diff options
Diffstat (limited to 'tools/src/h5repack/h5repack_refs.c')
| -rw-r--r-- | tools/src/h5repack/h5repack_refs.c | 546 |
1 files changed, 281 insertions, 265 deletions
diff --git a/tools/src/h5repack/h5repack_refs.c b/tools/src/h5repack/h5repack_refs.c index 5baabb6..78957c6 100644 --- a/tools/src/h5repack/h5repack_refs.c +++ b/tools/src/h5repack/h5repack_refs.c @@ -15,17 +15,15 @@ #include "h5diff.h" #include "h5tools.h" - /*------------------------------------------------------------------------- * local functions *------------------------------------------------------------------------- */ -static const char* MapIdToName(hid_t refobj_id,trav_table_t *travt); -static int copy_refs_attr(hid_t loc_in, hid_t loc_out, - trav_table_t *travt, hid_t fidout); -static herr_t update_ref_value(hid_t obj_id, H5R_type_t ref_type, void *ref_in, - hid_t fid_out, void *ref_out, trav_table_t *travt); +static const char *MapIdToName(hid_t refobj_id, trav_table_t *travt); +static int copy_refs_attr(hid_t loc_in, hid_t loc_out, trav_table_t *travt, hid_t fidout); +static herr_t update_ref_value(hid_t obj_id, H5R_type_t ref_type, void *ref_in, hid_t fid_out, void *ref_out, + trav_table_t *travt); /*------------------------------------------------------------------------- * Function: do_copy_refobjs @@ -37,35 +35,33 @@ static herr_t update_ref_value(hid_t obj_id, H5R_type_t ref_type, void *ref_in, *------------------------------------------------------------------------- */ -int do_copy_refobjs(hid_t fidin, - hid_t fidout, - trav_table_t *travt, - pack_opt_t *options) /* repack options */ +int +do_copy_refobjs(hid_t fidin, hid_t fidout, trav_table_t *travt, pack_opt_t *options) /* repack options */ { - hid_t grp_in = H5I_INVALID_HID; /* read group ID */ - hid_t grp_out = H5I_INVALID_HID; /* write group ID */ - hid_t dset_in = H5I_INVALID_HID; /* read dataset ID */ - hid_t dset_out = H5I_INVALID_HID; /* write dataset ID */ - hid_t type_in = H5I_INVALID_HID; /* named type ID */ - hid_t dcpl_id = H5I_INVALID_HID; /* dataset creation property list ID */ - hid_t space_id = H5I_INVALID_HID; /* space ID */ - hid_t ftype_id = H5I_INVALID_HID; /* file data type ID */ - hid_t mtype_id = H5I_INVALID_HID; /* 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 */ + hid_t grp_in = H5I_INVALID_HID; /* read group ID */ + hid_t grp_out = H5I_INVALID_HID; /* write group ID */ + hid_t dset_in = H5I_INVALID_HID; /* read dataset ID */ + hid_t dset_out = H5I_INVALID_HID; /* write dataset ID */ + hid_t type_in = H5I_INVALID_HID; /* named type ID */ + hid_t dcpl_id = H5I_INVALID_HID; /* dataset creation property list ID */ + hid_t space_id = H5I_INVALID_HID; /* space ID */ + hid_t ftype_id = H5I_INVALID_HID; /* file data type ID */ + hid_t mtype_id = H5I_INVALID_HID; /* 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; - named_dt_t *named_dt_head = NULL; /* Pointer to the stack of named datatypes copied */ - int ret_value = 0; + int k; + named_dt_t * named_dt_head = NULL; /* Pointer to the stack of named datatypes copied */ + int ret_value = 0; /*------------------------------------------------------------------------- - * browse - *------------------------------------------------------------------------- - */ - for(i = 0; i < travt->nobjs; i++) { - switch(travt->objs[i].type) { + * browse + *------------------------------------------------------------------------- + */ + for (i = 0; i < travt->nobjs; i++) { + switch (travt->objs[i].type) { /*------------------------------------------------------------------------- * H5TRAV_TYPE_GROUP *------------------------------------------------------------------------- @@ -75,27 +71,28 @@ int do_copy_refobjs(hid_t fidin, * copy referenced objects in attributes *------------------------------------------------------------------------- */ - if((grp_out = H5Gopen2(fidout, travt->objs[i].name, H5P_DEFAULT)) < 0) + if ((grp_out = H5Gopen2(fidout, travt->objs[i].name, H5P_DEFAULT)) < 0) H5TOOLS_GOTO_ERROR((-1), "H5Gopen2 failed"); - if((grp_in = H5Gopen2(fidin, travt->objs[i].name, H5P_DEFAULT)) < 0) + if ((grp_in = H5Gopen2(fidin, travt->objs[i].name, H5P_DEFAULT)) < 0) H5TOOLS_GOTO_ERROR((-1), "H5Gopen2 failed"); - if(copy_refs_attr(grp_in, grp_out, travt, fidout) < 0) + if (copy_refs_attr(grp_in, grp_out, travt, fidout) < 0) H5TOOLS_GOTO_ERROR((-1), "copy_refs_attr failed"); - if(H5Gclose(grp_out) < 0) + if (H5Gclose(grp_out) < 0) H5TOOLS_GOTO_ERROR((-1), "H5Gclose failed"); - if(H5Gclose(grp_in) < 0) + if (H5Gclose(grp_in) < 0) H5TOOLS_GOTO_ERROR((-1), "H5Gclose