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Commit 89bff5c

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douglasjacobsendouglasjacobsen
committed
Add missing value to registry and attribute lists
This commit updates the definition of registry to parse the missing_value attribute from variable definitions. The missing_value is then provided through the field types, in case a core wants to set elements to have this value. Additionally, missing_value is added to each field as an attribute so external tools can access what value is missing for each field independently. Additionally, it adds _FillValue, and sets the defaul values of both _FillValue and missing_value to be the NetCDF defined fill value for the correct type.
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‎src/framework/mpas_field_types.inc‎

Copy file name to clipboardExpand all lines: src/framework/mpas_field_types.inc
+13Lines changed: 13 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -21,6 +21,7 @@
2121
character (len=StrKIND), dimension(5) :: dimNames
2222
integer, dimension(5) :: dimSizes
2323
real (kind=RKIND) :: defaultValue
24+
real (kind=RKIND) :: missingValue
2425
logical :: isDecomposed
2526
logical :: hasTimeDimension
2627
logical :: isActive
@@ -53,6 +54,7 @@
5354
character (len=StrKIND), dimension(4) :: dimNames
5455
integer, dimension(4) :: dimSizes
5556
real (kind=RKIND) :: defaultValue
57+
real (kind=RKIND) :: missingValue
5658
logical :: isDecomposed
5759
logical :: hasTimeDimension
5860
logical :: isActive
@@ -86,6 +88,7 @@
8688
character (len=StrKIND), dimension(3) :: dimNames
8789
integer, dimension(3) :: dimSizes
8890
real (kind=RKIND) :: defaultValue
91+
real (kind=RKIND) :: missingValue
8992
logical :: isDecomposed
9093
logical :: hasTimeDimension
9194
logical :: isActive
@@ -118,6 +121,7 @@
118121
character (len=StrKIND), dimension(2) :: dimNames
119122
integer, dimension(2) :: dimSizes
120123
real (kind=RKIND) :: defaultValue
124+
real (kind=RKIND) :: missingValue
121125
logical :: isDecomposed
122126
logical :: hasTimeDimension
123127
logical :: isActive
@@ -150,6 +154,7 @@
150154
character (len=StrKIND), dimension(1) :: dimNames
151155
integer, dimension(1) :: dimSizes
152156
real (kind=RKIND) :: defaultValue
157+
real (kind=RKIND) :: missingValue
153158
logical :: isDecomposed
154159
logical :: hasTimeDimension
155160
logical :: isActive
@@ -180,6 +185,7 @@
180185
character (len=StrKIND) :: fieldName
181186
character (len=StrKIND), dimension(:), pointer :: constituentNames => null()
182187
real (kind=RKIND) :: defaultValue
188+
real (kind=RKIND) :: missingValue
183189
logical :: isDecomposed
184190
logical :: hasTimeDimension
185191
logical :: isActive
@@ -210,6 +216,7 @@
210216
character (len=StrKIND), dimension(:), pointer :: constituentNames => null()
211217
character (len=StrKIND), dimension(3) :: dimNames
212218
integer :: defaultValue
219+
integer :: missingValue
213220
integer, dimension(3) :: dimSizes
214221
logical :: isDecomposed
215222
logical :: hasTimeDimension
@@ -242,6 +249,7 @@
242249
character (len=StrKIND), dimension(:), pointer :: constituentNames => null()
243250
character (len=StrKIND), dimension(2) :: dimNames
244251
integer :: defaultValue
252+
integer :: missingValue
245253
integer, dimension(2) :: dimSizes
246254
logical :: isDecomposed
247255
logical :: hasTimeDimension
@@ -274,6 +282,7 @@
274282
character (len=StrKIND), dimension(:), pointer :: constituentNames => null()
275283
character (len=StrKIND), dimension(1) :: dimNames
276284
integer :: defaultValue
285+
integer :: missingValue
277286
integer, dimension(1) :: dimSizes
278287
logical :: isDecomposed
279288
logical :: hasTimeDimension
@@ -305,6 +314,7 @@
305314
character (len=StrKIND) :: fieldName
306315
character (len=StrKIND), dimension(:), pointer :: constituentNames => null()
307316
integer :: defaultValue
317+
integer :: missingValue
308318
logical :: isDecomposed
309319
logical :: hasTimeDimension
310320
logical :: isActive
@@ -336,6 +346,7 @@
336346
character (len=StrKIND), dimension(1) :: dimNames
337347
integer, dimension(1) :: dimSizes
338348
character (len=StrKIND) :: defaultValue
349+
character (len=StrKIND) :: missingValue
339350
logical :: isDecomposed
340351
logical :: hasTimeDimension
341352
logical :: isActive
@@ -366,6 +377,7 @@
366377
character (len=StrKIND) :: fieldName
367378
character (len=StrKIND), dimension(:), pointer :: constituentNames => null()
368379
character (len=StrKIND) :: defaultValue
380+
character (len=StrKIND) :: missingValue
369381
logical :: isDecomposed
370382
logical :: hasTimeDimension
371383
logical :: isActive
@@ -395,6 +407,7 @@
395407
character (len=StrKIND) :: fieldName
396408
character (len=StrKIND), dimension(:), pointer :: constituentNames => null()
397409
logical :: defaultValue
410+
logical :: missingValue
398411
logical :: isDecomposed
399412
logical :: hasTimeDimension
400413
logical :: isActive
Collapse file

