Changed setup_robin1.bash and Makefile for use on robin1 machine.
9 * Loop through one month of hourly history tapes from the Community Land Model
10 * and generate monthly statistics (means and standard deviations) of fields
17 #define HOURS_PER_DAY 24
18 #define MIN_PER_HOUR 60
19 #define SEC_PER_MIN 60
20 #define SEC_PER_HOUR (MIN_PER_HOUR * SEC_PER_MIN)
22 static char *metadata_vars[] = {
28 "hour", /* new metadata variable to be added to output files */
58 struct text_att *next;
59 struct text_att *prev;
84 static char *time_name = "time";
85 static char *time_bounds_name = "time_bounds";
86 static char *mcsec_name = "mcsec";
87 static char *history_name = "history";
88 static char *nsamples_name = "nsamples";
89 static char *hour_name = "hour", *hour_long_name = "hour of day",
91 static char *cell_method_name = "cell_method";
93 static int nmvars = sizeof(metadata_vars)/sizeof(*metadata_vars);
94 static int input_ncid, input_ndims, input_nvars, input_ngatts, input_unlimdimid;
95 static struct text_att *input_gatt_head = NULL;
96 static struct dim *input_dim_head = NULL, **input_dim_idx;
97 static struct var *input_var_head = NULL;
98 /* translation stuff */
99 static int *idid2mdid, *idid2sdid; /* dimension IDs */
101 static int mean_ncid, mean_ndims, mean_nvars, mean_ngatts, mean_unlimdimid;
102 static int mean_hour_dimid; /* special notes */
103 static struct dim *mean_dim_head = NULL;
104 static struct var *mean_var_head = NULL;
105 static int stddev_ncid, stddev_ndims, stddev_nvars, stddev_ngatts, stddev_unlimdimid;
106 static int stddev_hour_dimid; /* special notes */
107 static struct dim *stddev_dim_head = NULL;
108 static struct var *stddev_var_head = NULL;
110 char is_metadata(char *name)
114 for (i = 0; i < nmvars && strcmp(name, metadata_vars[i]); i++);
123 struct dim *dimlist_find_by_name(struct dim *head, char *name)
126 struct dim *p = NULL;
130 for (i = 0 ; i == 0 || node != head; i++) {
131 if (!strcmp(node->name, name))
142 struct var *varlist_find_by_name(struct var *head, char *name)
149 for (i = 0 ; (i == 0 || node != head) && strcmp(node->name, name); i++)
151 if (i && node == head)
160 void gattlist_add_node(struct text_att **headp, char *name, char *value)
162 struct text_att *head, *node;
166 if (!(node = (struct text_att *)malloc(sizeof(struct text_att)))) {
167 perror("gattlist_add_node");
171 if (!(node->name = strdup(name))) {
172 perror("gattlist_add_node");
175 if (!(node->value = strdup(value))) {
176 perror("gattlist_add_node");
188 node->prev = head->prev;
189 /* set this after setting node->prev from here */
191 /* set this after having set node->prev */
192 node->prev->next = node;
198 struct dim *dimlist_add_node(struct dim **headp, int dimid, char *name, size_t len)
200 struct dim *head, *node;
204 if (!(node = (struct dim *)malloc(sizeof(struct dim)))) {
205 perror("dimlist_add_node");
210 if (!(node->name = strdup(name))) {
211 perror("dimlist_add_node");
224 node->prev = head->prev;
225 /* set this after setting node->prev from here */
227 /* set this after having set node->prev */
228 node->prev->next = node;
234 void varlist_add_node(struct var **headp, int ncvarid, char *name,
235 nc_type nctype, int ndims, int *dimids, int natts, char FillFlag,
239 struct var *head, *node;
243 if (!(node = (struct var *)malloc(sizeof(struct var)))) {
244 perror("varlist_add_node");
248 node->ncvarid = ncvarid;
249 if (!(node->name = strdup(name))) {
250 perror("varlist_add_node");
253 node->nctype = nctype;
255 if (!(node->dimids = (int *)malloc(ndims * sizeof(int)))) {
256 perror("varlist_add_node");
259 for (i = 0; i < ndims; i++) node->dimids[i] = dimids[i];
261 node->metadata = is_metadata(name);
262 node->FillFlag = FillFlag;
263 node->FillValue = FillValue;
273 node->prev = head->prev;
274 /* set this after setting node->prev from here */
276 /* set this after having set node->prev */
277 node->prev->next = node;
283 void varlist_print(struct var *headp)
288 printf("Beginning of Variable List\n");
292 for (j = 0; j == 0 || node != headp; j++) {
293 printf("Variable %d (ptr=%ld):\n", j, (long)node);
294 printf("\tncvarid = %d\n", node->ncvarid);
295 printf("\tname = %s\n", node->name);
296 printf("\tnctype = %d\n", node->nctype);
297 printf("\tndims = %d\n", node->ndims);
298 printf("\tdimids =");
299 for (i = 0; i < node->ndims; i++)
300 printf(" %d", node->dimids[i]);
302 printf("\tnatts = %d\n", node->natts);
303 printf("\tmetadata = %d\n", (int)node->metadata);
304 printf("\tnext = %ld\n", (long)node->next);
305 printf("\tprev = %ld\n", (long)node->prev);
310 printf("\tList undefined\n");
313 printf("End of Variable List\n");
318 void wrap_nc(int status)
320 if (status != NC_NOERR) {
321 fprintf(stderr, "netCDF error: %s\n", nc_strerror(status));
