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#'Transform the coordinate system to -180 to 180 longitude of an infile
#'
#'@param infile Filename of input NetCDF file. This may include the directory
#' (character).
#'@param var Name of NetCDF variable (character).
#'@param outfile Filename of output NetCDF file. This may include the directory
#' (character).
#'@param nc Alternatively to \code{infile} you can specify the input as an
#' object of class `ncdf4` (as returned from \code{ncdf4::nc_open}).
#'
#'@return A NetCDF file including the coordinate system (-180 to 180 longitude) is
#' written.
#'@export
#'
#'@family data manipulation functions
cmsaf.transform.coordinate.system <- function(infile, var, outfile, nc = NULL){
# read .nc-file
file_data <- read_file(infile, var, nc = nc)
if (!is.null(nc)) nc_in <- nc
else nc_in <- nc_open(infile)
# read data from infile
dum_dat <- ncvar_get(
nc_in,
file_data$variable$name,
collapse_degen = FALSE
)
if (is.null(nc)) nc_close(nc_in)
# convert coordinate system
temp_file <- file.path(tempdir(),"temp_file.nc")
data.matrix <- t(as.matrix(dum_dat[,,1]))
r <- raster::raster(nrow=length(file_data$dimension_data$y), ncol=length(file_data$dimension_data$x))
raster::values(r) <- as.vector(t(data.matrix))
raster::extent(r) <- raster::extent(0, 360, -90, 90)
raster::rotate(r, filename=temp_file, format = "CDF", overwrite = TRUE, varname= var)
# read temp_file.nc
nc_in_tmp <- nc_open(temp_file)
# variables
#varnames <- names(nc_in_tmp$var)
dim_names <- names(nc_in_tmp$dim)
dimensions <- get_dimensions(nc_in_tmp, dim_names)
# use new coordinate system (180 to -180 for longitude)
dimension.data <- list(
x = nc_in_tmp$dim[[dimensions$names$x]]$vals,
y = nc_in_tmp$dim[[dimensions$names$y]]$vals
)
nc_close(nc_in_tmp)
vars_data <- list()
file_data$variable$prec <- "float"
nc34 <- 4 # use NetCDF 4
nc_format <- get_nc_version(nc34)
cmsaf_info <- paste0("Created with the CM SAF R Toolbox.")
time_data <- file_data$dimension_data$t
global_att_list <- names(file_data$global_att)
global_att_list <- global_att_list[toupper(global_att_list) %in% toupper(GLOBAL_ATT_DEFAULT)]
global_attributes <- file_data$global_att[global_att_list]
dims <- define_dims(file_data$grid$is_regular,
dimension.data$x,
dimension.data$y,
time_data,
NB2,
file_data$time_info$units,
with_time_bnds = FALSE)
vars <- define_vars(file_data$variable, dims, nc_format$compression, with_time_bnds = FALSE)
write_output_file(
outfile,
nc_format$force_v4,
vars,
vars_data,
file_data$variable$name,
file_data$grid$vars, file_data$grid$vars_data,
cmsaf_info,
file_data$time_info$calendar,
file_data$variable$attributes,
global_attributes,
with_time_bnds = FALSE,
write_result = FALSE
)
nc_out <- nc_open(outfile, write = TRUE)
for(i in 1:length(file_data$dimension_data$t)){
data.matrix <- t(as.matrix(dum_dat[,,i]))
r <- raster::raster(nrow=length(dimension.data$y), ncol=length(dimension.data$x))
raster::values(r) <- as.vector(t(data.matrix))
raster::extent(r) <- raster::extent(0, 360, -90, 90)
rr <- raster::rotate(r, varname = var)
dum_dat_temp <- as.array(t(raster::as.matrix(rr)))
ncvar_put(nc_out, vars[[1]], dum_dat_temp, start = c(1, 1, i), count = c(-1, -1, 1))
}
nc_close(nc_out)
# remove temp_file.nc
if(file.exists(temp_file)){
unlink(temp_file)
}
}
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