); PRINTVALSTREAM(rawoutstream, "4) h5repack -L -c 10 -s 20:dtype file1 file2\n"); @@ -283,7 +328,8 @@ static void usage(const char *prog) { * Return: Does not return *------------------------------------------------------------------------- */ -static void leave(int ret) +static void +leave(int ret) { h5tools_close(); HDexit(ret); @@ -297,15 +343,15 @@ static void leave(int ret) * Return: void, exit on error *------------------------------------------------------------------------- */ -static -int read_info(const char *filename, pack_opt_t *options) +static int +read_info(const char *filename, pack_opt_t *options) { - char stype[10] = {0, 0, 0, 0, 0, 0, 0, 0, 0, 0}; - char comp_info[1024]; + char stype[10] = {0, 0, 0, 0, 0, 0, 0, 0, 0, 0}; + char comp_info[1024]; FILE *fp = NULL; - char c; - int i; - int ret_value = EXIT_SUCCESS; + char c; + int i; + int ret_value = EXIT_SUCCESS; if (NULL == (fp = HDfopen(filename, "r"))) { error_msg("cannot open options file %s\n", filename); @@ -320,7 +366,7 @@ int read_info(const char *filename, pack_opt_t *options) break; /* Info indicator must be for layout or filter */ - if (HDstrcmp(stype,"-l") && HDstrcmp(stype, "-f")) { + if (HDstrcmp(stype, "-l") && HDstrcmp(stype, "-f")) { error_msg("bad file format for %s", filename); h5tools_setstatus(EXIT_FAILURE); ret_value = EXIT_FAILURE; @@ -434,16 +480,16 @@ set_sort_order(const char *form) * Purpose: parse command line input *------------------------------------------------------------------------- */ -static -int parse_command_line(int argc, const char **argv, pack_opt_t* options) +static int +parse_command_line(int argc, const char **argv, pack_opt_t *options) { h5tools_vol_info_t in_vol_info; h5tools_vol_info_t out_vol_info; - hbool_t custom_in_fapl = FALSE; - hbool_t custom_out_fapl = FALSE; - hid_t tmp_fapl = H5I_INVALID_HID; - int bound, opt; - int ret_value = 0; + hbool_t custom_in_fapl = FALSE; + hbool_t custom_out_fapl = FALSE; + hid_t tmp_fapl = H5I_INVALID_HID; + int bound, opt; + int ret_value = 0; /* Initialize fapl info structs */ HDmemset(&in_vol_info, 0, sizeof(h5tools_vol_info_t)); @@ -451,7 +497,7 @@ int parse_command_line(int argc, const char **argv, pack_opt_t* options) /* parse command line options */ while (EOF != (opt = get_option(argc, argv, s_opts, l_opts))) { - switch ((char) opt) { + switch ((char)opt) { /* -i for backward compatibility */ case 'i': @@ -502,8 +548,8 @@ int parse_command_line(int argc, const char **argv, pack_opt_t* options) break; case 'm': - options->min_comp = HDstrtoull(opt_arg , NULL, 0); - if ((int) options->min_comp <= 0) { + options->min_comp = HDstrtoull(opt_arg, NULL, 0); + if ((int)options->min_comp <= 0) { error_msg("invalid minimum compress size <%s>\n", opt_arg); h5tools_setstatus(EXIT_FAILURE); ret_value = -1; @@ -559,66 +605,64 @@ int parse_command_line(int argc, const char **argv, pack_opt_t* options) break; case 'c': - options->grp_compact = HDatoi( opt_arg ); + options->grp_compact = HDatoi(opt_arg); if (options->grp_compact > 0) options->latest = TRUE; /* must use latest format */ break; case 'd': - options->grp_indexed = HDatoi( opt_arg ); + options->grp_indexed = HDatoi(opt_arg); if (options->grp_indexed > 0) options->latest = TRUE; /* must use latest format */ break; - case 's': - { - int idx = 0; - int ssize = 0; - char *msgPtr = HDstrchr(opt_arg, ':'); - options->latest = TRUE; /* must use latest format */ - if (msgPtr == NULL) { - ssize = HDatoi(opt_arg); - for (idx = 0; idx < 5; idx++) - options->msg_size[idx] = ssize; - } - else { - char msgType[10]; - - HDstrcpy(msgType, msgPtr + 1); - msgPtr[0] = '\0'; - ssize = HDatoi( opt_arg ); - if (!HDstrncmp(msgType, "dspace", 6)) - options->msg_size[0] = ssize; - else if (!HDstrncmp(msgType, "dtype", 5)) - options->msg_size[1] = ssize; - else if (!HDstrncmp(msgType, "fill", 4)) - options->msg_size[2] = ssize; - else if (!HDstrncmp(msgType, "pline", 5)) - options->msg_size[3] = ssize; - else if (!HDstrncmp(msgType, "attr", 4)) - options->msg_size[4] = ssize; - } + case 's': { + int idx = 0; + int ssize = 0; + char *msgPtr = HDstrchr(opt_arg, ':'); + options->latest = TRUE; /* must use latest format */ + if (msgPtr == NULL) { + ssize = HDatoi(opt_arg); + for (idx = 0; idx < 5; idx++) + options->msg_size[idx] = ssize; } - break; + else { + char msgType[10]; + + HDstrcpy(msgType, msgPtr + 1); + msgPtr[0] = '\0'; + ssize = HDatoi(opt_arg); + if (!HDstrncmp(msgType, "dspace", 6)) + options->msg_size[0] = ssize; + else if (!HDstrncmp(msgType, "dtype", 5)) + options->msg_size[1] = ssize; + else if (!HDstrncmp(msgType, "fill", 4)) + options->msg_size[2] = ssize; + else if (!HDstrncmp(msgType, "pline", 5)) + options->msg_size[3] = ssize; + else if (!HDstrncmp(msgType, "attr", 4)) + options->msg_size[4] = ssize; + } + } break; case 'u': options->ublock_filename = opt_arg; break; case 'b': - options->ublock_size = (hsize_t) HDatol( opt_arg ); + options->ublock_size = (hsize_t)HDatol(opt_arg); break; case 'M': - options->meta_block_size = (hsize_t) HDatol( opt_arg ); + options->meta_block_size = (hsize_t)HDatol(opt_arg); break; case 't': - options->threshold = (hsize_t) HDatol( opt_arg ); + options->threshold = (hsize_t)HDatol(opt_arg); break; case 'a': - options->alignment = HDstrtoull(opt_arg , NULL, 0); + options->alignment = HDstrtoull(opt_arg, NULL, 0); if (options->alignment < 1) { error_msg("invalid alignment size\n", opt_arg); h5tools_setstatus(EXIT_FAILURE); @@ -627,30 +671,28 @@ int parse_command_line(int argc, const char **argv, pack_opt_t* options) } break; - case 'S': - { - char strategy[MAX_NC_NAME]; - - HDstrcpy(strategy, opt_arg); - if (!HDstrcmp(strategy, "FSM_AGGR")) - options->fs_strategy = H5F_FSPACE_STRATEGY_FSM_AGGR; - else if (!HDstrcmp(strategy, "PAGE")) - options->fs_strategy = H5F_FSPACE_STRATEGY_PAGE; - else if (!HDstrcmp(strategy, "AGGR")) - options->fs_strategy = H5F_FSPACE_STRATEGY_AGGR; - else if (!HDstrcmp(strategy, "NONE")) - options->fs_strategy = H5F_FSPACE_STRATEGY_NONE; - else { - error_msg("invalid file space management strategy\n", opt_arg); - h5tools_setstatus(EXIT_FAILURE); - ret_value = -1; - goto done; - } - if (options->fs_strategy == (H5F_fspace_strategy_t)0) - /* To distinguish the "specified" zero value */ - options->fs_strategy = (H5F_fspace_strategy_t)-1; + case 'S': { + char strategy[MAX_NC_NAME]; + + HDstrcpy(strategy, opt_arg); + if (!HDstrcmp(strategy, "FSM_AGGR")) + options->fs_strategy = H5F_FSPACE_STRATEGY_FSM_AGGR; + else if (!HDstrcmp(strategy, "PAGE")) + options->fs_strategy = H5F_FSPACE_STRATEGY_PAGE; + else if (!HDstrcmp(strategy, "AGGR")) + options->fs_strategy = H5F_FSPACE_STRATEGY_AGGR; + else if (!HDstrcmp(strategy, "NONE")) + options->fs_strategy = H5F_FSPACE_STRATEGY_NONE; + else { + error_msg("invalid file space management strategy\n", opt_arg); + h5tools_setstatus(EXIT_FAILURE); + ret_value = -1; + goto done; } - break; + if (options->fs_strategy == (H5F_fspace_strategy_t)0) + /* To distinguish the "specified" zero value */ + options->fs_strategy = (H5F_fspace_strategy_t)-1; + } break; case 'P': options->fs_persist = HDatoi(opt_arg); @@ -670,7 +712,7 @@ int parse_command_line(int argc, const char **argv, pack_opt_t* options) options->fs_pagesize = HDstrtoll(opt_arg, NULL, 0); if (options->fs_pagesize == 0) /* To distinguish the "specified" zero value */ - options->fs_pagesize = -1; + options->fs_pagesize = -1; break; case 'q': @@ -696,15 +738,15 @@ int parse_command_line(int argc, const char **argv, pack_opt_t* options) break; case '1': - in_vol_info.type = VOL_BY_VALUE; + in_vol_info.type = VOL_BY_VALUE; in_vol_info.u.value = (H5VL_class_value_t)HDatoi(opt_arg); - custom_in_fapl = TRUE; + custom_in_fapl = TRUE; break; case '2': - in_vol_info.type = VOL_BY_NAME; + in_vol_info.type = VOL_BY_NAME; in_vol_info.u.name = opt_arg; - custom_in_fapl = TRUE; + custom_in_fapl = TRUE; break; case '3': @@ -712,15 +754,15 @@ int parse_command_line(int argc, const char **argv, pack_opt_t* options) break; case '4': - out_vol_info.type = VOL_BY_VALUE; + out_vol_info.type = VOL_BY_VALUE; out_vol_info.u.value = (H5VL_class_value_t)HDatoi(opt_arg); - custom_out_fapl = TRUE; + custom_out_fapl = TRUE; break; case '5': - out_vol_info.type = VOL_BY_NAME; + out_vol_info.type = VOL_BY_NAME; out_vol_info.u.name = opt_arg; - custom_out_fapl = TRUE; + custom_out_fapl = TRUE; break; case '6': @@ -730,12 +772,12 @@ int parse_command_line(int argc, const char **argv, pack_opt_t* options) default: break; } /* end switch */ - } /* end while there are more options to parse */ + } /* end while there are more options to parse */ /* If neither -i nor -o given, get in and out files positionally */ if (0 == (has_i + has_o)) { if (argv[opt_ind] != NULL && argv[opt_ind + 1] != NULL) { - infile = argv[opt_ind]; + infile = argv[opt_ind]; outfile = argv[opt_ind + 1]; if (!HDstrcmp(infile, outfile)) { @@ -814,10 +856,11 @@ done: * Failure: EXIT_FAILURE(1) *------------------------------------------------------------------------- */ -int main(int argc, const char **argv) +int +main(int argc, const char **argv) { - pack_opt_t options; /*the global options */ - int parse_ret; + pack_opt_t options; /*the global options */ + int parse_ret; HDmemset(&options, 0, sizeof(pack_opt_t)); @@ -879,4 +922,3 @@ done: leave(h5tools_getstatus()); } - diff --git a/tools/src/h5repack/h5repack_opttable.c b/tools/src/h5repack/h5repack_opttable.c index 56fc12d..bb90b58 100644 --- a/tools/src/h5repack/h5repack_opttable.c +++ b/tools/src/h5repack/h5repack_opttable.c @@ -21,24 +21,25 @@ * Purpose: initialize a pack_info_t structure * * Return: void - *------------------------------------------------------------------------- + *------------------------------------------------------------------------- */ -void init_packobject(pack_info_t *obj) +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; + 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; + obj->refobj_id = -1; + obj->layout = H5D_LAYOUT_ERROR; + obj->nfilters = 0; } /*------------------------------------------------------------------------- @@ -50,7 +51,8 @@ void init_packobject(pack_info_t *obj) *------------------------------------------------------------------------- */ -static void aux_tblinsert_filter(pack_opttbl_t *table, unsigned int I, filter_info_t filt) +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; @@ -66,7 +68,8 @@ static void aux_tblinsert_filter(pack_opttbl_t *table, unsigned int I, filter_in * Return: void *------------------------------------------------------------------------- */ -static void aux_tblinsert_layout(pack_opttbl_t *table, unsigned int I, pack_info_t *pack) +static void +aux_tblinsert_layout(pack_opttbl_t *table, unsigned int I, pack_info_t *pack) { int k; @@ -75,15 +78,14 @@ static void aux_tblinsert_layout(pack_opttbl_t *table, unsigned int I, pack_info /* -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].