328 void get_dimensions(int ncid, int ndims, struct dim **dim_headp, struct dim ***in_dim_idxp)
331 char name[NC_MAX_NAME+1];
333 struct dim **in_dim_idx;
335 if (!(*in_dim_idxp = (struct dim **)malloc(ndims * sizeof(struct dim *)))) {
336 perror("*in_dim_idxp");
339 in_dim_idx = *in_dim_idxp;
341 for (i = 0; i < ndims; i++) {
342 wrap_nc(nc_inq_dim(ncid, i, name, &len));
343 in_dim_idx[i] = dimlist_add_node(dim_headp, i, name, len);
348 void get_gatts(int ncid, int ngatts, struct text_att **gatt_headp)
351 char name[NC_MAX_NAME+1], *value;
355 for (i = 0; i < ngatts; i++) {
356 wrap_nc(nc_inq_attname(ncid, NC_GLOBAL, i, name));
357 wrap_nc(nc_inq_att(ncid, NC_GLOBAL, name, &xtype, &len));
358 if (xtype != NC_CHAR) {
359 fprintf(stderr, "Global attribute %s is not of type NC_CHAR\n", name);
362 if (!(value = (char *)malloc((len+1)*sizeof(char)))) {
363 perror("get_gatts: value");
366 wrap_nc(nc_get_att_text(ncid, NC_GLOBAL, name, value));
367 value[(len+1-1)] = '\0';
368 gattlist_add_node(gatt_headp, name, value);
369 free(value); /* because gattlist_add_node() duplicates it */
375 void get_vars(int ncid, int nvars, struct var **var_headp)
377 int i, ndims, dimids[NC_MAX_VAR_DIMS], natts;
380 char name[NC_MAX_NAME+1], *fill_att_name = "_FillValue", FillFlag;
381 nc_type xtype, atype;
383 for (i = 0; i < nvars; i++) {
384 wrap_nc(nc_inq_var(ncid, i, name, &xtype, &ndims, dimids,
386 /* Check for _FillValue */
389 if (nc_inq_att(ncid, i, fill_att_name, &atype, &len)
391 if (atype == NC_FLOAT && len) {
392 wrap_nc(nc_get_att_float(ncid, i,
393 fill_att_name, &FillValue));
397 varlist_add_node(var_headp, i, name, xtype, ndims, dimids,
398 natts, FillFlag, FillValue);
404 int put_dimensions(struct dim *in_dim_head, int in_ndims, int in_unlimdimid,
405 size_t nsamples, int **in2outp, int out_ncid,
406 struct dim **out_dim_headp, int *out_unlimdimidp, int *out_hour_dimidp)
409 * Define dimensions on new files and build translation tables between
412 int j, dimid, ndims, *in2out;
418 if (!(*in2outp = (int *)malloc((in_ndims+1)*sizeof(int)))) {
419 perror("put_dimensions: in2outp");
426 for (j = 0; j == 0 || dnode != in_dim_head; j++) {
427 if (dnode->dimid == in_unlimdimid)
431 wrap_nc(nc_def_dim(out_ncid, dnode->name, len, &dimid));
432 dimlist_add_node(out_dim_headp, dimid, dnode->name, len);
434 in2out[dnode->dimid] = dimid;
435 if (dnode->dimid == in_unlimdimid)
436 *out_unlimdimidp = dimid;
438 * Just after the "time" dimension, add the new
439 * "nsamples" and "hour" dimensions.
441 if (!strcmp(dnode->name, time_name)) {
442 wrap_nc(nc_def_dim(out_ncid, nsamples_name, nsamples, &dimid));
443 dimlist_add_node(out_dim_headp, dimid, nsamples_name, nsamples);
446 wrap_nc(nc_def_dim(out_ncid, hour_name, HOURS_PER_DAY, &dimid));
447 dimlist_add_node(out_dim_headp, dimid, hour_name, HOURS_PER_DAY);
449 /* Track hour dimid for out files */
450 *out_hour_dimidp = dimid;
457 fprintf(stderr, "WARNING: No dimensions defined!\n");
463 int put_gatts(struct text_att *in_gatt_head, int out_ncid, char *out_history)
466 * Write out global attributes matching those of the input file.
467 * Change history attribute to the string passed in as an argument.
469 int j, hflag = 0, ngatts;
471 struct text_att *anode;
476 anode = in_gatt_head;
477 for (j = 0; j == 0 || anode != in_gatt_head; j++) {
478 if (!strcmp(anode->name, history_name)) {
483 value = anode->value;
484 wrap_nc(nc_put_att_text(out_ncid, NC_GLOBAL, anode->name, strlen(value), value));
488 /* If no history attribute on input, add one to the output */
490 wrap_nc(nc_put_att_text(out_ncid, NC_GLOBAL, history_name, strlen(out_history), out_history));
495 fprintf(stderr, "WARNING: No global attributes defined!\n");
501 int translate_dimids(struct dim **in_dim_idx, char metadata, int in_ndims, int *in_dimids, int *in2out, int *out_dimids, int hour_dimid)
504 * Translate between input dimension IDs and those for the output file.
505 * For normal time-based variables, add a new dimension for hour of
506 * day. For metadata variables, do not add new dimensions, even if
507 * it is time-based. Return (possibly new) number of dimensions.
511 for (i = ndims = 0; i < in_ndims; i++, ndims++) {
512 out_dimids[ndims] = in2out[in_dimids[i]];
513 if (!strcmp((in_dim_idx[in_dimids[i]])->name, time_name)
516 out_dimids[ndims] = hour_dimid;
523 int copy_att(char metadata, int stat_type, int in_natts, int in_ncid,
524 int in_varid, int out_ncid, int out_varid)
527 * Copy the attributes of the input variable to those of the output
528 * variable. If the variable is not a metadata variable, ensure that
529 * the cell_method attribute is set either to "time: mean" or
530 * "time: standard_deviation", depending on the output file type.