failed"); /*------------------------------------------------------------------------- * check for hard links *------------------------------------------------------------------------- */ - if(travt->objs[i].nlinks) - for(j = 0; j < travt->objs[i].nlinks; j++) - H5Lcreate_hard(fidout, travt->objs[i].name, H5L_SAME_LOC, travt->objs[i].links[j].new_name, H5P_DEFAULT, H5P_DEFAULT); + if (travt->objs[i].nlinks) + for (j = 0; j < travt->objs[i].nlinks; j++) + H5Lcreate_hard(fidout, travt->objs[i].name, H5L_SAME_LOC, + travt->objs[i].links[j].new_name, H5P_DEFAULT, H5P_DEFAULT); break; /*------------------------------------------------------------------------- @@ -103,26 +100,26 @@ int do_copy_refobjs(hid_t fidin, *------------------------------------------------------------------------- */ case H5TRAV_TYPE_DATASET: - if((dset_in = H5Dopen2(fidin, travt->objs[i].name, H5P_DEFAULT)) < 0) + if ((dset_in = H5Dopen2(fidin, travt->objs[i].name, H5P_DEFAULT)) < 0) H5TOOLS_GOTO_ERROR((-1), "H5Dopen2 failed"); - if((space_id = H5Dget_space(dset_in)) < 0) + if ((space_id = H5Dget_space(dset_in)) < 0) H5TOOLS_GOTO_ERROR((-1), "H5Dget_space failed"); - if((ftype_id = H5Dget_type(dset_in)) < 0) + if ((ftype_id = H5Dget_type(dset_in)) < 0) H5TOOLS_GOTO_ERROR((-1), "H5Dget_type failed"); - if((dcpl_id = H5Dget_create_plist(dset_in)) < 0) + if ((dcpl_id = H5Dget_create_plist(dset_in)) < 0) H5TOOLS_GOTO_ERROR((-1), "H5Dget_create_plist failed"); - if((rank = H5Sget_simple_extent_ndims(space_id)) < 0) + if ((rank = H5Sget_simple_extent_ndims(space_id)) < 0) H5TOOLS_GOTO_ERROR((-1), "H5Sget_simple_extent_ndims failed"); - if(H5Sget_simple_extent_dims(space_id, dims, NULL) < 0) + if (H5Sget_simple_extent_dims(space_id, dims, NULL) < 0) H5TOOLS_GOTO_ERROR((-1), "H5Sget_simple_extent_dims failed"); nelmts = 1; - for(k = 0; k < rank; k++) + for (k = 0; k < rank; k++) nelmts *= dims[k]; - if((mtype_id = H5Tget_native_type(ftype_id, H5T_DIR_DEFAULT)) < 0) + if ((mtype_id = H5Tget_native_type(ftype_id, H5T_DIR_DEFAULT)) < 0) H5TOOLS_GOTO_ERROR((-1), "H5Tget_native_type failed"); - if((msize = H5Tget_size(mtype_id)) == 0) + if ((msize = H5Tget_size(mtype_id)) == 0) H5TOOLS_GOTO_ERROR((-1), "H5Tget_size failed"); /*------------------------------------------------------------------------- @@ -132,7 +129,7 @@ int do_copy_refobjs(hid_t fidin, * 2) the internal filters might be turned off *------------------------------------------------------------------------- */ - if(h5tools_canreadf(NULL, dcpl_id) == 1) { + if (h5tools_canreadf(NULL, dcpl_id) == 1) { /*------------------------------------------------------------------------- * test for a valid output dataset *------------------------------------------------------------------------- @@ -144,75 +141,78 @@ int do_copy_refobjs(hid_t fidin, * we cannot just copy the buffers, but instead we recreate the reference *------------------------------------------------------------------------- */ - if(H5Tequal(mtype_id, H5T_STD_REF_OBJ)) { - hid_t refobj_id = H5I_INVALID_HID; - hobj_ref_t *refbuf = NULL; /* buffer for object references */ - hobj_ref_t *buf = NULL; - const char* refname; - unsigned u; + if (H5Tequal(mtype_id, H5T_STD_REF_OBJ)) { + hid_t refobj_id = H5I_INVALID_HID; + hobj_ref_t *refbuf = NULL; /* buffer for object references */ + hobj_ref_t *buf = NULL; + const char *refname; + unsigned u; /*------------------------------------------------------------------------- * read to memory *------------------------------------------------------------------------- */ - if(nelmts) { + if (nelmts) { buf = (hobj_ref_t *)HDmalloc((unsigned)(nelmts * msize)); - if(buf==NULL) { - HDprintf("cannot read into memory\n" ); + if (buf == NULL) { + HDprintf("cannot read into memory\n"); H5TOOLS_GOTO_ERROR((-1), "HDmalloc failed"); } /* end if */ - if(H5Dread(dset_in, mtype_id, H5S_ALL, H5S_ALL, H5P_DEFAULT, buf) < 0) + if (H5Dread(dset_in, mtype_id, H5S_ALL, H5S_ALL, H5P_DEFAULT, buf) < 0) H5TOOLS_GOTO_ERROR((-1), "H5Dread failed"); - refbuf = (hobj_ref_t*) HDcalloc((unsigned)nelmts, msize); - if(refbuf == NULL){ - HDprintf("cannot allocate memory\n" ); + refbuf = (hobj_ref_t *)HDcalloc((unsigned)nelmts, msize); + if (refbuf == NULL) { + HDprintf("cannot allocate memory\n"); H5TOOLS_GOTO_ERROR((-1), "HDcalloc failed"); } /* end if */ - for(u = 0; u < nelmts; u++) { - H5E_BEGIN_TRY { - if((refobj_id = H5Rdereference2(dset_in, H5P_DEFAULT, H5R_OBJECT, &buf[u])) < 0) + for (u = 0; u < nelmts; u++) { + H5E_BEGIN_TRY + { + if ((refobj_id = + H5Rdereference2(dset_in, H5P_DEFAULT, H5R_OBJECT, &buf[u])) < 