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]; + table->objs[I].chunk.chunk_lengths[k] = pack->chunk.chunk_lengths[k]; } } } @@ -100,10 +102,10 @@ static int aux_inctable(pack_opttbl_t *table, unsigned n_objs) { unsigned u; - int ret_value = 0; + int ret_value = 0; table->size += n_objs; - table->objs = (pack_info_t*) HDrealloc(table->objs, table->size * sizeof(pack_info_t)); + table->objs = (pack_info_t *)HDrealloc(table->objs, table->size * sizeof(pack_info_t)); if (table->objs == NULL) { H5TOOLS_INFO("not enough memory for options table"); ret_value = -1; @@ -116,27 +118,28 @@ aux_inctable(pack_opttbl_t *table, unsigned n_objs) return ret_value; } - /*------------------------------------------------------------------------- * Function: options_table_init * * Purpose: init options table * * Return: 0, ok, -1, fail - *------------------------------------------------------------------------- + *------------------------------------------------------------------------- */ -int options_table_init(pack_opttbl_t **tbl) { - unsigned int i; +int +options_table_init(pack_opttbl_t **tbl) +{ + unsigned int i; pack_opttbl_t *table; - int ret_value = 0; + int ret_value = 0; - if (NULL == (table = (pack_opttbl_t *) HDmalloc(sizeof(pack_opttbl_t)))) { + if (NULL == (table = (pack_opttbl_t *)HDmalloc(sizeof(pack_opttbl_t)))) { H5TOOLS_GOTO_ERROR((-1), "not enough memory for options table"); } - table->size = 30; + table->size = 30; table->nelems = 0; - if (NULL == (table->objs = (pack_info_t*) HDmalloc(table->size * sizeof(pack_info_t)))) { + if (NULL == (table->objs = (pack_info_t *)HDmalloc(table->size * sizeof(pack_info_t)))) { HDfree(table); H5TOOLS_GOTO_ERROR((-1), "not enough memory for options table"); } @@ -149,7 +152,6 @@ done: return ret_value; } - /*------------------------------------------------------------------------- * Function: options_table_free * @@ -159,7 +161,9 @@ done: *------------------------------------------------------------------------- */ -int options_table_free(pack_opttbl_t *table) { +int +options_table_free(pack_opttbl_t *table) +{ HDfree(table->objs); HDfree(table); return 0; @@ -171,15 +175,15 @@ 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; - hbool_t found = FALSE; - int ret_value = 0; + unsigned added = 0; + hbool_t found = FALSE; + int ret_value = 0; /* increase the size of the collection by N_OBJS if necessary */ if (table->nelems + n_objs >= table->size) @@ -193,7 +197,7 @@ options_add_layout(obj_list_t *obj_list, unsigned n_objs, pack_info_t *pack, pa /* linear table search */ for (i = 0; i < table->nelems; i++) { /*already on the table */ - if (HDstrcmp(obj_list[j].obj,table->objs[i].path) == 0) { + 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) { H5TOOLS_INFO("chunk information already inserted for <%s>\n", obj_list[j].obj); @@ -206,7 +210,7 @@ options_add_layout(obj_list_t *obj_list, unsigned n_objs, pack_info_t *pack, pa break; } } /* if */ - } /* i */ + } /* i */ if (!found) { /* keep the grow in a temp var */ @@ -220,14 +224,13 @@ options_add_layout(obj_list_t *obj_list, unsigned n_objs, pack_info_t *pack, pa -f dset1:GZIP=1 -l dset1,dset2:CHUNK=20x20 dset1 is already inserted, but dset2 must also be */ - else - if(found && HDstrcmp(obj_list[j].obj,table->objs[i].path) != 0) { - /* keep the grow in a temp var */ - I = table->nelems + added; - added++; - HDstrcpy(table->objs[I].path, obj_list[j].obj); - aux_tblinsert_layout(table, I, pack); - } + else if (found && HDstrcmp(obj_list[j].obj, table->objs[i].path) != 0) { + /* keep the grow in a temp var */ + I = table->nelems + added; + added++; + HDstrcpy(table->objs[I].path, obj_list[j].obj); + aux_tblinsert_layout(table, I, pack); + } } /* j */ } /* first time insertion */ @@ -258,8 +261,8 @@ int 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; - hbool_t found = FALSE; + unsigned added = 0; + hbool_t found = FALSE; /* increase the size of the collection by N_OBJS if necessary */ if (table->nelems + n_objs >= table->size) @@ -279,7 +282,7 @@ options_add_filter(obj_list_t *obj_list, unsigned n_objs, filter_info_t filt, pa found = TRUE; break; } /* if */ - } /* i */ + } /* i */ if (!found) { /* keep the grow in a temp var */ @@ -293,14 +296,13 @@ options_add_filter(obj_list_t *obj_list, unsigned n_objs, filter_info_t filt, pa -l dset1:CHUNK=20x20 -f dset1,dset2:GZIP=1 dset1 is already inserted, but dset2 must also be */ - else - if(found && HDstrcmp(obj_list[j].obj,table->objs[i].path) != 0) { - /* keep the grow in a temp var */ - I = table->nelems + added; - added++; - HDstrcpy(table->objs[I].path, obj_list[j].obj); - aux_tblinsert_filter(table, I, filt); - } + else if (found && HDstrcmp(obj_list[j].obj, table->objs[i].path) != 0) { + /* keep the grow in a temp var */ + I = table->nelems + added; + added++; + HDstrcpy(table->objs[I].path, obj_list[j].obj); + aux_tblinsert_filter(table, I, filt); + } } /* j */ } @@ -329,9 +331,11 @@ options_add_filter(obj_list_t *obj_list, unsigned n_objs, filter_info_t filt, pa *------------------------------------------------------------------------- */ -pack_info_t* options_get_object(const char *path, pack_opttbl_t *table) { +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 */ + 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 */ diff --git a/tools/src/h5repack/h5repack_parse.c b/tools/src/h5repack/h5repack_parse.c index 50ccd7a..b02f2cf 100644 --- a/tools/src/h5repack/h5repack_parse.c +++ b/tools/src/h5repack/h5repack_parse.c @@ -37,8 +37,9 @@ * "A,B:NONE" *------------------------------------------------------------------------- */ -obj_list_t* parse_filter(const char *str, unsigned *n_objs, filter_info_t *filt, - pack_opt_t *options, int *is_glb) { +obj_list_t * +parse_filter(const char *str, unsigned *n_objs, filter_info_t *filt, pack_opt_t *options, int *is_glb) +{ size_t i, m, u; char c; size_t len = HDstrlen(str); @@ -48,7 +49,7 @@ obj_list_t* parse_filter(const char *str, unsigned *n_objs, filter_info_t *filt, char scomp[16] = {0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}; char stype[16] = {0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}; char smask[16] = {0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}; - obj_list_t* obj_list = NULL; + obj_list_t *obj_list = NULL; unsigned pixels_per_block; /* initialize compression info */ @@ -59,7 +60,7 @@ obj_list_t* parse_filter(const char *str, unsigned *n_objs, filter_info_t *filt, for (i = 0, n = 0; i < len; i++) { c = str[i]; if (c == ':') { - end_obj = (int) i; + end_obj = (int)i; break; } if (c == ',') @@ -71,13 +72,13 @@ obj_list_t* parse_filter(const char *str, unsigned *n_objs, filter_info_t *filt, if (end_obj == -1) { /* apply to all objects */ options->all_filter = 1; - *is_glb = 1; - *n_objs = 1; + *is_glb = 1; + *n_objs = 1; } else *n_objs = n; - obj_list = (obj_list_t *) HDmalloc(n * sizeof(obj_list_t)); + 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; @@ -85,10 +86,10 @@ obj_list_t* parse_filter(const char *str, unsigned *n_objs, filter_info_t *filt, /* get object list */ if (end_obj > 0) - for (j = 0, k = 0, n = 0; j < (unsigned) end_obj; j++, k++) { - c = str[j]; + for (j = 0, k = 0, n = 0; j < (unsigned)end_obj; j++, k++) { + c = str[j]; sobj[k] = c; - if (c == ',' || j == (unsigned) (end_obj - 1)) { + if (c == ',' || j == (unsigned)(end_obj - 1)) { if (c == ',') sobj[k] = '\0'; else @@ -101,7 +102,7 @@ obj_list_t* parse_filter(const char *str, unsigned *n_objs, filter_info_t *filt, } } /* nothing after : */ - if (end_obj + 1 == (int) len) { + if (end_obj + 1 == (int)len) { if (obj_list) HDfree(obj_list); error_msg("input Error: Invalid compression type in <%s>\n", str); @@ -111,25 +112,25 @@ obj_list_t* parse_filter(const char *str, unsigned *n_objs, filter_info_t *filt, /* get filter additional parameters */ m = 0; for (i = (size_t)(end_obj + 1), k = 0, j = 0; i < len; i++, k++) { - c = str[i]; + c = str[i]; scomp[k] = c; if (c == '=' || i == len - 1) { - if (c == '=') { /*one more parameter */ + if (c == '=') { /*one more parameter */ scomp[k] = '\0'; /*cut space */ /*------------------------------------------------------------------------- - * H5Z_FILTER_SZIP - * szip has the format SZIP=<pixels per block,coding> - * pixels per block is a even number in 2-32 and coding method is 'EC' or 'NN' - * example SZIP=8,NN - *------------------------------------------------------------------------- - */ + * H5Z_FILTER_SZIP + * szip has the format SZIP=<pixels per block,coding> + * pixels per block is a even number in 2-32 and coding method is 'EC' or 'NN' + * example SZIP=8,NN + *------------------------------------------------------------------------- + */ if (HDstrcmp(scomp, "SZIP") == 0) { l = -1; /* mask index check */ for (m = 0, u = i + 1; u < len; u++, m++) { if (str[u] == ',') { stype[m] = '\0'; /* end digit of szip */ - l = 0; /* start EC or NN search */ - u++; /* skip ',' */ + l = 0; /* start EC or NN search */ + u++; /* skip ',' */ } c = str[u]; if (!HDisdigit(c) && l == -1) { @@ -145,10 +146,10 @@ obj_list_t* parse_filter(const char *str, unsigned *n_objs, filter_info_t *filt, l++; if (l == 2) { smask[l] = '\0'; - i = len - 1; /* end */ - if (HDstrcmp(smask,"NN") == 0) + i = len - 1; /* end */ + if (HDstrcmp(smask, "NN") == 0) filt->cd_values[j++] = H5_SZIP_NN_OPTION_MASK; - else if (HDstrcmp(smask,"EC") == 0) + else if (HDstrcmp(smask, "EC") == 0) filt->cd_values[j++] = H5_SZIP_EC_OPTION_MASK; else { error_msg("szip mask must be 'NN' or 'EC' \n"); @@ -157,29 +158,29 @@ obj_list_t* parse_filter(const char *str, unsigned *n_objs, filter_info_t *filt, } } } /* u */ - } /*if */ + } /*if */ /*------------------------------------------------------------------------- - * H5Z_FILTER_SCALEOFFSET - * scaleoffset has the format SOFF=<scale_factor,scale_type> - * scale_type can be - * integer datatype, H5Z_SO_INT (IN) - * float datatype using D-scaling method, H5Z_SO_FLOAT_DSCALE (DS) - * float datatype using E-scaling method, H5Z_SO_FLOAT_ESCALE (ES) , not yet implemented - * for integer datatypes, scale_factor denotes Minimum Bits - * for float datatypes, scale_factor denotes decimal scale factor - * examples - * SOFF=31,IN - * SOFF=3,DF - *------------------------------------------------------------------------- - */ + * H5Z_FILTER_SCALEOFFSET + * scaleoffset has the format SOFF=<scale_factor,scale_type> + * scale_type can be + * integer datatype, H5Z_SO_INT (IN) + * float datatype using D-scaling method, H5Z_SO_FLOAT_DSCALE (DS) + * float datatype using E-scaling method, H5Z_SO_FLOAT_ESCALE (ES) , not yet implemented + * for integer datatypes, scale_factor denotes Minimum Bits + * for float datatypes, scale_factor denotes decimal scale factor + * examples + * SOFF=31,IN + * SOFF=3,DF + *------------------------------------------------------------------------- + */ else if (HDstrcmp(scomp, "SOFF") == 0) { l = -1; /* mask index check */ for (m = 0, u = i + 1; u < len; u++, m++) { if (str[u] == ',') { stype[m] = '\0'; /* end digit */ - l = 0; /* start 'IN' , 'DS', or 'ES' search */ - u++; /* skip ',' */ + l = 0; /* start 'IN' , 'DS', or 'ES' search */ + u++; /* skip ',' */ } c = str[u]; if (!HDisdigit(c) && l == -1) { @@ -195,8 +196,8 @@ obj_list_t* parse_filter(const char *str, unsigned *n_objs, filter_info_t *filt, l++; if (l == 2) { smask[l] = '\0'; - i = len - 1; /* end */ - if (HDstrcmp(smask,"IN") == 0) + i = len - 1; /* end */ + if (HDstrcmp(smask, "IN") == 0) filt->cd_values[j++] = H5Z_SO_INT; else if (HDstrcmp(smask, "DS") == H5Z_SO_FLOAT_DSCALE) filt->cd_values[j++] = H5Z_SO_FLOAT_DSCALE; @@ -207,15 +208,15 @@ obj_list_t* parse_filter(const char *str, unsigned *n_objs, filter_info_t *filt, } } } /* u */ - } /*if */ + } /*if */ /*------------------------------------------------------------------------- - * User Defined - * has the format UD=<filter_number,filter_flag,cd_value_count,value_1[,value_2,...,value_N]> - * BZIP2 example - * UD=307,0,1,9 - *------------------------------------------------------------------------- - */ + * User Defined + * has the format + *UD=<filter_number,filter_flag,cd_value_count,value_1[,value_2,...,value_N]> BZIP2 