diff options
Diffstat (limited to 'tools/h5repack/h5repack_refs.c')
| -rw-r--r-- | tools/h5repack/h5repack_refs.c | 268 |
1 files changed, 134 insertions, 134 deletions
diff --git a/tools/h5repack/h5repack_refs.c b/tools/h5repack/h5repack_refs.c index 28c6c0b..99cd49f 100644 --- a/tools/h5repack/h5repack_refs.c +++ b/tools/h5repack/h5repack_refs.c @@ -19,14 +19,14 @@ #include "H5private.h" #include "h5repack.h" -static const char* MapIdToName(hid_t refobj_id, +static const char* MapIdToName(hid_t refobj_id, trav_table_t *travt); static void close_obj(H5G_obj_t obj_type, hid_t obj_id); -static int copy_refs_attr(hid_t loc_in, - hid_t loc_out, +static int copy_refs_attr(hid_t loc_in, + hid_t loc_out, pack_opt_t *options, trav_table_t *travt, hid_t fidout /* for saving references */ @@ -35,7 +35,7 @@ static int copy_refs_attr(hid_t loc_in, /*------------------------------------------------------------------------- * Function: do_copy_refobjs * - * Purpose: duplicate all referenced HDF5 objects in the file + * Purpose: duplicate all referenced HDF5 objects in the file * and create hard links * * Return: 0, ok, -1 no @@ -47,19 +47,19 @@ static int copy_refs_attr(hid_t loc_in, *------------------------------------------------------------------------- */ -int do_copy_refobjs(hid_t fidin, - hid_t fidout, +int do_copy_refobjs(hid_t fidin, + hid_t fidout, trav_table_t *travt, pack_opt_t *options) /* repack options */ { - hid_t grp_in=(-1); /* read group ID */ - hid_t grp_out=(-1); /* write group ID */ - hid_t dset_in=(-1); /* read dataset ID */ - hid_t dset_out=(-1); /* write dataset ID */ - hid_t type_in=(-1); /* named type ID */ - hid_t dcpl_id=(-1); /* dataset creation property list ID */ - hid_t space_id=(-1); /* space ID */ - hid_t ftype_id=(-1); /* file data type ID */ + hid_t grp_in=(-1); /* read group ID */ + hid_t grp_out=(-1); /* write group ID */ + hid_t dset_in=(-1); /* read dataset ID */ + hid_t dset_out=(-1); /* write dataset ID */ + hid_t type_in=(-1); /* named type ID */ + hid_t dcpl_id=(-1); /* dataset creation property list ID */ + hid_t space_id=(-1); /* space ID */ + hid_t ftype_id=(-1); /* file data type ID */ hid_t mtype_id=(-1); /* memory data type ID */ size_t msize; /* memory size of memory type */ hsize_t nelmts; /* number of elements in dataset */ @@ -72,7 +72,7 @@ int do_copy_refobjs(hid_t fidin, * browse *------------------------------------------------------------------------- */ - + for ( i = 0; i < travt->nobjs; i++) { switch ( travt->objs[i].type ) @@ -82,7 +82,7 @@ int do_copy_refobjs(hid_t fidin, *------------------------------------------------------------------------- */ case H5G_GROUP: - + /*------------------------------------------------------------------------- * check for hard links *------------------------------------------------------------------------- @@ -92,37 +92,37 @@ int do_copy_refobjs(hid_t fidin, { for ( j=0; j<travt->objs[i].nlinks; j++) { - H5Glink(fidout, + H5Glink(fidout, H5G_LINK_HARD, travt->objs[i].name, travt->objs[i].links[j].new_name); } } - + break; - + /*------------------------------------------------------------------------- * H5G_DATASET *------------------------------------------------------------------------- */ case H5G_DATASET: - - if ((dset_in=H5Dopen(fidin,travt->objs[i].name))<0) + + if ((dset_in=H5Dopen(fidin,travt->objs[i].name))<0) goto error; - if ((space_id=H5Dget_space(dset_in))<0) + if ((space_id=H5Dget_space(dset_in))<0) goto error; - if ((ftype_id=H5Dget_type (dset_in))<0) + if ((ftype_id=H5Dget_type (dset_in))<0) goto error; - if ((dcpl_id=H5Dget_create_plist(dset_in))<0) + 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++) + for (j=0; j<rank; j++) nelmts*=dims[j]; - + if ((mtype_id=h5tools_get_native_type(ftype_id))<0) goto error; @@ -133,11 +133,11 @@ int do_copy_refobjs(hid_t fidin, * check for external files *------------------------------------------------------------------------- */ - if ((next=H5Pget_external_count (dcpl_id))<0) + if ((next=H5Pget_external_count (dcpl_id))<0) goto error; /*------------------------------------------------------------------------- - * check if the dataset creation property list has filters that - * are not registered in the current configuration + * 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 *------------------------------------------------------------------------- @@ -152,10 +152,10 @@ int do_copy_refobjs(hid_t fidin, /*------------------------------------------------------------------------- * object references are a special case - * we cannot just copy the buffers, but instead we recreate the reference + * we cannot just copy the buffers, but instead we recreate the reference *------------------------------------------------------------------------- */ - if (H5Tequal(mtype_id, H5T_STD_REF_OBJ)) + if (H5Tequal(mtype_id, H5T_STD_REF_OBJ)) { H5G_obj_t obj_type; hid_t refobj_id; @@ -178,7 +178,7 @@ int do_copy_refobjs(hid_t fidin, } 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); @@ -192,7 +192,7 @@ int do_copy_refobjs(hid_t fidin, if ((refobj_id = H5Rdereference(dset_in,H5R_OBJECT,&buf[u]))<0) continue; } H5E_END_TRY; - /* get the name. a valid name could only occur in the + /* get the name. a valid name could only occur in the second traversal of the file */ if ((refname=MapIdToName(refobj_id,travt))!=NULL) { @@ -207,30 +207,30 @@ int do_copy_refobjs(hid_t fidin, close_obj(obj_type,refobj_id); }/* u */ }/*nelmts*/ - + /*------------------------------------------------------------------------- * create/write dataset/close *------------------------------------------------------------------------- */ - if ((dset_out=H5Dcreate(fidout,travt->objs[i].name,mtype_id,space_id,dcpl_id))<0) + if ((dset_out=H5Dcreate(fidout,travt->objs[i].name,mtype_id,space_id,dcpl_id))<0) goto error; if (nelmts) { if (H5Dwrite(dset_out,mtype_id,H5S_ALL,H5S_ALL,H5P_DEFAULT,refbuf)<0) goto error; } - + if (buf) free(buf); if (refbuf) free(refbuf); - + }/*H5T_STD_REF_OBJ*/ /*------------------------------------------------------------------------- * dataset region references *------------------------------------------------------------------------- */ - else if (H5Tequal(mtype_id, H5T_STD_REF_DSETREG)) + else if (H5Tequal(mtype_id, H5T_STD_REF_DSETREG)) { H5G_obj_t obj_type; hid_t refobj_id; @@ -254,12 +254,12 @@ int do_copy_refobjs(hid_t fidin, goto error; if ((obj_type = H5Rget_obj_type(dset_in,H5R_DATASET_REGION,buf))<0) goto error; - + /*------------------------------------------------------------------------- * create output *------------------------------------------------------------------------- */ - + refbuf=HDcalloc(sizeof(hdset_reg_ref_t),(size_t)nelmts); /*init to zero */ if ( refbuf==NULL){ printf( "cannot allocate memory\n" ); @@ -271,8 +271,8 @@ int do_copy_refobjs(hid_t fidin, if ((refobj_id = H5Rdereference(dset_in,H5R_DATASET_REGION,&buf[u]))<0) continue; } H5E_END_TRY; - - /* get the name. a valid name could only occur in the + + /* get the name. a valid name could only occur in the second traversal of the file */ if ((refname=MapIdToName(refobj_id,travt))!