Resolves Issue 99

.gitignore

@@ -19,3 +19,6 @@ sorc/rtofs_hycom.fd/esmf_4_0_0rp2/obj
 sorc/rtofs_hycom.fd/esmf_4_0_0rp2/make.out
 sorc/*/*.log
 
+# Ignore python cache
+ush/__pycache__/*
+

scripts/exrtofs_glo_ncoda_inc.sh

@@ -1,22 +1,5 @@
 #!/bin/sh
 set -xa
-###############################################################################
-####  UNIX Script Documentation Block                                         #
-#                                                                             #
-# Script name:         exrtofs_glo_ncoda_inc.sh                               #
-# Script description:                                                         #
-#                                                                             #
-# Author:        Dan Iredell     Org: NP23         Date: 2020-07-30           #
-#                                                                             #
-# Abstract: Remap an archive file to an NCODA analysis, new layer depths.     #
-#                                                                             #
-# Sub-scripts called:                                                         #
-#                                                                             #
-# Script history log:                                                         #
-# 2020-07-30  Dan Iredell                                                     #
-# 2023-02-08  Dmitry Dukhovskoy modified for updated ncoda_archv_lyrinc       #
-#                                                                             #
-###############################################################################
 
 export PS4='$SECONDS + '
 
@@ -70,7 +53,6 @@ types=salint_lyr_1o${SIZN}
 typeu=uucurr_lyr_1o${SIZN}
 typev=vvcurr_lyr_1o${SIZN}
 typep=lyrprs_lyr_1o${SIZN}
-typec=icecov_sfc_1o${SIZN}
 
 ln -sf  $COMINm1/rtofs_glo.t00z.n00.archv.a    archv.${archday}.a
 ln -sf  $COMINm1/rtofs_glo.t00z.n00.archv.b    archv.${archday}.b
@@ -118,25 +100,9 @@ else
    msg="$COMIN/ncoda/hycom_var/restart/${typep}_${dtg}_0000_analinc is missing"
    err_exit $msg
 fi
-# Ice Coverage
-if [ -e $COMIN/ncoda/hycom_var/restart/${typec}_${dtg}_0000_analfld ]; then
-   ln -sf  $COMIN/ncoda/hycom_var/restart/${typec}_${dtg}_0000_analfld ./icecov_${dtg}_analfld
-else
-   msg="$COMIN/ncoda/hycom_var/restart/${typec}_${dtg}_0000_analfld is missing"
-   err_exit $msg
-fi
 
-#create ssmi.r file
-rm -f ssmi1.a ssmi2.a ssmi.$dtg.r
-$EXECrtofs/rtofs_raw2hycom icecov_${dtg}_analfld $IDM $JDM 999.00 ssmi1.a > ssmi1.b
-err=$?; export err ; err_chk
-echo " error from rtofs_raw2hycom=",$err
-$EXECrtofs/rtofs_hycom_expr ssmi1.a "ONE" $IDM $JDM  0.01 0 ssmi2.a > ssmi2.b
-err=$?; export err ; err_chk
-echo " error from rtofs_hycom_expr=",$err
-$EXECrtofs/rtofs_hycom2raw8 ssmi2.a $IDM $JDM 1 1 $IDM $JDMA ssmi.$dtg.r
-err=$?; export err ; err_chk
-echo " error from rtofs_hycom2raw8=",$err
+# Create sea ice concentration file: sic.nc
+$USHrtofs/rtofs_glo_ice_update.sh
 
 ar=archv_1_inc.${archday}
 rm -f $ar.[a,b]

scripts/load_py_modules.sh

@@ -0,0 +1,7 @@
+#!/bin/bash
+
+export py_mod="ve/evs/2.0_py312"
+
+module use /apps/dev/modulefiles/
+module load ${py_mod}
+module list