example + * UD=307,0,1,9 + *------------------------------------------------------------------------- + */ else if (HDstrcmp(scomp, "UD") == 0) { l = -1; /* filter number index check */ f = -1; /* filter flag index check */ @@ -225,15 +226,15 @@ obj_list_t* parse_filter(const char *str, unsigned *n_objs, filter_info_t *filt, stype[q] = '\0'; /* end digit */ if (l == -1) { filt->filtn = HDatoi(stype); - l = 0; + l = 0; } else if (f == -1) { filt->filt_flag = (unsigned)HDstrtoul(stype, NULL, 0); - f = 0; + f = 0; } else if (p == -1) { filt->cd_nelmts = HDstrtoull(stype, NULL, 0); - p = 0; + p = 0; } else { filt->cd_values[j++] = (unsigned)HDstrtoul(stype, NULL, 0); @@ -260,9 +261,9 @@ obj_list_t* parse_filter(const char *str, unsigned *n_objs, filter_info_t *filt, } /*if */ /*------------------------------------------------------------------------- - * all other filters - *------------------------------------------------------------------------- - */ + * all other filters + *------------------------------------------------------------------------- + */ else { /* here we could have 1 or 2 digits */ for (m = 0, u = i + 1; u < len; u++, m++) { @@ -279,36 +280,36 @@ obj_list_t* parse_filter(const char *str, unsigned *n_objs, filter_info_t *filt, stype[m] = '\0'; } /*if */ - filt->cd_values[j++] = (unsigned) HDstrtoul(stype, NULL, 0); - if(filt->cd_nelmts == 0) + filt->cd_values[j++] = (unsigned)HDstrtoul(stype, NULL, 0); + if (filt->cd_nelmts == 0) j = 0; i += m; /* jump */ } else if (i == len - 1) { /*no more parameters */ scomp[k + 1] = '\0'; - no_param = 1; + no_param = 1; } /*------------------------------------------------------------------------- - * translate from string to filter symbol - *------------------------------------------------------------------------- - */ + * translate from string to filter symbol + *------------------------------------------------------------------------- + */ /*------------------------------------------------------------------------- - * H5Z_FILTER_NONE - *------------------------------------------------------------------------- - */ + * H5Z_FILTER_NONE + *------------------------------------------------------------------------- + */ if (HDstrcmp(scomp, "NONE") == 0) { - filt->filtn = H5Z_FILTER_NONE; + filt->filtn = H5Z_FILTER_NONE; filt->cd_nelmts = 0; } /*------------------------------------------------------------------------- - * H5Z_FILTER_DEFLATE - *------------------------------------------------------------------------- - */ + * H5Z_FILTER_DEFLATE + *------------------------------------------------------------------------- + */ else if (HDstrcmp(scomp, "GZIP") == 0) { - filt->filtn = H5Z_FILTER_DEFLATE; + filt->filtn = H5Z_FILTER_DEFLATE; filt->cd_nelmts = 1; if (no_param) { /*no more parameters, GZIP must have parameter */ if (obj_list) @@ -319,11 +320,11 @@ obj_list_t* parse_filter(const char *str, unsigned *n_objs, filter_info_t *filt, } /*------------------------------------------------------------------------- - * H5Z_FILTER_SZIP - *------------------------------------------------------------------------- - */ + * H5Z_FILTER_SZIP + *------------------------------------------------------------------------- + */ else if (HDstrcmp(scomp, "SZIP") == 0) { - filt->filtn = H5Z_FILTER_SZIP; + filt->filtn = H5Z_FILTER_SZIP; filt->cd_nelmts = 2; if (no_param) { /*no more parameters, SZIP must have parameter */ if (obj_list) @@ -334,11 +335,11 @@ obj_list_t* parse_filter(const char *str, unsigned *n_objs, filter_info_t *filt, } /*------------------------------------------------------------------------- - * H5Z_FILTER_SHUFFLE - *------------------------------------------------------------------------- - */ + * H5Z_FILTER_SHUFFLE + *------------------------------------------------------------------------- + */ else if (HDstrcmp(scomp, "SHUF") == 0) { - filt->filtn = H5Z_FILTER_SHUFFLE; + filt->filtn = H5Z_FILTER_SHUFFLE; filt->cd_nelmts = 0; if (m > 0) { /*shuffle does not have parameter */ if (obj_list) @@ -348,11 +349,11 @@ obj_list_t* parse_filter(const char *str, unsigned *n_objs, filter_info_t *filt, } } /*------------------------------------------------------------------------- - * H5Z_FILTER_FLETCHER32 - *------------------------------------------------------------------------- - */ + * H5Z_FILTER_FLETCHER32 + *------------------------------------------------------------------------- + */ else if (HDstrcmp(scomp, "FLET") == 0) { - filt->filtn = H5Z_FILTER_FLETCHER32; + filt->filtn = H5Z_FILTER_FLETCHER32; filt->cd_nelmts = 0; if (m > 0) { /*shuffle does not have parameter */ if (obj_list) @@ -362,11 +363,11 @@ obj_list_t* parse_filter(const char *str, unsigned *n_objs, filter_info_t *filt, } } /*------------------------------------------------------------------------- - * H5Z_FILTER_NBIT - *------------------------------------------------------------------------- - */ + * H5Z_FILTER_NBIT + *------------------------------------------------------------------------- + */ else if (HDstrcmp(scomp, "NBIT") == 0) { - filt->filtn = H5Z_FILTER_NBIT; + filt->filtn = H5Z_FILTER_NBIT; filt->cd_nelmts = 0; if (m > 0) { /*nbit does not have parameter */ if (obj_list) @@ -376,11 +377,11 @@ obj_list_t* parse_filter(const char *str, unsigned *n_objs, filter_info_t *filt, } } /*------------------------------------------------------------------------- - * H5Z_FILTER_SCALEOFFSET - *------------------------------------------------------------------------- - */ + * H5Z_FILTER_SCALEOFFSET + *------------------------------------------------------------------------- + */ else if (HDstrcmp(scomp, "SOFF") == 0) { - filt->filtn = H5Z_FILTER_SCALEOFFSET; + filt->filtn = H5Z_FILTER_SCALEOFFSET; filt->cd_nelmts = 2; if (no_param) { /*no more parameters, SOFF must have parameter */ if (obj_list) @@ -390,9 +391,9 @@ obj_list_t* parse_filter(const char *str, unsigned *n_objs, filter_info_t *filt, } } /*------------------------------------------------------------------------- - * User Defined Filter - *------------------------------------------------------------------------- - */ + * User Defined Filter + *------------------------------------------------------------------------- + */ else if (HDstrcmp(scomp, "UD") == 0) { /* parameters does not match count */ if (filt->cd_nelmts != j) { @@ -413,56 +414,55 @@ obj_list_t* parse_filter(const char *str, unsigned *n_objs, filter_info_t *filt, } /*i*/ /*------------------------------------------------------------------------- - * check valid parameters - *------------------------------------------------------------------------- - */ + * check valid parameters + *------------------------------------------------------------------------- + */ switch (filt->filtn) { - /*------------------------------------------------------------------------- - * H5Z_FILTER_DEFLATE - *------------------------------------------------------------------------- - */ - case H5Z_FILTER_DEFLATE: - if (filt->cd_values[0] > 9) { - if (obj_list) - HDfree(obj_list); - error_msg("invalid compression parameter in <%s>\n", str); - HDexit(EXIT_FAILURE); - } - break; /*------------------------------------------------------------------------- - * H5Z_FILTER_SZIP - *------------------------------------------------------------------------- - */ - case H5Z_FILTER_SZIP: - pixels_per_block = filt->cd_values[0]; - if ((pixels_per_block % 2) == 1) { - if (obj_list) - HDfree(obj_list); - error_msg("pixels_per_block is not even in <%s>\n", str); - HDexit(EXIT_FAILURE); - } - if (pixels_per_block > H5_SZIP_MAX_PIXELS_PER_BLOCK) { - if (obj_list) - HDfree(obj_list); - error_msg("pixels_per_block is too large in <%s>\n", str); - HDexit(EXIT_FAILURE); - } - if ((HDstrcmp(smask,"NN") != 0) && (HDstrcmp(smask,"EC") != 0)) { - if (obj_list) - HDfree(obj_list); - error_msg("szip mask must be 'NN' or 'EC' \n"); - HDexit(EXIT_FAILURE); - } - break; - default: - break; + * H5Z_FILTER_DEFLATE + *------------------------------------------------------------------------- + */ + case H5Z_FILTER_DEFLATE: + if (filt->cd_values[0] > 9) { + if (obj_list) + HDfree(obj_list); + error_msg("invalid compression parameter in <%s>\n", str); + HDexit(EXIT_FAILURE); + } + break; + /*------------------------------------------------------------------------- + * H5Z_FILTER_SZIP + *------------------------------------------------------------------------- + */ + case H5Z_FILTER_SZIP: + pixels_per_block = filt->cd_values[0]; + if ((pixels_per_block % 2) == 1) { + if (obj_list) + HDfree(obj_list); + error_msg("pixels_per_block is not even in <%s>\n", str); + HDexit(EXIT_FAILURE); + } + if (pixels_per_block > H5_SZIP_MAX_PIXELS_PER_BLOCK) { + if (obj_list) + HDfree(obj_list); + error_msg("pixels_per_block is too large in <%s>\n", str); + HDexit(EXIT_FAILURE); + } + if ((HDstrcmp(smask, "NN") != 0) && (HDstrcmp(smask, "EC") != 0)) { + if (obj_list) + HDfree(obj_list); + error_msg("szip mask must be 'NN' or 'EC' \n"); + HDexit(EXIT_FAILURE); + } + break; + default: + break; }; return obj_list; } - /*------------------------------------------------------------------------- * Function: parse_layout * @@ -484,9 +484,11 @@ obj_list_t* parse_filter(const char *str, unsigned *n_objs, filter_info_t *filt, * *------------------------------------------------------------------------- */ -obj_list_t* parse_layout(const char *str, unsigned *n_objs, pack_info_t *pack, /* info about layout needed */ -pack_opt_t *options) { - obj_list_t* obj_list = NULL; +obj_list_t * +parse_layout(const char *str, unsigned *n_objs, pack_info_t *pack, /* info about layout needed */ + pack_opt_t *options) +{ + obj_list_t *obj_list = NULL; unsigned i, j, n; char c; size_t len = HDstrlen(str); @@ -503,7 +505,7 @@ pack_opt_t *options) { for (i = 0, n = 0; i < len; i++) { c = str[i]; if (c == ':') - end_obj = (int) i; + end_obj = (int)i; if (c == ',') n++; } @@ -513,7 +515,7 @@ pack_opt_t *options) { } n++; - obj_list = (obj_list_t*) HDmalloc(n * sizeof(obj_list_t)); + 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; @@ -522,10 +524,10 @@ pack_opt_t *options) { /* get object list */ if (end_obj > 0) - for (j = 0, k = 0, n = 0; j < (unsigned) end_obj; j++, k++) { - c = str[j]; + for (j = 0, k = 0, n = 0; j < (unsigned)end_obj; j++, k++) { + c = str[j]; sobj[k] = c; - if (c == ',' || j == (unsigned) (end_obj - 1)) { + if (c == ',' || j == (unsigned)(end_obj - 1)) { if (c == ',') sobj[k] = '\0'; else @@ -538,7 +540,7 @@ pack_opt_t *options) { } /* nothing after : */ - if (end_obj + 1 == (int) len) { + if (end_obj + 1 == (int)len) { if (obj_list) HDfree(obj_list); error_msg("in parse layout, no characters after : in <%s>\n", str); @@ -546,7 +548,7 @@ pack_opt_t *options) { } /* get layout info */ - for (j = (unsigned) (end_obj + 1), n = 0; n <= 5; j++, n++) { + for (j = (unsigned)(end_obj + 1), n = 0; n <= 5; j++, n++) { if (n == 5) { slayout[n] = '\0'; /*cut string */ if (HDstrcmp(slayout, "COMPA") == 0) @@ -561,16 +563,16 @@ pack_opt_t *options) { } } else { - c = str[j]; + c = str[j]; slayout[n] = c; } } /* j */ if (pack->layout == H5D_CHUNKED) { /*------------------------------------------------------------------------- - * get chunk info - *------------------------------------------------------------------------- - */ + * get chunk info + *------------------------------------------------------------------------- + */ k = 0; if (j > len) { if (obj_list) @@ -580,7 +582,7 @@ pack_opt_t *options) { } for (i = j, c_index = 0; i < len; i++) { - c = str[i]; + c = str[i]; sdim[k] = c; k++; /*increment sdim index */ @@ -593,8 +595,8 @@ pack_opt_t *options) { if (c == 'x' || i == len - 1) { if (c == 'x') { - sdim[k - 1] = '\0'; - k = 0; + sdim[k - 1] = '\0'; + k = 0; pack->chunk.chunk_lengths[c_index] = HDstrtoull(sdim, NULL, 0); if (pack->chunk.chunk_lengths[c_index] == 0) { if (obj_list) @@ -606,8 +608,8 @@ pack_opt_t *options) { } else if (i == len - 1) { /*no more parameters */ sdim[k] = '\0'; - k = 0; - if (HDstrcmp(sdim,"NONE") == 0) { + k = 0; + if (HDstrcmp(sdim, "NONE") == 0) { pack->chunk.rank = -2; } else { @@ -621,9 +623,9 @@ pack_opt_t *options) { pack->chunk.rank = c_index + 1; } } /*if */ - } /*if c=='x' || i==len-1 */ - } /*i*/ - } /*H5D_CHUNKED*/ + } /*if c=='x' || i==len-1 */ + } /*i*/ + } /*H5D_CHUNKED*/ return obj_list; } diff --git a/tools/src/h5repack/h5repack_refs.c b/tools/src/h5repack/h5repack_refs.c index 5baabb6..78957c6 100644 --- a/tools/src/h5repack/h5repack_refs.c +++ b/tools/src/h5repack/h5repack_refs.c @@ -15,17 +15,15 @@ #include "h5diff.h" #include "h5tools.h" - /*------------------------------------------------------------------------- * local functions *------------------------------------------------------------------------- */ -static const char* MapIdToName(hid_t refobj_id,trav_table_t *travt); -static int copy_refs_attr(hid_t loc_in, hid_t loc_out, - trav_table_t *travt, hid_t fidout); -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); +static const char *MapIdToName(hid_t refobj_id, trav_table_t *travt); +static int copy_refs_attr(hid_t loc_in, hid_t loc_out, trav_table_t *travt, hid_t fidout); +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); /*------------------------------------------------------------------------- * Function: do_copy_refobjs @@ -37,35 +35,33 @@ static herr_t update_ref_value(hid_t obj_id, H5R_type_t ref_type, void *ref_in, *------------------------------------------------------------------------- */ -int do_copy_refobjs(hid_t fidin, - hid_t fidout, - trav_table_t *travt, - pack_opt_t *options) /* repack options */ +int +do_copy_refobjs(hid_t fidin, hid_t fidout, trav_table_t *travt, pack_opt_t *options) /* repack options */ { - hid_t grp_in = H5I_INVALID_HID; /* read group ID */ - hid_t grp_out = H5I_INVALID_HID; /* write group ID */ - hid_t dset_in = H5I_INVALID_HID; /* read dataset ID */ - hid_t dset_out = H5I_INVALID_HID; /* write dataset ID */ - hid_t type_in = H5I_INVALID_HID; /* named type ID */ - hid_t dcpl_id = H5I_INVALID_HID; /* dataset creation property list ID */ - hid_t space_id = H5I_INVALID_HID; /* space ID */ - hid_t ftype_id = H5I_INVALID_HID; /* file data type ID */ - hid_t mtype_id = H5I_INVALID_HID; /* 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 */ + hid_t grp_in = H5I_INVALID_HID; /* read group ID */ + hid_t grp_out = H5I_INVALID_HID; /* write group ID */ + hid_t dset_in = H5I_INVALID_HID; /* read dataset ID */ + hid_t dset_out = H5I_INVALID_HID; /* write dataset ID */ + hid_t type_in = H5I_INVALID_HID; /* named type ID */ + hid_t dcpl_id = H5I_INVALID_HID; /* dataset creation property list ID */ + hid_t space_id = H5I_INVALID_HID; /* space ID */ + hid_t ftype_id = H5I_INVALID_HID; /* file data type ID */ + hid_t mtype_id = H5I_INVALID_HID; /* 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 */ - int ret_value = 0; + int k; + named_dt_t * named_dt_head = NULL; /* Pointer to the stack of named datatypes copied */ + int ret_value = 0; /*------------------------------------------------------------------------- - * browse - *------------------------------------------------------------------------- - */ - for(i = 0; i < travt->nobjs; i++) { - switch(travt->objs[i].type) { + * browse + *------------------------------------------------------------------------- + */ + for (i = 0; i < travt->nobjs; i++) { + switch (travt->objs[i].type) { /*------------------------------------------------------------------------- * H5TRAV_TYPE_GROUP *------------------------------------------------------------------------- @@ -75,27 +71,28 @@ int do_copy_refobjs(hid_t fidin, * copy referenced objects in attributes *------------------------------------------------------------------------- */ - if((grp_out = H5Gopen2(fidout, travt->objs[i].name, H5P_DEFAULT)) < 0) + if ((grp_out = H5Gopen2(fidout, travt->objs[i].name, H5P_DEFAULT)) < 0) H5TOOLS_GOTO_ERROR((-1), "H5Gopen2 failed"); - if((grp_in = H5Gopen2(fidin, travt->objs[i].name, H5P_DEFAULT)) < 0) + if ((grp_in = H5Gopen2(fidin, travt->objs[i].name, H5P_DEFAULT)) < 0) H5TOOLS_GOTO_ERROR((-1), "H5Gopen2 failed"); - if(copy_refs_attr(grp_in, grp_out, travt, fidout) < 0) + if (copy_refs_attr(grp_in, grp_out, travt, fidout) < 0) H5TOOLS_GOTO_ERROR((-1), "copy_refs_attr failed"); - if(H5Gclose(grp_out) < 0) + if (H5Gclose(grp_out) < 0) H5TOOLS_GOTO_ERROR((-1), "H5Gclose failed"); - if(H5Gclose(grp_in) < 0) + if (H5Gclose(grp_in) < 0) H5TOOLS_GOTO_ERROR((-1), "H5Gclose failed"); /*------------------------------------------------------------------------- * 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); + 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; /*------------------------------------------------------------------------- @@ -103,26 +100,26 @@ int do_copy_refobjs(hid_t fidin, *------------------------------------------------------------------------- */ case H5TRAV_TYPE_DATASET: - if((dset_in = H5Dopen2(fidin, travt->objs[i].name, H5P_DEFAULT)) < 0) + if ((dset_in = H5Dopen2(fidin, travt->objs[i].name, H5P_DEFAULT)) < 0) H5TOOLS_GOTO_ERROR((-1), "H5Dopen2 failed"); - if((space_id = H5Dget_space(dset_in)) < 0) + if ((space_id = H5Dget_space(dset_in)) < 0) H5TOOLS_GOTO_ERROR((-1), "H5Dget_space failed"); - if((ftype_id = H5Dget_type(dset_in)) < 0) + if ((ftype_id = H5Dget_type(dset_in)) < 0) H5TOOLS_GOTO_ERROR((-1), "H5Dget_type failed"); - if((dcpl_id = H5Dget_create_plist(dset_in)) < 0) + if ((dcpl_id = H5Dget_create_plist(dset_in)) < 0) H5TOOLS_GOTO_ERROR((-1), "H5Dget_create_plist failed"); - if((rank = H5Sget_simple_extent_ndims(space_id)) < 0) + if ((rank = H5Sget_simple_extent_ndims(space_id)) < 0) H5TOOLS_GOTO_ERROR((-1), "H5Sget_simple_extent_ndims failed"); - if(H5Sget_simple_extent_dims(space_id, dims, NULL) < 0) + if (H5Sget_simple_extent_dims(space_id, dims, NULL) < 0) H5TOOLS_GOTO_ERROR((-1), "H5Sget_simple_extent_dims failed"); nelmts = 1; - for(k = 0; k < rank; k++) + for (k = 0; k < rank; k++) nelmts *= dims[k]; - if((mtype_id = H5Tget_native_type(ftype_id, H5T_DIR_DEFAULT)) < 0) + if ((mtype_id = H5Tget_native_type(ftype_id, H5T_DIR_DEFAULT)) < 0) H5TOOLS_GOTO_ERROR((-1), "H5Tget_native_type failed"); - if((msize = H5Tget_size(mtype_id)) == 0) + if ((msize = H5Tget_size(mtype_id)) == 0) H5TOOLS_GOTO_ERROR((-1), "H5Tget_size failed"); /*------------------------------------------------------------------------- @@ -132,7 +129,7 @@ int do_copy_refobjs(hid_t fidin, * 2) the internal filters might be turned off *------------------------------------------------------------------------- */ - if(h5tools_canreadf(NULL, dcpl_id) == 1) { + if (h5tools_canreadf(NULL, dcpl_id) == 1) { /*------------------------------------------------------------------------- * test for a valid output dataset *------------------------------------------------------------------------- @@ -144,75 +141,78 @@ int do_copy_refobjs(hid_t fidin, * we cannot just copy the buffers, but instead we recreate the reference *------------------------------------------------------------------------- */ - if(H5Tequal(mtype_id, H5T_STD_REF_OBJ)) { - hid_t refobj_id = H5I_INVALID_HID; - hobj_ref_t *refbuf = NULL; /* buffer for object references */ - hobj_ref_t *buf = NULL; - const char* refname; - unsigned u; + if (H5Tequal(mtype_id, H5T_STD_REF_OBJ)) { + hid_t refobj_id = H5I_INVALID_HID; + hobj_ref_t *refbuf = NULL; /* buffer for object references */ + hobj_ref_t *buf = NULL; + const char *refname; + unsigned u; /*------------------------------------------------------------------------- * read to memory *------------------------------------------------------------------------- */ - if(nelmts) { + if (nelmts) { buf = (hobj_ref_t *)HDmalloc((unsigned)(nelmts * msize)); - if(buf==NULL) { - HDprintf("cannot read into memory\n" ); + if (buf == NULL) { + HDprintf("cannot read into memory\n"); H5TOOLS_GOTO_ERROR((-1), "HDmalloc failed"); } /* end if */ - if(H5Dread(dset_in, mtype_id, H5S_ALL, H5S_ALL, H5P_DEFAULT, buf) < 0) + if (H5Dread(dset_in, mtype_id, H5S_ALL, H5S_ALL, H5P_DEFAULT, buf) < 0) H5TOOLS_GOTO_ERROR((-1), "H5Dread failed"); - refbuf = (hobj_ref_t*) HDcalloc((unsigned)nelmts, msize); - if(refbuf == NULL){ - HDprintf("cannot allocate memory\n" ); + refbuf = (hobj_ref_t *)HDcalloc((unsigned)nelmts, msize); + if (refbuf == NULL) { + HDprintf("cannot allocate memory\n"); H5TOOLS_GOTO_ERROR((-1), "HDcalloc failed"); } /* end if */ - for(u = 0; u < nelmts; u++) { - H5E_BEGIN_TRY { - if((refobj_id = H5Rdereference2(dset_in, H5P_DEFAULT, H5R_OBJECT, &buf[u])) < 0) + for (u = 0; u < nelmts; u++) { + H5E_BEGIN_TRY + { + if ((refobj_id = + H5Rdereference2(dset_in, H5P_DEFAULT, H5R_OBJECT, &buf[u])) < 0) continue; - } H5E_END_TRY; + } + H5E_END_TRY; /* get the name. a valid name could only occur * in the second traversal of the file */ - if((refname = MapIdToName(refobj_id, travt)) != NULL) { + if ((refname = MapIdToName(refobj_id, travt)) != NULL) { /* create the reference, -1 parameter for objects */ - if(H5Rcreate(&refbuf[u], fidout, refname, H5R_OBJECT, (hid_t)-1) < 0) + if (H5Rcreate(&refbuf[u], fidout, refname, H5R_OBJECT, (hid_t)-1) < 0) H5TOOLS_GOTO_ERROR((-1), "H5Rcreate failed"); - if(options->verbose) { - HDprintf(FORMAT_OBJ,"dset",travt->objs[i].name ); + if (options->verbose) { + HDprintf(FORMAT_OBJ, "dset", travt->objs[i].name); HDprintf("object <%s> object reference created to <%s>\n", - travt->objs[i].name, - refname); + travt->objs[i].name, refname); } } /*refname*/ if (H5Oclose(refobj_id) < 0) H5TOOLS_ERROR((-1), "H5Oclose refob failed"); } /* u */ - } /*nelmts*/ + } /*nelmts*/ /*------------------------------------------------------------------------- * create/write dataset/close *------------------------------------------------------------------------- */ - if((dset_out = H5Dcreate2(fidout, travt->objs[i].name, mtype_id, space_id, H5P_DEFAULT, dcpl_id, H5P_DEFAULT)) < 0) + if ((dset_out = H5Dcreate2(fidout, travt->objs[i].name, mtype_id, space_id, + H5P_DEFAULT, dcpl_id, H5P_DEFAULT)) < 0) H5TOOLS_GOTO_ERROR((-1), "H5Dcreate2 failed"); - if(nelmts) - if(H5Dwrite(dset_out, mtype_id, H5S_ALL, H5S_ALL, H5P_DEFAULT, refbuf) < 0) + if (nelmts) + if (H5Dwrite(dset_out, mtype_id, H5S_ALL, H5S_ALL, H5P_DEFAULT, refbuf) < 0) H5TOOLS_GOTO_ERROR((-1), "H5Dwrite failed"); - if(buf) + if (buf) HDfree(buf); - if(refbuf) + if (refbuf) HDfree(refbuf); - /*------------------------------------------------------ - * copy attrs - *----------------------------------------------------*/ - if(copy_attr(dset_in, dset_out, &named_dt_head, travt, options) < 0) + /*------------------------------------------------------ + * copy attrs + *----------------------------------------------------*/ + if (copy_attr(dset_in, dset_out, &named_dt_head, travt, options) < 0) H5TOOLS_GOTO_ERROR((-1), "copy_attr failed"); } /*H5T_STD_REF_OBJ*/ @@ -220,87 +220,93 @@ int do_copy_refobjs(hid_t fidin, * dataset region references *------------------------------------------------------------------------- */ - else if(H5Tequal(mtype_id, H5T_STD_REF_DSETREG)) { + else if (H5Tequal(mtype_id, H5T_STD_REF_DSETREG)) { hid_t