def test_H_sigma(self):
_energy_min = 0.004
_energy_max = 1
_energy_step = 0.01
o_reso = Resonance(energy_min=_energy_min,
energy_max=_energy_max,
energy_step=_energy_step,
database=self.database)
_layer_1 = 'H2'
_thickness_1 = 0.025 # mm
_layer_2 = 'H'
_thickness_2 = 0.01
_layer_3 = 'CH4'
_thickness_3 = 0.01
_layer_4 = 'ZrH'
_thickness_4 = 0.01
o_reso.add_layer(formula=_layer_1, thickness=_thickness_1)
o_reso.add_layer(formula=_layer_2, thickness=_thickness_2)
o_reso.add_layer(formula=_layer_3, thickness=_thickness_3)
o_reso.add_layer(formula=_layer_4, thickness=_thickness_4)
layer1_sigma = o_reso.stack_sigma[_layer_1]['H']['1-H']['sigma_b_raw'][
0]
layer2_sigma = o_reso.stack_sigma[_layer_2]['H']['1-H']['sigma_b_raw'][
0]
layer3_sigma = o_reso.stack_sigma[_layer_3]['H']['1-H']['sigma_b_raw'][
0]
layer4_sigma = o_reso.stack_sigma[_layer_4]['H']['1-H']['sigma_b_raw'][
0]
self.assertNotEqual(layer1_sigma, layer2_sigma)
self.assertNotEqual(layer1_sigma, layer3_sigma)
self.assertNotEqual(layer1_sigma, layer4_sigma)
self.assertNotEqual(layer2_sigma, layer3_sigma)
self.assertNotEqual(layer2_sigma, layer4_sigma)
self.assertNotEqual(layer3_sigma, layer4_sigma)
def test_element_metadata_via_add_layer_initialization(self):
"""assert __element_metadata is correctly populated using add layer initialization"""
o_reso = Resonance(database=self.database)
# layer 1
layer1 = 'CoAg'
thickness1 = 0.025
o_reso.add_layer(formula=layer1, thickness=thickness1)
# layer 2
layer2 = 'Ag'
thickness2 = 0.1
o_reso.add_layer(formula=layer2, thickness=thickness2)
stack = o_reso.stack
# molar mass
co_mass_expected = 58.9332
ag_mass_expected = 107.8682
self.assertEqual(co_mass_expected,
stack['CoAg']['Co']['molar_mass']['value'])
self.assertEqual(ag_mass_expected,
stack['CoAg']['Ag']['molar_mass']['value'])
self.assertEqual(ag_mass_expected,
stack['Ag']['Ag']['molar_mass']['value'])
# density
co_density_expected = 8.9
ag_density_expected = 10.5
self.assertEqual(co_density_expected,
stack['CoAg']['Co']['density']['value'])
self.assertEqual(ag_density_expected,
stack['Ag']['Ag']['density']['value'])
def test_abundance(self):
"""assert"""
o_reso = Resonance(database=self.database)
o_reso.add_layer(formula='C', thickness=1)
self.assertAlmostEqual(
o_reso.stack['C']['C']['isotopes']['isotopic_ratio'][0],
0.9893,
delta=0.0001)
self.assertAlmostEqual(
o_reso.stack['C']['C']['isotopes']['isotopic_ratio'][1],
0.0107,
delta=0.0001)
def setUp(self):
_energy_min = 1
_energy_max = 50
_energy_step = 0.1
_layer_1 = 'Co'
_thickness_1 = 0.025 # mm
o_reso = Resonance(energy_min=_energy_min,
energy_max=_energy_max,
energy_step=_energy_step,
database=self.database)
o_reso.add_layer(formula=_layer_1, thickness=_thickness_1)
self.o_reso = o_reso
def test_duplicated_layer_name(self):
o_reso = Resonance(database=self.database)
# layer 1
layer1 = 'CoAg'
thickness1 = 0.025
o_reso.add_layer(formula=layer1, thickness=thickness1)
# Duplicated layer name
layer2 = 'CoAg'
thickness2 = 0.01
self.assertRaises(ValueError,
o_reso.add_layer,
formula=layer2,
thickness=thickness2)
def _fill_iso_to_items(name, stack=None, database='ENDF_VII'):
if '*' not in name:
raise ValueError(
"'*' is needed to retrieve all isotopes of '{}' ".format(name))
else:
ele_name = name.replace('*', '')
if stack is None:
o_reso = Resonance(database=database)
o_reso.add_layer(formula=ele_name, thickness=1)
stack = o_reso.stack
