19 #include "nc4internal.h"
20 #include "ncdispatch.h"
21 #include "hdf5internal.h"
23 #include "hdf5debug.h"
26 #ifdef HAVE_INTTYPES_H
27 #define __STDC_FORMAT_MACROS
31 #define NC_HDF5_MAX_NAME 1024
42 flag_atts_dirty(NCindex *attlist) {
44 NC_ATT_INFO_T *att = NULL;
51 for(i=0;i<ncindexsize(attlist);i++) {
52 att = (NC_ATT_INFO_T*)ncindexith(attlist,i);
53 if(att == NULL)
continue;
77 rec_reattach_scales(NC_GRP_INFO_T *grp,
int dimid, hid_t dimscaleid)
80 NC_GRP_INFO_T *child_grp;
84 assert(grp && grp->hdr.name && dimid >= 0 && dimscaleid >= 0);
85 LOG((3,
"%s: grp->hdr.name %s", __func__, grp->hdr.name));
88 for (i = 0; i < ncindexsize(grp->children); i++)
90 child_grp = (NC_GRP_INFO_T*)ncindexith(grp->children, i);
92 if ((retval = rec_reattach_scales(child_grp, dimid, dimscaleid)))
97 for (i = 0; i < ncindexsize(grp->vars); i++)
99 NC_HDF5_VAR_INFO_T *hdf5_var;
101 var = (NC_VAR_INFO_T*)ncindexith(grp->vars,i);
102 assert(var && var->format_var_info);
104 hdf5_var = (NC_HDF5_VAR_INFO_T*)var->format_var_info;
105 assert(hdf5_var != NULL);
106 for (d = 0; d < var->ndims; d++)
108 if (var->dimids[d] == dimid && !hdf5_var->dimscale)
110 LOG((2,
"%s: attaching scale for dimid %d to var %s",
111 __func__, var->dimids[d], var->hdr.name));
114 if (H5DSattach_scale(hdf5_var->hdf_datasetid,
117 hdf5_var->dimscale_attached[d] = NC_TRUE;
142 rec_detach_scales(NC_GRP_INFO_T *grp,
int dimid, hid_t dimscaleid)
145 NC_GRP_INFO_T *child_grp;
149 assert(grp && grp->hdr.name && dimid >= 0 && dimscaleid >= 0);
150 LOG((3,
"%s: grp->hdr.name %s", __func__, grp->hdr.name));
153 for(i=0;i<ncindexsize(grp->children);i++) {
154 child_grp = (NC_GRP_INFO_T*)ncindexith(grp->children,i);
155 if(child_grp == NULL)
continue;
156 if ((retval = rec_detach_scales(child_grp, dimid, dimscaleid)))
161 for (i = 0; i < ncindexsize(grp->vars); i++)
163 NC_HDF5_VAR_INFO_T *hdf5_var;
164 var = (NC_VAR_INFO_T*)ncindexith(grp->vars, i);
165 assert(var && var->format_var_info);
166 hdf5_var = (NC_HDF5_VAR_INFO_T *)var->format_var_info;
168 for (d = 0; d < var->ndims; d++)
170 if (var->dimids[d] == dimid && !hdf5_var->dimscale)
172 LOG((2,
"%s: detaching scale for dimid %d to var %s",
173 __func__, var->dimids[d], var->hdr.name));
176 if (hdf5_var->dimscale_attached && hdf5_var->dimscale_attached[d])
178 if (H5DSdetach_scale(hdf5_var->hdf_datasetid,
181 hdf5_var->dimscale_attached[d] = NC_FALSE;
202 nc4_open_var_grp2(NC_GRP_INFO_T *grp,
int varid, hid_t *dataset)
205 NC_HDF5_VAR_INFO_T *hdf5_var;
207 assert(grp && grp->format_grp_info && dataset);
210 if (!(var = (NC_VAR_INFO_T *)ncindexith(grp->vars, varid)))
212 assert(var && var->hdr.id == varid && var->format_var_info);
213 hdf5_var = (NC_HDF5_VAR_INFO_T *)var->format_var_info;
216 if (!hdf5_var->hdf_datasetid)
218 NC_HDF5_GRP_INFO_T *hdf5_grp;
219 hdf5_grp = (NC_HDF5_GRP_INFO_T *)grp->format_grp_info;
221 if ((hdf5_var->hdf_datasetid = H5Dopen2(hdf5_grp->hdf_grpid,
222 var->hdr.name, H5P_DEFAULT)) < 0)
226 *dataset = hdf5_var->hdf_datasetid;
249 nc4_get_hdf_typeid(NC_FILE_INFO_T *h5,
nc_type xtype,
250 hid_t *hdf_typeid,
int endianness)
252 NC_TYPE_INFO_T *type;
256 assert(hdf_typeid && h5);
268 if ((
typeid = H5Tcopy(H5T_C_S1)) < 0)
270 if (H5Tset_strpad(
typeid, H5T_STR_NULLTERM) < 0)
272 if(H5Tset_cset(
typeid, H5T_CSET_ASCII) < 0)
276 *hdf_typeid =
typeid;
281 if ((
typeid = H5Tcopy(H5T_C_S1)) < 0)
283 if (H5Tset_size(
typeid, H5T_VARIABLE) < 0)
285 if(H5Tset_cset(
typeid, H5T_CSET_UTF8) < 0)
289 *hdf_typeid =
typeid;
300 typeid = H5T_STD_I8LE;
302 typeid = H5T_STD_I8BE;
304 typeid = H5T_NATIVE_SCHAR;
309 typeid = H5T_STD_I16LE;
311 typeid = H5T_STD_I16BE;
313 typeid = H5T_NATIVE_SHORT;
318 typeid = H5T_STD_I32LE;
320 typeid = H5T_STD_I32BE;
322 typeid = H5T_NATIVE_INT;
327 typeid = H5T_STD_U8LE;
329 typeid = H5T_STD_U8BE;
331 typeid = H5T_NATIVE_UCHAR;
336 typeid = H5T_STD_U16LE;
338 typeid = H5T_STD_U16BE;
340 typeid = H5T_NATIVE_USHORT;
345 typeid = H5T_STD_U32LE;
347 typeid = H5T_STD_U32BE;
349 typeid = H5T_NATIVE_UINT;
354 typeid = H5T_STD_I64LE;
356 typeid = H5T_STD_I64BE;
358 typeid = H5T_NATIVE_LLONG;
363 typeid = H5T_STD_U64LE;
365 typeid = H5T_STD_U64BE;
367 typeid = H5T_NATIVE_ULLONG;
372 typeid = H5T_IEEE_F32LE;
374 typeid = H5T_IEEE_F32BE;
376 typeid = H5T_NATIVE_FLOAT;
381 typeid = H5T_IEEE_F64LE;
383 typeid = H5T_IEEE_F64BE;
385 typeid = H5T_NATIVE_DOUBLE;
390 if (nc4_find_type(h5, xtype, &type))
394 typeid = ((NC_HDF5_TYPE_INFO_T *)type->format_type_info)->hdf_typeid;
400 if ((*hdf_typeid = H5Tcopy(
typeid)) < 0)
404 assert(*hdf_typeid != -1);
407 if (
typeid > 0 && H5Tclose(
typeid) < 0)
427 put_att_grpa(NC_GRP_INFO_T *grp,
int varid, NC_ATT_INFO_T *att)
429 NC_HDF5_GRP_INFO_T *hdf5_grp;
