#!/usr/bin/env python
# -*- coding: utf-8 -*-
#
# Copyright (c) 2018 Piero Dalle Pezze
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
# in the Software without restriction, including without limitation the rights
# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
# copies of the Software, and to permit persons to whom the Software is
# furnished to do so, subject to the following conditions:
#
# The above copyright notice and this permission notice shall be included in all
# copies or substantial portions of the Software.
#
# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
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# SOFTWARE.
from sbpipe.simul.copasi import copasi as copasi_simul
from sbpipe.simul import pl_simul
[docs]def pe_collect(inputdir,
outputdir,
fileout_final_estims,
fileout_all_estims,
copasi=True):
"""
Collect the results so that they can be processed.
:param inputdir: the input folder containing the data
:param outputdir: the output folder to stored the collected results
:param fileout_final_estims: the name of the file containing the best estimations
:param fileout_all_estims: the name of the file containing all the estimations
:param copasi: True if COPASI was used to generate the data.
"""
if copasi:
simulator = copasi_simul.Copasi()
else:
simulator = pl_simul.PLSimul()
# Collect and summarises the parameter estimation results
try:
files_num = simulator.get_best_fits(inputdir, outputdir, fileout_final_estims)
simulator.get_all_fits(inputdir, outputdir, fileout_all_estims)
# print('Files retrieved: ' + str(files_num))
except Exception as e:
print("simulator: " + simulator + " not found.")
import traceback
print(traceback.format_exc())