Newer
Older
#'@description This function allows to create a 's2dv_cube' object by passing
#'information through its parameters. This function will be needed if the data
#'hasn't been loaded using CST_Load or has been transformed with other methods.
#'A 's2dv_cube' object has many different components including metadata. This
#'function will allow to create 's2dv_cube' objects even if not all elements
#'are defined and for each expected missed parameter a warning message will be
#'returned.
#'
#'@author Perez-Zanon Nuria, \email{nuria.perez@bsc.es}
#'
#'@param data an array with any number of named dimensions, typically an object
#' output from CST_Load, with the following dimensions: dataset, member, sdate,
#'ftime, lat and lon.
#'@param lon an array with one dimension containing the longitudes and
#'attributes: dim, cdo_grid_name, data_across_gw, array_across_gw, first_lon,
#'last_lon and projection.
#'@param lat an array with one dimension containing the latitudes and
#'attributes: dim, cdo_grid_name, first_lat, last_lat and projection.
#'@param Variable a list of two elements: \code{varName} a character string
#'indicating the abbreviation of a variable name and \code{level} a character
#'string indicating the level (e.g., "2m"), if it is not required it could be
#' set as NULL.
#'@param Datasets a named list with the dataset model with two elements:
#'\code{InitiatlizationDates}, containing a list of the start dates for each
#'member named with the names of each member, and \code{Members} containing a
#'vector with the member names (e.g., "Member_1")
#'@param Dates a named list of one to two elements: The first element,
#'\code{start}, is an array of dimensions (sdate, time) with the POSIX initial
#'date of each forecast time of each starting date. The second element,
#'\code{end} (optional), is an array of dimensions (sdate, time) with the POSIX
# final date of each forecast time of each starting date.
#'@param time_dims a vector of strings containing the names of the temporal
#'dimensions found in \code{data}.
#'@param when a time stamp of the date issued by the Load() call to obtain the
#'data.
#'@param source_files a vector of character strings with complete paths to all
#'the found files involved in the Load() call.
#'@return The function returns an object of class 's2dv_cube'.
#'@seealso \code{\link[s2dv]{Load}} and \code{\link{CST_Load}}
#'exp_original <- 1:100
#'dim(exp_original) <- c(lat = 2, time = 10, lon = 5)
#'exp2 <- s2dv_cube(data = exp_original, lon = seq(-10, 10, 5), lat = c(45, 50))
#'exp3 <- s2dv_cube(data = exp_original, lon = seq(-10, 10, 5), lat = c(45, 50),
#'exp4 <- s2dv_cube(data = exp_original, lon = seq(-10, 10, 5), lat = c(45, 50),
#' Variable = list(varName = 'tas', level = '2m'),
#' Dates = list(start = paste0(rep("01", 10), rep("01", 10), 1990:1999),
#' end = paste0(rep("31", 10), rep("01", 10), 1990:1999)))
#'exp5 <- s2dv_cube(data = exp_original, lon = seq(-10, 10, 5), lat = c(45, 50),
#' Variable = list(varName = 'tas', level = '2m'),
#' Dates = list(start = paste0(rep("01", 10), rep("01", 10), 1990:1999),
#' end = paste0(rep("31", 10), rep("01", 10), 1990:1999)),
#'exp6 <- s2dv_cube(data = exp_original, lon = seq(-10, 10, 5), lat = c(45, 50),
#' Variable = list(varName = 'tas', level = '2m'),
#' Dates = list(start = paste0(rep("01", 10), rep("01", 10), 1990:1999),
#' end = paste0(rep("31", 10), rep("01", 10), 1990:1999)),
#'exp7 <- s2dv_cube(data = exp_original, lon = seq(-10, 10, 5), lat = c(45, 50),
#' Variable = list(varName = 'tas', level = '2m'),
#' Dates = list(start = paste0(rep("01", 10), rep("01", 10), 1990:1999),
#' end = paste0(rep("31", 10), rep("01", 10), 1990:1999)),
#' when = "2019-10-23 19:15:29 CET",
#' source_files = c("/path/to/file1.nc", "/path/to/file2.nc"),
#' Datasets = list(
#' exp1 = list(InitializationsDates = list(Member_1 = "01011990",
#' Members = "Member_1"))))
#'class(exp7)
#'dim(exp_original) <- c(dataset = 1, member = 1, sdate = 2, ftime = 5, lat = 2, lon = 5)
#'exp8 <- s2dv_cube(data = exp_original, lon = seq(-10, 10, 5), lat = c(45, 50),
#' Variable = list(varName = 'tas', level = '2m'),
#' Dates = list(start = paste0(rep("01", 10), rep("01", 10), 1990:1999),
#' end = paste0(rep("31", 10), rep("01", 10), 1990:1999)))
s2dv_cube <- function(data, lon = NULL, lat = NULL, Variable = NULL, Datasets = NULL,
Dates = NULL, time_dims = NULL, when = NULL, source_files = NULL) {
if (is.null(data) | !is.array(data) | is.null(names(dim(data)))) {
stop("Parameter 'data' must be an array with named dimensions.")
}
dims <- dim(data)
if (is.null(lon)) {
warning("Parameter 'lon' is not provided but data contains a ",
"longitudinal dimension.")
} else {
warning("Parameter 'lon' is not provided so the data is from an ",
"unknown location.")
}
104
105
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
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
}
if (is.null(lat)) {
if (any(c('lat', 'latitude') %in% names(dims))) {
warning("Parameter 'lat' is not provided but data contains a ",
"latitudinal dimension.")
} else {
warning("Parameter 'lat' is not provided so the data is from an ",
"unknown location.")