534 char name[NC_MAX_NAME+1], cmflag = 0;
535 char *cell_methods[] = { "time: mean", "time: standard_deviation" };
537 for (i = natts = 0; i < in_natts; i++, natts++) {
538 wrap_nc(nc_inq_attname(in_ncid, in_varid, i, name));
539 if (!strcmp(name, cell_method_name) && !metadata) {
540 wrap_nc(nc_put_att_text(out_ncid, out_varid, cell_method_name, strlen(cell_methods[stat_type]), cell_methods[stat_type]));
544 wrap_nc(nc_copy_att(in_ncid, in_varid, name, out_ncid, out_varid));
547 * If no cell_method attribute was specified for a non-metadata
548 * variable on the input file, add the appropriate cell_method anyway
549 * on the output file.
551 if (!cmflag && !metadata) {
552 wrap_nc(nc_put_att_text(out_ncid, out_varid, cell_method_name, strlen(cell_methods[stat_type]), cell_methods[stat_type]));
559 int define_vars(int in_ncid, struct dim **in_dim_idx, struct var *in_var_head,
560 int *in2out, int out_ncid, int hour_dimid, struct var **out_var_headp,
564 * Define variables on output file and copy attributes from input file.
565 * Return number of variables defined.
567 int j, varid, nvars, ndims, dimids[NC_MAX_VAR_DIMS], natts;
575 * March through input variables creating (mostly) the same
576 * variables on the output file.
578 for (j = 0; j == 0 || vnode != in_var_head; j++) {
579 ndims = translate_dimids(in_dim_idx, vnode->metadata, vnode->ndims, vnode->dimids, in2out, dimids, hour_dimid);
580 wrap_nc(nc_def_var(out_ncid, vnode->name, vnode->nctype, ndims, dimids, &varid));
581 natts = copy_att(vnode->metadata, stat_type, vnode->natts, in_ncid, vnode->ncvarid, out_ncid, varid);
582 varlist_add_node(out_var_headp, varid, vnode->name, vnode->nctype, ndims, dimids, natts, vnode->FillFlag, vnode->FillValue);
585 * Just after the "time" variable, add the new "hour"
586 * variable for hour of day.
588 if (!strcmp(vnode->name, time_name)) {
590 dimids[0] = hour_dimid;
591 wrap_nc(nc_def_var(out_ncid, hour_name, NC_FLOAT, ndims, dimids, &varid));
592 wrap_nc(nc_put_att_text(out_ncid, varid, "long_name", strlen(hour_long_name), hour_long_name));
593 wrap_nc(nc_put_att_text(out_ncid, varid, "units", strlen(hour_units), hour_units));
594 varlist_add_node(out_var_headp, varid, hour_name, NC_FLOAT, ndims, dimids, 2, 0, 0.0);
602 fprintf(stderr, "WARNING: No variables defined!\n");
608 void *alloc_var(nc_type nctype, size_t len)
614 if (!(val = (float *)malloc((len) * sizeof(float)))) {
615 perror("alloc_var: val");
620 if (!(val = (int *)malloc((len) * sizeof(int)))) {
621 perror("alloc_var: val");
626 if (!(val = (double *)malloc((len) * sizeof(double)))) {
627 perror("alloc_var: val");
632 if (!(val = (char *)malloc(((len)+1) * sizeof(char)))) {
633 perror("alloc_var: val");
638 fprintf(stderr, "netCDF external data type %d not supported\n", nctype);
645 void *read_var(int ncid, int varid, nc_type nctype, int ndims, int *dimids, struct dim **dim_idx)
648 size_t len = (size_t)1;
651 /* Figure out the total size */
652 for (i = 0; i < ndims; i++) len *= (dim_idx[dimids[i]])->len;
654 val = alloc_var(nctype, len);
658 wrap_nc(nc_get_var_float(ncid, varid, val));
661 wrap_nc(nc_get_var_int(ncid, varid, val));
664 wrap_nc(nc_get_var_double(ncid, varid, val));
667 wrap_nc(nc_get_var_text(ncid, varid, val));
670 fprintf(stderr, "netCDF external data type %d not supported\n", nctype);
677 void *read_timeslice(int ncid, int varid, nc_type nctype, int ndims, int *dimids, struct dim **dim_idx, size_t tslice)
680 size_t len = (size_t)1, start[NC_MAX_VAR_DIMS], count[NC_MAX_VAR_DIMS];
683 /* Make sure time is really the first dimension */
684 if (strcmp((dim_idx[dimids[0]])->name, time_name)) {
685 fprintf(stderr, "read_timeslice: %s is not first dimension of variable!\n", time_name);
689 * Figure out the total size for the slice (start at second dimension)
690 * and build start/count vectors.