430 hid_t datasetid = 0, locid;
431 hid_t attid = 0, spaceid = 0, file_typeid = 0;
432 hid_t existing_att_typeid = 0, existing_attid = 0, existing_spaceid = 0;
436 int phoney_data = 99;
439 assert(att->hdr.name && grp && grp->format_grp_info);
440 LOG((3,
"%s: varid %d att->hdr.id %d att->hdr.name %s att->nc_typeid %d "
441 "att->len %d", __func__, varid, att->hdr.id, att->hdr.name,
442 att->nc_typeid, att->len));
445 hdf5_grp = (NC_HDF5_GRP_INFO_T *)grp->format_grp_info;
448 if (grp->nc4_info->no_write)
453 locid = hdf5_grp->hdf_grpid;
456 if ((retval = nc4_open_var_grp2(grp, varid, &datasetid)))
464 if ((retval = nc4_get_hdf_typeid(grp->nc4_info, att->nc_typeid,
474 else if (att->vldata)
476 else if (att->stdata)
489 size_t string_size = dims[0];
493 if ((spaceid = H5Screate(H5S_NULL)) < 0)
498 if ((spaceid = H5Screate(H5S_SCALAR)) < 0)
501 if (H5Tset_size(file_typeid, string_size) < 0)
503 if (H5Tset_strpad(file_typeid, H5T_STR_NULLTERM) < 0)
510 if ((spaceid = H5Screate(H5S_NULL)) < 0)
515 if ((spaceid = H5Screate_simple(1, dims, NULL)) < 0)
521 if ((attr_exists = H5Aexists(locid, att->hdr.name)) < 0)
528 if ((existing_attid = H5Aopen(locid, att->hdr.name, H5P_DEFAULT)) < 0)
532 if ((existing_att_typeid = H5Aget_type(existing_attid)) < 0)
536 if ((existing_spaceid = H5Aget_space(existing_attid)) < 0)
538 if ((npoints = H5Sget_simple_extent_npoints(existing_spaceid)) < 0)
543 if (!H5Tequal(file_typeid, existing_att_typeid) ||
544 (att->nc_typeid !=
NC_CHAR && npoints != att->len))
549 if (H5Adelete(locid, att->hdr.name) < 0)
554 if ((attid = H5Acreate1(locid, att->hdr.name, file_typeid, spaceid,
559 if (H5Awrite(attid, file_typeid, data) < 0)
567 if (H5Awrite(existing_attid, file_typeid, data) < 0)
576 if ((attid = H5Acreate1(locid, att->hdr.name, file_typeid, spaceid,
581 if (H5Awrite(attid, file_typeid, data) < 0)
586 if (file_typeid && H5Tclose(file_typeid))
588 if (attid > 0 && H5Aclose(attid) < 0)
590 if (existing_att_typeid && H5Tclose(existing_att_typeid))
592 if (existing_attid > 0 && H5Aclose(existing_attid) < 0)
594 if (spaceid > 0 && H5Sclose(spaceid) < 0)
596 if (existing_spaceid > 0 && H5Sclose(existing_spaceid) < 0)
613 write_attlist(NCindex *attlist,
int varid, NC_GRP_INFO_T *grp)
619 for(i = 0; i < ncindexsize(attlist); i++)
621 att = (NC_ATT_INFO_T *)ncindexith(attlist, i);
625 LOG((4,
"%s: writing att %s to varid %d", __func__, att->hdr.name, varid));
626 if ((retval = put_att_grpa(grp, varid, att)))
628 att->dirty = NC_FALSE;
629 att->created = NC_TRUE;
649 write_coord_dimids(NC_VAR_INFO_T *var)
651 NC_HDF5_VAR_INFO_T *hdf5_var;
652 hsize_t coords_len[1];
653 hid_t c_spaceid = -1, c_attid = -1;
656 assert(var && var->format_var_info);
659 hdf5_var = (NC_HDF5_VAR_INFO_T *)var->format_var_info;
662 coords_len[0] = var->ndims;
663 if ((c_spaceid = H5Screate_simple(1, coords_len, coords_len)) < 0)
667 if ((c_attid = H5Acreate1(hdf5_var->hdf_datasetid, COORDINATES,
668 H5T_NATIVE_INT, c_spaceid, H5P_DEFAULT)) < 0)
672 if (H5Awrite(c_attid, H5T_NATIVE_INT, var->dimids) < 0)
676 if (c_spaceid >= 0 && H5Sclose(c_spaceid) < 0)
678 if (c_attid >= 0 && H5Aclose(c_attid) < 0)
696 write_quantize_att(NC_VAR_INFO_T *var)
698 NC_HDF5_VAR_INFO_T *hdf5_var;
700 hid_t c_spaceid = -1, c_attid = -1;
704 assert(var && var->format_var_info);
707 hdf5_var = (NC_HDF5_VAR_INFO_T *)var->format_var_info;
710 switch (var->quantize_mode)
726 if ((c_spaceid = H5Screate_simple(1, &len, &len)) < 0)
730 if ((c_attid = H5Acreate1(hdf5_var->hdf_datasetid, att_name,
731 H5T_NATIVE_INT, c_spaceid, H5P_DEFAULT)) < 0)
735 if (H5Awrite(c_attid, H5T_NATIVE_INT, &var->nsd) < 0)
739 if (c_spaceid >= 0 && H5Sclose(c_spaceid) < 0)
741 if (c_attid >= 0 && H5Aclose(c_attid) < 0)
757 write_netcdf4_dimid(hid_t datasetid,
int dimid)
759 hid_t dimid_spaceid = -1, dimid_attid = -1;
764 if ((dimid_spaceid = H5Screate(H5S_SCALAR)) < 0)
768 if ((attr_exists = H5Aexists(datasetid, NC_DIMID_ATT_NAME)) < 0)
771 dimid_attid = H5Aopen_by_name(datasetid,
".", NC_DIMID_ATT_NAME,
772 H5P_DEFAULT, H5P_DEFAULT);
775 dimid_attid = H5Acreate1(datasetid, NC_DIMID_ATT_NAME,
776 H5T_NATIVE_INT, dimid_spaceid, H5P_DEFAULT);
782 LOG((4,
"%s: writing secret dimid %d", __func__, dimid));
783 if (H5Awrite(dimid_attid, H5T_NATIVE_INT, &dimid) < 0)
788 if (dimid_spaceid >= 0 && H5Sclose(dimid_spaceid) < 0)
790 if (dimid_attid >= 0 && H5Aclose(dimid_attid) < 0)
811 var_create_dataset(NC_GRP_INFO_T *grp, NC_VAR_INFO_T *var, nc_bool_t write_dimid)
813 NC_HDF5_GRP_INFO_T *hdf5_grp;
814 NC_HDF5_VAR_INFO_T *hdf5_var;
815 hid_t plistid = 0, access_plistid = 0,
typeid = 0, spaceid = 0;
816 hsize_t chunksize[H5S_MAX_RANK], dimsize[H5S_MAX_RANK], maxdimsize[H5S_MAX_RANK];
819 NC_DIM_INFO_T *dim = NULL;
