diff options
Diffstat (limited to 'hl')
43 files changed, 847 insertions, 621 deletions
diff --git a/hl/CMakeLists.txt b/hl/CMakeLists.txt index 5061c6c..9391231 100644 --- a/hl/CMakeLists.txt +++ b/hl/CMakeLists.txt @@ -2,6 +2,14 @@ cmake_minimum_required (VERSION 3.12) project (HDF5_HL C) #----------------------------------------------------------------------------- +# Option to use new-style references with dimension scale APIs +#----------------------------------------------------------------------------- +option (HDF5_DIMENSION_SCALES_NEW_REF "Use new-style references with dimension scale APIs" OFF) +if (HDF5_DIMENSION_SCALES_NEW_REF) + set (H5_DIMENSION_SCALES_WITH_NEW_REF 1) +endif () + +#----------------------------------------------------------------------------- # List Source files #----------------------------------------------------------------------------- diff --git a/hl/c++/test/ptableTest.cpp b/hl/c++/test/ptableTest.cpp index ab49303..33199f1 100644 --- a/hl/c++/test/ptableTest.cpp +++ b/hl/c++/test/ptableTest.cpp @@ -223,7 +223,7 @@ TestGetNext() for (record = 1; record < 6; record++) wrapper.AppendPacket(&record); - /* Ensure that we can interate through the records and get the right ones */ + /* Ensure that we can iterate through the records and get the right ones */ for (i = 1; i < 6; i++) { wrapper.GetNextPacket(&record); if (record != i) @@ -237,7 +237,7 @@ TestGetNext() if (error < 0) goto error; - /* Ensure that we can interate through the records and get the right ones */ + /* Ensure that we can iterate through the records and get the right ones */ for (i = 1; i < 6; i++) { error = wrapper.GetNextPacket(&record); if (record != i || error < 0) @@ -622,7 +622,7 @@ TestHDFFV_9758() s1[i].a = static_cast<int>(i); s1[i].b = 1.0F * static_cast<float>(i * i); s1[i].c = 1.0 / static_cast<double>(i + 1); - HDsprintf(s1[i].d, "string%" PRIuHSIZE "", i); + HDsnprintf(s1[i].d, STRING_LENGTH, "string%" PRIuHSIZE "", i); s1[i].e = static_cast<int>(100 + i); } diff --git a/hl/examples/ex_image1.c b/hl/examples/ex_image1.c index ead1715..1294ab3 100644 --- a/hl/examples/ex_image1.c +++ b/hl/examples/ex_image1.c @@ -56,10 +56,10 @@ main(void) H5IMmake_image_8bit(file_id, "image1", (hsize_t)WIDTH, (hsize_t)HEIGHT, buf); /* make a palette */ - H5IMmake_palette(file_id, "pallete", pal_dims, pal); + H5IMmake_palette(file_id, "palette", pal_dims, pal); /* attach the palette to the image */ - H5IMlink_palette(file_id, "image1", "pallete"); + H5IMlink_palette(file_id, "image1", "palette"); /* close the file. */ H5Fclose(file_id); diff --git a/hl/fortran/src/H5DSff.F90 b/hl/fortran/src/H5DSff.F90 index b241e9a..bbd9918 100644 --- a/hl/fortran/src/H5DSff.F90 +++ b/hl/fortran/src/H5DSff.F90 @@ -216,7 +216,7 @@ CONTAINS END SUBROUTINE H5DSis_attached_f ! -! H5DSiterate_scales: Impliment in F2003 +! H5DSiterate_scales: Implement in F2003 ! !------------------------------------------------------------------------- diff --git a/hl/fortran/src/H5HL_buildiface.F90 b/hl/fortran/src/H5HL_buildiface.F90 index 4f34575..ca66ebf 100644 --- a/hl/fortran/src/H5HL_buildiface.F90 +++ b/hl/fortran/src/H5HL_buildiface.F90 @@ -14,7 +14,7 @@ ! ! NOTES ! This program uses the Fortran 2008 intrinsic function STORAGE_SIZE or SIZEOF -! depending on availablity.It generates code that makes use of +! depending on availability.It generates code that makes use of ! STORAGE_SIZE/SIZEOF in H5fortran_detect.f90. STORAGE_SIZE is standard ! compliant and should always be chosen over SIZEOF. ! diff --git a/hl/fortran/src/H5LTfc.c b/hl/fortran/src/H5LTfc.c index e87a9d3..4cb9265 100644 --- a/hl/fortran/src/H5LTfc.c +++ b/hl/fortran/src/H5LTfc.c @@ -319,11 +319,9 @@ h5ltset_attribute_c(hid_t_f *loc_id, size_t_f *namelen, _fcd dsetname, size_t_f else if ((size_t)*sizeof_val == sizeof(double)) ret = H5LT_set_attribute_numerical(c_loc_id, c_name, c_attrname, c_size, H5T_NATIVE_DOUBLE, (const double *)buf); -#if H5_SIZEOF_LONG_DOUBLE != 0 else if ((size_t)*sizeof_val == sizeof(long double)) ret = H5LT_set_attribute_numerical(c_loc_id, c_name, c_attrname, c_size, H5T_NATIVE_LDOUBLE, (const long double *)buf); -#endif else goto done; } @@ -413,10 +411,8 @@ h5ltget_attribute_c(hid_t_f *loc_id, size_t_f *namelen, _fcd dsetname, size_t_f ret = H5LTget_attribute(c_loc_id, c_name, c_attrname, H5T_NATIVE_FLOAT, buf); else if ((size_t)*sizeof_val == sizeof(double)) ret = H5LTget_attribute(c_loc_id, c_name, c_attrname, H5T_NATIVE_DOUBLE, buf); -#if H5_SIZEOF_LONG_DOUBLE != 0 else if ((size_t)*sizeof_val == sizeof(long double)) ret = H5LTget_attribute(c_loc_id, c_name, c_attrname, H5T_NATIVE_LDOUBLE, buf); -#endif else goto done; } diff --git a/hl/fortran/src/H5LTff.F90 b/hl/fortran/src/H5LTff.F90 index ba4b770..a4ab247 100644 --- a/hl/fortran/src/H5LTff.F90 +++ b/hl/fortran/src/H5LTff.F90 @@ -88,7 +88,7 @@ MODULE H5LT_CONST TYPE(C_PTR), VALUE :: buf ! data buffer CHARACTER(KIND=C_CHAR), DIMENSION(*), INTENT(in) :: dtype ! flag indicating the datatype of the ! the buffer: - ! R=Real, D=DOUBLE, I=Interger, C=Character + ! R=Real, D=DOUBLE, I=Integer, C=Character INTEGER(size_t) :: SizeOf_buf ! Sizeof the buf datatype END FUNCTION h5ltset_attribute_c END INTERFACE @@ -107,7 +107,7 @@ MODULE H5LT_CONST TYPE(C_PTR), VALUE :: buf ! data buffer CHARACTER(KIND=C_CHAR), DIMENSION(*), INTENT(in) :: dtype ! flag indicating the datatype of the ! the buffer: - ! R=Real, D=DOUBLE, I=Interger + ! R=Real, D=DOUBLE, I=Integer INTEGER(size_t), INTENT(in) :: SizeOf_buf ! Sizeof the buf data type END FUNCTION h5ltget_attribute_c END INTERFACE diff --git a/hl/fortran/src/H5TBfc.c b/hl/fortran/src/H5TBfc.c index 23e3377..91c420b 100644 --- a/hl/fortran/src/H5TBfc.c +++ b/hl/fortran/src/H5TBfc.c @@ -83,7 +83,7 @@ h5tbmake_table_c(size_t_f *namelen1, _fcd name1, hid_t_f *loc_id, size_t_f *name (tmp = (char *)HD5f2cstring(field_names, (size_t) * (max_char_size_field_names) * (size_t)num_elem))) HGOTO_DONE(FAIL) /* - * move data from temorary buffer + * move data from temporary buffer */ tmp_p = tmp; for (i = 0; i < num_elem; i++) { @@ -188,7 +188,7 @@ h5tbmake_table_ptr_c(size_t_f *namelen1, _fcd name1, hid_t_f *loc_id, size_t_f * (tmp = (char *)HD5f2cstring(field_names, (size_t) * (max_char_size_field_names) * (size_t)num_elem))) HGOTO_DONE(FAIL) /* - * move data from temorary buffer + * move data from temporary buffer */ tmp_p = tmp; for (i = 0; i < num_elem; i++) { diff --git a/hl/fortran/src/H5TBff.F90 b/hl/fortran/src/H5TBff.F90 index 35a88b8..82f34a8 100644 --- a/hl/fortran/src/H5TBff.F90 +++ b/hl/fortran/src/H5TBff.F90 @@ -961,7 +961,7 @@ CONTAINS INTEGER(size_t), DIMENSION(1:nfields), INTENT(inout) :: field_offsets ! field offsets INTEGER(size_t), INTENT(inout):: type_size ! type size INTEGER(size_t) :: namelen ! name length - INTEGER(size_t) :: maxlen ! maxiumum length of input field names + INTEGER(size_t) :: maxlen ! maximum length of input field names INTEGER(size_t), DIMENSION(1:nfields) :: namelen2 ! name lengths INTEGER(size_t) :: c_maxlen_out ! maximum character length of a field array element END FUNCTION h5tbget_field_info_c diff --git a/hl/fortran/test/tsttable.F90 b/hl/fortran/test/tsttable.F90 index a77068c..e7bd88e 100644 --- a/hl/fortran/test/tsttable.F90 +++ b/hl/fortran/test/tsttable.F90 @@ -172,11 +172,11 @@ SUBROUTINE test_table1() ! offset = 0 field_offset(1) = offset - offset = offset + type_sizec ! Offset of the second memeber is 2 + offset = offset + type_sizec ! Offset of the second member is 2 field_offset(2) = offset - offset = offset + type_sizei ! Offset of the second memeber is 6 + offset = offset + type_sizei ! Offset of the second member is 6 field_offset(3) = offset - offset = offset + type_sized ! Offset of the second memeber is 14 + offset = offset + type_sized ! Offset of the second member is 14 field_offset(4) = offset !------------------------------------------------------------------------- @@ -571,7 +571,7 @@ SUBROUTINE test_table2() INTEGER(HSIZE_T), PARAMETER :: nrecords = 8 ! nrecords CHARACTER(len=8), PARAMETER :: filename = "f2tab.h5" ! File name - CHARACTER(LEN=5), PARAMETER :: table_name = "tabel" ! table name + CHARACTER(LEN=5), PARAMETER :: table_name = "table" ! table name CHARACTER(LEN=10), PARAMETER :: table_name_fill = "tabel_fill" ! table name ! Define field information diff --git a/hl/src/H5DO.c b/hl/src/H5DO.c index 3bdb4e2..1703669 100644 --- a/hl/src/H5DO.c +++ b/hl/src/H5DO.c @@ -182,7 +182,7 @@ H5DOappend(hid_t dset_id, hid_t dxpl_id, unsigned axis, size_t extension, hid_t if (FAIL == H5Sselect_hyperslab(new_space_id, H5S_SELECT_SET, start, stride, count, block)) goto done; - /* The # of elemnts in the new extended dataspace */ + /* The # of elements in the new extended dataspace */ if ((snelmts = H5Sget_select_npoints(new_space_id)) < 0) goto done; nelmts = (hsize_t)snelmts; diff --git a/hl/src/H5DS.c b/hl/src/H5DS.c index 2bd4046..387419b 100644 --- a/hl/src/H5DS.c +++ b/hl/src/H5DS.c @@ -18,7 +18,40 @@ /* Local routines */ static herr_t H5DS_is_reserved(hid_t did); -static hid_t H5DS_get_REFLIST_type(void); + +/*------------------------------------------------------------------------- + * Function: H5DSwith_new_ref + * + * Purpose: Determines if new references are used with dimension scales. + * The function H5DSwith_new_ref takes any object identifier and checks + * if new references are used for dimension scales. Currently, + * new references are used when non-native VOL connector is used or when + * H5_DIMENSION_SCALES_WITH_NEW_REF is set up via configure option. + * + * Return: Non-negative on success/Negative on failure + * + *------------------------------------------------------------------------- + */ +herr_t +H5DSwith_new_ref(hid_t obj_id, hbool_t *with_new_ref) +{ + hbool_t config_flag = FALSE; + hbool_t native = FALSE; + + if (!with_new_ref) + return FAIL; + + if (H5VLobject_is_native(obj_id, &native) < 0) + return FAIL; + +#ifdef H5_DIMENSION_SCALES_WITH_NEW_REF + config_flag = TRUE; +#endif + + *with_new_ref = (config_flag || !native); + + return SUCCEED; +} /*------------------------------------------------------------------------- * Function: H5DSset_scale @@ -55,7 +88,7 @@ H5DSset_scale(hid_t dsid, const char *dimname) return FAIL; /*------------------------------------------------------------------------- - * check if the dataset is a dataset wich has references to dimension scales + * check if the dataset is a dataset which has references to dimension scales *------------------------------------------------------------------------- */ @@ -106,22 +139,34 @@ H5DSset_scale(hid_t dsid, const char *dimname) herr_t H5DSattach_scale(hid_t did, hid_t dsid, unsigned int idx) { - int has_dimlist; - int has_reflist; - int is_ds; - hssize_t nelmts; - hid_t sid; /* space ID */ - hid_t tid = -1; /* attribute type ID */ - hid_t ntid = -1; /* attribute native type ID */ - hid_t aid = -1; /* attribute ID */ - int rank; /* rank of dataset */ - hsize_t dims[1]; /* dimension of the "REFERENCE_LIST" array */ - ds_list_t dsl; /* attribute data in the DS pointing to the dataset */ - ds_list_t * dsbuf = NULL; /* array of attribute data in the DS pointing to the dataset */ - hobj_ref_t ref_to_ds; /* reference to the DS */ - hobj_ref_t ref_j; /* iterator reference */ - hvl_t * buf = NULL; /* VL buffer to store in the attribute */ - hid_t dsid_j; /* DS dataset ID in DIMENSION_LIST */ + int has_dimlist; + int has_reflist; + int is_ds; + hssize_t nelmts; + hid_t sid, sid_w; /* space ID */ + hid_t tid = H5I_INVALID_HID; /* attribute type ID */ + hid_t ntid = H5I_INVALID_HID; /* attribute native type ID */ + hid_t aid = H5I_INVALID_HID; /* attribute ID */ + int rank; /* rank of dataset */ + hsize_t dims[1]; /* dimension of the "REFERENCE_LIST" array */ + + ds_list_t dsl; /* attribute data in the DS pointing to the dataset */ + ds_list_t *dsbuf = NULL; /* array of attribute data in the DS pointing to the dataset */ + ds_list_t *dsbuf_w = + NULL; /* array of "REFERENCE_LIST" attribute data to write when adding new reference to a dataset */ + hobj_ref_t ref_to_ds; /* reference to the DS */ + hobj_ref_t