=NULL) { @@ -282,7 +282,7 @@ int do_copy_refobjs(hid_t fidin, /* create the reference, we need the space_id */ if (H5Rcreate(&refbuf[u],fidout,refname,H5R_DATASET_REGION,region_id)<0) goto error; - if (H5Sclose(region_id)<0) + if (H5Sclose(region_id)<0) goto error; if (options->verbose) printf("object <%s> region reference created to <%s>\n", @@ -292,18 +292,18 @@ int do_copy_refobjs(hid_t fidin, close_obj(obj_type,refobj_id); }/* u */ }/*nelmts*/ - + /*------------------------------------------------------------------------- * create/write dataset/close *------------------------------------------------------------------------- */ - if ((dset_out=H5Dcreate(fidout,travt->objs[i].name,mtype_id,space_id,dcpl_id))<0) + if ((dset_out=H5Dcreate(fidout,travt->objs[i].name,mtype_id,space_id,dcpl_id))<0) goto error; if (nelmts) { if (H5Dwrite(dset_out,mtype_id,H5S_ALL,H5S_ALL,H5P_DEFAULT,refbuf)<0) goto error; } - + if (buf) free(buf); if (refbuf) @@ -317,19 +317,19 @@ int do_copy_refobjs(hid_t fidin, */ else { - if ((dset_out=H5Dopen(fidout,travt->objs[i].name))<0) + if ((dset_out=H5Dopen(fidout,travt->objs[i].name))<0) goto error; } assert(dset_out!=FAIL); - + /*------------------------------------------------------------------------- * copy referenced objects in attributes *------------------------------------------------------------------------- */ - if (copy_refs_attr(dset_in,dset_out,options,travt,fidout)<0) + if (copy_refs_attr(dset_in,dset_out,options,travt,fidout)<0) goto error; - + /*------------------------------------------------------------------------- * check for hard links @@ -338,92 +338,92 @@ int do_copy_refobjs(hid_t fidin, if (travt->objs[i].nlinks) { for ( j=0; j<travt->objs[i].nlinks; j++){ - H5Glink(fidout, + H5Glink(fidout, H5G_LINK_HARD, travt->objs[i].name, travt->objs[i].links[j].new_name); } } - if (H5Dclose(dset_out)<0) + if (H5Dclose(dset_out)<0) goto error; }/*can_read*/ - + /*------------------------------------------------------------------------- * close *------------------------------------------------------------------------- */ - - if (H5Tclose(ftype_id)<0) + + if (H5Tclose(ftype_id)<0) goto error; - if (H5Tclose(mtype_id)<0) + if (H5Tclose(mtype_id)<0) goto error; - if (H5Pclose(dcpl_id)<0) + if (H5Pclose(dcpl_id)<0) goto error; - if (H5Sclose(space_id)<0) + if (H5Sclose(space_id)<0) goto error; - if (H5Dclose(dset_in)<0) + if (H5Dclose(dset_in)<0) goto error; - + break; - + /*------------------------------------------------------------------------- * H5G_TYPE *------------------------------------------------------------------------- */ case H5G_TYPE: - - if ((type_in = H5Topen (fidin,travt->objs[i].name))<0) + + if ((type_in = H5Topen (fidin,travt->objs[i].name))<0) goto error; - - if (H5Tclose(type_in)<0) + + 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 + * 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) + + if ((grp_out = H5Gopen(fidout,"/"))<0) goto error; - - if ((grp_in = H5Gopen(fidin,"/"))<0) + + if ((grp_in = H5Gopen(fidin,"/"))<0) goto error; - - if (copy_refs_attr(grp_in,grp_out,options,travt,fidout)<0) + + if (copy_refs_attr(grp_in,grp_out,options,travt,fidout)<0) goto error; - - if (H5Gclose(grp_out)<0) + + if (H5Gclose(grp_out)<0) goto error; - if (H5Gclose(grp_in)<0) + if (H5Gclose(grp_in)<0) goto error; - + return 0; - + error: H5E_BEGIN_TRY { H5Gclose(grp_in); @@ -437,7 +437,7 @@ error: H5Tclose(type_in); } H5E_END_TRY; return -1; - + } @@ -445,7 +445,7 @@ error: * Function: copy_refs_attr * * Purpose: duplicate all referenced HDF5 located in attributes - * relative to LOC_IN, which is