822 unsigned int* params = NULL;
824 assert(grp && grp->format_grp_info && var && var->format_var_info);
826 LOG((3,
"%s:: name %s", __func__, var->hdr.name));
829 hdf5_grp = (NC_HDF5_GRP_INFO_T *)grp->format_grp_info;
830 hdf5_var = (NC_HDF5_VAR_INFO_T *)var->format_var_info;
833 if ((plistid = H5Pcreate(H5P_DATASET_CREATE)) < 0)
835 if ((access_plistid = H5Pcreate(H5P_DATASET_ACCESS)) < 0)
839 if (H5Pset_obj_track_times(plistid, 0) < 0)
843 if ((retval = nc4_get_hdf_typeid(grp->nc4_info, var->type_info->hdr.id, &
typeid,
844 var->type_info->endianness)))
851 if (H5Pset_fill_time(plistid, H5D_FILL_TIME_NEVER) < 0)
856 if ((retval = nc4_get_fill_value(grp->nc4_info, var, &fillp)))
862 if (var->type_info->nc_type_class ==
NC_STRING)
864 if (H5Pset_fill_value(plistid,
typeid, fillp) < 0)
873 hid_t fill_typeid = 0;
875 if ((retval = nc4_get_hdf_typeid(grp->nc4_info, var->type_info->hdr.id, &fill_typeid,
878 if (H5Pset_fill_value(plistid, fill_typeid, fillp) < 0)
880 if (H5Tclose(fill_typeid) < 0)
884 if (H5Tclose(fill_typeid) < 0)
896 if(var->filters != NULL) {
898 NClist* filters = (NClist*)var->filters;
899 for(j=0;j<nclistlength(filters);j++) {
900 struct NC_HDF5_Filter* fi = (
struct NC_HDF5_Filter*)nclistget(filters,j);
901 if(fi->filterid == H5Z_FILTER_FLETCHER32) {
902 if(H5Pset_fletcher32(plistid) < 0)
904 }
else if(fi->filterid == H5Z_FILTER_SHUFFLE) {
905 if(H5Pset_shuffle(plistid) < 0)
907 }
else if(fi->filterid == H5Z_FILTER_DEFLATE) {
911 level = (int)fi->params[0];
912 if(H5Pset_deflate(plistid, level) < 0)
914 }
else if(fi->filterid == H5Z_FILTER_SZIP) {
919 options_mask = (int)fi->params[0];
920 bits_per_pixel = (
int)fi->params[1];
921 if(H5Pset_szip(plistid, options_mask, bits_per_pixel) < 0)
924 herr_t code = H5Pset_filter(plistid, fi->filterid,
930 fi->nparams, fi->params);
946 for (d = 0; d < var->ndims; d++) {
948 assert(dim && dim->hdr.id == var->dimids[d]);
956 if (nclistlength((NClist*)var->filters) == 0 &&
957 (var->chunksizes == NULL || !var->chunksizes[0]) && !unlimdim)
962 for (d = 0; d < var->ndims; d++)
965 assert(dim && dim->hdr.id == var->dimids[d]);
966 dimsize[d] = dim->unlimited ? NC_HDF5_UNLIMITED_DIMSIZE : dim->len;
967 maxdimsize[d] = dim->unlimited ? H5S_UNLIMITED : (hsize_t)dim->len;
970 if (var->chunksizes[d])
971 chunksize[d] = var->chunksizes[d];
975 if (var->type_info->nc_type_class ==
NC_STRING)
976 type_size =
sizeof(
char *);
978 type_size = var->type_info->size;
984 chunksize[d] = pow((
double)DEFAULT_CHUNK_SIZE/type_size,
985 1/(
double)(var->ndims - unlimdim));
989 if (!dim->unlimited && chunksize[d] > dim->len)
990 chunksize[d] = dim->len;
993 var->chunksizes[d] = chunksize[d];
999 if ((spaceid = H5Screate_simple(var->ndims, dimsize, maxdimsize)) < 0)
1004 if ((spaceid = H5Screate(H5S_SCALAR)) < 0)
1013 if (H5Pset_layout(plistid, H5D_CONTIGUOUS) < 0)
1018 if (H5Pset_layout(plistid, H5D_COMPACT) < 0)
1021 else if (var->ndims)
1023 if (H5Pset_chunk(plistid, var->ndims, chunksize) < 0)
1028 if (!grp->nc4_info->no_attr_create_order) {
1029 if (H5Pset_attr_creation_order(plistid, H5P_CRT_ORDER_TRACKED|
1030 H5P_CRT_ORDER_INDEXED) < 0)
1035 if (var->storage ==
NC_CHUNKED && var->chunkcache.size)
1036 if (H5Pset_chunk_cache(access_plistid, var->chunkcache.nelems,
1037 var->chunkcache.size, var->chunkcache.preemption) < 0)
1041 name_to_use = var->alt_name ? var->alt_name : var->hdr.name;
1042 LOG((4,
"%s: about to H5Dcreate2 dataset %s of type 0x%x", __func__,
1043 name_to_use,
typeid));
1044 if ((hdf5_var->hdf_datasetid = H5Dcreate2(hdf5_grp->hdf_grpid, name_to_use,
typeid,
1045 spaceid, H5P_DEFAULT, plistid, access_plistid)) < 0)
1047 var->created = NC_TRUE;
1048 var->is_new_var = NC_FALSE;
1054 if ((retval = write_coord_dimids(var)))
1060 if (hdf5_var->dimscale)
1062 if (H5DSset_scale(hdf5_var->hdf_datasetid, var->hdr.name) < 0)
1073 if ((retval = write_netcdf4_dimid(hdf5_var->hdf_datasetid, var->dimids[0])))
1081 if (var->quantize_mode)
1082 if ((retval = write_quantize_att(var)))
1086 if ((retval = write_attlist(var->att, var->hdr.id, grp)))
1090 var->attr_dirty = NC_FALSE;
1094 if (
typeid > 0 && H5Tclose(
typeid) < 0)
1096 if (plistid > 0 && H5Pclose(plistid) < 0)
1098 if (access_plistid > 0 && H5Pclose(access_plistid) < 0)
1100 if (spaceid > 0 && H5Sclose(spaceid) < 0)
1104 if (var->type_info->nc_type_class ==
NC_VLEN)
1106 else if (var->type_info->nc_type_class ==
NC_STRING && *(
char **)fillp)
1107 free(*(
char **)fillp);
1128 nc4_adjust_var_cache(NC_GRP_INFO_T *grp, NC_VAR_INFO_T *var)
1130 size_t chunk_size_bytes = 1;
1138 #ifdef USE_PARALLEL4
1140 if (grp->nc4_info->parallel)
1145 for (d = 0; d < var->ndims; d++)
1146 chunk_size_bytes *= var->chunksizes[d];
