/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * Copyright by the Board of Trustees of the University of Illinois. * * All rights reserved. * * * * This file is part of HDF5. The full HDF5 copyright notice, including * * terms governing use, modification, and redistribution, is contained in * * the files COPYING and Copyright.html. COPYING can be found at the root * * of the source code distribution tree; Copyright.html can be found at the * * root level of an installed copy of the electronic HDF5 document set and * * is linked from the top-level documents page. It can also be found at * * http://hdf.ncsa.uiuc.edu/HDF5/doc/Copyright.html. If you do not have * * access to either file, you may request a copy from hdfhelp@ncsa.uiuc.edu. * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ #include #include #include #include "H5private.h" #include "h5repack.h" /*------------------------------------------------------------------------- * Function: copy_objects * * Purpose: duplicate all HDF5 objects in the file * * Return: 0, ok, -1 no * * Programmer: Pedro Vicente, pvn@ncsa.uiuc.edu * * Date: October, 23, 2003 * *------------------------------------------------------------------------- */ int copy_objects(const char* fnamein, const char* fnameout, pack_opt_t *options) { hid_t fidin; hid_t fidout; trav_table_t *travt=NULL; /*------------------------------------------------------------------------- * open the files *------------------------------------------------------------------------- */ /* disable error reporting */ H5E_BEGIN_TRY { /* Open the files */ if ((fidin=H5Fopen(fnamein,H5F_ACC_RDONLY,H5P_DEFAULT))<0 ){ printf("h5repack: <%s>: No such file or directory\n", fnamein ); exit(1); } if ((fidout=H5Fcreate(fnameout,H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT))<0 ){ printf("h5repack: <%s>: Could not create file\n", fnameout ); exit(1); } /* enable error reporting */ } H5E_END_TRY; if (options->verbose) printf("Making file <%s>...\n",fnameout); /* init table */ trav_table_init(&travt); /* get the list of objects in the file */ if (h5trav_gettable(fidin,travt)<0) goto out; #if defined (H5_REPACK_DEBUG) h5trav_printtable(travt); #endif /*------------------------------------------------------------------------- * do the copy *------------------------------------------------------------------------- */ if(do_copy_objects(fidin,fidout,travt,options)<0) { printf("h5repack: <%s>: Could not copy data to: %s\n", fnamein, fnameout); goto out; } /*------------------------------------------------------------------------- * do the copy of referenced objects * and create hard links *------------------------------------------------------------------------- */ if(do_copy_refobjs(fidin,fidout,travt,options)<0) { printf("h5repack: <%s>: Could not copy data to: %s\n", fnamein, fnameout); goto out; } /* free table */ trav_table_free(travt); /*------------------------------------------------------------------------- * close *------------------------------------------------------------------------- */ H5Fclose(fidin); H5Fclose(fidout); return 0; /*------------------------------------------------------------------------- * out *------------------------------------------------------------------------- */ out: H5E_BEGIN_TRY { H5Fclose(fidin); H5Fclose(fidout); trav_table_free(travt); } H5E_END_TRY; return -1; } /*------------------------------------------------------------------------- * Function: do_copy_objects * * Purpose: duplicate all HDF5 objects in the file * * Return: 0, ok, -1 no * * Programmer: Pedro Vicente, pvn@ncsa.uiuc.edu * * Date: October, 23, 2003 * *------------------------------------------------------------------------- */ int do_copy_objects(hid_t fidin, hid_t fidout, trav_table_t *travt, pack_opt_t *options) /* repack options */ { hid_t grp_in; /* group ID */ hid_t grp_out; /* group ID */ hid_t dset_in; /* read dataset ID */ hid_t dset_out; /* write dataset ID */ hid_t type_in; /* named type ID */ hid_t type_out; /* named type ID */ hid_t dcpl_id; /* dataset creation property list ID */ hid_t space_id; /* space ID */ hid_t ftype_id; /* file data type ID */ hid_t mtype_id; /* memory data type ID */ size_t msize; /* memory size of memory type */ void *buf=NULL; /* data buffer */ hsize_t nelmts; /* number of elements in 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 i, j; /*------------------------------------------------------------------------- * copy