0) continue; - } H5E_END_TRY; + } + 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) { + if ((refname = MapIdToName(refobj_id, travt)) != NULL) { /* create the reference, -1 parameter for objects */ - if(H5Rcreate(&refbuf[u], fidout, refname, H5R_OBJECT, (hid_t)-1) < 0) + if (H5Rcreate(&refbuf[u], fidout, refname, H5R_OBJECT, (hid_t)-1) < 0) H5TOOLS_GOTO_ERROR((-1), "H5Rcreate failed"); - if(options->verbose) { - HDprintf(FORMAT_OBJ,"dset",travt->objs[i].name ); + if (options->verbose) { + HDprintf(FORMAT_OBJ, "dset", travt->objs[i].name); HDprintf("object <%s> object reference created to <%s>\n", - travt->objs[i].name, - refname); + travt->objs[i].name, refname); } } /*refname*/ if (H5Oclose(refobj_id) < 0) H5TOOLS_ERROR((-1), "H5Oclose refob failed"); } /* u */ - } /*nelmts*/ + } /*nelmts*/ /*------------------------------------------------------------------------- * create/write dataset/close *------------------------------------------------------------------------- */ - if((dset_out = H5Dcreate2(fidout, travt->objs[i].name, mtype_id, space_id, H5P_DEFAULT, dcpl_id, H5P_DEFAULT)) < 0) + if ((dset_out = H5Dcreate2(fidout, travt->objs[i].name, mtype_id, space_id, + H5P_DEFAULT, dcpl_id, H5P_DEFAULT)) < 0) H5TOOLS_GOTO_ERROR((-1), "H5Dcreate2 failed"); - if(nelmts) - if(H5Dwrite(dset_out, mtype_id, H5S_ALL, H5S_ALL, H5P_DEFAULT, refbuf) < 0) + if (nelmts) + if (H5Dwrite(dset_out, mtype_id, H5S_ALL, H5S_ALL, H5P_DEFAULT, refbuf) < 0) H5TOOLS_GOTO_ERROR((-1), "H5Dwrite failed"); - if(buf) + if (buf) HDfree(buf); - if(refbuf) + if (refbuf) HDfree(refbuf); - /*------------------------------------------------------ - * copy attrs - *----------------------------------------------------*/ - if(copy_attr(dset_in, dset_out, &named_dt_head, travt, options) < 0) + /*------------------------------------------------------ + * copy attrs + *----------------------------------------------------*/ + if (copy_attr(dset_in, dset_out, &named_dt_head, travt, options) < 0) H5TOOLS_GOTO_ERROR((-1), "copy_attr failed"); } /*H5T_STD_REF_OBJ*/ @@ -220,87 +220,93 @@ int do_copy_refobjs(hid_t fidin, * dataset region references *------------------------------------------------------------------------- */ - else if(H5Tequal(mtype_id, H5T_STD_REF_DSETREG)) { + else if (H5Tequal(mtype_id, H5T_STD_REF_DSETREG)) { hid_t refobj_id = H5I_INVALID_HID; - hdset_reg_ref_t *refbuf = NULL; /* input buffer for region references */ - hdset_reg_ref_t *buf = NULL; /* output buffer */ - const char* refname; + 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) { + if (nelmts) { buf = (hdset_reg_ref_t *)HDmalloc((unsigned)(nelmts * msize)); - if(buf == NULL) { + if (buf == NULL) { HDprintf("cannot read into memory\n"); H5TOOLS_GOTO_ERROR((-1), "HDmalloc failed"); } /* end if */ - if(H5Dread(dset_in, mtype_id, H5S_ALL, H5S_ALL, H5P_DEFAULT, buf) < 0) + if (H5Dread(dset_in, mtype_id, H5S_ALL, H5S_ALL, H5P_DEFAULT, buf) < 0) H5TOOLS_GOTO_ERROR((-1), "H5Dread failed"); /*------------------------------------------------------------------------- * create output *------------------------------------------------------------------------- */ - refbuf = (hdset_reg_ref_t *)HDcalloc(sizeof(hdset_reg_ref_t), (size_t)nelmts); /*init to zero */ - if(refbuf == NULL) { + refbuf = (hdset_reg_ref_t *)HDcalloc(sizeof(hdset_reg_ref_t), + (size_t)nelmts); /*init to zero */ + if (refbuf == NULL) { HDprintf("cannot allocate memory\n"); H5TOOLS_GOTO_ERROR((-1), "HDcalloc failed"); } /* end if */ - for(u = 0; u < nelmts; u++) { - H5E_BEGIN_TRY { - if((refobj_id = H5Rdereference2(dset_in, H5P_DEFAULT, H5R_DATASET_REGION, &buf[u])) < 0) + for (u = 0; u < nelmts; u++) { + H5E_BEGIN_TRY + { + if ((refobj_id = H5Rdereference2(dset_in, H5P_DEFAULT, H5R_DATASET_REGION, + &buf[u])) < 0) continue; - } H5E_END_TRY; + } + 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 = H5I_INVALID_HID; /* region id of the referenced dataset */ + if ((refname = MapIdToName(refobj_id, travt)) != NULL) { + hid_t region_id = + H5I_INVALID_HID; /* region id of the referenced dataset */ - if((region_id = H5Rget_region(dset_in, H5R_DATASET_REGION, &buf[u])) < 0) + if ((region_id = H5Rget_region(dset_in, H5R_DATASET_REGION, &buf[u])) < 0) H5TOOLS_GOTO_ERROR((-1), "H5Rget_region failed"); /* create the reference, we need the space_id */ - if(H5Rcreate(&refbuf[u], fidout, refname, H5R_DATASET_REGION, region_id) < 0) + if (H5Rcreate(&refbuf[u], fidout, refname, H5R_DATASET_REGION, + region_id) < 0) H5TOOLS_GOTO_ERROR((-1), "H5Rcreate