1147 if (var->type_info->size)
1148 chunk_size_bytes *= var->type_info->size;
1150 chunk_size_bytes *=
sizeof(
char *);
1155 if (var->chunkcache.size == CHUNK_CACHE_SIZE)
1156 if (chunk_size_bytes > var->chunkcache.size)
1158 var->chunkcache.size = chunk_size_bytes * DEFAULT_CHUNKS_IN_CACHE;
1159 if (var->chunkcache.size > MAX_DEFAULT_CACHE_SIZE)
1160 var->chunkcache.size = MAX_DEFAULT_CACHE_SIZE;
1161 if ((retval = nc4_reopen_dataset(grp, var)))
1184 commit_type(NC_GRP_INFO_T *grp, NC_TYPE_INFO_T *type)
1186 NC_HDF5_GRP_INFO_T *hdf5_grp;
1187 NC_HDF5_TYPE_INFO_T *hdf5_type;
1188 hid_t base_hdf_typeid;
1191 assert(grp && grp->format_grp_info && type && type->format_type_info);
1194 hdf5_grp = (NC_HDF5_GRP_INFO_T *)grp->format_grp_info;
1195 hdf5_type = (NC_HDF5_TYPE_INFO_T *)type->format_type_info;
1198 if (type->committed)
1204 NC_FIELD_INFO_T *field;
1205 hid_t hdf_base_typeid, hdf_typeid;
1208 if ((hdf5_type->hdf_typeid = H5Tcreate(H5T_COMPOUND, type->size)) < 0)
1210 LOG((4,
"creating compound type %s hdf_typeid 0x%x", type->hdr.name,
1211 hdf5_type->hdf_typeid));
1213 for(i=0;i<nclistlength(type->u.c.field);i++)
1215 field = (NC_FIELD_INFO_T *)nclistget(type->u.c.field, i);
1217 if ((retval = nc4_get_hdf_typeid(grp->nc4_info, field->nc_typeid,
1218 &hdf_base_typeid, type->endianness)))
1227 for (d = 0; d < field->ndims; d++)
1228 dims[d] = field->dim_size[d];
1229 if ((hdf_typeid = H5Tarray_create1(hdf_base_typeid, field->ndims,
1232 if (H5Tclose(hdf_base_typeid) < 0)
1236 if (H5Tclose(hdf_base_typeid) < 0)
1240 hdf_typeid = hdf_base_typeid;
1241 LOG((4,
"inserting field %s offset %d hdf_typeid 0x%x", field->hdr.name,
1242 field->offset, hdf_typeid));
1243 if (H5Tinsert(hdf5_type->hdf_typeid, field->hdr.name, field->offset,
1246 if (H5Tclose(hdf_typeid) < 0)
1250 else if (type->nc_type_class ==
NC_VLEN)
1253 if ((retval = nc4_get_hdf_typeid(grp->nc4_info, type->u.v.base_nc_typeid,
1254 &base_hdf_typeid, type->endianness)))
1258 if ((hdf5_type->hdf_typeid = H5Tvlen_create(base_hdf_typeid)) < 0)
1261 else if (type->nc_type_class ==
NC_OPAQUE)
1264 if ((hdf5_type->hdf_typeid = H5Tcreate(H5T_OPAQUE, type->size)) < 0)
1267 else if (type->nc_type_class ==
NC_ENUM)
1269 NC_ENUM_MEMBER_INFO_T *enum_m;
1272 if (nclistlength(type->u.e.enum_member) == 0)
1276 if ((retval = nc4_get_hdf_typeid(grp->nc4_info, type->u.e.base_nc_typeid,
1277 &base_hdf_typeid, type->endianness)))
1281 if ((hdf5_type->hdf_typeid = H5Tenum_create(base_hdf_typeid)) < 0)
1285 for(i=0;i<nclistlength(type->u.e.enum_member);i++) {
1286 enum_m = (NC_ENUM_MEMBER_INFO_T*)nclistget(type->u.e.enum_member,i);
1287 if (H5Tenum_insert(hdf5_type->hdf_typeid, enum_m->name, enum_m->value) < 0)
1293 LOG((0,
"Unknown class: %d", type->nc_type_class));
1298 if (H5Tcommit1(hdf5_grp->hdf_grpid, type->hdr.name, hdf5_type->hdf_typeid) < 0)
1300 type->committed = NC_TRUE;
1301 LOG((4,
"just committed type %s, HDF typeid: 0x%x", type->hdr.name,
1302 hdf5_type->hdf_typeid));
1307 if ((hdf5_type->native_hdf_typeid = H5Tget_native_type(hdf5_type->hdf_typeid,
1308 H5T_DIR_DEFAULT)) < 0)
1325 write_nc3_strict_att(hid_t hdf_grpid)
1327 hid_t attid = 0, spaceid = 0;
1334 if ((attr_exists = H5Aexists(hdf_grpid, NC3_STRICT_ATT_NAME)) < 0)
1341 if ((spaceid = H5Screate(H5S_SCALAR)) < 0)
1343 if ((attid = H5Acreate1(hdf_grpid, NC3_STRICT_ATT_NAME,
1344 H5T_NATIVE_INT, spaceid, H5P_DEFAULT)) < 0)
1346 if (H5Awrite(attid, H5T_NATIVE_INT, &one) < 0)
1350 if (spaceid > 0 && (H5Sclose(spaceid) < 0))
1352 if (attid > 0 && (H5Aclose(attid) < 0))
1370 create_group(NC_GRP_INFO_T *grp)
1372 NC_HDF5_GRP_INFO_T *hdf5_grp, *parent_hdf5_grp;
1376 assert(grp && grp->format_grp_info && grp->parent &&
1377 grp->parent->format_grp_info);
1380 hdf5_grp = (NC_HDF5_GRP_INFO_T *)grp->format_grp_info;
1381 parent_hdf5_grp = (NC_HDF5_GRP_INFO_T *)grp->parent->format_grp_info;
1382 assert(parent_hdf5_grp->hdf_grpid);
1386 if ((gcpl_id = H5Pcreate(H5P_GROUP_CREATE)) < 0)
1390 if (H5Pset_obj_track_times(gcpl_id, 0) < 0)
1394 if (H5Pset_link_creation_order(gcpl_id, H5P_CRT_ORDER_TRACKED|H5P_CRT_ORDER_INDEXED) < 0)
1398 if (!grp->nc4_info->no_attr_create_order) {
1399 if (H5Pset_attr_creation_order(gcpl_id, H5P_CRT_ORDER_TRACKED|H5P_CRT_ORDER_INDEXED) < 0)
1404 if ((hdf5_grp->hdf_grpid = H5Gcreate2(parent_hdf5_grp->hdf_grpid, grp->hdr.name,
1405 H5P_DEFAULT, gcpl_id, H5P_DEFAULT)) < 0)
1409 if (gcpl_id > -1 && H5Pclose(gcpl_id) < 0)
1412 if (hdf5_grp->hdf_grpid > 0 && H5Gclose(hdf5_grp->hdf_grpid) < 0)
1430 attach_dimscales(NC_GRP_INFO_T *grp)
1433 NC_HDF5_VAR_INFO_T *hdf5_var;
1437 for (v = 0; v < ncindexsize(grp->vars); v++)
1440 var = (NC_VAR_INFO_T *)ncindexith(grp->vars, v);
1441 assert(var && var->format_var_info);