‎src/framework/mpas_io.F‎

Copy file name to clipboardExpand all lines: src/framework/mpas_io.F
+8Lines changed: 8 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -22,6 +22,14 @@ module mpas_io
2222
#else
2323
integer, parameter :: PIO_REALKIND = PIO_DOUBLE
2424
#endif
25+
26+
integer, parameter :: MPAS_INT_FILLVAL = NF_FILL_INT
27+
character, parameter :: MPAS_CHAR_FILLVAL = achar(NF_FILL_CHAR)
28+
#ifdef SINGLE_PRECISION
29+
real (kind=RKIND), parameter :: MPAS_REAL_FILLVAL = NF_FILL_FLOAT
30+
#else
31+
real (kind=RKIND), parameter :: MPAS_REAL_FILLVAL = NF_FILL_DOUBLE
32+
#endif
2533

2634
interface MPAS_io_get_var
2735
module procedure MPAS_io_get_var_int0d
Collapse file

‎src/tools/registry/gen_inc.c‎

Copy file name to clipboardExpand all lines: src/tools/registry/gen_inc.c
+68-26Lines changed: 68 additions & 26 deletions
Original file line numberDiff line numberDiff line change
@@ -424,7 +424,7 @@ int build_dimension_information(ezxml_t registry, ezxml_t var, int *ndims, int *
424424
}/*}}}*/
425425

426426

427-
int get_field_information(const char *vartype, const char *varval, char *default_value, int *type){/*{{{*/
427+
int get_field_information(const char *vartype, const char *varval, char *default_value, const char *varmissval, char *missing_value, int *type){/*{{{*/
428428
if (strcmp(vartype, "real") == 0){
429429
(*type) = REAL;
430430
if(!varval){
@@ -448,6 +448,29 @@ int get_field_information(const char *vartype, const char *varval, char *default
448448
}
449449
}
450450

451+
if (strcmp(vartype, "real") == 0){
452+
(*type) = REAL;
453+
if(!varmissval){
454+
snprintf(missing_value, 1024, "MPAS_REAL_FILLVAL");
455+
} else {
456+
snprintf(missing_value, 1024, "%s", varmissval);
457+
}
458+
} else if (strcmp(vartype, "integer") == 0){
459+
(*type) = INTEGER;
460+
if(!varmissval){
461+
snprintf(missing_value, 1024, "MPAS_INT_FILLVAL");
462+
} else {
463+
snprintf(missing_value, 1024, "%s", varmissval);
464+
}
465+
} else if (strcmp(vartype, "text") == 0){
466+
(*type) = CHARACTER;
467+
if(!varmissval){
468+
snprintf(missing_value, 1024, "MPAS_CHAR_FILLVAL");
469+
} else {
470+
snprintf(missing_value, 1024, "'%s'", varmissval);
471+
}
472+
}
473+
451474
return 0;
452475
}/*}}}*/
453476

@@ -952,7 +975,7 @@ int parse_var_array(FILE *fd, ezxml_t registry, ezxml_t superStruct, ezxml_t var
952975