iso_list = stack[ele_name][ele_name]['isotopes']['list']
_path_to_iso = []
for _each_iso in iso_list:
_path_to_iso.append(_shape_items(_each_iso))
return _path_to_iso
def test_layer_density_locked_if_defined_during_initialization_add_layer(
self):
"""assert the layer density is locked if defined at the beginning using add_layer"""
o_reso = Resonance(database=self.database)
# layer 1
layer1 = 'CoAg'
thickness1 = 0.025
density = 8.9
o_reso.add_layer(formula=layer1, thickness=thickness1, density=density)
# layer 2
layer2 = 'Ag'
thickness2 = 0.1
o_reso.add_layer(formula=layer2, thickness=thickness2)
density_lock_before = 8.9
density_lock_after = o_reso.stack['CoAg']['density']['value']
self.assertEqual(density_lock_after, density_lock_before)
density_unlock_expected = 10.5
density_unlock_after = o_reso.stack['Ag']['density']['value']
self.assertEqual(density_unlock_after, density_unlock_expected)
def test_adding_layer(self):
"""assert adding_layer works"""
o_reso = Resonance(database=self.database)
# layer 1
layer1 = 'CoAg'
thickness1 = 0.025
o_reso.add_layer(formula=layer1, thickness=thickness1)
# layer 2
layer2 = 'Ag'
thickness2 = 0.1
density2 = 0.5
o_reso.add_layer(formula=layer2,
thickness=thickness2,
density=density2)
returned_stack = o_reso.stack
expected_stack = {
'CoAg': {
'elements': ['Co', 'Ag'],
'stoichiometric_ratio': [1, 1],
'thickness': {
'value': 0.025,
'units': 'mm'
},
'density': {
'value': 9.7,
'units': 'g/cm3'
},
'Co': {
'isotopes': {
'file_names': ['Co-58.csv', 'Co-59.csv'],
'list': ['58-Co', '59-Co'],
'mass': {
'value': [57.9357576, 58.9332002],
'units': 'g/mol',
},
'isotopic_ratio': [0.0, 1.0],
},
'density': {
'value': 8.9,
'units': 'g/cm3'
},
'molar_mass': {
'value': 58.9332,
'units': 'g/mol'
},
},
'Ag': {
'isotopes': {
'file_names': ['Ag-107.csv', 'Ag-109.csv'],
'list': ['107-Ag', '109-Ag'],
'mass': {
'value': [106.905093, 108.904756],
'units': 'g/mol',
},
'isotopic_ratio': [0.51839, 0.48161000],
},
'density': {
'value': 10.5,
'units': 'g/cm3'
},
'molar_mass': {
'value': 107.8682,
'units': 'g/cm3'
},
},
},
'Ag': {
'elements': ['Ag'],
'stoichiometric_ratio': [1],
'thickness': {
'value': 0.1,
'units': 'mm'
},
'density': {
'value': 0.5,
'units': 'g/cm3'
},
'Ag': {
'isotopes': {
'file_names': ['Ag-107.csv', 'Ag-109.csv'],
'list': ['107-Ag', '109-Ag'],
'mass': {
'value': [106.905093, 108.904756],
'units': 'g/mol',
},
'isotopic_ratio': [0.51839, 0.48161000],
},
'density': {
'value': 10.5,
'units': 'g/cm3'
},
'molar_mass': {
'value': 107.8682,
'units': 'g/mol'
},
},
},
}
# CoAg
# elements
self.assertEqual(returned_stack['CoAg']['elements'],
expected_stack['CoAg']['elements'])
# atomic_atomic_ratio
self.assertEqual(returned_stack['CoAg']['stoichiometric_ratio'],
expected_stack['CoAg']['stoichiometric_ratio'])
# thickness
self.assertEqual(returned_stack['CoAg']['thickness']['value'],
expected_stack['CoAg']['thickness']['value'])
self.assertEqual(returned_stack['CoAg']['thickness']['units'],
expected_stack['CoAg']['thickness']['units'])
# isotopes Co
# file names
self.assertEqual(
returned_stack['CoAg']['Co']['isotopes']['file_names'],
expected_stack['CoAg']['Co']['isotopes']['file_names'])
# list
self.assertEqual(returned_stack['CoAg']['Co']['isotopes']['list'],
expected_stack['CoAg']['Co']['isotopes']['list'])
# mass
self.assertEqual(
returned_stack['CoAg']['Co']['isotopes']['mass']['value'],
expected_stack['CoAg']['Co']['isotopes']['mass']['value'])