1442 hdf5_var = (NC_HDF5_VAR_INFO_T *)var->format_var_info;
1446 if (hdf5_var->dimscale)
1450 for (d = 0; d < var->ndims; d++)
1453 if (hdf5_var->dimscale_attached)
1455 if (!hdf5_var->dimscale_attached[d])
1458 assert(var->dim[d] && var->dim[d]->hdr.id == var->dimids[d] &&
1459 var->dim[d]->format_dim_info);
1461 LOG((2,
"%s: attaching scale for dimid %d to var %s",
1462 __func__, var->dimids[d], var->hdr.name));
1465 if (var->dim[d]->coord_var)
1466 dsid = ((NC_HDF5_VAR_INFO_T *)(var->dim[d]->coord_var->format_var_info))->hdf_datasetid;
1468 dsid = ((NC_HDF5_DIM_INFO_T *)var->dim[d]->format_dim_info)->hdf_dimscaleid;
1472 if (H5DSattach_scale(hdf5_var->hdf_datasetid, dsid, d) < 0)
1474 hdf5_var->dimscale_attached[d] = NC_TRUE;
1494 var_exists(hid_t grpid,
char *name, nc_bool_t *exists)
1502 if ((link_exists = H5Lexists(grpid, name, H5P_DEFAULT)) < 0)
1509 if (H5Gget_objinfo(grpid, name, 1, &statbuf) < 0)
1512 if (H5G_DATASET == statbuf.type)
1535 remove_coord_atts(hid_t hdf_datasetid)
1541 if ((attr_exists = H5Aexists(hdf_datasetid, NC_DIMID_ATT_NAME)) < 0)
1545 if (H5Adelete(hdf_datasetid, NC_DIMID_ATT_NAME) < 0)
1550 if ((attr_exists = H5Aexists(hdf_datasetid,
1551 HDF5_DIMSCALE_CLASS_ATT_NAME)) < 0)
1555 if (H5Adelete(hdf_datasetid, HDF5_DIMSCALE_CLASS_ATT_NAME) < 0)
1558 if ((attr_exists = H5Aexists(hdf_datasetid,
1559 HDF5_DIMSCALE_NAME_ATT_NAME)) < 0)
1563 if (H5Adelete(hdf_datasetid, HDF5_DIMSCALE_NAME_ATT_NAME) < 0)
1584 write_var(NC_VAR_INFO_T *var, NC_GRP_INFO_T *grp, nc_bool_t write_dimid)
1586 NC_HDF5_GRP_INFO_T *hdf5_grp;
1587 NC_HDF5_VAR_INFO_T *hdf5_var;
1588 nc_bool_t replace_existing_var = NC_FALSE;
1591 assert(var && var->format_var_info && grp && grp->format_grp_info);
1593 LOG((4,
"%s: writing var %s", __func__, var->hdr.name));
1596 hdf5_grp = (NC_HDF5_GRP_INFO_T *)grp->format_grp_info;
1597 hdf5_var = (NC_HDF5_VAR_INFO_T *)var->format_var_info;
1601 if (var->created && var->fill_val_changed)
1603 replace_existing_var = NC_TRUE;
1604 var->fill_val_changed = NC_FALSE;
1610 flag_atts_dirty(var->att);
1617 if (var->became_coord_var)
1619 if ((NC_DIM_INFO_T *)ncindexlookup(grp->dim, var->hdr.name))
1623 if ((retval = var_exists(hdf5_grp->hdf_grpid, var->hdr.name, &exists)))
1629 replace_existing_var = NC_TRUE;
1630 flag_atts_dirty(var->att);
1637 if (replace_existing_var)
1642 if ((d1 = (NC_DIM_INFO_T *)ncindexlookup(grp->dim, var->hdr.name)))
1645 assert(d1->format_dim_info && d1->hdr.name);
1647 if ((retval = var_exists(hdf5_grp->hdf_grpid, var->hdr.name, &exists)))
1655 dsid = ((NC_HDF5_VAR_INFO_T *)d1->coord_var->format_var_info)->hdf_datasetid;
1657 dsid = ((NC_HDF5_DIM_INFO_T *)d1->format_dim_info)->hdf_dimscaleid;
1663 if ((retval = rec_detach_scales(grp->nc4_info->root_grp,
1664 var->dimids[0], dsid)))
1672 if (var->was_coord_var && hdf5_var->dimscale_attached)
1679 if ((retval = remove_coord_atts(hdf5_var->hdf_datasetid)))
1683 for (d = 0; d < var->ndims; d++)
1685 if (hdf5_var->dimscale_attached[d])
1688 assert(var->dim[d] && var->dim[d]->hdr.id == var->dimids[d] &&
1689 var->dim[d]->format_dim_info);
1692 if (var->dim[d]->coord_var)
1693 dsid = ((NC_HDF5_VAR_INFO_T *)var->dim[d]->coord_var->format_var_info)->hdf_datasetid;
1695 dsid = ((NC_HDF5_DIM_INFO_T *)var->dim[d]->format_dim_info)->hdf_dimscaleid;
1699 if (H5DSdetach_scale(hdf5_var->hdf_datasetid, dsid, d) < 0)
1701 hdf5_var->dimscale_attached[d] = NC_FALSE;
1707 if (replace_existing_var)
1710 if (hdf5_var->hdf_datasetid && H5Dclose(hdf5_var->hdf_datasetid) < 0)
1712 hdf5_var->hdf_datasetid = 0;
1715 if (H5Gunlink(hdf5_grp->hdf_grpid, var->hdr.name) < 0)
1720 if (var->is_new_var || replace_existing_var)
1722 if ((retval = var_create_dataset(grp, var, write_dimid)))
1727 if (write_dimid && var->ndims)
1728 if ((retval = write_netcdf4_dimid(hdf5_var->hdf_datasetid,
1733 if (replace_existing_var)
1737 if(hdf5_var->dimscale)
1739 if ((retval = rec_reattach_scales(grp->nc4_info->root_grp,
1740 var->dimids[0], hdf5_var->hdf_datasetid)))
1747 if (hdf5_var->dimscale_attached)
1748 memset(hdf5_var->dimscale_attached, 0,
sizeof(nc_bool_t) * var->ndims);
1753 var->was_coord_var = NC_FALSE;
1754 var->became_coord_var = NC_FALSE;
1757 if (var->attr_dirty)
1760 if ((retval = write_attlist(var->att, var->hdr.id, grp)))
1762 var->attr_dirty = NC_FALSE;
1782 nc4_create_dim_wo_var(NC_DIM_INFO_T *dim)
1784 NC_HDF5_DIM_INFO_T *hdf5_dim;
1785 NC_HDF5_GRP_INFO_T *hdf5_grp;
1786 hid_t spaceid = -1, create_propid = -1;
1787 hsize_t dims[1], max_dims[1], chunk_dims[1] = {1};
1791 LOG((4,
"%s: creating dim %s", __func__, dim->hdr.name));
1794 assert(!dim->coord_var);
1797 hdf5_grp = (NC_HDF5_GRP_INFO_T *)dim->container->format_grp_info;