694 for (i = 1; i < ndims; i++) {
696 count[i] = (dim_idx[dimids[i]])->len;
697 len *= (dim_idx[dimids[i]])->len;
700 val = alloc_var(nctype, len);
704 wrap_nc(nc_get_vara_float(ncid, varid, start, count, val));
707 wrap_nc(nc_get_vara_int(ncid, varid, start, count, val));
710 wrap_nc(nc_get_vara_double(ncid, varid, start, count, val));
713 wrap_nc(nc_get_vara_text(ncid, varid, start, count, val));
716 fprintf(stderr, "netCDF external data type %d not supported\n", nctype);
723 void write_var(int ncid, int varid, nc_type nctype, void *val)
727 wrap_nc(nc_put_var_float(ncid, varid, val));
730 wrap_nc(nc_put_var_int(ncid, varid, val));
733 wrap_nc(nc_put_var_double(ncid, varid, val));
736 wrap_nc(nc_put_var_text(ncid, varid, val));
739 fprintf(stderr, "netCDF external data type %d not supported\n", nctype);
746 void write_timeslice(int ncid, int varid, nc_type nctype, int ndims, int *dimids, struct dim **dim_idx, void *val, size_t tslice)
749 size_t start[NC_MAX_VAR_DIMS], count[NC_MAX_VAR_DIMS];
751 /* Make sure time is really the first dimension */
752 if (strcmp((dim_idx[dimids[0]])->name, time_name)) {
753 fprintf(stderr, "write_timeslice: %s is not first dimension of variable!\n", time_name);
757 /* Build start/count vectors */
760 for (i = 1; i < ndims; i++) {
762 count[i] = (dim_idx[dimids[i]])->len;
767 wrap_nc(nc_put_vara_float(ncid, varid, start, count, val));
770 wrap_nc(nc_put_vara_int(ncid, varid, start, count, val));
773 wrap_nc(nc_put_vara_double(ncid, varid, start, count, val));
776 wrap_nc(nc_put_vara_text(ncid, varid, start, count, val));
779 fprintf(stderr, "netCDF external data type %d not supported\n", nctype);
786 void copy_metadata(int in_ncid, struct var *in_var_head,
787 struct dim **in_dim_idx, int out_ncid, struct var *out_var_head,
791 float hr[HOURS_PER_DAY];
792 struct var *in_vnode, *out_vnode;
795 for (i = 0; i < HOURS_PER_DAY; i++) hr[i] = (float)i;
798 in_vnode = in_var_head;
800 * March through input variables to stuff metadata values into
801 * the new output files. NOTE: Time-based metadata variables
802 * should contain only the last (time-slice) value (from all
805 for (j = 0; j == 0 || in_vnode != in_var_head; j++) {
806 if (in_vnode->metadata) {
807 out_vnode = varlist_find_by_name(out_var_head, in_vnode->name);
808 if (strcmp((input_dim_idx[in_vnode->dimids[0]])->name, time_name)) {
809 /* time is not the first dimension */
811 printf("Copying metadata variable %s\n",
814 val = read_var(in_ncid, in_vnode->ncvarid, in_vnode->nctype, in_vnode->ndims, in_vnode->dimids, in_dim_idx);
815 write_var(out_ncid, out_vnode->ncvarid, out_vnode->nctype, val);
818 /* time is the first dimension */
820 printf("Copying last value of \
821 time-based metadata variable %s\n", in_vnode->name);
823 val = read_timeslice(in_ncid, in_vnode->ncvarid, in_vnode->nctype, in_vnode->ndims, in_vnode->dimids, in_dim_idx, ((input_dim_idx[in_vnode->dimids[0]])->len - 1));
824 if (!strcmp(in_vnode->name, time_bounds_name))
825 write_timeslice(out_ncid, out_vnode->ncvarid, out_vnode->nctype, in_vnode->ndims, in_vnode->dimids, in_dim_idx, tbounds, 0);
827 write_timeslice(out_ncid, out_vnode->ncvarid, out_vnode->nctype, in_vnode->ndims, in_vnode->dimids, in_dim_idx, val, 0);
831 * Just after the "time" variable, write out
832 * the "hour" variable values.
834 if (!strcmp(in_vnode->name, time_name)) {
835 out_vnode = varlist_find_by_name(out_var_head, hour_name);
836 write_var(out_ncid, out_vnode->ncvarid,
837 out_vnode->nctype, hr);
842 printf("Skipping variable %s\n",
846 in_vnode = in_vnode->next;
853 void get_time_bounds(char *first_fname, char *last_fname, double *tbounds)
855 int time_dimid, time_bounds_varid;
856 size_t time_len, time_bounds_index[2];
859 /* Open first input file */
860 wrap_nc(nc_open(first_fname, NC_NOWRITE, &input_ncid));
861 /* Get dimension ID of the time dimension */
862 wrap_nc(nc_inq_dimid(input_ncid, time_name, &time_dimid));
863 /* Get length of time dimension */
864 wrap_nc(nc_inq_dimlen(input_ncid, time_dimid, &time_len));
865 /* Get variable ID of time_bounds variable */
866 wrap_nc(nc_inq_varid(input_ncid, time_bounds_name, &time_bounds_varid));
867 /* Set index for reading the first value of time_bounds from the
868 * first timeslice of the first file */
869 time_bounds_index[0] = time_bounds_index[1] = 0;
871 wrap_nc(nc_get_var1_double(input_ncid, time_bounds_varid,
872 time_bounds_index, &bnd1));
873 /* If the first and last file are not the same, close the first one and
874 * open the second one */
875 if (strcmp(first_fname, last_fname)) {
876 /* Close the first input file */
877 wrap_nc(nc_close(input_ncid));
878 /* Open the last input file */