the suppplied object list *------------------------------------------------------------------------- */ for ( i = 0; i < travt->nobjs; i++) { switch ( travt->objs[i].type ) { /*------------------------------------------------------------------------- * H5G_GROUP *------------------------------------------------------------------------- */ case H5G_GROUP: if (options->verbose) printf(" %-10s %s\n", "group",travt->objs[i].name ); if ((grp_out=H5Gcreate(fidout,travt->objs[i].name, 0))<0) goto error; if((grp_in = H5Gopen (fidin,travt->objs[i].name))<0) goto error; /*------------------------------------------------------------------------- * copy attrs *------------------------------------------------------------------------- */ if (copy_attr(grp_in,grp_out,options)<0) goto error; if (H5Gclose(grp_out)<0) goto error; if (H5Gclose(grp_in)<0) goto error; break; /*------------------------------------------------------------------------- * H5G_DATASET *------------------------------------------------------------------------- */ case H5G_DATASET: if (options->verbose) printf(" %-10s %s\n", "dataset",travt->objs[i].name ); if ((dset_in=H5Dopen(fidin,travt->objs[i].name))<0) goto error; if ((space_id=H5Dget_space(dset_in))<0) goto error; if ((ftype_id=H5Dget_type (dset_in))<0) goto error; if ((dcpl_id=H5Dget_create_plist(dset_in))<0) goto error; if ( (rank=H5Sget_simple_extent_ndims(space_id))<0) goto error; if ( H5Sget_simple_extent_dims(space_id,dims,NULL)<0) goto error; nelmts=1; for (j=0; jverbose) print_filters(dcpl_id); /*------------------------------------------------------------------------- * object 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 ( ! H5Tequal(mtype_id, H5T_STD_REF_OBJ) ) { /* the information about the object to be filtered/"layouted" */ pack_info_t obj; init_packobject(&obj); /* get the storage size of the input dataset */ dsize_in=H5Dget_storage_size(dset_in); /*------------------------------------------------------------------------- * read to memory *------------------------------------------------------------------------- */ buf=(void *) HDmalloc((unsigned)(nelmts*msize)); if ( buf==NULL){ printf( "cannot read into memory\n" ); goto error; } if (H5Dread(dset_in,mtype_id,H5S_ALL,H5S_ALL,H5P_DEFAULT,buf)<0) goto error; /*------------------------------------------------------------------------- * apply the layout; check first if the object is to be modified. * if the layout could not be applied, continue *------------------------------------------------------------------------- */ if (layout_this(dcpl_id,travt->objs[i].name,options,&obj)) { if (apply_layout(dcpl_id,&obj)<0) continue; } /*------------------------------------------------------------------------- * apply the filter; check first if the object is to be filtered. * if the filter could not be applied, continue *------------------------------------------------------------------------- */ if (filter_this(travt->objs[i].name,options,&obj)) { /* filters require CHUNK layout; if we do not have one define a default */ if (obj.chunk.rank==0) { obj.chunk.rank=rank; for (j=0; jobjs[i].name,ftype_id,space_id,dcpl_id))<0) goto error; if (dsize_in) { if (H5Dwrite(dset_out,mtype_id,H5S_ALL,H5S_ALL,H5P_DEFAULT,buf)<0) goto error; } /*------------------------------------------------------------------------- * copy attrs *------------------------------------------------------------------------- */ if (copy_attr(dset_in,dset_out,options)<0) goto error; /*------------------------------------------------------------------------- * store the storage sizes *------------------------------------------------------------------------- */ dsize_out=H5Dget_storage_size(dset_out); /*close */ if (H5Dclose(dset_out)<0) goto error; if (buf) free(buf); }/*H5T_STD_REF_OBJ*/ /*------------------------------------------------------------------------- * close *------------------------------------------------------------------------- */ if (H5Tclose(ftype_id)<0) goto error; if (H5Tclose(mtype_id)<0) goto error; if (H5Pclose(dcpl_id)<0) goto error; if (H5Sclose(space_id)<0) goto error; if (H5Dclose(dset_in)<0) goto error; break; /*------------------------------------------------------------------------- * H5G_TYPE *------------------------------------------------------------------------- */ case H5G_TYPE: if ((type_in = H5Topen (fidin,travt->objs[i].name))<0) goto