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#'Conversion of 'startR_array' or 'list' objects to 's2dv_cube'
#'
#'This function converts data loaded using startR package or s2dv
#'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 or a list output from function \code{Load}
#' from s2dv package. Any other object class will not be accepted.
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#'@param remove_attrs_coords A logical value indicating whether to remove the
#' attributes of the coordinates (TRUE) or not (FALSE) when the data is loaded
#' from Start(). It is TRUE by default.
#'@param remove_null A logical value indicating whether to remove the elements
#' that are NULL (TRUE) or not (FALSE) of the output object. It is TRUE by
#' default.
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#'
#'@return The function returns an 's2dv_cube' object to be easily used with
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#'functions \code{CST} from CSTools and CSIndicators packages. The object is
#'mainly a list with the following elements:\cr
#'\itemize{
#' \item{'data', array with named dimensions.}
#' \item{'dims', named vector of the data dimensions.}
#' \item{'coords', named list with elements of the coordinates corresponding to
#' the dimensions of the data parameter. 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. The attribute 'indices' indicates wether the
#' coordinate is an index vector (TRUE) or not (FALSE).}
#' \item{'attrs', named list with elements:
#' \itemize{
#' \item{'Dates', array with named temporal dimensions of class 'POSIXct' from
#' time values in the data.}
#' \item{'Variable', has the following components:
#' \itemize{
#' \item{'varName', with the short name of the loaded variable as specified
#' in the parameter 'var'.}
#' \item{'level', with information on the pressure level of the variable.
#' Is kept to NULL by now.}
#' }
#' }
#' \item{'Datasets', character strings indicating the names of the dataset.}
#' \item{'source_files', a vector of character strings with complete paths to
#' all the found files involved in loading the data.}
#' \item{'when', a time stamp of the date issued by the Start() or Load() call to
#' obtain the data.}
#' \item{'load_parameters', it contains the components used in the arguments to
#' load the data from Start() or Load() functions.}
#' }
#' }
#'@seealso \code{\link{s2dv_cube}}, \code{\link[s2dv]{Load}},
#'\code{\link[startR]{Start}} and \code{\link{CST_Load}}
#'repos <- '/esarchive/exp/ecmwf/system5_m1/monthly_mean/$var$_f6h/$var$_$sdate$.nc'
#'data <- Start(dat = repos,
#' var = 'tas',
#' sdate = c('20170101', '20180101'),
#' latitude = indices(1:5),
#' longitude = indices(1:5),
#' return_vars = list(latitude = 'dat', longitude = 'dat', time = 'sdate'),
#' retrieve = TRUE)
#'data <- as.s2dv_cube(data)
#'class(data)
#'startDates <- c('20001101', '20011101', '20021101',
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#' '20031101', '20041101', '20051101')
#' nmember = 2, sdates = startDates,
#' leadtimemax = 3, latmin = 10, latmax = 30,
#' lonmin = -10, lonmax = 10, output = 'lonlat')
#'data <- as.s2dv_cube(data)
#'class(data)
#'}
#'@export
as.s2dv_cube <- function(object, remove_attrs_coords = TRUE, remove_null = TRUE) {
if (is.list(object) & length(object) == 11) {
if (is.null(object) || (is.null(object$mod) && is.null(object$obs))) {
stop("The s2dv::Load call did not return any data.")
