From 8b115bb24bb99e96e4f9aea8920ce6f1e9382150 Mon Sep 17 00:00:00 2001
From: Charlie Koven <cdkoven@lbl.gov>
Date: Fri, 19 Jan 2018 13:01:34 -0800
Subject: [PATCH] added script modify_fates_paramfile.py

---
 tools/modify_fates_paramfile.py | 95 +++++++++++++++++++++++++++++++++
 1 file changed, 95 insertions(+)
 create mode 100755 tools/modify_fates_paramfile.py

diff --git a/tools/modify_fates_paramfile.py b/tools/modify_fates_paramfile.py
new file mode 100755
index 00000000..c81a944b
--- /dev/null
+++ b/tools/modify_fates_paramfile.py
@@ -0,0 +1,95 @@
+#!/usr/bin/env python
+
+#### this script modifies a FATES parameter file. It accepts the following flags
+# --var or --variable: variable.
+# --pft or --PFT: PFT number. If this is missing, script will assume that its a global variable that is being modified.
+# --input or --fin: input filename.
+# --output or --fout: output filename.  If missing, will assume its directly modifying the input file, and will prompt unless -O is specified
+# --O or --overwrite: overwrite output file without asking.
+# --value or --val: value to put in variable
+####
+
+
+# =======================================================================================
+# =======================================================================================
+
+import numpy as np
+import os
+from scipy.io import netcdf as nc
+import argparse
+import shutil
+
+# ========================================================================================
+# ========================================================================================
+#                                        Main
+# ========================================================================================
+# ========================================================================================
+
+def main():
+    parser = argparse.ArgumentParser(description='Parse command line arguments to this script.')
+    #
+    parser.add_argument('--var','--variable', dest='varname', type=str, help="What variable to modify? Required.", required=True)
+    parser.add_argument('--pft','--PFT', dest='pftnum', type=int, help="PFT number to modify. If this is missing, will assume a global variable.")
+    parser.add_argument('--fin', '--input', dest='inputfname', type=str, help="Input filename.  Required.", required=True)
+    parser.add_argument('--fout','--output', dest='outputfname', type=str, help="Output filename.  Required.", required=True)
+    parser.add_argument('--val', '--value', dest='val', type=float, help="New value of PFT variable.  Required.", required=True)
+    parser.add_argument('--O','--overwrite', dest='overwrite', help="If present, automatically overwrite the output file.", action="store_true")
+    #
+    args = parser.parse_args()
+    # print(args.varname, args.pftnum, args.inputfname, args.outputfname, args.val, args.overwrite)
+    #
+    # check to see if output file exists
+    if os.path.isfile(args.outputfname):
+        if args.overwrite:
+            print('replacing file: '+args.outputfname)
+            os.remove(args.outputfname)
+        else:
+            raise ValueError('Output file already exists and overwrite flag not specified for filename: '+args.outputfname)
+    #
+    shutil.copyfile(args.inputfname, args.outputfname)
+    #
+    ncfile = nc.netcdf_file(args.outputfname, 'a')
+    #
+    var = ncfile.variables[args.varname]
+    #
+    ### check to make sure that, if a PFT is specified, the variable has a PFT dimension, and if not, then it doesn't. and also that shape is reasonable.
+    ndim_file = len(var.dimensions)
+    ispftvar = False
+    for i in range(ndim_file):
+        if var.dimensions[i] == 'fates_pft':
+            ispftvar = True
+            npft_file = var.shape[i]
+            pftdim = 0
+        else:
+            npft_file = None
+            pftdim = None
+    if args.pftnum == None and ispftvar:
+        raise ValueError('pft value is missing but variable has pft dimension.')
+    if args.pftnum != None and not ispftvar:
+        raise ValueError('pft value is present but variable does not have pft dimension.')
+    if ndim_file > 1:
+        raise ValueError('variable dimensionality is too high for this script')
+    if ndim_file == 1 and not ispftvar:
+        raise ValueError('variable dimensionality is too high for this script')
+    if args.pftnum != None and ispftvar:
+        if args.pftnum > npft_file:
+            raise ValueError('PFT specified ('+str(args.pftnum)+') is larger than the number of PFTs in the file ('+str(npft_file)+').')
+        if pftdim == 0:
+            var[args.pftnum-1] = args.val
+    elif args.pftnum == None and not ispftvar:
+        var[:] = args.val
+    else:
+        raise ValueError('Nothing happened somehow.')
+    #
+    #
+    ncfile.close()
+
+
+
+
+# =======================================================================================
+# This is the actual call to main
+   
+if __name__ == "__main__":
+    main()
+