1798 hdf5_dim = (NC_HDF5_DIM_INFO_T *)dim->format_dim_info;
1801 if ((create_propid = H5Pcreate(H5P_DATASET_CREATE)) < 0)
1805 if (H5Pset_obj_track_times(create_propid, 0) < 0)
1810 max_dims[0] = dim->len;
1816 max_dims[0] = H5S_UNLIMITED;
1817 if (H5Pset_chunk(create_propid, 1, chunk_dims) < 0)
1822 if ((spaceid = H5Screate_simple(1, dims, max_dims)) < 0)
1826 if (!dim->container->nc4_info->no_attr_create_order) {
1827 if (H5Pset_attr_creation_order(create_propid, H5P_CRT_ORDER_TRACKED|
1828 H5P_CRT_ORDER_INDEXED) < 0)
1832 LOG((4,
"%s: about to H5Dcreate1 a dimscale dataset %s", __func__,
1834 if ((hdf5_dim->hdf_dimscaleid = H5Dcreate2(hdf5_grp->hdf_grpid, dim->hdr.name,
1835 H5T_IEEE_F32BE, spaceid,
1836 H5P_DEFAULT, create_propid,
1843 sprintf(dimscale_wo_var,
"%s%10d", DIM_WITHOUT_VARIABLE, (
int)dim->len);
1844 if (H5DSset_scale(hdf5_dim->hdf_dimscaleid, dimscale_wo_var) < 0)
1850 if ((retval = write_netcdf4_dimid(hdf5_dim->hdf_dimscaleid, dim->hdr.id)))
1854 if (spaceid > 0 && H5Sclose(spaceid) < 0)
1856 if (create_propid > 0 && H5Pclose(create_propid) < 0)
1874 write_dim(NC_DIM_INFO_T *dim, NC_GRP_INFO_T *grp, nc_bool_t write_dimid)
1876 NC_HDF5_DIM_INFO_T *hdf5_dim;
1879 assert(dim && dim->format_dim_info && grp && grp->format_grp_info);
1882 hdf5_dim = (NC_HDF5_DIM_INFO_T *)dim->format_dim_info;
1888 if (!hdf5_dim->hdf_dimscaleid)
1889 if ((retval = nc4_create_dim_wo_var(dim)))
1895 NC_VAR_INFO_T *v1 = NULL;
1897 assert(dim->unlimited);
1901 v1 = dim->coord_var;
1904 NC_HDF5_VAR_INFO_T *hdf5_v1;
1908 hdf5_v1 = (NC_HDF5_VAR_INFO_T *)v1->format_var_info;
1912 if (!(new_size = malloc(v1->ndims *
sizeof(hsize_t))))
1914 for (d1 = 0; d1 < v1->ndims; d1++)
1916 assert(v1->dim[d1] && v1->dim[d1]->hdr.id == v1->dimids[d1]);
1917 new_size[d1] = v1->dim[d1]->len;
1919 if (H5Dset_extent(hdf5_v1->hdf_datasetid, new_size) < 0)
1929 if (write_dimid && hdf5_dim->hdf_dimscaleid)
1930 if ((retval = write_netcdf4_dimid(hdf5_dim->hdf_dimscaleid, dim->hdr.id)))
1951 nc4_rec_write_metadata(NC_GRP_INFO_T *grp, nc_bool_t bad_coord_order)
1953 NC_DIM_INFO_T *dim = NULL;
1954 NC_VAR_INFO_T *var = NULL;
1955 NC_GRP_INFO_T *child_grp = NULL;
1956 int coord_varid = -1;
1962 assert(grp && grp->hdr.name &&
1963 ((NC_HDF5_GRP_INFO_T *)(grp->format_grp_info))->hdf_grpid);
1964 LOG((3,
"%s: grp->hdr.name %s, bad_coord_order %d", __func__, grp->hdr.name,
1968 if ((retval = write_attlist(grp->att,
NC_GLOBAL, grp)))
1973 dim = (NC_DIM_INFO_T *)ncindexith(grp->dim, dim_index);
1974 var = (NC_VAR_INFO_T *)ncindexith(grp->vars, var_index);
1981 nc_bool_t found_coord, wrote_coord;
1985 for (found_coord = NC_FALSE; dim && !found_coord; )
1987 if (!dim->coord_var)
1989 if ((retval = write_dim(dim, grp, bad_coord_order)))
1994 coord_varid = dim->coord_var->hdr.id;
1995 found_coord = NC_TRUE;
1997 dim = (NC_DIM_INFO_T *)ncindexith(grp->dim, ++dim_index);
2002 for (wrote_coord = NC_FALSE; var && !wrote_coord; )
2004 if ((retval = write_var(var, grp, bad_coord_order)))
2006 if (found_coord && var->hdr.id == coord_varid)
2007 wrote_coord = NC_TRUE;
2008 var = (NC_VAR_INFO_T *)ncindexith(grp->vars, ++var_index);
2013 if (!grp->nc4_info->no_dimscale_attach) {
2014 if ((retval = attach_dimscales(grp)))
2019 for (i = 0; i < ncindexsize(grp->children); i++)
2021 child_grp = (NC_GRP_INFO_T *)ncindexith(grp->children, i);
2023 if ((retval = nc4_rec_write_metadata(child_grp, bad_coord_order)))
2039 nc4_rec_write_groups_types(NC_GRP_INFO_T *grp)
2041 NC_GRP_INFO_T *child_grp;
2042 NC_HDF5_GRP_INFO_T *hdf5_grp;
2043 NC_TYPE_INFO_T *type;
2047 assert(grp && grp->hdr.name && grp->format_grp_info);
2048 LOG((3,
"%s: grp->hdr.name %s", __func__, grp->hdr.name));
2051 hdf5_grp = (NC_HDF5_GRP_INFO_T *)grp->format_grp_info;
2054 if (!hdf5_grp->hdf_grpid)
2055 if ((retval = create_group(grp)))
2061 if ((retval = write_nc3_strict_att(hdf5_grp->hdf_grpid)))
2065 for(i=0;i<ncindexsize(grp->type);i++) {
2066 type = (NC_TYPE_INFO_T *)ncindexith(grp->type, i);
2068 if ((retval = commit_type(grp, type)))
2073 for(i=0;i<ncindexsize(grp->children);i++) {
2074 if((child_grp = (NC_GRP_INFO_T*)ncindexith(grp->children,i)) == NULL)
continue;
2075 if ((retval = nc4_rec_write_groups_types(child_grp)))
2095 nc4_rec_match_dimscales(NC_GRP_INFO_T *grp)
2103 assert(grp && grp->hdr.name);
2104 LOG((4,
"%s: grp->hdr.name %s", __func__, grp->hdr.name));
2107 for (i = 0; i < ncindexsize(grp->children); i++)
2109 g = (NC_GRP_INFO_T*)ncindexith(grp->children, i);
2111 if ((retval = nc4_rec_match_dimscales(g)))
2117 for (i = 0; i < ncindexsize(grp->vars); i++)
2119 NC_HDF5_VAR_INFO_T *hdf5_var;
2124 var = (NC_VAR_INFO_T*)ncindexith(grp->vars, i);
2125 assert(var && var->format_var_info);
2126 hdf5_var = (NC_HDF5_VAR_INFO_T *)var->format_var_info;