ref_j; /* iterator reference */ + + /* Variables to be used when new references are used */ + nds_list_t ndsl; + nds_list_t *ndsbuf = NULL; + nds_list_t *ndsbuf_w = NULL; + H5R_ref_t nref_to_ds; + H5R_ref_t nref_j; + hbool_t is_new_ref; + + hvl_t * buf = NULL; /* VL buffer to store in the attribute */ + hid_t dsid_j; /* DS dataset ID in DIMENSION_LIST */ H5O_info2_t oi1, oi2; H5I_type_t it1, it2; int i; @@ -159,6 +204,14 @@ H5DSattach_scale(hid_t did, hid_t dsid, unsigned int idx) return FAIL; } /* end if */ + /*------------------------------------------------------------------------- + * determine if old or new references should be used + *------------------------------------------------------------------------- + */ + + if (H5DSwith_new_ref(did, &is_new_ref) < 0) + return FAIL; + /* get ID type */ if ((it1 = H5Iget_type(did)) < 0) return FAIL; @@ -209,14 +262,23 @@ H5DSattach_scale(hid_t did, hid_t dsid, unsigned int idx) * and one to the dataset, saved in "REFERENCE_LIST" *------------------------------------------------------------------------- */ - /* create a reference for the >>DS<< dataset */ - if (H5Rcreate(&ref_to_ds, dsid, ".", H5R_OBJECT, (hid_t)-1) < 0) - return FAIL; - - /* create a reference for the >>data<< dataset */ - if (H5Rcreate(&dsl.ref, did, ".", H5R_OBJECT, (hid_t)-1) < 0) - return FAIL; + if (is_new_ref) { + /* create a reference for the >>DS<< dataset */ + if (H5Rcreate_object(dsid, ".", H5P_DEFAULT, &nref_to_ds) < 0) + return FAIL; + /* create a reference for the >>data<< dataset */ + if (H5Rcreate_object(did, ".", H5P_DEFAULT, &ndsl.ref) < 0) + return FAIL; + } + else { + /* create a reference for the >>DS<< dataset */ + if (H5Rcreate(&ref_to_ds, dsid, ".", H5R_OBJECT, (hid_t)-1) < 0) + return FAIL; + /* create a reference for the >>data<< dataset */ + if (H5Rcreate(&dsl.ref, did, ".", H5R_OBJECT, (hid_t)-1) < 0) + return FAIL; + } /* try to find the attribute "DIMENSION_LIST" on the >>data<< dataset */ if ((has_dimlist = H5LT_find_attribute(did, DIMENSION_LIST)) < 0) return FAIL; @@ -234,9 +296,14 @@ H5DSattach_scale(hid_t did, hid_t dsid, unsigned int idx) return FAIL; /* create the type for the attribute "DIMENSION_LIST" */ - if ((tid = H5Tvlen_create(H5T_STD_REF_OBJ)) < 0) - goto out; - + if (is_new_ref) { + if ((tid = H5Tvlen_create(H5T_STD_REF)) < 0) + goto out; + } + else { + if ((tid = H5Tvlen_create(H5T_STD_REF_OBJ)) < 0) + goto out; + } /* create the attribute */ if ((aid = H5Acreate2(did, DIMENSION_LIST, tid, sid, H5P_DEFAULT, H5P_DEFAULT)) < 0) goto out; @@ -252,24 +319,32 @@ H5DSattach_scale(hid_t did, hid_t dsid, unsigned int idx) } /* store the REF information in the index of the dataset that has the DS */ - buf[idx].len = 1; - buf[idx].p = HDmalloc(1 * sizeof(hobj_ref_t)); - ((hobj_ref_t *)buf[idx].p)[0] = ref_to_ds; - + buf[idx].len = 1; + if (is_new_ref) { + buf[idx].p = HDmalloc(1 * sizeof(H5R_ref_t)); + ((H5R_ref_t *)buf[idx].p)[0] = nref_to_ds; + } + else { + buf[idx].p = HDmalloc(1 * sizeof(hobj_ref_t)); + ((hobj_ref_t *)buf[idx].p)[0] = ref_to_ds; + } /* write the attribute with the reference */ if (H5Awrite(aid, tid, buf) < 0) goto out; /* close */ - if (H5Treclaim(tid, sid, H5P_DEFAULT, buf) < 0) - goto out; + if (is_new_ref) { + if (H5Rdestroy(&nref_to_ds) < 0) + goto out; + } if (H5Sclose(sid) < 0) goto out; if (H5Tclose(tid) < 0) goto out; if (H5Aclose(aid) < 0) goto out; - + HDfree(buf[idx].p); + buf[idx].p = NULL; HDfree(buf); buf = NULL; } @@ -302,12 +377,20 @@ H5DSattach_scale(hid_t did, hid_t dsid, unsigned int idx) /* iterate all the REFs in this dimension IDX */ for (i = 0; i < (int)buf[idx].len; i++) { /* get the reference */ - ref_j = ((hobj_ref_t *)buf[idx].p)[i]; + if (is_new_ref) { + nref_j = ((H5R_ref_t *)buf[idx].p)[i]; - /* get the scale id for this REF */ - if ((dsid_j = H5Rdereference2(did, H5P_DEFAULT, H5R_OBJECT, &ref_j)) < 0) - goto out; + /* get the scale id for this REF */ + if ((dsid_j = H5Ropen_object(&nref_j, H5P_DEFAULT, H5P_DEFAULT)) < 0) + goto out; + } + else { + ref_j = ((hobj_ref_t *)buf[idx].p)[i]; + /* get the scale id for this REF */ + if ((dsid_j = H5Rdereference2(did, H5P_DEFAULT, H5R_OBJECT, &ref_j)) < 0) + goto out; + } /* get info for DS in the parameter list */ if (H5Oget_info3(dsid, &oi1, H5O_INFO_BASIC) < 0) goto out; @@ -335,17 +418,33 @@ H5DSattach_scale(hid_t did, hid_t dsid, unsigned int idx) /* we are adding one more DS to this dimension */ if (buf[idx].len > 0) { buf[idx].len++; - len = buf[idx].len; - buf[idx].p = HDrealloc(buf[idx].p, len * sizeof(hobj_ref_t)); - ((hobj_ref_t *)buf[idx].p)[len - 1] = ref_to_ds; + len = buf[idx].len; + if (is_new_ref) { + buf[idx].p = HDrealloc(buf[idx].p, len * sizeof(H5R_ref_t)); + ((H5R_ref_t *)buf[idx].p)[len - 1] = nref_to_ds; + } + else { + buf[idx].p = HDrealloc(buf[idx].p, len * sizeof(hobj_ref_t)); + ((hobj_ref_t *)buf[idx].p)[len - 1] = ref_to_ds; + } } /* end if */ else { /* store the REF information in the index of the dataset that has the DS */ - buf[idx].len = 1; - buf[idx].p = HDmalloc(sizeof(hobj_ref_t)); - ((hobj_ref_t *)buf[idx].p)[0] = ref_to_ds; + buf[idx].len = 1; + if (is_new_ref) { + buf[idx].p = HDmalloc(sizeof(H5R_ref_t)); + ((H5R_ref_t *)buf[idx].p)[0] = nref_to_ds; + } + else { + buf[idx].p = HDmalloc(sizeof(hobj_ref_t)); + ((hobj_ref_t *)buf[idx].p)[0] = ref_to_ds; + } } /* end else */ } /* end if */ + else { + if (is_new_ref && H5Rdestroy(&nref_to_ds) < 0) + goto out; + } /* write the attribute with the new references */ if (H5Awrite(aid, tid, buf) < 0) @@ -385,29 +484,40 @@ H5DSattach_scale(hid_t did, hid_t dsid, unsigned int idx) goto out; /* create the compound datatype for the attribute "REFERENCE_LIST" */ - if ((tid = H5Tcreate(H5T_COMPOUND, sizeof(ds_list_t))) < 0) - goto out; - - /* insert reference field */ - if (H5Tinsert(tid, "dataset", HOFFSET(ds_list_t, ref), H5T_STD_REF_OBJ) < 0) - goto out; - - /* insert dimension idx of the dataset field */ - if (H5Tinsert(tid, "dimension", HOFFSET(ds_list_t, dim_idx), H5T_NATIVE_INT) < 0) - goto out; + if (is_new_ref) { + if ((tid = H5Tcreate(H5T_COMPOUND, sizeof(nds_list_t))) < 0) + goto out; + if (H5Tinsert(tid, "dataset", HOFFSET(nds_list_t, ref), H5T_STD_REF) < 0) + goto out; + if (H5Tinsert(tid, "dimension", HOFFSET(nds_list_t, dim_idx), H5T_NATIVE_UINT) < 0) + goto out; + } + else { + if ((tid = H5Tcreate(H5T_COMPOUND, sizeof(ds_list_t))) < 0) + goto out; + if (H5Tinsert(tid, "dataset", HOFFSET(ds_list_t, ref), H5T_STD_REF_OBJ) < 0) + goto out; + if (H5Tinsert(tid, "dimension", HOFFSET(ds_list_t, dim_idx), H5T_NATIVE_UINT) < 0) + goto out; + } /* create the attribute */ if ((aid = H5Acreate2(dsid, REFERENCE_LIST, tid, sid, H5P_DEFAULT, H5P_DEFAULT)) < 0) goto out; /* store the IDX information */ - dsl.dim_idx = idx; - - /* write the attribute with the reference */ - if (H5Awrite(aid, tid, &dsl) < 0) - goto out; - - /* close */ + if (is_new_ref) { + ndsl.dim_idx = idx; + if (H5Awrite(aid, tid, &ndsl) < 0) + goto out; + if (H5Rdestroy(&ndsl.ref) < 0) + goto out; + } + else { + dsl.dim_idx = idx; + if (H5Awrite(aid, tid, &dsl) < 0) + goto out; + } if (H5Sclose(sid) < 0) goto out; if (H5Tclose(tid) < 0) @@ -421,6 +531,9 @@ H5DSattach_scale(hid_t did, hid_t dsid, unsigned int idx) *------------------------------------------------------------------------- */ else if (has_reflist == 1) { + hid_t tmp_id; /* Temporary DS dataset ID to recreate reference */ + int j; + if ((aid = H5Aopen(dsid, REFERENCE_LIST, H5P_DEFAULT)) < 0) goto out; @@ -428,7 +541,7 @@ H5DSattach_scale(hid_t did, hid_t dsid, unsigned int idx) goto out; /* get native type to read attribute REFERENCE_LIST */ - if ((ntid = H5DS_get_REFLIST_type()) < 0) + if ((ntid = H5Tget_native_type(tid, H5T_DIR_ASCEND)) < 0) goto out; /* get and save the old reference(s) */ @@ -439,17 +552,22 @@ H5DSattach_scale(hid_t did, hid_t dsid, unsigned int idx) goto out; nelmts++; - - dsbuf = (ds_list_t *)HDmalloc((size_t)nelmts * sizeof(ds_list_t)); - if (dsbuf == NULL) - goto out; - - if (H5Aread(aid, ntid, dsbuf) < 0) - goto out; + if (is_new_ref) { + ndsbuf = (nds_list_t *)HDmalloc((size_t)nelmts * sizeof(nds_list_t)); + if (ndsbuf == NULL) + goto out; + if (H5Aread(aid, ntid, ndsbuf) < 0) + goto out; + } + else { + dsbuf = (ds_list_t *)HDmalloc((size_t)nelmts * sizeof(ds_list_t)); + if (dsbuf == NULL) + goto out; + if (H5Aread(aid, ntid, dsbuf) < 0) + goto out; + } /* close */ - if (H5Sclose(sid) < 0) - goto out; if (H5Aclose(aid) < 0) goto out; @@ -458,40 +576,93 @@ H5DSattach_scale(hid_t did, hid_t dsid, unsigned int idx) *------------------------------------------------------------------------- */ + /* Allocate new buffer to copy old references and add new one */ + + if (is_new_ref) { + ndsbuf_w = (nds_list_t *)HDmalloc((size_t)nelmts * sizeof(nds_list_t)); + if (ndsbuf_w == NULL) + goto out; + } + else { + dsbuf_w = (ds_list_t *)HDmalloc((size_t)nelmts * sizeof(ds_list_t)); + if (dsbuf_w == NULL) + goto out; + } + /* Recreate the references we read from the existing "REFERENCE_LIST" attribute */ + for (j = 0; j < nelmts - 1; j++) { + if (is_new_ref) { + ndsbuf_w[j].dim_idx = ndsbuf[j].dim_idx; + tmp_id = H5Ropen_object(&ndsbuf[j].ref, H5P_DEFAULT, H5P_DEFAULT); + if (tmp_id < 0) + goto out; + if (H5Rcreate_object(tmp_id, ".", H5P_DEFAULT, &ndsbuf_w[j].ref) < 0) { + H5Dclose(tmp_id); + goto out; + } + } + else { + dsbuf_w[j] = dsbuf[j]; + } + } + /* store the IDX information (index of the dataset that has the DS) */ + if (is_new_ref) { + ndsl.dim_idx = idx; + ndsbuf_w[nelmts - 1] = ndsl; + } + else { + dsl.dim_idx = idx; + dsbuf_w[nelmts - 1] = dsl; + } + /* the attribute must be deleted, in order to the new one can reflect the changes*/ if (H5Adelete(dsid, REFERENCE_LIST) < 0) goto out; - /* store the IDX information (index of the dataset that has the DS) */ - dsl.dim_idx = idx; - dsbuf[nelmts - 1] = dsl; - /* create a new data space for the new references array */ dims[0] = (hsize_t)nelmts; - if ((sid = H5Screate_simple(1, dims, NULL)) < 0) + if ((sid_w = H5Screate_simple(1, dims, NULL)) < 0) goto out; /* create the attribute again with the changes of space */ - if ((aid = H5Acreate2(dsid, REFERENCE_LIST, tid, sid, H5P_DEFAULT, H5P_DEFAULT)) < 0) + if ((aid = H5Acreate2(dsid, REFERENCE_LIST, tid, sid_w, H5P_DEFAULT, H5P_DEFAULT)) < 0) goto out; /* write the attribute with the new references */ - if (H5Awrite(aid, ntid, dsbuf) < 0) - goto out; - - /* close */ + if (is_new_ref) { + if (H5Awrite(aid, ntid, ndsbuf_w) < 0) + goto out; + if (H5Treclaim(tid, sid, H5P_DEFAULT, ndsbuf_w) < 0) + goto out; + } + else { + if (H5Awrite(aid, ntid, dsbuf_w) < 0) + goto out; + if (H5Treclaim(tid, sid, H5P_DEFAULT, dsbuf_w) < 0) + goto out; + } if (H5Sclose(sid) < 0) goto out; + if (H5Sclose(sid_w) < 0) + goto out; if (H5Tclose(tid) < 0) goto out; if (H5Aclose(aid) < 0) goto out; if (H5Tclose(ntid) < 0) goto out; - - HDfree(dsbuf); - dsbuf = NULL; + if (is_new_ref) { + HDfree(ndsbuf); + dsbuf = NULL; + HDfree(ndsbuf_w); + dsbuf = NULL; + } + else { + HDfree(dsbuf); + dsbuf = NULL; + HDfree(dsbuf_w); + dsbuf = NULL; + } } /* has_reflist */ /*------------------------------------------------------------------------- @@ -515,6 +686,8 @@ out: HDfree(buf); if (dsbuf) HDfree(dsbuf); + if (dsbuf_w) + HDfree(dsbuf_w); H5E_BEGIN_TRY { @@ -554,27 +727,35 @@ out: herr_t H5DSdetach_scale(hid_t did, hid_t dsid, unsigned int idx) { - int has_dimlist; - int has_reflist; - hssize_t nelmts; - hid_t dsid_j; /* DS dataset ID in DIMENSION_LIST */ - hid_t did_i; /* dataset ID in REFERENCE_LIST */ - hid_t sid; /* space ID */ - hid_t tid = -1; /* attribute type ID */ - hid_t ntid = -1; /* attribute native type ID */ - hid_t aid = -1; /* attribute ID */ - int rank; /* rank of dataset */ - ds_list_t * dsbuf = NULL; /* array of attribute data in the DS pointing to the dataset */ - hsize_t dims[1]; /* dimension of the "REFERENCE_LIST" array */ - hobj_ref_t ref; /* reference to the DS */ - hvl_t * buf = NULL; /* VL buffer to store in the attribute */ - int i; - size_t j; - hssize_t ii; - H5O_info2_t did_oi, dsid_oi, tmp_oi; - int found_dset = 0, found_ds = 0; - int have_ds = 0; - htri_t is_scale; + int has_dimlist; + int has_reflist; + hssize_t nelmts; + hid_t dsid_j; /* DS dataset ID in DIMENSION_LIST */ + hid_t did_i; /* dataset ID in REFERENCE_LIST */ + hid_t sid = H5I_INVALID_HID; /* space ID */ + hid_t sid_w = H5I_INVALID_HID; /* space ID */ + hid_t tid = H5I_INVALID_HID; /* attribute type ID */ + hid_t ntid = H5I_INVALID_HID; /* attribute native type ID */ + hid_t aid = H5I_INVALID_HID; /* attribute ID */ + int rank; /* rank of dataset */ + nds_list_t * ndsbuf = NULL; /* array of attribute data in the DS pointing to the dataset */ + nds_list_t * ndsbuf_w = NULL; /* array of attribute data in the DS pointing to the dataset to write*/ + ds_list_t * dsbuf = NULL; /* array of attribute data in the DS pointing to the dataset */ + ds_list_t * dsbuf_w = NULL; /* array of attribute data in the DS pointing to the dataset to write*/ + hsize_t dims[1]; /* dimension of the "REFERENCE_LIST" array */ + H5R_ref_t nref; + hobj_ref_t ref; /* reference to the DS */ + hvl_t * buf = NULL; /* VL buffer to store in the attribute */ + int i; + size_t j; + hssize_t ii; + H5O_info2_t did_oi, dsid_oi, tmp_oi; + int found_dset = 0, found_ds = 0; + int have_ds = 0; + htri_t is_scale; + hbool_t is_new_ref; + unsigned int tmp_idx; + hid_t tmp_id; /*------------------------------------------------------------------------- * parameter checking @@ -612,9 +793,17 @@ H5DSdetach_scale(hid_t did, hid_t dsid, unsigned int idx) } /* end if */ /*------------------------------------------------------------------------- - * Find "DIMENSION_LIST" + * determine if old or new references should be used + *------------------------------------------------------------------------- + */ + if (H5DSwith_new_ref(did, &is_new_ref) < 0) + return FAIL; + + /*------------------------------------------------------------------------- + * find "DIMENSION_LIST" *------------------------------------------------------------------------- */ + /* try to find the attribute "DIMENSION_LIST" on the >>data<< dataset */ if ((has_dimlist = H5LT_find_attribute(did, DIMENSION_LIST)) < 0) return FAIL; @@ -676,13 +865,22 @@ H5DSdetach_scale(hid_t did, hid_t dsid, unsigned int idx) /* reset */ if (buf[idx].len > 0) { for (j = 0; j < buf[idx].len; j++) { - /* get the reference */ - ref = ((hobj_ref_t *)buf[idx].p)[j]; + if (is_new_ref) { + /* get the reference */ + nref = ((H5R_ref_t *)buf[idx].p)[j]; - /* get the DS id */ - if ((dsid_j = H5Rdereference2(did, H5P_DEFAULT, H5R_OBJECT, &ref)) < 0) - goto out; + /* get the scale id for this REF */ + if ((dsid_j = H5Ropen_object(&nref, H5P_DEFAULT, H5P_DEFAULT)) < 0) + goto out; + } + else { + /* get the reference */ + ref = ((hobj_ref_t *)buf[idx].p)[j]; + /* get the DS id */ + if ((dsid_j = H5Rdereference2(did, H5P_DEFAULT, H5R_OBJECT, &ref)) < 0) + goto out; + } /* get info for this DS */ if (H5Oget_info3(dsid_j, &tmp_oi, H5O_INFO_BASIC) < 0) goto out; @@ -708,8 +906,14 @@ H5DSdetach_scale(hid_t did, hid_t dsid, unsigned int idx) size_t len = buf[idx].len; - if (j < len - 1) - ((hobj_ref_t *)buf[idx].p)[j] = ((hobj_ref_t *)buf[idx].p)[len - 1]; + if (j < len - 1) { + if (is_new_ref) { + ((H5R_ref_t *)buf[idx].p)[j] = ((H5R_ref_t *)buf[idx].p)[len - 1]; + } + else { + ((hobj_ref_t *)buf[idx].p)[j] = ((hobj_ref_t *)buf[idx].p)[len - 1]; + } + } len = --buf[idx].len; if (len == 0) { HDfree(buf[idx].p); @@ -770,7 +974,7 @@ H5DSdetach_scale(hid_t did, hid_t dsid, unsigned int idx) goto out; /* get native type to read attribute REFERENCE_LIST */ - if ((ntid = H5DS_get_REFLIST_type()) < 0) + if ((ntid = H5Tget_native_type(tid, H5T_DIR_ASCEND)) < 0) goto out; /* get and save the old reference(s) */ @@ -780,22 +984,65 @@ H5DSdetach_scale(hid_t did, hid_t dsid, unsigned int idx) if ((nelmts = H5Sget_simple_extent_npoints(sid)) < 0) goto out; - dsbuf = (ds_list_t *)HDmalloc((size_t)nelmts * sizeof(ds_list_t)); - if (dsbuf == NULL) - goto out; - - if (H5Aread(aid, ntid, dsbuf) < 0) - goto out; - + if (is_new_ref) { + ndsbuf = (nds_list_t *)HDmalloc((size_t)nelmts * sizeof(nds_list_t)); + if (ndsbuf == NULL) + goto out; + if (H5Aread(aid, ntid, ndsbuf) < 0) + goto out; + ndsbuf_w = (nds_list_t *)HDmalloc((size_t)nelmts * sizeof(nds_list_t)); + if (ndsbuf_w == NULL) + goto out; + } + else { + dsbuf = (ds_list_t *)HDmalloc((size_t)nelmts * sizeof(ds_list_t)); + if (dsbuf == NULL) + goto out; + if (H5Aread(aid, ntid, dsbuf) < 0) + goto out; + dsbuf_w = (ds_list_t *)HDmalloc((size_t)nelmts * sizeof(ds_list_t)); + if (dsbuf_w == NULL) + goto out; + } + /* Recreate the references we read from the existing "REFERENCE_LIST" attribute */ + for (i = 0; i < nelmts; i++) { + if (is_new_ref) { + ndsbuf_w[i].dim_idx = ndsbuf[i].dim_idx; + tmp_id = H5Ropen_object(&ndsbuf[i].ref, H5P_DEFAULT, H5P_DEFAULT); + if (tmp_id < 0) + goto out; + if (H5Rcreate_object(tmp_id, ".", H5P_DEFAULT, &ndsbuf_w[i].ref) < 0) { + H5Dclose(tmp_id); + goto out; + } + H5Dclose(tmp_id); + } + else { + dsbuf_w[i] = dsbuf[i]; + } + } for (ii = 0; ii < nelmts; ii++) { /* First check if we have the same dimension index */ - if (idx == dsbuf[ii].dim_idx) { + if (is_new_ref) { + tmp_idx = ndsbuf_w[ii].dim_idx; + } + else { + tmp_idx = dsbuf_w[ii].dim_idx; + } + if (idx == tmp_idx) { /* get the reference to the dataset */ - ref = dsbuf[ii].ref; - - /* get the dataset id */ - if ((did_i = H5Rdereference2(did, H5P_DEFAULT, H5R_OBJECT, &ref)) < 0) - goto out; + if (is_new_ref) { + /* get the dataset id */ + nref = ndsbuf_w[ii].ref; + if ((did_i = H5Ropen_object(&nref, H5P_DEFAULT, H5P_DEFAULT)) < 0) + goto out; + } + else { + /* get the dataset id */ + ref = dsbuf_w[ii].ref; + if ((did_i = H5Rdereference2(did, H5P_DEFAULT, H5R_OBJECT, &ref)) < 0) + goto out; + } /* get info for this dataset */ if (H5Oget_info3(did_i, &tmp_oi, H5O_INFO_BASIC) < 0) @@ -813,7 +1060,12 @@ H5DSdetach_scale(hid_t did, hid_t dsid, unsigned int idx) goto out; if (!token_cmp) { /* copy the last one to replace the one which is found */ - dsbuf[ii] = dsbuf[nelmts - 1]; + if (is_new_ref) { + ndsbuf_w[ii] = ndsbuf_w[nelmts - 1]; + } + else { + dsbuf_w[ii] = dsbuf_w[nelmts - 1]; + } nelmts--; found_dset = 1; break; @@ -822,9 +1074,7 @@ H5DSdetach_scale(hid_t did, hid_t dsid, unsigned int idx) } /* if we have the same dimension index */ } /* ii */ - /* close space and attribute */ - if (H5Sclose(sid) < 0) - goto out; + /* close attribute */ if (H5Aclose(aid) < 0) goto out; @@ -851,32 +1101,69 @@ H5DSdetach_scale(hid_t did, hid_t dsid, unsigned int idx) /* create a new data space for the new references array */ dims[0] = (hsize_t)nelmts; - if ((sid = H5Screate_simple(1, dims, NULL)) < 0) + if ((sid_w = H5Screate_simple(1, dims, NULL)) < 0) goto out; /* create the attribute again with the changes of space */ - if ((aid = H5Acreate2(dsid, REFERENCE_LIST, tid, sid, H5P_DEFAULT, H5P_DEFAULT)) < 0) + if ((aid = H5Acreate2(dsid, REFERENCE_LIST, tid, sid_w, H5P_DEFAULT, H5P_DEFAULT)) < 0) goto out; /* write the new attribute with the new references */ - if (H5Awrite(aid, ntid, dsbuf) < 0) - goto out; + if (is_new_ref) { + if (H5Awrite(aid, ntid, ndsbuf_w) < 0) + goto out; + } + else { + if (H5Awrite(aid, ntid, dsbuf_w) < 0) + goto out; + } - /* close space and attribute */ - if (H5Sclose(sid) < 0) - goto out; if (H5Aclose(aid) < 0) goto out; } /* nelmts */ + /* Free references */ + if (is_new_ref) { + if (H5Treclaim(tid, sid, H5P_DEFAULT, ndsbuf) < 0) + goto out; + if (H5Sclose(sid) < 0) + goto out; + if (sid_w > 0) { + if (H5Treclaim(tid, sid_w, H5P_DEFAULT, ndsbuf_w) < 0) + goto out; + if (H5Sclose(sid_w) < 0) + goto out; + } + } + else { + if (H5Treclaim(tid, sid, H5P_DEFAULT, dsbuf) < 0) + goto out; + if (H5Sclose(sid) < 0) + goto out; + if (sid_w > 0) { + if (H5Treclaim(tid, sid_w, H5P_DEFAULT, dsbuf_w) < 0) + goto out; + if (H5Sclose(sid_w) < 0) + goto out; + } + } /* close type */ if (H5Tclose(tid) < 0) goto out; if (H5Tclose(ntid) < 0) goto out; - - HDfree(dsbuf); - dsbuf = NULL; + if (is_new_ref) { + HDfree(ndsbuf); + HDfree(ndsbuf_w); + ndsbuf = NULL; + ndsbuf_w = NULL; + } + else { + HDfree(dsbuf); + HDfree(dsbuf_w); + dsbuf = NULL; + dsbuf_w = NULL; + } return SUCCEED; @@ -889,12 +1176,20 @@ out: H5Tclose(ntid); H5Tclose(tid); + if (ndsbuf) { + HDfree(ndsbuf); + ndsbuf = NULL; + } + if (ndsbuf_w) { + HDfree(ndsbuf_w); + ndsbuf_w = NULL; + } if (dsbuf) { HDfree(dsbuf); dsbuf = NULL; } if (buf) { - /* Failure occured before H5Treclaim was called; + /* Failure occurred before H5Treclaim was called; free the pointers allocated when we read data in */ for (i = 0; i < rank; i++) { if (buf[i].p) @@ -936,21 +1231,24 @@ H5DSis_attached(hid_t did, hid_t dsid, unsigned int idx) int has_dimlist; int has_reflist; hssize_t nelmts; - hid_t sid; /* space ID */ - hid_t tid = -1; /* attribute type ID */ - hid_t ntid = -1; /* attribute native type ID */ - hid_t aid = -1; /* attribute ID */ - int rank; /* rank of dataset */ - ds_list_t * dsbuf = NULL; /* array of attribute data in the DS pointing to the dataset */ - hobj_ref_t ref; /* reference to the DS */ - hvl_t * buf = NULL; /* VL buffer to store in the attribute */ - hid_t dsid_j; /* DS dataset ID in DIMENSION_LIST */ - hid_t did_i; /* dataset ID in REFERENCE_LIST */ + hid_t sid; /* space ID */ + hid_t tid = H5I_INVALID_HID; /* attribute type ID */ + hid_t ntid = H5I_INVALID_HID; /* attribute native type ID */ + hid_t aid = H5I_INVALID_HID; /* attribute ID */ + int rank; /* rank of dataset */ + nds_list_t *ndsbuf = NULL; /* array of attribute data in the DS pointing to the dataset */ + ds_list_t * dsbuf = NULL; /* array of attribute data in the DS pointing to the dataset */ + H5R_ref_t nref; /* reference to the DS */ + hobj_ref_t ref; /* reference to the DS */ + hvl_t * buf = NULL; /* VL buffer to store in the attribute */ + hid_t dsid_j; /* DS dataset ID in DIMENSION_LIST */ + hid_t did_i; /* dataset ID in REFERENCE_LIST */ H5O_info2_t oi1, oi2, oi3, oi4; H5I_type_t it1, it2; int i; int found_dset = 0, found_ds = 0; htri_t is_scale; + hbool_t is_new_ref; /*------------------------------------------------------------------------- * parameter checking @@ -982,6 +1280,14 @@ H5DSis_attached(hid_t did, hid_t dsid, unsigned int idx) return FAIL; } /* end if */ + /*------------------------------------------------------------------------- + * determine if old or new references should be used + *------------------------------------------------------------------------- + */ + + if (H5DSwith_new_ref(did, &is_new_ref) < 0) + return FAIL; + /* get ID type */ if ((it1 = H5Iget_type(did)) < 0) return FAIL; @@ -1042,12 +1348,22 @@ H5DSis_attached(hid_t did, hid_t dsid, unsigned int idx) /* iterate all the REFs in this dimension IDX */ for (i = 0; i < (int)buf[idx].len; i++) { - /* get the reference */ - ref = ((hobj_ref_t *)buf[idx].p)[i]; + if (is_new_ref) { + /* get the reference */ + nref = ((H5R_ref_t *)buf[idx].p)[i]; - /* get the scale id for this REF */ - if ((dsid_j = H5Rdereference2(did, H5P_DEFAULT, H5R_OBJECT, &ref)) < 0) - goto out; + /* get the scale id for this REF */ + if ((dsid_j = H5Ropen_object(&nref, H5P_DEFAULT, H5P_DEFAULT)) < 0) + goto out; + } + else { + /* get the reference */ + ref = ((hobj_ref_t *)buf[idx].p)[i]; + + /* get the scale id for this REF */ + if ((dsid_j = H5Rdereference2(did, H5P_DEFAULT, H5R_OBJECT, &ref)) < 0) + goto out; + } /* get info for DS in the parameter list */ if (H5Oget_info3(dsid, &oi1, H5O_INFO_BASIC) < 0) @@ -1107,7 +1423,7 @@ H5DSis_attached(hid_t did, hid_t dsid, unsigned int idx) goto out; /* get native type to read REFERENCE_LIST attribute */ - if ((ntid = H5DS_get_REFLIST_type()) < 0) + if ((ntid = H5Tget_native_type(tid, H5T_DIR_ASCEND)) < 0) goto out; /* get and save the old reference(s) */ @@ -1117,13 +1433,20 @@ H5DSis_attached(hid_t did, hid_t dsid, unsigned int idx) if ((nelmts = H5Sget_simple_extent_npoints(sid)) < 0) goto out; - dsbuf = (ds_list_t *)HDmalloc((size_t)nelmts * sizeof(ds_list_t)); - - if (dsbuf == NULL) - goto out; - - if (H5Aread(aid, ntid, dsbuf) < 0) - goto out; + if (is_new_ref) { + ndsbuf = (nds_list_t *)HDmalloc((size_t)nelmts * sizeof(nds_list_t)); + if (ndsbuf == NULL) + goto out; + if (H5Aread(aid, ntid, ndsbuf) < 0) + goto out; + } + else { + dsbuf = (ds_list_t *)HDmalloc((size_t)nelmts * sizeof(ds_list_t)); + if (dsbuf == NULL) + goto out; + if (H5Aread(aid, ntid, dsbuf) < 0) + goto out; + } /*------------------------------------------------------------------------- * iterate @@ -1131,40 +1454,58 @@ H5DSis_attached(hid_t did, hid_t dsid, unsigned int idx) */ for (i = 0; i < nelmts; i++) { - /* get the reference */ - ref = dsbuf[i].ref; - /* the reference was not deleted */ - if (ref) { + if (is_new_ref) { + nref = ndsbuf[i].ref; + /* get the dataset id */ + if ((did_i = H5Ropen_object(&nref, H5P_DEFAULT, H5P_DEFAULT)) < 0) + goto out; + } + else { + ref = dsbuf[i].ref; /* get the dataset id */ if ((did_i = H5Rdereference2(did, H5P_DEFAULT, H5R_OBJECT, &ref)) < 0) goto out; + } - /* get info for dataset in the parameter list */ - if (H5Oget_info3(did, &oi3, H5O_INFO_BASIC) < 0) - goto out; + /* get info for dataset in the parameter list */ + if (H5Oget_info3(did, &oi3, H5O_INFO_BASIC) < 0) + goto out; - /* get info for this dataset */ - if (H5Oget_info3(did_i, &oi4, H5O_INFO_BASIC) < 0) - goto out; + /* get info for this dataset */ + if (H5Oget_info3(did_i, &oi4, H5O_INFO_BASIC) < 0) + goto out; - /* same object */ - if (oi3.fileno == oi4.fileno) { - int token_cmp; + /* same object */ + if (oi3.fileno == oi4.fileno) { + int token_cmp; - if (H5Otoken_cmp(did, &oi3.token, &oi4.token, &token_cmp) < 0) - goto out; + if (H5Otoken_cmp(did, &oi3.token, &oi4.token, &token_cmp) < 0) + goto out; + if (is_new_ref) { + if (!token_cmp && (idx == ndsbuf[i].dim_idx)) + found_dset = 1; + } + else { if (!token_cmp && (idx == dsbuf[i].dim_idx)) found_dset = 1; - } /* end if */ + } + } /* end if */ - /* close the dereferenced dataset */ - if (H5Dclose(did_i) < 0) - goto out; - } /* if */ - } /* i */ + /* close the dereferenced dataset */ + if (H5Dclose(did_i) < 0) + goto out; + } /* for */ /* close */ + if (is_new_ref) { + if (H5Treclaim(ntid, sid, H5P_DEFAULT, ndsbuf) < 0) + goto out; + } + else { + if (H5Treclaim(ntid, sid, H5P_DEFAULT, dsbuf) < 0) + goto out; + } if (H5Sclose(sid) < 0) goto out; if (H5Tclose(ntid) < 0) @@ -1174,8 +1515,14 @@ H5DSis_attached(hid_t did, hid_t dsid, unsigned int idx) if (H5Aclose(aid) < 0) goto out; - HDfree(dsbuf); - dsbuf = NULL; + if (ndsbuf) { + HDfree(ndsbuf); + ndsbuf = NULL; + } + if (dsbuf) { + HDfree(dsbuf); + dsbuf = NULL; + } } /* has_reflist */ if (found_ds && found_dset) @@ -1198,6 +1545,10 @@ out: HDfree(buf); buf = NULL; } + if (ndsbuf) { + HDfree(ndsbuf); + ndsbuf = NULL; + } if (dsbuf) { HDfree(dsbuf); dsbuf = NULL; @@ -1249,17 +1600,19 @@ H5DSiterate_scales(hid_t did, unsigned int dim, int *ds_idx, H5DS_iterate_t visi { hid_t scale_id; int rank; - hobj_ref_t ref; /* reference to the DS */ - hid_t sid; /* space ID */ - hid_t tid = -1; /* attribute type ID */ - hid_t aid = -1; /* attribute ID */ - hvl_t * buf = NULL; /* VL buffer to store in the attribute */ - H5I_type_t it; /* ID type */ + H5R_ref_t nref; /* reference to the DS */ + hobj_ref_t ref; /* reference to the DS */ + hid_t sid; /* space ID */ + hid_t tid = H5I_INVALID_HID; /* attribute type ID */ + hid_t aid = H5I_INVALID_HID; /* attribute ID */ + hvl_t * buf = NULL; /* VL buffer to store in the attribute */ + H5I_type_t it; /* ID type */ herr_t ret_value = 0; int j_idx; int nscales; int has_dimlist; int i; + hbool_t is_new_ref; /*------------------------------------------------------------------------- * parameter checking @@ -1272,7 +1625,15 @@ H5DSiterate_scales(hid_t did, unsigned int dim, int *ds_idx, H5DS_iterate_t visi if (H5I_DATASET != it) return FAIL; - /* get the number of scales assotiated with this DIM */ + /*------------------------------------------------------------------------- + * determine if old or new references should be used + *------------------------------------------------------------------------- + */ + + if (H5DSwith_new_ref(did, &is_new_ref) < 0) + return FAIL; + + /* get the number of scales associated with this DIM */ if ((nscales = H5DSget_num_scales(did, dim)) < 0) return FAIL; @@ -1330,17 +1691,32 @@ H5DSiterate_scales(hid_t did, unsigned int dim, int *ds_idx, H5DS_iterate_t visi /* iterate */ for (i = j_idx; i < nscales; i++) { - /* get the reference */ - ref = ((hobj_ref_t *)buf[dim].p)[i]; - - /* disable error reporting, the ID might refer to a deleted dataset */ - H5E_BEGIN_TRY - { - /* get the DS id */ - if ((scale_id = H5Rdereference2(did, H5P_DEFAULT, H5R_OBJECT, &ref)) < 0) - goto out; + if (is_new_ref) { + /* get the reference */ + nref = ((H5R_ref_t *)buf[dim].p)[i]; + + /* disable error reporting, the ID might refer to a deleted dataset */ + H5E_BEGIN_TRY + { + /* get the DS id */ + if ((scale_id = H5Ropen_object(&nref, H5P_DEFAULT, H5P_DEFAULT)) < 0) + goto out; + } + H5E_END_TRY; + } + else { + /* get the reference */ + ref = ((hobj_ref_t *)buf[dim].p)[i]; + + /* disable error reporting, the ID might refer to a deleted dataset */ + H5E_BEGIN_TRY + { + /* get the DS id */ + if ((scale_id = H5Rdereference2(did, H5P_DEFAULT, H5R_OBJECT, &ref)) < 0) + goto out; + } + H5E_END_TRY; } - H5E_END_TRY; /* set the return IDX OUT value at current scale index */ if (ds_idx != NULL) { @@ -1413,12 +1789,12 @@ herr_t H5DSset_label(hid_t did, unsigned int idx, const char *label) { int has_labels; - hid_t sid = -1; /* space ID */ - hid_t tid = -1; /* attribute type ID */ - hid_t aid = -1; /* attribute ID */ - int rank; /* rank of dataset */ - hsize_t dims[1]; /* dimensions of dataset */ - H5I_type_t it; /* ID type */ + hid_t sid = H5I_INVALID_HID; /* space ID */ + hid_t tid = H5I_INVALID_HID; /* attribute type ID */ + hid_t aid = H5I_INVALID_HID; /* attribute ID */ + int rank; /* rank of dataset */ + hsize_t dims[1]; /* dimensions of dataset */ + H5I_type_t it; /* ID type */ unsigned int i; union { /* union is needed to eliminate compiler warnings about */ char ** buf; /* discarding the 'const' qualifier in the free */ @@ -1616,12 +1992,12 @@ ssize_t H5DSget_label(hid_t did, unsigned int idx, char *label, size_t size) { int has_labels; - hid_t sid = -1; /* space ID */ - hid_t tid = -1; /* attribute type ID */ - hid_t aid = -1; /* attribute ID */ - int rank; /* rank of dataset */ - char ** buf = NULL; /* buffer to store in the attribute */ - H5I_type_t it; /* ID type */ + hid_t sid = H5I_INVALID_HID; /* space ID */ + hid_t tid = H5I_INVALID_HID; /* attribute type ID */ + hid_t aid = H5I_INVALID_HID; /* attribute ID */ + int rank; /* rank of dataset */ + char ** buf = NULL; /* buffer to store in the attribute */ + H5I_type_t it; /* ID type */ size_t nbytes = 0; size_t copy_len; int i; @@ -1764,10 +2140,10 @@ out: ssize_t H5DSget_scale_name(hid_t did, char *name, size_t size) { - hid_t aid; /* attribute ID */ - hid_t tid = -1; /* attribute type ID */ - hid_t sid; /* space ID */ - H5I_type_t it; /* ID type */ + hid_t aid = H5I_INVALID_HID; /* attribute ID */ + hid_t tid = H5I_INVALID_HID; /* attribute type ID */ + hid_t sid = H5I_INVALID_HID; /* space ID */ + H5I_type_t it; /* ID type */ size_t nbytes; size_t copy_len; int has_name; @@ -1881,13 +2257,13 @@ out: htri_t H5DSis_scale(hid_t did) { - hid_t tid = -1; /* attribute type ID */ - hid_t aid = -1; /* attribute ID */ - herr_t attr_class; /* has the "CLASS" attribute */ - htri_t is_ds = -1; /* set to "not a dimension scale" */ - H5I_type_t it; /* type of identifier */ - char * buf = NULL; /* buffer to read name of attribute */ - size_t string_size; /* size of storage for the attribute */ + hid_t tid = H5I_INVALID_HID; /* attribute type ID */ + hid_t aid = H5I_INVALID_HID; /* attribute ID */ + herr_t attr_class; /* has the "CLASS" attribute */ + htri_t is_ds = -1; /* set to "not a dimension scale" */ + H5I_type_t it; /* type of identifier */ + char * buf = NULL; /* buffer to read name of attribute */ + size_t string_size; /* size of storage for the attribute */ H5T_class_t type_class; H5T_str_t strpad; @@ -1995,12 +2371,12 @@ int H5DSget_num_scales(hid_t did, unsigned int idx) { int has_dimlist; - hid_t sid; /* space ID */ - hid_t tid = -1; /* attribute type ID */ - hid_t aid = -1; /* attribute ID */ - int rank; /* rank of dataset */ - hvl_t * buf = NULL; /* VL buffer to store in the attribute */ - H5I_type_t it; /* ID type */ + hid_t sid; /* space ID */ + hid_t tid = H5I_INVALID_HID; /* attribute type ID */ + hid_t aid = H5I_INVALID_HID; /* attribute ID */ + int rank; /* rank of dataset */ + hvl_t * buf = NULL; /* VL buffer to store in the attribute */ + H5I_type_t it; /* ID type */ int nscales; /*------------------------------------------------------------------------- @@ -2112,12 +2488,12 @@ out: static herr_t H5DS_is_reserved(hid_t did) { - int has_class; - hid_t tid = -1; - hid_t aid = -1; - char * buf; /* Name of attribute */ - hsize_t storage_size; /* Size of storage for attribute */ - herr_t ret; + int has_class; + hid_t tid = H5I_INVALID_HID; + hid_t aid = H5I_INVALID_HID; + char * buf = NULL; /* Name of attribute */ + size_t string_size; /* Size of storage for attribute */ + herr_t ret; /* try to find the attribute "CLASS" on the dataset */ if ((has_class = H5LT_find_attribute(did, "CLASS")) < 0) @@ -2142,10 +2518,10 @@ H5DS_is_reserved(hid_t did) goto out; /* allocate buffer large enough to hold string */ - if ((storage_size = H5Aget_storage_size(aid)) == 0) + if ((string_size = H5Tget_size(tid)) == 0) goto out; - buf = (char *)HDmalloc((size_t)storage_size * sizeof(char) + 1); + buf = (char *)HDmalloc((size_t)string_size * sizeof(char)); if (buf == NULL) goto out; @@ -2174,51 +2550,11 @@ H5DS_is_reserved(hid_t did) out: H5E_BEGIN_TRY { + if (buf) + HDfree(buf); H5Tclose(tid); H5Aclose(aid); } H5E_END_TRY; return FAIL; } - -/*------------------------------------------------------------------------- - * Function: H5DS_get_REFLIST_type - * - * Purpose: This is a helper function to return a native type for - * the REFERENCE_LIST attribute. - * - * Return: Type identifier on success and negative on failure - * - * Programmer: Elena Pourmal - * - * Date: May 22, 2010 - * - *------------------------------------------------------------------------- - */ -static hid_t -H5DS_get_REFLIST_type(void) -{ - hid_t ntid_t = -1; - - /* Build native type that corresponds to compound datatype - used to store ds_list_t structure in the REFERENCE_LIST - attribute */ - - if ((ntid_t = H5Tcreate(H5T_COMPOUND, sizeof(ds_list_t))) < 0) - goto out; - - if (H5Tinsert(ntid_t, "dataset", HOFFSET(ds_list_t, ref), H5T_STD_REF_OBJ) < 0) - goto out; - - if (H5Tinsert(ntid_t, "dimension", HOFFSET(ds_list_t, dim_idx), H5T_NATIVE_INT) < 0) - goto out; - - return ntid_t; -out: - H5E_BEGIN_TRY - { - H5Tclose(ntid_t); - } - H5E_END_TRY; - return FAIL; -} diff --git a/hl/src/H5DSprivate.h b/hl/src/H5DSprivate.h index 0403a4c..ede0209 100644 --- a/hl/src/H5DSprivate.h +++ b/hl/src/H5DSprivate.h @@ -20,12 +20,18 @@ /* public LT prototypes */ #include "H5DSpublic.h" -/* attribute type of a DS dataset */ +/* attribute type of a DS dataset when old references are used*/ typedef struct ds_list_t { hobj_ref_t ref; /* object reference */ unsigned int dim_idx; /* dimension index of the dataset */ } ds_list_t; +/* attribute type of a DS dataset when new references are used*/ +typedef struct nds_list_t { + H5R_ref_t ref; + unsigned int dim_idx; /* dimension index of the dataset */ +} nds_list_t; + /*------------------------------------------------------------------------- * private functions *------------------------------------------------------------------------- diff --git a/hl/src/H5DSpublic.h b/hl/src/H5DSpublic.h index 7306cbc..979a173 100644 --- a/hl/src/H5DSpublic.h +++ b/hl/src/H5DSpublic.h @@ -25,6 +25,8 @@ typedef herr_t (*H5DS_iterate_t)(hid_t dset, unsigned dim, hid_t scale, void *vi extern "C" { #endif +H5_HLDLL herr_t H5DSwith_new_ref(hid_t obj_id, hbool_t *with_new_ref); + H5_HLDLL herr_t H5DSattach_scale(hid_t did, hid_t dsid, unsigned int idx); H5_HLDLL herr_t H5DSdetach_scale(hid_t did, hid_t dsid, unsigned int idx); diff --git a/hl/src/H5LT.c b/hl/src/H5LT.c index 8f2b33f..238bbf2 