953976
const char *structname, *structlevs, *structpackages;
954977
const char *substructname;
955-
const char *vararrname, *vararrtype, *vararrdims, *vararrpersistence, *vararrdefaultval, *vararrpackages;
978+
const char *vararrname, *vararrtype, *vararrdims, *vararrpersistence, *vararrdefaultval, *vararrpackages, *vararrmissingval;
956979
const char *varname, *varpersistence, *vartype, *vardims, *varunits, *vardesc, *vararrgroup, *varstreams, *vardefaultval, *varpackages;
957980
const char *varname2, *vararrgroup2, *vararrname_in_code;
958981
const char *varname_in_code;
@@ -974,6 +997,7 @@ int parse_var_array(FILE *fd, ezxml_t registry, ezxml_t superStruct, ezxml_t var
974997
char pointer_name[1024];
975998
char spacing[1024], sub_spacing[1024];
976999
char default_value[1024];
1000+
char missing_value[1024];
9771001

9781002
structname = ezxml_attr(superStruct, "name");
9791003

@@ -986,6 +1010,7 @@ int parse_var_array(FILE *fd, ezxml_t registry, ezxml_t superStruct, ezxml_t var
9861010
vararrdims = ezxml_attr(var_arr_xml, "dimensions");
9871011
vararrpersistence = ezxml_attr(var_arr_xml, "persistence");
9881012
vararrdefaultval = ezxml_attr(var_arr_xml, "default_value");
1013+
vararrmissingval = ezxml_attr(var_arr_xml, "missing_value");
9891014
vararrpackages = ezxml_attr(var_arr_xml, "packages");
9901015
vararrtimelevs = ezxml_attr(var_arr_xml, "time_levs");
9911016
vararrname_in_code = ezxml_attr(var_arr_xml, "name_in_code");
@@ -1016,7 +1041,7 @@ int parse_var_array(FILE *fd, ezxml_t registry, ezxml_t superStruct, ezxml_t var
10161041
snprintf(spacing, 1024, " ");
10171042

10181043
// Determine field type and default value.
1019-
get_field_information(vararrtype, vararrdefaultval, default_value, &type);
1044+
get_field_information(vararrtype, vararrdefaultval, default_value, vararrmissingval, missing_value, &type);
10201045

10211046
// Determine ndims, hasTime, and decomp type
10221047
build_dimension_information(registry, var_arr_xml, &ndims, &hasTime, &decomp);
@@ -1290,25 +1315,26 @@ int parse_var_array(FILE *fd, ezxml_t registry, ezxml_t superStruct, ezxml_t var
12901315
vardesc = ezxml_attr(var_xml, "description");
12911316
varunits = ezxml_attr(var_xml, "units");
12921317

1293-
if ( vardesc != NULL || varunits != NULL) {
1294-
if(!varname_in_code){
1295-
varname_in_code = ezxml_attr(var_xml, "name");
1296-
}
1318+
if(!varname_in_code){
1319+
varname_in_code = ezxml_attr(var_xml, "name");
1320+
}
12971321

1298-
fortprintf(fd, " if (associated(newSubPool)) then\n");
1299-
fortprintf(fd, " call mpas_pool_get_dimension(newSubPool, 'index_%s', const_index)\n", varname_in_code);
1300-
fortprintf(fd, " end if\n");
1301-
fortprintf(fd, " if (const_index > 0) then\n", spacing);
1302-
if ( vardesc != NULL ) {
1303-
fortprintf(fd, " call mpas_add_att(%s(%d) %% attLists(const_index) %% attList, 'long_name', '%s')\n", pointer_name, time_lev, vardesc);
1304-
}
1322+
fortprintf(fd, " if (associated(newSubPool)) then\n");
1323+
fortprintf(fd, " call mpas_pool_get_dimension(newSubPool, 'index_%s', const_index)\n", varname_in_code);
1324+
fortprintf(fd, " end if\n");
1325+
fortprintf(fd, " if (const_index > 0) then\n", spacing);
1326+
if ( vardesc != NULL ) {
1327+
fortprintf(fd, " call mpas_add_att(%s(%d) %% attLists(const_index) %% attList, 'long_name', '%s')\n", pointer_name, time_lev, vardesc);
1328+
}
13051329

1306-
if ( varunits != NULL ) {
1307-
fortprintf(fd, " call mpas_add_att(%s(%d) %% attLists(const_index) %% attList, 'units', '%s')\n", pointer_name, time_lev, varunits);
1308-
}
1309-
fortprintf(fd, " %s(%d) %% constituentNames(const_index) = '%s'\n", pointer_name, time_lev, varname);
1310-
fortprintf(fd, " end if\n", spacing);
1330+
if ( varunits != NULL ) {
1331+
fortprintf(fd, " call mpas_add_att(%s(%d) %% attLists(const_index) %% attList, 'units', '%s')\n", pointer_name, time_lev, varunits);
13111332
}
1333+
1334+
fortprintf(fd, " call mpas_add_att(%s(%d) %% attLists(const_index) %% attList, 'missing_value', %s)\n", pointer_name, time_lev, missing_value);
1335+
fortprintf(fd, " call mpas_add_att(%s(%d) %% attLists(const_index) %% attList, '_FillValue', %s)\n", pointer_name, time_lev, missing_value);
1336+
fortprintf(fd, " %s(%d) %% constituentNames(const_index) = '%s'\n", pointer_name, time_lev, varname);
1337+
fortprintf(fd, " end if\n", spacing);
13121338
}
13131339

