def test_setPhaseDefinition(cal):
calc = CryspyCalculator('')
interface = QtCalculatorInterface(calc)
interface.setPhaseDefinition(phase_path)
phase_added = interface.getPhase('Fe3O4')
phase_ref = cal.getPhase('Fe3O4')
assert phase_added['phasename'] == phase_ref['phasename']
assert phase_added['spacegroup']['crystal_system'].value == phase_ref[
'spacegroup']['crystal_system'].value
assert phase_added['spacegroup'][
'space_group_name_HM_ref'].value == phase_ref['spacegroup'][
'space_group_name_HM_ref'].value
assert phase_added['spacegroup'][
'space_group_IT_number'].value == phase_ref['spacegroup'][
'space_group_IT_number'].value
assert phase_added['spacegroup']['origin_choice'].value == phase_ref[
'spacegroup']['origin_choice'].value
assert phase_added['cell']['length_a'].value == phase_ref['cell'][
'length_a'].value
assert phase_added['cell']['length_b'].value == phase_ref['cell'][
'length_b'].value
assert phase_added['cell']['length_c'].value == phase_ref['cell'][
'length_c'].value
assert phase_added['cell']['angle_alpha'].value == phase_ref['cell'][
'angle_alpha'].value
assert phase_added['cell']['angle_beta'].value == phase_ref['cell'][
'angle_beta'].value
assert phase_added['cell']['angle_gamma'].value == phase_ref['cell'][
'angle_gamma'].value
assert phase_added['atoms']['Fe3A']['fract_x'].value == phase_ref['atoms'][
'Fe3A']['fract_x'].value
assert phase_added['atoms']['Fe3B']['fract_y'].value == phase_ref['atoms'][
'Fe3B']['fract_y'].value
assert phase_added['atoms']['O']['fract_z'].value == phase_ref['atoms'][
'O']['fract_z'].value
def test_calculator_info():
info = CryspyCalculator.calculatorInfo()
assert isinstance(info, dict)
keys = info.keys()
assert 'name' in keys
assert info['name'] == 'CrysPy'
assert 'version' in keys
assert 'url' in keys
def test_addExperimentDefinition(cal):
calc = CryspyCalculator('')
interface = CalculatorInterface(calc)
interface.addExperimentDefinition(exp_path)
exp_added = interface.getExperiment('pd')
exp_ref = cal.getExperiment('pd')
assert exp_added['name'] == exp_ref['name']
assert exp_added['wavelength'].value == exp_ref['wavelength'].value
assert exp_added['offset'].value == exp_ref['offset'].value
assert exp_added['phase']['Fe3O4']['name'] == exp_ref['phase']['Fe3O4']['name']
assert exp_added['phase']['Fe3O4']['scale'].value == exp_ref['phase']['Fe3O4']['scale'].value
def test_setExperimentDefinitionFromString():
calc = CryspyCalculator()
interface = CalculatorInterface(calc)
interface.setPhaseDefinition(phase_path)
with open(exp_path, 'r') as file_reader:
exp_content = file_reader.read()
interface.addExperimentDefinitionFromString(exp_content)
experiment_dict = interface.project_dict['experiments']
assert len(experiment_dict) == 1
assert len(experiment_dict['pd']) == 10
# wavelength
assert len(experiment_dict['pd']['wavelength']) == 5
assert experiment_dict['pd']['wavelength'].value == 0.84
assert experiment_dict['pd']['wavelength']['url'] == ''
# offset
assert len(experiment_dict['pd']['offset']) == 5
assert experiment_dict['pd']['offset'].value == -0.385404
assert experiment_dict['pd']['offset']['store']['error'] == 0.0
assert experiment_dict['pd']['offset']['store']['refine'] is False
# phase
assert len(experiment_dict['pd']['phase']) == 1
assert len(experiment_dict['pd']['phase']['Fe3O4']['scale']) == 5
assert experiment_dict['pd']['phase']['Fe3O4']['scale'].value == 0.02381
assert experiment_dict['pd']['phase']['Fe3O4']['scale']['store']['refine'] is False
assert experiment_dict['pd']['phase']['Fe3O4']['scale']['store']['error'] == 0.0