100644 --- a/hl/src/H5LT.c +++ b/hl/src/H5LT.c @@ -1856,46 +1856,6 @@ H5LTset_attribute_double(hid_t loc_id, const char *obj_name, const char *attr_na } /*------------------------------------------------------------------------- - * Function: find_attr - * - * Purpose: operator function used by H5LT_find_attribute - * - * Programmer: Pedro Vicente - * - * Date: June 21, 2001 - * - * Comments: - * - * Modifications: - * - *------------------------------------------------------------------------- - */ -static herr_t -find_attr(H5_ATTR_UNUSED hid_t loc_id, const char *name, H5_ATTR_UNUSED const H5A_info_t *ainfo, - void *op_data) -{ - int ret = H5_ITER_CONT; - - /* check the arguments */ - if (name == NULL) - return H5_ITER_CONT; - - /* Shut compiler up */ - (void)loc_id; - (void)ainfo; - - /* Define a positive value for return value if the attribute was found. This will - * cause the iterator to immediately return that positive value, - * indicating short-circuit success - */ - - if (HDstrncmp(name, (char *)op_data, MAX(HDstrlen((char *)op_data), HDstrlen(name))) == 0) - ret = H5_ITER_STOP; - - return ret; -} - -/*------------------------------------------------------------------------- * Function: H5LTfind_attribute * * Purpose: Inquires if an attribute named attr_name exists attached to @@ -1926,32 +1886,22 @@ H5LTfind_attribute(hid_t loc_id, const char *attr_name) * * Date: June 21, 2001 * - * Comments: - * The function uses H5Aiterate2 with the operator function find_attr - * * Return: - * Success: The return value of the first operator that - * returns non-zero, or zero if all members were - * processed with no operator returning non-zero. + * Success: Positive if the attribute exists attached to the + * object loc_id. Zero if the attribute does not + * exist attached to the object loc_id. * * Failure: Negative if something goes wrong within the - * library, or the negative value returned by one - * of the operators. + * library. * *------------------------------------------------------------------------- */ -/* H5Aiterate wants a non-const pointer but we have a const pointer in the API - * call. It's safe to ignore this because we control the callback, don't - * modify the op_data buffer (i.e.: attr_name) during the traversal, and the - * library never modifies that buffer. - */ -H5_GCC_CLANG_DIAG_OFF("cast-qual") herr_t H5LT_find_attribute(hid_t loc_id, const char *attr_name) { - return H5Aiterate2(loc_id, H5_INDEX_NAME, H5_ITER_INC, NULL, find_attr, (void *)attr_name); + htri_t attr_exists = H5Aexists(loc_id, attr_name); + return (attr_exists < 0) ? (herr_t)-1 : (attr_exists) ? (herr_t)1 : (herr_t)0; } -H5_GCC_CLANG_DIAG_ON("cast-qual") /*------------------------------------------------------------------------- * Function: H5LTget_attribute_ndims @@ -2579,11 +2529,9 @@ H5LT_dtype_to_text(hid_t dtype, char *dt_str, H5LT_lang_t lang, size_t *slen, hb } else if (H5Tequal(dtype, H5T_NATIVE_DOUBLE)) { HDsnprintf(dt_str, *slen, "H5T_NATIVE_DOUBLE"); -#if H5_SIZEOF_LONG_DOUBLE != 0 } else if (H5Tequal(dtype, H5T_NATIVE_LDOUBLE)) { HDsnprintf(dt_str, *slen, "H5T_NATIVE_LDOUBLE"); -#endif } else { HDsnprintf(dt_str, *slen, "undefined float"); diff --git a/hl/src/H5LTpublic.h b/hl/src/H5LTpublic.h index f19d353..a6c7c84 100644 --- a/hl/src/H5LTpublic.h +++ b/hl/src/H5LTpublic.h @@ -19,7 +19,7 @@ #define H5LT_FILE_IMAGE_DONT_COPY 0x0002 /* The HDF5 lib won't copy */ /* user supplied image buffer. The same image is open with the core driver. */ #define H5LT_FILE_IMAGE_DONT_RELEASE 0x0004 /* The HDF5 lib won't */ -/* deallocate user supplied image buffer. The user application is reponsible */ +/* deallocate user supplied image buffer. The user application is responsible */ /* for doing so. */ #define H5LT_FILE_IMAGE_ALL 0x0007 diff --git a/hl/test/CMakeTests.cmake b/hl/test/CMakeTests.cmake index 44208e3..e532253 100644 --- a/hl/test/CMakeTests.cmake +++ b/hl/test/CMakeTests.cmake @@ -31,7 +31,9 @@ set (HL_REFERENCE_TEST_FILES dslat.txt dslon.txt test_ds_be.h5 + test_ds_be_new_ref.h5 test_ds_le.h5 + test_ds_le_new_ref.h5 test_ld.h5 ) diff --git a/hl/test/gen_test_ds.c b/hl/test/gen_test_ds.c index a56e6cf..d7a9f44 100644 --- a/hl/test/gen_test_ds.c +++ b/hl/test/gen_test_ds.c @@ -63,7 +63,11 @@ static int test_foreign_scaleattached(const char *filename); #define SCALE_4_NAME "scalename_4_" #define FILENAME "test_ds_" -#define FILEEXT ".h5" +#ifdef H5_DIMENSION_SCALES_WITH_NEW_REF +#define FILEEXT "_new_ref.h5" +#else +#define FILEEXT ".h5" +#endif /*------------------------------------------------------------------------- * the main program diff --git a/hl/test/test_ds.c b/hl/test/test_ds.c index 964e13f..12b6840 100644 --- a/hl/test/test_ds.c +++ b/hl/test/test_ds.c @@ -137,10 +137,15 @@ static int test_attach_detach(void); #define DIM0_LABEL "Latitude" #define DIM1_LABEL "Longitude" +#ifdef H5_DIMENSION_SCALES_WITH_NEW_REF +#define FOREIGN_FILE1 "test_ds_le_new_ref.h5" +#define FOREIGN_FILE2 "test_ds_be_new_ref.h5" +#else #define FOREIGN_FILE1 "test_ds_le.h5" #define FOREIGN_FILE2 "test_ds_be.h5" -#define FILENAME "test_ds" -#define FILEEXT ".h5" +#endif +#define FILENAME "test_ds" +#define FILEEXT ".h5" #define FILE1 "test_ds3.h5" #define FILE2 "test_ds4.h5" @@ -161,10 +166,15 @@ static int test_attach_detach(void); int main(void) { - int nerrors = 0; + hid_t file_id = H5I_INVALID_HID; + int nerrors = 0; /* create file to be used in following tests */ - if (create_test_file("1") < 0) { + if ((file_id = create_test_file("1")) < 0) { + nerrors = 1; + goto error; + } + if (H5Fclose(file_id) < 0) { nerrors = 1; goto error; } @@ -179,7 +189,11 @@ main(void) nerrors += test_long_scalenames("1") < 0 ? 1 : 0; nerrors += test_float_scalenames("1") < 0 ? 1 : 0; nerrors += test_numberofscales("1") < 0 ? 1 : 0; - if (create_test_file("2") < 0) { + if ((file_id = create_test_file("2")) < 0) { + nerrors = 1; + goto error; + } + if (H5Fclose(file_id) < 0) { nerrors = 1; goto error; } @@ -254,10 +268,9 @@ open_test_file(const char *fileext) herr_t create_char_dataset(hid_t fid, const char *dsidx, int fulldims) { - int rank = 3; - int rankds = 1; - hsize_t dims[3] = {DIM1_SIZE, DIM2_SIZE, DIM3_SIZE}; - char buf[DIM1_SIZE * DIM2_SIZE * DIM3_SIZE]; + int rank = 3; + int rankds = 1; + hsize_t dims[3] = {DIM1_SIZE, DIM2_SIZE, DIM3_SIZE}; hsize_t s1_dim[1] = {DIM1_SIZE}; hsize_t s2_dim[1] = {DIM2_SIZE}; hsize_t s3_dim[1] = {DIM3_SIZE}; @@ -275,7 +288,7 @@ create_char_dataset(hid_t fid, const char *dsidx, int fulldims) HDsnprintf(name, sizeof(name), "%s%s", DATASET_NAME, dsidx); /* make a dataset */ - if (H5LTmake_dataset_char(fid, name, rank, dims, buf) >= 0) { + if (H5LTmake_dataset_char(fid, name, rank, dims, NULL) >= 0) { if (fulldims == 0) { /* make a DS dataset for the first dimension */ if (create_DS1_char_datasets(fid, dsidx, rankds, s1_dim, s1_wbuf, NULL) < 0) @@ -309,10 +322,9 @@ create_char_dataset(hid_t fid, const char *dsidx, int fulldims) herr_t create_short_dataset(hid_t fid, const char *dsidx, int fulldims) { - int rank = 3; - int rankds = 1; - hsize_t dims[3] = {DIM1_SIZE, DIM2_SIZE, DIM3_SIZE}; - short buf[DIM1_SIZE * DIM2_SIZE * DIM3_SIZE]; + int rank = 3; + int rankds = 1; + hsize_t dims[3] = {DIM1_SIZE, DIM2_SIZE, DIM3_SIZE}; hsize_t s1_dim[1] = {DIM1_SIZE}; hsize_t s2_dim[1] = {DIM2_SIZE}; hsize_t s3_dim[1] = {DIM3_SIZE}; @@ -330,7 +342,7 @@ create_short_dataset(hid_t fid, const char *dsidx, int fulldims) HDsnprintf(name, sizeof(name), "%s%s", DATASET_NAME, dsidx); /* make a dataset */ - if (H5LTmake_dataset_short(fid, name, rank, dims, buf) >= 0) { + if (H5LTmake_dataset_short(fid, name, rank, dims, NULL) >= 0) { if (fulldims == 0) { /* make a DS dataset for the first dimension */ if (create_DS1_short_datasets(fid, dsidx, rankds, s1_dim, s1_wbuf, NULL) < 0) @@ -364,10 +376,9 @@ create_short_dataset(hid_t fid, const char *dsidx, int fulldims) herr_t create_int_dataset(hid_t fid, const char *dsidx, int fulldims) { - int rank = RANK; - int rankds = 1; - hsize_t dims[RANK] = {DIM1_SIZE, DIM2_SIZE}; - int buf[DIM1_SIZE * DIM2_SIZE]; + int rank = RANK; + int rankds = 1; + hsize_t dims[RANK] = {DIM1_SIZE, DIM2_SIZE}; hsize_t s1_dim[1] = {DIM1_SIZE}; hsize_t s2_dim[1] = {DIM2_SIZE}; int s1_wbuf[DIM1_SIZE] = {10, 20, 30}; @@ -380,7 +391,7 @@ create_int_dataset(hid_t fid, const char *dsidx, int fulldims) HDsnprintf(name, sizeof(name), "%s%s", DATASET_NAME, dsidx); /* make a dataset */ - if (H5LTmake_dataset_int(fid, name, rank, dims, buf) >= 0) { + if (H5LTmake_dataset_int(fid, name, rank, dims, NULL) >= 0) { if (fulldims == 0) { /* make a DS dataset for the first dimension */ if (create_DS1_int_datasets(fid, dsidx, rankds, s1_dim, s1_wbuf, NULL) < 0) @@ -409,7 +420,6 @@ create_long_dataset(hid_t fid, const char *dsname, const char *dsidx, int fulldi int rank = 4; int rankds = 1; hsize_t dims[4] = {DIM1_SIZE, DIM2_SIZE, DIM3_SIZE, DIM4_SIZE}; - long * buf = NULL; hsize_t s1_dim[1] = {DIM1_SIZE}; hsize_t s2_dim[1] = {DIM2_SIZE}; hsize_t s3_dim[1] = {DIM3_SIZE}; @@ -429,12 +439,8 @@ create_long_dataset(hid_t fid, const char *dsname, const char *dsidx, int fulldi long s43_wbuf[DIM4_SIZE] = {180, 180}; long s44_wbuf[DIM4_SIZE] = {280, 280}; - /* Allocate buffer */ - if (NULL == (buf = (long *)HDmalloc(sizeof(long) * DIM1_SIZE * DIM2_SIZE * DIM3_SIZE * DIM4_SIZE))) - goto error; - /* make a dataset */ - if (H5LTmake_dataset_long(fid, dsname, rank, dims, buf) >= 0) { + if (H5LTmake_dataset_long(fid, dsname, rank, dims, NULL) >= 0) { if (fulldims == 0) { /* make a DS dataset for the first dimension */ if (create_DS1_long_datasets(fid, dsidx, rankds, s1_dim, s1_wbuf, NULL) < 0) @@ -471,23 +477,18 @@ create_long_dataset(hid_t fid, const char *dsname, const char *dsidx, int fulldi else goto error; - HDfree(buf); - return SUCCEED; error: - HDfree(buf); - return FAIL; } herr_t create_float_dataset(hid_t fid, const char *dsidx, int fulldims) { - int rank = RANK; - int rankds = 1; - hsize_t dims[RANK] = {DIM1_SIZE, DIM2_SIZE}; - float buf[DIM1_SIZE * DIM2_SIZE]; + int rank = RANK; + int rankds = 1; + hsize_t dims[RANK] = {DIM1_SIZE, DIM2_SIZE}; hsize_t s1_dim[1] = {DIM1_SIZE}; hsize_t s2_dim[1] = {DIM2_SIZE}; float s1_wbuf[DIM1_SIZE] = {10, 20, 30}; @@ -500,7 +501,7 @@ create_float_dataset(hid_t fid, const char *dsidx, int fulldims) HDsnprintf(name, sizeof(name), "%s%s", DATASET_NAME, dsidx); /* make a dataset */ - if (H5LTmake_dataset_float(fid, name, rank, dims, buf) >= 0) { + if (H5LTmake_dataset_float(fid, name, rank, dims, NULL) >= 0) { if (fulldims == 0) { /* make a DS dataset for the first dimension */ if (create_DS1_float_datasets(fid, dsidx, rankds, s1_dim, s1_wbuf, NULL) < 0) @@ -3020,7 +3021,7 @@ test_simple(void) } /*------------------------------------------------------------------------- - * dettach for DIM0 + * detach for DIM0 *------------------------------------------------------------------------- */ @@ -3318,11 +3319,11 @@ test_simple(void) goto out; dim = 0; - /* iterate trough the 1st dimension of "dset_a" and verify that its DS is valid */ + /* iterate through the 1st dimension of "dset_a" and verify that its DS is valid */ if (H5DSiterate_scales(did, dim, NULL, verify_scale, NULL) < 0) goto out; - /* iterate trough the 2nd dimension of "dset_a" and verify that its DS is valid + /* iterate through the 2nd dimension of "dset_a" and verify that its DS is valid start at DS index 2 */ dim = 1; scale_idx = 2; @@ -3343,11 +3344,11 @@ test_simple(void) goto out; dim = 0; - /* iterate trough the 1st dimension of "dset_a" and read the DS */ + /* iterate through the 1st dimension of "dset_a" and read the DS */ if (H5DSiterate_scales(did, dim, NULL, read_scale, s1_wbuf) < 0) goto out; - /* iterate trough the 2nd dimension of "dset_a" and read the DS + /* iterate through the 2nd dimension of "dset_a" and read the DS start at DS index 2 */ dim = 1; scale_idx = 2; @@ -3380,9 +3381,9 @@ test_simple(void) goto out; { int match_size; /* does this scale size matches the dataset DIM size */ - int idx = 0; /* scale index to start iterating, on return, index where iterator stoped */ + int idx = 0; /* scale index to