ush/convert_bin_inc_to_nc.py

@@ -0,0 +1,89 @@
+#!/usr/bin/env python3
+
+"""
+Convert analysis increments or (2d) fields from NCODA analysis
+from binary to netcdf format.
+"""
+
+import os
+import sys
+import argparse
+import numpy as np
+import xarray as xr
+
+from utils import bin_to_nc_2d
+
+# --------------------------------------------------------------------------- #
+# 1. User Inputs
+# --------------------------------------------------------------------------- #
+get_inputs = argparse.ArgumentParser(
+    prog='convert_bin_inc_to_nc.py',
+    description='To convert RTOFS-DA output from binary to netcdf format.',
+    formatter_class=argparse.ArgumentDefaultsHelpFormatter
+)
+
+get_inputs.add_argument('--topog_file', type=str,
+    help='Path to topography file (NetCDF)',
+    required=True)
+
+get_inputs.add_argument('--input_file', type=str,
+    help='Name of NCODA binary output, including path',
+    required=True)
+
+get_inputs.add_argument('--var_name', type=str,
+    help='2-d variable name: icecov, icethk, icetmp, or mixlyr',
+    default="icecov")
+
+get_inputs.add_argument('--output_path', type=str,
+    help='Path to where output file is to be saved',
+    required=True)
+
+get_inputs.add_argument('--plot', action='store_true',
+    help='If present, generate a diagnostic plot of the output file',
+    default=False)
+
+args = get_inputs.parse_args()
+
+# Assign variables
+topo_file   = args.topog_file
+input_file  = args.input_file
+var_name    = args.var_name
+output_path = args.output_path
+
+# --------------------------------------------------------------------------- #
+# 2. Safety Checks
+# --------------------------------------------------------------------------- #
+
+if not os.path.isfile(topo_file):
+    sys.exit(f"ERROR: Topography file not found at: {topo_file}")
+
+if not os.path.isfile(input_file):
+    sys.exit(f"ERROR: NCODA binary file not found at: {input_file}")
+
+allowed_vars = ["icecov", "icethk", "icetmp", "mixlyr"]
+if var_name not in allowed_vars:
+    # Exit code 2 to distinguish from path errors
+    print(f"ERROR: Variable '{var_name}' is not in allowed list: {allowed_vars}")
+    sys.exit(2)
+
+if not os.path.isdir(output_path):
+    sys.exit(f"ERROR: Output path does not exist: {output_path}")
+
+if not os.access(output_path, os.W_OK):
+    sys.exit(f"ERROR: Output path is not writable: {output_path}")
+
+print(f"STATUS: All inputs validated. Beginning conversion for {var_name}...")
+
+# --------------------------------------------------------------------------- #
+# 3. Execution
+# --------------------------------------------------------------------------- #
+bin_to_nc_2d(input_file, var_name, output_path, topo_file)
+
+# --------------------------------------------------------------------------- #
+# 4. Plotting (Optional)
+# --------------------------------------------------------------------------- #
+if args.plot:
+    from utils import plot_var
+    # Use the name generated by bin_to_nc_2d
+    out_nc_file = os.path.join(output_path, f"{os.path.basename(input_file)}.nc")
+    plot_var(out_nc_file, var_name, output_path)

ush/rtofs_glo2d_ice.sh

@@ -1,47 +1,103 @@
 #!/bin/sh
-#
-###############################################################################
-####  UNIX Script Documentation Block                                         #
-#                                                                             #
-# Script name:         rtofs_glo2d_1hrly.sh                                   #
-# Script description:                                                         #
-#                                                                             #
-# Authors: Bhavani Rajan & Ilya Rivin  Org: NP23         Date: 2020-07-02     #
-#                                                                             #
-# Abstract: This script creates the surface ice fields for RTOFS-Global       #
-#           every 1 or 3 hours in netCDF format                               #
-#                                                                             #
-# Sub-scripts called:                                                         #
-#                                                                             # 
-# Executables called:                                                         #
-#                    rtofs_archv2ncdf2d                                       #
-#                                                                             # 
-#                                                                             #
-# Imported variables:                                                         #
-#                    RUN                                                      #
-#                    modID                                                    #
-#                    fhr                                                      #
-#                    EXECrtofs                                                #
-#                    PARMglobal                                               #
-#                    mode                                                     #
-#                                                                             #
-#                                                                             #
-# Script history log:                                                         #
-# XXXX-XX-XXX  Joe Dow                                                        #
-#                                                                             #
-###############################################################################
-
-set -x
-typeset -Z3 fhr
-
-echo "*** Started script $0 on hostname "$(hostname)' at time '$(date)
-
-export CDF021=${RUN}_${modID}_2ds_${mode}${fhr}_ice.nc
-
-export pgm="rtofs_archv2ncdf2d"
-. prep_step
-startmsg
-${EXECrtofs}/rtofs_field2ncdf2d < ${PARMrtofs}/${RUN}_${modID}.${inputgrid}.field2ncdf2d.in >> $pgmout 2>>errfile 
-export err=$? ; err_chk
-
-echo "*** Finished script $0 on hostname "$(hostname)' at time '$(date)
+
+if [[ $# -ne 4 ]]; then
+  echo " "
+  echo "Usage: "
+  echo "$0" "topog_file ncoda_file variable_name output_path"
+  echo " "
+  echo "Example inputs: "
+  echo "topog_file:    depth_GLBb0.08_09m11ob2_mom6.nc"
+  echo "ncoda_file:    icecov_20251215_analfld"
+  echo "variable_name: options: icecov, icethk, icetmp, mixlyr"
+  echo "output_path:   /lfs/h2/emc/stmp/santha.akella/test/"
+  echo " "
+  exit 1
+fi
+echo " "
+
+set -ux
+
+msg="$(basename -- "$0") JOB has begun on $(hostname) at $(date)"
+postmsg "$msg"
+
+# Allowed variable names
+allowed_variables=("icecov" "icethk" "icetmp" "mixlyr")
+
+is_not_allowed=true
+# --------------------------------------------------------------------------- #
+
+# Check for validity of inputs
+topog_file=$1
+ncoda_file=$2
+var_name=$3
+output_path=$4
+
+# Is there is a topography file in the "fix/", it is needed.
+if [[ ! -f "${topog_file}" ]]; then
+  echo "A topography file is needed for this script to work."
+  echo "Check in ${FIXrtofs} for depth_*.nc"
+  exit 1
+fi
+
+# Ice coverage file
+if [[ ! -f "${ncoda_file}" ]]; then
+  echo "A NCODA binary file is needed for this script to work."
+  echo "For example: icecov_yyyymmdd00_analfld"
+  exit 1
+fi
+
+# Variable name
+if [[ -z "${var_name}" ]]; then
+  echo "Variable name (string) is empty. Valid options are: icecov, icethk, icetmp, mixlyr."
+  exit 1
+fi
+
+# Loop through the  allowed variables to check for a match
+for val in "${allowed_variables[@]}"; do
+  if [ "${var_name}" = "$val" ]; then
+    is_not_allowed=false
+    break # Exit loop early if a match is found
+  fi
+done
+
+# Check the flag set within the loop
+if [ "$is_not_allowed" = true ]; then
+    echo "Error: variable name '${var_name}' is not an allowed value."
+    echo "Valid options are: icecov, icethk, icetmp, mixlyr."
+    exit 2
+fi
+
+# Output path check
+if [[ ! -d "${output_path}" ]]; then
+  echo "Error: Output path '${output_path}' does not exist or is not a directory."
+  exit 1
+fi
+
+if [[ ! -w "${output_path}" ]]; then
+  echo "Error: Output path '${output_path}' is not writable. Check permissions."
+  exit 1
+fi
+# --------------------------------------------------------------------------- #
+
+# Load module(s) that provide python packages (such as xarray)
+#source ${HOMErtofs}/scripts/load_py_modules.sh
+
+echo "Converting format for ${var_name}..."
+
+set +x  # Turn off tracing to keep the log clean
+$USHrtofs/convert_bin_inc_to_nc.py --topog_file "${topog_file}" \
+                                   --input_file "${ncoda_file}" \
+                                   --var_name   "${var_name}" \
+                                   --output_path "${output_path}" 2>&1 | tee output.log
+
+# Get the exit code of the Python script, NOT the tee command
+err=${PIPESTATUS[0]}
+export err
+set -x  # Turn tracing back on
+
+# Run error check
+err_chk
+echo " error from convert_bin_inc_to_nc.py = $err"
+
+msg="THE $(basename -- "$0") JOB HAS ENDED NORMALLY on $(hostname) at $(date)"
+postmsg "$msg"