self.assertEqual(
returned_stack['CoAg']['Co']['isotopes']['mass']['units'],
expected_stack['CoAg']['Co']['isotopes']['mass']['units'])
# atomic_ratio Co
self.assertAlmostEqual(
returned_stack['CoAg']['Co']['isotopes']['isotopic_ratio'][0],
expected_stack['CoAg']['Co']['isotopes']['isotopic_ratio'][0],
delta=0.0001)
self.assertAlmostEqual(
returned_stack['CoAg']['Co']['isotopes']['isotopic_ratio'][1],
expected_stack['CoAg']['Co']['isotopes']['isotopic_ratio'][1],
delta=0.0001)
# isotopic_ratio Ag
self.assertAlmostEqual(
returned_stack['CoAg']['Ag']['isotopes']['isotopic_ratio'][0],
expected_stack['CoAg']['Ag']['isotopes']['isotopic_ratio'][0],
delta=0.0001)
self.assertAlmostEqual(
returned_stack['CoAg']['Ag']['isotopes']['isotopic_ratio'][1],
expected_stack['CoAg']['Ag']['isotopes']['isotopic_ratio'][1],
delta=0.0001)
# layer density
self.assertEqual(returned_stack['Ag']['density']['value'],
expected_stack['Ag']['density']['value'])
self.assertAlmostEqual(returned_stack['CoAg']['density']['value'],
expected_stack['CoAg']['density']['value'],
delta=0.1)
# element density
self.assertEqual(returned_stack['CoAg']['Ag']['density']['value'],
expected_stack['CoAg']['Ag']['density']['value'])
self.assertEqual(returned_stack['CoAg']['Co']['density']['value'],
expected_stack['CoAg']['Co']['density']['value'])
# molar mass
self.assertEqual(returned_stack['CoAg']['Ag']['molar_mass']['value'],
expected_stack['CoAg']['Ag']['molar_mass']['value'])
self.assertEqual(returned_stack['CoAg']['Co']['molar_mass']['value'],
expected_stack['CoAg']['Co']['molar_mass']['value'])
class Simulation(object):
# Input sample name or names as str, case sensitive
def __init__(self, energy_min=1e-5, energy_max=1000, energy_step=0.01, database='ENDF_VIII'):
"""
initialize the a Simulation() using the Resonance() in ImagingReso
:param energy_min:
:type energy_min:
:param energy_max:
:type energy_max:
:param energy_step:
:type energy_step:
:param database:
:type database:
"""
self.energy_min = energy_min
self.energy_max = energy_max
self.energy_step = energy_step
self.database = database
self.o_reso = Resonance(energy_min=energy_min,
energy_max=energy_max,
energy_step=energy_step,
database=database)
self.neutron_pulse = None
self.layer_list = []
self.layer = fit_util.Layer()
self.x_tof_us = None
self.y_att = None
def add_layer(self, layer: str, thickness_mm: float, density_gcm3=np.NaN):
"""
:param layer:
:type layer:
:param thickness_mm:
:type thickness_mm:
:param density_gcm3:
:type density_gcm3:
:return:
:rtype:
"""
self.o_reso.add_layer(formula=layer,
thickness=thickness_mm,
density=density_gcm3)
self.layer_list.append(layer)
self.layer.add_layer(layer=layer, thickness_mm=thickness_mm, density_gcm3=density_gcm3)
def add_Layer(self, layer: Layer):
"""
Add layer using Layer class
:param layer:
"""
for _each_layer in list(layer.info.keys()):
self.add_layer(layer=_each_layer,
thickness_mm=layer.info[_each_layer]['thickness']['value'],
density_gcm3=layer.info[_each_layer]['density']['value'])
def set_isotopic_ratio(self, layer, element, new_isotopic_ratio_list):
"""
Set isotopic ratios for picked element and update x y values to pass
:param layer:
:param element:
:param new_isotopic_ratio_list:
:return: x in eV
y in attenuation
"""
if type(new_isotopic_ratio_list) is not list:
raise ValueError("{} is not a list".format(new_isotopic_ratio_list))
