Newer
Older
#'Save objects of class 's2dv_cube' to data in NetCDF format
#'
#'@author Perez-Zanon Nuria, \email{nuria.perez@bsc.es}
#'
#'@description This function allows to divide and save a object of class
#''s2dv_cube' into a NetCDF file, allowing to reload the saved data using
#'\code{Start} function from StartR package. If the original 's2dv_cube' object
#'has been created from \code{CST_Start()}, then it can be reloaded with
#'@param data An object of class \code{s2dv_cube}.
#'@param destination A character string containing the directory name in which
#' to save the data. NetCDF file for each starting date are saved into the
#' folder tree: \cr
#' destination/Dataset/variable/. By default the function
#' creates and saves the data into the working directory.
#'@param sdate_dim A character string indicating the name of the start date
#' dimension. By default, it is set to 'sdate'. It can be NULL if there is no
#' start date dimension.
#'@param ftime_dim A character string indicating the name of the forecast time
#' dimension. By default, it is set to 'time'. It can be NULL if there is no
#' forecast time dimension.
#'@param dat_dim A character string indicating the name of dataset dimension.
#' By default, it is set to 'dataset'. It can be NULL if there is no dataset
#' dimension.
#'@param var_dim A character string indicating the name of variable dimension.
#' By default, it is set to 'var'. It can be NULL if there is no variable
#' dimension.
#'@param memb_dim A character string indicating the name of the member dimension.
#' By default, it is set to 'member'. It can be NULL if there is no member
#'@param startdates A vector of dates that will be used for the filenames
#' when saving the data in multiple files. It must be a vector of the same
#' length as the start date dimension of data. It must be a vector of class
#' \code{Dates}, \code{'POSIXct'} or character with lenghts between 1 and 10.
#' If it is NULL, the coordinate corresponding the the start date dimension or
#' the first Date of each time step will be used as the name of the files.
#' It is NULL by default.
Eva Rifà
committed
#'@param drop_dims A vector of character strings indicating the dimension names
#' of length 1 that need to be dropped in order that they don't appear in the
#' netCDF file. It is NULL by default (optional).
#'@param single_file A logical value indicating if all object is saved in a
#' single file (TRUE) or in multiple files (FALSE). When it is FALSE,
#' the array is separated for Datasets, variable and start date. It is FALSE
#' by default.
#'@param extra_string A character string to be include as part of the file name,
#' for instance, to identify member or realization. It would be added to the
#' file name between underscore characters.
#'@return Multiple or single NetCDF files containing the data array.\cr
#'\item{\code{single_file = TRUE}}{
#' All data is saved in a single file located in the specified destination
#' path with the following name:
#' <variable_name>_<extra_string>_<first_sdate>_<last_sdate>.nc. Multiple
#' variables are saved separately in the same file. The forecast time units
#' is extracted from the frequency of the time steps (hours, days, months).
#' The first value of forecast time is 1. If no frequency is found, the units
#' will be 'hours since' each start date and the time steps are assumed to be
#' equally spaced.
#'}
#'\item{\code{single_file = FALSE}}{
#' The data array is subset and stored into multiple files. Each file
#' contains the data subset for each start date, variable and dataset. Files
#' with different variables and Datasets are stored in separated directories
#' within the following directory tree: destination/Dataset/variable/.
#' The name of each file will be:
#' <variable_name>_<extra_string>_<sdate>.nc.
#'}
#'
#'@seealso \code{\link[startR]{Start}}, \code{\link{as.s2dv_cube}} and
#'\code{\link{s2dv_cube}}
#'data <- lonlat_temp$exp
#'CST_SaveExp(data = data, destination = destination, ftime_dim = 'time',
#' var_dim = NULL, ftime_dim = 'time', var_dim = NULL)
#'@import ncdf4
#'@importFrom s2dv Reorder
#'@importFrom ClimProjDiags Subset
#'@import multiApply
CST_SaveExp <- function(data, destination = "./", sdate_dim = 'sdate',
ftime_dim = 'time', dat_dim = 'dataset',
var_dim = 'var', memb_dim = 'member',
Eva Rifà
committed
startdates = NULL, drop_dims = NULL,
single_file = FALSE, extra_string = NULL) {
if (!inherits(data, 's2dv_cube')) {
stop("Parameter 'data' must be of the class 's2dv_cube', ",
"as output by CSTools::CST_Load.")
}
# Check object structure
if (!all(c('data', 'attrs') %in% names(data))) {
stop("Parameter 'data' must have at least 'data' and 'attrs' elements ",
"within the 's2dv_cube' structure.")
}
if (!inherits(data$attrs, 'list')) {
stop("Level 'attrs' must be a list with at least 'Dates' element.")
}
if (!all(c('coords') %in% names(data))) {
warning("Element 'coords' not found. No coordinates will be used.")
