ml2pl_in.sh

#!/bin/bash

# Author: Lionel GUEZ

# This script is a wrapper for a Fortran program. For an explanation
# of programming choices, see notes.

# Do not run several instances of this script in parallel in the same
# directory. File names are not made different for different
# instances.

##set -x

# Absolute path to Fortran executable:
executable=@CMAKE_INSTALL_FULL_LIBEXECDIR@/ml2pl

# Set up the necessary environment:
if [[ -f @CMAKE_INSTALL_FULL_LIBEXECDIR@/ml2pl_runtime_env.sh ]]
then
    source @CMAKE_INSTALL_FULL_LIBEXECDIR@/ml2pl_runtime_env.sh
fi

USAGE="usage: ml2pl.sh [OPTION]... input-file output-file [pressure-file]

Interpolates NetCDF variables from model levels to pressure
levels.

Options:
   -h                       : this help message
   -p variable              : name of 4-dimensional variable in the input file
                              or in the pressure file containing the
                              pressure field at model levels
   -v variable[,variable...]: names of variables you want to interpolate, 
                              or extrapolate if target pressure level is below
                              surface
   -w variable[,variable...]: names of variables you want to interpolate, 
                              or set to 0 if target pressure level is below
                              surface
   -m variable[,variable...]: names of variables you want to interpolate, 
                              or set to missing if target pressure level is 
                              below surface

The target pressure levels should be in a file called
\"press_levels.txt\", in the same unit as input pressure field. For further
information, see https://github.com/lguez/Ml2pl."

while getopts hp:v:w:m: name
  do
  case $name in
      p) 
	  pressure_var=$OPTARG;;
      v) 
	  variable_list_v=$OPTARG;;
      w) 
	  variable_list_w=$OPTARG;;
      m) 
	  variable_list_m=$OPTARG;;
      h)
	  echo "$USAGE" >&2
	  exit;;
      \?)
	  echo "Use option -h for help"
	  exit 1;;
  esac
done

if [[ -n $pressure_var ]]
then
    # For Climaf, remove pressure_var from variable lists:

    variable_list_v=`echo $variable_list_v | sed -e 's/'$pressure_var'//g' -e s'/,,*/,/g' -e s'/^,//' -e 's/,$//'`
    
    variable_list_w=`echo $variable_list_w | sed -e 's/'$pressure_var'//g' -e s'/,,*/,/g' -e s'/^,//' -e 's/,$//'`

    variable_list_m=`echo $variable_list_m | sed -e 's/'$pressure_var'//g' -e s'/,,*/,/g' -e s'/^,//' -e 's/,$//'`
fi

if [[ -z $variable_list_v && -z $variable_list_w && -z $variable_list_m ]]
    then
    echo "Specify at least one variable, following -v, -w or -m."
    echo "Use option -h for help"
    exit 1
fi

shift $((OPTIND - 1))

if (($# <= 1))
then
    echo "Missing input or output file."
    echo "Use option -h for help"
    exit 1
elif (($# >= 4))
then
    echo "Too many arguments."
    echo "Use option -h for help"
    exit 1
fi

set -e

if [[ ! -x $executable ]]
    then
    echo "$executable not found or not executable"
    exit 1
fi

if [[ ! -f $1 ]]
    then
    echo "ml2pl.sh: $1 not found"
    exit 1
fi

if [[ ! -f "press_levels.txt" ]]
    then
    echo "ml2pl.sh: press_levels.txt not found"
    echo "Use option -h for help"
    exit 1
fi

if (($# == 2))
then
    ln -sf $1 input_file_ml2pl.nc
else
    # $# == 3

    if [[ ! -f $3 ]]
    then
	echo "ml2pl.sh: $3 not found"
	exit 1
    fi

    cp $3 input_file_ml2pl.nc
    ncks --append ${variable_list_v:+--variable=$variable_list_v} \
	${variable_list_w:+--variable=$variable_list_w} \
	${variable_list_m:+--variable=$variable_list_m} $1 input_file_ml2pl.nc
    echo "Appended $1 to $3."
fi

output_file=$2

IFS=","

if [[ -z $variable_list_v ]]
then
    nv=0
else
    set $variable_list_v
    nv=$#
fi

if [[ -z $variable_list_w ]]
then
    nw=0
else
    set $variable_list_w
    nw=$#
fi

# Create the list of variables:
set $variable_list_v $variable_list_w $variable_list_m
for my_var in $*
  do
  echo $my_var
done >variable_list_ml2pl.txt

# Run the Fortran program:
$executable <<EOF
$nv
$nw
"$pressure_var"
EOF
# (Quotes around $pressure_var are necessary for the case when
# pressure_var is not defined.)

mv output_file_ml2pl.nc $output_file

# Clean up:
rm input_file_ml2pl.nc variable_list_ml2pl.txt