13141340

@@ -1356,7 +1382,7 @@ int parse_var(FILE *fd, ezxml_t registry, ezxml_t superStruct, ezxml_t currentVa
13561382
const char *structtimelevs, *vartimelevs;
13571383
const char *structname, *structlevs, *structpackages;
13581384
const char *substructname;
1359-
const char *varname, *varpersistence, *vartype, *vardims, *varunits, *vardesc, *vararrgroup, *varstreams, *vardefaultval, *varpackages;
1385+
const char *varname, *varpersistence, *vartype, *vardims, *varunits, *vardesc, *vararrgroup, *varstreams, *vardefaultval, *varpackages, *varmissingval;
13601386
const char *varname2, *vararrgroup2;
13611387
const char *varname_in_code;
13621388
const char *streamname, *streamname2;
@@ -1373,6 +1399,7 @@ int parse_var(FILE *fd, ezxml_t registry, ezxml_t superStruct, ezxml_t currentVa
13731399
char pointer_name[1024];
13741400
char package_spacing[1024];
13751401
char default_value[1024];
1402+
char missing_value[1024];
13761403

13771404
var_xml = currentVar;
13781405

@@ -1390,6 +1417,7 @@ int parse_var(FILE *fd, ezxml_t registry, ezxml_t superStruct, ezxml_t currentVa
13901417
varname_in_code = ezxml_attr(var_xml, "name_in_code");
13911418
varunits = ezxml_attr(var_xml, "units");
13921419
vardesc = ezxml_attr(var_xml, "description");
1420+
varmissingval = ezxml_attr(var_xml, "missing_value");
13931421

13941422
if(!varname_in_code){
13951423
varname_in_code = ezxml_attr(var_xml, "name");
@@ -1412,9 +1440,8 @@ int parse_var(FILE *fd, ezxml_t registry, ezxml_t superStruct, ezxml_t currentVa
14121440

14131441
fortprintf(fd, "! Define variable %s\n", varname);
14141442

1415-
14161443
// Determine field type and default value.
1417-
get_field_information(vartype, vardefaultval, default_value, &type);
1444+
get_field_information(vartype, vardefaultval, default_value, varmissingval, missing_value, &type);
14181445

14191446
// Determine ndims, hasTime, and decomp type
14201447
build_dimension_information(registry, var_xml, &ndims, &hasTime, &decomp);
@@ -1469,8 +1496,9 @@ int parse_var(FILE *fd, ezxml_t registry, ezxml_t superStruct, ezxml_t currentVa
14691496
free(tofree);
14701497
}
14711498

1499+
fortprintf(fd, " %s(%d) %% defaultValue = %s\n", pointer_name, time_lev, default_value);
1500+
fortprintf(fd, " %s(%d) %% defaultValue = %s\n", pointer_name, time_lev, default_value);
14721501
if ( ndims > 0 ) {
1473-
fortprintf(fd, " %s(%d) %% defaultValue = %s\n", pointer_name, time_lev, default_value);
14741502
fortprintf(fd, " nullify(%s(%d) %% array)\n", pointer_name, time_lev);
14751503
} else {
14761504
fortprintf(fd, " %s(%d) %% scalar = %s\n", pointer_name, time_lev, default_value);
@@ -1490,6 +1518,9 @@ int parse_var(FILE *fd, ezxml_t registry, ezxml_t superStruct, ezxml_t currentVa
14901518
fortprintf(fd, " call mpas_add_att(%s(%d) %% attLists(1) %% attList, 'long_name', '%s')\n", pointer_name, time_lev, vardesc);
14911519
}
14921520

1521+
fortprintf(fd, " call mpas_add_att(%s(%d) %% attLists(1) %% attList, 'missing_value', %s)\n", pointer_name, time_lev, missing_value);
1522+
fortprintf(fd, " call mpas_add_att(%s(%d) %% attLists(1) %% attList, '_FillValue', %s)\n", pointer_name, time_lev, missing_value);
1523+
14931524
fortprintf(fd, " %s(%d) %% block => block\n", pointer_name, time_lev);
14941525