879 wrap_nc(nc_open(last_fname, NC_NOWRITE, &input_ncid));
880 /* Get dimension ID of the time dimension */
881 wrap_nc(nc_inq_dimid(input_ncid, time_name, &time_dimid));
882 /* Get length of time dimension */
883 wrap_nc(nc_inq_dimlen(input_ncid, time_dimid, &time_len));
884 /* Get variable ID of time_bounds variable */
885 wrap_nc(nc_inq_varid(input_ncid, time_bounds_name,
886 &time_bounds_varid));
888 /* Set index for reading the second value of time_bounds from the
889 * last timeslice of the last file */
890 time_bounds_index[0] = time_len - 1; time_bounds_index[1] = 1;
892 wrap_nc(nc_get_var1_double(input_ncid, time_bounds_varid,
893 time_bounds_index, &bnd2));
895 /* Close the last input file */
896 wrap_nc(nc_close(input_ncid));
904 void open_inout(char *first_fname, char *last_fname, char *mean_fname, char *stddev_fname, char *flist, size_t nsamples)
906 char *mean_history_gatt, *stddev_history_gatt,
907 *mean_prefix="Statistical means from history files:",
908 *stddev_prefix="Statistical standard deviations from history files:";
912 * Construct strings for history global attributes for the two output
915 if (!(mean_history_gatt = (char *)malloc((strlen(mean_prefix) + strlen(flist)+1)*sizeof(char)))) {
916 perror("open_inout:mean_history_gatt");
919 if (!(stddev_history_gatt = (char *)malloc((strlen(stddev_prefix) + strlen(flist)+1)*sizeof(char)))) {
920 perror("open_inout:stddev_history_gatt");
923 sprintf(mean_history_gatt, "%s%s", mean_prefix, flist);
924 sprintf(stddev_history_gatt, "%s%s", stddev_prefix, flist);
926 /* The two time_bounds values must be handled explicitly by obtaining
927 * the first one from the first file and the last one from the last
928 * file. These are then passed to copy_metadata() below. */
929 get_time_bounds(first_fname, last_fname, tbounds);
931 fprintf(stderr, "Got back tbounds=%lf,%lf\n", tbounds[0], tbounds[1]);
934 /* Open last input file */
935 wrap_nc(nc_open(last_fname, NC_NOWRITE, &input_ncid));
936 /* Inquire about number of dimensions, variables, global attributes
937 * and the ID of the unlimited dimension
939 wrap_nc(nc_inq(input_ncid, &input_ndims, &input_nvars, &input_ngatts,
941 /* Grab dimension IDs and lengths from input file */
942 get_dimensions(input_ncid, input_ndims, &input_dim_head, &input_dim_idx);
943 /* Grab desired global attributes from input file */
944 get_gatts(input_ncid, input_ngatts, &input_gatt_head);
945 /* Grab variable IDs and attributes from input file */
946 get_vars(input_ncid, input_nvars, &input_var_head);
948 varlist_print(input_var_head);
950 /* Create netCDF files for monthly means and standard deviations */
951 /* Create new netCDF files */
952 wrap_nc(nc_create(mean_fname, NC_NOCLOBBER, &mean_ncid));
953 wrap_nc(nc_create(stddev_fname, NC_NOCLOBBER, &stddev_ncid));
954 /* Define dimensions */
955 mean_ndims = put_dimensions(input_dim_head, input_ndims,
956 input_unlimdimid, nsamples, &idid2mdid, mean_ncid,
957 &mean_dim_head, &mean_unlimdimid, &mean_hour_dimid);
958 stddev_ndims = put_dimensions(input_dim_head, input_ndims,
959 input_unlimdimid, nsamples, &idid2sdid, stddev_ncid,
960 &stddev_dim_head, &stddev_unlimdimid, &stddev_hour_dimid);
961 /* Define variables and their attributes */
962 mean_nvars = define_vars(input_ncid, input_dim_idx, input_var_head,
963 idid2mdid, mean_ncid, mean_hour_dimid, &mean_var_head,
965 stddev_nvars = define_vars(input_ncid, input_dim_idx, input_var_head,
966 idid2sdid, stddev_ncid, stddev_hour_dimid, &stddev_var_head,
968 /* Store global attributes */
969 mean_ngatts = put_gatts(input_gatt_head, mean_ncid, mean_history_gatt);
970 stddev_ngatts = put_gatts(input_gatt_head, stddev_ncid,
971 stddev_history_gatt);
972 /* End define mode */
973 wrap_nc(nc_enddef(mean_ncid));
974 wrap_nc(nc_enddef(stddev_ncid));
975 /* Write out metdata variables that do not depend on "time" */
976 copy_metadata(input_ncid, input_var_head, input_dim_idx, mean_ncid,
977 mean_var_head, tbounds);
978 copy_metadata(input_ncid, input_var_head, input_dim_idx, stddev_ncid,
979 stddev_var_head, tbounds);
981 wrap_nc(nc_close(input_ncid));
986 size_t count_samples(int nifnames, char **input_fnames)
989 char name[NC_MAX_NAME+1];
992 for (i = 0; i < nifnames; i++) {
993 /* Open input file */
994 wrap_nc(nc_open(input_fnames[i], NC_NOWRITE, &input_ncid));
996 * Inquire about number of dimensions, variables, global
997 * attributes and the ID of the unlimited dimension
999 wrap_nc(nc_inq(input_ncid, &input_ndims, &input_nvars,
1000 &input_ngatts, &input_unlimdimid));
1001 wrap_nc(nc_inq_dim(input_ncid, input_unlimdimid, name, &len));
1002 if (strcmp(name, time_name)) {
1003 fprintf(stderr, "%s is not the unlimited dimension for file %s!\n", time_name, input_fnames[i]);