# Check if layer exist
if layer not in self.layer_list:
raise ValueError('Layer {} does not exist.'.format(layer))
# Check if element exist
_formula = re.findall(r'([A-Z][a-z]*)(\d*)', layer)
_elements = []
for _element in _formula:
_single_element = list(_element)[0]
_elements.append(_single_element)
if element not in _elements:
raise ValueError('Element {} specified does not exist in {} layer.'.format(element, layer))
self.o_reso.set_isotopic_ratio(compound=layer, element=element, list_ratio=new_isotopic_ratio_list)
# self.x_simu = np.array(self.o_reso.total_signal['energy_eV']).round(5)
# self.y_simu = np.array(self.o_reso.total_signal['attenuation'])
def get_x(self, x_type, offset_us=None, source_to_detector_m=None, t_unit='us',
t_start_us=None, time_resolution_us=None, num_offset=0):
"""
Get x by specified type
:param x_type:
:type x_type:
:param offset_us:
:type offset_us:
:param source_to_detector_m:
:type source_to_detector_m:
:return: x in specified type
:rtype: np.array
"""
fit_util.check_if_in_list(x_type, fit_util.x_type_list)
_x = np.array(self.o_reso.total_signal['energy_eV']).round(5)
x = fit_util.convert_energy_to(x=_x,
x_type=x_type,
offset_us=offset_us,
source_to_detector_m=source_to_detector_m,
t_unit=t_unit,
t_start_us=t_start_us,
time_resolution_us=time_resolution_us,
num_offset=num_offset)
return x
def get_y(self, y_type):
"""
Get x by specified type
:param y_type:
:type y_type:
:return: y in specified type
:rtype: np.array
"""
fit_util.check_if_in_list(y_type, fit_util.y_type_list)
y = self.o_reso.total_signal[y_type]
return y
def _convolve_beam_shapes(self, source_to_detector_m, conv_proton, proton_params={}, model_index=1):
_file_path = os.path.abspath(os.path.dirname(__file__))
_rel_path_to_neutron1 = 'data/_data_for_tutorial/neutron_pulse/source_section_1.dat'
_rel_path_to_neutron2 = 'data/_data_for_tutorial/neutron_pulse/source_section_2.dat'
path1 = os.path.join(_file_path, _rel_path_to_neutron1)
path2 = os.path.join(_file_path, _rel_path_to_neutron2)
self.neutron_pulse = NeutronPulse(path1, model_index=model_index)
self.neutron_pulse.load_shape_each(path2)
self.neutron_pulse.fit_shape(e_min=1, e_max=500,
drop=False, norm=True,
check_each=False,
save_fig=False,
overwrite_csv=False)
self.neutron_pulse.fit_params(check_each=False, loglog_fit=True, overwrite_csv=False)
self.neutron_pulse.make_shape(e_ev=self.get_x(x_type='energy'), t_interp=None, for_sum=True, norm=False,
source_to_detector_m=source_to_detector_m,
conv_proton=conv_proton, proton_params=proton_params,
overwrite_csv=False)
tof_beam_shape_df = self.neutron_pulse.shape_tof_df_interp.set_index('tof_us')
tof_trans_df = tof_beam_shape_df * self.o_reso.total_signal['transmission']
tof_beam_shape_df['sum'] = tof_beam_shape_df.sum(axis=1)
tof_trans_df['sum'] = tof_trans_df.sum(axis=1)
# print(tof_beam_shape_df)
# print(tof_trans_df)
self.x_tof_us = np.array(tof_beam_shape_df.index)
self.y_att = 1 - np.array(tof_trans_df['sum'] / tof_beam_shape_df['sum'])
def peak_map(self, x_type, y_type, thres=0.15, min_dist=20, impr_reso=True,
offset_us=None, source_to_detector_m=None, t_unit='us',
t_start_us=None, time_resolution_us=None, num_offset=0,
):
"""
Get peak map for each element and/or isotope
:param thres:
:type thres:
:param min_dist:
:type min_dist:
:param impr_reso:
:type impr_reso:
:return:
:rtype:
"""
if len(self.layer_list) == 0:
raise ValueError("No layer has been added.")
