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test_diffraction_objects.py
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from pathlib import Path
import numpy as np
import pytest
from freezegun import freeze_time
from diffpy.utils.scattering_objects.diffraction_objects import DiffractionObject, wavelength_warning_emsg
params = [
( # Default
[
"",
None,
"",
[np.empty(0), np.empty(0)],
[np.empty(0), np.empty(0)],
[np.empty(0), np.empty(0)],
{},
],
[
"",
None,
"",
[np.empty(0), np.empty(0)],
[np.empty(0), np.empty(0)],
[np.empty(0), np.empty(0)],
{},
],
True,
),
( # Compare same attributes
[
"test",
0.71,
"x-ray",
[np.array([1, 2]), np.array([3, 4])],
[np.array([1, 2]), np.array([3, 4])],
[np.array([1, 2]), np.array([3, 4])],
{"thing1": 1, "thing2": "thing2"},
],
[
"test",
0.7100001,
"x-ray",
[np.array([1.00001, 2.00001]), np.array([3.00001, 4.00001])],
[np.array([1.00001, 2.00001]), np.array([3.00001, 4.00001])],
[np.array([1.00001, 2.00001]), np.array([3.00001, 4.00001])],
{"thing1": 1, "thing2": "thing2"},
],
True,
),
( # Different names
[
"test1",
None,
"",
[np.empty(0), np.empty(0)],
[np.empty(0), np.empty(0)],
[np.empty(0), np.empty(0)],
{},
],
[
"test2",
None,
"",
[np.empty(0), np.empty(0)],
[np.empty(0), np.empty(0)],
[np.empty(0), np.empty(0)],
{},
],
False,
),
( # Different wavelengths
[
"",
0.71,
"",
[np.empty(0), np.empty(0)],
[np.empty(0), np.empty(0)],
[np.empty(0), np.empty(0)],
{},
],
[
"",
0.711,
"",
[np.empty(0), np.empty(0)],
[np.empty(0), np.empty(0)],
[np.empty(0), np.empty(0)],
{},
],
False,
),
( # Different wavelengths
[
"",
0.71,
"",
[np.empty(0), np.empty(0)],
[np.empty(0), np.empty(0)],
[np.empty(0), np.empty(0)],
{},
],
[
"",
None,
"",
[np.empty(0), np.empty(0)],
[np.empty(0), np.empty(0)],
[np.empty(0), np.empty(0)],
{},
],
False,
),
( # Different scat_quantity
[
"",
None,
"",
[np.empty(0), np.empty(0)],
[np.empty(0), np.empty(0)],
[np.empty(0), np.empty(0)],
{},
],
[
"",
None,
"x-ray",
[np.empty(0), np.empty(0)],
[np.empty(0), np.empty(0)],
[np.empty(0), np.empty(0)],
{},
],
False,
),
( # Different on_q
[
"",
None,
"",
[np.array([1, 2]), np.array([3, 4])],
[np.empty(0), np.empty(0)],
[np.empty(0), np.empty(0)],
{},
],
[
"",
None,
"",
[np.array([1.01, 2]), np.array([3, 4])],
[np.empty(0), np.empty(0)],
[np.empty(0), np.empty(0)],
{},
],
False,
),
( # Different on_tth
[
"",
None,
"",
[np.empty(0), np.empty(0)],
[np.array([1, 2]), np.array([3, 4])],
[np.empty(0), np.empty(0)],
{},
],
[
"",
None,
"",
[np.empty(0), np.empty(0)],
[np.array([1.01, 2]), np.array([3, 4])],
[np.empty(0), np.empty(0)],
{},
],
False,
),
( # Different on_d
[
"",
None,
"",
[np.empty(0), np.empty(0)],
[np.empty(0), np.empty(0)],
[np.array([1, 2]), np.array([3, 4])],
{},
],
[
"",
None,
"",
[np.empty(0), np.empty(0)],
[np.empty(0), np.empty(0)],
[np.array([1.01, 2]), np.array([3, 4])],
{},
],
False,
),
( # Different metadata
[
"",
None,
"",
[np.empty(0), np.empty(0)],
[np.empty(0), np.empty(0)],
[np.empty(0), np.empty(0)],
{"thing1": 0, "thing2": "thing2"},
],
[
"",
None,
"",
[np.empty(0), np.empty(0)],
[np.empty(0), np.empty(0)],
[np.empty(0), np.empty(0)],
{"thing1": 1, "thing2": "thing2"},
],
False,
),
]
@pytest.mark.parametrize("inputs1, inputs2, expected", params)
def test_diffraction_objects_equality(inputs1, inputs2, expected):
diffraction_object1 = DiffractionObject()
diffraction_object2 = DiffractionObject()
diffraction_object1_attributes = [key for key in diffraction_object1.__dict__ if not key.startswith("_")]
for i, attribute in enumerate(diffraction_object1_attributes):