start iterating, on return, index where iterator stopped */ - /* iterate trough all the dimensions */ + /* iterate through all the dimensions */ for (dim = 0; dim < (unsigned)rank; dim++) { if ((match_size = H5DSiterate_scales(did, dim, &idx, match_dim_scale, NULL)) < 0) goto out; @@ -3474,9 +3475,9 @@ test_simple(void) goto out; { int match_size; /* does this scale size matches the dataset DIM size */ - int idx; /* scale index to start iterating, on return, index where iterator stoped */ + int idx; /* scale index to start iterating, on return, index where iterator stopped */ - /* iterate trough all the dimensions */ + /* iterate through all the dimensions */ for (dim = 0; dim < (unsigned)rank; dim++) { /* always start at 1st scale */ idx = 0; @@ -4024,7 +4025,7 @@ test_errors(void) PASSED(); /*------------------------------------------------------------------------- - * try to attach a scale to an image, pallete or table + * try to attach a scale to an image, palette or table *------------------------------------------------------------------------- */ @@ -4035,7 +4036,7 @@ test_errors(void) goto out; /* make a palette */ - if (H5IMmake_palette(fid, "pallete", pal_dims, NULL) < 0) + if (H5IMmake_palette(fid, "palette", pal_dims, NULL) < 0) goto out; /* open the previous written "ds_b" */ @@ -4247,7 +4248,7 @@ test_iterators(void) if ((did = H5Dopen2(fid, "dset_a", H5P_DEFAULT)) < 0) goto out; - /* try to iterate trough the 1st dimension of "dset_a", return error */ + /* try to iterate through the 1st dimension of "dset_a", return error */ if (H5DSiterate_scales(did, 0, NULL, verify_scale, NULL) < 0) goto out; @@ -4268,7 +4269,7 @@ test_iterators(void) if ((did = H5Dopen2(fid, "dset_a", H5P_DEFAULT)) < 0) goto out; - /* try to iterate trough the 3rd dimension of "dset_a", return error */ + /* try to iterate through the 3rd dimension of "dset_a", return error */ if (H5DSiterate_scales(did, 3, NULL, verify_scale, NULL) == SUCCEED) goto out; @@ -4305,7 +4306,7 @@ test_iterators(void) goto out; } - /* iterate trough the 1st dimension of "dset_a" */ + /* iterate through the 1st dimension of "dset_a" */ if (H5DSiterate_scales(did, 0, NULL, op_continue, NULL) < 0) goto out; diff --git a/hl/test/test_ds_be_new_ref-32bit.h5 b/hl/test/test_ds_be_new_ref-32bit.h5 Binary files differnew file mode 100644 index 0000000..ee327e9 --- /dev/null +++ b/hl/test/test_ds_be_new_ref-32bit.h5 diff --git a/hl/test/test_ds_be_new_ref.h5 b/hl/test/test_ds_be_new_ref.h5 Binary files differnew file mode 100644 index 0000000..eddfa02 --- /dev/null +++ b/hl/test/test_ds_be_new_ref.h5 diff --git a/hl/test/test_ds_le_new_ref.h5 b/hl/test/test_ds_le_new_ref.h5 Binary files differnew file mode 100644 index 0000000..8625d77 --- /dev/null +++ b/hl/test/test_ds_le_new_ref.h5 diff --git a/hl/test/test_file_image.c b/hl/test/test_file_image.c index bde8adc..4448e41 100644 --- a/hl/test/test_file_image.c +++ b/hl/test/test_file_image.c @@ -109,12 +109,13 @@ test_file_image(size_t open_images, size_t nflags, const unsigned *flags) input_flags[i] = flags[(nflags + i) % nflags]; /* allocate name buffer for image i */ - filename[i] = (char *)HDmalloc(sizeof(char) * 32); + size_t filenamelength = sizeof(char) * 32; + filename[i] = (char *)HDmalloc(filenamelength); if (!filename[i]) FAIL_PUTS_ERROR("HDmalloc() failed"); /* create file name */ - HDsprintf(filename[i], "image_file%d.h5", (int)i); + HDsnprintf(filename[i], filenamelength, "image_file%d.h5", (int)i); /* create file */ if ((file_id[i] = H5Fcreate(filename[i], H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT)) < 0) @@ -243,7 +244,7 @@ test_file_image(size_t open_images, size_t nflags, const unsigned *flags) */ HDmemset((uint8_t *)tmp_ptr + SUPER_STATUS_FLAGS_OFF_V0_V1, (int)0, (size_t)SUPER_STATUS_FLAGS_SIZE_V0_V1); - /* Does the comparision */ + /* Does the comparison */ if (HDmemcmp(tmp_ptr, buf_ptr[i], (size_t)buf_size[i]) != 0) FAIL_PUTS_ERROR("comparison of TMP vfd and user buffer failed"); /* Free the temporary buffer */ diff --git a/hl/test/test_h5do_compat.c b/hl/test/test_h5do_compat.c index c554ae7..6f19d4b 100644 --- a/hl/test/test_h5do_compat.c +++ b/hl/test/test_h5do_compat.c @@ -31,7 +31,7 @@ * * Purpose: Test the basic functionality of H5DOwrite_chunk * - * Return: Success: An identifer for the dataset used in the tests + * Return: Success: An identifier for the dataset used in the tests * Failure: H5I_INVALID_HID * *------------------------------------------------------------------------- diff --git a/hl/test/test_image.c b/hl/test/test_image.c index 81340c1..4997df6 100644 --- a/hl/test/test_image.c +++ b/hl/test/test_image.c @@ -219,7 +219,7 @@ test_simple(void) *------------------------------------------------------------------------- */ - HL_TESTING2("pallete functions"); + HL_TESTING2("palette functions"); if (H5IMget_npalettes(fid, IMAGE1_NAME, &npals) < 0) goto out; @@ -422,7 +422,7 @@ test_data(void) /*------------------------------------------------------------------------- * palette #4. blue-red - * make a palette whith blue to red colors + * make a palette with blue to red colors *------------------------------------------------------------------------- */ for (i = 0, n = 0; i < 256 * 3; i += 3, n++) { @@ -650,7 +650,7 @@ test_generate(void) HL_TESTING2("make indexed image from land data"); for (i = 0; i < n_elements; i++) { - if (data[i] < 0.0f) + if (data[i] < 0.0F) image_data[i] = 0; else image_data[i] = (unsigned char)((255 * data[i]) / xmax); @@ -671,10 +671,10 @@ test_generate(void) HL_TESTING2("make indexed image from sea data"); for (i = 0; i < n_elements; i++) { - if (data[i] > 0.0f) + if (data[i] > 0.0F) image_data[i] = 0; else { - image_data[i] = (unsigned char)((255.0f * (data[i] - xmin)) / (xmax - xmin)); + image_data[i] = (unsigned char)((255.0F * (data[i] - xmin)) / (xmax - xmin)); } } diff --git a/hl/test/test_ld.c b/hl/test/test_ld.c index dc5755c..150d04c 100644 --- a/hl/test/test_ld.c +++ b/hl/test/test_ld.c @@ -189,7 +189,7 @@ typedef struct set_t { * This will fail on heiwa and amani when VALID_FIELDS1 is "field1,field3,field4" * because of alignment problems: * amani and heiwa - 8 byte alignment - * jam - 4 byte alignemnt + * jam - 4 byte alignment * This will need to be fixed in the library for H5Tget_native_type(). */ /* VALID_FIELDS1 "field1,field2.a,field3,field4" */ @@ -213,8 +213,8 @@ typedef struct test_valid_fields2 { #define TEST_BUF_SIZE 100 int * iibuf; /* buffer for storing retrieved elements */ int * ibuf; /* buffer for storing retrieved elements (integer) */ -set_t * cbuf; /* buffer for storing retrieved elemnets (compound) */ -set_t * ccbuf; /* buffer for storing retrieved elemnets (compound) */ +set_t * cbuf; /* buffer for storing retrieved elements (compound) */ +set_t * ccbuf; /* buffer for storing retrieved elements (compound) */ test_valid_fields1 *vbuf1; /* buffer for storing retrieved elements (FIELDS1) */ test_valid_fields2 *vbuf2; /* buffer for storing retrieved elements (FIELDS2) */ diff --git a/hl/test/test_packet.c b/hl/test/test_packet.c index 5f30d4b..e8b90f7 100644 --- a/hl/test/test_packet.c +++ b/hl/test/test_packet.c @@ -47,7 +47,7 @@ typedef struct particle_t { */ static particle_t testPart[NRECORDS] = {{"zero", 0, 0, 0.0F, 0.0}, {"one", 10, 10, 1.0F, 10.0}, {"two", 20, 20, 2.0F, 20.0}, {"three", 30, 30, 3.0F, 30.0}, - {"Four", 40, 40, 4.0F, 40.0}, {"Five", 50, 50, 5.0F, 50.0}, + {"four", 40, 40, 4.0F, 40.0}, {"five", 50, 50, 5.0F, 50.0}, {"six", 60, 60, 6.0F, 60.0}, {"seven", 70, 70, 7.0F, 70.0}}; /*------------------------------------------------------------------------- diff --git a/hl/test/test_packet_vlen.c b/hl/test/test_packet_vlen.c index c668a07..aa88a6c 100644 --- a/hl/test/test_packet_vlen.c +++ b/hl/test/test_packet_vlen.c @@ -109,7 +109,7 @@ test_VLof_atomic(void) if (ret < 0) goto error; - HDsprintf(msg, "The number of packets in the packet table must be %u\n", NRECORDS); + HDsnprintf(msg, sizeof(msg), "The number of packets in the packet table must be %u\n", NRECORDS); VERIFY(count == NRECORDS, msg); /* Read all five packets back */ @@ -246,7 +246,7 @@ test_VLof_comptype(void) if (ret < 0) goto error; - HDsprintf(msg, "The number of packets in the packet table must be %u\n", NRECORDS); + HDsnprintf(msg, sizeof(msg), "The number of packets in the packet table must be %u\n", NRECORDS); VERIFY(count == NRECORDS, msg); /* Read all five packets back */ @@ -418,7 +418,7 @@ test_compound_VL_VLtype(void) if (ret < 0) goto error; - HDsprintf(msg, "The number of packets in the packet table must be %u\n", NRECORDS); + HDsnprintf(msg, sizeof(msg), "The number of packets in the packet table must be %u\n", NRECORDS); VERIFY(count == NRECORDS, msg); /* Read all five packets back */ @@ -539,8 +539,8 @@ test_VLof_VLtype(void) HDfprintf(stderr, "Cannot allocate memory for VL data! uu=%u\n", uu); goto error; } - t1->len = vv * 1; - for (ww = 0; ww < (vv * 1); ww++) + t1->len = vv + 1; + for (ww = 0; ww < (vv + 1); ww++) ((unsigned int *)t1->p)[ww] = uu * 100 + vv * 10 + ww; } /* end for */ } /* end for */ @@ -582,7 +582,7 @@ test_VLof_VLtype(void) if (ret < 0) goto error; - HDsprintf(msg, "The number of packets in the packet table must be %u\n", NRECORDS); + HDsnprintf(msg, sizeof(msg), "The number of packets in the packet table must be %u\n", NRECORDS); VERIFY(count == NRECORDS, msg); /* Read all five packets back */ @@ -677,7 +677,7 @@ error: /* An error has occurred. Clean up and exit. */ * * Description: * - Added a fixed-length packet table to the file for variety - * - Use the helper funtion verify_ptlengthtype to test H5PTis_varlen + * - Use the helper function verify_ptlengthtype to test H5PTis_varlen * on each packet table. * * 2016/01/27 -BMR @@ -1144,7 +1144,7 @@ testfl_VLof_atomic(void) if (ret < 0) goto error; - HDsprintf(msg, "The number of packets in the packet table must be %u\n", NRECORDS); + HDsnprintf(msg, sizeof(msg), "The number of packets in the packet table must be %u\n", NRECORDS); VERIFY(count == NRECORDS, msg); /* Read all five packets back */ @@ -1281,7 +1281,7 @@ testfl_VLof_comptype(void) if (ret < 0) goto error; - HDsprintf(msg, "The number of packets in the packet table must be %u\n", NRECORDS); + HDsnprintf(msg, sizeof(msg), "The number of packets in the packet table must be %u\n", NRECORDS); VERIFY(count == NRECORDS, msg); /* Read all five packets back */ @@ -1453,7 +1453,7 @@ testfl_compound_VL_VLtype(void) if (ret < 0) goto error; - HDsprintf(msg, "The number of packets in the packet table must be %u\n", NRECORDS); + HDsnprintf(msg, sizeof(msg), "The number of packets in the packet table must be %u\n", NRECORDS); VERIFY(count == NRECORDS, msg); /* Read all five packets back */ @@ -1617,7 +1617,7 @@ testfl_VLof_VLtype(void) if (ret < 0) goto error; - HDsprintf(msg, "The number of packets in the packet table must be %u\n", NRECORDS); + HDsnprintf(msg, sizeof(msg), "The number of packets in the packet table must be %u\n", NRECORDS); VERIFY(count == NRECORDS, msg); /* Read all five packets back */ diff --git a/hl/test/test_table.c b/hl/test/test_table.c index 6199e27..90a930c 100644 --- a/hl/test/test_table.c +++ b/hl/test/test_table.c @@ -1464,7 +1464,7 @@ test_table(hid_t fid, int do_write) HL_TESTING2("getting field info"); - /* alocate */ + /* allocate */ names_out = (char **)HDmalloc(sizeof(char *) * (size_t)NFIELDS); for (i = 0; i < NFIELDS; i++) { names_out[i] = (char *)HDmalloc(sizeof(char) * 255); diff --git a/hl/tools/gif2h5/decompress.c b/hl/tools/gif2h5/decompress.c index 64d9643..ca33f86 100644 --- a/hl/tools/gif2h5/decompress.c +++ b/hl/tools/gif2h5/decompress.c @@ -178,7 +178,7 @@ Decompress(GIFIMAGEDESC *GifImageDesc, GIFHEAD *GifHead) DataMask = (1 << ((GifHead->PackedField & 0x07) + 1)) - 1; Raster = GifImageDesc->GIFImage; - /* Check for image seperator */ + /* Check for image separator */ /* Now read in values from the image descriptor */ IWidth = GifImageDesc->ImageWidth; @@ -193,7 +193,7 @@ Decompress(GIFIMAGEDESC *GifImageDesc, GIFHEAD *GifHead) */ /* - * Start reading the raster data. First we get the intial code size and + * Start