}
# metadata
if (is.null(data$attrs$Variable$metadata)) {
warning("No metadata found in element Variable from attrs.")
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
if (!inherits(data$attrs$Variable$metadata, 'list')) {
stop("Element metadata from Variable element in attrs must be a list.")
}
if (!any(names(data$attrs$Variable$metadata) %in% names(data$coords))) {
warning("Metadata is not found for any coordinate.")
} else if (!any(names(data$attrs$Variable$metadata) %in%
data$attrs$Variable$varName)) {
warning("Metadata is not found for any variable.")
}
}
# Dates
if (is.null(data$attrs$Dates)) {
stop("Element 'Dates' from 'attrs' level cannot be NULL.")
}
if (is.null(dim(data$attrs$Dates))) {
stop("Element 'Dates' from 'attrs' level must have time dimensions.")
}
# sdate_dim
if (!is.null(sdate_dim)) {
if (!is.character(sdate_dim)) {
stop("Parameter 'sdate_dim' must be a character string.")
}
if (length(sdate_dim) > 1) {
warning("Parameter 'sdate_dim' has length greater than 1 and ",
"only the first element will be used.")
sdate_dim <- sdate_dim[1]
}
} else if (length(dim(data$attrs$Dates)) == 1) {
sdate_dim <- 'sdate'
dim(data$data) <- c(sdate = 1, dim(data$data))
data$dims <- dim(data$data)
dim(data$attrs$Dates) <- c(sdate = 1, dim(data$attrs$Dates))
data$coords[[sdate_dim]] <- data$attrs$Dates[1]
}
# startdates
if (is.null(startdates)) {
startdates <- data$coords[[sdate_dim]]
if (!is.character(startdates)) {
warning(paste0("Parameter 'startdates' is not a character string, ",
"it will not be used."))
startdates <- data$coords[[sdate_dim]]
}
if (!is.null(sdate_dim)) {
if (dim(data$data)[sdate_dim] != length(startdates)) {
warning(paste0("Parameter 'startdates' doesn't have the same length ",
"as dimension '", sdate_dim,"', it will not be used."))
startdates <- data$coords[[sdate_dim]]
}
}
}
SaveExp(data = data$data,
destination = destination,
Dates = data$attrs$Dates,
coords = data$coords,
varname = data$attrs$Variable$varName,
metadata = data$attrs$Variable$metadata,
Datasets = data$attrs$Datasets,
dat_dim = dat_dim, sdate_dim = sdate_dim,
ftime_dim = ftime_dim, var_dim = var_dim,
Eva Rifà
committed
memb_dim = memb_dim,
drop_dims = drop_dims,
extra_string = extra_string,
single_file = single_file)
}
#'Save a multidimensional array with metadata to data in NetCDF format
#'@description This function allows to save a data array with metadata into a
#'NetCDF file, allowing to reload the saved data using \code{Start} function
#'from StartR package. If the original 's2dv_cube' object has been created from
#'\code{CST_Start()}, then it can be reloaded with \code{Start()}.
#'
#'@author Perez-Zanon Nuria, \email{nuria.perez@bsc.es}
#'
#'@param data A multi-dimensional array with named dimensions.
#'@param destination A character string indicating the path where to store the
#' NetCDF files.
#'@param Dates A named array of dates with the corresponding sdate and forecast
#' time dimension.
#'@param coords A named list with elements of the coordinates corresponding to
#' the dimensions of the data parameter. The names and length of each element
#' must correspond to the names of the dimensions. If any coordinate is not
#' provided, it is set as an index vector with the values from 1 to the length
#' of the corresponding dimension.
#'@param varname A character string indicating the name of the variable to be
#'@param metadata A named list where each element is a variable containing the
#' corresponding information. The information must be contained in a list of
#' lists for each variable.
#'@param Datasets A vector of character string indicating the names of the
#' datasets.
#'@param startdates A vector of dates that will be used for the filenames
#' when saving the data in multiple files. It must be a vector of the same
#' length as the start date dimension of data. It must be a vector of class
#' \code{Dates}, \code{'POSIXct'} or character with lenghts between 1 and 10.
#' If it is NULL, the first Date of each time step will be used as the name of
#' the files. It is NULL by default.
#'@param sdate_dim A character string indicating the name of the start date
#' dimension. By default, it is set to 'sdate'. It can be NULL if there is no
#' start date dimension.
#'@param ftime_dim A character string indicating the name of the forecast time
#' dimension. By default, it is set to 'time'. It can be NULL if there is no
#' forecast time dimension.
#'@param dat_dim A character string indicating the name of dataset dimension.
#' By default, it is set to 'dataset'. It can be NULL if there is no dataset
#' dimension.
#'@param var_dim A character string indicating the name of variable dimension.
#' By default, it is set to 'var'. It can be NULL if there is no variable
#' dimension.
#'@param memb_dim A character string indicating the name of the member dimension.