setattr(diffraction_object1, attribute, inputs1[i])
setattr(diffraction_object2, attribute, inputs2[i])
assert (diffraction_object1 == diffraction_object2) == expected
def _test_valid_diffraction_objects(actual_diffraction_object, function, expected_array):
if actual_diffraction_object.wavelength is None:
with pytest.warns(UserWarning) as warn_record:
getattr(actual_diffraction_object, function)()
assert str(warn_record[0].message) == wavelength_warning_emsg
actual_array = getattr(actual_diffraction_object, function)()
return np.allclose(actual_array, expected_array)
params_q_to_tth = [
# UC1: User specified empty q values (without wavelength)
([None, [], []], [[]]),
# UC2: User specified empty q values (with wavelength)
([4 * np.pi, [], []], [[]]),
# UC3: User specified valid q values (without wavelength)
([None, [0, 0.2, 0.4, 0.6, 0.8, 1], [1, 2, 3, 4, 5, 6]], [[]]),
# UC4: User specified valid q values (with wavelength)
# expected tth values are 2*arcsin(q) in degrees
(
[4 * np.pi, [0, 0.2, 0.4, 0.6, 0.8, 1], [1, 2, 3, 4, 5, 6]],
[[0, 23.07392, 47.15636, 73.73980, 106.26020, 180]],
),
]
@pytest.mark.parametrize("inputs, expected", params_q_to_tth)
def test_q_to_tth(inputs, expected):
actual = DiffractionObject(wavelength=inputs[0])
actual.on_q = [inputs[1], inputs[2]]
expected_tth = expected[0]
assert _test_valid_diffraction_objects(actual, "q_to_tth", expected_tth)
params_q_to_tth_bad = [
# UC1: user specified invalid q values that result in tth > 180 degrees
(
[4 * np.pi, [0.2, 0.4, 0.6, 0.8, 1, 1.2], [1, 2, 3, 4, 5, 6]],
[
ValueError,
"The supplied q-array and wavelength will result in an impossible two-theta. "
"Please check these values and re-instantiate the DiffractionObject with correct values.",
],
),
# UC2: user specified a wrong wavelength that result in tth > 180 degrees
(
[100, [0, 0.2, 0.4, 0.6, 0.8, 1], [1, 2, 3, 4, 5, 6]],
[
ValueError,
"The supplied q-array and wavelength will result in an impossible two-theta. "
"Please check these values and re-instantiate the DiffractionObject with correct values.",
],
),
# UC3: user specified a q array that does not match the length of intensity array (without wavelength)
(
[None, [0, 0.2, 0.4, 0.6, 0.8, 1], [1, 2, 3, 4, 5]],
[RuntimeError, "Please ensure q array and intensity array are of the same length."],
),
# UC4: user specified a q array that does not match the length of intensity array (with wavelength)
(
[4 * np.pi, [0, 0.2, 0.4, 0.6, 0.8, 1], [1, 2, 3, 4, 5]],
[RuntimeError, "Please ensure q array and intensity array are of the same length."],
),
# UC5: user specified a non-numeric value in q array (without wavelength)
(
[None, [0, 0.2, 0.4, 0.6, 0.8, "invalid"], [1, 2, 3, 4, 5, 6]],
[TypeError, "Invalid value found in q array. Please ensure all values are numeric."],
),
# UC5: user specified a non-numeric value in q array (with wavelength)
(
[4 * np.pi, [0, 0.2, 0.4, 0.6, 0.8, "invalid"], [1, 2, 3, 4, 5, 6]],
[TypeError, "Invalid value found in q array. Please ensure all values are numeric."],
),
]
@pytest.mark.parametrize("inputs, expected", params_q_to_tth_bad)
def test_q_to_tth_bad(inputs, expected):
actual = DiffractionObject(wavelength=inputs[0])
actual.on_q = [inputs[1], inputs[2]]
with pytest.raises(expected[0], match=expected[1]):
actual.q_to_tth()
params_tth_to_q = [
# UC1: User specified empty tth values (without wavelength)
([None, [], []], [[]]),
# UC2: User specified empty tth values (with wavelength)
([4 * np.pi, [], []], [[]]),