failed"); - if(H5Sclose(region_id) < 0) + if (H5Sclose(region_id) < 0) H5TOOLS_GOTO_ERROR((-1), "H5Sclose failed"); - if(options->verbose) { - HDprintf(FORMAT_OBJ,"dset",travt->objs[i].name ); + if (options->verbose) { + HDprintf(FORMAT_OBJ, "dset", travt->objs[i].name); HDprintf("object <%s> region reference created to <%s>\n", - travt->objs[i].name, - refname); + travt->objs[i].name, refname); } } /*refname*/ if (H5Oclose(refobj_id) < 0) H5TOOLS_ERROR((-1), "H5Oclose refobj_id failed"); } /* u */ - } /*nelmts*/ + } /*nelmts*/ /*------------------------------------------------------------------------- * create/write dataset/close *------------------------------------------------------------------------- */ - if((dset_out = H5Dcreate2(fidout, travt->objs[i].name, mtype_id, space_id, H5P_DEFAULT, dcpl_id, H5P_DEFAULT)) < 0) + if ((dset_out = H5Dcreate2(fidout, travt->objs[i].name, mtype_id, space_id, + H5P_DEFAULT, dcpl_id, H5P_DEFAULT)) < 0) H5TOOLS_GOTO_ERROR((-1), "H5Dcreate2 failed"); - if(nelmts) - if(H5Dwrite(dset_out, mtype_id, H5S_ALL, H5S_ALL, H5P_DEFAULT, refbuf) < 0) + if (nelmts) + if (H5Dwrite(dset_out, mtype_id, H5S_ALL, H5S_ALL, H5P_DEFAULT, refbuf) < 0) H5TOOLS_GOTO_ERROR((-1), "H5Dwrite failed"); - if(buf) + if (buf) HDfree(buf); - if(refbuf) + if (refbuf) HDfree(refbuf); - /*----------------------------------------------------- - * copy attrs - *----------------------------------------------------*/ - if(copy_attr(dset_in, dset_out, &named_dt_head, travt, options) < 0) + /*----------------------------------------------------- + * copy attrs + *----------------------------------------------------*/ + if (copy_attr(dset_in, dset_out, &named_dt_head, travt, options) < 0) H5TOOLS_GOTO_ERROR((-1), "copy_attr failed"); } /* H5T_STD_REF_DSETREG */ /*------------------------------------------------------------------------- @@ -308,7 +314,7 @@ int do_copy_refobjs(hid_t fidin, *------------------------------------------------------------------------- */ else { - if((dset_out = H5Dopen2(fidout, travt->objs[i].name, H5P_DEFAULT)) < 0) + if ((dset_out = H5Dopen2(fidout, travt->objs[i].name, H5P_DEFAULT)) < 0) H5TOOLS_GOTO_ERROR((-1), "H5Dopen2 failed"); } /* end else */ @@ -316,18 +322,19 @@ int do_copy_refobjs(hid_t fidin, * copy referenced objects in attributes *------------------------------------------------------------------------- */ - if(copy_refs_attr(dset_in, dset_out, travt, fidout) < 0) + if (copy_refs_attr(dset_in, dset_out, travt, fidout) < 0) H5TOOLS_GOTO_ERROR((-1), "copy_refs_attr failed"); /*------------------------------------------------------------------------- * check for hard links *------------------------------------------------------------------------- */ - if(travt->objs[i].nlinks) - for(j = 0; j < travt->objs[i].nlinks; j++) - H5Lcreate_hard(fidout, travt->objs[i].name, H5L_SAME_LOC, travt->objs[i].links[j].new_name, H5P_DEFAULT, H5P_DEFAULT); + if (travt->objs[i].nlinks) + for (j = 0; j < travt->objs[i].nlinks; j++) + H5Lcreate_hard(fidout, travt->objs[i].name, H5L_SAME_LOC, + travt->objs[i].links[j].new_name, H5P_DEFAULT, H5P_DEFAULT); - if(H5Dclose(dset_out) < 0) + if (H5Dclose(dset_out) < 0) H5TOOLS_GOTO_ERROR((-1), "H5Dclose failed"); } /*can_read*/ @@ -335,15 +342,15 @@ int do_copy_refobjs(hid_t fidin, * close *------------------------------------------------------------------------- */ - if(H5Tclose(ftype_id) < 0) + if (H5Tclose(ftype_id) < 0) H5TOOLS_GOTO_ERROR((-1), "H5Tclose failed"); - if(H5Tclose(mtype_id) < 0) + if (H5Tclose(mtype_id) < 0) H5TOOLS_GOTO_ERROR((-1), "H5Tclose failed"); - if(H5Pclose(dcpl_id) < 0) + if (H5Pclose(dcpl_id) < 0) H5TOOLS_GOTO_ERROR((-1), "H5Pclose failed"); - if(H5Sclose(space_id) < 0) + if (H5Sclose(space_id) < 0) H5TOOLS_GOTO_ERROR((-1), "H5Sclose failed"); - if(H5Dclose(dset_in) < 0) + if (H5Dclose(dset_in) < 0) H5TOOLS_GOTO_ERROR((-1), "H5Dclose failed"); break; @@ -352,9 +359,9 @@ int do_copy_refobjs(hid_t fidin, *------------------------------------------------------------------------- */ case H5TRAV_TYPE_NAMED_DATATYPE: - if((type_in = H5Topen2(fidin, travt->objs[i].name, H5P_DEFAULT)) < 0) + if ((type_in = H5Topen2(fidin, travt->objs[i].name, H5P_DEFAULT)) < 0) H5TOOLS_GOTO_ERROR((-1), "H5Topen2 failed"); - if(H5Tclose(type_in) < 0) + if (H5Tclose(type_in) < 0) H5TOOLS_GOTO_ERROR((-1), "H5Tclose failed"); break; @@ -374,7 +381,7 @@ int do_copy_refobjs(hid_t fidin, default: break; } /* end switch */ - } /* end for */ + } /* end for */ /* Finalize (link) the stack of named datatypes (if any) * This