#' By default, it is set to 'member'. It can be NULL if there is no member
#' dimension.
Eva Rifà
committed
#'@param drop_dims A vector of character strings indicating the dimension names
#' of length 1 that need to be dropped in order that they don't appear in the
#' netCDF file. It is NULL by default (optional).
#'@param single_file A logical value indicating if all object is saved in a
#' unique file (TRUE) or in separated directories (FALSE). When it is FALSE,
#' the array is separated for Datasets, variable and start date. It is FALSE
Eva Rifà
committed
#' by default (optional).
#'@param extra_string A character string to be include as part of the file name,
#' for instance, to identify member or realization. It would be added to the
Eva Rifà
committed
#' file name between underscore characters (optional).
#'@return Multiple or single NetCDF files containing the data array.\cr
#'\item{\code{single_file = TRUE}}{
#' All data is saved in a single file located in the specified destination
#' path with the following name:
#' <variable_name>_<extra_string>_<first_sdate>_<last_sdate>.nc. Multiple
#' variables are saved separately in the same file. The forecast time units
#' is extracted from the frequency of the time steps (hours, days, months).
#' The first value of forecast time is 1. If no frequency is found, the units
#' will be 'hours since' each start date and the time steps are assumed to be
#' equally spaced.
#'}
#'\item{\code{single_file = FALSE}}{
#' The data array is subset and stored into multiple files. Each file
#' contains the data subset for each start date, variable and dataset. Files
#' with different variables and Datasets are stored in separated directories
#' within the following directory tree: destination/Dataset/variable/.
#' The name of each file will be:
#' <variable_name>_<extra_string>_<sdate>.nc.
#'}
#'data <- lonlat_temp$exp$data
#'lon <- lonlat_temp$exp$coords$lon
#'lat <- lonlat_temp$exp$coords$lat
#'coords <- list(lon = lon, lat = lat)
#'Datasets <- lonlat_temp$exp$attrs$Datasets
#'varname <- 'tas'
#'Dates <- lonlat_temp$exp$attrs$Dates
#'destination = './'
#'metadata <- lonlat_temp$exp$attrs$Variable$metadata
#'SaveExp(data = data, destination = destination, coords = coords,
#' Datasets = Datasets, varname = varname, Dates = Dates,
#' metadata = metadata, single_file = TRUE, ftime_dim = 'time',
#'@import ncdf4
#'@importFrom s2dv Reorder
#'@import multiApply
#'@importFrom ClimProjDiags Subset
SaveExp <- function(data, destination = "./", Dates = NULL, coords = NULL,
varname = NULL, metadata = NULL, Datasets = NULL,
startdates = NULL, dat_dim = 'dataset', sdate_dim = 'sdate',
ftime_dim = 'time', var_dim = 'var', memb_dim = 'member',
Eva Rifà
committed
drop_dims = NULL, single_file = FALSE, extra_string = NULL) {
## Initial checks
# data
if (is.null(data)) {
stop("Parameter 'data' cannot be NULL.")
}
dimnames <- names(dim(data))
if (is.null(dimnames)) {
stop("Parameter 'data' must be an array with named dimensions.")
}
# destination
if (!is.character(destination) | length(destination) > 1) {
stop("Parameter 'destination' must be a character string of one element ",
"indicating the name of the file (including the folder if needed) ",
"where the data will be saved.")
}
# Dates
if (!is.null(Dates)) {
if (!inherits(Dates, "POSIXct") & !inherits(Dates, "Date")) {
stop("Parameter 'Dates' must be of 'POSIXct' or 'Dates' class.")
}
if (is.null(dim(Dates))) {
stop("Parameter 'Dates' must have dimension names.")
}
}
Eva Rifà
committed
# drop_dims
if (!is.null(drop_dims)) {
if (!is.character(drop_dims) | any(!drop_dims %in% names(dim(data)))) {
warning("Parameter 'drop_dims' must be character string containing ",
"the data dimension names to be dropped. It will not be used.")
} else if (!all(dim(data)[drop_dims] %in% 1)) {
warning("Parameter 'drop_dims' can only contain dimension names ",
"that are of length 1. It will not be used.")
} else {
data <- Subset(x = data, along = drop_dims,
indices = lapply(1:length(drop_dims), function(x) 1),
drop = 'selected')
dimnames <- names(dim(data))
}
}
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
# coords
if (!is.null(coords)) {
if (!all(names(coords) %in% dimnames)) {
coords <- coords[-which(!names(coords) %in% dimnames)]
}
for (i_coord in dimnames) {
if (i_coord %in% names(coords)) {
if (length(coords[[i_coord]]) != dim(data)[i_coord]) {
warning(paste0("Coordinate '", i_coord, "' has different lenght as ",
"its dimension and it will not be used."))
coords[[i_coord]] <- 1:dim(data)[i_coord]
}
} else {
warning(paste0("Coordinate '", i_coord, "' is not provided ",
"and it will be set as index in element coords."))
coords[[i_coord]] <- 1:dim(data)[i_coord]
}
}
} else {
coords <- sapply(dimnames, function(x) 1:dim(data)[x])
}
# varname
if (is.null(varname)) {
warning("Parameter 'varname' is NULL. It will be assigned to 'X'.")
varname <- 'X'
} else if (length(varname) > 1) {
multiple_vars <- TRUE
} else {
multiple_vars <- FALSE
}
if (!all(sapply(varname, is.character))) {
stop("Parameter 'varname' must be a character string with the ",
"variable names.")
