def test_create_export_csv_file_created(self):
"""Assert the correct output CSV file is created"""
_handler = BraggEdge(material = 'Fe', number_of_bragg_edges = 4)
_filename = 'remove_me.txt'
_handler.export(filename = _filename, file_type = 'csv')
self.assertTrue(os.path.isfile(_filename))
os.remove(_filename) #cleanup temp file
def test_create_export_csv_file_created(self):
"""Assert the correct output CSV file is created"""
_handler = BraggEdge(material = 'Fe', number_of_bragg_edges = 4)
_filename = 'remove_me.txt'
_handler.export(filename = _filename, file_type = 'csv')
self.assertTrue(os.path.isfile('remove_me_Fe.txt'))
os.remove('remove_me_Fe.txt') #cleanup temp file
def test_create_export_csv_metadata(self):
"""Assert the correct metadata data are created for Fe when using create output file"""
_handler = BraggEdge(material = 'Fe', number_of_bragg_edges = 4)
_metadata = _handler._format_metadata()
self.assertEqual("Material: Fe", _metadata[0])
self.assertEqual("Lattice : 2.8664Angstroms", _metadata[1])
self.assertEqual("Crystal Structure: BCC", _metadata[2])
self.assertEqual("Using local metadata Table: True", _metadata[3])
def test_create_export_csv_metadata(self):
"""Assert the correct metadata data are created for Fe when using create output file"""
_handler = BraggEdge(material = 'Fe', number_of_bragg_edges = 4)
_metadata = _handler._format_metadata('Fe')
self.assertEqual("Material: Fe", _metadata[0])
self.assertEqual("Lattice : 2.8664Angstroms", _metadata[1])
self.assertEqual("Crystal Structure: BCC", _metadata[2])
self.assertEqual("Using local metadata Table: True", _metadata[3])
def test_create_export_csv_data(self):
"""Assert the correct data are created for Fe when using create output file"""
_handler = BraggEdge(material = 'Fe', number_of_bragg_edges = 4)
_data = _handler._format_data('Fe')
self.assertEqual(1, _data[0][0])
self.assertAlmostEqual(2.02685, _data[0][3], delta = 0.0001)
self.assertAlmostEqual(4.05370, _data[0][4], delta = 0.0001)
self.assertAlmostEqual(1.17020, _data[2][3], delta = 0.0001)
self.assertAlmostEqual(2.34041, _data[2][4], delta = 0.0001)
def test_create_export_csv_data(self):
"""Assert the correct data are created for Fe when using create output file"""
_handler = BraggEdge(material = 'Fe', number_of_bragg_edges = 4)
_data = _handler._format_data()
self.assertEqual(1, _data[0][0])
self.assertAlmostEqual(2.02685, _data[0][3], delta = 0.0001)
self.assertAlmostEqual(4.05370, _data[0][4], delta = 0.0001)
self.assertAlmostEqual(1.17020, _data[2][3], delta = 0.0001)
self.assertAlmostEqual(2.34041, _data[2][4], delta = 0.0001)
def test_retrieve_correct_metadata_for_single_local_material(self):
"""Assert the correct metadata are retrieved for a single local material"""
new_material = [{'name': 'Ta', 'lattice': 0.5, 'crystal_structure': 'BCC'}]
_handler = BraggEdge(new_material = new_material)
_metadata = _handler.metadata
self.assertEqual(0.5, _metadata['lattice']['Ta'])
self.assertEqual('BCC', _metadata['crystal_structure']['Ta'])
def test_calculate_experimental_lattice_with_value_and_error_different_size(self):
"""Assert in BraggEdge - bragg edge value and error have different sizes"""
_handler = BraggEdge(material = 'Fe', number_of_bragg_edges = 4)
exp_bragg_value = np.array([1,2,3])
exp_bragg_error = np.array([0.1, 0.2])
