diff options
| -rw-r--r-- | tools/h5repack/h5repack_refs.c | 1333 |
1 files changed, 666 insertions, 667 deletions
diff --git a/tools/h5repack/h5repack_refs.c b/tools/h5repack/h5repack_refs.c index d94c250..4757552 100644 --- a/tools/h5repack/h5repack_refs.c +++ b/tools/h5repack/h5repack_refs.c @@ -13,7 +13,6 @@ * access to either file, you may request a copy from help@hdfgroup.org. * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ - #include <stdlib.h> #include <string.h> #include <stdio.h> @@ -50,403 +49,403 @@ int do_copy_refobjs(hid_t fidin, 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 mtype_id=(-1); /* 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; - -/*------------------------------------------------------------------------- - * browse - *------------------------------------------------------------------------- - */ - - for ( i = 0; i < travt->nobjs; i++) - { - switch ( travt->objs[i].type ) - { - /*------------------------------------------------------------------------- - * H5G_GROUP - *------------------------------------------------------------------------- - */ - case H5G_GROUP: - - /*------------------------------------------------------------------------- - * copy referenced objects in attributes - *------------------------------------------------------------------------- - */ - - if ((grp_out=H5Gopen(fidout,travt->objs[i].name))<0) - goto error; - if((grp_in = H5Gopen (fidin,travt->objs[i].name))<0) - goto error; - if (copy_refs_attr(grp_in,grp_out,options,travt,fidout)<0) - goto error; - if (H5Gclose(grp_out)<0) - goto error; - if (H5Gclose(grp_in)<0) - goto error; - - /*------------------------------------------------------------------------- - * check for hard links - *------------------------------------------------------------------------- - */ - - if (travt->objs[i].nlinks) - { - for ( j=0; j<travt->objs[i].nlinks; j++) - { - 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) - 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 (k=0; k<rank; k++) - nelmts*=dims[k]; - - if ((mtype_id=h5tools_get_native_type(ftype_id))<0) - goto error; - - if ((msize=H5Tget_size(mtype_id))==0) - goto error; - - -/*------------------------------------------------------------------------- - * 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((NULL),dcpl_id)==1) - { -/*------------------------------------------------------------------------- - * test for a valid output dataset - *------------------------------------------------------------------------- - */ - dset_out = FAIL; - -/*------------------------------------------------------------------------- - * 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_t1 obj_type; - hid_t refobj_id; - hobj_ref_t *refbuf=NULL; /* buffer for object references */ - hobj_ref_t *buf=NULL; - const char* refname; - unsigned u; - - /*------------------------------------------------------------------------- - * read to memory + 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 */ + int rank; /* rank of dataset */ + hsize_t dims[H5S_MAX_RANK]; /* dimensions of dataset */ + unsigned int i, j; + int k; + + /*------------------------------------------------------------------------- + * browse *------------------------------------------------------------------------- */ - - if (nelmts) + + for ( i = 0; i < travt->nobjs; i++) { - 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=HDcalloc((unsigned)nelmts,msize); - if ( refbuf==NULL){ - printf( "cannot allocate memory\n" ); - goto error; - } - for ( u=0; u<nelmts; u++) - { - H5E_BEGIN_TRY { - 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 - second traversal of the file */ - if ((refname=MapIdToName(refobj_id,travt))!=NULL) - { - /* create the reference, -1 parameter for objects */ - if (H5Rcreate(&refbuf[u],fidout,refname,H5R_OBJECT,-1)<0) - goto error; - if (options->verbose) - printf("object <%s> object reference created to <%s>\n", - travt->objs[i].name, - refname); - }/*refname*/ - close_obj(obj_type,refobj_id); - }/* u */ - }/*nelmts*/ - + switch ( travt->objs[i].type ) + { + /*------------------------------------------------------------------------- + * H5G_GROUP + *------------------------------------------------------------------------- + */ + case H5G_GROUP: + + /*------------------------------------------------------------------------- + * copy referenced objects in attributes + *------------------------------------------------------------------------- + */ + + if ((grp_out=H5Gopen(fidout,travt->objs[i].name))<0) + goto error; + if((grp_in = H5Gopen (fidin,travt->objs[i].name))<0) + goto error; + if (copy_refs_attr(grp_in,grp_out,options,travt,fidout)<0) + goto error; + if (H5Gclose(grp_out)<0) + goto error; + if (H5Gclose(grp_in)<0) + goto error; + + /*------------------------------------------------------------------------- + * check for hard links + *------------------------------------------------------------------------- + */ + + if (travt->objs[i].nlinks) + { + for ( j=0; j<travt->objs[i].nlinks; j++) + { + 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) + 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 (k=0; k<rank; k++) + nelmts*=dims[k]; + + if ((mtype_id=h5tools_get_native_type(ftype_id))<0) + goto error; + + if ((msize=H5Tget_size(mtype_id))==0) + goto error; + + + /*------------------------------------------------------------------------- + * 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((NULL),dcpl_id)==1) + { + /*------------------------------------------------------------------------- + * test for a valid output dataset + *------------------------------------------------------------------------- + */ + dset_out = FAIL; + + /*------------------------------------------------------------------------- + * 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_t1 obj_type; + hid_t refobj_id; + hobj_ref_t *refbuf=NULL; /* buffer for object references */ + hobj_ref_t *buf=NULL; + const char* refname; + unsigned u; + + /*------------------------------------------------------------------------- + * read to memory + *------------------------------------------------------------------------- + */ + + if (nelmts) + { + 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=HDcalloc((unsigned)nelmts,msize); + if ( refbuf==NULL){ + printf( "cannot allocate memory\n" ); + goto error; + } + for ( u=0; u<nelmts; u++) + { + H5E_BEGIN_TRY { + 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 + second traversal of the file */ + if ((refname=MapIdToName(refobj_id,travt))!=NULL) + { + /* create the reference, -1 parameter for objects */ + if (H5Rcreate(&refbuf[u],fidout,refname,H5R_OBJECT,-1)<0) + goto error; + if (options->verbose) + printf("object <%s> object reference created to <%s>\n", + travt->objs[i].name, + refname); + }/*refname*/ + 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) + 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)) + { + H5G_obj_t1 obj_type; + hid_t refobj_id; + 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) + { + 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_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" ); + goto error; + } + for ( u=0; u<nelmts; u++) + { + H5E_BEGIN_TRY { + 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 + second traversal of the file */ + if ((refname=MapIdToName(refobj_id,travt))!=NULL) + { + hid_t region_id; /* region id of the referenced dataset */ + if ((region_id = H5Rget_region(dset_in,H5R_DATASET_REGION,&buf[u]))<0) + goto error; + /* 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) + goto error; + if (options->verbose) + printf("object <%s> region reference created to <%s>\n", + travt->objs[i].name, + refname); + }/*refname*/ + 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) + 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_DSETREG */ + + + /*------------------------------------------------------------------------- + * not references, open previously created object in 1st traversal + *------------------------------------------------------------------------- + */ + else + { + 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) + goto error; + + + /*------------------------------------------------------------------------- + * check for hard links + *------------------------------------------------------------------------- + */ + if (travt->objs[i].nlinks) + { + for ( j=0; j<travt->objs[i].nlinks; j++){ + H5Glink(fidout, + H5G_LINK_HARD, + travt->objs[i].name, + travt->objs[i].links[j].new_name); + } + } + + if (H5Dclose(dset_out)<0) + goto error; + + }/*can_read*/ + /*------------------------------------------------------------------------- - * create/write dataset/close - *------------------------------------------------------------------------- - */ - 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)) - { - H5G_obj_t1 obj_type; - hid_t refobj_id; - 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 + * close *------------------------------------------------------------------------- */ - if (nelmts) - { - 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_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" ); - goto error; - } - for ( u=0; u<nelmts; u++) - { - H5E_BEGIN_TRY { - 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 - second traversal of the file */ - if ((refname=MapIdToName(refobj_id,travt))!=NULL) - { - hid_t region_id; /* region id of the referenced dataset */ - if ((region_id = H5Rget_region(dset_in,H5R_DATASET_REGION,&buf[u]))<0) + + if (H5Tclose(ftype_id)<0) goto error; - /* create the reference, we need the space_id */ - if (H5Rcreate(&refbuf[u],fidout,refname,H5R_DATASET_REGION,region_id)<0) + if (H5Tclose(mtype_id)<0) goto error; - if (H5Sclose(region_id)<0) + if (H5Pclose(dcpl_id)<0) goto error; - if (options->verbose) - printf("object <%s> region reference created to <%s>\n", - travt->objs[i].name, - refname); - }/*refname*/ - close_obj(obj_type,refobj_id); - }/* u */ - }/*nelmts*/ - + if (H5Sclose(space_id)<0) + goto error; + if (H5Dclose(dset_in)<0) + goto error; + + break; + /*------------------------------------------------------------------------- - * create/write dataset/close - *------------------------------------------------------------------------- - */ - 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_DSETREG */ - - -/*------------------------------------------------------------------------- - * not