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Merge pull request #314 from rgknox/rgknox-tools-pftindexswapper
Add python script for manipulating PFT parameter files
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‎tools/FatesPFTIndexSwapper.py‎

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#!/usr/bin/env python
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# =======================================================================================
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#
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# This python script will open an input FATES parameter file, and given a list of PFT
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# indices supplied by the user, will create a new parameter file with PFTs entries cloned
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# from the original file as-per the list of indices supplied by the user.
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#
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# First Added, Ryan Knox: Thu Jan 11 13:36:14 PST 2018
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# =======================================================================================
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import numpy as np
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import sys
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import getopt
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import code # For development: code.interact(local=locals())
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from datetime import datetime
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from scipy.io import netcdf
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import matplotlib.pyplot as plt
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# =======================================================================================
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# Parameters
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# =======================================================================================
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pft_dim_name = 'fates_pft'
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class timetype:
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# This is time, like the thing that always goes forward and cant be seen
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# or touched, insert creative riddle here
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def __init__(self,ntimes):
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self.year = -9*np.ones((ntimes))
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self.month = -9*np.ones((ntimes))
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# This is a floating point decimal day
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self.day = -9.0*np.ones((ntimes))
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# This is a decimal datenumber
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self.datenum = -9.0*np.ones((ntimes))
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def usage():
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print('')
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print('=======================================================================')
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print('')
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print(' python FatesPFTIndexSwapper.py -h --pft-indices <integer position> ')
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print(' --fin <netcdf-file-in> ')
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print(' --fout <netcdf-file-out>')
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print('')
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print('')
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print(' -h --help ')
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print(' print this help message')
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print('')
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print('')
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print(' --pft-indices <integer positions ie 1,1,2,3,5,7>')
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print(' This is a comma delimited list of integer positions of the PFTs')
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print(' to be copied into the new file. Note that first pft position')
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print(' is treated as 1 (not C or python like), and any order or multiples')
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print(' of indices can be chosen')
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print('')
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print('')
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print(' --fin <netcdf-file-in>')
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print(' This is the full path to the netcdf file you are basing off of')
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print('')
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print('')
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print(' --fout <netcdf-file-out>')
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print(' This is the full path to the netcdf file you are writing to.')
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print('')
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print('')
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print('=======================================================================')
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def interp_args(argv):
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argv.pop(0) # The script itself is the first argument, forget it
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# Name of the conversion file
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input_fname = "none"
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output_fname = "none"
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donor_pft_indices = -9
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donot_pft_indices_str = ''
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try:
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opts, args = getopt.getopt(argv, 'h',["fin=","fout=","pft-indices="])
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except getopt.GetoptError as err:
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print('Argument error, see usage')
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usage()
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sys.exit(2)
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for o, a in opts:
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if o in ("-h", "--help"):
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usage()
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sys.exit(0)
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elif o in ("--fin"):
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input_fname = a
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elif o in ("--fout"):
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output_fname = a
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elif o in ("--pft-indices"):
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donor_pft_indices_str = a.strip()
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else:
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assert False, "unhandled option"
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if (input_fname == "none"):
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print("You must specify an input file:\n\n")
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usage()
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sys.exit(2)
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if (output_fname == "none"):
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print("You must specify an output file:\n\n")
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usage()
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sys.exit(2)
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if (donor_pft_indices_str == ''):
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print("You must specify at least one donor pft index!\n\n")
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usage()
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sys.exit(2)
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else:
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donor_pft_indices = []
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for strpft in donor_pft_indices_str.split(','):
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donor_pft_indices.append(int(strpft))
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return (input_fname,output_fname,donor_pft_indices)
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# ========================================================================================
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# ========================================================================================
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# Main
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# ========================================================================================
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# ========================================================================================
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def main(argv):
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# Interpret the arguments to the script
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[input_fname,output_fname,donor_pft_indices] = interp_args(argv)
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num_pft_out = len(donor_pft_indices)
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# Open the netcdf files
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fp_out = netcdf.netcdf_file(output_fname, 'w')
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fp_in = netcdf.netcdf_file(input_fname, 'r')
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for key, value in sorted(fp_in.dimensions.iteritems()):
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if(key==pft_dim_name):
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fp_out.createDimension(key,int(num_pft_out))
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print('Creating Dimension: {}={}'.format(key,num_pft_out))
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else:
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fp_out.createDimension(key,int(value))
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print('Creating Dimension: {}={}'.format(key,value))
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for key, value in sorted(fp_in.variables.iteritems()):
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print('Creating Variable: ',key)
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# code.interact(local=locals())
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out_var = fp_out.createVariable(key,'f',(fp_in.variables.get(key).dimensions))
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in_var = fp_in.variables.get(key)
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out_var.units = in_var.units
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out_var.long_name = in_var.long_name
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# Idenfity if this variable has pft dimension
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pft_dim_found = -1
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pft_dim_len = len(fp_in.variables.get(key).dimensions)
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for idim, name in enumerate(fp_in.variables.get(key).dimensions):
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# Manipulate data
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if(name==pft_dim_name):
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pft_dim_found = idim
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# Copy over the input data
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# Tedious, but I have to permute through all combinations of dimension position
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if( pft_dim_len == 0 ):
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out_var.assignValue(float(fp_in.variables.get(key).data))
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elif(pft_dim_found==-1):
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out_var[:] = in_var[:]
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elif( (pft_dim_found==0) & (pft_dim_len==1) ): # 1D fates_pft
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tmp_out = np.zeros([num_pft_out])
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for id,ipft in enumerate(donor_pft_indices):
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tmp_out[id] = fp_in.variables.get(key).data[ipft-1]
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out_var[:] = tmp_out
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elif( (pft_dim_found==1) & (pft_dim_len==2) ): # 2D hdyro_organ - fate_pft
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dim2_len = fp_in.dimensions.get(fp_in.variables.get(key).dimensions[0])
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tmp_out = np.zeros([dim2_len,num_pft_out])
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for id,ipft in enumerate(donor_pft_indices):
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for idim in range(0,dim2_len):
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tmp_out[idim,id] = fp_in.variables.get(key).data[idim,ipft-1]
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out_var[:] = tmp_out
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else:
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print('This variable has a dimensioning that we have not considered yet.')
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print('Please add this condition to the logic above this statement.')
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print('Aborting')
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exit(2)
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fp_out.history = "This file was made from FatesPFTIndexSwapper.py \n Input File = {} \n Indices = {}"\
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.format(input_fname,donor_pft_indices)
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#var_out.mode = var.mode
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#fp.flush()
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fp_in.close()
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fp_out.close()
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print('Cloneing complete!')
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exit(0)
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# =======================================================================================
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# This is the actual call to main
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if __name__ == "__main__":
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main(sys.argv)
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‎tools/modify_fates_paramfile.py‎

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