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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.
#'@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.
#'@return The function returns an 's2dv_cube' object to be easily used with
#'functions \code{CST} from CSTools and CSIndicators packages. The structure
#'is the following:\cr\cr
#'\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.
#'}
#'\item{attrs}{
#' Named list with elements: Dates, Variable, Datasets, source_files, when and load_parameters.
#'}
#'@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'),
#' 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, remove_attrs_coords = TRUE, remove_null = TRUE) {
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
}
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$data)) {
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# attrs
object$attrs <- within(object, rm(list = c('data')))
object <- within(object, rm(list = names(object$attrs)))
dates <- object$attrs$Dates$start
dim(dates) <- dim(object$data)[c('sdate','ftime')]
object$attrs$Dates <- dates
# dims
object$dims <- dim(object$data)
# coords
object$coords <- sapply(names(dim(object$data)),function(x) NULL)
# sdate
object$coords$sdate <- object$attrs$load_parameters$sdates
# lon
if (!is.null(object$attrs$lon)) {
if (isTRUE(remove_attrs_coords)) {
object$coords$lon <- as.vector(object$attrs$lon)
} else {
object$coords$lon <- object$attrs$lon
}
object$attrs <- within(object$attrs, rm(lon))
}
# lat
if (!is.null(object$attrs$lat)) {
if (isTRUE(remove_attrs_coords)) {
object$coords$lat <- as.vector(object$attrs$lat)
} else {
object$coords$lat <- object$attrs$lat
}
object$attrs <- within(object$attrs, rm(lat))
}
# member
object$coords$member <- 1:object$dims['member']
# dataset
object$coords$dataset <- 1:object$dims['dataset']
# ftime
object$coords$ftime <- 1:object$dims['ftime']
# remove NULL values
if (isTRUE(remove_null)) {
object <- .rmNullObs(object)
}
object <- object[c('data','dims','coords','attrs')]
class(object) <- 's2dv_cube'
result$exp <- object
}
if (!is.null(obs$data)) {
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# attrs
obs$attrs <- within(obs, rm(list = c('data', 'not_found_files')))
obs <- within(obs, rm(list = names(obs$attrs)))
dates <- obs$attrs$Dates$start
dim(dates) <- dim(obs$data)[c('sdate','ftime')]
obs$attrs$Dates <- dates
# dims
obs$dims <- dim(obs$data)
# coords
obs$coords <- sapply(names(dim(obs$data)),function(x) NULL)
## sdate
obs$coords$sdate <- obs$attrs$load_parameters$sdates
# lon
if (!is.null(obs$attrs$lon)) {
if (isTRUE(remove_attrs_coords)) {
obs$coords$lon <- as.vector(obs$attrs$lon)
} else {
obs$coords$lon <- obs$attrs$lon
}
obs$attrs <- within(obs$attrs, rm(lon))
}
# lat
if (!is.null(obs$attrs$lat)) {
if (isTRUE(remove_attrs_coords)) {
obs$coords$lat <- as.vector(obs$attrs$lat)
} else {
obs$coords$lat <- obs$attrs$lat
}
obs$attrs <- within(obs$attrs, rm(lat))
}
# member
obs$coords$member <- 1:obs$dims['member']
# dataset
obs$coords$dataset <- 1:obs$dims['dataset']
# ftime
obs$coords$ftime <- 1:obs$dims['ftime']
# remove NULL values
if (isTRUE(remove_null)) {
obs <- .rmNullObs(obs)
}
obs <- obs[c('data','dims','coords','attrs')]
class(obs) <- 's2dv_cube'
result$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 (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]])
}
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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]]
}
} else {
result$coords[[i_coord]] <- 1:dims[i_coord]
}
} else {
print(paste0("Length of coordinate", i_coord, "in FileSelector is more than 1.")) # Can this be TRUE?
}
} else if (i_coord %in% VariablesCommon) { # coords in common
coord_in_common <- attributes(object)$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
}
} else {
result$coords[[i_coord]] <- 1:dims[i_coord]
}
} else if (!is.null(VariablesDat)) { # coords in dat
if (i_coord %in% VariablesDat) {
coord_in_dat <- attributes(object)$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$coords[[i_coord]] <- coord_in_dat
}
} else {
result$coords[[i_coord]] <- 1:dims[i_coord]
}
} else {
result$coords[[i_coord]] <- 1:dims[i_coord]
}
} else { # missing other dims
result$coords[[i_coord]] <- 1:dims[i_coord]
## 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.")