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Commit 3f53aa44 authored by Nicolau Manubens's avatar Nicolau Manubens
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Merge branch 'master' of http://earth.bsc.es/gitlab/es/easyNCDF

parents 32e2ddb4 6297b73e
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R/ArrayToNc.R
View file @ 3f53aa44
ArrayToNc <- function(arrays, file_path) {
ArrayToNetCDF <- function(arrays, file_path) {
# Check parameter arrays.
if (is.array(arrays)) {
arrays <- list(arrays)
......@@ -98,7 +98,7 @@ ArrayToNc <- function(arrays, file_path) {
if (!('vals' %in% names(dim_info))) {
dim_info[['vals']] <- 1:dim_info[['len']]
} else {
if (!is.numeric(dim_info[['vals']])) {
if (!(is.numeric(dim_info[['vals']]))) {
stop("The provided 'vals' for the ", k, "th dimension in the ", i, "th array must be a numeric vector.")
}
if (dim_info[['units']] == '') {
......@@ -301,7 +301,7 @@ ArrayToNc <- function(arrays, file_path) {
}
ncatt_put(ncdf_object, defined_vars[[var_counter]]$name, 'coordinates', paste(coords, collapse = ' '))
}
attrs_to_skip <- which(names(var_info) %in% c('addOffset', 'scaleFact', 'coordinates'))
attrs_to_skip <- which(names(var_info) %in% c('addOffset', 'scaleFact', 'coordinates', 'dim'))
attrs_to_add <- names(var_info)
if (length(attrs_to_skip) > 0) {
attrs_to_add <- attrs_to_add[-attrs_to_skip]
......@@ -318,5 +318,3 @@ ArrayToNc <- function(arrays, file_path) {
nc_close(ncdf_object)
invisible(NULL)
}
a2nc <- ArrayToNc
R/ArrayToNetCDF.R deleted 100644 → 0
View file @ 32e2ddb4
ArrayToNetCDF <- function(arrays, file_path) {
# Check parameter arrays.
if (is.array(arrays)) {
arrays <- list(arrays)
}
if (any(!sapply(arrays, function(x) is.array(x) && (is.numeric(x) || is.logical(x))))) {
stop("The parameter 'arrays' must be one or a list of numeric or logical arrays.")
}
# Check parameter file_path.
if (!is.character(file_path)) {
stop("Parameter 'file_path' must be a character string.")
}
defined_dims <- list()
defined_vars <- list()
global_attrs <- list()
var_dim <- NULL
for (i in 1:length(arrays)) {
array_attrs <- attributes(arrays[[i]])
if ('variables' %in% names(array_attrs)) {
vars_info <- array_attrs[['variables']]
array_attrs <- array_attrs[-which(names(array_attrs) == 'variables')]
} else {
vars_info <- NULL
}
global_attrs[names(array_attrs)] <- array_attrs
var_dim <- which(names(dim(arrays[[i]])) %in% c('var', 'variable'))
if (length(var_dim) > 0) {
var_dim <- var_dim[1]
num_vars <- dim(arrays[[i]])[var_dim]
} else {
var_dim <- NULL
num_vars <- 1
}
# Defining ncdf4 variable objects
for (j in 1:num_vars) {
var_info <- vars_info[[j]]
if (length(var_info) == 0) {
var_info <- list()
}
dim_names <- names(dim(arrays[[i]]))
if (!is.null(dim_names)) {
if (any(is.na(dim_names) | (sapply(dim_names, nchar) == 0))) {
stop("The provided arrays must have all named dimensions or ",
"all unnamed dimensions.")
}
}
provided_dims <- sapply(var_info$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 {
if (!(is.numeric(dim_info[['vals']]))) {
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))) {
var_info[['prec']] <- 'float'
} 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
}
}
nc_close(ncdf_object)
invisible(NULL)
}
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