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#'Save multidimensional R arrays into NetCDF files
#'
#'@author N. Manubens \email{nicolau.manubens@bsc.es}
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#'@description This function takes as input one or a list of multidimensional R arrays and stores them in a NetCDF file, using the \code{ncdf4} package. The full path and name of the resulting file must be specified. Metadata can be attached to the arrays and propagated into the NetCDF file in 3 possible ways:\cr
#' \itemize{
#' \item{Via the list names if a list of arrays is provided:}{Each name in the input list, corresponding to one multidimensional array, will be interpreted as the name of the variable it contains.\cr
#'E.g:\cr
#' \code{
#'ArrayToNc(arrays = list(temperature = array(1:9, c(3, 3))),
#' file_path = 'example.nc')
#' }
#' }
#' \item{Via the dimension names of each provided array:}{The dimension names of each of the provided arrays will be interpreted as names for the dimensions of the NetCDF files. Read further for special dimension names that will trigger special behaviours, such as 'time' and 'var'.\cr
#'E.g:\cr
#' \code{
#'temperature <- array(rnorm(100 * 50 * 10), dim = c(100, 50, 10))
#'names(dim(temperature)) <- c('longitude', 'latitude', 'time')
#'ArrayToNc(list(temperature = temperature), file_path = 'example.nc')
#' }
#' }
#' \item{Via the attribute 'variables' of each provided array:}{The arrays can be provided with metadata in an attribute named 'variables', which is expected to be a named list of named lists, where the names of the container list are the names of the variables present in the provided array, and where each sub-list contains metadata for each of the variables. The attribute names and values supported in the sub-lists must follow the same format the package \code{ncdf4} uses to represent the NetCDF file headers.\cr
#'E.g:\cr
#' \code{
#'a <- array(1:400, dim = c(5, 10, 4, 2))
#'metadata <- list(
#' tos = list(addOffset = 100,
#' scaleFact = 10,
#' dim = list(list(name = 'time',
#' unlim = FALSE)))
#' )
#'attr(a, 'variables') <- metadata
#'names(dim(a)) <- c('lat', 'lon', 'time', 'var')
#'ArrayToNc(a, 'tmp.nc')
#' }
#' }
#' }
#'The special dimension names are 'var'/'variable' and 'time'.\cr
#'If a dimension is named 'var' or 'variable', \code{ArrayToNc} will interpret each array entry along such dimension corresponds to a separate new variable, hence will create a new variable inside the NetCDF file and will use it to store all the data in the provided array for the corresponding entry along the 'var'/'variable' dimension.\cr
#'If a dimension is named 'time', by default it will be interpreted and built as an unlimited dimension. The 'time' dimension must be the last dimension of the array (the right-most). If a 'var'/'variable' dimension is present, the 'time' dimension can be also placed on its left (i.e. the one before the last dimension). The default behaviour of creating the 'time' as unlimited dimension can be disabled by setting manually the attribute \code{unlim = FALSE}, as shown in the previous example.\cr\cr
#'\code{a2nc} is an alias of \code{ArrayToNc}.
#'
#'@param arrays One or a list of multidimensional data arrays. The list can be provided with names, which will be interpreted as variable names. The arrays can be provided with dimension names. The arrays can be provided with metadata in the attribute 'variables' (read section Description for details).
#'@param file_path Path and name of the NetCDF file to be created.
#'
#'@return This function returns NULL.