_stack_signal = self.o_reso.stack_signal
_layer_list = self.layer_list
# _x_energy = _stack_signal[_layer_list[0]][_layer_list[0]]['energy_eV']
_x = self.get_x(x_type=x_type,
offset_us=offset_us,
source_to_detector_m=source_to_detector_m,
t_unit=t_unit,
t_start_us=t_start_us,
time_resolution_us=time_resolution_us,
num_offset=num_offset
)
# _x = sorted(_x)
peak_map = {}
for _ele in _layer_list:
# Isotope
for _iso in self.o_reso.stack[_ele][_ele]['isotopes']['list']:
peak_map[_iso] = {}
_iso_y = _stack_signal[_ele][_ele][_iso]['attenuation']
_peak_df = fit_util.find_peak(x=_x, y=_iso_y, x_name='x',
thres=thres, min_dist=min_dist,
imprv_reso=impr_reso)
if y_type == 'transmission':
_peak_df['y'] = 1 - _peak_df['y']
peak_map[_iso]['ideal'] = _peak_df
# Element
peak_map[_ele] = {}
_ele_y = _stack_signal[_ele][_ele]['attenuation']
_peak_df = fit_util.find_peak(x=_x, y=_ele_y, x_name='x',
thres=thres, min_dist=min_dist,
imprv_reso=impr_reso)
if y_type == 'transmission':
_peak_df['y'] = 1 - _peak_df['y']
peak_map[_ele]['ideal'] = _peak_df
peak_map_dict = {'peak_map': peak_map,
'x_type': x_type,
'y_type': y_type}
return peak_map_dict
def plot(self, y_type='attenuation', x_type='energy',
logx=False, logy=False,
mixed=True, all_layers=False, all_elements=False,
all_isotopes=False, items_to_plot=None, time_unit='us', offset_us=0.,
source_to_detector_m=16.,
t_start_us=1,
time_resolution_us=0.16,
ax_mpl=None,
fmt='-', ms=2, lw=1.5, alpha=1):
if len(self.layer_list) == 0:
raise ValueError("No layer has been added.")
if items_to_plot is not None:
# shape format of items
items = fit_util.Items(o_reso=self.o_reso, database=self.database)
items_to_plot = items.shaped(items_list=items_to_plot)
ax = self.o_reso.plot(y_axis=y_type, x_axis=x_type, mixed=mixed,
all_layers=all_layers, all_elements=all_elements,
all_isotopes=all_isotopes, items_to_plot=items_to_plot,
source_to_detector_m=source_to_detector_m,
offset_us=offset_us,
time_resolution_us=time_resolution_us,
time_unit=time_unit,
t_start_us=t_start_us,
ax_mpl=ax_mpl,
logx=logx,
logy=logy,
# plotly=plotly
fmt=fmt,
ms=ms,
lw=lw,
alpha=alpha)
return ax
def export(self, output_type='clip', filename=None, x_type='energy', y_type='attenuation',
all_layers=False, all_elements=False, all_isotopes=False, items_to_export=None,
offset_us=0., source_to_detector_m=16.,
t_start_us=1, time_resolution_us=0.16, time_unit='us'):
if items_to_export is not None:
# Shape items
items = fit_util.Items(o_reso=self.o_reso, database=self.database)
items_to_export = items.shaped(items_list=items_to_export)
_df = self.o_reso.export(output_type=output_type,
filename=filename,
x_axis=x_type,
y_axis=y_type,
all_layers=all_layers,
all_elements=all_elements,
all_isotopes=all_isotopes,
items_to_export=items_to_export,
offset_us=offset_us,
source_to_detector_m=source_to_detector_m,
t_start_us=t_start_us,
time_resolution_us=time_resolution_us,
time_unit=time_unit)
return _df