ush/rtofs_glo_ice_update.sh

@@ -0,0 +1,56 @@
+#!/bin/sh
+
+#
+# Abstract:
+# - Input:  NCODA (data assimilation) output sea ice coverage (binary format).
+# - Output: Converts to netcdf format (used by the sea ice model).
+#
+set -xa
+
+export PS4='$SECONDS + '
+
+cd $DATA
+
+msg="$(basename -- "$0") JOB has begun on $(hostname) at $(date)"
+postmsg "$msg"
+# --------------------------------------------------------------------------- #
+
+# 1. Set up inputs for run
+
+dtg=${PDYm1}00
+
+echo $dtg
+
+IDM=$(cat ${BLKDATA_FILE} | grep idm | cut -d' ' -f1 | tr -d '[:space:]')
+JDM=$(cat ${BLKDATA_FILE} | grep jdm | cut -d' ' -f1 | tr -d '[:space:]')
+SIZN="${IDM}x${JDM}"
+
+# 2. Link to ncoda var ice coverage restart file
+
+typec=icecov_sfc_1o${SIZN}
+
+if [ -e $COMIN/ncoda/hycom_var/restart/${typec}_${dtg}_0000_analfld ]; then
+   ln -sf  $COMIN/ncoda/hycom_var/restart/${typec}_${dtg}_0000_analfld ./icecov_${dtg}_analfld
+else
+   msg="$COMIN/ncoda/hycom_var/restart/${typec}_${dtg}_0000_analfld is missing"
+   err_exit $msg
+fi
+
+# 3. Link in topo files
+
+ln -f -s ${FIXrtofs}/depth_GLBb0.08_09m11ob2_mom6.nc depth_GLBb0.08_09m11ob2_mom6.nc
+
+# 4. Create sic.nc file
+
+$USHrtofs/rtofs_glo2d_ice.sh depth_GLBb0.08_09m11ob2_mom6.nc icecov_${dtg}_analfld icecov ${DATA}
+err=$?; export err ; err_chk
+echo " error from rtofs_glo2d_ice.sh=",$err
+
+if [ -f "icecov_${dtg}_analfld.nc" ]; then
+    mv "icecov_${dtg}_analfld.nc" sic.nc
+else
+    echo "WARNING: icecov_${dtg}_analfld.nc not found. Skipping rename."
+fi
+
+msg="THE $(basename -- "$0") JOB HAS ENDED NORMALLY on $(hostname) at $(date)"
+postmsg "$msg"