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#'Conversion of 'startR_array' or 'list' objects to 's2dv_cube'
#'
#'This function converts data loaded using startR package or s2dverification Load function into a 's2dv_cube' object.
#'
#'@author Perez-Zanon Nuria, \email{nuria.perez@bsc.es}
#'@author Nicolau Manubens, \email{nicolau.manubens@bsc.es}
#'
#'@param object an object of class 'startR_array' generated from function \code{Start} from startR package (version 0.1.3 from earth.bsc.es/gitlab/es/startR) or a list output from function \code{Load} from s2dverification package.
#'
#'@return The function returns a 's2dv_cube' object to be easily used with functions \code{CST} from CSTools package.
#'
#'@seealso \code{\link{s2dv_cube}}, \code{\link[s2dverification]{Load}}, \code{\link[startR]{Start}} and \code{\link{CST_Load}}
#'@examples
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#'repos <- '/esarchive/exp/ecmwf/system5_m1/monthly_mean/$var$_f6h/$var$_$sdate$.nc'
#'data <- Start(dat = repos,
#' var = 'tas',
#' sdate = c('20170101', '20180101'),
#' ensemble = indices(1:20),
#' time = 'all',
#' latitude = 'all',
#' longitude = indices(1:40),
#' return_vars = list(latitude = 'dat', longitude = 'dat', time = 'sdate'),
#' retrieve = TRUE)
#'data <- as.s2dv_cube(data)
#'class(data)
#'startDates <- c('20001101', '20011101', '20021101',
#' '20031101', '20041101', '20051101')
#'data <- Load(var = 'tas', exp = 'system5c3s',
#' nmember = 15, sdates = startDates,
#' leadtimemax = 3, latmin = 27, latmax = 48,
#' lonmin = -12, lonmax = 40, output = 'lonlat')
#'data <- as.s2dv_cube(data)
#'class(data)
#'}
#'@export
as.s2dv_cube <- function(object) {
if (is.list(object)) {
if (is.null(object) || (is.null(object$mod) && is.null(object$obs))) {
stop("The s2dverification::Load call did not return any data.")
}
obs <- object
obs$mod <- NULL
object$obs <- NULL
names(object)[[1]] <- 'data'
names(obs)[[1]] <- 'data'
remove_matches <- function(v, patterns) {
if (length(v) > 0) {
matches <- c()
for (pattern in patterns) {
matches <- c(matches, which(grepl(pattern, v)))
}
if (length(matches) > 0) {
v <- v[-matches]
}
}
v
}
harmonize_patterns <- function(v) {
matches <- grepl('.*\\.nc$', v)
if (sum(!matches) > 0) {
match_indices <- which(!matches)
v[match_indices] <- sapply(v[match_indices], function(x) paste0(x, '*'))
}
v <- glob2rx(v)
v <- gsub('\\$.*\\$', '*', v)
v
}
if (!is.null(obs$data)) {
obs$Datasets$exp <- NULL
obs$Datasets <- obs$Datasets$obs
obs_path_patterns <- sapply(obs$Datasets, function(x) attr(x, 'source'))
obs_path_patterns <- harmonize_patterns(obs_path_patterns)
}
if (!is.null(object$data)) {
object$Datasets$obs <- NULL
object$Datasets <- object$Datasets$exp
exp_path_patterns <- sapply(object$Datasets, function(x) attr(x, 'source'))
exp_path_patterns <- harmonize_patterns(exp_path_patterns)
}
if (!is.null(obs$data) && !is.null(object$data)) {
obs$source_files <- remove_matches(obs$source_files,
exp_path_patterns)
obs$not_found_files <- remove_matches(obs$not_found_files,
exp_path_patterns)
object$source_files <- remove_matches(object$source_files,
obs_path_patterns)
object$not_found_files <- remove_matches(object$not_found_files,
obs_path_patterns)
}
result <- list()
if (!is.null(object$data)) {
class(object) <- 's2dv_cube'
result$exp <- object
}
if (!is.null(obs$data)) {
class(obs) <- 's2dv_cube'
result$obs <- obs
}
if (is.list(result)) {
if (is.null(result$exp)) {
result <- result$obs
} else if (is.null(result$obs)) {
result <- result$exp
} else {
warning("The output is a list of two 's2dv_cube' objects",
" corresponding to 'exp' and 'obs'.")
}
}
} else if (class(object) == 'startR_array') {
result <- list()
result$data <- as.vector(object)
dim(result$data) <- dim(object)
dat_attr_names <- names(attributes(object)$Variables$dat1)
common_attr_names <- names(attributes(object)$Variables$common)
# $lon
known_lon_names <- s2dv:::.KnownLonNames()
if (!is.null(dat_attr_names[which(dat_attr_names %in% known_lon_names)]) &
!identical(dat_attr_names[which(dat_attr_names %in% known_lon_names)], character(0))) {
result$lon <- attributes(object)$Variables$dat1[[dat_attr_names[which(dat_attr_names %in% known_lon_names)]]]
} else if (!is.null(common_attr_names[which(common_attr_names %in% known_lon_names)]) &
!identical(common_attr_names[which(common_attr_names %in% known_lon_names)], character(0))) {
result$lon <- attributes(object)$Variables$common[[common_attr_names[which(common_attr_names %in% known_lon_names)]]]
} else {
warning("'lon' is not found in this object.")
result$lon <- NULL
}
# $lat
known_lat_names <- s2dv:::.KnownLatNames()
if (!is.null(dat_attr_names[which(dat_attr_names %in% known_lat_names)]) &
!identical(dat_attr_names[which(dat_attr_names %in% known_lat_names)], character(0))) {
result$lat <- attributes(object)$Variables$dat1[[dat_attr_names[which(dat_attr_names %in% known_lat_names)]]]
} else if (!is.null(common_attr_names[which(common_attr_names %in% known_lat_names)]) &
!identical(common_attr_names[which(common_attr_names %in% known_lat_names)], character(0))) {
result$lat <- attributes(object)$Variables$common[[common_attr_names[which(common_attr_names %in% known_lat_names)]]]
} else {
warning("'lat' is not found in this object.")
result$lat <- NULL
}
vars <- which(!common_attr_names %in% c("time", known_lon_names, known_lat_names))
if (length(vars) > 1) {
warning("More than one variable has been provided and ",
"only the first one '", common_attr_names[vars[1]],"' will be used.")
vars <- vars[1]
}
Variable <- list()
Variable$varName <- names(attributes(object)$Variables$common)[vars]
attr(Variable, 'variable') <- attributes(object)$Variables$common[[vars]]
result$Variable <- Variable
dims <- dim(object)
if (any(c('sdate', 'sdates') %in% names(dims))) {
n_sdates <- dims[which(names(dims) == 'sdate' | names(dims) == 'sdates')]
sdates <- attributes(object)$Variables$common$time[1 : n_sdates]
} else {
sdates <- attributes(object)$Variables$common$time[1]
}
Dataset <- list(list(InitializationDates = list(Member_1 = sdates)))
names(Dataset) <- list(deparse(substitute(object)))
result$Datasets <- Dataset
result$Dates$start <- attributes(object)$Variables$common$time
result$when <- Sys.time()
result$source_files <- as.vector(attributes(object)$Files)
result$load_parameters <- attributes(object)$FileSelectors
class(result) <- 's2dv_cube'
} else {
stop("The class of parameter 'object' is not implemented",
" to be converted into 's2dv_cube' class yet.")