obtained either from + * relative to LOC_IN, which is obtained either from * loc_id = H5Gopen( fid, name); * loc_id = H5Dopen( fid, name); * loc_id = H5Topen( fid, name); @@ -459,17 +459,17 @@ error: *------------------------------------------------------------------------- */ -static int copy_refs_attr(hid_t loc_in, - hid_t loc_out, +static int copy_refs_attr(hid_t loc_in, + hid_t loc_out, pack_opt_t *options, trav_table_t *travt, hid_t fidout /* for saving references */ ) { - hid_t attr_id=-1; /* attr ID */ - hid_t attr_out=-1; /* attr ID */ - hid_t space_id=-1; /* space ID */ - hid_t ftype_id=-1; /* file data type ID */ + hid_t attr_id=-1; /* attr ID */ + hid_t attr_out=-1; /* attr ID */ + hid_t space_id=-1; /* space ID */ + hid_t ftype_id=-1; /* file data type ID */ hid_t mtype_id=-1; /* memory data type ID */ size_t msize; /* memory size of type */ hsize_t nelmts; /* number of elements in dataset */ @@ -479,9 +479,9 @@ static int copy_refs_attr(hid_t loc_in, int n, j; unsigned u; - if ((n = H5Aget_num_attrs(loc_in))<0) + if ((n = H5Aget_num_attrs(loc_in))<0) goto error; - + for ( u = 0; u < (unsigned)n; u++) { @@ -490,32 +490,32 @@ static int copy_refs_attr(hid_t loc_in, *------------------------------------------------------------------------- */ /* open attribute */ - if ((attr_id = H5Aopen_idx(loc_in, u))<0) + if ((attr_id = H5Aopen_idx(loc_in, u))<0) goto error; - + /* get name */ - if (H5Aget_name( attr_id, 255, name )<0) + 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++) + for (j=0; j<rank; j++) nelmts*=dims[j]; if ((mtype_id=h5tools_get_native_type(ftype_id))<0) @@ -526,10 +526,10 @@ static int copy_refs_attr(hid_t loc_in, /*------------------------------------------------------------------------- * object references are a special case - * we cannot just copy the buffers, but instead we recreate the reference + * we cannot just copy the buffers, but instead we recreate the reference *------------------------------------------------------------------------- */ - if (H5Tequal(mtype_id, H5T_STD_REF_OBJ)) + if (H5Tequal(mtype_id, H5T_STD_REF_OBJ)) { H5G_obj_t obj_type; hid_t refobj_id; @@ -537,7 +537,7 @@ static int copy_refs_attr(hid_t loc_in, unsigned k; const char* refname; hobj_ref_t *buf=NULL; - + /*------------------------------------------------------------------------- * read input to memory *------------------------------------------------------------------------- @@ -552,7 +552,7 @@ static int copy_refs_attr(hid_t loc_in, } 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); @@ -566,7 +566,7 @@ static int copy_refs_attr(hid_t loc_in, if ((refobj_id = H5Rdereference(attr_id,H5R_OBJECT,&buf[k]))<0) goto error; } H5E_END_TRY; - /* get the name. a valid name could only occur in the + /* get the name. a valid name could only occur in the second traversal of the file */ if ((refname=MapIdToName(refobj_id,travt))!=NULL) { @@ -579,34 +579,34 @@ static int copy_refs_attr(hid_t loc_in, close_obj(obj_type,refobj_id); }/* k */ }/*nelmts*/ - + /*------------------------------------------------------------------------- - * copy + * copy *------------------------------------------------------------------------- */ - + if ((attr_out=H5Acreate(loc_out,name,ftype_id,space_id,H5P_DEFAULT))<0) goto error; if (nelmts) { if(H5Awrite(attr_out,mtype_id,refbuf)<0) goto error; } - - if (H5Aclose(attr_out)<0) + + if (H5Aclose(attr_out)<0) goto error; if (refbuf) free(refbuf); if (buf) free(buf); - + }/*H5T_STD_REF_OBJ*/ /*------------------------------------------------------------------------- * dataset