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update_input_file.py
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update_input_file.py
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"""
Update an existing mcmcfit input file using the results of a
previous chain.
"""
import argparse
import configobj
import numpy as np
from mcmc_utils import flatchain, readchain_dask as readchain
def update_entry(name, input_dict, newval):
fields = input_dict[name].split(' ')
fields = [v for v in fields if v != '']
fields[0] = str(newval)
input_dict[name] = ' '.join(fields)
if __name__ == "__main__":
parser = argparse.ArgumentParser()
parser.add_argument("-t", "--thin", action="store", type=int,
default=10, help="thinning for chain (default=10)")
parser.add_argument('input_file', help='mcmc input file')
parser.add_argument('chain_file', help='chain output file')
args = parser.parse_args()
input_dict = configobj.ConfigObj(args.input_file)
print("Reading in the chain")
chain = readchain(args.chain_file)
nwalkers, nsteps, npars = chain.shape
fchain = flatchain(chain, npars, thin=args.thin)
# get param names from chain file
firstLine = open(args.chain_file).readline()
# first entry is walker number - strip
fields = firstLine.strip().split()[1:]
# strip "core" from core params
for i in range(len(fields)):
if 'core' in fields[i]:
fields[i] = fields[i].split("_")[0]
# get median values
vals = np.median(fchain, axis=0)
# update
for n, v in zip(fields, vals):
if n in input_dict:
print("\nUpdating the entry:")
print("n: {}".format(n))
print("v: {}".format(v))
update_entry(n, input_dict, v)
input_dict.write()