#'
#'@import ncdf4
#'@importFrom ClimProjDiags Subset
#'@importFrom stats setNames
#'@examples
#' \dontrun{
#'# Minimal use case
#'ArrayToNc(array(1:9, c(3, 3)), 'tmp.nc')
#'# Works with arrays of any number of dimensions
#'ArrayToNc(array(1:27, c(3, 3, 3)), 'tmp.nc')
#'
#'# Arrays can also be provided in [named] lists
#'ArrayToNc(list(tos = array(1:27, c(3, 3, 3))), 'tmp.nc')
#'
#'# Or with dimension names
#'# 'var' dimension name will generate multiple variables in the
#'# resulting NetCDF file
#'a <- array(1:27, dim = c(3, 3, 3))
#'names(dim(a)) <- c('lon', 'lat', 'var')
#'ArrayToNc(a, 'tmp.nc')
#'
#'# 'variable' as dimension name will do the same
#'a <- array(1:27, dim = c(3, 3, 3))
#'names(dim(a)) <- c('lon', 'lat', 'variable')
#'ArrayToNc(a, 'tmp.nc')
#'
#'# The 'time' dimension will be built as unlimited dimension, by default
#'a <- array(1:1600, dim = c(10, 20, 4, 2))
#'names(dim(a)) <- c('lat', 'lon', 'time', 'var')
#'ArrayToNc(a, 'tmp.nc')
#'
#'# The dimension 'var'/'variable' can be in any position and can have any length
#'a <- array(1:1600, dim = c(10, 20, 4, 2))
#'names(dim(a)) <- c('lat', 'var', 'lon', 'time')
#'ArrayToNc(a, 'tmp.nc')
#'
#'# Multiple arrays can be provided in a list
#'a <- array(1:400, dim = c(5, 10, 4, 2))
#'names(dim(a)) <- c('lat', 'lon', 'time', 'var')
#'ArrayToNc(list(a, a), 'tmp.nc')
#'
#'# If no dimension names are given to an array, new names will be automatically
#'# generated
#'a <- array(1:400, dim = c(5, 10, 4, 2))
#'b <- array(1:400, dim = c(5, 11, 4, 2))
#'names(dim(a)) <- c('lat', 'lon', 'time', 'var')
#'ArrayToNc(list(a, b), 'tmp.nc')
#'
#'# Metadata can be provided for each variable in each array, via the
#'# attribute 'variables'. In this example the metadata is empty.
#'a <- array(1:400, dim = c(5, 10, 4, 2))
#'metadata <- list(
#' tos = list(),
#' tas = list())
#'attr(a, 'variables') <- metadata
#'names(dim(a)) <- c('lat', 'lon', 'time', 'var')
#'ArrayToNc(a, 'tmp.nc')
#'
#'# Variable names can be manually specified
#'a <- array(1:400, dim = c(5, 10, 4, 2))
#'metadata <- list(
#' tos = list(name = 'name1'),
#' tas = list(name = 'name2'))
#'attr(a, 'variables') <- metadata
#'names(dim(a)) <- c('lat', 'lon', 'time', 'var')
#'ArrayToNc(a, 'tmp.nc')
#'# Units can be specified
#'a <- array(1:400, dim = c(5, 10, 4, 2))
#'metadata <- list(
#' tos = list(units = 'K'),
#' tas = list(units = 'K'))
#'attr(a, 'variables') <- metadata
#'names(dim(a)) <- c('lat', 'lon', 'time', 'var')
#'ArrayToNc(a, 'tmp.nc')
#'
#'# addOffset and scaleFactor can be specified
#'a <- array(1:400, dim = c(5, 10, 4, 2))
#'metadata <- list(
#' tos = list(addOffset = 100,
#' scaleFact = 10),
#' tas = list(addOffset = 100,
#' scaleFact = 10))
#'attr(a, 'variables') <- metadata
#'names(dim(a)) <- c('lat', 'lon', 'time', 'var')
#'ArrayToNc(a, 'tmp.nc')
#'
#'# Global attributes can be specified
#'a <- array(rnorm(10), dim = c(a = 5, b = 2))
#'attrs <- list(variables =
#' list(tas = list(var_attr_1 = 'test_1_var',
#' var_attr_2 = 2)),
#' global_attrs = list(global_attr_name_1 = 'test_1_global',
#' global_attr_name_2 = 2))
#'attributes(a) <- c(attributes(a), attrs)
#'ArrayToNc(a, 'tmp.nc')
#'
#'# Unlimited dimensions can be manually created
#'a <- array(1:400, dim = c(5, 10, 4, 2))
#'metadata <- list(
#' tos = list(addOffset = 100,
#' scaleFact = 10,
#' dim = list(list(name = 'unlimited',
#' unlim = TRUE))),
#' tas = list(addOffset = 100,
#' scaleFact = 10,
#' dim = list(list(name = 'unlimited',
#' unlim = TRUE))))
#'attr(a, 'variables') <- metadata
#'names(dim(a)) <- c('lat', 'lon', 'unlimited', 'var')
#'ArrayToNc(a, 'tmp.nc')
#'
#'# A 'time' dimension can be built without it necessarily being unlimited
#'a <- array(1:400, dim = c(5, 10, 4, 2))
#'metadata <- list(
#' tos = list(addOffset = 100,
#' scaleFact = 10,
#' dim = list(list(name = 'time',
#' unlim = FALSE))),
#' tas = list(addOffset = 100,
#' scaleFact = 10,
#' dim = list(list(name = 'time',
#' unlim = FALSE))))
#'attr(a, 'variables') <- metadata
#'names(dim(a)) <- c('lat', 'lon', 'time', 'var')
#'ArrayToNc(a, 'tmp.nc')
#'