1007 printf("%ld samples in %s\n", (long)len, input_fnames[i]);
1009 wrap_nc(nc_close(input_ncid));
1015 void alloc_means_stddevs(size_t d1, size_t d2, double ***meansp, double ***stddevsp, size_t ***cell_samplesp)
1018 * Allocate space for arrays of means and standard deviations by
1022 size_t **cell_samples;
1023 double **means, **stddevs;
1025 if (!(*meansp = (double **)malloc(HOURS_PER_DAY * sizeof(double *)))) {
1026 perror("alloc_means_stddevs:*meansp");
1029 if (!(*stddevsp = (double **)malloc(HOURS_PER_DAY * sizeof(double *)))) {
1030 perror("alloc_means_stddevs:*stddevsp");
1033 if (!(*cell_samplesp = (size_t **)malloc(HOURS_PER_DAY * sizeof(size_t *)))) {
1034 perror("alloc_means_stddevs:*cell_samplesp");
1039 stddevs = *stddevsp;
1040 cell_samples = *cell_samplesp;
1042 for (i = 0; i < HOURS_PER_DAY; i++) {
1043 if (!(means[i] = (double *)malloc(d1 * d2 * sizeof(double)))) {
1044 perror("alloc_means_stddevs:means[i]");
1047 if (!(stddevs[i] = (double *)malloc(d1 * d2 * sizeof(double)))) {
1048 perror("alloc_means_stddevs:stddevs[i]");
1051 if (!(cell_samples[i] = (size_t *)malloc(d1 * d2 * sizeof(size_t)))) {
1052 perror("alloc_means_stddevs:cell_samples[i]");
1060 void init_means_stddevs(size_t d1, size_t d2, double **means, double **stddevs, size_t **cell_samples, float FillValue)
1064 for (hr = 0; hr < HOURS_PER_DAY; hr++) {
1065 for (i = 0; i < d1; i++) {
1066 #pragma _CRI concurrent
1067 for (j = 0; j < d2; j++) {
1069 means[hr][pos] = FillValue;
1070 stddevs[hr][pos] = FillValue;
1071 cell_samples[hr][pos] = 0;
1079 void reset_cell_samples(size_t d1, size_t d2, size_t **cell_samples)
1083 for (hr = 0; hr < HOURS_PER_DAY; hr++) {
1084 for (i = 0; i < d1; i++) {
1085 #pragma _CRI concurrent
1086 for (j = 0; j < d2; j++) {
1088 cell_samples[hr][pos] = 0;
1096 void free_means_stddevs(double **means, double **stddevs, size_t **cell_samples)
1099 * Free space from arrays of means and standard deviations by
1104 for (i = 0; i < HOURS_PER_DAY; i++) {
1107 free(cell_samples[i]);
1117 void add_to_means_float(float *val, int sec, size_t d1, size_t d2,
1118 char FillFlag, float FillValue, double **means, size_t **cell_samples)
1122 hr = (int)floor((double)sec/(double)SEC_PER_HOUR);
1124 for (i = 0; i < d1; i++) {
1125 #pragma _CRI concurrent
1126 for (j = 0; j < d2; j++) {
1128 if (!FillFlag || (FillFlag && val[pos] != FillValue)) {
1129 if (cell_samples[hr][pos] == 0)
1130 means[hr][pos] = (double)val[pos];
1132 means[hr][pos] += (double)val[pos];
1133 ++cell_samples[hr][pos];
1141 void add_to_means_double(double *val, int sec, size_t d1, size_t d2,
1142 char FillFlag, float FillValue, double **means, size_t **cell_samples)
1146 hr = (int)floor((double)sec/(double)SEC_PER_HOUR);
1148 for (i = 0; i < d1; i++) {
1149 #pragma _CRI concurrent
1150 for (j = 0; j < d2; j++) {
1152 if (!FillFlag || (FillFlag && val[pos] != FillValue)) {
1153 if (cell_samples[hr][pos] == 0)
1154 means[hr][pos] = val[pos];
1156 means[hr][pos] += val[pos];
1157 ++cell_samples[hr][pos];
1166 void divide_means(size_t d1, size_t d2, double **means, size_t **cell_samples)
1170 for (hr = 0; hr < HOURS_PER_DAY; hr++) {
1171 for (i = 0; i < d1; i++) {
1172 #pragma _CRI concurrent
1173 for (j = 0; j < d2; j++) {
1175 if (cell_samples[hr][pos] != 0) {
1176 means[hr][pos] /= (double)cell_samples[hr][pos];
1185 void add_to_stddevs_float(float *val, int sec, size_t d1, size_t d2,
1186 char FillFlag, float FillValue, double **means, double **stddevs,
1187 size_t **cell_samples)
1192 hr = (int)floor((double)sec/(double)SEC_PER_HOUR);
1194 for (i = 0; i < d1; i++) {
1195 #pragma _CRI concurrent
1196 for (j = 0; j < d2; j++) {
1198 if (!FillFlag || (FillFlag && val[pos] != FillValue
1199 && means[hr][pos] != FillValue)) {
1200 delta = means[hr][pos] - (double)val[pos];
1201 if (cell_samples[hr][pos] == 0)
1202 stddevs[hr][pos] = delta * delta;
1204 stddevs[hr][pos] += delta * delta;
1205 ++cell_samples[hr][pos];
1213 void add_to_stddevs_double(double *val, int sec, size_t d1, size_t d2,
1214 char FillFlag, float FillValue, double **means, double **stddevs,
1215 size_t **cell_samples)
1220 hr = (int)floor((double)sec/(double)SEC_PER_HOUR);
1222 for (i = 0; i < d1; i++) {
1223 #pragma _CRI concurrent
1224 for (j = 0; j < d2; j++) {
1226 if (!FillFlag || (FillFlag && val[pos] != FillValue
1227 && means[hr][pos] != FillValue)) {
1228 delta = means[hr][pos] - val[pos];
1229 if (cell_samples[hr][pos] == 0)
1230 stddevs[hr][pos] = delta * delta;
1232 stddevs[hr][pos] += delta * delta;
1233 ++cell_samples[hr][pos];
1242 void divide_sqrt_stddevs(size_t d1, size_t d2, double **stddevs, size_t **cell_samples)