refobj_id = H5I_INVALID_HID; - hdset_reg_ref_t *refbuf = NULL; /* input buffer for region references */ - hdset_reg_ref_t *buf = NULL; /* output buffer */ - const char* refname; + hdset_reg_ref_t *refbuf = NULL; /* input buffer for region references */ + hdset_reg_ref_t *buf = NULL; /* output buffer */ + const char * refname; unsigned u; /*------------------------------------------------------------------------- * read input to memory *------------------------------------------------------------------------- */ - if(nelmts) { + if (nelmts) { buf = (hdset_reg_ref_t *)HDmalloc((unsigned)(nelmts * msize)); - if(buf == NULL) { + if (buf == NULL) { HDprintf("cannot read into memory\n"); H5TOOLS_GOTO_ERROR((-1), "HDmalloc failed"); } /* end if */ - if(H5Dread(dset_in, mtype_id, H5S_ALL, H5S_ALL, H5P_DEFAULT, buf) < 0) + if (H5Dread(dset_in, mtype_id, H5S_ALL, H5S_ALL, H5P_DEFAULT, buf) < 0) H5TOOLS_GOTO_ERROR((-1), "H5Dread failed"); /*------------------------------------------------------------------------- * create output *------------------------------------------------------------------------- */ - refbuf = (hdset_reg_ref_t *)HDcalloc(sizeof(hdset_reg_ref_t), (size_t)nelmts); /*init to zero */ - if(refbuf == NULL) { + refbuf = (hdset_reg_ref_t *)HDcalloc(sizeof(hdset_reg_ref_t), + (size_t)nelmts); /*init to zero */ + if (refbuf == NULL) { HDprintf("cannot allocate memory\n"); H5TOOLS_GOTO_ERROR((-1), "HDcalloc failed"); } /* end if */ - for(u = 0; u < nelmts; u++) { - H5E_BEGIN_TRY { - if((refobj_id = H5Rdereference2(dset_in, H5P_DEFAULT, H5R_DATASET_REGION, &buf[u])) < 0) + for (u = 0; u < nelmts; u++) { + H5E_BEGIN_TRY + { + if ((refobj_id = H5Rdereference2(dset_in, H5P_DEFAULT, H5R_DATASET_REGION, + &buf[u])) < 0) continue; - } H5E_END_TRY; + } + H5E_END_TRY; /* get the name. a valid name could only occur * in the second traversal of the file */ - if((refname = MapIdToName(refobj_id, travt)) != NULL) { - hid_t region_id = H5I_INVALID_HID; /* region id of the referenced dataset */ + if ((refname = MapIdToName(refobj_id, travt)) != NULL) { + hid_t region_id = + H5I_INVALID_HID; /* region id of the referenced dataset */ - if((region_id = H5Rget_region(dset_in, H5R_DATASET_REGION, &buf[u])) < 0) + if ((region_id = H5Rget_region(dset_in, H5R_DATASET_REGION, &buf[u])) < 0) H5TOOLS_GOTO_ERROR((-1), "H5Rget_region failed"); /* create the reference, we need the space_id */ - if(H5Rcreate(&refbuf[u], fidout, refname, H5R_DATASET_REGION, region_id) < 0) + if (H5Rcreate(&refbuf[u], fidout, refname, H5R_DATASET_REGION, + region_id) < 0) H5TOOLS_GOTO_ERROR((-1), "H5Rcreate failed"); - if(H5Sclose(region_id) < 0) + if (H5Sclose(region_id) < 0) H5TOOLS_GOTO_ERROR((-1), "H5Sclose failed"); - if(options->verbose) { - HDprintf(FORMAT_OBJ,"dset",travt->objs[i].name ); + if (options->verbose) { + HDprintf(FORMAT_OBJ, "dset", travt->objs[i].name); HDprintf("object <%s> region reference created to <%s>\n", - travt->objs[i].name, - refname); + travt->objs[i].name, refname); } } /*refname*/ if (H5Oclose(refobj_id) < 0) H5TOOLS_ERROR((-1), "H5Oclose refobj_id failed"); } /* u */ - } /*nelmts*/ + } /*nelmts*/ /*------------------------------------------------------------------------- * create/write dataset/close *------------------------------------------------------------------------- */ - if((dset_out = H5Dcreate2(fidout, travt->objs[i].name, mtype_id, space_id, H5P_DEFAULT, dcpl_id, H5P_DEFAULT)) < 0) + if ((dset_out = H5Dcreate2(fidout, travt->objs[i].name, mtype_id, space_id, + H5P_DEFAULT, dcpl_id, H5P_DEFAULT)) < 0) H5TOOLS_GOTO_ERROR((-1), "H5Dcreate2 failed"); - if(nelmts) - if(H5Dwrite(dset_out, mtype_id, H5S_ALL, H5S_ALL, H5P_DEFAULT, refbuf) < 0) + if (nelmts) + if (H5Dwrite(dset_out, mtype_id, H5S_ALL, H5S_ALL, H5P_DEFAULT, refbuf) < 0) H5TOOLS_GOTO_ERROR((-1), "H5Dwrite failed"); - if(buf) + if (buf) HDfree(buf); - if(refbuf) + if (refbuf) HDfree(refbuf); - /*----------------------------------------------------- - * copy attrs - *----------------------------------------------------*/ - if(copy_attr(dset_in, dset_out, &named_dt_head, travt, options) < 0) + /*----------------------------------------------------- + * copy attrs + *----------------------------------------------------*/ + if (copy_attr(dset_in, dset_out, &named_dt_head, travt, options) < 0) H5TOOLS_GOTO_ERROR((-1), "copy_attr failed"); } /* H5T_STD_REF_DSETREG */ /*------------------------------------------------------------------------- @@ -308,7 +314,7 @@ int do_copy_refobjs(hid_t fidin, *------------------------------------------------------------------------- */ else { - if((dset_out = H5Dopen2(fidout, travt->objs[i].name, H5P_DEFAULT)) < 0) + if ((dset_out = H5Dopen2(fidout, travt->objs[i].name, H5P_DEFAULT)) < 0) H5TOOLS_GOTO_ERROR((-1), "H5Dopen2 failed"); } /* end else */ @@ -316,18 +322,19 @@ int do_copy_refobjs(hid_t fidin, * copy referenced objects in attributes *------------------------------------------------------------------------- */ - if(copy_refs_attr(dset_in, dset_out, travt, fidout) < 0) + if (copy_refs_attr(dset_in, dset_out, travt, fidout) < 0) H5TOOLS_GOTO_ERROR((-1), "copy_refs_attr failed"); /*------------------------------------------------------------------------- * 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); + 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); - if(H5Dclose(dset_out) < 0) + if (H5Dclose(dset_out) < 0) H5TOOLS_GOTO_ERROR((-1), "H5Dclose failed"); } /*can_read*/ @@ -335,15 +342,15 @@ int do_copy_refobjs(hid_t fidin, * close *------------------------------------------------------------------------- */ - if(H5Tclose(ftype_id) < 0) + if (H5Tclose(ftype_id) < 0) H5TOOLS_GOTO_ERROR((-1), "H5Tclose failed"); - if(H5Tclose(mtype_id) < 0) + if (H5Tclose(mtype_id) < 0) H5TOOLS_GOTO_ERROR((-1), "H5Tclose failed"); - if(H5Pclose(dcpl_id) < 0) + if (H5Pclose(dcpl_id) < 0) H5TOOLS_GOTO_ERROR((-1), "H5Pclose failed"); - if(H5Sclose(space_id) < 0) + if (H5Sclose(space_id) < 0) H5TOOLS_GOTO_ERROR((-1), "H5Sclose failed"); - if(H5Dclose(dset_in) < 0) + if (H5Dclose(dset_in) < 0) H5TOOLS_GOTO_ERROR((-1), "H5Dclose failed"); break; @@ -352,9 +359,9 @@ int do_copy_refobjs(hid_t fidin, *------------------------------------------------------------------------- */ case H5TRAV_TYPE_NAMED_DATATYPE: - if((type_in = H5Topen2(fidin, travt->objs[i].name, H5P_DEFAULT)) < 0) + if ((type_in = H5Topen2(fidin, travt->objs[i].name, H5P_DEFAULT)) < 0) H5TOOLS_GOTO_ERROR((-1), "H5Topen2 failed"); - if(H5Tclose(type_in) < 0) + if (H5Tclose(type_in) < 0) H5TOOLS_GOTO_ERROR((-1), "H5Tclose failed"); break; @@ -374,7 +381,7 @@ int do_copy_refobjs(hid_t fidin, default: break; } /* end switch */ - } /* end for */ + } /* end for */ /* Finalize (link) the stack of named datatypes (if any) * This function is paired with copy_named_datatype() which is called @@ -386,7 +393,8 @@ int do_copy_refobjs(hid_t fidin, return ret_value; done: - H5E_BEGIN_TRY { + H5E_BEGIN_TRY + { H5Gclose(grp_in); H5Gclose(grp_out); H5Pclose(dcpl_id); @@ -397,12 +405,12 @@ done: H5Tclose(mtype_id); H5Tclose(type_in); named_datatype_free(&named_dt_head, 1); - } H5E_END_TRY; + } + H5E_END_TRY; return ret_value; } - /*------------------------------------------------------------------------- * Function: copy_refs_attr * @@ -425,91 +433,87 @@ done: *------------------------------------------------------------------------- */ -static int copy_refs_attr(hid_t loc_in, - hid_t loc_out, - trav_table_t *travt, - hid_t fidout) /* for saving references */ +static int +copy_refs_attr(hid_t loc_in, hid_t loc_out, trav_table_t *travt, hid_t fidout) /* for saving references */ { - hid_t attr_id = H5I_INVALID_HID; /* attr ID */ - hid_t attr_out = H5I_INVALID_HID; /* attr ID */ - hid_t space_id = H5I_INVALID_HID; /* space ID */ - hid_t ftype_id = H5I_INVALID_HID; /* file data type ID */ - hid_t mtype_id = H5I_INVALID_HID; /* 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 */ + hid_t attr_id = H5I_INVALID_HID; /* attr ID */ + hid_t attr_out = H5I_INVALID_HID; /* attr ID */ + hid_t space_id = H5I_INVALID_HID; /* space ID */ + hid_t ftype_id = H5I_INVALID_HID; /* file data type ID */ + hid_t mtype_id = H5I_INVALID_HID; /* 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_info2_t oinfo; /* Object info */ + H5O_info2_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; - unsigned *ref_comp_index = NULL; - size_t *ref_comp_size = NULL; + hbool_t is_ref = 0, is_ref_vlen = 0, is_ref_array = 0, is_ref_comp = 0; + void * refbuf = NULL; + void * buf = NULL; + unsigned * ref_comp_index = NULL; + size_t * ref_comp_size = NULL; int ref_comp_field_n = 0; - int ret_value = 0; + int ret_value = 0; - if(H5Oget_info3(loc_in, &oinfo, H5O_INFO_NUM_ATTRS) < 0) + if (H5Oget_info3(loc_in, &oinfo, H5O_INFO_NUM_ATTRS) < 0) H5TOOLS_GOTO_ERROR((-1), "H5Oget_info failed"); - for(u = 0; u < (unsigned)oinfo.num_attrs; u++) { + for (u = 0; u < (unsigned)oinfo.num_attrs; u++) { is_ref = is_ref_vlen = is_ref_array = is_ref_comp = 0; /* open attribute */ - if((attr_id = H5Aopen_by_idx(loc_in, ".", H5_INDEX_CRT_ORDER, H5_ITER_INC, (hsize_t)u, H5P_DEFAULT, H5P_DEFAULT)) < 0) + if ((attr_id = H5Aopen_by_idx(loc_in, ".", H5_INDEX_CRT_ORDER, H5_ITER_INC, (hsize_t)u, H5P_DEFAULT, + H5P_DEFAULT)) < 0) H5TOOLS_GOTO_ERROR((-1), "H5Aopen_by_idx failed"); /* get the file datatype */ - if((ftype_id = H5Aget_type(attr_id)) < 0) + if ((ftype_id = H5Aget_type(attr_id)) < 0) H5TOOLS_GOTO_ERROR((-1), "H5Aget_type failed"); type_class = H5Tget_class(ftype_id); - if((mtype_id = H5Tget_native_type(ftype_id, H5T_DIR_DEFAULT)) < 0) + if ((mtype_id = H5Tget_native_type(ftype_id, H5T_DIR_DEFAULT)) < 0) H5TOOLS_GOTO_ERROR((-1), "H5Tget_native_type failed"); - if((msize = H5Tget_size(mtype_id)) == 0) + if ((msize = H5Tget_size(mtype_id)) == 0) H5TOOLS_GOTO_ERROR((-1), "H5Tget_size failed"); is_ref = (type_class == H5T_REFERENCE); - if(type_class == H5T_VLEN ) { + if (type_class == H5T_VLEN) { hid_t base_type = H5Tget_super(ftype_id); is_ref_vlen = (H5Tget_class(base_type) == H5T_REFERENCE); - msize = H5Tget_size(base_type); + msize = H5Tget_size(base_type); if (H5Tclose(base_type) < 0) H5TOOLS_ERROR((-1), "H5Tclose base_type failed"); } - else if(type_class == H5T_ARRAY ) { + else if (type_class == H5T_ARRAY) { hid_t base_type = H5Tget_super(ftype_id); is_ref_array = (H5Tget_class(base_type) == H5T_REFERENCE); - msize = H5Tget_size(base_type); + msize = H5Tget_size(base_type); if (H5Tclose(base_type) < 0) H5TOOLS_GOTO_ERROR((-1), "H5Tclose base_type failed"); } - else if(type_class == H5T_COMPOUND) { - int nmembers = H5Tget_nmembers(ftype_id) ; + else if (type_class == H5T_COMPOUND) { + int nmembers = H5Tget_nmembers(ftype_id); if (nmembers < 1) H5TOOLS_GOTO_ERROR((-1), "H5Tget_nmembers failed"); - ref_comp_index = (unsigned *)HDmalloc((size_t)nmembers*sizeof(unsigned)); - ref_comp_size = (size_t *)HDmalloc((size_t)nmembers*sizeof(ref_comp_size)); + ref_comp_index = (unsigned *)HDmalloc((size_t)nmembers * sizeof(unsigned)); + ref_comp_size = (size_t *)HDmalloc((size_t)nmembers * sizeof(ref_comp_size)); ref_comp_field_n = 0; - for (i=0; i<(unsigned)nmembers; i++) { + for (i = 0; i < (unsigned)nmembers; i++) { hid_t mtid = H5Tget_member_type(ftype_id, i); 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_size[ref_comp_field_n] = H5Tget_size(mtid); ref_comp_field_n++; } if (H5Tclose(mtid) < 0) @@ -539,7 +543,6 @@ static int copy_refs_attr(hid_t loc_in, is_ref_comp = (ref_comp_field_n > 0); } - if (!