# Multiple arrays with data for multiple variables can be saved into a
# NetCDF file at once.
#'tos <- array(1:400, dim = c(5, 10, 4))
#'metadata <- list(tos = list(units = 'K'))
#'attr(tos, 'variables') <- metadata
#'names(dim(tos)) <- c('lat', 'lon', 'time')
#'lon <- seq(0, 360 - 360 / 10, length.out = 10)
#'dim(lon) <- length(lon)
#'metadata <- list(lon = list(units = 'degrees_east'))
#'attr(lon, 'variables') <- metadata
#'names(dim(lon)) <- 'lon'
#'lat <- seq(-90, 90, length.out = 5)
#'dim(lat) <- length(lat)
#'metadata <- list(lat = list(units = 'degrees_north'))
#'attr(lat, 'variables') <- metadata
#'names(dim(lat)) <- 'lat'
#'ArrayToNc(list(tos, lon, lat), 'tmp.nc')
#'}
#'
#'@export
# Check parameter arrays.
if (is.array(arrays)) {
arrays <- list(arrays)
}
if (any(!sapply(arrays, function(x) is.array(x) && (is.numeric(x) || is.logical(x))))) {
stop("The parameter 'arrays' must be one or a list of numeric or logical arrays.")
}
# Check parameter file_path.
if (!is.character(file_path)) {
stop("Parameter 'file_path' must be a character string.")
}
defined_dims <- list()
defined_vars <- list()
global_attrs <- list()
var_dim <- NULL
for (i in 1:length(arrays)) {
array_attrs <- attributes(arrays[[i]])
if ('variables' %in% names(array_attrs)) {
vars_info <- array_attrs[['variables']]
array_attrs <- array_attrs[-which(names(array_attrs) == 'variables')]
} else {
vars_info <- NULL
}
#global_attrs[names(array_attrs)] <- array_attrs
if ('global_attrs' %in% names(array_attrs)) {
global_attrs <- c(global_attrs, array_attrs[['global_attrs']])
}
var_dim <- which(names(dim(arrays[[i]])) %in% c('var', 'variable'))
if (length(var_dim) > 0) {
var_dim <- var_dim[1]
num_vars <- dim(arrays[[i]])[var_dim]
} else {
var_dim <- NULL
num_vars <- 1
}
# Defining ncdf4 variable objects
for (j in 1:num_vars) {
var_info <- vars_info[[j]]
if (length(var_info) == 0) {
var_info <- list()
}
dim_names <- names(dim(arrays[[i]]))
if (!is.null(dim_names)) {
if (any(is.na(dim_names) | (sapply(dim_names, nchar) == 0))) {
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stop("The provided arrays must have all named dimensions or ",
"all unnamed dimensions.")