obs <- object
obs$mod <- NULL
object$obs <- NULL
names(object)[[1]] <- 'data' # exp
names(obs)[[1]] <- 'data' # obs
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
}
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)
} else {
obs_exist <- FALSE
if (!is.null(object$data)) {
object$Datasets$obs <- NULL
object$Datasets <- object$Datasets$exp
exp_path_patterns <- sapply(object$Datasets, function(x) attr(x, 'source'))
exp_path_patterns <- harmonize_patterns(exp_path_patterns)
} else {
exp_exist <- FALSE
}
if (!is.null(obs$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$not_found_files, obs_path_patterns)
# obs and exp
if (obs_exist & exp_exist) {
obs_exp = list(obs = obs, exp = object)
} else if (obs_exist & !exp_exist) {
obs_exp = list(obs = obs)
} else {
obs_exp = list(exp = object)
}
i <- 0
for (obj_i in obs_exp) {
i <- i + 1
obj_i$attrs <- within(obj_i, rm(list = c('data')))
obj_i <- within(obj_i, rm(list = names(obj_i$attrs)))
dates <- obj_i$attrs$Dates$start
if (!is.null(dates)) {
dim(dates) <- dim(obj_i$data)[c('ftime', 'sdate')]
obj_i$attrs$Dates <- dates
}
obj_i$dims <- dim(obj_i$data)
obj_i$coords <- sapply(names(dim(obj_i$data)),function(x) NULL)
obj_i$coords$sdate <- obj_i$attrs$load_parameters$sdates
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attr(obj_i$coords$sdate, 'indices') <- FALSE
if (!is.null(obj_i$attrs$lon)) {
obj_i$coords$lon <- as.vector(obj_i$attrs$lon)
obj_i$coords$lon <- obj_i$attrs$lon
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attr(obj_i$coords$lon, 'indices') <- FALSE
obj_i$attrs <- within(obj_i$attrs, rm(lon))
if (!is.null(obj_i$attrs$lat)) {
obj_i$coords$lat <- as.vector(obj_i$attrs$lat)
obj_i$coords$lat <- obj_i$attrs$lat
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attr(obj_i$coords$lat, 'indices') <- FALSE
obj_i$attrs <- within(obj_i$attrs, rm(lat))
obj_i$coords$member <- 1:obj_i$dims['member']
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attr(obj_i$coords$member, 'indices') <- TRUE
obj_i$coords$dataset <- 1:obj_i$dims['dataset']
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attr(obj_i$coords$dataset, 'indices') <- TRUE
obj_i$coords$ftime <- 1:obj_i$dims['ftime']
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attr(obj_i$coords$ftime, 'indices') <- TRUE
obj_i <- obj_i[c('data','dims','coords','attrs')]
class(obj_i) <- 's2dv_cube'
if (names(obs_exp)[[i]] == 'exp') {
result$exp <- obj_i
} else {
result$obs <- obj_i
if (is.list(result)) {
if (is.null(result$exp)) {
result <- result$obs
} else if (is.null(result$obs)) {
result <- result$exp
} else {
warning("The output is a list of two 's2dv_cube' objects",
" corresponding to 'exp' and 'obs'.")
}
} else if (inherits(object,'startR_array')) {
# From Start:
result <- list()
result$data <- as.vector(object)
dims <- dim(object)
dim(result$data) <- dims
result$dims <- dims
## coords
result$coords <- sapply(names(dims), function(x) NULL)
# Find coordinates
FileSelector <- attributes(object)$FileSelectors
VariablesCommon <- names(attributes(object)$Variables$common)
dat <- names(FileSelector)[1]
VariablesDat <- names(attributes(object)$Variables[[dat]])
for (i_coord in names(dims)) {
if (i_coord %in% names(FileSelector[[dat]])) { # coords in FileSelector
coord_in_fileselector <- FileSelector[[dat]][which(i_coord == names(FileSelector[[dat]]))]
if (length(coord_in_fileselector) == 1) {
if (length(coord_in_fileselector[[i_coord]][[1]]) == dims[i_coord]) {
if (i_coord %in% c('var', 'vars')) {
varName <- as.vector(coord_in_fileselector[[i_coord]][[1]])
}
if (remove_attrs_coords) {
result$coords[[i_coord]] <- as.vector(coord_in_fileselector[[i_coord]][[1]])
} else {
result$coords[[i_coord]] <- coord_in_fileselector[[i_coord]][[1]]
}
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attr(result$coords[[i_coord]], 'indices') <- FALSE
} else {
result$coords[[i_coord]] <- 1:dims[i_coord]
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attr(result$coords[[i_coord]], 'indices') <- TRUE
}
} else {
print(paste0("Length of coordinate", i_coord, "in FileSelector is more than 1.")) # Can this be TRUE?