(is_ref || is_ref_vlen || is_ref_array || is_ref_comp)) { if (H5Tclose(mtype_id) < 0) H5TOOLS_ERROR((-1), "H5Tclose mtype_id failed"); @@ -551,31 +554,30 @@ static int copy_refs_attr(hid_t loc_in, } /* get name */ - if(H5Aget_name(attr_id, 255, name) < 0) + if (H5Aget_name(attr_id, 255, name) < 0) H5TOOLS_GOTO_ERROR((-1), "H5Aget_name failed"); /* get the dataspace handle */ - if((space_id = H5Aget_space(attr_id)) < 0) + if ((space_id = H5Aget_space(attr_id)) < 0) H5TOOLS_GOTO_ERROR((-1), "H5Aget_space failed"); /* get dimensions */ - if((rank = H5Sget_simple_extent_dims(space_id, dims, NULL)) < 0) + if ((rank = H5Sget_simple_extent_dims(space_id, dims, NULL)) < 0) H5TOOLS_GOTO_ERROR((-1), "H5Sget_simple_extent_dims failed"); - /*------------------------------------------------------------------------- - * elements - *------------------------------------------------------------------------- - */ + * elements + *------------------------------------------------------------------------- + */ nelmts = 1; - for(j = 0; j < (unsigned)rank; j++) + for (j = 0; j < (unsigned)rank; j++) nelmts *= dims[j]; if (is_ref_array) { - unsigned array_rank = 0; - hsize_t array_size = 1; - hsize_t array_dims[H5S_MAX_RANK]; - hid_t base_type = H5Tget_super(ftype_id); + unsigned array_rank = 0; + hsize_t array_size = 1; + hsize_t array_dims[H5S_MAX_RANK]; + hid_t base_type = H5Tget_super(ftype_id); msize = H5Tget_size(base_type); if (H5Tclose(base_type) < 0) @@ -583,153 +585,163 @@ static int copy_refs_attr(hid_t loc_in, array_rank = (unsigned)H5Tget_array_ndims(mtype_id); H5Tget_array_dims2(mtype_id, array_dims); - for(j = 0; j <array_rank; j++) + for (j = 0; j < array_rank; j++) array_size *= array_dims[j]; nelmts *= array_size; } - if((attr_out = H5Acreate2(loc_out, name, ftype_id, space_id, H5P_DEFAULT, H5P_DEFAULT)) < 0) + if ((attr_out = H5Acreate2(loc_out, name, ftype_id, space_id, H5P_DEFAULT, H5P_DEFAULT)) < 0) H5TOOLS_GOTO_ERROR((-1), "H5Acreate2 failed"); - if (nelmts>0) { + if (nelmts > 0) { /* handle object references */ - if((is_ref || is_ref_array) && (H5R_OBJ_REF_BUF_SIZE==msize)) { + if ((is_ref || is_ref_array) && (H5R_OBJ_REF_BUF_SIZE == msize)) { buf = (hobj_ref_t *)HDmalloc((unsigned)(nelmts * msize)); - if(buf == NULL) { + if (buf == NULL) { HDprintf("cannot read into memory\n"); H5TOOLS_GOTO_ERROR((-1), "HDmalloc failed"); } /* end if */ - if(H5Aread(attr_id, mtype_id, buf) < 0) + if (H5Aread(attr_id, mtype_id, buf) < 0) H5TOOLS_GOTO_ERROR((-1), "H5Aread failed"); refbuf = (hobj_ref_t *)HDcalloc((unsigned)nelmts, msize); - if(refbuf == NULL) { + if (refbuf == NULL) { HDprintf("cannot allocate memory\n"); H5TOOLS_GOTO_ERROR((-1), "HDcalloc failed"); } /* end if */ - for(i = 0; i < (unsigned)nelmts; i++) - if(update_ref_value(attr_id, H5R_OBJECT, &((hobj_ref_t *)buf)[i], fidout, &((hobj_ref_t *)refbuf)[i], travt) < 0) + for (i = 0; i < (unsigned)nelmts; i++) + if (update_ref_value(attr_id, H5R_OBJECT, &((hobj_ref_t *)buf)[i], fidout, + &((hobj_ref_t *)refbuf)[i], travt) < 0) continue; } /* H5T_STD_REF_OBJ */ /* handle region references */ - else if((is_ref || is_ref_array) && (H5R_DSET_REG_REF_BUF_SIZE == msize)) { + else if ((is_ref || is_ref_array) && (H5R_DSET_REG_REF_BUF_SIZE == msize)) { buf = (hdset_reg_ref_t *)HDmalloc((unsigned)(nelmts * msize)); - if(buf == NULL) { - HDprintf( "cannot read into memory\n" ); + if (buf == NULL) { + HDprintf("cannot read into memory\n"); H5TOOLS_GOTO_ERROR((-1), "HDmalloc failed"); } /* end if */ - if(H5Aread(attr_id, mtype_id, buf) < 0) + if (H5Aread(attr_id, mtype_id, buf) < 0) H5TOOLS_GOTO_ERROR((-1), "H5Aread failed"); /*------------------------------------------------------------------------- * create output *------------------------------------------------------------------------- */ - refbuf = (hdset_reg_ref_t *)HDcalloc(sizeof(hdset_reg_ref_t), (size_t)nelmts); /*init to zero */ - if(refbuf == NULL) { - HDprintf( "cannot allocate memory\n" ); + refbuf = + (hdset_reg_ref_t *)HDcalloc(sizeof(hdset_reg_ref_t), (size_t)nelmts); /*init to zero */ + if (refbuf == NULL) { + HDprintf("cannot allocate memory\n"); H5TOOLS_GOTO_ERROR((-1), "HDcalloc failed"); } /* end if */ - for(i = 0; i < (unsigned)nelmts; i++) - if(update_ref_value(attr_id, H5R_DATASET_REGION, &((hdset_reg_ref_t *)buf)[i], fidout, &((hdset_reg_ref_t *)refbuf)[i], travt) < 0) + for (i = 0; i < (unsigned)nelmts; i++) + if (update_ref_value(attr_id, H5R_DATASET_REGION, &((hdset_reg_ref_t *)buf)[i], fidout, + &((hdset_reg_ref_t *)refbuf)[i], travt) < 0) continue; } /* H5T_STD_REF_DSETREG */ else if (is_ref_vlen) { /* handle VLEN of references */ - buf = (hvl_t *)HDmalloc((unsigned)(nelmts * sizeof(hvl_t))); + buf = (hvl_t *)HDmalloc((unsigned)(nelmts * sizeof(hvl_t))); refbuf = buf; /* reuse the read buffer for write */ - if(buf == NULL) { - HDprintf( "cannot read into memory\n" ); + if (buf == NULL) { + HDprintf("cannot read into memory\n"); H5TOOLS_GOTO_ERROR((-1), "HDmalloc failed"); } /* end if */ - if(H5Aread(attr_id, mtype_id, buf) < 0) + if (H5Aread(attr_id, mtype_id, buf) < 0) H5TOOLS_GOTO_ERROR((-1), "H5Aread failed"); - if (H5R_OBJ_REF_BUF_SIZE==msize) { + if (H5R_OBJ_REF_BUF_SIZE == msize) { hobj_ref_t ref_out; - for (i=0; i<(unsigned)nelmts; i++) { + for (i = 0; i < (unsigned)nelmts; i++) { hobj_ref_t *ptr = (hobj_ref_t *)((hvl_t *)buf)[i].p; - for (j=0; j<((hvl_t *)buf)[i].len; j++ ) { - if (update_ref_value(attr_id, H5R_OBJECT, &(ptr[j]), fidout, &ref_out, travt)<0) + for (j = 0; j < ((hvl_t *)buf)[i].len; j++) { + if (update_ref_value(attr_id, H5R_OBJECT, &(ptr[j]), fidout, &ref_out, travt) < 0) continue; HDmemcpy(&(ptr[j]), &ref_out, msize); } - } /* for (i=0; i<nelems; i++) */ + } /* for (i=0; i<nelems; i++) */ } else if (H5R_DSET_REG_REF_BUF_SIZE == msize) { hdset_reg_ref_t ref_out; - for (i=0; i<(unsigned)nelmts; i++) { + for (i = 0; i < (unsigned)nelmts; i++) { hdset_reg_ref_t *ptr = (hdset_reg_ref_t *)((hvl_t *)buf)[i].p; - for (j=0; j<((hvl_t *)buf)[i].len; j++ ) { - if (update_ref_value(attr_id, H5R_DATASET_REGION, &(ptr[j]), fidout, &ref_out, travt)<0) + for (j = 0; j < ((hvl_t *)buf)[i].len; j++) { + if (update_ref_value(attr_id, H5R_DATASET_REGION, &(ptr[j]), fidout, &ref_out, + travt) < 0) continue; HDmemcpy(&(ptr[j]), &ref_out, msize); } - } /* for (i=0; i<nelems; i++) */ + } /* for (i=0; i<nelems; i++) */ } } /* else if (is_ref_vlen) */ else if (is_ref_comp) { /* handle ref fields in a compound */ - buf = HDmalloc((unsigned)(nelmts * msize)); + buf = HDmalloc((unsigned)(nelmts * msize)); refbuf = buf; /* reuse the read buffer for write */ - if(buf == NULL) { - HDprintf( "cannot read into memory\n" ); + if (buf == NULL) { + HDprintf("cannot read into memory\n"); H5TOOLS_GOTO_ERROR((-1), "HDmalloc failed"); } /* end if */ - if(H5Aread(attr_id, mtype_id, buf) < 0) + if (H5Aread(attr_id, mtype_id, buf) < 0) H5TOOLS_GOTO_ERROR((-1), "H5Aread failed"); - for (i=0; i<(unsigned)nelmts; i++) { - for (j=0; j<(unsigned)ref_comp_field_n; j++) { + for (i = 0; i < (unsigned)nelmts; i++) { + for (j = 0; j < (unsigned)ref_comp_field_n; j++) { if (ref_comp_size[j] == H5R_OBJ_REF_BUF_SIZE) { - size_t idx = (i * msize) + H5Tget_member_offset(mtype_id, ref_comp_index[j]); + size_t idx = (i * msize) + H5Tget_member_offset(mtype_id, ref_comp_index[j]); hobj_ref_t ref_out; - if (update_ref_value(attr_id, H5R_OBJECT, (hobj_ref_t *)((void *)(((char *)buf)+idx)), fidout, &ref_out, travt) < 0) /* Extra (void *) cast to quiet "cast to create alignment" warning - 2019/07/05, QAK */ + if (update_ref_value(attr_id, H5R_OBJECT, + (hobj_ref_t *)((void *)(((char *)buf) + idx)), fidout, + &ref_out, + travt) < 0) /* Extra (void *) cast to quiet "cast to create + alignment" warning - 2019/07/05, QAK */ continue; - HDmemcpy(((char *)buf)+idx, &ref_out, ref_comp_size[j]); + HDmemcpy(((char *)buf) + idx, &ref_out, ref_comp_size[j]); } /* if */ else if (ref_comp_size[j] == H5R_DSET_REG_REF_BUF_SIZE) { size_t idx = i * msize + H5Tget_member_offset(mtype_id, ref_comp_index[j]); hdset_reg_ref_t ref_out; - if (update_ref_value(attr_id, H5R_DATASET_REGION, (hdset_reg_ref_t *)(((char *)buf)+idx), fidout, &ref_out, travt)<0) + if (update_ref_value(attr_id, H5R_DATASET_REGION, + (hdset_reg_ref_t *)(((char *)buf) + idx), fidout, &ref_out, + travt) < 0) continue; - HDmemcpy(((char *)buf)+idx, &ref_out, ref_comp_size[j]); + HDmemcpy(((char *)buf) + idx, &ref_out, ref_comp_size[j]); } /* else if */ - } /* j */ - } /* i */ - } /* else if (is_ref_comp) */ + } /* j */ + } /* i */ + } /* else if (is_ref_comp) */ - if(H5Awrite(attr_out, mtype_id, refbuf) < 0) + if (H5Awrite(attr_out, mtype_id, refbuf) < 0) H5TOOLS_GOTO_ERROR((-1), "H5Awrite failed"); if (is_ref_vlen && buf) - H5Treclaim (mtype_id, space_id, H5P_DEFAULT, buf); + H5Treclaim(mtype_id, space_id, H5P_DEFAULT, buf); } /* if (nelmts) */ if (refbuf == buf) refbuf = NULL; /* set it to NULL to avoid double free since buf and refbuf are the same. */ - if(buf) { + if (buf) { HDfree(buf); buf = NULL; } - if(refbuf) { + if (refbuf) { HDfree(refbuf); refbuf = NULL; } @@ -744,27 +756,27 @@ static int copy_refs_attr(hid_t loc_in, ref_comp_size = NULL; } - if(H5Aclose(attr_out) < 0) + if (H5Aclose(attr_out) < 0) H5TOOLS_GOTO_ERROR((-1), "H5Aclose failed"); /*------------------------------------------------------------------------- - * close - *------------------------------------------------------------------------- - */ - if(H5Tclose(ftype_id) < 0) + * close + *------------------------------------------------------------------------- + */ + if (H5Tclose(ftype_id) < 0) H5TOOLS_GOTO_ERROR((-1), "H5Tclose failed"); - if(H5Tclose(mtype_id) < 0) + if (H5Tclose(mtype_id) < 0) H5TOOLS_GOTO_ERROR((-1), "H5Tclose failed"); - if(H5Sclose(space_id) < 0) + if (H5Sclose(space_id) < 0) H5TOOLS_GOTO_ERROR((-1), "H5Sclose failed"); - if(H5Aclose(attr_id) < 0) + if (H5Aclose(attr_id) < 0) H5TOOLS_GOTO_ERROR((-1), "H5Aclose failed"); } /* for(u = 0; u < (unsigned)oinfo.num_attrs; u++) */ done: - if(refbuf) + if (refbuf) HDfree(refbuf); - if(buf) + if (buf) HDfree(buf); if (ref_comp_index) @@ -773,13 +785,15 @@ done: if (ref_comp_size) HDfree(ref_comp_size); - H5E_BEGIN_TRY { + H5E_BEGIN_TRY + { H5Tclose(ftype_id); H5Tclose(mtype_id); H5Sclose(space_id); H5Aclose(attr_id); H5Aclose(attr_out); - } H5E_END_TRY; + } + H5E_END_TRY; return ret_value; } @@ -791,32 +805,32 @@ done: * *------------------------------------------------------------------------- */ -static const char* +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++) { - if(travt->objs[u].type == (h5trav_type_t)H5O_TYPE_DATASET || - travt->objs[u].type == (h5trav_type_t)H5O_TYPE_GROUP || - travt->objs[u].type == (h5trav_type_t)H5O_TYPE_NAMED_DATATYPE) { - H5O_info2_t ref_oinfo; /* Stat for the refobj id */ + for (u = 0; u < travt->nobjs; u++) { + if (travt->objs[u].type == (h5trav_type_t)H5O_TYPE_DATASET || + travt->objs[u].type == (h5trav_type_t)H5O_TYPE_GROUP || + travt->objs[u].type == (h5trav_type_t)H5O_TYPE_NAMED_DATATYPE) { + H5O_info2_t ref_oinfo; /* Stat for the refobj id */ int token_cmp; /* obtain information to identify the referenced object uniquely */ - if(H5Oget_info3(refobj_id, &ref_oinfo, H5O_INFO_BASIC) < 0) + if (H5Oget_info3(refobj_id, &ref_oinfo, H5O_INFO_BASIC) < 0) goto out; - if(H5Otoken_cmp(refobj_id, &ref_oinfo.token, &travt->objs[u].obj_token, &token_cmp) < 0) + if (H5Otoken_cmp(refobj_id, &ref_oinfo.token, &travt->objs[u].obj_token, &token_cmp) < 0) goto out; - if(!token_cmp) { + if (!token_cmp) { ret = travt->objs[u].name; goto