}
# metadata
if (is.null(metadata)) {
warning("Parameter 'metadata' is not provided so the metadata saved ",
"will be incomplete.")
}
# single_file
if (!inherits(single_file, 'logical')) {
warning("Parameter 'single_file' must be a logical value. It will be ",
"set as FALSE.")
single_file <- FALSE
if (!is.null(extra_string)) {
if (!is.character(extra_string)) {
stop("Parameter 'extra_string' must be a character string.")
}
}
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
465
466
467
468
469
470
471
472
473
474
475
476
477
478
479
480
481
482
## Dimensions checks
# Spatial coordinates
if (!any(dimnames %in% .KnownLonNames()) |
!any(dimnames %in% .KnownLatNames())) {
lon_dim <- NULL
lat_dim <- NULL
} else {
lon_dim <- dimnames[which(dimnames %in% .KnownLonNames())]
lat_dim <- dimnames[which(dimnames %in% .KnownLatNames())]
if (length(lon_dim) > 1) {
warning("Found more than one longitudinal dimension. Only the first one ",
"will be used.")
lon_dim <- lon_dim[1]
}
if (length(lat_dim) > 1) {
warning("Found more than one latitudinal dimension. Only the first one ",
"will be used.")
lat_dim <- lat_dim[1]
}
}
# ftime_dim
if (!is.null(ftime_dim)) {
if (!is.character(ftime_dim)) {
stop("Parameter 'ftime_dim' must be a character string.")
}
if (!all(ftime_dim %in% dimnames)) {
stop("Parameter 'ftime_dim' is not found in 'data' dimension.")
}
if (length(ftime_dim) > 1) {
warning("Parameter 'ftime_dim' has length greater than 1 and ",
"only the first element will be used.")
ftime_dim <- ftime_dim[1]
}
}
# sdate_dim
if (!is.null(sdate_dim)) {
if (!is.character(sdate_dim)) {
stop("Parameter 'sdate_dim' must be a character string.")
}
if (length(sdate_dim) > 1) {
warning("Parameter 'sdate_dim' has length greater than 1 and ",
"only the first element will be used.")
sdate_dim <- sdate_dim[1]
}
if (!all(sdate_dim %in% dimnames)) {
stop("Parameter 'sdate_dim' is not found in 'data' dimension.")
}
}
# memb_dim
if (!is.null(memb_dim)) {
if (!is.character(memb_dim)) {
stop("Parameter 'memb_dim' must be a character string.")
}
if (!all(memb_dim %in% dimnames)) {
stop("Parameter 'memb_dim' is not found in 'data' dimension. Set it ",
"as NULL if there is no member dimension.")
}
}
# dat_dim
if (!is.null(dat_dim)) {
if (!is.character(dat_dim)) {
stop("Parameter 'dat_dim' must be a character string.")
}
if (!all(dat_dim %in% dimnames)) {
stop("Parameter 'dat_dim' is not found in 'data' dimension. Set it ",
"as NULL if there is no Datasets dimension.")
}
if (length(dat_dim) > 1) {
warning("Parameter 'dat_dim' has length greater than 1 and ",
"only the first element will be used.")
dat_dim <- dat_dim[1]
}
n_datasets <- dim(data)[dat_dim]
} else {
n_datasets <- 1
}
# var_dim
if (!is.null(var_dim)) {
if (!is.character(var_dim)) {
stop("Parameter 'var_dim' must be a character string.")
}
if (!all(var_dim %in% dimnames)) {
stop("Parameter 'var_dim' is not found in 'data' dimension. Set it ",
"as NULL if there is no variable dimension.")
