def from_config(filename):
'''Opens a config file and reads the fields/subfields required for setting up
the analysis while ignoring the irrelavant ones. Returns a dictionary of the
collected information.
:param filename: Name of file to read.
:type filename: str
'''
config = configparser.RawConfigParser()
config.optionxform = lambda option: option
config_data = {}
with open(filename, 'r') as file:
config.read_file(file)
n = 1
for section in config.sections():
if not is_analysis_settings(config, section):
continue
init = config[section]['init']
params = config[section]['parameter_values']
tspan = config[section]['tspan']
solver_args = config[section].get('solver_args')
fixed_parameters = config[section].get('fixed_parameters')
parameter_bounds = config[section].get('parameter_bounds')
units = config[section].get('units')
init = eval_init_string(init)
tspan = eval_tspan_string(tspan)
params = eval_params_string(params)
solver_args = string_to_dict(solver_args) if solver_args else {}
fixed_parameters = string_to_list_string(
fixed_parameters) if fixed_parameters else []
parameter_bounds = string_to_dict_array(
parameter_bounds) if parameter_bounds else {}
units = string_to_dict(units) if units else {}
config_data[n] = {
'system_type': section,
'init': init,
'params': params,
'tspan': tspan,
'solver_args': solver_args,
'fixed_parameters': fixed_parameters,
'parameter_bounds': parameter_bounds,
'units': units
}
n += 1
return config_data
def from_config(filename):
'''Opens a config file and reads the fields/subfields required for setting up
the analysis while ignoring the irrelavant ones. Returns a dictionary of the
collected information.
:param filename: Name of file to read.
:type filename: str
'''
config = configparser.RawConfigParser()
config.optionxform = lambda option: option
config_data = {}
with open(filename, 'r') as file:
config.read_file(file)
n = 1
for section in config.sections():
if not is_analysis_settings(config, section):
continue
parameter_values = config[section].get('parameter_values')
measured_states = config[section].get('measured_states')
input_conditions = config[section].get('input_conditions')
decomposition = config[section].get('decomposition')
init = config[section].get('init')
units = config[section].get('units')
measured_states = string_to_list_string(measured_states) if measured_states else []
input_conditions = string_to_dict(input_conditions) if input_conditions else {}
parameter_values = string_to_dict(parameter_values) if parameter_values else {}
units = string_to_dict(units) if units else {}
init = eval_init_string(init) if init else {}
if decomposition:
temp = ''.join([s for s in decomposition if s in ['[', ']']])
if '[[' in temp:
decomposition = decomposition.strip()
decomposition = decomposition[1: len(decomposition)-1]
else:
decomposition = []
decomposition = [s.strip() for s in split_at_top_level(decomposition)]
decomposition = [[v.strip() for v in s.replace(']', '').replace('[', '').split(',')] for s in decomposition]
for key in init:
try:
next(iter(init[key]))
if len(init[key]) != 1:
raise Exception('Error in init. Only one value allowed.')
except:
pass
config_data[n] = {'system_type' : section,
'parameter_values' : parameter_values,
'init' : init,
'input_conditions' : input_conditions,
'measured_states' : measured_states,
'decomposition' : decomposition,
'units' : units
}
n += 1
return config_data
def from_config(filename, sampler='sa'):
'''Opens a config file and reads the fields/subfields required for setting up
the analysis while ignoring the irrelavant ones. Returns a dictionary of the
collected information.
:param filename: Name of file to read.
:type filename: str
:param sampler: "sa" for simulated annealing; "bh" for scipy's basin hopping;
"da" for scipy's dual annealing; "de" for scipy's differential evolution;
defaults to "sa"
:type sampler: str, optional
'''
config = configparser.RawConfigParser()
config.optionxform = lambda option: option
config_data = {}
with open(filename, 'r') as file:
config.read_file(file)
n = 1
for section in config.sections():
if not is_analysis_settings(config, section):
continue
solver_args = config[section].get('solver_args')
fixed_parameters = config[section].get('fixed_parameters')
parameter_bounds = config[section].get('parameter_bounds')
priors = config[section].get('priors')
step_size = config[section].get('step_size')
init = config[section].get('init')
tspan = config[section].get('tspan')
sa_args = config[section].get('sa_args')
de_args = config[section].get('de_args')
bh_args = config[section].get('bh_args')
da_args = config[section].get('da_args')
guess = config[section].get('guess')
units = config[section].get('units')
tspan = eval_tspan_string(tspan)
init = eval_init_string(init) if init else {}
solver_args = string_to_dict(solver_args) if solver_args else {}
fixed_parameters = string_to_list_string(fixed_parameters) if fixed_parameters else []
parameter_bounds = string_to_dict_array(parameter_bounds) if parameter_bounds else {}
priors = string_to_dict(priors) if priors else {}
step_size = string_to_dict(step_size) if step_size else {}
sa_args = string_to_dict(sa_args) if sa_args else {}
de_args = string_to_dict(de_args) if de_args else {}
bh_args = string_to_dict(bh_args) if bh_args else {}
da_args = string_to_dict(da_args) if da_args else {}
guess = eval_params_string(guess) if guess else {}
units = string_to_dict(units) if units else {}
if sampler == 'sa':
config_data[n] = {'system_type' : section, 'guess' : guess, 'priors' : priors,
'solver_args' : solver_args, 'parameter_bounds' : parameter_bounds,
'step_size' : step_size, 'fixed_parameters' : fixed_parameters,
'units' : units, 'init' : init, 'tspan' : tspan, 'sa_args':sa_args
}
elif sampler == 'de':
config_data[n] = {'system_type' : section, 'guess' : guess, 'priors' : priors,
'solver_args' : solver_args, 'parameter_bounds' : parameter_bounds,
'de_args' : de_args, 'fixed_parameters' : fixed_parameters,
'units' : units, 'init' : init, 'tspan' : tspan
}
elif sampler == 'bh':
config_data[n] = {'system_type' : section, 'guess' : guess, 'priors' : priors,
'solver_args' : solver_args, 'parameter_bounds' : parameter_bounds,
'step_size' : step_size, 'fixed_parameters' : fixed_parameters,
'bh_args' : bh_args, 'units' : units, 'init' : init, 'tspan' : tspan
}
elif sampler == 'da':
config_data[n] = {'system_type' : section, 'guess' : guess, 'priors' : priors,
'solver_args' : solver_args, 'parameter_bounds' : parameter_bounds,
'da_args' : da_args, 'fixed_parameters' : fixed_parameters,
'units' : units, 'init' : init, 'tspan' : tspan
}
n += 1
return config_data