out; } - } /* end if */ - } /* u */ + } /* end if */ + } /* u */ out: return ret; @@ -828,13 +842,14 @@ out: * 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) +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) { const char *ref_obj_name; - hid_t space_id = H5I_INVALID_HID; + hid_t space_id = H5I_INVALID_HID; hid_t ref_obj_id = H5I_INVALID_HID; - herr_t ret_value = SUCCEED; + herr_t ret_value = SUCCEED; ref_obj_id = H5Rdereference2(obj_id, H5P_DEFAULT, ref_type, ref_in); if (ref_obj_id < 0) @@ -850,15 +865,16 @@ static herr_t update_ref_value(hid_t obj_id, H5R_type_t ref_type, void *ref_in, H5TOOLS_GOTO_ERROR(FAIL, "H5Rget_region failed"); } - if(H5Rcreate(ref_out, fid_out, ref_obj_name, ref_type, space_id) < 0) + if (H5Rcreate(ref_out, fid_out, ref_obj_name, ref_type, space_id) < 0) H5TOOLS_GOTO_ERROR(FAIL, "H5Rcreate failed"); done: - H5E_BEGIN_TRY { - H5Sclose(space_id); - H5Oclose(ref_obj_id); - } H5E_END_TRY; + H5E_BEGIN_TRY + { + H5Sclose(space_id); + H5Oclose(ref_obj_id); + } + H5E_END_TRY; return ret_value; } - diff --git a/tools/src/h5repack/h5repack_verify.c b/tools/src/h5repack/h5repack_verify.c index 7bb5dfd..4149729 100644 --- a/tools/src/h5repack/h5repack_verify.c +++ b/tools/src/h5repack/h5repack_verify.c @@ -17,13 +17,12 @@ /* number of members in an array */ #ifndef NELMTS -# define NELMTS(X) (sizeof(X)/sizeof(X[0])) +#define NELMTS(X) (sizeof(X) / sizeof(X[0])) #endif static int verify_layout(hid_t pid, pack_info_t *obj); static int verify_filters(hid_t pid, hid_t tid, int nfilters, filter_info_t *filter); - /*------------------------------------------------------------------------- * Function: h5repack_verify * @@ -39,62 +38,62 @@ static int verify_filters(hid_t pid, hid_t tid, int nfilters, filter_info_t *fil int h5repack_verify(const char *in_fname, const char *out_fname, pack_opt_t *options) { - hid_t fidin = H5I_INVALID_HID; /* file ID for input file*/ - hid_t fidout = H5I_INVALID_HID; /* file ID for output file*/ - hid_t did = H5I_INVALID_HID; /* dataset ID */ - hid_t pid = H5I_INVALID_HID; /* dataset creation property list ID */ - hid_t sid = H5I_INVALID_HID; /* space ID */ - hid_t tid = H5I_INVALID_HID; /* type ID */ - int ok = 1; /* step results */ - unsigned int i; - trav_table_t *travt = NULL; - hid_t fcpl_in = H5I_INVALID_HID; /* file creation property for input file */ - hid_t fcpl_out = H5I_INVALID_HID; /* 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 */ - int ret_value = 0; + hid_t fidin = H5I_INVALID_HID; /* file ID for input file*/ + hid_t fidout = H5I_INVALID_HID; /* file ID for output file*/ + hid_t did = H5I_INVALID_HID; /* dataset ID */ + hid_t pid = H5I_INVALID_HID; /* dataset creation property list ID */ + hid_t sid = H5I_INVALID_HID; /* space ID */ + hid_t tid = H5I_INVALID_HID; /* type ID */ + int ok = 1; /* step results */ + unsigned int i; + trav_table_t * travt = NULL; + hid_t fcpl_in = H5I_INVALID_HID; /* file creation property for input file */ + hid_t fcpl_out = H5I_INVALID_HID; /* 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 */ + int ret_value = 0; /* open the output file */ - if((fidout = H5Fopen(out_fname, H5F_ACC_RDONLY, H5P_DEFAULT)) < 0 ) + if ((fidout = H5Fopen(out_fname, H5F_ACC_RDONLY, H5P_DEFAULT)) < 0) H5TOOLS_GOTO_ERROR((-1), "H5Fopen failed on <%s>", out_fname); - 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]; + 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]; - /*------------------------------------------------------------------------- - * open - *------------------------------------------------------------------------- - */ - if((did = H5Dopen2(fidout, name, H5P_DEFAULT)) < 0) + /*------------------------------------------------------------------------- + * open + *------------------------------------------------------------------------- + */ + if ((did = H5Dopen2(fidout, name, H5P_DEFAULT)) < 0) H5TOOLS_GOTO_ERROR((-1), "H5Dopen2 failed on <%s>", name); - if((sid = H5Dget_space(did)) < 0) + if ((sid = H5Dget_space(did)) < 0) H5TOOLS_GOTO_ERROR((-1), "H5Dget_space failed"); - if((pid = H5Dget_create_plist(did)) < 0) + if ((pid = H5Dget_create_plist(did)) < 0) H5TOOLS_GOTO_ERROR((-1), "H5Dget_create_plist failed"); - if((tid = H5Dget_type(did)) < 0) + if ((tid = H5Dget_type(did)) < 0) H5TOOLS_GOTO_ERROR((-1), "H5Dget_type failed"); - /*------------------------------------------------------------------------- - * filter check - *------------------------------------------------------------------------- - */ - if(verify_filters(pid, tid, obj->nfilters, obj->filter) <= 0) + /*------------------------------------------------------------------------- + * filter check + *------------------------------------------------------------------------- + */ + if (verify_filters(pid, tid, obj->nfilters, obj->filter) <= 0) ok = 0; - /*------------------------------------------------------------------------- - * layout check - *------------------------------------------------------------------------- - */ - if((obj->layout != -1) && (verify_layout(pid, obj) == 0)) + /*------------------------------------------------------------------------- + * layout check + *------------------------------------------------------------------------- + */ + if ((obj->layout != -1) && (verify_layout(pid, obj) == 0)) ok = 0; - /*------------------------------------------------------------------------- - * close - *------------------------------------------------------------------------- - */ + /*------------------------------------------------------------------------- + * close + *------------------------------------------------------------------------- + */ if (H5Pclose(pid) < 0) H5TOOLS_GOTO_ERROR((-1), "H5Pclose failed"); if (H5Sclose(sid) < 0) @@ -105,65 +104,65 @@ h5repack_verify(const char *in_fname, const char *out_fname, pack_opt_t *options H5TOOLS_GOTO_ERROR((-1), "H5Tclose failed"); } - /*------------------------------------------------------------------------- - * check for the "all" objects option - *------------------------------------------------------------------------- - */ + /*------------------------------------------------------------------------- + * 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 */ trav_table_init(fidout, &travt); /* get the list of objects in the file */ - if(h5trav_gettable(fidout, travt) < 0) + if (h5trav_gettable(fidout, travt) < 0) H5TOOLS_GOTO_ERROR((-1), "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) { - /*------------------------------------------------------------------------- - * open - *------------------------------------------------------------------------- - */ - if((did = H5Dopen2(fidout, name, H5P_DEFAULT)) < 0) + if (travt->objs[i].type == H5TRAV_TYPE_DATASET) { + /*------------------------------------------------------------------------- + * open + *------------------------------------------------------------------------- + */ + if ((did = H5Dopen2(fidout, name, H5P_DEFAULT)) < 0) H5TOOLS_GOTO_ERROR((-1), "H5Dopen2 failed on <%s>", name); - if((sid = H5Dget_space(did)) < 0) + if ((sid = H5Dget_space(did)) < 0) H5TOOLS_GOTO_ERROR((-1), "H5Dget_space failed"); - if((pid = H5Dget_create_plist(did)) < 0) + if ((pid = H5Dget_create_plist(did)) < 0) H5TOOLS_GOTO_ERROR((-1), "H5Dget_create_plist failed"); - if((tid = H5Dget_type(did)) < 0) + if ((tid = H5Dget_type(did)) < 0) H5TOOLS_GOTO_ERROR((-1), "H5Dget_type failed"); - /*------------------------------------------------------------------------- - * filter check - *------------------------------------------------------------------------- - */ - if(options->all_filter == 1) { - if(verify_filters(pid, tid, options->n_filter_g, options->filter_g) <= 0) + /*------------------------------------------------------------------------- + * filter check + *------------------------------------------------------------------------- + */ + if (options->all_filter == 1) { + if (verify_filters(pid, tid, options->n_filter_g, options->filter_g) <= 0) ok = 0; } - /*------------------------------------------------------------------------- - * layout check - *------------------------------------------------------------------------- - */ - if(options->all_layout == 1) { + /*------------------------------------------------------------------------- + * layout check + *------------------------------------------------------------------------- + */ + if (options->all_layout == 1) { pack_info_t pack; init_packobject(&pack); pack.layout = options->layout_g; - pack.chunk = options->chunk_g; - if(verify_layout(pid, &pack) == 0) + pack.chunk = options->chunk_g; + if (verify_layout(pid, &pack) == 0) ok = 0; } - /*------------------------------------------------------------------------- - * close - *------------------------------------------------------------------------- - */ + /*------------------------------------------------------------------------- + * close + *------------------------------------------------------------------------- + */ if (H5Pclose(pid) < 0) H5TOOLS_GOTO_ERROR((-1), "H5Pclose failed"); if (H5Sclose(sid) < 0) @@ -173,45 +172,47 @@ h5repack_verify(const char *in_fname, const char *out_fname, pack_opt_t *options if (H5Tclose(tid) < 0) H5TOOLS_GOTO_ERROR((-1), "H5Tclose failed"); } /* if */ - } /* i */ + } /* i */ /* free table */ trav_table_free(travt); travt = NULL; } - /*------------------------------------------------------------------------- - * Verify that file space info are set as expected - *------------------------------------------------------------------------- - */ + /*------------------------------------------------------------------------- + * Verify that file space info are set as expected + *------------------------------------------------------------------------- + */ /* open the input file */ - if((fidin = H5Fopen(in_fname, H5F_ACC_RDONLY, H5P_DEFAULT)) < 0) + if ((fidin = H5Fopen(in_fname, H5F_ACC_RDONLY, H5P_DEFAULT)) < 0) H5TOOLS_GOTO_ERROR((-1), "H5Fopen failed on file <%s>", in_fname); /* Get file creation property list for input file */ - if((fcpl_in = H5Fget_create_plist(fidin)) < 0) + if ((fcpl_in = H5Fget_create_plist(fidin)) < 0) H5TOOLS_GOTO_ERROR((-1), "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) - H5TOOLS_GOTO_ERROR((-1), "H5Pget_file_space_strategy failed to retrieve file space strategy & threshold"); + if (H5Pget_file_space_strategy(fcpl_in, &in_strategy, &in_persist, &in_threshold) < 0) + H5TOOLS_GOTO_ERROR((-1), + "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) + if (H5Pget_file_space_page_size(fcpl_in, &in_pagesize) < 0) H5TOOLS_GOTO_ERROR((-1), "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) + if ((fcpl_out = H5Fget_create_plist(fidout)) < 0) H5TOOLS_GOTO_ERROR((-1), "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) - H5TOOLS_GOTO_ERROR((-1), "H5Pget_file_space_strategy failed to retrieve file space strategy & threshold"); + if (H5Pget_file_space_strategy(fcpl_out, &out_strategy, &out_persist, &out_threshold) < 0) + H5TOOLS_GOTO_ERROR((-1), + "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) + if (H5Pget_file_space_page_size(fcpl_out, &out_pagesize) < 0) H5TOOLS_GOTO_ERROR((-1), "H5Pget_file_space_page_size failed to retrieve file space page size"); /* @@ -219,12 +220,12 @@ h5repack_verify(const char *in_fname, const char *out_fname, pack_opt_t *options * If -S option is not set, the file space handling strategy should be * 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)) + if (options->fs_strategy) { + if (out_strategy != (options->fs_strategy == (H5F_fspace_strategy_t)-1 ? 