}
if (length(var_dim) > 1) {
warning("Parameter 'var_dim' has length greater than 1 and ",
"only the first element will be used.")
var_dim <- var_dim[1]
}
n_vars <- dim(data)[var_dim]
} else {
n_vars <- 1
}
# minimum dimensions
if (all(dimnames %in% c(var_dim, dat_dim))) {
if (!single_file) {
warning("Parameter data has only ",
paste(c(var_dim, dat_dim), collapse = ' and '), " dimensions ",
"and it cannot be splitted in multiple files. All data will ",
"be saved in a single file.")
single_file <- TRUE
}
}
# Dates dimension check
if (!is.null(Dates)) {
if (all(names(dim(Dates)) == c(ftime_dim, sdate_dim)) |
all(names(dim(Dates)) == c(sdate_dim, ftime_dim))) {
if (is.null(startdates)) {
startdates <- Subset(Dates, along = ftime_dim, 1, drop = 'selected')
} else if ((!inherits(startdates, "POSIXct") & !inherits(startdates, "Date")) &&
(!is.character(startdates) | (any(nchar(startdates) > 10) | any(nchar(startdates) < 1)))) {
warning("Parameter 'startdates' should be a character string containing ",
"the start dates in the format 'yyyy-mm-dd', 'yyyymmdd', 'yyyymm', ",
"'POSIXct' or 'Dates' class. Files will be named with Dates instead.")
startdates <- Subset(Dates, along = ftime_dim, 1, drop = 'selected')
if (!is.null(format(startdates, "%Y%m%d"))) {
startdates <- format(startdates, "%Y%m%d")
}
} else if (all(dim(Dates)[!names(dim(Dates)) %in% c(ftime_dim, sdate_dim)] == 1)) {
dim(Dates) <- dim(Dates)[names(dim(Dates)) %in% c(ftime_dim, sdate_dim)]
} else {
stop("Parameter 'Dates' must have start date dimension and ",
"forecast time dimension.")
}
}
# startdates
if (is.null(startdates)) {
if (is.null(sdate_dim)) {
startdates <- 'XXX'
} else {
startdates <- rep('XXX', dim(data)[sdate_dim])
}
} else {
if (is.null(sdate_dim)) {
if (length(startdates) != 1) {
warning("Parameter 'startdates' has length more than 1. Only first ",
"value will be used.")
startdates <- startdates[[1]]
}
}
}
# Datasets
if (is.null(Datasets)) {
if (!single_file) {
warning("Parameter 'Datasets' is NULL. Files will be saved with a ",
"directory name of 'XXX'.")
}
Datasets <- rep('XXX', n_datasets )
if (inherits(Datasets, 'list')) {
Datasets <- names(Datasets)
if (n_datasets > length(Datasets)) {
warning("Dimension 'Datasets' in 'data' is greater than those listed in ",
"element 'Datasets' and the first element will be reused.")
Datasets <- c(Datasets, rep(Datasets[1], n_datasets - length(Datasets)))
} else if (n_datasets < length(Datasets)) {
warning("Dimension 'Datasets' in 'data' is smaller than those listed in ",
"element 'Datasets' and only the firsts elements will be used.")
Datasets <- Datasets[1:n_datasets]
## Unknown dimensions check
alldims <- c(dat_dim, var_dim, sdate_dim, lon_dim, lat_dim, memb_dim, ftime_dim)
if (!all(dimnames %in% alldims)) {
unknown_dims <- dimnames[which(!dimnames %in% alldims)]
memb_dim <- c(memb_dim, unknown_dims)
alldims <- c(dat_dim, var_dim, sdate_dim, lon_dim, lat_dim, memb_dim, ftime_dim)
}
# Reorder
if (any(dimnames != alldims)) {
data <- Reorder(data, alldims)
dimnames <- names(dim(data))
if (!is.null(attr(data, 'dimensions'))) {
attr(data, 'dimensions') <- dimnames
}
}
## NetCDF dimensions definition
defined_dims <- NULL
extra_info_dim <- NULL
if (is.null(Dates)) {
filedims <- dimnames[which(!dimnames %in% c(dat_dim, var_dim))]
} else {
filedims <- dimnames[which(!dimnames %in% c(dat_dim, var_dim, sdate_dim, ftime_dim))]
}
for (i_coord in filedims) {
dim_info <- list()
# vals
if (i_coord %in% names(coords)) {
if (is.numeric(coords[[i_coord]])) {
dim_info[['vals']] <- as.vector(coords[[i_coord]])
} else {
dim_info[['vals']] <- 1:dim(data)[i_coord]
}
dim_info[['vals']] <- 1:dim(data)[i_coord]
573
574
575
576
577
578
579
580
581
582
583
584
585
586
587
588
589
590
591
592
593
594
595
596
597
598
599
600
601
602
603
604
605
606
607
608
609
610
611
612
613
614
615
616
617
618
619
620
621
622
623
624
625
626
627
628
629
630
631
632
633
634
635
636
637
638
639
640
641
642
643
644
645
646
647
648
649
# name
dim_info[['name']] <- i_coord
# len
dim_info[['len']] <- as.numeric(dim(data)[i_coord])
# unlim
dim_info[['unlim']] <- FALSE
# create_dimvar
dim_info[['create_dimvar']] <- TRUE
## metadata
if (i_coord %in% names(metadata)) {
if ('variables' %in% names(attributes(metadata[[i_coord]]))) {
# from Start: 'lon' or 'lat'
attrs <- attributes(metadata[[i_coord]])[['variables']][[i_coord]]
i_coord_info <- attrs[!sapply(attrs, inherits, 'list')]
} else if (inherits(metadata[[i_coord]], 'list')) {
# from Start and Load: main var
i_coord_info <- metadata[[i_coord]]
} else if (!is.null(attributes(metadata[[i_coord]]))) {
# from Load
i_coord_info <- attributes(metadata[[i_coord]])
} else {
stop("Metadata is not correct.")
