cycle2interp.sh

#!/bin/sh

##########################################################################
# The MIT License
#
# Copyright (c) engeir
#
# Permission is hereby granted, free of charge,
# to any person obtaining a copy of this software and
# associated documentation files (the "Software"), to
# deal in the Software without restriction, including
# without limitation the rights to use, copy, modify,
# merge, publish, distribute, sublicense, and/or sell
# copies of the Software, and to permit persons to whom
# the Software is furnished to do so,
# subject to the following conditions:
#
# The above copyright notice and this permission notice
# shall be included in all copies or substantial portions of the Software.
#
# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
# EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
# OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT.
# IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR
# ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT,
# TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE
# SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
##########################################################################

#
# Description: Create file used in the CESM2 that works with the INTERP_MISSING_MONTHS mode,
# from a file meant to be run in CYCLE mode.
#
# Dependencies: NCO - http://research.jisao.washington.edu/data_sets/nco/
#               reset_date_variable - https://gist.github.com/engeir/7ba0e74b2856222ac1cefb105af43b3b#file-reset_date_variable-py
#
# Usage:
#   1. Run with some netCDF file as the first argument
#     `cycle2interp.sh in.nc`
#
# Needs a python environment with the netcdf4 package installed, and the NCO command line
# tools.
#
# Shell: POSIX compliant
# Author: Eirik R. Enger
#

if ! command -v ncks >/dev/null 2>&1; then
    echo "Cannot access NCO commands"
    exit 1
fi

ncks -d time,'1850-1-1 0:00:0.0','1851-1-1 0:00:0.0' "$1" 1850.nc

ncap2 -s 'time=time+(1-1850)*365' 1850.nc 1.nc
ncap2 -s 'time=time+(9999-1850)*365' 1850.nc 9999.nc

if ncdump -h "$1" | grep 'time = UNLIMITED' >/dev/null 2>&1; then
    cp 1.nc 1_un.nc
    cp 9999.nc 9999_un.nc
else
    ncks --mk_rec_dmn time 1.nc 1_un.nc
    ncks --mk_rec_dmn time 9999.nc 9999_un.nc
fi
  
# Make a backup and save to the original name.
mv "$1" "$1".bak
ncrcat -h 1_un.nc 9999_un.nc "$1"

echo "$1" | reset_date_variable.py

# Clean up
rm 1850.nc 1.nc 9999.nc 1_un.nc 9999_un.nc

reset_date_variable.py

#!/bin/python

##########################################################################
# The MIT License
#
# Copyright (c) engeir
#
# Permission is hereby granted, free of charge,
# to any person obtaining a copy of this software and
# associated documentation files (the "Software"), to
# deal in the Software without restriction, including
# without limitation the rights to use, copy, modify,
# merge, publish, distribute, sublicense, and/or sell
# copies of the Software, and to permit persons to whom
# the Software is furnished to do so,
# subject to the following conditions:
#
# The above copyright notice and this permission notice
# shall be included in all copies or substantial portions of the Software.
#
# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
# EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
# OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT.
# IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR
# ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT,
# TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE
# SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
##########################################################################

#
# Description: Re-write the year of the "date" variable of a netCDF file. The first
# 12 elements are set to year 1, the rest to year 9999.
#
# Dependencies: netCDF4 - https://pypi.org/project/netCDF4/
#
# Usage:
#   1. Run the script with the filename as stdin
#     `echo "in.nc" | reset_date_variable.py`
#
# Author: Eirik R. Enger
#

import os
import sys

import netCDF4 as nc


def rewrite_date_variable() -> None:
    # Check file path
    data = sys.stdin.readlines()
    new_path = data[0].strip("\n")
    if not isinstance(new_path, str) or new_path[-3:] != ".nc":
        raise TypeError(f"Are you sure {new_path} is a valid netCDF file?")
    if not os.path.exists(new_path):
        raise FileNotFoundError(f"Cannot find file named {new_path}.")

    # Open file
    with nc.Dataset(new_path, "r+") as ncfile:
        # Fix values
        for i, d in enumerate(ncfile.variables["date"][:]):
            n = 1 if i < 12 else 9999
            ncfile.variables["date"][i] = d % 10000 + n * 10000


if __name__ == "__main__":
    rewrite_date_variable()