def test_get_quant_fluor_data_dict():
"""Tests for 'get_quant_fluor_data_dict': basic tests for consistensy of the returned dictionary"""
for standard_data in _standard_data_sample:
quant_fluor_data_dict = get_quant_fluor_data_dict(standard_data,
incident_energy=12.0)
# Will raise exception is schema is not satisfied
jsonschema.validate(instance=quant_fluor_data_dict,
schema=_xrf_quant_fluor_schema)
assert quant_fluor_data_dict["name"] == standard_data[
"name"], "Dictionary element 'name' is incorrect"
assert (quant_fluor_data_dict["serial"] == standard_data["serial"]
), "Dictionary element 'serial' is incorrect"
assert (quant_fluor_data_dict["description"] ==
standard_data["description"]
), "Dictionary element 'description' is incorrect"
eline_set = set()
# The 'mass' is not actual mass. If elements has multiple emission lines activated, then
# the mass (density) of the element will be counted multiple times. There is no
# physical meaning in the computed value: it is used to verify the sum of densities in
# the 'element_lines' dictionary of emission lines in 'quant_fluor_data_dict'
mass_sum_expected = 0
for cmpd, mass in standard_data["compounds"].items():
em_dict = split_compound_mass(cmpd, mass)
for el, ms in em_dict.items():
elines = generate_eline_list([el], incident_energy=12.0)
n_elines = len(elines)
if n_elines:
mass_sum_expected += n_elines * ms
eline_set.update(elines)
eline_out_list = list(quant_fluor_data_dict["element_lines"].keys())
assert len(eline_out_list) == len(
eline_set), "The number of emission lines is not as expected"
assert (
set(eline_out_list) == eline_set
), "Generated object contains emission lines that are different from expected"
mass_sum = sum([
_["density"]
for _ in quant_fluor_data_dict["element_lines"].values()
])
assert (
mass_sum == mass_sum_expected
), "The total mass (density) of the components is different from expected"
def test_split_compound_mass(formula, elements, n_atoms):
mass_total = 10.0
data = split_compound_mass(formula, mass_total)
# Basic checks for proper parsing
assert len(data) == len(
elements), "The number of parsed elements is incorrect"
assert set(elements) == set(
data.keys()), "The set of parsed elements is incorrect"
# Make sure that the sum of mass of each element equals to total mass
npt.assert_almost_equal(
np.sum(list(data.values())),
mass_total,
err_msg="The computed mass is not distributed properly among elements")
def test_split_compound_mass_fail(formula):
with pytest.raises(RuntimeError,
match=f"Invalid chemical formula.*{formula}"):
split_compound_mass(formula, 10.0)