2144 for (d = 0; d < ndims; d++)
2146 if (var->dim[d] == NULL) {
2147 nc4_find_dim(grp, var->dimids[d], &var->dim[d], NULL);
2153 if (!hdf5_var->dimscale)
2159 if (hdf5_var->dimscale_hdf5_objids)
2161 for (d = 0; d < var->ndims; d++)
2163 nc_bool_t finished = NC_FALSE;
2164 LOG((5,
"%s: var %s has dimscale info...", __func__, var->hdr.name));
2167 for (g = grp; g && !finished; g = g->parent)
2170 for (j = 0; j < ncindexsize(g->dim); j++)
2173 NC_HDF5_DIM_INFO_T *hdf5_dim;
2174 dim = (NC_DIM_INFO_T *)ncindexith(g->dim, j);
2175 assert(dim && dim->format_dim_info);
2176 hdf5_dim = (NC_HDF5_DIM_INFO_T *)dim->format_dim_info;
2180 #
if H5_VERSION_GE(1,12,0)
2182 if (H5Otoken_cmp(hdf5_var->hdf_datasetid, &hdf5_var->dimscale_hdf5_objids[d].token, &hdf5_dim->hdf5_objid.token, &token_cmp) < 0)
2185 if (hdf5_var->dimscale_hdf5_objids[d].fileno == hdf5_dim->hdf5_objid.fileno &&
2188 if (hdf5_var->dimscale_hdf5_objids[d].fileno[0] == hdf5_dim->hdf5_objid.fileno[0] &&
2189 hdf5_var->dimscale_hdf5_objids[d].objno[0] == hdf5_dim->hdf5_objid.objno[0] &&
2190 hdf5_var->dimscale_hdf5_objids[d].fileno[1] == hdf5_dim->hdf5_objid.fileno[1] &&
2191 hdf5_var->dimscale_hdf5_objids[d].objno[1] == hdf5_dim->hdf5_objid.objno[1])
2194 LOG((4,
"%s: for dimension %d, found dim %s", __func__,
2196 var->dimids[d] = dim->hdr.id;
2203 LOG((5,
"%s: dimid for this dimscale is %d", __func__,
2204 var->type_info->hdr.id));
2211 hsize_t *h5dimlen = NULL, *h5dimlenmax = NULL;
2215 if ((spaceid = H5Dget_space(hdf5_var->hdf_datasetid)) < 0)
2221 if (!(h5dimlen = malloc(var->ndims *
sizeof(hsize_t))))
2223 if (!(h5dimlenmax = malloc(var->ndims *
sizeof(hsize_t))))
2228 if ((dataset_ndims = H5Sget_simple_extent_dims(spaceid, h5dimlen,
2229 h5dimlenmax)) < 0) {
2234 if (dataset_ndims != var->ndims) {
2243 if (H5Sget_simple_extent_type(spaceid) != H5S_SCALAR)
2248 if (H5Sclose(spaceid) < 0) {
2257 for (d = 0; d < var->ndims; d++)
2262 for(match=-1,k=0;k<ncindexsize(grp->dim);k++) {
2263 if((dim = (NC_DIM_INFO_T*)ncindexith(grp->dim,k)) == NULL)
continue;
2264 if ((dim->len == h5dimlen[d]) &&
2265 ((h5dimlenmax[d] == H5S_UNLIMITED && dim->unlimited) ||
2266 (h5dimlenmax[d] != H5S_UNLIMITED && !dim->unlimited)))
2274 sprintf(phony_dim_name,
"phony_dim_%d", grp->nc4_info->next_dimid);
2275 LOG((3,
"%s: creating phony dim for var %s", __func__, var->hdr.name));
2276 if ((retval = nc4_dim_list_add(grp, phony_dim_name, h5dimlen[d], -1, &dim)))
2283 if (!(dim->format_dim_info = calloc(1,
sizeof(NC_HDF5_DIM_INFO_T))))
2285 if (h5dimlenmax[d] == H5S_UNLIMITED)
2286 dim->unlimited = NC_TRUE;
2290 var->dimids[d] = dim->hdr.id;
2316 reportobject(
int uselog, hid_t
id,
unsigned int type)
2318 char name[NC_HDF5_MAX_NAME];
2320 const char*
typename = NULL;
2321 long long printid = (
long long)
id;
2323 len = H5Iget_name(
id, name, NC_HDF5_MAX_NAME);
2328 case H5F_OBJ_FILE:
typename =
"File";
break;
2329 case H5F_OBJ_DATASET:
typename =
"Dataset";
break;
2330 case H5F_OBJ_GROUP:
typename =
"Group";
break;
2331 case H5F_OBJ_DATATYPE:
typename =
"Datatype";
break;
2333 typename =
"Attribute";
2334 len = H5Aget_name(
id, NC_HDF5_MAX_NAME, name);
2335 if(len < 0) len = 0;
2338 default:
typename =
"<unknown>";
break;
2342 LOG((0,
"Type = %s(%lld) name='%s'",
typename,printid,name));
2346 fprintf(stderr,
"Type = %s(%lld) name='%s'",
typename,printid,name);
2362 reportopenobjectsT(
int uselog, hid_t fid,
int ntypes,
unsigned int* otypes)
2366 size_t maxobjs = -1;
2367 hid_t* idlist = NULL;
2372 LOG((0,
"\nReport: open objects on %lld",(
long long)fid));
2375 fprintf(stdout,
"\nReport: open objects on %lld\n",(
long long)fid);
2376 maxobjs = H5Fget_obj_count(fid,H5F_OBJ_ALL);
2377 if(idlist != NULL) free(idlist);
2378 idlist = (hid_t*)malloc(
sizeof(hid_t)*maxobjs);
2379 for(t=0;t<ntypes;t++) {
2380 unsigned int ot = otypes[t];
2381 ocount = H5Fget_obj_ids(fid,ot,maxobjs,idlist);
2382 for(i=0;i<ocount;i++) {
2383 hid_t o = idlist[i];
2384 reportobject(uselog,o,ot);
2387 if(idlist != NULL) free(idlist);
2399 reportopenobjects(
int uselog, hid_t fid)
2401 unsigned int OTYPES[5] = {H5F_OBJ_FILE, H5F_OBJ_DATASET, H5F_OBJ_GROUP,
2402 H5F_OBJ_DATATYPE, H5F_OBJ_ATTR};
2404 reportopenobjectsT(uselog, fid ,5, OTYPES);
2415 showopenobjects5(NC_FILE_INFO_T* h5)
2417 NC_HDF5_FILE_INFO_T *hdf5_info;
2419 assert(h5 && h5->format_file_info);
2420 hdf5_info = (NC_HDF5_FILE_INFO_T *)h5->format_file_info;
2422 fprintf(stderr,
"===== begin showopenobjects =====\n");
2423 reportopenobjects(0,hdf5_info->hdfid);
2424 fprintf(stderr,
"===== end showopenobjects =====\n");
2437 showopenobjects(
int ncid)
2439 NC_FILE_INFO_T* h5 = NULL;
2442 if (nc4_find_nc_grp_h5(ncid, NULL, NULL, &h5) !=
NC_NOERR)