14951526
}
@@ -1690,7 +1721,7 @@ int generate_struct_links(FILE *fd, int curLevel, ezxml_t superStruct, ezxml_t r
16901721
const char *structname;
16911722
const char *vartimelevs;
16921723
const char *varname, *vardims, *vartype;
1693-
const char *vardefaultval;
1724+
const char *vardefaultval, *varmissingval;
16941725
const char *varname_in_code;
16951726
int depth;
16961727
int err;
@@ -1701,6 +1732,7 @@ int generate_struct_links(FILE *fd, int curLevel, ezxml_t superStruct, ezxml_t r
17011732
char *string, *tofree, *token;
17021733
char pointer_name[1024];
17031734
char default_value[1024];
1735+
char missing_value[1024];
17041736

17051737
depth = curLevel + 1;
17061738

@@ -1743,6 +1775,7 @@ int generate_struct_links(FILE *fd, int curLevel, ezxml_t superStruct, ezxml_t r
17431775
vartimelevs = ezxml_attr(var_arr_xml, "time_levs");
17441776
vartype = ezxml_attr(var_arr_xml, "type");
17451777
vardefaultval = ezxml_attr(var_arr_xml, "default_value");
1778+
varmissingval = ezxml_attr(var_arr_xml, "missing_value");
17461779

17471780
if(!vartimelevs){
17481781
vartimelevs = ezxml_attr(subStruct, "time_levs");
@@ -1757,8 +1790,12 @@ int generate_struct_links(FILE *fd, int curLevel, ezxml_t superStruct, ezxml_t r
17571790
time_levs = 1;
17581791
}
17591792

1793+
if(!varmissingval){
1794+
varmissingval = vardefaultval;
1795+
}
1796+
17601797
// Determine field type and default value.
1761-
get_field_information(vartype, vardefaultval, default_value, &type);
1798+
get_field_information(vartype, vardefaultval, default_value, varmissingval, missing_value, &type);
17621799

17631800
// Determine number of dimensions
17641801
// and decomp type
@@ -1809,6 +1846,7 @@ int generate_struct_links(FILE *fd, int curLevel, ezxml_t superStruct, ezxml_t r
18091846
vartimelevs = ezxml_attr(var_xml, "time_levs");
18101847
vartype = ezxml_attr(var_xml, "type");
18111848
vardefaultval = ezxml_attr(var_xml, "default_value");
1849+
varmissingval = ezxml_attr(var_xml, "missing_value");
18121850
varname_in_code = ezxml_attr(var_xml, "name_in_code");
18131851

18141852
if(!vartimelevs){
@@ -1828,8 +1866,12 @@ int generate_struct_links(FILE *fd, int curLevel, ezxml_t superStruct, ezxml_t r
18281866
varname_in_code = ezxml_attr(var_xml, "name");
18291867
}
18301868

1869+
if(!varmissingval){
1870+
varmissingval = vardefaultval;
1871+
}
1872+
18311873
// Determine field type and default value.
1832-
get_field_information(vartype, vardefaultval, default_value, &type);
1874+
get_field_information(vartype, vardefaultval, default_value, varmissingval, missing_value, &type);
18331875

18341876
// Determine number of dimensions
18351877
// and decomp type
Collapse file

‎src/tools/registry/gen_inc.h‎

Copy file name to clipboardExpand all lines: src/tools/registry/gen_inc.h
+1-1Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -17,7 +17,7 @@ int add_package_to_list(const char * package, const char * package_list);
1717
int build_struct_package_lists(ezxml_t currentPosition, char * out_packages);
1818
int get_dimension_information(ezxml_t registry, const char *test_dimname, int *has_time, int *decomp);
1919
int build_dimension_information(ezxml_t registry, ezxml_t var, int *ndims, int *has_time, int *decomp);
20-
int get_field_information(const char *vartype, const char *varval, char *default_value, int *type);
20+
int get_field_information(const char *vartype, const char *varval, char *default_value, const char *varmissval, char *missing_value, int *type);
2121
int write_set_field_pointer(FILE *fd, const char *spacing, const char *iterator_name, const char *pool_name);
2222
void write_default_namelist(ezxml_t registry);
2323
int parse_packages_from_registry(ezxml_t registry);

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