Rewrite CDS CMIP6 NetCDF files to fix lat_bnds and lon_bnds problem

rewrite_netcdf.R

#!/usr/bin/env Rscript
# NetCDF rewrite - Data downloaded from CDS had some funny dimensions
# CDO did not like it. So rewriting
# usage: rewrite_netcdf input.nc output.nc 

library(ncdf4)

# processin arguments ####

args <- commandArgs(trailingOnly = TRUE)
if (length(args) != 2) {
    print("usage: rewrite_netcdf input.nc output.nc ")
    stop('Provide needed arguments')
}

arq <- args[1]
path <- dirname(args[1])
nome_base <- basename(arq)
variable <- unlist(strsplit(nome_base, '_'))[1]

# opening data  and attributes ####
infile <- nc_open(arq)

xsize <- infile$dim$lon$len
ysize <- infile$dim$lat$len
atributos <- ncatt_get(infile, 0)
var_atrib <- ncatt_get(infile, variable)

# creating output file ####
lon <- ncvar_get(infile, 'lon')
lat <- ncvar_get(infile, 'lat')
tvals <- ncvar_get(infile, 'time')

tunits <- ncatt_get(infile, 'time', 'units')

londim <- ncdim_def('lon', 'degrees_east', lon, longname = 'longitude')
latdim <- ncdim_def('lat', 'degrees_north', lat, longname = 'latitude')
timedim <- ncdim_def('time', tunits$value, tvals, longname = 'time')

var_def <- ncvar_def(variable, var_atrib$units, list(londim, latdim, timedim), 
                     var_atrib[['_FillValue']])

outfile <- nc_create(args[2],
                     list(var_def), force_v4 = TRUE)

# copying data to output files  ####
# in chunks to save memory

anos <- ceiling(length(tvals) / 365)

for (i in 1:anos) {
    sid <- (i - 1)*365 + 1
    if (i == anos) {
        # ultimo grupo.
        nts <- length(tvals) - (i-1) * 365
    } else {
        nts <- 365
    }
    dados <- ncvar_get(infile, variable,
                       start = c(1, 1, sid),
                       count = c(xsize, ysize, nts))

    ncvar_put(outfile, variable, dados,
              start = c(1,1, sid),
              count = c(xsize, ysize, nts))
}


# Updating output file attributes ####
ncatt_put(outfile, 'lon', 'axis', 'X')
ncatt_put(outfile, 'lat', 'axis', 'Y')
ncatt_put(outfile, 'time', 'axis', 'T')

atributos$history <- paste(atributos$history, ';', Sys.time(),
                           'NetCDF rewrite to work with CDO using rewrite_netcdf.R (DCV, Embrapa CNPTIA)')

for (a in names(atributos)) {
    ncatt_put(outfile, 0, a, atributos[[a]])
}

var_atrib$history <- paste(var_atrib$history, ';',
                           Sys.time(),
                           'NetCDF rewrite to work with CDO using rewrite_netcdf.R (DCV, Embrapa CNPTIA)')

# fillvalue does not work here. remove from attribute list
ncatt_put(outfile, variable, 'missing_value', var_atrib[['missing_value']])
var_atrib[['_FillValue']] <- NULL
var_atrib[['missing_value']] <- NULL

for (a in names(var_atrib)) {
    ncatt_put(outfile, variable, a, var_atrib[[a]])
}


nc_close(outfile)