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#'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_Load()}, 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.
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#'@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.
#'@param units_time_since A logical value indicating if the time units are
#' saved as 'time unit since' (e.g. 'horurs since') (TRUE) or as time unit
#' index (e.g. days, months, or hours) (FALSE). It is set as TRUE by default.
#'@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}}
#'CST_SaveExp(data = data, destination = destination, ftime_dim = 'ftime',
#' var_dim = 'var', dat_dim = 'dataset')
#'@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',
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startdates = NULL, drop_dims = NULL,
single_file = FALSE, extra_string = NULL,
units_time_since = TRUE) {
stop("Parameter 'data' must be of the class 's2dv_cube'.")
# 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.")
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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,
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memb_dim = memb_dim,
drop_dims = drop_dims,
single_file = single_file,
units_time_since = units_time_since)
}
#'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_Load()}, then it can be reloaded with \code{Load()}.
#'
#'@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. If there is no sdate_dim, you can set it to NULL.
#' It must have ftime_dim 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.
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#'@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
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#' 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
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#' file name between underscore characters (optional).
#'@param units_time_since A logical value indicating if the time units are
#' saved as 'time unit since' (e.g. 'horurs since') (TRUE) or as time unit
#' index (e.g. days, months, or hours) (FALSE). It is set as TRUE by default.
#'@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_st$exp$data
#'lon <- lonlat_temp_st$exp$coords$lon
#'lat <- lonlat_temp_st$exp$coords$lat
#'Datasets <- lonlat_temp_st$exp$attrs$Datasets
#'Dates <- lonlat_temp_st$exp$attrs$Dates
#'metadata <- lonlat_temp_st$exp$attrs$Variable$metadata
#'SaveExp(data = data, destination = destination, coords = coords,
#' Datasets = Datasets, varname = varname, Dates = Dates,
#' metadata = metadata, single_file = TRUE, ftime_dim = 'ftime',
#' var_dim = 'var', dat_dim = 'dataset')
#'@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',
drop_dims = NULL, single_file = FALSE, extra_string = NULL,
units_time_since = TRUE) {
## 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.")
}
}
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# 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))
}
}
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# 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.")
}
}
# units_time_since
if (!is.logical(units_time_since)) {
warning("Parameter 'units_time_since' must be a logical value. It will be ",
"set as TRUE.")
units_time_since <- TRUE
}
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## 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(c(ftime_dim, sdate_dim) %in% names(dim(Dates)))) {
if (any(!names(dim(Dates)) %in% c(ftime_dim, sdate_dim))) {
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 only sdate_dim and ftime_dim dimensions.")
}
}
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 (any(ftime_dim %in% names(dim(Dates)))) {
if (all(dim(Dates)[!names(dim(Dates)) %in% c(ftime_dim)] == 1)) {
dim(Dates) <- dim(Dates)[names(dim(Dates)) %in% c(ftime_dim, sdate_dim)]
}
}
}
# 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]
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# 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)
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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(sdate_dim)) {
sdates <- Dates[1]
# ftime definition
leadtimes <- as.numeric(Dates - sdates)/3600
save_hours_since <- TRUE
} else {
# 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)]
# ftime definition
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)
leadtimes <- Subset(differ_ftime, along = sdate_dim, 1, drop = 'selected')
if (all(apply(differ_ftime, 1, function(x){length(unique(x)) == 1}))) {
if (!units_time_since) save_hours_since <- FALSE
} else {
warning("Time steps are not equal for all start dates. Only ",
"forecast time values for the first start date will be saved ",
"correctly.")
}
}
if (!save_hours_since) {
if (all(diff(leadtimes/24) == 1)) {
# daily values
dim_time <- list(ncdim_def(name = ftime_dim, units = 'days',
vals = round(leadtimes/24) + 1,
longname = ftime_dim, unlim = TRUE))
names(dim_time) <- ftime_dim
defined_dims <- c(defined_dims, dim_time)
} else if (all(diff(leadtimes/24) %in% c(28, 29, 30, 31))) {
# monthly values
dim_time <- list(ncdim_def(name = ftime_dim, units = 'months',
vals = round(leadtimes/730) + 1,
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',
vals = leadtimes + 1,
calendar = 'proleptic_gregorian',
longname = ftime_dim, unlim = TRUE))
names(dim_time) <- ftime_dim
defined_dims <- c(defined_dims, dim_time)
}
} else {
# Save in units 'hours since'
dim_time <- list(ncdim_def(name = ftime_dim,
units = paste('hours since',
paste(sdates, collapse = ', ')),
vals = leadtimes,
longname = ftime_dim, unlim = TRUE))
names(dim_time) <- ftime_dim
defined_dims <- c(defined_dims, dim_time)
}
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}
# 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")
nc <- substr(extra_string, nchar(extra_string)-2, nchar(extra_string))
if (nc == ".nc") {
file_name <- extra_string
} else {
file_name <- paste0(extra_string, ".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']] <- ''
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# 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)
}