}
}
if (is.null(Variable)) {
warning("Parameter 'Variable' is not provided so the metadata ",
"of 's2dv_cube' object will be incomplete.")
}
if (is.null(Datasets)) {
warning("Parameter 'Datasets' is not provided so the metadata ",
"of 's2dv_cube' object will be incomplete.")
}
if (is.null(Dates)) {
if (!is.null(time_dims)) {
if (any(time_dims %in% names(dims))) {
warning("Parameter 'Dates' is not provided but data contains a ",
"temporal dimension.")
} else {
warning("Data does not contain any of the temporal dimensions ",
"in 'time_dims'.")
}
} else if (any(c('time', 'ftime', 'sdate') %in% names(dims))) {
warning("Parameter 'Dates' is not provided but data contains a ",
"temporal dimension.")
} else {
warning("Parameter 'Dates' is not provided so the data is from an ",
"unknown time period.")
}
}
if (is.null(when)) {
warning("Parameter 'when' is not provided so the metadata ",
"of 's2dv_cube' object will be incomplete.")
}
if (is.null(source_files)) {
warning("Parameter 'source_files' is not provided so the metadata ",
"of 's2dv_cube' object will be incomplete.")
}
if (!is.null(Variable)) {
if (!is.list(Variable)) {
Variable <- list(Variable)
}
if (names(Variable)[1] != 'varName' | names(Variable)[2] != 'level') {
warning("The name of the first element of parameter 'Variable' is ",
"expected to be 'varName' and the second 'level'.")
}
if (!is.character(Variable[[1]])) {
warning("The element 'Varname' of parameter 'Variable' must be ",
"a character.")
}
}
# Dimensions comparison
## lon
if (!is.null(lon)) {
if (any(names(dims) %in% c('lon', 'longitude'))) {
name_lon <- names(dims[names(dims) %in% c('lon', 'longitude')])
if (dims[name_lon] != length(lon) & dims[name_lon] != 1) {
stop("Length of parameter 'lon' doesn't match the length of ",
"longitudinal dimension in parameter 'data'.")
}
if (!is.null(names(dim(lon))) && !identical(name_lon, names(dim(lon)))) {
stop("The dimension name of parameter 'lon' is not consistent ",
"with data dimension name for longitude.")
} else {
dim(lon) <- length(lon)
names(dim(lon)) <- name_lon
} else if (!is.null(names(dim(lon))) && names(dim(lon)) %in% names(dims)) {
name_lon <- names(dims[names(dim(lon))])
if (length(lon) != dims[name_lon]) {
stop("The length of the longitudinal dimension doesn't match ",
"with the length of 'lon' parameter.")
} else {
warning(paste0("Detected the longitude dimension name to be ", names(dim(lon)),
", which is not the expected names ('lon' or 'longitude') by s2dv_cube."))
}
} else {
stop("Parameter 'lon' is provided but data doesn't contain a ",
"longitudinal dimension.")
}
if (!is.null(lat)) {
if (any(names(dims) %in% c('lat', 'latitude'))) {
name_lat <- names(dims[names(dims) %in% c('lat', 'latitude')])
if (dims[name_lat] != length(lat) & dims[name_lat] != 1) {
stop("Length of parameter 'lat' doesn't match the length of ",
"longitudinal dimension in parameter 'data'.")
if (!is.null(names(dim(lat))) && !identical(name_lat, names(dim(lat)))) {
stop("The dimension name of parameter 'lat' is not consistent ",
"with data dimension name for latitude.")
} else {
dim(lat) <- length(lat)
names(dim(lat)) <- name_lat
}
} else if (!is.null(names(dim(lat))) && names(dim(lat)) %in% names(dims)) {
name_lat <- names(dims[names(dim(lat))])
if (length(lat) != dims[name_lat]) {
stop("The length of the latgitudinal dimension doesn't match ",
"with the length of 'lat' parameter.")
} else {
warning(paste0("Detected the latitude dimension name to be ", names(dim(lat)),
", which is not the expected names ('lat' or 'latitude') by s2dv_cube."))
}
} else {
stop("Parameter 'lat' is provided but data doesn't contain a ",
"latitudinal dimension.")
}
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
## Dates
if (!is.null(Dates)) {
if (!is.list(Dates)) {
stop("Parameter 'Dates' must be a list.")
} else {
if (length(Dates) > 2) {
warning("Parameter 'Dates' is a list with more than 2 ",
"elements and only the first two will be used.")
Dates <- Dates[1 : 2]
}
if (names(Dates)[1] != 'start') {
warning("The name of the first element of parameter 'Dates' ",
"is expected to be 'start'.")
}
if (length(Dates) == 2) {
if (names(Dates)[2] != 'end') {
warning("The name of the second element of parameter 'Dates' ",
"is expected to be 'end'.")
}
if (length(Dates[[1]]) != length(Dates[[2]])) {
stop("The length of the elements in parameter 'Dates' must ",
"be equal.")
}
}
if (!is.null(time_dims)) {
time_dims <- dims[names(dims) %in% time_dims]
} else {
warning("Parameter 'time_dims' is not provided, assigning 'sdate', ",
"'time' and 'ftime' as default time dimension names.")
time_dims <- dims[names(dims) %in% c('sdate', 'time', 'ftime')]
}
if (prod(time_dims) != length(Dates[[1]])) {
stop("The length of the temporal dimension doesn't match ",
"the length of elements in parameter 'Dates'.")
}
object <- list(data = data, lon = lon, lat = lat, Variable = Variable,
Datasets = Datasets, Dates = Dates, time_dims = time_dims,
when = when, source_files = source_files)
class(object) <- 's2dv_cube'
return(object)
}