1246 for (hr = 0; hr < HOURS_PER_DAY; hr++) {
1247 for (i = 0; i < d1; i++) {
1248 #pragma _CRI concurrent
1249 for (j = 0; j < d2; j++) {
1251 if (cell_samples[hr][pos] != 0) {
1252 stddevs[hr][pos] /= (double)cell_samples[hr][pos];
1253 stddevs[hr][pos] = sqrt(stddevs[hr][pos]);
1263 void read_and_compute(int nifnames, char **input_fnames, size_t d1, size_t d2, char *var_name, nc_type nctype, int level, int ndims, char FillFlag, float FillValue, int stat_type, double **means, double **stddevs, size_t **cell_samples)
1267 size_t len, start[NC_MAX_VAR_DIMS], count[NC_MAX_VAR_DIMS];
1268 char name[NC_MAX_NAME+1];
1271 /* Allocate space for timeslice */
1272 val = alloc_var(nctype, (d1 * d2));
1274 for (i = 0; i < nifnames; i++) {
1276 printf("\tOpening %s", input_fnames[i]);
1277 if (ndims > 3) printf(" to retrieve level %d", level);
1278 if (stat_type == MEAN_TYPE)
1279 printf(" for computing means\n");
1281 printf(" for computing stddevs\n");
1283 /* Open input file */
1284 wrap_nc(nc_open(input_fnames[i], NC_NOWRITE, &input_ncid));
1286 * Inquire about number of dimensions, variables, global
1287 * attributes and the ID of the unlimited dimension
1289 wrap_nc(nc_inq(input_ncid, &input_ndims, &input_nvars,
1290 &input_ngatts, &input_unlimdimid));
1291 wrap_nc(nc_inq_dim(input_ncid, input_unlimdimid, name, &len));
1292 if (strcmp(name, time_name)) {
1293 fprintf(stderr, "%s is not the unlimited dimension for file %s!\n", time_name, input_fnames[i]);
1296 /* Get seconds of day variable */
1297 wrap_nc(nc_inq_varid(input_ncid, mcsec_name, &varid));
1298 if (!(mcsec = (int *)malloc(len * sizeof(int)))) {
1299 perror("read_and_compute:mcsec");
1302 wrap_nc(nc_get_var_int(input_ncid, varid, mcsec));
1303 /* Get variable ID for requested variable */
1304 wrap_nc(nc_inq_varid(input_ncid, var_name, &varid));
1305 /* Retrieve time slice of desired variable */
1306 for (ts = 0; ts < len; ts++) {
1309 start[(ndims-2)] = 0;
1310 count[(ndims-2)] = d1;
1311 start[(ndims-1)] = 0;
1312 count[(ndims-1)] = d2;
1319 wrap_nc(nc_get_vara_float(input_ncid, varid, start, count, val));
1320 if (stat_type == MEAN_TYPE)
1321 add_to_means_float(val, mcsec[ts], d1, d2, FillFlag, FillValue, means, cell_samples);
1323 add_to_stddevs_float(val, mcsec[ts], d1, d2, FillFlag, FillValue, means, stddevs, cell_samples);
1326 wrap_nc(nc_get_vara_double(input_ncid, varid, start, count, val));
1327 if (stat_type == MEAN_TYPE)
1328 add_to_means_double(val, mcsec[ts], d1, d2, FillFlag, FillValue, means, cell_samples);
1330 add_to_stddevs_double(val, mcsec[ts], d1, d2, FillFlag, FillValue, means, stddevs, cell_samples);
1333 fprintf(stderr, "netCDF external data type %d not supported\n", nctype);
1338 /* Free mcsec vector */
1340 /* Close input file */
1341 wrap_nc(nc_close(input_ncid));
1343 /* Divide sums by number of samples */
1344 if (stat_type == MEAN_TYPE)
1345 divide_means(d1, d2, means, cell_samples);
1347 divide_sqrt_stddevs(d1, d2, stddevs, cell_samples);
1349 /* Free working variable array */
1355 float *double_to_float(size_t len, double *dvar)
1360 if (!(fvar = (float *)malloc(len * sizeof(float)))) {
1361 perror("double_to_float:fvar");
1365 for (i = 0; i < len; i++)
1366 fvar[i] = (float)dvar[i];
1371 void write_var_hours(int ncid, int varid, nc_type nctype, size_t d1, size_t d2,
1372 int level, int ndims, double **var_hours)
1374 /* Output dimensions should be one larger than input dimensions */
1376 size_t start[NC_MAX_VAR_DIMS], count[NC_MAX_VAR_DIMS];
1379 if (nctype == NC_FLOAT) {
1380 if (!(fvar = (float *)malloc(d1 * d2 * sizeof(float)))) {
1381 perror("write_var_hours:fvar");
1386 for (hr = 0; hr < HOURS_PER_DAY; hr++) {
1388 count[0] = 1; /* time */
1390 count[1] = 1; /* hour */
1391 start[(ndims-2)] = 0;
1392 count[(ndims-2)] = d1;
1393 start[(ndims-1)] = 0;
1394 count[(ndims-1)] = d2;
1401 for (i = 0; i < (d1 * d2); i++)
1402 fvar[i] = (float)var_hours[hr][i];
1403 wrap_nc(nc_put_vara_float(ncid, varid, start, count, fvar));
1406 wrap_nc(nc_put_vara_double(ncid, varid, start, count, var_hours[hr]));
1409 fprintf(stderr, "netCDF external data type %d not supported\n", nctype);
1414 if (nctype == NC_FLOAT)
1420 void compute_stats(int nifnames, char **input_fnames, size_t nsamples)
1423 size_t d1, d2, **cell_samples;
1424 double **means, **stddevs;
1425 struct var *in_vnode, *out_vnode;
1427 if (input_var_head) {
1428 in_vnode = input_var_head;
1429 /* March through non-metadata variables to compute stats */
1430 for (j = 0; j == 0 || in_vnode != input_var_head; j++) {
1431 if (!in_vnode->metadata) {
1432 /* Make sure time is really the first dimension */
1433 if (strcmp((input_dim_idx[in_vnode->dimids[0]])->name, time_name)) {