function is paired with copy_named_datatype() which is called @@ -386,7 +393,8 @@ int do_copy_refobjs(hid_t fidin, return ret_value; done: - H5E_BEGIN_TRY { + H5E_BEGIN_TRY + { H5Gclose(grp_in); H5Gclose(grp_out); H5Pclose(dcpl_id); @@ -397,12 +405,12 @@ done: H5Tclose(mtype_id); H5Tclose(type_in); named_datatype_free(&named_dt_head, 1); - } H5E_END_TRY; + } + H5E_END_TRY; return ret_value; } - /*------------------------------------------------------------------------- * Function: copy_refs_attr * @@ -425,91 +433,87 @@ done: *------------------------------------------------------------------------- */ -static int copy_refs_attr(hid_t loc_in, - hid_t loc_out, - trav_table_t *travt, - hid_t fidout) /* for saving references */ +static int +copy_refs_attr(hid_t loc_in, hid_t loc_out, trav_table_t *travt, hid_t fidout) /* for saving references */ { - hid_t attr_id = H5I_INVALID_HID; /* attr ID */ - hid_t attr_out = H5I_INVALID_HID; /* attr ID */ - hid_t space_id = H5I_INVALID_HID; /* space ID */ - hid_t ftype_id = H5I_INVALID_HID; /* file data type ID */ - hid_t mtype_id = H5I_INVALID_HID; /* memory data type ID */ - size_t msize; /* memory size of type */ - hsize_t nelmts; /* number of elements in dataset */ - hsize_t dims[H5S_MAX_RANK];/* dimensions of dataset */ + hid_t attr_id = H5I_INVALID_HID; /* attr ID */ + hid_t attr_out = H5I_INVALID_HID; /* attr ID */ + hid_t space_id = H5I_INVALID_HID; /* space ID */ + hid_t ftype_id = H5I_INVALID_HID; /* file data type ID */ + hid_t mtype_id = H5I_INVALID_HID; /* memory data type ID */ + size_t msize; /* memory size of type */ + hsize_t nelmts; /* number of elements in dataset */ + hsize_t dims[H5S_MAX_RANK]; /* dimensions of dataset */ char name[255]; - H5O_info2_t oinfo; /* Object info */ + H5O_info2_t oinfo; /* Object info */ unsigned u, i, j; int rank; H5T_class_t type_class = -1; - hbool_t is_ref = 0, - is_ref_vlen = 0, - is_ref_array = 0, - is_ref_comp = 0; - void *refbuf = NULL; - void *buf = NULL; - unsigned *ref_comp_index = NULL; - size_t *ref_comp_size = NULL; + hbool_t is_ref = 0, is_ref_vlen = 0, is_ref_array = 0, is_ref_comp = 0; + void * refbuf = NULL; + void * buf = NULL; + unsigned * ref_comp_index = NULL; + size_t * ref_comp_size = NULL; int ref_comp_field_n = 0; - int ret_value = 0; + int ret_value = 0; - if(H5Oget_info3(loc_in, &oinfo, H5O_INFO_NUM_ATTRS) < 0) + if (H5Oget_info3(loc_in, &oinfo, H5O_INFO_NUM_ATTRS) < 0) H5TOOLS_GOTO_ERROR((-1), "H5Oget_info failed"); - for(u = 0; u < (unsigned)oinfo.num_attrs; u++) { + for (u = 0; u < (unsigned)oinfo.num_attrs; u++) { is_ref = is_ref_vlen = is_ref_array = is_ref_comp = 0; /* open attribute */ - if((attr_id = H5Aopen_by_idx(loc_in, ".", H5_INDEX_CRT_ORDER, H5_ITER_INC, (hsize_t)u, H5P_DEFAULT, H5P_DEFAULT)) < 0) + if ((attr_id = H5Aopen_by_idx(loc_in, ".", H5_INDEX_CRT_ORDER, H5_ITER_INC, (hsize_t)u, H5P_DEFAULT, + H5P_DEFAULT)) < 0) H5TOOLS_GOTO_ERROR((-1), "H5Aopen_by_idx failed"); /* get the file datatype */ - if((ftype_id = H5Aget_type(attr_id)) < 0) + if ((ftype_id = H5Aget_type(attr_id)) < 0) H5TOOLS_GOTO_ERROR((-1), "H5Aget_type failed"); type_class = H5Tget_class(ftype_id); - if((mtype_id = H5Tget_native_type(ftype_id, H5T_DIR_DEFAULT)) < 0) + if ((mtype_id = H5Tget_native_type(ftype_id, H5T_DIR_DEFAULT)) < 0) H5TOOLS_GOTO_ERROR((-1), "H5Tget_native_type failed"); - if((msize = H5Tget_size(mtype_id)) == 0) + if ((msize = H5Tget_size(mtype_id)) == 0) H5TOOLS_GOTO_ERROR((-1), "H5Tget_size failed"); is_ref = (type_class == H5T_REFERENCE); - if(type_class == H5T_VLEN ) { + if (type_class == H5T_VLEN) { hid_t base_type = H5Tget_super(ftype_id); is_ref_vlen = (H5Tget_class(base_type) == H5T_REFERENCE); - msize = H5Tget_size(base_type); + msize = H5Tget_size(base_type); if (H5Tclose(base_type) < 0) H5TOOLS_ERROR((-1), "H5Tclose base_type failed"); } - else if(type_class == H5T_ARRAY ) { + else if (type_class == H5T_ARRAY) { hid_t base_type = H5Tget_super(ftype_id); is_ref_array = (H5Tget_class(base_type) == H5T_REFERENCE); - msize = H5Tget_size(base_type); + msize = H5Tget_size(base_type); if (H5Tclose(base_type) < 0) H5TOOLS_GOTO_ERROR((-1), "H5Tclose base_type failed"); } - else if(type_class == H5T_COMPOUND) { - int nmembers = H5Tget_nmembers(ftype_id) ; + else if (type_class == H5T_COMPOUND) { + int nmembers = H5Tget_nmembers(ftype_id); if (nmembers < 1) H5TOOLS_GOTO_ERROR((-1), "H5Tget_nmembers failed"); - ref_comp_index = (unsigned *)HDmalloc((size_t)nmembers*sizeof(unsigned)); - ref_comp_size = (size_t *)HDmalloc((size_t)nmembers*sizeof(ref_comp_size)); + ref_comp_index = (unsigned *)HDmalloc((size_t)nmembers * sizeof(unsigned)); + ref_comp_size = (size_t *)HDmalloc((size_t)nmembers * sizeof(ref_comp_size)); ref_comp_field_n = 0; - for (i=0; i<(unsigned)nmembers; i++) { + for (i = 0; i < (unsigned)nmembers; i++) { hid_t mtid = H5Tget_member_type(ftype_id, i); if ((H5Tget_class(mtid) == H5T_REFERENCE)) { ref_comp_index[ref_comp_field_n] = i; - ref_comp_size[ref_comp_field_n] = H5Tget_size(mtid); + ref_comp_size[ref_comp_field_n] = H5Tget_size(mtid); ref_comp_field_n++; } if (H5Tclose(mtid) < 0) @@ -539,7 +543,6 @@ static int copy_refs_attr(hid_t loc_in, is_ref_comp = (ref_comp_field_n > 0); } - if (!