error; if ((type_out = H5Tcopy(type_in))<0) goto error; if ((H5Tcommit(fidout,travt->objs[i].name,type_out))<0) goto error; /*------------------------------------------------------------------------- * copy attrs *------------------------------------------------------------------------- */ if (copy_attr(type_in,type_out,options)<0) goto error; if (H5Tclose(type_in)<0) goto error; if (H5Tclose(type_out)<0) goto error; if (options->verbose) printf(" %-10s %s\n","datatype",travt->objs[i].name ); break; /*------------------------------------------------------------------------- * H5G_LINK *------------------------------------------------------------------------- */ case H5G_LINK: { H5G_stat_t statbuf; char *targbuf=NULL; if (H5Gget_objinfo(fidin,travt->objs[i].name,FALSE,&statbuf)<0) goto error; targbuf = malloc(statbuf.linklen); if (H5Gget_linkval(fidin,travt->objs[i].name,statbuf.linklen,targbuf)<0) goto error; if (H5Glink(fidout, H5G_LINK_SOFT, targbuf, /* current name of object */ travt->objs[i].name /* new name of object */ )<0) goto error; free(targbuf); if (options->verbose) printf(" %-10s %s\n","link",travt->objs[i].name ); } break; default: if (options->verbose) printf(" %-10s %s\n","User defined object",travt->objs[i].name); break; } } /*------------------------------------------------------------------------- * the root is a special case, we get an ID for the root group * and copy its attributes using that ID * it must be done last, because the attributes might contain references to * objects in the object list *------------------------------------------------------------------------- */ if ((grp_out = H5Gopen(fidout,"/"))<0) goto error; if ((grp_in = H5Gopen(fidin,"/"))<0) goto error; if (copy_attr(grp_in,grp_out,options)<0) goto error; if (H5Gclose(grp_out)<0) goto error; if (H5Gclose(grp_in)<0) goto error; return 0; error: H5E_BEGIN_TRY { H5Gclose(grp_in); H5Gclose(grp_out); H5Pclose(dcpl_id); H5Sclose(space_id); H5Dclose(dset_in); H5Dclose(dset_out); H5Tclose(ftype_id); H5Tclose(mtype_id); H5Tclose(type_in); H5Tclose(type_out); if (buf) free(buf); } H5E_END_TRY; return -1; } /*------------------------------------------------------------------------- * Function: copy_attr * * Purpose: copy attributes located in LOC_IN, which is obtained either from * loc_id = H5Gopen( fid, name); * loc_id = H5Dopen( fid, name); * loc_id = H5Topen( fid, name); * * Return: 0, ok, -1 no * * Programmer: Pedro Vicente, pvn@ncsa.uiuc.edu * * Date: October, 28, 2003 * *------------------------------------------------------------------------- */ int copy_attr(hid_t loc_in, hid_t loc_out, pack_opt_t *options ) { hid_t attr_id; /* attr ID */ hid_t attr_out; /* attr ID */ hid_t space_id; /* space ID */ hid_t ftype_id; /* file data type ID */ hid_t mtype_id; /* memory data type ID */ size_t msize; /* memory size of type */ void *buf; /* data buffer */ hsize_t nelmts; /* number of elements in dataset */ int rank; /* rank of dataset */ hsize_t dims[H5S_MAX_RANK];/* dimensions of dataset */ char name[255]; int n, j; unsigned u; if ((n = H5Aget_num_attrs(loc_in))<0) goto error; for ( u = 0; u < (unsigned)n; u++) { /* set data buffer to NULL each iteration we might not use it in the case of references */ buf=NULL; /*------------------------------------------------------------------------- * open *------------------------------------------------------------------------- */ /* open attribute */ if ((attr_id = H5Aopen_idx(loc_in, u))<0) goto error; /* get name */ if (H5Aget_name( attr_id, 255, name )<0) goto error; /* get the file datatype */ if ((ftype_id = H5Aget_type( attr_id )) < 0 ) goto error; /* get the dataspace handle */ if ((space_id = H5Aget_space( attr_id )) < 0 ) goto error; /* get dimensions */ if ( (rank = H5Sget_simple_extent_dims(space_id, dims, NULL)) < 0 ) goto error; nelmts=1; for (j=0; jverbose) printf(" %-13s %s\n", "attr", name); /*------------------------------------------------------------------------- * close *------------------------------------------------------------------------- */ if (H5Tclose(ftype_id)<0) goto error; if (H5Tclose(mtype_id)<0) goto error; if (H5Sclose(space_id)<0) goto error; if (H5Aclose(attr_id)<0) goto error; } /* u */ return 0; error: H5E_BEGIN_TRY { H5Tclose(ftype_id); H5Tclose(mtype_id); H5Sclose(space_id); H5Aclose(attr_id); H5Aclose(attr_out); if (buf) free(buf); } H5E_END_TRY; return -1; }