#!/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 # --s or --silent: don't write anything on successful execution. #### # # Written by C. Koven, 2018 # # ======================================================================================= # ======================================================================================= import os from scipy.io import netcdf as nc import argparse import shutil import tempfile import sys import datetime import time import numpy as np import code # For development: code.interact(local=dict(globals(), **locals())) # ======================================================================================== # ======================================================================================== # 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 and --pftname are missing and --allPFTs is not specified, will assume a global variable.") parser.add_argument('--pftname', '--PFTname', dest='pftname', type=str, help="Name of PFT to modify. alternate argument to --pft or --allpfts") parser.add_argument('--allPFTs', '--allpfts', dest='allpfts', help="apply to all PFT indices. Cannot use at same time as --pft argument.", action="store_true") 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=str, help="New value of PFT variable. Must be interpretable as either a real number or a comma-separated list of real numbers. Required.", required=True) parser.add_argument('--O','--overwrite', dest='overwrite', help="If present, automatically overwrite the output file.", action="store_true") parser.add_argument('--silent', '--s', dest='silent', help="prevent writing of output.", action="store_true") parser.add_argument('--nohist', dest='nohist', help="prevent recording of the edit in the history attribute of the output file", action="store_true") parser.add_argument('--changeshape', dest='changeshape', help="allow script to change shape of specified variable, and all other variables with the relevant dimension, if necessary", action="store_true") parser.add_argument('--all',dest='varall',help="replace all values for the specified parameter, supercedes other flags",action="store_true") # args = parser.parse_args() # # work with the file in some random temporary place so that if something goes wrong, # then nothing happens to original file and it doesn't make a persistent output file tempdir = tempfile.mkdtemp() tempfilename = os.path.join(tempdir, 'temp_fates_param_file.nc') ncfile_old = None rename_pft = False if args.varall: # val_list = args.val.split(',') # output_vec = [float(valstr) for valstr in val_list] outputval = np.fromstring(args.val, sep=',', dtype=np.float64) else: try: outputval = float(args.val) if args.changeshape: raise Exception except: try: #print('output variable not interpretable as real. trying array') outputval = np.fromstring(args.val, sep=',', dtype=np.float32) if len(outputval) == 0: raise RuntimeError('output variable needs to have size greater than zero') except: if args.varname != 'fates_pftname': raise RuntimeError('output variable not interpretable as real or array') else: rename_pft = True # # try: shutil.copyfile(args.inputfname, tempfilename) # ncfile = nc.netcdf_file(tempfilename, '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) if args.varall: # Calculate total number of values expected nvals = 1 #code.interact(local=dict(globals(), **locals())) for i in range(ndim_file): nvals = nvals*np.prod(var.shape[i]) if(len(outputval) != nvals): print('Input vector is not the same size as the in-file array for {}'.format(args.varname)) print('total size = {}, you specified = {} values'.format(nvals,len(outputval))) exit(2) if(ndim_file==2): ii = 0 for i in range(var.shape[0]): for j in range(var.shape[1]): var[i,j] = outputval[ii] ii=ii+1 elif(ndim_file==1): for i in range(var.shape[0]): var[i] = outputval[i] elif(ndim_file==0): var.assignValue(outputval[0]) else: print("Unhandled dimension size in modify_fates_paramfile.py") print("using --all flag") exit(2) else: ispftvar = False # for purposes of current state of this script, assume 1D if ndim_file > 2: raise ValueError('variable dimensionality is too high for this script') for i in range(ndim_file): if var.dimensions[i] == 'fates_pft': ispftvar = True npft_file = var.shape[i] pftdim = i otherdimpresent = False elif var.dimensions[i] in ['fates_history_age_bins','fates_history_size_bins', \ 'fates_history_coage_bins','fates_history_height_bins', \ 'fates_history_damage_bins', 'fates_NCWD','fates_litterclass','fates_leafage_class', \ 'fates_plant_organs','fates_hydr_organs','fates_hlm_pftno', \ 'fates_leafage_class']: otherdimpresent = True otherdimname = var.dimensions[i] otherdimlength = var.shape[i] elif var.dimensions[i] == 'fates_string_length' and rename_pft: otherdimpresent = True otherdimname = var.dimensions[i] otherdimlength = var.shape[i] else: raise ValueError('variable dimension not handled in this script') # if args.changeshape: ### if we are allowing the script to change the shape of the variable, ### then we need to figure out if that's really a thing that needs to happen. ### first identify what dimension we would change the shape of if we had to. length_specified = len(outputval) if length_specified != otherdimlength: ### ok, we find ourselves in the situation where we need to rewrite the netcdf ### from scratch with its revised shape. # # first lets chech to make sure the dimension we are changing can be changed without breaking things. plastic_dimensions_list = ['fates_history_age_bins','fates_history_size_bins', \ 'fates_history_coage_bins','fates_history_height_bins', \ 'fates_leafage_class'] if otherdimname not in plastic_dimensions_list: raise ValueError('asking to change the shape of a dimension, '+\ otherdimname+', that will probably break things') else: print('WARNING: we need to change the dimension of '+otherdimname) ### close the file that's open and start over. ncfile.close() os.remove(tempfilename) ncfile = nc.netcdf_file(tempfilename, 'w') ncfile_old = nc.netcdf_file(args.inputfname, 'r') # try: ncfile.history = ncfile_old.history except: print('no history') # ### copy over and, when needed, modify the dimensions for name, dimlength in ncfile_old.dimensions.items(): #print(name, dimlength) if name != otherdimname: ncfile.createDimension(name, dimlength) else: ncfile.createDimension(name, length_specified) #print(name, length_specified) # ### copy over and, when needed, modify the variables for name, variable in ncfile_old.variables.items(): variabledims = variable.dimensions #print(name, variabledims) x = ncfile.createVariable(name, variable.data.dtype, variable.dimensions) try: x.units = variable.units except: print('no units') try: x.long_name = variable.long_name except: print('no long name') # if len(variable.dimensions) > 0: if not otherdimname in variable.dimensions: x[:] = variable[:] else: if len(variable.dimensions) == 1: if length_specified > otherdimlength: print('WARNING: Variable '+name+ \ ' has a dimension that has been reshaped.'+\ ' New length is longer than old, so its been filled in with zeros.') x[0:otherdimlength] = variable[0:otherdimlength] x[otherdimlength:length_specified] = 0 else: print('WARNING: Variable '+name+' has a dimension that has been reshaped.'+\ ' New length is shorter than old, so its been truncated.') x[0:length_specified] = variable[0:length_specified] elif len(variable.dimensions) == 2: if length_specified > otherdimlength: print('WARNING: Variable '+name+' has a dimension that has been reshaped.'+\ ' New length is longer than old, so its been filled in with zeros.') x[0:otherdimlength,:] = variable[0:otherdimlength,:] x[otherdimlength:length_specified,:] = 0 else: print('WARNING: Variable '+name+' has a dimension that has been reshaped.'+\ ' New length is shorter than old, so its been truncated.') x[0:length_specified,:] = variable[0:length_specified,:] else: x.assignValue(float(variable.data)) # var = ncfile.variables[args.varname] else: # declare as none for now ncfile_old = None # if (args.pftnum == None and args.pftname == None and ispftvar) and not args.allpfts: raise ValueError('pft value is missing but variable has pft dimension.') if (args.pftnum != None or args.pftname != None) and args.allpfts: raise ValueError("can't specify both a PFT number and the argument allPFTs.") if (args.pftnum != None or args.pftname != None) and not ispftvar: raise ValueError('pft value is present but variable does not have pft dimension.') if (args.pftnum != None and args.pftname != None): raise ValueError('can only specify pft number or name, not both.') if (args.pftnum == None or args.pftname != None) and not args.allpfts and ispftvar: ## now we need to figure out what the number of the pft that has been given a name argument pftnamelist = [] npftnames = ncfile.variables['fates_pftname'].shape[0] for i in range(npftnames): pftname_bytelist = list(ncfile.variables['fates_pftname'][i,:]) pftname_stringlist = [i.decode('utf-8') for i in pftname_bytelist] pftnamelist.append(''.join(pftname_stringlist).strip()) n_times_pft_listed = pftnamelist.count(args.pftname.strip()) if n_times_pft_listed != 1: raise ValueError('can only index by PFT name if the chosen PFT name occurs once and only once.') pftnum = pftnamelist.index(args.pftname.strip()) args.pftnum=pftnum +1 if args.pftnum != None and ispftvar: if not rename_pft: 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: if not args.silent: 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(outputval)) var[args.pftnum-1] = outputval if pftdim == 1: if not args.silent: 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(outputval)) var[:,args.pftnum-1] = outputval else: pftname_in_bytelist = list(ncfile.variables['fates_pftname'][args.pftnum-1,:]) pftname_in_stringlist = [i.decode('utf-8') for i in pftname_in_bytelist] print('replacing prior value of pft name for PFT '+str(args.pftnum)+', which was "'+''.join(pftname_in_stringlist).strip()+'", with new value of "'+args.val+'"') var[args.pftnum-1] = args.val.ljust(otherdimlength) elif args.allpfts and ispftvar: if pftdim == 0: if not args.silent: print('replacing prior values of variable '+args.varname+', for all PFTs, which were '+str(var[:])+', with new value of '+str(outputval)) var[:] = outputval if pftdim == 1: if not args.silent: print('replacing prior values of variable '+args.varname+', for all PFTs, which were '+str(var[:])+', with new value of '+str(outputval)) var[:] = outputval elif args.pftnum == None and not ispftvar and ndim_file > 0: if not otherdimpresent: if not args.silent: print('replacing prior value of variable '+args.varname+', which was '+str(var[:])+', with new value of '+str(outputval)) var[:] = outputval else: #print(var.shape) #print(outputval.shape) if not args.silent: print('replacing prior value of variable '+args.varname+', which was '+str(var[:])+', with new value of '+str(outputval)) var[:] = outputval elif ndim_file < 1: if not args.silent: print('replacing prior value of scalar variable '+args.varname+', which was '+str(var.data)+', with new value of '+str(outputval)) var.assignValue(outputval) else: raise ValueError('Nothing happened somehow.') # if not args.nohist: # write to the netcdf file history attribute what you just did. actionstring = 'modify_fates_paramfile.py '+' '.join(sys.argv[1:]) timestampstring = datetime.datetime.fromtimestamp(time.time()).strftime('%a %b %d %Y, %H:%M:%S') # oldhiststr = ncfile.history.decode('utf-8') newhiststr = oldhiststr + "\n "+timestampstring + ': ' + actionstring ncfile.history = newhiststr # ncfile.close() if type(ncfile_old) != type(None): ncfile_old.close() # # # now move file from temporary location to final location # # check to see if output file exists if os.path.isfile(args.outputfname): if args.overwrite: if not args.silent: 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.move(tempfilename, args.outputfname) shutil.rmtree(tempdir, ignore_errors=True) except: shutil.rmtree(tempdir, ignore_errors=True) raise # ======================================================================================= # This is the actual call to main if __name__ == "__main__": main()