0 : options->fs_strategy)) H5TOOLS_GOTO_ERROR((-1), "file space strategy not set as unexpected"); } else { - if(out_strategy != in_strategy) + if (out_strategy != in_strategy) H5TOOLS_GOTO_ERROR((-1), "file space strategy not set as unexpected"); } @@ -233,12 +234,12 @@ h5repack_verify(const char *in_fname, const char *out_fname, pack_opt_t *options * If the -P option is not set, the free-space persist status should be * 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)) + if (options->fs_persist) { + if (out_persist != (hbool_t)(options->fs_persist == (-1) ? FALSE : options->fs_persist)) H5TOOLS_GOTO_ERROR((-1), "free-space persist status not set as unexpected"); } else { - if(out_persist != in_persist) + if (out_persist != in_persist) H5TOOLS_GOTO_ERROR((-1), "free-space persist status not set as unexpected"); } @@ -247,12 +248,12 @@ h5repack_verify(const char *in_fname, const char *out_fname, pack_opt_t *options * If the -T option is not set, the threshold should be the same as the * input file's threshold size. */ - if(options->fs_threshold) { - if(out_threshold != (hsize_t)(options->fs_threshold == (-1) ? 0 : options->fs_threshold)) + if (options->fs_threshold) { + if (out_threshold != (hsize_t)(options->fs_threshold == (-1) ? 0 : options->fs_threshold)) H5TOOLS_GOTO_ERROR((-1), "threshold not set as unexpected"); } else { - if(out_threshold != in_threshold) + if (out_threshold != in_threshold) H5TOOLS_GOTO_ERROR((-1), "threshold not set as unexpected"); } @@ -261,20 +262,20 @@ h5repack_verify(const char *in_fname, const char *out_fname, pack_opt_t *options * If the -G option is not set, the file space page size should be * 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)) + if (options->fs_pagesize) { + if (out_pagesize != (hsize_t)(options->fs_pagesize == (-1) ? 0 : options->fs_pagesize)) H5TOOLS_GOTO_ERROR((-1), "file space page size not set as unexpected"); } else { /* "-G" is not set */ - if(out_pagesize != in_pagesize) + if (out_pagesize != in_pagesize) H5TOOLS_GOTO_ERROR((-1), "file space page size not set as unexpected"); - } ret_value = ok; done: - H5E_BEGIN_TRY { + H5E_BEGIN_TRY + { H5Pclose(fcpl_in); H5Pclose(fcpl_out); H5Pclose(pid); @@ -285,7 +286,8 @@ done: H5Fclose(fidout); if (travt) trav_table_free(travt); - } H5E_END_TRY; + } + H5E_END_TRY; return ret_value; } /* h5repack_verify() */ @@ -305,13 +307,14 @@ done: *------------------------------------------------------------------------- */ -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 */ - int nfilters; /* number of filters */ - int rank; /* rank */ - int i; /* index */ + hsize_t chsize[64]; /* chunk size in elements */ + H5D_layout_t layout; /* layout */ + int nfilters; /* number of filters */ + int rank; /* rank */ + int i; /* index */ /* check if we have filters in the input object */ if ((nfilters = H5Pget_nfilters(pid)) < 0) @@ -328,8 +331,8 @@ int verify_layout(hid_t pid, pack_info_t *obj) 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; @@ -353,49 +356,50 @@ int verify_layout(hid_t pid, pack_info_t *obj) *------------------------------------------------------------------------- */ -int h5repack_cmp_pl(const char *fname1, hid_t fname1_fapl, const char *fname2, hid_t fname2_fapl) +int +h5repack_cmp_pl(const char *fname1, hid_t fname1_fapl, const char *fname2, hid_t fname2_fapl) { - hid_t fid1 = H5I_INVALID_HID; /* file ID */ - hid_t fid2 = H5I_INVALID_HID; /* file ID */ - hid_t dset1 = H5I_INVALID_HID; /* dataset ID */ - hid_t dset2 = H5I_INVALID_HID; /* dataset ID */ - hid_t gid = H5I_INVALID_HID; /* group ID */ - hid_t dcpl1 = H5I_INVALID_HID; /* dataset creation property list ID */ - hid_t dcpl2 = H5I_INVALID_HID; /* dataset creation property list ID */ - hid_t gcplid = H5I_INVALID_HID; /* group creation property list */ - unsigned crt_order_flag1; /* group creation order flag */ - unsigned crt_order_flag2; /* group creation order flag */ + hid_t fid1 = H5I_INVALID_HID; /* file ID */ + hid_t fid2 = H5I_INVALID_HID; /* file ID */ + hid_t dset1 = H5I_INVALID_HID; /* dataset ID */ + hid_t dset2 = H5I_INVALID_HID; /* dataset ID */ + hid_t gid = H5I_INVALID_HID; /* group ID */ + hid_t dcpl1 = H5I_INVALID_HID; /* dataset creation property list ID */ + hid_t dcpl2 = H5I_INVALID_HID; /* dataset creation property list ID */ + hid_t gcplid = H5I_INVALID_HID; /* 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; int ret_value = 1; - /*------------------------------------------------------------------------- - * open the files - *------------------------------------------------------------------------- - */ + /*------------------------------------------------------------------------- + * open the files + *------------------------------------------------------------------------- + */ /* Open the files */ if ((fid1 = h5tools_fopen(fname1, H5F_ACC_RDONLY, fname1_fapl, TRUE, NULL, 0)) < 0) H5TOOLS_GOTO_ERROR((-1), "h5tools_fopen failed <%s>: %s", fname1, H5FOPENERROR); if ((fid2 = h5tools_fopen(fname2, H5F_ACC_RDONLY, fname2_fapl, TRUE, NULL, 0)) < 0) H5TOOLS_GOTO_ERROR((-1), "h5tools_fopen failed <%s>: %s", fname2, H5FOPENERROR); - /*------------------------------------------------------------------------- - * get file table list of objects - *------------------------------------------------------------------------- - */ + /*------------------------------------------------------------------------- + * get file table list of objects + *------------------------------------------------------------------------- + */ /* Initialize indexing options */ h5trav_set_index(sort_by, sort_order); /* init table */ trav_table_init(fid1, &trav); - if(h5trav_gettable(fid1, trav) < 0) + if (h5trav_gettable(fid1, trav) < 0) H5TOOLS_GOTO_ERROR((-1), "h5trav_gettable failed"); - /*------------------------------------------------------------------------- - * traverse the suppplied object list - *------------------------------------------------------------------------- - */ - for(i = 0; i < trav->nobjs; i++) { - if(trav->objs[i].type == H5TRAV_TYPE_GROUP) { + /*------------------------------------------------------------------------- + * traverse the suppplied object list + *------------------------------------------------------------------------- + */ + 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) H5TOOLS_GOTO_ERROR((-1), "H5Gopen2 failed on first <%s>", trav->objs[i].name); if ((gcplid = H5Gget_create_plist(gid)) < 0) @@ -421,40 +425,40 @@ int h5repack_cmp_pl(const char *fname1, hid_t fname1_fapl, const char *fname2, h if (crt_order_flag1 != crt_order_flag2) H5TOOLS_GOTO_ERROR(0, "property lists failed for <%s> are different", trav->objs[i].name); } - else if(trav->objs[i].type == H5TRAV_TYPE_DATASET) { - if((dset1 = H5Dopen2(fid1, trav->objs[i].name, H5P_DEFAULT)) < 0) + else if (trav->objs[i].type == H5TRAV_TYPE_DATASET) { + if ((dset1 = H5Dopen2(fid1, trav->objs[i].name, H5P_DEFAULT)) < 0) H5TOOLS_GOTO_ERROR((-1), "H5Dopen2 failed on first <%s>", trav->objs[i].name); - if((dset2 = H5Dopen2(fid2, trav->objs[i].name, H5P_DEFAULT)) < 0) + if ((dset2 = H5Dopen2(fid2, trav->objs[i].name, H5P_DEFAULT)) < 0) H5TOOLS_GOTO_ERROR((-1), "H5Dopen2 failed on second <%s>", trav->objs[i].name); - if((dcpl1 = H5Dget_create_plist(dset1)) < 0) + if ((dcpl1 = H5Dget_create_plist(dset1)) < 0) H5TOOLS_GOTO_ERROR((-1), "H5Dget_create_plist failed"); - if((dcpl2 = H5Dget_create_plist(dset2)) < 0) + if ((dcpl2 = H5Dget_create_plist(dset2)) < 0) H5TOOLS_GOTO_ERROR((-1), "H5Dget_create_plist failed"); - /*------------------------------------------------------------------------- - * compare the property lists - *------------------------------------------------------------------------- - */ - if((ret_value = H5Pequal(dcpl1, dcpl2)) < 0) + /*------------------------------------------------------------------------- + * compare the property lists + *------------------------------------------------------------------------- + */ + if ((ret_value = H5Pequal(dcpl1, dcpl2)) < 0) H5TOOLS_GOTO_ERROR((-1), "H5Pequal failed"); - if(ret_value == 0) + if (ret_value == 0) H5TOOLS_GOTO_ERROR(0, "property lists failed for <%s> are different", trav->objs[i].name); - /*------------------------------------------------------------------------- - * close - *------------------------------------------------------------------------- - */ - if(H5Pclose(dcpl1) < 0) + /*------------------------------------------------------------------------- + * close + *------------------------------------------------------------------------- + */ + if (H5Pclose(dcpl1) < 0) H5TOOLS_GOTO_ERROR((-1), "H5Pclose failed"); - if(H5Pclose(dcpl2) < 0) + if (H5Pclose(dcpl2) < 0) H5TOOLS_GOTO_ERROR((-1), "H5Pclose failed"); - if(H5Dclose(dset1) < 0) + if (H5Dclose(dset1) < 0) H5TOOLS_GOTO_ERROR((-1), "H5Dclose failed"); - if(H5Dclose(dset2) < 0) + if (H5Dclose(dset2) < 0) H5TOOLS_GOTO_ERROR((-1), "H5Dclose failed"); } /*if*/ - } /*for*/ + } /*for*/ done: H5E_BEGIN_TRY @@ -467,14 +471,14 @@ done: H5Fclose(fid2); H5Pclose(gcplid); H5Gclose(gid); - if(trav) + if (trav) trav_table_free(trav); - } H5E_END_TRY; + } + H5E_END_TRY; return ret_value; } - /*------------------------------------------------------------------------- * Function: verify_filters * @@ -489,27 +493,25 @@ done: *------------------------------------------------------------------------- */ -static -int verify_filters(hid_t pid, hid_t tid, int nfilters, filter_info_t *filter) +static int +verify_filters(hid_t pid, hid_t tid, int nfilters, filter_info_t *filter) { - int nfilters_dcpl; /* number of filters in DCPL*/ - unsigned filt_flags; /* filter flags */ - H5Z_filter_t filtn; /* filter identification number */ - unsigned cd_values[20]; /* filter client data values */ - size_t cd_nelmts; /* filter client number of values */ - char f_name[256]; /* filter name */ - size_t size; /* type size */ - int i; /* index */ - unsigned j; /* index */ + int nfilters_dcpl; /* number of filters in DCPL*/ + unsigned filt_flags; /* filter flags */ + H5Z_filter_t filtn; /* filter identification number */ + unsigned cd_values[20]; /* filter client data values */ + size_t cd_nelmts; /* filter client number of values */ + char f_name[256]; /* filter name */ + size_t size; /* type size */ + int i; /* index */ + unsigned j; /* index */ /* get information about filters */ - if((nfilters_dcpl = H5Pget_nfilters(pid)) < 0) + if ((nfilters_dcpl = H5Pget_nfilters(pid)) < 0) return -1; /* 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) + if (!nfilters_dcpl && nfilters == 1 && filter[0].filtn == H5Z_FILTER_NONE) return 1; /* else the numbers of filters must match */ @@ -523,8 +525,8 @@ int verify_filters(hid_t pid, hid_t tid, int nfilters, filter_info_t *filter) 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); + filtn = H5Pget_filter2(pid, (unsigned)i, &filt_flags, &cd_nelmts, cd_values, sizeof(f_name), f_name, + NULL); /* filter ID */ if (filtn < 0) @@ -535,7 +537,7 @@ int verify_filters(hid_t pid, hid_t tid, int nfilters, filter_info_t *filter) /* compare client data values. some filters do return local values */ switch (filtn) { case H5Z_FILTER_NONE: - break; + break; case H5Z_FILTER_SHUFFLE: /* 1 private client value is returned by DCPL */ @@ -543,7 +545,7 @@ int verify_filters(hid_t pid, hid_t tid, int nfilters, filter_info_t *filter) return 0; /* get dataset's type size */ - if((size = H5Tget_size(tid)) <= 0) + if ((size = H5Tget_size(tid)) <= 0) return -1; /* the private client value holds the dataset's type size */ |