Newer
Older
#'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 remain
#' attributes from coordinates (FALSE) or not (TRUE) when the data is loaded from
#' Start(). It is TRUE by default.
#'@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[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) {
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$data)) {
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
# attrs
object$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$dims['ftime']
# remove NULL values
object$attrs$load_parameters$maskmod[sapply(object$attrs$load_parameters$maskmod, is.null)] <- NULL
object$attrs$load_parameters$maskobs[sapply(object$attrs$load_parameters$maskobs, is.null)] <- NULL
object$attrs$load_parameters[sapply(object$attrs$load_parameters, is.null)] <- NULL
object <- object[c('data','dims','coords','attrs')]
class(object) <- 's2dv_cube'
result$exp <- object
}
if (!is.null(obs$data)) {
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
# attrs
obs$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$dims['ftime']
# remove NULL values
obs$attrs$load_parameters$maskmod[sapply(obs$attrs$load_parameters$maskmod, is.null)] <- NULL
obs$attrs$load_parameters$maskobs[sapply(obs$attrs$load_parameters$maskobs, is.null)] <- NULL
obs$attrs$load_parameters[sapply(obs$attrs$load_parameters, is.null)] <- NULL
obs <- obs[c('data','dims','coords','attrs')]
class(obs) <- 's2dv_cube'
result$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 (class(object) == 'startR_array') {
result <- list()
result$data <- as.vector(object)
# lon name
known_lon_names <- s2dv:::.KnownLonNames()
# lat name
known_lat_names <- s2dv:::.KnownLatNames()
names_dat <- names(attributes(object)$FileSelectors)
names_vars <- as.vector(attributes(object)$FileSelectors[[names_dat[1]]]$var[[1]])
variables_common <- names(attributes(object)$Variables$common)
name_time_dim <- variables_common[!variables_common %in% names_vars]
name_time_dim <- name_time_dim[which(!name_time_dim %in% known_lon_names & !name_time_dim %in% known_lat_names)]
dates <- attributes(object)$Variables$common[[name_time_dim]]
# dims
dims <- dim(object)
dim(result$data) <- dims
result$dims <- dims
# coords
result$coords <- sapply(names(dims),function(x) NULL)
dat <- names_dat[1]
dat_attr_names <- names(attributes(object)$Variables[[dat]])
# lon
known_lon_names <- s2dv:::.KnownLonNames()
lon_name_dat <- dat_attr_names[which(dat_attr_names %in% known_lon_names)]
lon_name_common <- variables_common[which(variables_common %in% known_lon_names)]
if (!is.null(lon_name_dat) & !identical(lon_name_dat, character(0))) {
if (isTRUE(remove_attrs_coords)) {
result$coords[[lon_name_dat]] <- as.vector(attributes(object)$Variables[[dat]][[lon_name_dat]])
} else {
result$coords[[lon_name_dat]] <- attributes(object)$Variables[[dat]][[lon_name_dat]]
}
} else if (!is.null(lon_name_common) & !identical(lon_name_common, character(0))) {
if (isTRUE(remove_attrs_coords)) {
result$coords[[lon_name_common]] <- as.vector(attributes(object)$Variables$common[[lon_name_common]])
result$coords[[lon_name_common]] <- attributes(object)$Variables$common[[lon_name_common]]
} else {
warning("'lon' is not found in this object.")
}
# lat
known_lat_names <- s2dv:::.KnownLatNames()
lat_name_dat <- dat_attr_names[which(dat_attr_names %in% known_lat_names)]
lat_name_common <- variables_common[which(variables_common %in% known_lat_names)]
if (!is.null(lat_name_dat) & !identical(lat_name_dat, character(0))) {
if (isTRUE(remove_attrs_coords)) {
result$coords[[lat_name_dat]] <- as.vector(attributes(object)$Variables[[dat]][[lat_name_dat]])
result$coords[[lat_name_dat]] <- attributes(object)$Variables[[dat]][[lat_name_dat]]
} else if (!is.null(lat_name_common) & !identical(lat_name_common, character(0))) {
if (isTRUE(remove_attrs_coords)) {
result$coords[[lat_name_common]] <- as.vector(attributes(object)$Variables$common[[lat_name_common]])
result$coords[[lat_name_common]] <- attributes(object)$Variables$common[[lat_name_common]]
} else {
warning("'lat' is not found in this object.")
}
if (any(name_time_dim %in% names(dims))) {
n_sdates <- dims[which(names(dims) == 'sdate' | names(dims) == 'sdates')]
sdate_name <- names(dims)[which(names(dims) %in% c('sdate', 'sdates'))]
sdates <- attributes(object)$FileSelectors[[dat]][[sdate_name]]
# result$coords[[sdate_name]] <- as.vector(attributes(object)$FileSelectors[[dat]][[sdate_name]][[1]])
} else {
if (any(c('sdate', 'sdates', 'sweek', 'sday', 'time') %in% names(dims))) {
name_time_dim <- names(dims)[which(names(dims) %in% c('sdate', 'sdates', 'sweek', 'sday', 'syear', 'time'))]
sdates <- NULL
sdate_name <- NULL
}
# missing other dims
result$coords <- sapply(names(result$coords), function(x) {
if (is.null(result$coords[[x]])) {
result$coords[[x]] <- 1:result$dims[x]
} else {
result$coords[[x]] <- result$coords[[x]]
}
})
Variable <- list()
if (all(names_vars %in% variables_common)) {
Variable$varName <- names_vars
attr(Variable, 'variable') <- attributes(object)$Variables$common[[names_vars]]
if (isTRUE(remove_attrs_coords)) {
attr(Variable, "variable")$dim <- NULL
}
result$attrs$Variable <- Variable
} else if (all(names_vars %in% dat_attr_names)) {
Variable$varName <- names_vars
for (var in names_vars) {
attr(Variable, var) <- attributes(object)$Variables[[dat]][[var]]
}
}
if (isTRUE(remove_attrs_coords)) {
attr(Variable, "variable")$dim <- NULL
result$attrs$Variable <- Variable
result$attrs$Datasets <- names_dat
for (i in 2:length(names_dat)) {
if (!is.null(lon_name_dat)) {
if (any(result$coords[[lon_name_dat]] != as.vector(attributes(object)$Variables[[names_dat[i]]][[lon_name_dat]]))) {
warning("'lon' values are different for different datasets. Only values from the first will be used.")
}
}
if (!is.null(lat_name_dat)) {
if (any(result$coords[[lat_name_dat]] != as.vector(attributes(object)$Variables[[names_dat[i]]][[lat_name_dat]]))) {
warning("'lat' values are different for different datasets. Only values from the first will be used.")
}
}
}
Dataset <- list(list(InitializationDates = list(Member_1 = sdates)))
names(Dataset) <- list(deparse(substitute(object)))
result$attrs$Datasets <- Dataset
result$attrs$Dates <- dates
result$attrs$when <- Sys.time()
result$attrs$source_files <- as.vector(attributes(object)$Files)
result$attrs$load_parameters <- attributes(object)$FileSelectors
} else {
stop("The class of parameter 'object' is not implemented",
" to be converted into 's2dv_cube' class yet.")