diff options
Diffstat (limited to 'tools/h5repack/h5repack_refs.c')
| -rw-r--r-- | tools/h5repack/h5repack_refs.c | 600 |
1 files changed, 600 insertions, 0 deletions
diff --git a/tools/h5repack/h5repack_refs.c b/tools/h5repack/h5repack_refs.c new file mode 100644 index 0000000..cd5fe80 --- /dev/null +++ b/tools/h5repack/h5repack_refs.c @@ -0,0 +1,600 @@ +/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * + * 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 <stdlib.h> +#include <string.h> +#include <stdio.h> +#include "H5private.h" +#include "h5repack.h" + + +/*------------------------------------------------------------------------- + * Function: do_copy_refobjs + * + * Purpose: duplicate all referenced HDF5 objects in the file + * + * Return: 0, ok, -1 no + * + * Programmer: Pedro Vicente, pvn@ncsa.uiuc.edu + * + * Date: December, 10, 2003 + * + *------------------------------------------------------------------------- + */ + +int do_copy_refobjs(hid_t fidin, + hid_t fidout, + int nobjects, /* number of objects */ + trav_info_t *travi, /* array of object names */ + 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 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 */ + hsize_t nelmts; /* number of elements in dataset */ + int rank; /* rank of dataset */ + hsize_t dims[H5S_MAX_RANK];/* dimensions of dataset */ + int i, j; + + /* initialize to test for non reference cases */ + +/*------------------------------------------------------------------------- + * browse + *------------------------------------------------------------------------- + */ + + for ( i = 0; i < nobjects; i++) + { + + switch ( travi[i].type ) + { + /*------------------------------------------------------------------------- + * H5G_GROUP + *------------------------------------------------------------------------- + */ + case H5G_GROUP: + + if((grp_in = H5Gopen (fidin,travi[i].name))<0) + goto error; + + if (H5Gclose(grp_in)<0) + goto error; + + break; + + /*------------------------------------------------------------------------- + * H5G_DATASET + *------------------------------------------------------------------------- + */ + case H5G_DATASET: + + if ((dset_in=H5Dopen(fidin,travi[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; j<rank; j++) + nelmts*=dims[j]; + if ((mtype_id=H5Tget_native_type(ftype_id,H5T_DIR_DEFAULT))<0) + goto error; + if ((msize=H5Tget_size(mtype_id))==0) + goto error; + + +/*------------------------------------------------------------------------- + * object references are a special case + * we cannot just copy the buffers, but instead we recreate the reference + *------------------------------------------------------------------------- + */ + if (H5Tequal(mtype_id, H5T_STD_REF_OBJ)) + { + H5G_obj_t obj_type; + hid_t refobj_id; + hobj_ref_t *refbuf; + const char* refname; + hobj_ref_t *buf; + + /*------------------------------------------------------------------------- + * 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; + + + if ((obj_type = H5Rget_obj_type(dset_in,H5R_OBJECT,buf))<0) + goto error; + refbuf=HDmalloc((unsigned)nelmts*msize); + if ( refbuf==NULL){ + printf( "cannot allocate memory\n" ); + goto error; + } + for ( j=0; j<nelmts; j++) + { + if ((refobj_id = H5Rdereference(dset_in,H5R_OBJECT,&buf[j]))<0) + goto error; + + /* get the name. a valid name could only occur in the + second traversal of the file */ + if ((refname=MapIdToName(refobj_id,nobjects,travi,options))!=NULL) + { + /* create the reference */ + if (H5Rcreate(&refbuf[j],fidout,refname,H5R_OBJECT,-1)<0) + goto error; + + if (options->verbose) + printf("object <%s> reference created to <%s>\n",travi[i].name,refname); + } + close_obj(obj_type,refobj_id); + }/* j */ + + + + /*------------------------------------------------------------------------- + * create/write dataset/close + *------------------------------------------------------------------------- + */ + if ((dset_out=H5Dcreate(fidout,travi[i].name,ftype_id,space_id,dcpl_id))<0) + goto error; + if (H5Dwrite(dset_out,mtype_id,H5S_ALL,H5S_ALL,H5P_DEFAULT,refbuf)<0) + goto error; + + free(buf); + free(refbuf); + + }/*H5T_STD_REF_OBJ*/ + + + /*------------------------------------------------------------------------- + * open previously created object in 1st traversal + *------------------------------------------------------------------------- + */ + + else + { + if ((dset_out=H5Dopen(fidout,travi[i].name))<0) + goto error; + } + + /*------------------------------------------------------------------------- + * copy referenced objects in attributes + *------------------------------------------------------------------------- + */ + + if (do_copy_refobjs_inattr(dset_in,dset_out,options,nobjects,travi,fidout)<0) + goto error; + + + /*------------------------------------------------------------------------- + * 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; + if (H5Dclose(dset_out)<0) + goto error; + + + break; + + /*------------------------------------------------------------------------- + * H5G_TYPE + *------------------------------------------------------------------------- + */ + case H5G_TYPE: + + if ((type_in = H5Topen (fidin,travi[i].name))<0) + goto error; + + if (H5Tclose(type_in)<0) + goto error; + + + break; + + + /*------------------------------------------------------------------------- + * H5G_LINK + *------------------------------------------------------------------------- + */ + + case H5G_LINK: + + /*nothing to do */ + break; + + default: + + 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 (do_copy_refobjs_inattr(grp_in,grp_out,options,nobjects,travi,fidout)<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); + } H5E_END_TRY; + return -1; + +} + + +/*------------------------------------------------------------------------- + * Function: do_copy_refobjs_inattr + * + * 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 do_copy_refobjs_inattr(hid_t loc_in, + hid_t loc_out, + pack_opt_t *options, + int nobjects, /* number of objects */ + trav_info_t *travi, /* array of object names */ + hid_t fidout /* for saving references */ + ) +{ + 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 */ + 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++) + { + +/*------------------------------------------------------------------------- + * 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; + + + /*------------------------------------------------------------------------- + * elements + *------------------------------------------------------------------------- + */ + nelmts=1; + for (j=0; j<rank; j++) + nelmts*=dims[j]; + if ((mtype_id=H5Tget_native_type(ftype_id,H5T_DIR_DEFAULT))<0) + goto error; + if ((msize=H5Tget_size(mtype_id))==0) + goto error; + + + +/*------------------------------------------------------------------------- + * object references are a special case + * we cannot just copy the buffers, but instead we recreate the reference + *------------------------------------------------------------------------- + */ + if (H5Tequal(mtype_id, H5T_STD_REF_OBJ)) + { + H5G_obj_t obj_type; + hid_t refobj_id; + hobj_ref_t *refbuf; + int i; + const char* refname; + hobj_ref_t *buf; + + + buf=(void *) HDmalloc((unsigned)(nelmts*msize)); + if ( buf==NULL){ + printf( "cannot read into memory\n" ); + goto error; + } + if (H5Aread(attr_id,mtype_id,buf)<0) + goto error; + + if ((obj_type = H5Rget_obj_type(attr_id,H5R_OBJECT,buf))<0) + goto error; + refbuf=HDmalloc((unsigned)nelmts*msize); + if ( refbuf==NULL){ + printf( "cannot allocate memory\n" ); + goto error; + } + for ( i=0; i<nelmts; i++) + { + if ((refobj_id = H5Rdereference(attr_id,H5R_OBJECT,&buf[i]))<0) + goto error; + + /* get the name. a valid name could only occur in the + second traversal of the file */ + if ((refname=MapIdToName(refobj_id,nobjects,travi,options))!=NULL) + { + /* create the reference */ + if (H5Rcreate(&refbuf[i],fidout,refname,H5R_OBJECT,-1)<0) + goto error; + + if (options->verbose) + printf("object <%s> reference created to <%s>\n",name,refname); + } + close_obj(obj_type,refobj_id); + }/* i */ + + + /*------------------------------------------------------------------------- + * copy + *------------------------------------------------------------------------- + */ + + if ((attr_out=H5Acreate(loc_out,name,ftype_id,space_id,H5P_DEFAULT))<0) + goto error; + if(H5Awrite(attr_out,mtype_id,refbuf)<0) + goto error; + + if (H5Aclose(attr_out)<0) + goto error; + + free(refbuf); + free(buf); + + }/*H5T_STD_REF_OBJ*/ + + +/*------------------------------------------------------------------------- + * 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); + } H5E_END_TRY; + return -1; +} + +/*------------------------------------------------------------------------- + * Function: close_obj + * + * Purpose: Auxiliary function to close an object + * + *------------------------------------------------------------------------- + */ + +static void close_obj(H5G_obj_t obj_type, hid_t obj_id) +{ + + switch (obj_type) { + case H5G_GROUP: + H5Gclose(obj_id); + break; + case H5G_DATASET: + H5Dclose(obj_id); + break; + case H5G_TYPE: + H5Tclose(obj_id); + break; + default: + assert(0); + break; + } +} + +/*------------------------------------------------------------------------- + * Function: MapIdToName + * + * Purpose: map an object ID to a name + * + *------------------------------------------------------------------------- + */ + +const char* MapIdToName(hid_t refobj_id, + int nobjects, /* number of objects */ + trav_info_t *travi, /* array of object names */ + pack_opt_t *options) /* repack options */ +{ + hid_t id; + hid_t fid; + int i; + + if ((fid = H5Iget_file_id(refobj_id))<0) + { + assert(0); + return NULL; + } + + + for ( i=0; i<nobjects; i++) + { + switch ( travi[i].type ) + { + + /*------------------------------------------------------------------------- + * H5G_GROUP + *------------------------------------------------------------------------- + */ + + case H5G_GROUP: + + + break; + + /*------------------------------------------------------------------------- + * H5G_DATASET + *------------------------------------------------------------------------- + */ + + case H5G_DATASET: + + if ((id = H5Dopen(fid,travi[i].name))<0) + { + assert(0); + return NULL; + } + + if (H5Dclose(id)<0) + { + assert(0); + return NULL; + } + + if (id==refobj_id) + { + H5Fclose(fid); + return travi[i].name; + } + + + break; + + /*------------------------------------------------------------------------- + * H5G_TYPE + *------------------------------------------------------------------------- + */ + + case H5G_TYPE: + + + + break; + + + /*------------------------------------------------------------------------- + * H5G_LINK + *------------------------------------------------------------------------- + */ + + case H5G_LINK: + break; + + default: + assert(0); + break; + + } + + + } /* i */ + + if (H5Fclose(fid)<0) + return NULL; + + return NULL; +} |