}
# len
if ('size' %in% names(i_coord_info)) {
if (i_coord_info[['size']] != dim(data)[i_coord]) {
dim_info[['original_len']] <- i_coord_info[['size']]
i_coord_info[['size']] <- NULL
}
}
# units
if (!('units' %in% names(i_coord_info))) {
dim_info[['units']] <- ''
} else {
dim_info[['units']] <- i_coord_info[['units']]
i_coord_info[['units']] <- NULL
}
# calendar
if (!('calendar' %in% names(i_coord_info))) {
dim_info[['calendar']] <- NA
} else {
dim_info[['calendar']] <- i_coord_info[['calendar']]
i_coord_info[['calendar']] <- NULL
}
# longname
if ('long_name' %in% names(i_coord_info)) {
dim_info[['longname']] <- i_coord_info[['long_name']]
i_coord_info[['long_name']] <- NULL
} else if ('longname' %in% names(i_coord_info)) {
dim_info[['longname']] <- i_coord_info[['longname']]
i_coord_info[['longname']] <- NULL
} else {
if (i_coord %in% .KnownLonNames()) {
dim_info[['longname']] <- 'longitude'
} else if (i_coord %in% .KnownLatNames()) {
dim_info[['longname']] <- 'latitude'
}
}
# extra information
if (!is.null(names(i_coord_info))) {
extra_info_dim[[i_coord]] <- i_coord_info
}
} else {
# units
dim_info[['units']] <- "adim"
# longname
dim_info[['longname']] <- i_coord
# calendar
dim_info[['calendar']] <- NA
}
new_dim <- list(ncdim_def(name = dim_info[['name']], units = dim_info[['units']],
vals = dim_info[['vals']], unlim = dim_info[['unlim']],
create_dimvar = dim_info[['create_dimvar']],
calendar = dim_info[['calendar']],
longname = dim_info[['longname']]))
names(new_dim) <- i_coord
defined_dims <- c(defined_dims, new_dim)
652
653
654
655
656
657
658
659
660
661
662
663
664
665
666
667
668
669
670
671
672
673
674
675
676
677
678
679
680
681
682
683
684
685
686
687
688
689
690
691
692
693
694
695
696
697
698
699
defined_vars <- list()
if (!single_file) {
for (i in 1:n_datasets) {
path <- file.path(destination, Datasets[i], varname)
for (j in 1:n_vars) {
dir.create(path[j], recursive = TRUE)
startdates <- gsub("-", "", startdates)
dim(startdates) <- c(length(startdates))
names(dim(startdates)) <- sdate_dim
if (is.null(dat_dim) & is.null(var_dim)) {
data_subset <- data
} else if (is.null(dat_dim)) {
data_subset <- Subset(data, c(var_dim), list(j), drop = 'selected')
} else if (is.null(var_dim)) {
data_subset <- Subset(data, along = c(dat_dim), list(i), drop = 'selected')
} else {
data_subset <- Subset(data, c(dat_dim, var_dim), list(i, j), drop = 'selected')
}
if (is.null(Dates)) {
input_data <- list(data_subset, startdates)
target_dims <- list(c(lon_dim, lat_dim, memb_dim, ftime_dim), NULL)
} else {
input_data <- list(data_subset, startdates, Dates)
target_dims = list(c(lon_dim, lat_dim, memb_dim, ftime_dim), NULL, ftime_dim)
}
Apply(data = input_data,
target_dims = target_dims,
fun = .saveExp,
destination = path[j],
defined_dims = defined_dims,
ftime_dim = ftime_dim,
varname = varname[j],
metadata_var = metadata[[varname[j]]],
extra_info_dim = extra_info_dim,
extra_string = extra_string)
}
}
} else {
# Datasets definition
# From here
if (!is.null(dat_dim)) {
new_dim <- list(ncdim_def(name = dat_dim, units = "adim",
vals = 1 : dim(data)[dat_dim],
longname = 'Datasets', create_dimvar = TRUE))
names(new_dim) <- dat_dim
defined_dims <- c(new_dim, defined_dims)
extra_info_dim[[dat_dim]] <- list(Datasets = paste(Datasets, collapse = ', '))
}
first_sdate <- last_sdate <- NULL
if (!is.null(Dates)) {
# sdate definition
sdates <- Subset(Dates, along = ftime_dim, 1, drop = 'selected')
differ <- as.numeric((sdates - sdates[1])/3600)
new_dim <- list(ncdim_def(name = sdate_dim, units = paste('hours since', sdates[1]),
vals = differ,
longname = sdate_dim, create_dimvar = TRUE))
names(new_dim) <- sdate_dim
defined_dims <- c(defined_dims, new_dim)
first_sdate <- sdates[1]
last_sdate <- sdates[length(sdates)]
Dates <- Reorder(Dates, c(ftime_dim, sdate_dim))