2443 fprintf(stderr,
"failed\n");
2445 showopenobjects5(h5);
2461 NC4_hdf5get_libversion(
unsigned* major,
unsigned* minor,
unsigned* release)
2463 if(H5get_libversion(major,minor,release) < 0)
2479 NC4_hdf5get_superblock(
struct NC_FILE_INFO* h5,
int* idp)
2481 NC_HDF5_FILE_INFO_T *hdf5_info;
2486 assert(h5 && h5->format_file_info);
2487 hdf5_info = (NC_HDF5_FILE_INFO_T *)h5->format_file_info;
2489 if((plist = H5Fget_create_plist(hdf5_info->hdfid)) < 0)
2491 if(H5Pget_version(plist, &super, NULL, NULL, NULL) < 0)
2493 if(idp) *idp = (int)super;
2495 if(plist >= 0) H5Pclose(plist);
2499 static int NC4_strict_att_exists(NC_FILE_INFO_T*);
2500 static int NC4_walk(hid_t,
int*);
2528 NC4_isnetcdf4(
struct NC_FILE_INFO* h5)
2536 exists = NC4_strict_att_exists(h5);
2542 stat = NC4_walk(((NC_HDF5_GRP_INFO_T *)(h5->root_grp->format_grp_info))->hdf_grpid,
2547 isnc4 = (count >= 2);
2562 NC4_strict_att_exists(NC_FILE_INFO_T *h5)
2568 grpid = ((NC_HDF5_GRP_INFO_T *)(h5->root_grp->format_grp_info))->hdf_grpid;
2571 if ((attr_exists = H5Aexists(grpid, NC3_STRICT_ATT_NAME)) < 0)
2573 return (attr_exists?1:0);
2586 NC4_walk(hid_t gid,
int* countp)
2595 char name[NC_HDF5_MAX_NAME];
2598 err = H5Gget_num_objs(gid, &nobj);
2599 if(err < 0)
return err;
2601 for(i = 0; i < nobj; i++) {
2603 len = H5Gget_objname_by_idx(gid,(hsize_t)i,name,(
size_t)NC_HDF5_MAX_NAME);
2604 if(len < 0)
return len;
2606 otype = H5Gget_objtype_by_idx(gid,(
size_t)i);
2609 grpid = H5Gopen1(gid,name);
2610 NC4_walk(grpid,countp);
2615 if(strcmp(name,
"phony_dim")==0)
2616 *countp = *countp + 1;
2617 dsid = H5Dopen1(gid,name);
2618 na = H5Aget_num_attrs(dsid);
2619 for(j = 0; j < na; j++) {
2620 hid_t aid = H5Aopen_idx(dsid,(
unsigned int) j);
2622 const NC_reservedatt* ra;
2623 ssize_t len = H5Aget_name(aid, NC_HDF5_MAX_NAME, name);
2624 if(len < 0)
return len;
2627 ra = NC_findreserved(name);
2629 *countp = *countp + 1;
EXTERNL int nc_free_vlen(nc_vlen_t *vl)
Free memory in a VLEN object.
Main header file for the C API.
#define NC_EBADTYPE
Not a netcdf data type.
#define NC_UINT
unsigned 4-byte int
#define NC_ENDIAN_NATIVE
In HDF5 files you can set the endianness of variables with nc_def_var_endian().
#define NC_EFILTER
Filter operation failed.
#define NC_QUANTIZE_GRANULARBR_ATT_NAME
When quantization is used for a variable, an attribute of the appropriate name is added.
#define NC_INT
signed 4 byte integer
#define NC_ENDIAN_BIG
In HDF5 files you can set the endianness of variables with nc_def_var_endian().
#define NC_MAX_VAR_DIMS
max per variable dimensions
#define NC_BYTE
signed 1 byte integer
#define NC_EPERM
Write to read only.
#define NC_QUANTIZE_BITROUND
Use BitRound quantization.
#define NC_EDIMSCALE
Problem with HDF5 dimscales.
#define NC_VLEN
vlen (variable-length) types
#define NC_NAT
Not A Type.
#define NC_DOUBLE
double precision floating point number
#define NC_UBYTE
unsigned 1 byte int
#define NC_FLOAT
single precision floating point number
#define NC_ENOMEM
Memory allocation (malloc) failure.
#define NC_COMPOUND
compound types
#define NC_CHUNKED
In HDF5 files you can set storage for each variable to be either contiguous or chunked,...
#define NC_SHORT
signed 2 byte integer
#define NC_QUANTIZE_GRANULARBR
Use Granular BitRound quantization.
#define NC_QUANTIZE_BITGROOM
Use BitGroom quantization.
#define NC_ENUM
enum types
#define NC_INT64
signed 8-byte int
#define NC_EATTMETA
Problem with attribute metadata.
#define NC_EHDFERR
Error at HDF5 layer.
#define NC_CONTIGUOUS
In HDF5 files you can set storage for each variable to be either contiguous or chunked,...
#define NC_GLOBAL
Attribute id to put/get a global attribute.
#define NC_UINT64
unsigned 8-byte int
#define NC_COMPACT
In HDF5 files you can set storage for each variable to be either contiguous or chunked,...
#define NC_EFILEMETA
Problem with file metadata.
#define NC_ENOTVAR
Variable not found.
#define NC_EINVAL
Invalid Argument.
#define NC_CLASSIC_MODEL
Enforce classic model on netCDF-4.
#define NC_ENDIAN_LITTLE
In HDF5 files you can set the endianness of variables with nc_def_var_endian().
#define NC_MAX_NAME
Maximum for classic library.
#define NC_NOERR
No Error.
#define NC_EDIMMETA
Problem with dimension metadata.
#define NC_USHORT
unsigned 2-byte int
#define NC_OPAQUE
opaque types
#define NC_QUANTIZE_BITGROOM_ATT_NAME
When quantization is used for a variable, an attribute of the appropriate name is added.
#define NC_CHAR
ISO/ASCII character.
#define NC_EVARMETA
Problem with variable metadata.
#define NC_QUANTIZE_BITROUND_ATT_NAME
When quantization is used for a variable, an attribute of the appropriate name is added.
int nc_type
The nc_type type is just an int.
This is the type of arrays of vlens.