# background
assert len(experiment_dict['pd']['background']) == 3
assert experiment_dict['pd']['background']['4.5']['ttheta'] == 4.5
assert len(experiment_dict['pd']['background']['4.5']['intensity']) == 5
assert experiment_dict['pd']['background']['4.5']['intensity'].value == 256.0
assert experiment_dict['pd']['background']['80.0']['ttheta'] == 80.0
assert len(experiment_dict['pd']['background']['80.0']['intensity']) == 5
assert experiment_dict['pd']['background']['80.0']['intensity'].value == 65.0
# resolution
assert len(experiment_dict['pd']['resolution']) == 5
assert len(experiment_dict['pd']['resolution']['u']) == 5
assert experiment_dict['pd']['resolution']['u'].value == 16.9776
assert experiment_dict['pd']['resolution']['u']['store']['refine'] is False
assert len(experiment_dict['pd']['resolution']['y']) == 5
assert experiment_dict['pd']['resolution']['v'].value == -2.8357
assert experiment_dict['pd']['resolution']['v']['store']['error'] == 0.0
assert experiment_dict['pd']['resolution']['v']['store']['hide'] is False
# measured_pattern
assert len(experiment_dict['pd']['measured_pattern']) == 9
assert 5.0 in experiment_dict['pd']['measured_pattern']['x']
assert len(experiment_dict['pd']['measured_pattern'].y_obs_lower) == 381
assert experiment_dict['pd']['measured_pattern'].y_obs_lower[380] == pytest.approx(762.959046)
def test_addPhaseToExp():
calc = CryspyCalculator('')
interface = CalculatorInterface(calc)
interface.addExperimentDefinition(exp_path)
interface.addPhaseDefinition(phase_path)
interface.removePhaseFromExp('pd', 'Fe3O4')
interface.addPhaseToExp('pd', 'Fe3O4', scale=1.0)
exp_ref = interface.getExperiment('pd')
assert exp_ref['name'] == 'pd'
assert 'Fe3O4' in exp_ref['phase'].keys()
assert exp_ref['phase']['Fe3O4']['scale'].value == 1.0
def test_setPhaseDefinition_EmptyStr():
calc = CryspyCalculator('')
interface = CalculatorInterface(calc)
interface.setPhaseDefinition('')
def test_setPhaseDefinition_None():
calc = CryspyCalculator('')
interface = CalculatorInterface(calc)
interface.setPhaseDefinition(None)
def test_creation_Empty():
calc = CryspyCalculator()
interface = CalculatorInterface(calc)
def test_creation_WrongStr():
path = os.path.join(test_data, 'mainf.cif')
calc = CryspyCalculator(path)
interface = CalculatorInterface(calc)
def test_creation_None():
calc = CryspyCalculator(None)
interface = CalculatorInterface(calc)
def cal():
calc = CryspyCalculator(file_path)
interface = CalculatorInterface(calc)
return interface
def test_creation_EmptyStr():
calc = CryspyCalculator('')
interface = QtCalculatorInterface(calc)
Performing a fit
================
This demonstrates an example of how to load an example and create a interface to a cryspy calculator and then fit a
value.
"""
import os
from easyInterface.Utils.Helpers import getExamplesDir
from easyInterface.Diffraction.Calculators import CryspyCalculator
from easyInterface.Diffraction.Interface import CalculatorInterface
data_dir = getExamplesDir()
main_rcif = os.path.join(data_dir, 'PbSO4_powder-1d_neutrons-unpol_D1A(ILL)',
'main.cif')
calculator = CryspyCalculator(main_rcif)
interface = CalculatorInterface(calculator)
print(interface.project_dict)
phase_ids = interface.phasesIds()
print(phase_ids)
phase = interface.getPhase(phase_ids[0])
phase['phasename'] = 'PbSO5'
interface.addPhase(phase)
interface.removePhase('PbSO5')
phase = interface.getPhase(phase_ids[0])
def test_creationEmptyFile():
calc = CryspyCalculator('baah')
assert calc._phase_names == []
def cal():
calc = CryspyCalculator(file_path)
return calc