(is_ref || is_ref_vlen || is_ref_array || is_ref_comp)) { if (H5Tclose(mtype_id) < 0) H5TOOLS_ERROR((-1), "H5Tclose mtype_id failed"); @@ -551,31 +554,30 @@ static int copy_refs_attr(hid_t loc_in, } /* get name */ - if(H5Aget_name(attr_id, 255, name) < 0) + if (H5Aget_name(attr_id, 255, name) < 0) H5TOOLS_GOTO_ERROR((-1), "H5Aget_name failed"); /* get the dataspace handle */ - if((space_id = H5Aget_space(attr_id)) < 0) + if ((space_id = H5Aget_space(attr_id)) < 0) H5TOOLS_GOTO_ERROR((-1), "H5Aget_space failed"); /* get dimensions */ - if((rank = H5Sget_simple_extent_dims(space_id, dims, NULL)) < 0) + if ((rank = H5Sget_simple_extent_dims(space_id, dims, NULL)) < 0) H5TOOLS_GOTO_ERROR((-1), "H5Sget_simple_extent_dims failed"); - /*------------------------------------------------------------------------- - * elements - *------------------------------------------------------------------------- - */ + * elements + *------------------------------------------------------------------------- + */ nelmts = 1; - for(j = 0; j < (unsigned)rank; j++) + for (j = 0; j < (unsigned)rank; j++) nelmts *= dims[j]; if (is_ref_array) { - unsigned array_rank = 0; - hsize_t array_size = 1; - hsize_t array_dims[H5S_MAX_RANK]; - hid_t base_type = H5Tget_super(ftype_id); + unsigned array_rank = 0; + hsize_t array_size = 1; + hsize_t array_dims[H5S_MAX_RANK]; + hid_t base_type = H5Tget_super(ftype_id); msize = H5Tget_size(base_type); if (H5Tclose(base_type) < 0) @@ -583,153 +585,163 @@ static int copy_refs_attr(hid_t loc_in, array_rank = (unsigned)H5Tget_array_ndims(mtype_id); H5Tget_array_dims2(mtype_id, array_dims); - for(j = 0; j <array_rank; j++) + for (j = 0; j < array_rank; j++) array_size *= array_dims[j]; nelmts *= array_size; } - if((attr_out = H5Acreate2(loc_out, name, ftype_id, space_id, H5P_DEFAULT, H5P_DEFAULT)) < 0) + if ((attr_out = H5Acreate2(loc_out, name, ftype_id, space_id, H5P_DEFAULT, H5P_DEFAULT)) < 0) H5TOOLS_GOTO_ERROR((-1), "H5Acreate2 failed"); - if (nelmts>0) { + if (nelmts > 0) { /* handle object references */ - if((is_ref || is_ref_array) && (H5R_OBJ_REF_BUF_SIZE==msize)) { + if ((is_ref || is_ref_array) && (H5R_OBJ_REF_BUF_SIZE == msize)) { buf = (hobj_ref_t *)HDmalloc((unsigned)(nelmts * msize)); - if(buf == NULL) { + if (buf == NULL) { HDprintf("cannot read into memory\n"); H5TOOLS_GOTO_ERROR((-1), "HDmalloc failed"); } /* end if */ - if(H5Aread(attr_id, mtype_id, buf) < 0) + if (H5Aread(attr_id, mtype_id, buf) < 0) H5TOOLS_GOTO_ERROR((-1), "H5Aread failed"); refbuf = (hobj_ref_t *)HDcalloc((unsigned)nelmts, msize); - if(refbuf == NULL) { + if (refbuf == NULL) { HDprintf("cannot allocate memory\n"); H5TOOLS_GOTO_ERROR((-1), "HDcalloc failed"); } /* end if */ - for(i = 0; i < (unsigned)nelmts; i++) - if(update_ref_value(attr_id, H5R_OBJECT, &((hobj_ref_t *)buf)[i], fidout, &((hobj_ref_t *)refbuf)[i], travt) < 0) + for (i = 0; i < (unsigned)nelmts; i++) + if (update_ref_value(attr_id, H5R_OBJECT, &((hobj_ref_t *)buf)[i], fidout, + &((hobj_ref_t *)refbuf)[i], travt) < 0) continue; } /* H5T_STD_REF_OBJ */ /* handle region references */ - else if((is_ref || is_ref_array) && (H5R_DSET_REG_REF_BUF_SIZE == msize)) { + else if ((is_ref || is_ref_array) && (H5R_DSET_REG_REF_BUF_SIZE == msize)) { buf = (hdset_reg_ref_t *)HDmalloc((unsigned)(nelmts * msize)); - if(buf == NULL) { - HDprintf( "cannot read into memory\n" ); + if (buf == NULL) { + HDprintf("cannot read into memory\n"); H5TOOLS_GOTO_ERROR((-1), "HDmalloc failed"); } /* end if */ - if(H5Aread(attr_id, mtype_id, buf) < 0) + if (H5Aread(attr_id, mtype_id, buf) < 0) H5TOOLS_GOTO_ERROR((-1), "H5Aread failed"); /*------------------------------------------------------------------------- * create output *------------------------------------------------------------------------- */ - refbuf = (hdset_reg_ref_t *)HDcalloc(sizeof(hdset_reg_ref_t), (size_t)nelmts); /*init to zero */ - if(refbuf == NULL) { - HDprintf( "cannot allocate memory\n" ); + refbuf = + (hdset_reg_ref_t *)HDcalloc(sizeof(hdset_reg_ref_t), (size_t)nelmts); /*init to zero */ + if (refbuf == NULL) { + HDprintf("cannot allocate memory\n"); H5TOOLS_GOTO_ERROR((-1), "HDcalloc failed"); } /* end if */ - for(i = 0; i < (unsigned)nelmts; i++) - if(update_ref_value(attr_id, H5R_DATASET_REGION, &((hdset_reg_ref_t *)buf)[i], fidout, &((hdset_reg_ref_t *)refbuf)[i], travt) < 0) + for (i = 0; i < (unsigned)nelmts; i++) + if (update_ref_value(attr_id, H5R_DATASET_REGION, &((hdset_reg_ref_t *)buf)[i], fidout, + &((hdset_reg_ref_t *)refbuf)[i], travt) < 0) continue; } /* H5T_STD_REF_DSETREG */ else if (is_ref_vlen) { /* handle VLEN of references */ - buf = (hvl_t *)HDmalloc((unsigned)(nelmts * sizeof(hvl_t))); + buf = (hvl_t *)HDmalloc((unsigned)(nelmts * sizeof(hvl_t))); refbuf = buf; /* reuse the read buffer for write */ - if(buf == NULL) { - HDprintf( "cannot read into memory\n" ); + if (buf == NULL) { + HDprintf("cannot read into memory\n"); H5TOOLS_GOTO_ERROR((-1), "HDmalloc failed"); } /* end if */ - if(H5Aread(attr_id, mtype_id, buf) < 0) + if (H5Aread(attr_id, mtype_id, buf) < 0) H5TOOLS_GOTO_ERROR((-1), "H5Aread failed"); - if (H5R_OBJ_REF_BUF_SIZE==msize) { + if (H5R_OBJ_REF_BUF_SIZE == msize) { hobj_ref_t ref_out; - for (i=0; i<(unsigned)nelmts; i++) { + for (i = 0; i < (unsigned)nelmts; i++) { hobj_ref_t *ptr = (hobj_ref_t *)((hvl_t *)buf)[i].p; - for (j=0; j<((hvl_t *)buf)[i].len; j++ ) { - if (update_ref_value(attr_id, H5R_OBJECT, &(ptr[j]), fidout, &ref_out, travt)<0) + for (j = 0; j < ((hvl_t *)buf)[i].len; j++) { + if (update_ref_value(attr_id, H5R_OBJECT, &(ptr[j]), fidout, &ref_out, travt) < 0) continue; HDmemcpy(&(ptr[j]), &ref_out, msize); } - } /* for (i=0; i<nelems; i++) */ + } /* for (i=0; i<nelems; i++) */ } else if (H5R_DSET_REG_REF_BUF_SIZE == msize) { hdset_reg_ref_t ref_out; - for (i=0; i<(unsigned)nelmts; i++) { + for (i = 0; i < (unsigned)nelmts; i++) { hdset_reg_ref_t *ptr = (hdset_reg_ref_t *)((hvl_t *)buf)[i].p; - for (j=0; j<((hvl_t *)buf)[i].len; j++ ) { - if (update_ref_value(attr_id, H5R_DATASET_REGION, &(ptr[j]), fidout, &ref_out, travt)<0) + for (j = 0; j < ((hvl_t *)buf)[i].len; j++) { + if (update_ref_value(attr_id, H5R_DATASET_REGION, &(ptr[j]), fidout, &ref_out, + travt) < 0) continue; HDmemcpy(&(ptr[j]), &ref_out, msize); } - } /* for (i=0; i<nelems; i++) */ + } /* for (i=0; i<nelems; i++) */ } } /* else if (is_ref_vlen) */ else if (is_ref_comp) { /* handle ref fields in a compound */ - buf = HDmalloc((unsigned)(nelmts * msize)); + buf = HDmalloc((unsigned)(nelmts * msize)); refbuf = buf; /* reuse the read buffer for write */ - if(buf == NULL) { - HDprintf( "cannot read into memory\n" ); + if (buf == NULL) { + HDprintf("cannot read into memory\n"); H5TOOLS_GOTO_ERROR((-1), "HDmalloc failed"); } /* end if */ - if(H5Aread(attr_id, mtype_id, buf) < 0) + if (H5Aread(attr_id, mtype_id, buf) < 0) H5TOOLS_GOTO_ERROR((-1), "H5Aread failed"); - for (i=0; i<(unsigned)nelmts; i++) { - for (j=0; j<(unsigned)ref_comp_field_n; j++) { + for (i = 0; i < (unsigned)nelmts; i++) { + for (j = 0; j < (unsigned)ref_comp_field_n; j++) { if (ref_comp_size[j] == H5R_OBJ_REF_BUF_SIZE) { - size_t idx = (i * msize) + H5Tget_member_offset(mtype_id, ref_comp_index[j]); + size_t idx = (i * msize) + H5Tget_member_offset(mtype_id, ref_comp_index[j]); hobj_ref_t ref_out; - if (update_ref_value(attr_id, H5R_OBJECT, (hobj_ref_t *)((void *)(((char *)buf)+idx)), fidout, &ref_out, travt) < 0) /* Extra (void *) cast to quiet "cast to create alignment" warning - 2019/07/05, QAK */ + if (update_ref_value(attr_id, H5R_OBJECT, + (hobj_ref_t *)((void *)(((char *)buf) + idx)), fidout, + &ref_out, + travt) < 0) /* Extra (void *) cast to quiet "cast to create + alignment" warning - 2019/07/05, QAK */ continue; - HDmemcpy(((char *)buf)+idx, &ref_out, ref_comp_size[j]); + HDmemcpy(((char *)buf) + idx, &ref_out, ref_comp_size[j]); } /* if */ else if (ref_comp_size[j] == H5R_DSET_REG_REF_BUF_SIZE) { size_t idx = i * msize + H5Tget_member_offset(mtype_id, ref_comp_index[j]); hdset_reg_ref_t ref_out; - if (update_ref_value(attr_id, H5R_DATASET_REGION, (hdset_reg_ref_t *)(((char *)buf)+idx), fidout, &ref_out, travt)<0) + if (update_ref_value(attr_id, H5R_DATASET_REGION, + (hdset_reg_ref_t *)(((char *)buf) + idx), fidout, &ref_out, + travt) < 0) continue; - HDmemcpy(((char *)buf)+idx, &ref_out, ref_comp_size[j]); + HDmemcpy(((char *)buf) + idx, &ref_out, ref_comp_size[j]); } /* else if */ - } /* j */ - } /* i */ - } /* else if (is_ref_comp) */ + } /* j */ + } /* i */ + } /* else if (is_ref_comp) */ - if(H5Awrite(attr_out, mtype_id, refbuf) < 0) + if (H5Awrite(attr_out, mtype_id, refbuf) < 0) H5TOOLS_GOTO_ERROR((-1), "H5Awrite failed"); if (is_ref_vlen && buf) - H5Treclaim (mtype_id, space_id, H5P_DEFAULT, buf); + H5Treclaim(mtype_id, space_id, H5P_DEFAULT, buf); } /* if (nelmts) */ if (refbuf == buf) refbuf = NULL; /* set it to NULL to avoid double free since buf and refbuf are the same. */ - if(buf) { + if (buf) { HDfree(buf); buf = NULL; } - if(refbuf) { + if (refbuf) { HDfree(refbuf); refbuf = NULL; } @@ -744,27 +756,27 @@ static int copy_refs_attr(hid_t loc_in, ref_comp_size = NULL; } - if(H5Aclose(attr_out) < 0) + if (H5Aclose(attr_out) < 0) H5TOOLS_GOTO_ERROR((-1), "H5Aclose failed"); /*------------------------------------------------------------------------- - * close - *------------------------------------------------------------------------- - */ - if(H5Tclose(ftype_id) < 0) + * close + *------------------------------------------------------------------------- + */ + if (H5Tclose(ftype_id) < 0) H5TOOLS_GOTO_ERROR((-1), "H5Tclose failed"); - if(H5Tclose(mtype_id) < 0) + if (H5Tclose(mtype_id) < 0) H5TOOLS_GOTO_ERROR((-1), "H5Tclose failed"); - if(H5Sclose(space_id) < 0) + if (H5Sclose(space_id) < 0) H5TOOLS_GOTO_ERROR((-1), "H5Sclose failed"); - if(H5Aclose(attr_id) < 0) + if (H5Aclose(attr_id) < 0) H5TOOLS_GOTO_ERROR((-1), "H5Aclose failed"); } /* for(u = 0; u < (unsigned)oinfo.num_attrs; u++) */ done: - if(refbuf) + if (refbuf) HDfree(refbuf); - if(buf) + if (buf) HDfree(buf); if (ref_comp_index) @@ -773,13 +785,15 @@ done: if (ref_comp_size) HDfree(ref_comp_size); - H5E_BEGIN_TRY { + H5E_BEGIN_TRY + { H5Tclose(ftype_id); H5Tclose(mtype_id); H5Sclose(space_id); H5Aclose(attr_id); H5Aclose(attr_out); - } H5E_END_TRY; + } + H5E_END_TRY; return ret_value; } @@ -791,32 +805,32 @@ done: * *------------------------------------------------------------------------- */ -static const char* +static const char * MapIdToName(hid_t refobj_id, trav_table_t *travt) { unsigned int u; - const char *ret = NULL; + const char * ret = NULL; /* linear search */ - for(u = 0; u < travt->nobjs; u++) { - if(travt->objs[u].type == (h5trav_type_t)H5O_TYPE_DATASET || - travt->objs[u].type == (h5trav_type_t)H5O_TYPE_GROUP || - travt->objs[u].type == (h5trav_type_t)H5O_TYPE_NAMED_DATATYPE) { - H5O_info2_t ref_oinfo; /* Stat for the refobj id */ + for (u = 0; u < travt->nobjs; u++) { + if (travt->objs[u].type == (h5trav_type_t)H5O_TYPE_DATASET || + travt->objs[u].type == (h5trav_type_t)H5O_TYPE_GROUP || + travt->objs[u].type == (h5trav_type_t)H5O_TYPE_NAMED_DATATYPE) { + H5O_info2_t ref_oinfo; /* Stat for the refobj id */ int token_cmp; /* obtain information to identify the referenced object uniquely */ - if(H5Oget_info3(refobj_id, &ref_oinfo, H5O_INFO_BASIC) < 0) + if (H5Oget_info3(refobj_id, &ref_oinfo, H5O_INFO_BASIC) < 0) goto out; - if(H5Otoken_cmp(refobj_id, &ref_oinfo.token, &travt->objs[u].obj_token, &token_cmp) < 0) + if (H5Otoken_cmp(refobj_id, &ref_oinfo.token, &travt->objs[u].obj_token, &token_cmp) < 0) goto out; - if(!token_cmp) { + if (!token_cmp) { ret = travt->objs[u].name; goto out; } - } /* end if */ - } /* u */ + } /* end if */ + } /* u */ out: return ret; @@ -828,13 +842,14 @@ out: * Purpose: Update a reference value *------------------------------------------------------------------------- */ -static herr_t update_ref_value(hid_t obj_id, H5R_type_t ref_type, void *ref_in, - hid_t fid_out, void *ref_out, trav_table_t *travt) +static herr_t +update_ref_value(hid_t obj_id, H5R_type_t ref_type, void *ref_in, hid_t fid_out, void *ref_out, + trav_table_t *travt) { const char *ref_obj_name; - hid_t space_id = H5I_INVALID_HID; + hid_t space_id = H5I_INVALID_HID; hid_t ref_obj_id = H5I_INVALID_HID; - herr_t ret_value = SUCCEED; + herr_t ret_value = SUCCEED; ref_obj_id = H5Rdereference2(obj_id, H5P_DEFAULT, ref_type, ref_in); if (ref_obj_id < 0) @@ -850,15 +865,16 @@ static herr_t update_ref_value(hid_t obj_id, H5R_type_t ref_type, void *ref_in, H5TOOLS_GOTO_ERROR(FAIL, "H5Rget_region failed"); } - if(H5Rcreate(ref_out, fid_out, ref_obj_name, ref_type, space_id) < 0) + if (H5Rcreate(ref_out, fid_out, ref_obj_name, ref_type, space_id) < 0) H5TOOLS_GOTO_ERROR(FAIL, "H5Rcreate failed"); done: - H5E_BEGIN_TRY { - H5Sclose(space_id); - H5Oclose(ref_obj_id); - } H5E_END_TRY; + H5E_BEGIN_TRY + { + H5Sclose(space_id); + H5Oclose(ref_obj_id); + } + H5E_END_TRY; return ret_value; } - |