def runTest(self):
loader = VesuvioLoadHelper('single',
'spectrum',
'Vesuvio_IP_file_test.par',
load_log_files=False)
self._tof_input = VesuvioTOFFitInput('15039-15045', None, 'forward',
loader)
def fit_tof(runs, flags, iterations=1, convergence_threshold=None):
# Retrieve vesuvio input data
vesuvio_loader = VesuvioLoadHelper(
flags['diff_mode'], flags['fit_mode'], flags['ip_file'],
flags.get('bin_parameters', None),
_extract_bool_from_flags('load_log_files', flags))
vesuvio_input = VesuvioTOFFitInput(runs, flags.get('container_runs', None),
flags.get('spectra', None),
vesuvio_loader)
if flags.get('ms_enabled', True):
hydrogen_constraints = flags['ms_flags'].pop("HydrogenConstraints",
None)
ms_helper = VesuvioMSHelper(**flags['ms_flags'])
if hydrogen_constraints is not None:
ms_helper.add_hydrogen_constraints(hydrogen_constraints)
else:
ms_helper = VesuvioMSHelper()
intensity_string = _create_intensity_constraint_str(
flags['intensity_constraints'])
fit_helper = VesuvioTOFFitHelper(
_create_background_str(flags.get('background', None)),
intensity_string, _create_user_defined_ties_str(flags['masses']),
flags.get('max_fit_iterations', 5000), flags['fit_minimizer'])
corrections_helper = VesuvioCorrectionsHelper(
_extract_bool_from_flags('gamma_correct', flags, False),
_extract_bool_from_flags('ms_enabled', flags),
flags.get('fixed_gamma_scaling', 0.0),
flags.get('fixed_container_scaling', 0.0), intensity_string)
create_mass_profile = _mass_profile_generator(MaterialBuilder())
profiles = [create_mass_profile(profile) for profile in flags['masses']]
mass_profile_collection = MassProfileCollection2D.from_collection(
MassProfileCollection(profiles), vesuvio_input.spectra_number)
fit_namer = VesuvioFitNamer.from_vesuvio_input(vesuvio_input,
flags['fit_mode'])
vesuvio_fit_routine = VesuvioTOFFitRoutine(ms_helper, fit_helper,
corrections_helper,
mass_profile_collection,
fit_namer)
vesuvio_output, result, exit_iteration = vesuvio_fit_routine(
vesuvio_input, iterations, convergence_threshold,
_extract_bool_from_flags('output_verbose_corrections', flags, False),
_extract_bool_from_flags('calculate_caad', flags, False))
result = result if len(result) > 1 else result[0]
return result, vesuvio_output.fit_parameters_workspace, vesuvio_output.chi2_values, exit_iteration