self.assertRaises(ValueError, _handler.get_experimental_lattice_parameter, exp_bragg_value,
exp_bragg_error)
def test_calculate_hkl_for_single_local_material(self):
"""Assert the hkl calculation is correct for a single local material"""
new_material = [{'name': 'Ta', 'lattice': 5.0, 'crystal_structure': 'BCC'}]
_handler = BraggEdge(new_material = new_material)
_hkl = _handler.hkl
self.assertEqual(_hkl['Ta'][0], [1, 1, 0])
self.assertEqual(_hkl['Ta'][1], [2, 0, 0])
def update_lattice_and_crystal_when_index_selected(self, source='load_data',
fill_lattice_flag=True,
fill_crystal_structure_flag=True):
_element = self.get_element_selected(source=source)
try:
_handler = BraggEdge(material = _element)
_crystal_structure = _handler.metadata['crystal_structure'][_element]
_lattice = str(_handler.metadata['lattice'][_element])
except KeyError:
# look for element in local list of element
_handler = self.retrieve_handler_from_local_bragg_edge_list(material = _element)
_crystal_structure = _handler['crystal_structure']
_lattice = _handler['lattice']
if source == 'load_data':
_index = self.parent.ui.list_of_elements.currentIndex()
self.parent.ui.list_of_elements_2.setCurrentIndex(_index)
else:
_index = self.parent.ui.list_of_elements_2.currentIndex()
self.parent.ui.list_of_elements.setCurrentIndex(_index)
if fill_lattice_flag:
self.parent.ui.lattice_parameter.setText(_lattice)
self.parent.ui.lattice_parameter_2.setText(_lattice)
if fill_crystal_structure_flag:
self.set_crystal_structure(_crystal_structure)
def __init__(self, parent=None):
self.parent = parent
o_gui = GuiHandler(parent=self.parent)
element_name = str(
o_gui.get_text_selected(ui=self.parent.ui.list_of_elements))
lattice_value = np.float(
o_gui.get_text(ui=self.parent.ui.lattice_parameter))
crystal_structure = str(
o_gui.get_text_selected(ui=self.parent.ui.crystal_structure))
_element_dictionary = {
'name': element_name,
'lattice': lattice_value,
'crystal_structure': crystal_structure
}
_handler = BraggEdge(new_material=[_element_dictionary])
self.parent.selected_element_bragg_edges_array = _handler.bragg_edges[
element_name]
self.parent.selected_element_hkl_array = _handler.hkl[element_name]
self.parent.selected_element_name = element_name
# modified the fitting window list of h,k,l if window is alive
if self.parent.fitting_ui:
hkl_list = _handler.hkl[element_name]
str_hkl_list = [
"{},{},{}".format(_hkl[0], _hkl[1], _hkl[2])
for _hkl in hkl_list
]
self.parent.fitting_ui.ui.hkl_list_ui.clear()
self.parent.fitting_ui.ui.hkl_list_ui.addItems(str_hkl_list)
self.parent.fitting_ui.ui.material_groupBox.setTitle(element_name)
def test_retrieving_correct_number_and_first_2_values_hkl_for_Si(self):
"""Assert the correct hkl first 2values are returned for Si, and the correct number"""
_handler = BraggEdge(material = 'Si', number_of_bragg_edges = 4)
_hkl = _handler.hkl['Si']
self.assertEqual([1, 1, 1], _hkl[0])
self.assertEqual([2, 0, 0], _hkl[1])
self.assertEqual(4, len(_hkl))
def test_calculating_bragg_edges_for_Fe(self):
"""Assert the first 3 bragg_edges are correct for Fe"""
_handler = BraggEdge(material = 'Fe', number_of_bragg_edges = 4)
_bragg_edges = _handler.bragg_edges['Fe']
self.assertAlmostEqual(4.0537, _bragg_edges[0], delta = 0.001)
self.assertAlmostEqual(2.8664, _bragg_edges[1], delta = 0.001)
self.assertAlmostEqual(2.3404, _bragg_edges[2], delta = 0.001)