}
}
provided_dims <- sapply(var_info$dim, '[[', 'name')
var_built_dims <- NULL
for (k in 1:length(dim(arrays[[i]]))) {
if (!identical(k, var_dim)) {
final_dim_position <- k - ifelse(!is.null(var_dim) && k > var_dim, 1, 0)
dim_name <- dim_names[k]
if (!is.null(dim_name) && (dim_name %in% provided_dims)) {
dim_info <- var_info$dim[[which(provided_dims == dim_name)]]
} else {
dim_info <- list()
}
if (!('name' %in% names(dim_info))) {
if (!is.null(dim_name)) {
dim_info[['name']] <- dim_name
} else {
dim_info[['name']] <- paste0('dim', final_dim_position)
}
} else {
if (!is.character(dim_info[['name']])) {
stop("The provided 'name' for the ", k, "th dimension in the ", i, "th array must be a character string.")
}
dim_info[['name']] <- dim_info[['name']][1]
}
if (!('len' %in% names(dim_info))) {
dim_info[['len']] <- unname(dim(arrays[[i]])[k])
} else {
if (!is.numeric(dim_info[['len']])) {
stop("The provided 'len' for the ", k, "th dimension in the ", i, "th array must be a numeric value.")
}
dim_info[['len']] <- as.integer(round(dim_info[['len']][1]))
if (dim_info[['len']] != dim(arrays[[i]])[k]) {
stop("The provided 'len' for the ", k, "th dimension in the ", i, "th array does not match the actual length of the provided array.")
}
}
if (!('unlim' %in% names(dim_info))) {
dim_info[['unlim']] <- ifelse(dim_info[['name']] == 'time', TRUE, FALSE)
} else {
if (!is.logical(dim_info[['unlim']])) {
stop("The provided 'unlim' for the ", k, "th dimension in the ", i, "th array must be a logical value.")
}
dim_info[['unlim']] <- dim_info[['unlim']][1]
}
if (!('units' %in% names(dim_info))) {
dim_info[['units']] <- ''
} else {
if (!is.character(dim_info[['units']])) {
stop("The provided 'units' for the ", k, "th dimension in the ", i, "th array must be a character string.")
}
dim_info[['units']] <- dim_info[['units']][1]
}
if (!('vals' %in% names(dim_info))) {
dim_info[['vals']] <- 1:dim_info[['len']]
} else {
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stop("The provided 'vals' for the ", k, "th dimension in the ", i, "th array must be a numeric vector.")
}
if (dim_info[['units']] == '') {
dim_info[['vals']] <- as.integer(dim_info[['vals']])
}
if (length(dim_info[['vals']]) != dim_info[['len']]) {
stop("The length of the provided 'vals' for the ", k, "th dimension in the ", i, "th array does not match the length of the provided array.")
}
}
if (!('create_dimvar' %in% names(dim_info))) {
if (dim_info[['units']] == '') {
dim_info[['create_dimvar']] <- FALSE
} else {
dim_info[['create_dimvar']] <- TRUE
}
} else {
if (!is.logical(dim_info[['create_dimvar']])) {
stop("The provided 'create_dimvar' for the ", k, "th dimension in the ", i, "th array must be a logical value.")
}
dim_info[['create_dimvar']] <- dim_info[['create_dimvar']][1]
if (dim_info[['units']] != '' && !dim_info[['create_dimvar']]) {
stop("Provided 'units' for the ", k, "th dimension in the ", i, "th array but 'create_dimvar' set to FALSE.")
}
}
if (!('calendar' %in% names(dim_info))) {
dim_info[['calendar']] <- NA
} else {
if (!is.character(dim_info[['calendar']])) {
stop("The provided 'calendar' for the ", k, "th dimension in the ", i, "th array must be a character string.")
}
dim_info[['calendar']] <- dim_info[['calendar']][1]
}
if (!('longname' %in% names(dim_info))) {
dim_info[['longname']] <- dim_info[['name']]
} else {
if (!is.character(dim_info[['longname']])) {
stop("The provided 'longname' for the ", k, "th dimension in the ", i, "th array must be a character string.")
