def test_cs_different_units():
e = XrfElement('Fe')
# test at different energies
for eng in range(10, 20):
cs1 = np.array([v for k, v in e.cs(eng).all]) # unit in cm2/g
cs2 = np.array([v for k, v in e.csb(eng).all]) # unit in barns/atom
cs1 /= cs1[0]
cs2 /= cs2[0]
# ratio should be the same no matter which unit is used
assert_array_almost_equal(cs1, cs2, decimal=10)
def test_cs_different_units():
e = XrfElement('Fe')
# test at different energies
for eng in range(10, 20):
cs1 = np.array([v for k, v in e.cs(eng).all]) # unit in cm2/g
cs2 = np.array([v for k, v in e.csb(eng).all]) # unit in barns/atom
cs1 /= cs1[0]
cs2 /= cs2[0]
# ratio should be the same no matter which unit is used
assert_array_almost_equal(cs1, cs2, decimal=10)
def test_element_data():
"""
smoke test of all elements
"""
data1 = []
data2 = []
name_list = []
for i in range(100):
e = XrfElement(i+1)
data1.append(e.cs(10)['Ka1'])
name_list.append(e.name)
for item in name_list:
e = XrfElement(item)
data2.append(e.cs(10)['Ka1'])
assert_array_equal(data1, data2)
return
def smoke_test_element_creation():
prev_element = None
elements = [elm for abbrev, elm in six.iteritems(basic)
if isinstance(abbrev, int)]
elements.sort()
for element in elements:
Z = element.Z
element.mass
element.density
sym = element.sym
inits = [Z, sym, sym.upper(), sym.lower(), sym.swapcase()]
element = None
for init in inits:
element = XrfElement(init)
# obtain the next four attributes to make sure the XrayLibWrap is
# working
element.bind_energy
element.fluor_yield
element.jump_factor
element.emission_line.all
if prev_element is not None:
# compare prev_element to element
assert_equal(prev_element.__lt__(element), True)
assert_equal(prev_element < element, True)
assert_equal(prev_element.__eq__(element), False)
assert_equal(prev_element == element, False)
assert_equal(prev_element >= element, False)
assert_equal(prev_element > element, False)
# compare element to prev_element
assert_equal(element < prev_element, False)
assert_equal(element.__lt__(prev_element), False)
assert_equal(element <= prev_element, False)
assert_equal(element.__eq__(prev_element), False)
assert_equal(element == prev_element, False)
assert_equal(element >= prev_element, True)
assert_equal(element > prev_element, True)
prev_element = element
def test_element_creation():
prev_element = None
elements = [elm for abbrev, elm in six.iteritems(basic)
if isinstance(abbrev, int)]
elements.sort()
for element in elements:
Z = element.Z
element.mass
element.density
sym = element.sym
inits = [Z, sym, sym.upper(), sym.lower(), sym.swapcase()]
element = None
for init in inits:
element = XrfElement(init)
# obtain the next four attributes to make sure the XrayLibWrap is
# working
element.bind_energy
element.fluor_yield
element.jump_factor
element.emission_line.all
if prev_element is not None:
# compare prev_element to element
assert_equal(prev_element.__lt__(element), True)
assert_equal(prev_element < element, True)
assert_equal(prev_element.__eq__(element), False)
assert_equal(prev_element == element, False)
assert_equal(prev_element >= element, False)
assert_equal(prev_element > element, False)
# compare element to prev_element
assert_equal(element < prev_element, False)
assert_equal(element.__lt__(prev_element), False)
assert_equal(element <= prev_element, False)
assert_equal(element.__eq__(prev_element), False)
assert_equal(element == prev_element, False)
assert_equal(element >= prev_element, True)
assert_equal(element > prev_element, True)
prev_element = element
def test_element_data():
"""
smoke test of all elements
"""
data1 = []
data2 = []
name_list = []
for i in range(100):
e = XrfElement(i+1)
data1.append(e.cs(10)['Ka1'])
name_list.append(e.name)
for item in name_list:
e = XrfElement(item)
data2.append(e.cs(10)['Ka1'])
assert_array_equal(data1, data2)
return
def _get_elemental_line_parameters(*, elemental_line, incident_energy):
r"""
Retrieve information on all emission lines for the given element and the group (K, L or M)
at given incident energy. For each emission line, the information includes emission line name,
energy and ratio. The data is used for simulation of emission spectra of elements.
Parameters
----------
elemental_line: str
Elemental line name in the format ``Fe_K``, ``Ca_L``, etc.
incident_energy: float
Incident energy in keV
Returns
-------
List of dictionaries. Keys: ``name`` - emission line name, ``energy`` - energy of the
emission line, "ratio" - ratio of the emission line area to the area of ``a1`` line.
Raises
------
RuntimeError
Elemental line is not in the list of supported lines or the emission line is
incorrectly formatted.
"""
# Check format (Fe_K, Y_L, W_M etc.)
if not re.search(r"^[A-Z][a-z]?_[KLM]$", elemental_line):
raise RuntimeError(
f"Elemental line {elemental_line} has incorrect format")
element, line = elemental_line.split("_")
line_name = elemental_line
ALL_LINES = K_LINE + L_LINE + M_LINE
if line_name not in ALL_LINES:
raise RuntimeError(f"Elemental line {line_name} is not supported")
elemental_lines = []
# XrfElement class provides convenient access to xraylib library functions
e = XrfElement(element)
# Check if the emission line is activated (check if 'a1' line is active)
em_line_a1 = f"{line.lower()}a1"
i_line_a1 = e.cs(incident_energy)[em_line_a1]
if i_line_a1 > 0:
for num, item in enumerate(e.emission_line.all):
l_name = item[0] # Line name (ka1, kb2 etc.)
energy_v = item[1] # Energy (in kEv)
if line.lower() not in l_name:
continue
i_line = e.cs(incident_energy)[l_name]
ratio_v = i_line / i_line_a1
if energy_v == 0 or ratio_v == 0:
continue
elemental_lines.append({
"name": l_name,
"energy": energy_v,
"ratio": ratio_v
})
return elemental_lines