reading the raster data. First we get the initial code size and * compute decompressor constant values, based on this code size. */ diff --git a/hl/tools/gif2h5/gif.h b/hl/tools/gif2h5/gif.h index 1a8cfe4..5ea8633 100644 --- a/hl/tools/gif2h5/gif.h +++ b/hl/tools/gif2h5/gif.h @@ -129,7 +129,7 @@ typedef struct _GifCommentExtension { ** in the HDF file. ** I have assumed that the ImageDescriptors and GraphicControls follow ** one another, ie. I have not associated them with each other. The driver -** must assume a 1-1 correspondance. The same discussion with plain text +** must assume a 1-1 correspondence. The same discussion with plain text ** extension. */ typedef struct _GifToMem { diff --git a/hl/tools/gif2h5/gif2mem.c b/hl/tools/gif2h5/gif2mem.c index c66250b..44e18e0 100644 --- a/hl/tools/gif2h5/gif2mem.c +++ b/hl/tools/gif2h5/gif2mem.c @@ -40,7 +40,7 @@ Gif2Mem(GIFBYTE *MemGif, GIFTOMEM *GifMemoryStruct) { /* * The gif structure outline for passing data to memory is given in gif.h. - * These pointers are redunant, should take them out in ver. 2 + * These pointers are redundant, should take them out in ver. 2 */ GIFHEAD * gifHead; /* GIF Header structure */ GIFIMAGEDESC ** gifImageDesc; /* Logical Image Descriptor struct */ @@ -49,22 +49,22 @@ Gif2Mem(GIFBYTE *MemGif, GIFTOMEM *GifMemoryStruct) GIFCOMMENT ** gifComment; /* Comment Extension structure */ GIFGRAPHICCONTROL **gifGraphicControl; /* Graphic Control Extension strct */ - register GIFWORD i; /* Loop counter */ - GIFBYTE Identifier; /* Extension block identifier holder */ - GIFBYTE Label; /* Extension block label holder */ - GIFBYTE ImageCount; /* Count of the number of images in the file */ - GIFBYTE ImageArray; /* Keep the size of the array to store Images */ - GIFBYTE CommentCount; - GIFBYTE CommentArray; - GIFBYTE ApplicationCount; - GIFBYTE ApplicationArray; - GIFBYTE PlainTextCount; - GIFBYTE PlainTextArray; - GIFBYTE GCEflag; - GIFBYTE aTemp; - GIFBYTE j; - GIFBYTE w; /* Two more variables needed only while testing */ - GIFBYTE * b; /* Endian Ordering */ + GIFWORD i; /* Loop counter */ + GIFBYTE Identifier; /* Extension block identifier holder */ + GIFBYTE Label; /* Extension block label holder */ + GIFBYTE ImageCount; /* Count of the number of images in the file */ + GIFBYTE ImageArray; /* Keep the size of the array to store Images */ + GIFBYTE CommentCount; + GIFBYTE CommentArray; + GIFBYTE ApplicationCount; + GIFBYTE ApplicationArray; + GIFBYTE PlainTextCount; + GIFBYTE PlainTextArray; + GIFBYTE GCEflag; + GIFBYTE aTemp; + GIFBYTE j; + GIFBYTE w; /* Two more variables needed only while testing */ + GIFBYTE *b; /* Endian Ordering */ /* Allocate memory for the GIF structures */ /* Plug the structs into GifMemoryStruct at the end */ diff --git a/hl/tools/gif2h5/gifread.c b/hl/tools/gif2h5/gifread.c index dd9e5be..3a6bcae 100644 --- a/hl/tools/gif2h5/gifread.c +++ b/hl/tools/gif2h5/gifread.c @@ -50,15 +50,15 @@ GetByte(const GIFBYTE *MemGif) * Global Color Table (if any) from a GIF image file. The information * is stored in a GIFHEAD structure. * - * Returns: -1 if a FILE stream error occured during the read, - * otherwise 0 if no error occured. + * Returns: -1 if a FILE stream error occurred during the read, + * otherwise 0 if no error occurred. */ int ReadGifHeader(GIFHEAD * GifHead, /* Pointer to GIF header structure */ GIFBYTE **MemGif2) /* GIF image file input FILE stream */ { GIFWORD i; /* Loop counter */ - GIFWORD tableSize; /* Number of entires in the Global Color Table */ + GIFWORD tableSize; /* Number of entries in the Global Color Table */ GifHead->TableSize = 0; for (i = 0; i < 6; i++) { @@ -103,7 +103,7 @@ ReadGifHeader(GIFHEAD * GifHead, /* Pointer to GIF header structure */ return -1; #endif /* 0 */ - return 0; /* No FILE stream error occured */ + return 0; /* No FILE stream error occurred */ } /* @@ -116,8 +116,8 @@ ReadGifHeader(GIFHEAD * GifHead, /* Pointer to GIF header structure */ ** Note that the ImageSeparator field value in the GIFIMAGEDESC ** structure is assigned by the function calling ReadGifImageDesc(). ** -** Returns: -1 if a FILE stream error occured during the read, -** otherwise 0 if no error occured. +** Returns: -1 if a FILE stream error occurred during the read, +** otherwise 0 if no error occurred. */ int ReadGifImageDesc(GIFIMAGEDESC *GifImageDesc, /* Pointer to GIF image descriptor structure */ @@ -196,7 +196,7 @@ ReadGifImageDesc(GIFIMAGEDESC *GifImageDesc, /* Pointer to GIF image descriptor *TempPtr++ = *(*MemGif2)++; } while (ch1); - return (0); /* No FILE stream error occured */ + return (0); /* No FILE stream error occurred */ } /* @@ -205,8 +205,8 @@ ReadGifImageDesc(GIFIMAGEDESC *GifImageDesc, /* Pointer to GIF image descriptor ** Note that the Introducer and Label field values in the GIFGRAPHICCONTROL ** structure are assigned by the function calling ReadGifGraphicControl(). ** -** Returns: -1 if a FILE stream error occured during the read, -** otherwise 0 if no error occured. +** Returns: -1 if a FILE stream error occurred during the read, +** otherwise 0 if no error occurred. */ int ReadGifGraphicControl(GIFGRAPHICCONTROL *GifGraphicControl, /* Pointer to GC Extension structure */ @@ -219,7 +219,7 @@ ReadGifGraphicControl(GIFGRAPHICCONTROL *GifGraphicControl, /* Pointer to GC Ext GifGraphicControl->GCEDump[i] = *(*MemGif2)++; } - return (0); /* No FILE stream error occured */ + return (0); /* No FILE stream error occurred */ } /* @@ -228,8 +228,8 @@ ReadGifGraphicControl(GIFGRAPHICCONTROL *GifGraphicControl, /* Pointer to GC Ext ** Note that the Introducer and Label field values in the GIFLPLAINTEXT ** structure are assigned by the function calling ReadGifPlainText(). ** -** Returns: -1 if a FILE stream error occured during the read, -** otherwise 0 if no error occured. +** Returns: -1 if a FILE stream error occurred during the read, +** otherwise 0 if no error occurred. */ int ReadGifPlainText(GIFPLAINTEXT *GifPlainText, /* Pointer to Plain Text Extension structure */ @@ -256,7 +256,7 @@ ReadGifPlainText(GIFPLAINTEXT *GifPlainText, /* Pointer to Plain Text Extension return(-1); */ - return (0); /* No FILE stream error occured */ + return (0); /* No FILE stream error occurred */ } /* @@ -265,8 +265,8 @@ ReadGifPlainText(GIFPLAINTEXT *GifPlainText, /* Pointer to Plain Text Extension ** Note that the Introducer and Label field values in the GIFAPPLICATION ** structure are assigned by the function calling ReadGifApplication(). ** -** Returns: -1 if a FILE stream error occured during the read, -** otherwise 0 if no error occured. +** Returns: -1 if a FILE stream error occurred during the read, +** otherwise 0 if no error occurred. */ int ReadGifApplication(GIFAPPLICATION *GifApplication, /* Pointer to Application Extension structure */ @@ -292,7 +292,7 @@ ReadGifApplication(GIFAPPLICATION *GifApplication, /* Pointer to Application Ext return(-1); */ - return (0); /* No FILE stream error occured */ + return (0); /* No FILE stream error occurred */ } /* @@ -301,8 +301,8 @@ ReadGifApplication(GIFAPPLICATION *GifApplication, /* Pointer to Application Ext ** Note that the Introducer and Label field values in the GIFCOMMENT ** structure are assigned by the function calling ReadGifComment(). ** -** Returns: -1 if a FILE stream error occured during the read, -** otherwise 0 if no error occured. +** Returns: -1 if a FILE stream error occurred during the read, +** otherwise 0 if no error occurred. */ int ReadGifComment(GIFCOMMENT *GifComment, /* Pointer to GIF Comment Extension structure */ @@ -316,7 +316,7 @@ ReadGifComment(GIFCOMMENT *GifComment, /* Pointer to GIF Comment Extension struc GifComment->Terminator = 0; - return (0); /* No FILE stream error occured */ + return (0); /* No FILE stream error occurred */ } /* @@ -326,8 +326,8 @@ ReadGifComment(GIFCOMMENT *GifComment, /* Pointer to GIF Comment Extension struc ** A GIF "sub-block" is a single count byte followed by 1 to 255 ** additional data bytes. ** -** Returns: A NULL pointer if a memory allocation error occured, -** otherwise a valid pointer if no error occured. +** Returns: A NULL pointer if a memory allocation error occurred, +** otherwise a valid pointer if no error occurred. */ static GIFBYTE * ReadDataSubBlocks(GIFBYTE **MemGif2, /* GIF image file input FILE stream */ @@ -364,7 +364,7 @@ ReadDataSubBlocks(GIFBYTE **MemGif2, /* GIF image file input FILE stream if ((dataSize = *(*MemGif2)++) == 0) break; /* Block Terminator encountered */ - /* Increase the buffer size to accomodate the next sub-block */ + /* Increase the buffer size to accommodate the next sub-block */ if (!(ptr1 = ptr2 = (GIFBYTE *)realloc(ptr2, bufSize + dataSize + 1))) return ((GIFBYTE *)NULL); diff --git a/hl/tools/gif2h5/h52giftest.sh.in b/hl/tools/gif2h5/h52giftest.sh.in index 2f84ef6..4f4057f 100644 --- a/hl/tools/gif2h5/h52giftest.sh.in +++ b/hl/tools/gif2h5/h52giftest.sh.in @@ -46,7 +46,7 @@ TOOLTEST() # Verify the test runs with failure (return code is not 0) # Use for testing if tool can handle error conditions like -# illegal input, bad arguments, exeeding limits, ... +# illegal input, bad arguments, exceeding limits, ... TOOLTESTFAIL() { # for now, discard any error messages generated. diff --git a/hl/tools/gif2h5/hdfgifwr.c b/hl/tools/gif2h5/hdfgifwr.c index 21b14d1..7126da9 100644 --- a/hl/tools/gif2h5/hdfgifwr.c +++ b/hl/tools/gif2h5/hdfgifwr.c @@ -188,13 +188,13 @@ hdfWriteGIF(FILE *fp, byte *pic, int ptype, int w, int h, const byte *rmap, cons static void compress(int init_bits, FILE *outfile, byte *data, int len) { - register long fcode; - register int i = 0; - register int c; - register int ent; - register int disp; - register int hsize_reg; - register int hshift; + long fcode; + int i = 0; + int c; + int ent; + int disp; + int hsize_reg; + int hshift; /* * Set up the globals: g_init_bits - initial number of bits g_outfile - diff --git a/hl/tools/gif2h5/writehdf.c b/hl/tools/gif2h5/writehdf.c index 6ec6af4..b49e2a6 100644 --- a/hl/tools/gif2h5/writehdf.c +++ b/hl/tools/gif2h5/writehdf.c @@ -27,7 +27,7 @@ * Programmer: Unknown * * Modifications: pvn - * Use the HDF5 IMAGE API to write the HDF5 image and pallete + * Use the HDF5 IMAGE API to write the HDF5 image and palette * * Date: January, 31, 2006 * @@ -68,7 +68,7 @@ WriteHDF(GIFTOMEM GifMemoryStruct, char *HDFName) #endif /* UNUSED */ if ((file_id = H5Fcreate(HDFName, H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT)) < 0) { - /* error occured opening the HDF File for write */ + /* error occurred opening the HDF File for write */ fprintf(stderr, "HDF file could not be opened for writing\n"); fprintf(stderr, "NOTE: GIF file must be present in the same directory as the binary on UNIX systems.