region references *------------------------------------------------------------------------- */ - else if (H5Tequal(mtype_id, H5T_STD_REF_DSETREG)) + else if (H5Tequal(mtype_id, H5T_STD_REF_DSETREG)) { H5G_obj_t obj_type; hid_t refobj_id; @@ -619,8 +619,8 @@ static int copy_refs_attr(hid_t loc_in, * read input to memory *------------------------------------------------------------------------- */ - - if (nelmts) + + if (nelmts) { buf=(void *) HDmalloc((unsigned)(nelmts*msize)); if ( buf==NULL){ @@ -631,12 +631,12 @@ static int copy_refs_attr(hid_t loc_in, goto error; if ((obj_type = H5Rget_obj_type(attr_id,H5R_DATASET_REGION,buf))<0) goto error; - + /*------------------------------------------------------------------------- * create output *------------------------------------------------------------------------- */ - + refbuf=HDcalloc(sizeof(hdset_reg_ref_t),(size_t)nelmts); /*init to zero */ if ( refbuf==NULL){ printf( "cannot allocate memory\n" ); @@ -648,7 +648,7 @@ static int copy_refs_attr(hid_t loc_in, if ((refobj_id = H5Rdereference(attr_id,H5R_DATASET_REGION,&buf[k]))<0) continue; } H5E_END_TRY; - /* get the name. a valid name could only occur in the + /* get the name. a valid name could only occur in the second traversal of the file */ if ((refname=MapIdToName(refobj_id,travt))!=NULL) { @@ -658,7 +658,7 @@ static int copy_refs_attr(hid_t loc_in, /* create the reference, we need the space_id */ if (H5Rcreate(&refbuf[k],fidout,refname,H5R_DATASET_REGION,region_id)<0) goto error; - if (H5Sclose(region_id)<0) + if (H5Sclose(region_id)<0) goto error; if (options->verbose) printf("object <%s> region reference created to <%s>\n",name,refname); @@ -666,19 +666,19 @@ static int copy_refs_attr(hid_t loc_in, close_obj(obj_type,refobj_id); }/* k */ }/*nelmts */ - + /*------------------------------------------------------------------------- - * copy + * copy *------------------------------------------------------------------------- */ - + if ((attr_out=H5Acreate(loc_out,name,ftype_id,space_id,H5P_DEFAULT))<0) goto error; if (nelmts) { if(H5Awrite(attr_out,mtype_id,refbuf)<0) goto error; } - if (H5Aclose(attr_out)<0) + if (H5Aclose(attr_out)<0) goto error; if (refbuf) free(refbuf); @@ -696,7 +696,7 @@ static int copy_refs_attr(hid_t loc_in, if (H5Sclose(space_id)<0) goto error; if (H5Aclose(attr_id)<0) goto error; } /* u */ - + return 0; error: @@ -720,9 +720,9 @@ error: static void close_obj(H5G_obj_t obj_type, hid_t obj_id) { - H5E_BEGIN_TRY + H5E_BEGIN_TRY { - switch (obj_type) + switch (obj_type) { case H5G_GROUP: H5Gclose(obj_id); @@ -736,7 +736,7 @@ static void close_obj(H5G_obj_t obj_type, hid_t obj_id) default: break; } - } H5E_END_TRY; + } H5E_END_TRY; } /*------------------------------------------------------------------------- @@ -747,7 +747,7 @@ static void close_obj(H5G_obj_t obj_type, hid_t obj_id) *------------------------------------------------------------------------- */ -static const char* MapIdToName(hid_t refobj_id, +static const char* MapIdToName(hid_t refobj_id, trav_table_t *travt) { hid_t id; @@ -769,18 +769,18 @@ static const char* MapIdToName(hid_t refobj_id, /* linear search */ for ( i=0; i<travt->nobjs; i++) { - switch ( travt->objs[i].type ) + switch ( travt->objs[i].type ) { default: break; - + /*------------------------------------------------------------------------- * H5G_DATASET *------------------------------------------------------------------------- */ - + case H5G_DATASET: - + if ((id = H5Dopen(fid,travt->objs[i].name))<0) return NULL; if(H5Gget_objinfo(id, ".", 0, &objstat) <0) |