references, open previously created object in 1st traversal - *------------------------------------------------------------------------- - */ - else - { - 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) - goto error; - - -/*------------------------------------------------------------------------- - * check for hard links - *------------------------------------------------------------------------- - */ - if (travt->objs[i].nlinks) - { - for ( j=0; j<travt->objs[i].nlinks; j++){ - H5Glink(fidout, - H5G_LINK_HARD, - travt->objs[i].name, - travt->objs[i].links[j].new_name); - } - } - - if (H5Dclose(dset_out)<0) - goto error; - - }/*can_read*/ - - /*------------------------------------------------------------------------- - * close + * H5G_TYPE *------------------------------------------------------------------------- */ - - 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 (H5Tclose(type_in)<0) - goto error; - - break; - - /*------------------------------------------------------------------------- - * H5G_LINK - *------------------------------------------------------------------------- - */ - + + if ((type_in = H5Topen (fidin,travt->objs[i].name))<0) + goto error; + + if (H5Tclose(type_in)<0) + goto error; + + break; + + /*------------------------------------------------------------------------- + * H5G_LINK + *------------------------------------------------------------------------- + */ + case H5G_LINK: - - /*nothing to do */ - break; - + + /*nothing to do */ + break; + default: - - break; + + 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; - + goto error; + if ((grp_in = H5Gopen(fidin,"/"))<0) - goto error; - + goto error; + if (copy_refs_attr(grp_in,grp_out,options,travt,fidout)<0) - goto error; - + goto error; + if (H5Gclose(grp_out)<0) - goto error; + goto error; if (H5Gclose(grp_in)<0) - goto error; - + 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); + 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; - + } @@ -475,247 +474,247 @@ static int copy_refs_attr(hid_t loc_in, 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 mtype_id=-1; /* 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=h5tools_get_native_type(ftype_id))<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_t1 obj_type; - hid_t refobj_id; - hobj_ref_t *refbuf=NULL; - unsigned k; - const char* refname; - hobj_ref_t *buf=NULL; - - /*------------------------------------------------------------------------- - * read input to memory - *------------------------------------------------------------------------- - */ - - if (nelmts) - { - 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=HDcalloc((unsigned)nelmts,msize); - - if ( refbuf==NULL){ - printf( "cannot allocate memory\n" ); - goto error; - } - for ( k=0; k<nelmts; k++) - { - H5E_BEGIN_TRY { - 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 - second traversal of the file */ - if ((refname=MapIdToName(refobj_id,travt))!=NULL) - { - /* create the reference */ - if (H5Rcreate(&refbuf[k],fidout,refname,H5R_OBJECT,-1)<0) + 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 */ + 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; - if (options->verbose) - printf("object <%s> reference created to <%s>\n",name,refname); - } - close_obj(obj_type,refobj_id); - }/* k */ - }/*nelmts*/ - - /*------------------------------------------------------------------------- - * 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) - 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)) - { - H5G_obj_t1 obj_type; - hid_t refobj_id; - hdset_reg_ref_t *refbuf=NULL; /* input buffer for region references */ - hdset_reg_ref_t *buf=NULL; /* output buffer */ - const char* refname; - unsigned k; - - /*------------------------------------------------------------------------- - * read input to memory - *------------------------------------------------------------------------- - */ - - if (nelmts) + + for ( u = 0; u < (unsigned)n; u++) { - 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_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" ); - goto error; - } - for ( k=0; k<nelmts; k++) - { - H5E_BEGIN_TRY { - 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 - second traversal of the file */ - if ((refname=MapIdToName(refobj_id,travt))!=NULL) - { - hid_t region_id; /* region id of the referenced dataset */ - if ((region_id = H5Rget_region(attr_id,H5R_DATASET_REGION,&buf[k]))<0) - goto error; - /* 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) - goto error; - if (options->verbose) - printf("object <%s> region reference created to <%s>\n",name,refname); - } - close_obj(obj_type,refobj_id); - }/* k */ - }/*nelmts */ - + /*------------------------------------------------------------------------- - * 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) - goto error; - if (refbuf) - free(refbuf); - if (buf) - free(buf); - } /* H5T_STD_REF_DSETREG */ - -/*------------------------------------------------------------------------- - * 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; + * 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=h5tools_get_native_type(ftype_id))<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_t1 obj_type; + hid_t refobj_id; + hobj_ref_t *refbuf=NULL; + unsigned k; + const char* refname; + hobj_ref_t *buf=NULL; + + /*------------------------------------------------------------------------- + * read input to memory + *------------------------------------------------------------------------- + */ + + if (nelmts) + { + 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=HDcalloc((unsigned)nelmts,msize); + + if ( refbuf==NULL){ + printf( "cannot allocate memory\n" ); + goto error; + } + for ( k=0; k<nelmts; k++) + { + H5E_BEGIN_TRY { + 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 + second traversal of the file */ + if ((refname=MapIdToName(refobj_id,travt))!