}
dim_info[['longname']] <- dim_info[['longname']][1]
}
if (dim_info[['name']] %in% names(defined_dims)) {
items_to_check <- c('name', 'len', 'unlim', 'units', 'vals',
'create_dimvar', 'longname')
if (!identical(dim_info[items_to_check],
defined_dims[[dim_info[['name']]]][items_to_check]) ||
!(identical(dim_info[['calendar']], defined_dims[[dim_info[['name']]]][['calendar']]) ||
(is.na(dim_info[['calendar']]) && is.null(defined_dims[[dim_info[['name']]]][['calendar']])))) {
stop("The dimension '", dim_info[['name']], "' is ",
"defined or used more than once in the provided ",
"data but the dimension specifications do not ",
"match.")
}
} else {
new_dim <- list(ncdim_def(dim_info[['name']], dim_info[['units']],
dim_info[['vals']], dim_info[['unlim']],
dim_info[['create_dimvar']],
dim_info[['calendar']],
dim_info[['longname']]))
names(new_dim) <- dim_info[['name']]
defined_dims <- c(defined_dims, new_dim)
}
var_built_dims <- c(var_built_dims, dim_info[['name']])
}
}
if (!('name' %in% names(var_info))) {
var_name_from_md <- names(vars_info)[j]
var_name_from_ar <- names(arrays)[i]
if (is.character(var_name_from_md) &&
!is.na(var_name_from_md) &&
(nchar(var_name_from_md) > 0)) {
var_name <- var_name_from_md
} else if (is.character(var_name_from_ar) &&
!is.na(var_name_from_ar) &&
(nchar(var_name_from_ar) > 0)){
var_name <- var_name_from_ar
} else {
var_name <- paste0('var', i, '_', j)
}
var_info[['name']] <- var_name
} else {
if (!is.character(var_info[['name']])) {
stop("The provided 'name' for the ", j, "th variable in the ", i, "th array must be a character string.")
}
var_info[['name']] <- var_info[['name']][1]
}
if (!('units' %in% names(var_info))) {
var_info[['units']] <- ''
} else {
if (!is.character(var_info[['units']])) {
stop("The provided 'units' for the ", j, "th variable in the ", i, "th array must be a character string.")
}
var_info[['units']] <- var_info[['units']][1]
}
if (!('missval' %in% names(var_info))) {
var_info[['missval']] <- NULL
} else {
if (!is.numeric(var_info[['missval']])) {
stop("The provided 'missval' for the ", j, "th variable in the ", i, "th array must be a numeric value.")
}
var_info[['missval']] <- var_info[['missval']][1]
}
if (!('longname' %in% names(var_info))) {
var_info[['longname']] <- var_info[['name']]
} else {
if (!is.character(var_info[['longname']])) {
stop("The provided 'longname' for the ", j, "th variable in the ", i, "th array must be a character string.")
}
var_info[['longname']] <- var_info[['longname']][1]
}
if (!('prec' %in% names(var_info))) {
if (typeof(arrays[[i]]) == 'logical') {
var_info[['prec']] <- 'short'
} else if (typeof(arrays[[i]]) == 'character') {
var_info[['prec']] <- 'char'
} else if (typeof(arrays[[i]]) == 'integer') {
var_info[['prec']] <- 'integer'
} else {
var_info[['prec']] <- 'double'
}
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} else {
if (!is.character(var_info[['prec']])) {
stop("The provided 'prec' for the ", j, "th variable in the ", i, "th array must be a character string.")
}
var_info[['prec']] <- var_info[['prec']][1]
}
new_var <- list(ncvar_def(var_info[['name']], var_info[['units']],
defined_dims[var_built_dims],
var_info[['missval']],
var_info[['longname']], var_info[['prec']]))
names(new_var) <- var_info[['name']]
defined_vars <- c(defined_vars, new_var)
}
}
ncdf_object <- nc_create(file_path, defined_vars)