\n"); @@ -100,7 +100,7 @@ WriteHDF(GIFTOMEM GifMemoryStruct, char *HDFName) dims[1] = gifImageDesc->ImageWidth; /* create the image name */ - sprintf(ImageName, "Image%d", i); + snprintf(ImageName, sizeof(ImageName), "Image%d", i); /* write image */ if (H5IMmake_image_8bit(file_id, ImageName, dims[1], dims[0], (gifImageDesc->Image)) < 0) diff --git a/hl/tools/h5watch/CMakeLists.txt b/hl/tools/h5watch/CMakeLists.txt index be983ba..1ab473d 100644 --- a/hl/tools/h5watch/CMakeLists.txt +++ b/hl/tools/h5watch/CMakeLists.txt @@ -40,29 +40,6 @@ if (HDF5_ENABLE_FORMATTERS) endif () if (BUILD_TESTING AND HDF5_TEST_SWMR AND HDF5_TEST_SERIAL) - #-- Add swmr_check_compat_vfd program - set (hl_swmr_check_compat_vfd_SOURCES - ${HDF5_HL_TOOLS_H5WATCH_SOURCE_DIR}/swmr_check_compat_vfd.c - ) - add_executable (hl_swmr_check_compat_vfd ${hl_swmr_check_compat_vfd_SOURCES}) - target_compile_options(hl_swmr_check_compat_vfd PRIVATE "${HDF5_CMAKE_C_FLAGS}") - target_include_directories (hl_swmr_check_compat_vfd PRIVATE "${HDF5_SRC_DIR};${HDF5_SRC_BINARY_DIR};$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:${MPI_C_INCLUDE_DIRS}>") - if (NOT ONLY_SHARED_LIBS) - TARGET_C_PROPERTIES (hl_swmr_check_compat_vfd STATIC) - target_link_libraries (hl_swmr_check_compat_vfd PRIVATE ${HDF5_LIB_TARGET}) - else () - TARGET_C_PROPERTIES (hl_swmr_check_compat_vfd SHARED) - target_link_libraries (hl_swmr_check_compat_vfd PRIVATE ${HDF5_LIBSH_TARGET}) - endif () - set_target_properties (hl_swmr_check_compat_vfd PROPERTIES FOLDER tools/hl) - - #----------------------------------------------------------------------------- - # Add Target to clang-format - #----------------------------------------------------------------------------- - if (HDF5_ENABLE_FORMATTERS) - clang_format (HDF5_HL_TOOLS_H5WATCH_hl_swmr_check_compat_vfd_FORMAT hl_swmr_check_compat_vfd) - endif () - #-- Add extend_dset program set (extend_dset_SOURCES ${HDF5_HL_TOOLS_H5WATCH_SOURCE_DIR}/extend_dset.c diff --git a/hl/tools/h5watch/CMakeTests.cmake b/hl/tools/h5watch/CMakeTests.cmake index 60c099b..b2f689b 100644 --- a/hl/tools/h5watch/CMakeTests.cmake +++ b/hl/tools/h5watch/CMakeTests.cmake @@ -149,18 +149,22 @@ add_custom_target(H5WATCH_files ALL COMMENT "Copying files needed by H5WATCH tes # Check to see if the VFD specified by the HDF5_DRIVER environment variable # supports SWMR. -set (SWMR_INCOMPAT ${hl_swmr_check_compat_vfd}) +add_test ( + NAME H5WATCH-SWMR_INCOMPAT + COMMAND swmr_check_compat_vfd +) +set_tests_properties (H5WATCH-SWMR_INCOMPAT PROPERTIES FIXTURES_SETUP swmr_vfd_check_compat) -if (NOT SWMR_INCOMPAT) # Remove any output file left over from previous test run - add_test ( - NAME H5WATCH-clearall-objects - COMMAND ${CMAKE_COMMAND} -E remove WATCH.h5 - ) - if (last_test) - set_tests_properties (H5WATCH-clearall-objects PROPERTIES DEPENDS ${last_test}) - endif () - set (last_test "H5WATCH-clearall-objects") +add_test ( + NAME H5WATCH-clearall-objects + COMMAND ${CMAKE_COMMAND} -E remove WATCH.h5 +) +set_tests_properties (H5WATCH-clearall-objects PROPERTIES FIXTURES_REQUIRED swmr_vfd_check_compat) +if (last_test) + set_tests_properties (H5WATCH-clearall-objects PROPERTIES DEPENDS ${last_test}) +endif () +set (last_test "H5WATCH-clearall-objects") ################################################################################################# # # @@ -182,32 +186,32 @@ if (NOT SWMR_INCOMPAT) # # ################################################################################################# # create the output files to be used. - add_test (NAME H5WATCH-h5watchgentest COMMAND ${CMAKE_CROSSCOMPILING_EMULATOR} $<TARGET_FILE:h5watchgentest>) - set_tests_properties (H5WATCH-h5watchgentest PROPERTIES - WORKING_DIRECTORY "${PROJECT_BINARY_DIR}/testfiles" - DEPENDS "H5WATCH-clearall-objects" - ) - set_tests_properties (H5WATCH-h5watchgentest PROPERTIES FIXTURES_SETUP gen_test_watch) - set (last_test "H5WATCH-h5watchgentest") +add_test (NAME H5WATCH-h5watchgentest COMMAND ${CMAKE_CROSSCOMPILING_EMULATOR} $<TARGET_FILE:h5watchgentest>) +set_tests_properties (H5WATCH-h5watchgentest PROPERTIES + WORKING_DIRECTORY "${PROJECT_BINARY_DIR}/testfiles" + DEPENDS "H5WATCH-clearall-objects" +) +set_tests_properties (H5WATCH-h5watchgentest PROPERTIES FIXTURES_SETUP gen_test_watch) +set_tests_properties (H5WATCH-h5watchgentest PROPERTIES FIXTURES_REQUIRED swmr_vfd_check_compat) +set (last_test "H5WATCH-h5watchgentest") # Test on --help options - ADD_H5_TEST (w-help1 0 --help) +ADD_H5_TEST (w-help1 0 --help) # # Tests on expected failures - ADD_H5_ERR_TEST (w-err-dset1 1 WATCH.h5) - ADD_H5_ERR_TEST (w-err-dset2 1 WATCH.h5/group/DSET_CMPD) - ADD_H5_ERR_TEST (w-err-dset-none 1 WATCH.h5/DSET_NONE) - ADD_H5_ERR_TEST (w-err-dset-nomax 1 WATCH.h5/DSET_NOMAX) - ADD_H5_ERR_TEST (w-err-file 1 ../WATCH.h5/DSET_CMPD) - ADD_H5_TEST (w-err-width 1 --width=-8 WATCH.h5/DSET_ONE) - ADD_H5_TEST (w-err-poll 1 --polling=-8 WATCH.h5/DSET_ONE) - ADD_H5_TEST (w-err-poll0 1 --polling=0 WATCH.h5/DSET_ONE) +ADD_H5_ERR_TEST (w-err-dset1 1 WATCH.h5) +ADD_H5_ERR_TEST (w-err-dset2 1 WATCH.h5/group/DSET_CMPD) +ADD_H5_ERR_TEST (w-err-dset-none 1 WATCH.h5/DSET_NONE) +ADD_H5_ERR_TEST (w-err-dset-nomax 1 WATCH.h5/DSET_NOMAX) +ADD_H5_ERR_TEST (w-err-file 1 ../WATCH.h5/DSET_CMPD) +ADD_H5_TEST (w-err-width 1 --width=-8 WATCH.h5/DSET_ONE) +ADD_H5_TEST (w-err-poll 1 --polling=-8 WATCH.h5/DSET_ONE) +ADD_H5_TEST (w-err-poll0 1 --polling=0 WATCH.h5/DSET_ONE) # # Tests on invalid field names via --fields option for a compound typed dataset: DSET_CMPD - ADD_H5_ERR_TEST (w-err-cmpd1 1 --fields=fieldx WATCH.h5/DSET_CMPD) - ADD_H5_ERR_TEST (w-err-cmpd2 1 --fields=field1,field2. WATCH.h5/DSET_CMPD) - ADD_H5_ERR_TEST (w-err-cmpd3 1 --fields=field1,field2, WATCH.h5/DSET_CMPD) - ADD_H5_ERR_TEST (w-err-cmpd4 1 --fields=field1,field2.b.k WATCH.h5/DSET_CMPD) - ADD_H5_ERR_TEST (w-err-cmpd5 1 --fields=field1 --fields=field2.b.k WATCH.h5/DSET_CMPD) +ADD_H5_ERR_TEST (w-err-cmpd1 1 --fields=fieldx WATCH.h5/DSET_CMPD) +ADD_H5_ERR_TEST (w-err-cmpd2 1 --fields=field1,field2. WATCH.h5/DSET_CMPD) +ADD_H5_ERR_TEST (w-err-cmpd3 1 --fields=field1,field2, WATCH.h5/DSET_CMPD) +ADD_H5_ERR_TEST (w-err-cmpd4 1 --fields=field1,field2.b.k WATCH.h5/DSET_CMPD) +ADD_H5_ERR_TEST (w-err-cmpd5 1 --fields=field1 --fields=field2.b.k WATCH.h5/DSET_CMPD) # -endif () diff --git a/hl/tools/h5watch/Makefile.am b/hl/tools/h5watch/Makefile.am index 5112965..13bd820 100644 --- a/hl/tools/h5watch/Makefile.am +++ b/hl/tools/h5watch/Makefile.am @@ -24,7 +24,6 @@ AM_CPPFLAGS+=-I$(top_srcdir)/src -I$(top_srcdir)/tools/lib -I$(top_srcdir)/hl/sr # These are our main targets, the tools bin_PROGRAMS=h5watch -noinst_PROGRAMS=swmr_check_compat_vfd # Add h5watch specific linker flags here h5watch_LDFLAGS = $(LT_STATIC_EXEC) $(AM_LDFLAGS) @@ -38,7 +37,7 @@ if BUILD_TESTS_CONDITIONAL TEST_SCRIPT=testh5watch.sh check_SCRIPTS=$(TEST_SCRIPT) SCRIPT_DEPEND=swmr_check_compat_vfd$(EXEEXT) extend_dset$(EXEEXT) h5watch$(EXEEXT) - noinst_PROGRAMS+=h5watchgentest extend_dset + noinst_PROGRAMS=h5watchgentest extend_dset # Add extend_dset specific preprocessor flags here # (add the main test subdirectory to the include file path) extend_dset_CPPFLAGS=$(AM_CPPFLAGS) -I$(top_srcdir)/test diff --git a/hl/tools/h5watch/extend_dset.c b/hl/tools/h5watch/extend_dset.c index 282f5c2..7756506 100644 --- a/hl/tools/h5watch/extend_dset.c +++ b/hl/tools/h5watch/extend_dset.c @@ -83,7 +83,7 @@ extend_dset_two(const char *file, char *dname, int action1, int action2) size_t dtype_size; /* size of the dataset's datatype */ unsigned num_elmts; /* number of elements in the dataset */ int * ibuf = NULL; /* buffer for storing retrieved elements (integer) */ - set_t * cbuf = NULL; /* buffer for storing retrieved elemnets (compound) */ + set_t * cbuf = NULL; /* buffer for storing retrieved elements (compound) */ /* Allocate memory */ if (NULL == (ibuf = (int *)HDcalloc(TEST_BUF_SIZE, sizeof(int)))) @@ -237,7 +237,7 @@ extend_dset_one(const char *file, char *dname, int action) hsize_t count[1]; /* dimension sizes of appended data */ size_t dtype_size; /* size of the dataset's datatype */ int * ibuf = NULL; /* buffer for storing retrieved elements (integer) */ - set_t * cbuf = NULL; /* buffer for storing retrieved elemnets (compound) */ + set_t * cbuf = NULL; /* buffer for storing retrieved elements (compound) */ /* Allocate memory */ if (NULL == (ibuf = (int *)HDcalloc(TEST_BUF_SIZE, sizeof(int)))) @@ -392,7 +392,7 @@ error: *********************************************************************** */ int -main(int argc, const char *argv[]) +main(int argc, char *argv[]) { char *dname = NULL; char *fname = NULL; diff --git a/hl/tools/h5watch/h5watch.c b/hl/tools/h5watch/h5watch.c index afbc31d..5a6fe6f 100644 --- a/hl/tools/h5watch/h5watch.c +++ b/hl/tools/h5watch/h5watch.c @@ -51,7 +51,7 @@ static herr_t process_cmpd_fields(hid_t fid, char *dsetname); static herr_t check_dataset(hid_t fid, char *dsetname); static void leave(int ret); static void usage(const char *prog); -static void parse_command_line(int argc, const char *argv[]); +static void parse_command_line(int argc, const char *const *argv); /* * Command-line options: The user can only specify long-named parameters. @@ -174,9 +174,9 @@ doprint(hid_t did, const hsize_t *start, const hsize_t *block, int rank) } /* end else */ /* Floating point types should display full precision */ - sprintf(fmt_float, "%%1.%dg", FLT_DIG); + snprintf(fmt_float, sizeof(fmt_float), "%%1.%dg", FLT_DIG); info.fmt_float = fmt_float; - sprintf(fmt_double, "%%1.%dg", DBL_DIG); + snprintf(fmt_double, sizeof(fmt_double), "%%1.%dg", DBL_DIG); info.fmt_double = fmt_double; info.dset_format = "DSET-%s "; @@ -665,7 +665,7 @@ usage(const char *prog) *------------------------------------------------------------------------- */ static void -parse_command_line(int argc, const char *argv[]) +parse_command_line(int argc, const char *const *argv) { int opt; /* Command line option */ int tmp; @@ -790,7 +790,7 @@ catch_signal(int H5_ATTR_UNUSED signo) *------------------------------------------------------------------------- */ int -main(int argc, const char *argv[]) +main(int argc, char *argv[]) { char drivername[50]; /* VFD name */ char *fname = NULL; /* File name */ @@ -819,7 +819,7 @@ main(int argc, const char *argv[]) } /* parse command line options */ - parse_command_line(argc, argv); + parse_command_line(argc, (const char *const *)argv); if (argc <= H5_optind) { error_msg("missing dataset name\n"); @@ -921,7 +921,7 @@ main(int argc, const char *argv[]) } } - /* If everything is fine, start monitoring the datset */ + /* If everything is fine, start monitoring the dataset */ if (h5tools_getstatus() != EXIT_FAILURE) if (monitor_dataset(fid, dname) < 0) h5tools_setstatus(EXIT_FAILURE); diff --git a/hl/tools/h5watch/swmr_check_compat_vfd.c b/hl/tools/h5watch/swmr_check_compat_vfd.c deleted file mode 100644 index a2340bf..0000000 --- a/hl/tools/h5watch/swmr_check_compat_vfd.c +++ /dev/null @@ -1,55 +0,0 @@ -/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * - * Copyright by The HDF Group. * - * Copyright by the Board of Trustees of the University of Illinois. * - * All rights reserved. * - * * - * This file is part of HDF5. The full HDF5 copyright notice, including * - * terms governing use, modification, and redistribution, is contained in * - * the COPYING file, which can be found at the root of the source code * - * distribution tree, or in https://www.hdfgroup.org/licenses. * - * If you do not have access to either file, you may request a copy from * - * help@hdfgroup.org. * - * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ - -/* Purpose: This is a small program that checks if the HDF5_DRIVER - * environment variable is set to a value that supports SWMR. - * - * It is intended for use in shell scripts. - */ - -#include <stdlib.h> - -#include "H5private.h" - -/* This file needs to access the file driver testing code */ -#define H5FD_FRIEND /*suppress error about including H5FDpkg */ -#define H5FD_TESTING -#include "H5FDpkg.h" /* File drivers */ - -/*------------------------------------------------------------------------- - * Function: main - * - * Purpose: Inspects the HDF5_DRIVER environment variable, which - * determines the VFD that the test harness will use with - * the majority of the tests. - * - * Return: VFD supports SWMR: EXIT_SUCCESS - * - * VFD does not support SWMR - * or failure: EXIT_FAILURE - * - *------------------------------------------------------------------------- - */ -int -main(void) -{ - char *driver = NULL; - - driver = HDgetenv("HDF5_DRIVER"); - - if (H5FD__supports_swmr_test(driver)) - return EXIT_SUCCESS; - else - return EXIT_FAILURE; - -} /* end main() */ diff --git a/hl/tools/h5watch/testh5watch.sh.in b/hl/tools/h5watch/testh5watch.sh.in index 67ffcc3..0432384 100644 --- a/hl/tools/h5watch/testh5watch.sh.in +++ b/hl/tools/h5watch/testh5watch.sh.in @@ -13,10 +13,11 @@ # # Tests for the h5watch tool # +utils_testdir=@abs_top_builddir@/@H5_UTILS_TEST_BUILDDIR@ # Check to see if the VFD specified by the HDF5_DRIVER environment variable # supports SWMR. -./swmr_check_compat_vfd +$utils_testdir/swmr_check_compat_vfd rc=$? if [ $rc != 0 ] ; then echo @@ -66,10 +67,6 @@ fi nerrors=0 verbose=yes -# The build (current) directory might be different than the source directory. -if test -z "$srcdir"; then - srcdir=. -fi test -d ../testfiles || mkdir ../testfiles # Print a line-line message left justified in a field of 70 characters |