def parse(self):
"""
Parse the NIST problem file into a Fitting Problem.
:return: The fully parsed fitting problem
:rtype: fitbenchmarking.parsing.fitting_problem.FittingProblem
"""
fitting_problem = FittingProblem()
equation, data, starting_values, name = self._parse_line_by_line()
data = self._parse_data(data)
fitting_problem.data_x = data[:, 1]
fitting_problem.data_y = data[:, 0]
if len(data[0, :]) > 2:
fitting_problem.data_e = data[:, 2]
fitting_problem.name = name
# String containing a mathematical expression
fitting_problem.equation = self._parse_equation(equation)
fitting_problem.starting_values = starting_values
fitting_problem.function = \
nist_func_definition(function=fitting_problem.equation,
param_names=starting_values[0].keys())
return fitting_problem
def parse(self):
"""
Get data into a Fitting Problem via cutest.
:return: The fully parsed fitting problem
:rtype: fitbenchmarking.parsing.fitting_problem.FittingProblem
"""
self.mastsif_dir = TemporaryDirectory()
# set the MASTSIF environment variable so that pycutest
# can find the sif files
os.environ["MASTSIF"] = self.mastsif_dir.name
self._num_params = None
# get just the short filename (minus the .SIF)
fp = FittingProblem(self.options)
# Collect x and create new file with blank y
fname, fp.data_x, fp.data_y, fp.data_e = self._setup_data()
self._p = _import_problem(fname)
fp.name = self._p.name
fp.function = self._function # self._p.objcons
fp.jacobian = self._jacobian # self._p.lagjac
fp.equation = None
fp.starting_values = self._get_starting_values()
fp.start_x = None
fp.end_x = None
fp.format = "cutest"
# Create a list of x and f (function evaluation) and x and g (Jacobian
# evaluation).
# If a new x is given we will create and parse a new file
self._cache_f = [(fp.data_x, self._p.objcons)]
self._cache_g = [(fp.data_x, self._p.lagjac)]
return fp
def parse(self):
"""
Parse the NIST problem file into a Fitting Problem.
:return: The fully parsed fitting problem
:rtype: fitbenchmarking.parsing.fitting_problem.FittingProblem
"""
fitting_problem = FittingProblem(self.options)
equation, data, starting_values, name = self._parse_line_by_line()
data = self._parse_data(data)
fitting_problem.data_x = data[:, 1]
fitting_problem.data_y = data[:, 0]
if len(data[0, :]) > 2:
fitting_problem.data_e = data[:, 2]
fitting_problem.name = name
# String containing a mathematical expression
fitting_problem.equation = self._parse_equation(equation)
fitting_problem.starting_values = starting_values
fitting_problem.function = \
nist_func_definition(function=fitting_problem.equation,
param_names=starting_values[0].keys())
fitting_problem.format = "nist"
try:
jacobian = self._parse_jacobian(name)
fitting_problem.jacobian = \
nist_jacobian_definition(jacobian=jacobian,
param_names=starting_values[0].keys())
except NoJacobianError:
LOGGER.warn("WARNING: Could not find analytic Jacobian "
"information for {} problem".format(name))
return fitting_problem
def parse(self):
"""
Parse the Fitbenchmark problem file into a Fitting Problem.
:return: The fully parsed fitting problem
:rtype: fitbenchmarking.parsing.fitting_problem.FittingProblem
"""
fitting_problem = FittingProblem()
self._entries = self._get_data_problem_entries()
software = self._entries['software'].lower()
if not (software in import_success and import_success[software][0]):
e = import_success[software][1]
raise MissingSoftwareError('Requirements are missing for {} parser'
': {}'.format(software, e))
self._parsed_func = self._parse_function()
# NAME
fitting_problem.name = self._entries['name']
# DATA
data_points = self._get_data_points()
fitting_problem.data_x = data_points[:, 0]
fitting_problem.data_y = data_points[:, 1]
if data_points.shape[1] > 2:
fitting_problem.data_e = data_points[:, 2]
# FUNCTION
if software == 'mantid':
fitting_problem.function = self._create_mantid_function()
elif software == 'sasview':
fitting_problem.function = self._create_sasview_function()
# EQUATION
equation_count = len(self._parsed_func)
if equation_count == 1:
fitting_problem.equation = self._parsed_func[0]['name']
else:
fitting_problem.equation = '{} Functions'.format(equation_count)
if software == 'mantid':
# String containing the function name(s) and the starting parameter
# values for each function
fitting_problem._mantid_equation = self._entries['function']
# STARTING VALUES
fitting_problem.starting_values = self._get_starting_values()
# PARAMETER RANGES
vr = self._parse_range('parameter_ranges')
fitting_problem.value_ranges = vr if vr != {} else None
# FIT RANGES
fit_ranges = self._parse_range('fit_ranges')
try:
fitting_problem.start_x = fit_ranges['x'][0]
fitting_problem.end_x = fit_ranges['x'][1]
except KeyError:
pass
return fitting_problem