var_counter <- 1
# Putting the data and extra attributes.
for (i in 1:length(arrays)) {
array_attrs <- attributes(arrays[[i]])
if ('variables' %in% names(array_attrs)) {
vars_info <- array_attrs[['variables']]
} else {
vars_info <- NULL
}
var_dim <- which(names(dim(arrays[[i]])) %in% c('var', 'variable'))
if (length(var_dim) > 0) {
var_dim <- var_dim[1]
num_vars <- dim(arrays[[i]])[var_dim]
} else {
var_dim <- NULL
num_vars <- 1
}
for (j in 1:num_vars) {
var_info <- vars_info[[j]]
if (length(var_info) == 0) {
var_info <- list()
}
if (!('scaleFact' %in% names(var_info))) {
scale_factor <- 1
} else {
if (!is.numeric(var_info[['scaleFact']])) {
stop("The provided 'scaleFact' for the ", j, "th variable in the ", i, "th array must be a numeric value.")
}
scale_factor <- var_info[['scaleFact']][1]
}
if (!('addOffset' %in% names(var_info))) {
add_offset <- 0
} else {
if (!is.numeric(var_info[['addOffset']])) {
stop("The provided 'addOffset' for the ", j, "th variable in the ", i, "th array must be a numeric value.")
}
add_offset <- var_info[['addOffset']][1]
}
if (is.null(var_dim)) {
if (scale_factor != 1 || add_offset != 0) {
ncvar_put(ncdf_object, defined_vars[[var_counter]]$name,
(arrays[[i]] - add_offset) / scale_factor,
count = dim(arrays[[i]]))
} else {
ncvar_put(ncdf_object, defined_vars[[var_counter]]$name,
arrays[[i]],
count = dim(arrays[[i]]))
}
} else {
if (scale_factor != 1 || add_offset != 0) {
ncvar_put(ncdf_object, defined_vars[[var_counter]]$name,
(Subset(arrays[[i]], var_dim, j, drop = 'selected') - add_offset) / scale_factor,
count = dim(arrays[[i]])[-var_dim])
} else {
ncvar_put(ncdf_object, defined_vars[[var_counter]]$name,
Subset(arrays[[i]], var_dim, j, drop = 'selected'),
count = dim(arrays[[i]])[-var_dim])
}
}
if (scale_factor != 1 || add_offset != 0) {
ncatt_put(ncdf_object, defined_vars[[var_counter]]$name, 'scale_factor', scale_factor)
ncatt_put(ncdf_object, defined_vars[[var_counter]]$name, 'add_offset', add_offset)
}
if ('coordinates' %in% names(var_info)) {
if (!is.character(var_info[['coordinates']])) {
stop("The attribute 'coordinates' must be a character string.")
}
coords <- strsplit(var_info[['coordinates']], ' ')[[1]]
if (!(all(coords %in% sapply(defined_vars, '[[', 'name') |
coords %in% sapply(defined_dims[which(sapply(defined_dims, '[[', 'create_dimvar'))], '[[', 'name')))) {
coords <- coords[which(coords %in% sapply(defined_vars, '[[', 'name') |
coords %in% sapply(defined_dims[which(sapply(defined_dims, '[[', 'create_dimvar'))], '[[', 'name'))]
.warning("Some of the dimensions appearing in 'coordinates' have been removed because they point to undefined variables.")
ncatt_put(ncdf_object, defined_vars[[var_counter]]$name, 'coordinates', paste(coords, collapse = ' '))
attrs_to_skip <- which(names(var_info) %in% c('addOffset', 'scaleFact', 'coordinates', 'dim'))
attrs_to_add <- names(var_info)
if (length(attrs_to_skip) > 0) {
attrs_to_add <- attrs_to_add[-attrs_to_skip]
}
for (attribute_name in attrs_to_add) {
if (is.numeric(var_info[[attribute_name]]) ||
is.character(var_info[[attribute_name]])) {
ncatt_put(ncdf_object, defined_vars[[var_counter]]$name, attribute_name, var_info[[attribute_name]])
}
}
var_counter <- var_counter + 1
}
}
# Adding global attributes
if (length(global_attrs) > 0) {
for (attr_name in names(global_attrs)) {
ncatt_put(ncdf_object, 0, attr_name, global_attrs[[attr_name]])
}
}
nc_close(ncdf_object)
invisible(NULL)
}