}
} else if (i_coord %in% VariablesCommon) { # coords in common
coord_in_common <- attributes(object)$Variables$common[[which(i_coord == VariablesCommon)]]
if (inherits(coord_in_common, "POSIXct")) {
result$attrs$Dates <- coord_in_common
}
if (length(coord_in_common) == dims[i_coord]) {
if (remove_attrs_coords) {
if (inherits(coord_in_common, "POSIXct")) {
result$coords[[i_coord]] <- coord_in_common
} else {
result$coords[[i_coord]] <- as.vector(coord_in_common)
}
} else {
result$coords[[i_coord]] <- coord_in_common
}
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attr(result$coords[[i_coord]], 'indices') <- FALSE
} else {
result$coords[[i_coord]] <- 1:dims[i_coord]
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attr(result$coords[[i_coord]], 'indices') <- TRUE
}
} else if (!is.null(VariablesDat)) { # coords in dat
if (i_coord %in% VariablesDat) {
coord_in_dat <- attributes(object)$Variables[[dat]][[which(i_coord == VariablesDat)]]
if (inherits(coord_in_dat, "POSIXct")) {
result$attrs$Dates <- coord_in_dat
}
if (length(coord_in_dat) == dims[i_coord]) {
if (remove_attrs_coords) {
if (inherits(coord_in_dat, "POSIXct")) {
result$coords[[i_coord]] <- coord_in_dat
} else {
result$coords[[i_coord]] <- as.vector(coord_in_dat)
}
} else {
result$coords[[i_coord]] <- coord_in_dat
}
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attr(result$coords[[i_coord]], 'indices') <- FALSE
} else {
result$coords[[i_coord]] <- 1:dims[i_coord]
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attr(result$coords[[i_coord]], 'indices') <- TRUE
}
} else {
result$coords[[i_coord]] <- 1:dims[i_coord]
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attr(result$coords[[i_coord]], 'indices') <- TRUE
}
} else { # missing other dims
result$coords[[i_coord]] <- 1:dims[i_coord]
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attr(result$coords[[i_coord]], 'indices') <- TRUE
## varName
if (!is.null(varName)) {
result$attrs$Variable$varName <- varName
}
## Variables
for (var_type in names(attributes(object)$Variables)) {
if (!is.null(attributes(object)$Variables[[var_type]])) {
for (var in names(attributes(object)$Variables[[var_type]])) {
attr_variable <- attributes(object)$Variables[[var_type]][[var]]
if (is.null(result$attrs$Dates)) {
if (inherits(attr_variable, "POSIXct")) {
result$attrs$Dates <- attr_variable
}
}
## Datasets
if (length(names(FileSelector)) > 1) {
# lon name
known_lon_names <- .KnownLonNames()
lon_name_dat <- names(dims)[which(names(dims) %in% known_lon_names)]
# lat name
known_lat_names <- .KnownLatNames()
lat_name_dat <- names(dims)[which(names(dims) %in% known_lat_names)]
result$attrs$Datasets <- names(FileSelector)
for (i in 2:length(names(FileSelector))) {
if (!is.null(lon_name_dat)) {
if (any(result$coords[[lon_name_dat]] != as.vector(attributes(object)$Variables[[names(FileSelector)[i]]][[lon_name_dat]]))) {
warning("'lon' values are different for different datasets. Only values from the first will be used.")
}
}
if (!is.null(lat_name_dat)) {
if (any(result$coords[[lat_name_dat]] != as.vector(attributes(object)$Variables[[names(FileSelector)[i]]][[lat_name_dat]]))) {
warning("'lat' values are different for different datasets. Only values from the first will be used.")
}
}
}
result$attrs$Datasets <- names(FileSelector)
## source_files
result$attrs$source_files <- attributes(object)$Files
result$attrs$load_parameters <- attributes(object)$FileSelectors
## remove NULL values
if (isTRUE(remove_null)) {
result <- .rmNullObs(result)
}
} else {
stop("The class of parameter 'object' is not implemented",
" to be converted into 's2dv_cube' class yet.")