differ_ftime <- apply(Dates, 2, function(x){as.numeric((x - x[1])/3600)})
dim(differ_ftime) <- dim(Dates)
differ_ftime_subset <- Subset(differ_ftime, along = sdate_dim, 1, drop = 'selected')
if (all(apply(differ_ftime, 1, function(x){length(unique(x)) == 1}))) {
if (all(diff(differ_ftime_subset/24) == 1)) {
# daily values
dim_time <- list(ncdim_def(name = ftime_dim, units = 'days',
vals = round(differ_ftime_subset/24) + 1,
calendar = 'proleptic_gregorian',
longname = ftime_dim, unlim = TRUE))
names(dim_time) <- ftime_dim
defined_dims <- c(defined_dims, dim_time)
} else if (all(diff(differ_ftime_subset/24) %in% c(28, 29, 30, 31))) {
# monthly values
dim_time <- list(ncdim_def(name = ftime_dim, units = 'months',
calendar = 'proleptic_gregorian',
longname = ftime_dim, unlim = TRUE))
names(dim_time) <- ftime_dim
defined_dims <- c(defined_dims, dim_time)
} else {
# other frequency
dim_time <- list(ncdim_def(name = ftime_dim, units = 'hours',
calendar = 'proleptic_gregorian',
longname = ftime_dim, unlim = TRUE))
names(dim_time) <- ftime_dim
defined_dims <- c(defined_dims, dim_time)
}
} else {
warning("Time steps are not equal for all start dates. Only ",
"forecast time values for the first start date will be saved ",
"correctly.")
dim_time <- list(ncdim_def(name = ftime_dim,
units = paste('hours since',
paste(sdates, collapse = ', ')),
vals = differ_ftime_subset,
calendar = 'proleptic_gregorian',
longname = ftime_dim, unlim = TRUE))
names(dim_time) <- ftime_dim
defined_dims <- c(defined_dims, dim_time)
}
756
757
758
759
760
761
762
763
764
765
766
767
768
769
770
771
772
773
774
775
776
777
778
779
780
781
782
783
784
785
786
787
788
789
790
791
792
793
794
795
796
797
798
799
800
801
802
803
804
805
806
807
808
809
810
811
812
813
814
815
816
817
818
819
820
}
# var definition
defined_vars <- list()
extra_info_var <- NULL
for (j in 1:n_vars) {
var_info <- list()
i_var_info <- metadata[[varname[j]]][!sapply(metadata[[varname[j]]], inherits, 'list')]
## Define metadata
# name
var_info[['name']] <- varname[j]
# units
if ('units' %in% names(i_var_info)) {
var_info[['units']] <- i_var_info[['units']]
i_var_info[['units']] <- NULL
} else {
var_info[['units']] <- ''
}
# dim
var_info[['dim']] <- defined_dims
# missval
if ('missval' %in% names(i_var_info)) {
var_info[['missval']] <- i_var_info[['missval']]
i_var_info[['missval']] <- NULL
} else {
var_info[['missval']] <- NULL
}
# longname
if (any(c('longname', 'long_name') %in% names(i_var_info))) {
longname <- names(i_var_info)[which(names(i_var_info) %in% c('longname', 'long_name'))]
var_info[['longname']] <- i_var_info[[longname]]
i_var_info[[longname]] <- NULL
} else {
var_info[['longname']] <- varname[j]
}
# prec
if ('prec' %in% names(i_var_info)) {
var_info[['prec']] <- i_var_info[['prec']]
i_var_info[['prec']] <- NULL
} else {
prec <- typeof(data)
if (prec == 'character') {
var_info[['prec']] <- 'char'
}
if (any(prec %in% c('short', 'float', 'double', 'integer', 'char', 'byte'))) {
var_info[['prec']] <- prec
} else {
var_info[['prec']] <- 'double'
}
}
# extra information
if (!is.null(names(i_var_info))) {
extra_info_var[[varname[j]]] <- i_var_info
}
new_var <- list(ncvar_def(name = var_info[['name']],
units = var_info[['units']],
dim = var_info[['dim']],
missval = var_info[['missval']],
longname = var_info[['longname']],
prec = var_info[['prec']]))
names(new_var) <- varname[j]
defined_vars <- c(defined_vars, new_var)
}
if (is.null(extra_string)) {
gsub("-", "", first_sdate)
file_name <- paste0(paste(c(varname,
gsub("-", "", first_sdate),
gsub("-", "", last_sdate)),
collapse = '_'), ".nc")
file_name <- paste0(paste(c(varname, extra_string,
gsub("-", "", last_sdate)),
collapse = '_'), ".nc")
}
full_filename <- file.path(destination, file_name)