1434 fprintf(stderr, "compute_stats: %s is not first dimension of variable %s!\n", time_name, in_vnode->name);
1437 /* Figure out input dimensions */
1438 if (in_vnode->ndims < 3 || in_vnode->ndims > 4) {
1439 fprintf(stderr, "compute_stats: %s has %d dimensions!\n", in_vnode->name, in_vnode->ndims);
1442 /* Assume 2D output; find dimensions */
1443 d1 = (input_dim_idx[in_vnode->dimids[(in_vnode->ndims-2)]])->len;
1444 d2 = (input_dim_idx[in_vnode->dimids[(in_vnode->ndims-1)]])->len;
1445 if (in_vnode->ndims == 3)
1448 nlevels = (input_dim_idx[in_vnode->dimids[1]])->len;
1449 /* Allocate working space for means and stddevs */
1450 alloc_means_stddevs(d1, d2, &means, &stddevs, &cell_samples);
1451 init_means_stddevs(d1, d2, means, stddevs, cell_samples, in_vnode->FillValue);
1452 printf("Computing statistics for %s\n",
1454 /* Compute means and stddevs, then write them */
1455 for (k = 0; k < nlevels; k++) {
1456 /* Read and compute means */
1457 read_and_compute(nifnames, input_fnames, d1, d2, in_vnode->name, in_vnode->nctype, k, in_vnode->ndims, in_vnode->FillFlag, in_vnode->FillValue, MEAN_TYPE, means, stddevs, cell_samples);
1458 /* Find corresponding output variable on the mean output file */
1459 out_vnode = varlist_find_by_name(mean_var_head, in_vnode->name);
1460 /* Write out the means for this variable */
1461 write_var_hours(mean_ncid, out_vnode->ncvarid, out_vnode->nctype, d1, d2, k, out_vnode->ndims, means);
1462 /* Zero out cell_samples so they can be used as a flag again for computing stddevs */
1463 reset_cell_samples(d1, d2, cell_samples);
1464 /* Read and compute stddevs using means */
1465 read_and_compute(nifnames, input_fnames, d1, d2, in_vnode->name, in_vnode->nctype, k, in_vnode->ndims, in_vnode->FillFlag, in_vnode->FillValue, STDDEV_TYPE, means, stddevs, cell_samples);
1466 /* Find corresponding output variable on the stddev output file */
1467 out_vnode = varlist_find_by_name(stddev_var_head, in_vnode->name);
1468 /* Write out stddevs for this variable */
1469 write_var_hours(stddev_ncid, out_vnode->ncvarid, out_vnode->nctype, d1, d2, k, out_vnode->ndims, stddevs);
1472 /* Free working space for means and stddevs */
1473 free_means_stddevs(means, stddevs, cell_samples);
1475 in_vnode = in_vnode->next;
1481 void usage(char *program)
1483 fprintf(stderr, "Usage: %s -m mean.nc -s stddev.nc hist_file1.nc [ hist_file2.nc ... ]\n", program);
1484 fprintf(stderr, "WARNING: It is assumed that the list of input files is specified in time order!\n");
1488 int main(int argc, char **argv)
1490 int i, ic, nifnames;
1491 size_t len, pos, nsamples;
1492 char *mfname, *sfname, **ifnames, *flist;
1495 mfname = sfname = flist = NULL;
1499 printf("Number of metadata variables (nmvars) = %d\n", nmvars);
1503 /* check command-line flags and switches */
1504 while ((ic = getopt(argc, argv, "m:s:")) != -1) {
1507 if (!(mfname = strdup(optarg))) {
1513 if (!(sfname = strdup(optarg))) {
1522 fprintf(stderr, "Output file name for writing means required.\n");
1526 fprintf(stderr, "Output file name for writing standard deviations required.\n");
1530 if (optind < argc) {
1531 if (!(ifnames = (char **)malloc((argc-optind+1)*sizeof(char *)))) {
1535 for (i = optind; i < argc; i++) {
1536 if (!(ifnames[nifnames++] = strdup(argv[i]))) {
1537 perror("ifnames[nifnames++]");
1543 fprintf(stderr, "At least one input file name is required.\n");
1549 * Build list of input files to be included in the global history
1550 * attribute on the two outputs files.
1552 for (i = len = 0; i < nifnames; i++)
1553 len += strlen(ifnames[i]);
1554 len += nifnames + 1; /* space in front of every name + null terminator */
1555 if (!(flist = (char *)malloc(len * sizeof(char)))) {
1559 for (i = pos = 0; i < nifnames; pos += (strlen(ifnames[i])+1), i++)
1560 sprintf(&flist[pos], " %s", ifnames[i]);
1562 printf("flist=%s\n", flist);
1566 /* Open every file to count up the number of time samples. */
1567 nsamples = count_samples(nifnames, ifnames);
1569 printf("Number of samples across all files = %ld\n", (long)nsamples);
1574 * Open the *last* input file and the two output files (for mean and
1575 * standard deviation). Define dimensions, variables, and attributes
1576 * for the two output files based on the *last* input files. The
1577 * last file is used because some metadata variables will contain
1578 * only values from the last time slice from the period over which
1579 * the statistics are computed.
1581 open_inout(ifnames[0], ifnames[(nifnames-1)], mfname, sfname, flist,
1584 compute_stats(nifnames, ifnames, nsamples);
1586 /* Close the two output files */
1587 wrap_nc(nc_close(mean_ncid));
1588 wrap_nc(nc_close(stddev_ncid));