def test_calculating_d_spacing_values_for_Ni(self):
"""Assert the first 3 d_spacing are correct for Ni"""
_handler = BraggEdge(material = 'Ni', number_of_bragg_edges = 4)
_d_spacing = _handler.d_spacing['Ni']
self.assertAlmostEqual(2.0345, _d_spacing[0], delta = 0.001)
self.assertAlmostEqual(1.7619, _d_spacing[1], delta = 0.001)
self.assertAlmostEqual(1.2459, _d_spacing[2], delta = 0.001)
def test_retrieving_first_2_values_hkl_for_Fe(self):
"""Assert the correct hkl first 2 values are returned for Fe """
_handler = BraggEdge(material = 'Fe', number_of_bragg_edges = 4)
_hkl = _handler.hkl['Fe']
self.assertEqual([1, 1, 0], _hkl[0])
self.assertEqual([2, 0, 0], _hkl[1])
self.assertEqual([2, 1, 1], _hkl[2])
self.assertEqual([2, 2, 0], _hkl[3])
def init_material_widgets(self):
retrieve_material = RetrieveMaterialMetadata(material = 'all')
list_returned = retrieve_material.full_list_material()
self.parent.ui.list_of_elements.addItems(list_returned)
self.parent.ui.list_of_elements_2.addItems(list_returned)
_handler = BraggEdge(material= self.get_element_selected())
_crystal_structure = _handler.metadata['crystal_structure'][self.get_element_selected()]
_lattice = str(_handler.metadata['lattice'][self.get_element_selected()])
self.parent.ui.lattice_parameter.setText(_lattice)
self.parent.ui.lattice_parameter_2.setText(_lattice)
self.set_crystal_structure(_crystal_structure)
def test_create_export_unsuported_file_raise_error(self):
"""Assert in BraggEdge - NotImplementedError raised when trying to create unsuported output format"""
_handler = BraggEdge(material = 'Fe', number_of_bragg_edges = 4)
_filename = 'remove_me_Fe.txt'
self.assertRaises(NotImplementedError, _handler.export, _filename, 'do_not_exist_yet')
def test_calculate_experimental_lattice_with_no_input_provided(self):
"""Assert in BraggEdge - calculate exp. lattice - ValueError raised if no experimental bragg edge array provided """
_handler = BraggEdge(material = 'Fe', number_of_bragg_edges = 4)
self.assertRaises(ValueError, _handler.get_experimental_lattice_parameter)
def test_loading_single_material_in_list(self):
"""Assert in BraggEdge - single element Al data listed in a list correctly caluclated"""
_handler = BraggEdge(material = ['Al'], number_of_bragg_edges = 4)
def test_create_export_csv_no_file_raise_error(self):
"""Assert the IOError is raised when no file name given"""
_handler = BraggEdge(material = 'Fe', number_of_bragg_edges = 4)
self.assertRaises(IOError, _handler.export)
def test_printing_report(self):
"""Assert the metadata/hkl/braggedges are correctly output"""
_handler = BraggEdge(material = 'Ni', number_of_bragg_edges = 5)
def test_calculate_d_spacing_for_single_local_material(self):
"""Assert the d_spacing calculation is correct for a single local material"""
new_material = [{'name': 'Ta', 'lattice': 5.0, 'crystal_structure': 'BCC'}]
_handler = BraggEdge(new_material = new_material)
_d_spacing = _handler.d_spacing
self.assertAlmostEqual(_d_spacing['Ta'][0], 3.5355, delta = 0.0001)
def test_retrieving_correct_metadata_for_Ni(self):
"""Assert the correct metadata are returned for Ni"""
_handler = BraggEdge(material = 'Ni')
_metadata = _handler.metadata
self.assertAlmostEqual(3.5238, _metadata['lattice']['Ni'], delta = 0.01)
self.assertEqual('FCC', _metadata['crystal_structure']['Ni'])