file_nc <- nc_create(full_filename, defined_vars)
if (is.null(var_dim)) {
ncvar_put(file_nc, varname, vals = data)
} else {
for (j in 1:n_vars) {
ncvar_put(file_nc, defined_vars[[j]]$name,
vals = Subset(data, var_dim, j, drop = 'selected'))
}
}
# Additional dimension attributes
for (dim in names(defined_dims)) {
if (dim %in% names(extra_info_dim)) {
for (info_dim in names(extra_info_dim[[dim]])) {
add_info_dim <- paste0(extra_info_dim[[dim]][[info_dim]], collapse = ', ')
ncatt_put(file_nc, dim, info_dim, add_info_dim)
}
}
}
# Additional dimension attributes
for (var in names(defined_vars)) {
if (var %in% names(extra_info_var)) {
for (info_var in names(extra_info_var[[var]])) {
add_info_var <- paste0(extra_info_var[[var]][[info_var]], collapse = ', ')
ncatt_put(file_nc, var, info_var, add_info_var)
}
}
}
nc_close(file_nc)
}
}
.saveExp <- function(data, startdates = NULL, dates = NULL, destination = "./",
defined_dims, ftime_dim = 'time', varname = 'var',
metadata_var = NULL, extra_info_dim = NULL,
extra_string = NULL) {
# ftime_dim
if (!is.null(dates)) {
differ <- as.numeric((dates - dates[1])/3600)
dim_time <- list(ncdim_def(name = ftime_dim, units = paste('hours since', dates[1]),
vals = differ, calendar = 'proleptic_gregorian',
longname = ftime_dim, unlim = TRUE))
names(dim_time) <- ftime_dim
defined_dims <- c(defined_dims, dim_time)
## Define var metadata
var_info <- NULL
extra_info_var <- NULL
i_var_info <- metadata_var[!sapply(metadata_var, inherits, 'list')]
# name
var_info[['name']] <- varname
# units
if ('units' %in% names(i_var_info)) {
var_info[['units']] <- i_var_info[['units']]
i_var_info[['units']] <- NULL
} else {
var_info[['units']] <- ''
892
893
894
895
896
897
898
899
900
901
902
903
904
905
906
907
908
909
910
911
912
913
914
915
916
917
918
919
920
921
922
923
924
925
926
927
928
929
930
931
932
933
934
# dim
var_info[['dim']] <- defined_dims
# missval
if ('missval' %in% names(i_var_info)) {
var_info[['missval']] <- i_var_info[['missval']]
i_var_info[['missval']] <- NULL
} else {
var_info[['missval']] <- NULL
}
# longname
if (any(c('longname', 'long_name') %in% names(i_var_info))) {
longname <- names(i_var_info)[which(names(i_var_info) %in% c('longname', 'long_name'))]
var_info[['longname']] <- i_var_info[[longname]]
i_var_info[[longname]] <- NULL
} else {
var_info[['longname']] <- varname
}
# prec
if ('prec' %in% names(i_var_info)) {
var_info[['prec']] <- i_var_info[['prec']]
i_var_info[['prec']] <- NULL
} else {
prec <- typeof(data)
if (prec == 'character') {
var_info[['prec']] <- 'char'
}
if (any(prec %in% c('short', 'float', 'double', 'integer', 'char', 'byte'))) {
var_info[['prec']] <- prec
} else {
var_info[['prec']] <- 'double'
}
}
# extra information
if (!is.null(names(i_var_info))) {
extra_info_var <- i_var_info
}
datanc <- ncvar_def(name = var_info[['name']],
units = var_info[['units']],
dim = var_info[['dim']],
missval = var_info[['missval']],
longname = var_info[['longname']],
prec = var_info[['prec']])
file_name <- paste0(varname, "_", startdates, ".nc")
file_name <- paste0(varname, "_", extra_string, "_", startdates, ".nc")
full_filename <- file.path(destination, file_name)
file_nc <- nc_create(full_filename, datanc)
ncvar_put(file_nc, datanc, data)
# Additional attributes
for (dim in names(defined_dims)) {
if (dim %in% names(extra_info_dim)) {
for (info_dim in names(extra_info_dim[[dim]])) {
Eva Rifà
committed
add_info_dim <- paste0(extra_info_dim[[dim]][[info_dim]], collapse = ', ')
ncatt_put(file_nc, dim, info_dim, add_info_dim)
}
}
}
# Additional dimension attributes
if (!is.null(extra_info_var)) {
for (info_var in names(extra_info_var)) {
Eva Rifà
committed
add_info_var <- paste0(extra_info_var[[info_var]], collapse = ', ')
ncatt_put(file_nc, varname, info_var, add_info_var)
nc_close(file_nc)
}