# UC3: User specified valid tth values between 0-180 degrees (without wavelength)
(
[None, [0, 30, 60, 90, 120, 180], [1, 2, 3, 4, 5, 6]],
[[]],
),
# UC4: User specified valid tth values between 0-180 degrees (with wavelength)
# expected q vales are sin15, sin30, sin45, sin60, sin90
([4 * np.pi, [0, 30, 60, 90, 120, 180], [1, 2, 3, 4, 5, 6]], [[0, 0.258819, 0.5, 0.707107, 0.866025, 1]]),
]
@pytest.mark.parametrize("inputs, expected", params_tth_to_q)
def test_tth_to_q(inputs, expected):
actual = DiffractionObject(wavelength=inputs[0])
actual.on_tth = [inputs[1], inputs[2]]
expected_q = expected[0]
assert _test_valid_diffraction_objects(actual, "tth_to_q", expected_q)
params_tth_to_q_bad = [
# UC1: user specified an invalid tth value of > 180 degrees (without wavelength)
(
[None, [0, 30, 60, 90, 120, 181], [1, 2, 3, 4, 5, 6]],
[ValueError, "Two theta exceeds 180 degrees. Please check the input values for errors."],
),
# UC2: user specified an invalid tth value of > 180 degrees (with wavelength)
(
[4 * np.pi, [0, 30, 60, 90, 120, 181], [1, 2, 3, 4, 5, 6]],
[ValueError, "Two theta exceeds 180 degrees. Please check the input values for errors."],
),
# UC3: user specified a two theta array that does not match the length of intensity array (without wavelength)
(
[None, [0, 30, 60, 90, 120], [1, 2, 3, 4, 5, 6]],
[RuntimeError, "Please ensure two theta array and intensity array are of the same length."],
),
# UC4: user specified a two theta array that does not match the length of intensity array (with wavelength)
(
[4 * np.pi, [0, 30, 60, 90, 120], [1, 2, 3, 4, 5, 6]],
[RuntimeError, "Please ensure two theta array and intensity array are of the same length."],
),
# UC5: user specified a non-numeric value in two theta array (without wavelength)
(
[None, [0, 30, 60, 90, 120, "invalid"], [1, 2, 3, 4, 5, 6]],
[TypeError, "Invalid value found in two theta array. Please ensure all values are numeric."],
),
# UC6: user specified a non-numeric value in two theta array (with wavelength)
(
[4 * np.pi, [0, 30, 60, 90, 120, "invalid"], [1, 2, 3, 4, 5, 6]],
[TypeError, "Invalid value found in two theta array. Please ensure all values are numeric."],
),
]
@pytest.mark.parametrize("inputs, expected", params_tth_to_q_bad)
def test_tth_to_q_bad(inputs, expected):
actual = DiffractionObject(wavelength=inputs[0])
actual.on_tth = [inputs[1], inputs[2]]
with pytest.raises(expected[0], match=expected[1]):
actual.tth_to_q()
def test_dump(tmp_path, mocker):
x, y = np.linspace(0, 5, 6), np.linspace(0, 5, 6)
directory = Path(tmp_path)
file = directory / "testfile"
test = DiffractionObject()
test.wavelength = 1.54
test.name = "test"
test.scat_quantity = "x-ray"
test.insert_scattering_quantity(
x, y, "q", metadata={"thing1": 1, "thing2": "thing2", "package_info": {"package2": "3.4.5"}}
)
mocker.patch("importlib.metadata.version", return_value="3.3.0")
with freeze_time("2012-01-14"):
test.dump(file, "q")
with open(file, "r") as f:
actual = f.read()
expected = (
"[DiffractionObject]\nname = test\nwavelength = 1.54\nscat_quantity = x-ray\nthing1 = 1\n"
"thing2 = thing2\npackage_info = {'package2': '3.4.5', 'diffpy.utils': '3.3.0'}\n"
"creation_time = 2012-01-14 00:00:00\n\n"
"#### start data\n0.000000000000000000e+00 0.000000000000000000e+00\n"
"1.000000000000000000e+00 1.000000000000000000e+00\n"
"2.000000000000000000e+00 2.000000000000000000e+00\n"
"3.000000000000000000e+00 3.000000000000000000e+00\n"
"4.000000000000000000e+00 4.000000000000000000e+00\n"
"5.000000000000000000e+00 5.000000000000000000e+00\n"
)
assert actual == expected