diff options
Diffstat (limited to 'tools/h5repack/h5repack_copy.c')
| -rw-r--r-- | tools/h5repack/h5repack_copy.c | 237 |
1 files changed, 217 insertions, 20 deletions
diff --git a/tools/h5repack/h5repack_copy.c b/tools/h5repack/h5repack_copy.c index 8ab5a35..73f57e3 100644 --- a/tools/h5repack/h5repack_copy.c +++ b/tools/h5repack/h5repack_copy.c @@ -21,8 +21,21 @@ #include "h5tools.h" #include "h5tools_utils.h" -extern char *progname; +/*------------------------------------------------------------------------- +* typedefs +*------------------------------------------------------------------------- +*/ +typedef struct named_dt_t { + haddr_t addr_in; /* Address of 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; +/*------------------------------------------------------------------------- +* globals +*------------------------------------------------------------------------- +*/ +extern char *progname; /*------------------------------------------------------------------------- * macros @@ -36,7 +49,11 @@ extern char *progname; */ 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_attr(hid_t loc_in,hid_t loc_out,pack_opt_t *options); +static 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); +static 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); +static int named_datatype_free(named_dt_t **named_dt_head_p, int ignore_err); 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); @@ -506,6 +523,7 @@ int do_copy_objects(hid_t fidin, hid_t f_space_id=-1; /* file space ID */ hid_t ftype_id=-1; /* file type ID */ hid_t wtype_id=-1; /* read/write type ID */ + named_dt_t *named_dt_head=NULL; /* Pointer to the stack of named datatypes copied */ size_t msize; /* size of type */ hsize_t nelmts; /* number of elements in dataset */ int rank; /* rank of dataset */ @@ -522,6 +540,7 @@ int do_copy_objects(hid_t fidin, unsigned i; unsigned u; int is_ref=0; + htri_t is_named; /*------------------------------------------------------------------------- * copy the suppplied object list @@ -605,7 +624,7 @@ int do_copy_objects(hid_t fidin, * copy attrs *------------------------------------------------------------------------- */ - if(copy_attr(grp_in,grp_out,options) < 0) + if(copy_attr(grp_in, grp_out, &named_dt_head, travt, options) < 0) goto error; @@ -657,6 +676,14 @@ int do_copy_objects(hid_t fidin, goto error; if(H5T_REFERENCE == H5Tget_class(ftype_id)) is_ref = 1; + + /* Check if the datatype is committed */ + if((is_named = H5Tcommitted(ftype_id)) < 0) + goto error; + if(is_named) + if((wtype_id = copy_named_datatype(ftype_id, fidout, &named_dt_head, travt, options)) < 0) + goto error; + if(H5Tclose(ftype_id) < 0) goto error; if(H5Dclose(dset_in) < 0) @@ -672,7 +699,8 @@ int do_copy_objects(hid_t fidin, if ( options->op_tbl->nelems || options->all_filter == 1 || options->all_layout == 1 || - is_ref) + is_ref || + is_named) { int j; @@ -698,10 +726,13 @@ int do_copy_objects(hid_t fidin, nelmts *= dims[j]; } - if(options->use_native == 1) - wtype_id = h5tools_get_native_type(ftype_id); - else - wtype_id = H5Tcopy(ftype_id); + /* wtype_id will have already been set if using a named dtype */ + if(!is_named) { + if(options->use_native == 1) + wtype_id = h5tools_get_native_type(ftype_id); + else + wtype_id = H5Tcopy(ftype_id); + } /* end if */ if((msize = H5Tget_size(wtype_id)) == 0) goto error; @@ -933,7 +964,7 @@ int do_copy_objects(hid_t fidin, * copy attrs *------------------------------------------------------------------------- */ - if (copy_attr(dset_in,dset_out,options) < 0) + if (copy_attr(dset_in, dset_out, &named_dt_head, travt, options) < 0) goto error; /*close */ @@ -1004,7 +1035,7 @@ int do_copy_objects(hid_t fidin, goto error; if((dset_out = H5Dopen2(fidout, travt->objs[i].name, H5P_DEFAULT)) < 0) goto error; - if(copy_attr(dset_in, dset_out, options) < 0) + if(copy_attr(dset_in, dset_out, &named_dt_head, travt, options) < 0) goto error; if(H5Dclose(dset_in) < 0) goto error; @@ -1033,17 +1064,21 @@ int do_copy_objects(hid_t fidin, if((type_in = H5Topen2(fidin, travt->objs[i].name, H5P_DEFAULT)) < 0) goto error; - if((type_out = H5Tcopy(type_in)) < 0) + /* Copy the datatype anonymously */ + if((type_out = copy_named_datatype(type_in, fidout, &named_dt_head, + travt, options)) < 0) goto error; - if((H5Tcommit2(fidout, travt->objs[i].name, type_out, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT)) < 0) + /* Link in to group structure */ + if(H5Lcreate_hard(type_out, ".", fidout, travt->objs[i].name, + H5P_DEFAULT, H5P_DEFAULT) < 0) goto error; /*------------------------------------------------------------------------- * copy attrs *------------------------------------------------------------------------- */ - if(copy_attr(type_in, type_out, options) < 0) + if(copy_attr(type_in, type_out, &named_dt_head, travt, options) < 0) goto error; if(H5Tclose(type_in) < 0) @@ -1094,6 +1129,9 @@ int do_copy_objects(hid_t fidin, } /* i */ + /* Finalize (link) the stack of named datatypes (if any) */ + named_datatype_free(&named_dt_head, 0); + return 0; error: @@ -1110,6 +1148,7 @@ error: H5Tclose(wtype_id); H5Tclose(type_in); H5Tclose(type_out); + named_datatype_free(&named_dt_head, 1); } H5E_END_TRY; /* free */ if (buf!=NULL) @@ -1139,6 +1178,8 @@ error: 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 ) { @@ -1151,6 +1192,7 @@ int copy_attr(hid_t loc_in, void *buf=NULL; /* data buffer */ hsize_t nelmts; /* number of elements in dataset */ int rank; /* rank of dataset */ + htri_t is_named; /* Whether the datatype is named */ hsize_t dims[H5S_MAX_RANK];/* dimensions of dataset */ char name[255]; H5O_info_t oinfo; /* object info */ @@ -1182,6 +1224,27 @@ int copy_attr(hid_t loc_in, if ((ftype_id = H5Aget_type( attr_id )) < 0 ) goto error; + /* Check if the datatype is committed */ + if((is_named = H5Tcommitted(ftype_id)) < 0) + goto error; + if(is_named) { + hid_t fidout; + + /* Create out file id */ + if((fidout = H5Iget_file_id(loc_out)) < 0) + goto error; + + /* Copy named dt */ + if((wtype_id = copy_named_datatype(ftype_id, fidout, named_dt_head_p, + travt, options)) < 0) { + H5Fclose(fidout); + goto error; + } /* end if */ + + if(H5Fclose(fidout) < 0) + goto error; + } /* end if */ + /* get the dataspace handle */ if ((space_id = H5Aget_space( attr_id )) < 0 ) goto error; @@ -1194,10 +1257,13 @@ int copy_attr(hid_t loc_in, for (j=0; j<rank; j++) nelmts*=dims[j]; - if (options->use_native==1) - wtype_id = h5tools_get_native_type(ftype_id); - else - wtype_id = H5Tcopy(ftype_id); + /* wtype_id will have already been set if using a named dtype */ + if(!is_named) { + if (options->use_native==1) + wtype_id = h5tools_get_native_type(ftype_id); + else + wtype_id = H5Tcopy(ftype_id); + } /* end if */ if ((msize=H5Tget_size(wtype_id))==0) goto error; @@ -1234,7 +1300,7 @@ int copy_attr(hid_t loc_in, *------------------------------------------------------------------------- */ - if((attr_out = H5Acreate2(loc_out, name, ftype_id, space_id, H5P_DEFAULT, H5P_DEFAULT)) < 0) + if((attr_out = H5Acreate2(loc_out, name, wtype_id, space_id, H5P_DEFAULT, H5P_DEFAULT)) < 0) goto error; if(H5Awrite(attr_out, wtype_id, buf) < 0) goto error; @@ -1282,8 +1348,6 @@ error: } - - /*------------------------------------------------------------------------- * Function: print_dataset_info * @@ -1388,6 +1452,139 @@ static void print_dataset_info(hid_t dcpl_id, } } + +/*------------------------------------------------------------------------- +* Function: copy_named_datatype +* +* Purpose: Copies the specified datatype anonymously, and returns an open +* id for that datatype in the output file. The first time this +* is called it scans every named datatype in travt into a +* private stack, afterwards it simply scans that stack. The id +* returned must be closed after it is no longer needed. +* named_datatype_free must be called before the program exits +* to free the stack. +* +* Programmer: Neil Fortner +* +* Date: April 14, 2009 +* +*------------------------------------------------------------------------- +*/ +static hid_t +copy_named_datatype(hid_t type_in, hid_t fidout, named_dt_t **named_dt_head_p, trav_table_t *travt, pack_opt_t *options) +{ + named_dt_t *dt = *named_dt_head_p; /* Stack pointer */ + named_dt_t *dt_ret = NULL; /* Datatype to return */ + H5O_info_t oinfo; /* Object info of input dtype */ + hid_t ret_value = -1; /* The identifier of the named dtype in the out file */ + + if(H5Oget_info(type_in, &oinfo) < 0) + goto error; + + if(*named_dt_head_p) { + /* Stack already exists, search for the datatype */ + while(dt && dt->addr_in != oinfo.addr) + dt = dt->next; + + dt_ret = dt; + } else { + /* Create the stack */ + size_t i; + + for(i=0; i<travt->nobjs; i++) + if(travt->objs[i].type == H5TRAV_TYPE_NAMED_DATATYPE) { + /* Push onto the stack */ + if(NULL == (dt = (named_dt_t *) HDmalloc(sizeof(named_dt_t)))) + goto error; + dt->next = *named_dt_head_p; + *named_dt_head_p = dt; + + /* Update the address and id */ + dt->addr_in = travt->objs[i].objno; + dt->id_out = -1; + + /* Check if this type is the one requested */ + if(oinfo.addr == dt->addr_in) { + HDassert(!dt_ret); + dt_ret = dt; + } /* end if */ + } /* end if */ + } /* end else */ + + /* Handle the case that the requested datatype was not found. This is + * possible if the datatype was committed anonymously in the input file. */ + if(!dt_ret) { + /* Push the new datatype onto the stack */ + if(NULL == (dt_ret = (named_dt_t *) HDmalloc(sizeof(named_dt_t)))) + goto error; + dt_ret->next = *named_dt_head_p; + *named_dt_head_p = dt_ret; + + /* Update the address and id */ + dt_ret->addr_in = oinfo.addr; + dt_ret->id_out = -1; + } /* end if */ + + /* If the requested datatype does not yet exist in the output file, copy it + * anonymously */ + if(dt_ret->id_out < 0) { + if (options->use_native==1) + dt_ret->id_out = h5tools_get_native_type(type_in); + else + dt_ret->id_out = H5Tcopy(type_in); + if(dt_ret->id_out < 0) + goto error; + if(H5Tcommit_anon(fidout, dt_ret->id_out, H5P_DEFAULT, H5P_DEFAULT) < 0) + goto error; + } /* end if */ + + /* Set return value */ + ret_value = dt_ret->id_out; + + /* Increment the ref count on id_out, because the calling function will try + * to close it */ + if(H5Iinc_ref(ret_value) < 0) + goto error; + + return(ret_value); + +error: + return(-1); +} /* end copy_named_datatype */ + + +/*------------------------------------------------------------------------- +* Function: named_datatype_free +* +* Purpose: Frees the stack of named datatypes. +* +* Programmer: Neil Fortner +* +* Date: April 14, 2009 +* +*------------------------------------------------------------------------- +*/ +static int +named_datatype_free(named_dt_t **named_dt_head_p, int ignore_err) +{ + named_dt_t *dt = *named_dt_head_p; + + while(dt) { + /* Pop the datatype off the stack and free it */ + if(H5Tclose(dt->id_out) < 0 && !ignore_err) + goto error; + dt = dt->next; + HDfree(*named_dt_head_p); + *named_dt_head_p = dt; + } /* end while */ + + return 0; + +error: + return -1; +} /* end named_datatype_free */ + + /*------------------------------------------------------------------------- * Function: copy_user_block * |