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