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Merged
merged 11 commits into from
Nov 28, 2024
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q_to_tth & tth_to_q #178

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7841ff2
fix docstring and add error messages
yucongalicechen Nov 15, 2024
1b0fa19
add tests
yucongalicechen Nov 15, 2024
4e85b0a
edit error message
yucongalicechen Nov 20, 2024
a33482b
add more tests
yucongalicechen Nov 21, 2024
3efde28
add warning msg for wavelength, edit error msg
yucongalicechen Nov 25, 2024
a53461f
edit warning msg for wavelength, change index error to runtime error
yucongalicechen Nov 25, 2024
2a5a819
add functionality for handling error messages
yucongalicechen Nov 25, 2024
64d8693
remove docstring from private test functions
yucongalicechen Nov 26, 2024
728ff36
add news
yucongalicechen Nov 26, 2024
490486c
add example and utility
yucongalicechen Nov 26, 2024
d481253
edits on docs
yucongalicechen Nov 26, 2024
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183 changes: 134 additions & 49 deletions tests/diffpy/utils/scattering_objects/test_diffraction_objects.py
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Original file line number Diff line number Diff line change
Expand Up @@ -231,94 +231,179 @@ def test_diffraction_objects_equality(inputs1, inputs2, expected):
assert (diffraction_object1 == diffraction_object2) == expected


def test_q_to_tth():
# Valid q values that should result in 0-180 tth values after conversion
def _test_valid_diffraction_objects(actual_diffraction_object, function, expected_array):
"""Checks the behavior of the DiffractionObject:
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Test functions don't need docstring, though if it's ok to leave this now you did it.

when there is no wavelength, we expect the correct warning message and output,
otherwise, we only check the output matches the 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) == (
"INFO: no wavelength has been specified. You can continue "
"to use the DiffractionObject but some of its powerful features "
"will not be available. To specify a wavelength, you can use "
"DiffractionObject(wavelength=0.71)."
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0.71? Or something like "wavelength=) where you replace with the actual wavelength in the units of..." Etc. Also, are these the correct instructions? This seems to be instantiating a new DO not adding a wavelength to an existing DO.

Let's also make sure to add these instructions to the documentation.

)
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)
# expected tth values are 2*arcsin(q) in degrees
actual = DiffractionObject(wavelength=4 * np.pi)
setattr(actual, "on_q", [[0, 0.2, 0.4, 0.6, 0.8, 1], [1, 2, 3, 4, 5, 6]])
actual_tth = actual.q_to_tth()
expected_tth = [0, 23.07392, 47.15636, 73.73980, 106.26020, 180]
assert np.allclose(actual_tth, expected_tth)
(
[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 did not specify wavelength
# UC1: user specified invalid q values that result in tth > 180 degrees
(
[None, [0, 0.2, 0.4, 0.6, 0.8, 1]],
"Wavelength is not specified. Please provide a valid wavelength, "
"e.g., DiffractionObject(wavelength=0.71).",
[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.",
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Maybe add ."... With correct values"

],
),
# UC2: user specified invalid q values that result in tth > 180 degrees
# UC2: user specified a wrong wavelength that result in tth > 180 degrees
(
[4 * np.pi, [0.2, 0.4, 0.6, 0.8, 1, 1.2]],
"Wavelength * q > 4 * pi. Please check if you entered an incorrect wavelength or q value.",
[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. "
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See above. Also since we are reusing the error message do we want to minimize word by defining it in a variable once and reusing the variable in multiple tests?

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Yes I will store them in diffraction_objects.py file

"Please check these values and re-instantiate the DiffractionObject.",
],
),
# UC3: user specified a wrong wavelength that result in tth > 180 degrees
# UC3: user specified a q array that does not match the length of intensity array (without wavelength)
(
[100, [0, 0.2, 0.4, 0.6, 0.8, 1]],
"Wavelength * q > 4 * pi. Please check if you entered an incorrect wavelength or q value.",
[None, [0, 0.2, 0.4, 0.6, 0.8, 1], [1, 2, 3, 4, 5]],
[IndexError, "Please ensure q array and intensity array are the same length."],
),
# UC4: user specified an empty q array
([4 * np.pi, []], "Q array is empty. Please provide valid q values."),
# UC5: user specified a non-numeric value in q array
# 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, "invalid"]],
"Invalid value found in q array. Please ensure all values are numeric.",
[4 * np.pi, [0, 0.2, 0.4, 0.6, 0.8, 1], [1, 2, 3, 4, 5]],
[IndexError, "Please ensure q array and intensity array are the same length."],
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I think RunTime wrote may be more appropriate here since I think we will raise it ourselves?

),
# 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])
setattr(actual, "on_q", [inputs[1], [1, 2, 3, 4, 5, 6]])
with pytest.raises(ValueError):
actual.on_q = [inputs[1], inputs[2]]
with pytest.raises(expected[0], match=expected[1]):
actual.q_to_tth()


def test_tth_to_q():
# Valid tth values between 0-180 degrees
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
actual = DiffractionObject(wavelength=4 * np.pi)
setattr(actual, "on_tth", [[0, 30, 60, 90, 120, 180], [1, 2, 3, 4, 5, 6]])
actual_q = actual.tth_to_q()
expected_q = [0, 0.258819, 0.5, 0.707107, 0.866025, 1]
assert np.allclose(actual_q, expected_q)
(
[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 did not specify wavelength
# 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, 180]],
"Wavelength is not specified. Please provide a valid wavelength, "
"e.g., DiffractionObject(wavelength=0.71).",
[None, [0, 30, 60, 90, 120], [1, 2, 3, 4, 5, 6]],
[IndexError, "Please ensure two theta array and intensity array are the same length."],
),
# UC2: user specified an invalid tth value of > 180 degrees
# 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, 181]],
"Two theta exceeds 180 degrees. Please check the input values for errors.",
[4 * np.pi, [0, 30, 60, 90, 120], [1, 2, 3, 4, 5, 6]],
[IndexError, "Please ensure two theta array and intensity array are the same length."],
),
# UC3: user did not specify wavelength and specified invalid tth values
# UC5: user specified a non-numeric value in two theta array (without wavelength)
(
[None, [0, 30, 60, 90, 120, 181]],
"Wavelength is not specified. Please provide a valid wavelength, "
"e.g., DiffractionObject(wavelength=0.71).",
[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."],
),
# UC4: user specified an empty two theta array
([4 * np.pi, []], "Two theta array is empty. Please provide valid two theta values."),
# UC5: user specified a non-numeric value in two theta array
# UC6: user specified a non-numeric value in two theta array (with wavelength)
(
[4 * np.pi, [0, 30, 60, 90, 120, "invalid"]],
"Invalid value found in two theta array. Please ensure all values are numeric.",
[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])
setattr(actual, "on_tth", [inputs[1], [1, 2, 3, 4, 5, 6]])
with pytest.raises(ValueError, match=expected):
actual.on_tth = [inputs[1], inputs[2]]
with pytest.raises(expected[0], match=expected[1]):
actual.tth_to_q()


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