=NULL) + { + /* create the reference */ + if (H5Rcreate(&refbuf[k],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); + }/* k */ + }/*nelmts*/ + + /*------------------------------------------------------------------------- + * 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) + 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)) + { + H5G_obj_t1 obj_type; + hid_t refobj_id; + hdset_reg_ref_t *refbuf=NULL; /* input buffer for region references */ + hdset_reg_ref_t *buf=NULL; /* output buffer */ + const char* refname; + unsigned k; + + /*------------------------------------------------------------------------- + * read input to memory + *------------------------------------------------------------------------- + */ + + if (nelmts) + { + 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_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" ); + goto error; + } + for ( k=0; k<nelmts; k++) + { + H5E_BEGIN_TRY { + 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 + second traversal of the file */ + if ((refname=MapIdToName(refobj_id,travt))!=NULL) + { + hid_t region_id; /* region id of the referenced dataset */ + if ((region_id = H5Rget_region(attr_id,H5R_DATASET_REGION,&buf[k]))<0) + goto error; + /* 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) + goto error; + if (options->verbose) + printf("object <%s> region reference created to <%s>\n",name,refname); + } + close_obj(obj_type,refobj_id); + }/* k */ + }/*nelmts */ + + /*------------------------------------------------------------------------- + * 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) + goto error; + if (refbuf) + free(refbuf); + if (buf) + free(buf); + } /* H5T_STD_REF_DSETREG */ + + /*------------------------------------------------------------------------- + * 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; - + + return 0; + error: H5E_BEGIN_TRY { - H5Tclose(ftype_id); - H5Tclose(mtype_id); - H5Sclose(space_id); - H5Aclose(attr_id); - H5Aclose(attr_out); + H5Tclose(ftype_id); + H5Tclose(mtype_id); + H5Sclose(space_id); + H5Aclose(attr_id); + H5Aclose(attr_out); } H5E_END_TRY; return -1; } @@ -730,23 +729,23 @@ error: static void close_obj(H5G_obj_t1 obj_type, hid_t obj_id) { - H5E_BEGIN_TRY - { - 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: - break; - } - } H5E_END_TRY; + H5E_BEGIN_TRY + { + 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: + break; + } + } H5E_END_TRY; } /*------------------------------------------------------------------------- @@ -760,56 +759,56 @@ static void close_obj(H5G_obj_t1 obj_type, hid_t obj_id) static const char* MapIdToName(hid_t refobj_id, trav_table_t *travt) { - hid_t id; - hid_t fid; - H5G_stat_t refstat; /* Stat for the refobj id */ - H5G_stat_t objstat; /* Stat for objects in the file */ - unsigned int i; - - /* obtain information to identify the referenced object uniquely */ - if(H5Gget_objinfo(refobj_id, ".", 0, &refstat) <0) - return NULL; - - /* obtains the file ID given an object ID. This ID must be closed */ - if ((fid = H5Iget_file_id(refobj_id))<0) - { - return NULL; - } - - /* linear search */ - for ( i=0; i<travt->nobjs; i++) - { - 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) - return NULL; - if (H5Dclose(id)<0) + hid_t id; + hid_t fid; + H5G_stat_t refstat; /* Stat for the refobj id */ + H5G_stat_t objstat; /* Stat for objects in the file */ + unsigned int i; + + /* obtain information to identify the referenced object uniquely */ + if(H5Gget_objinfo(refobj_id, ".", 0, &refstat) <0) + return NULL; + + /* obtains the file ID given an object ID. This ID must be closed */ + if ((fid = H5Iget_file_id(refobj_id))<0) + { + return NULL; + } + + /* linear search */ + for ( i=0; i<travt->nobjs; i++) + { + 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) + return NULL; + if (H5Dclose(id)<0) + return NULL; + if (refstat.fileno[0]==objstat.fileno[0] && refstat.fileno[1]==objstat.fileno[1] + && refstat.objno[0]==objstat.objno[0] && refstat.objno[1]==objstat.objno[1]) + { + H5Fclose(fid); + return travt->objs[i].name; + } + break; + } /* switch */ + } /* i */ + + if (H5Fclose(fid)<0) + return NULL; + return NULL; - if (refstat.fileno[0]==objstat.fileno[0] && refstat.fileno[1]==objstat.fileno[1] - && refstat.objno[0]==objstat.objno[0] && refstat.objno[1]==objstat.objno[1]) - { - H5Fclose(fid); - return travt->objs[i].name; - } - break; - } /* switch */ - } /* i */ - - if (H5Fclose(fid)<0) - return NULL; - - return NULL; } |