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Merged
merged 11 commits into from
Nov 28, 2024
53 changes: 44 additions & 9 deletions src/diffpy/utils/scattering_objects/diffraction_objects.py
Original file line number Diff line number Diff line change
Expand Up @@ -17,6 +17,23 @@
"and specifying how to handle the mismatch."
)

wavelength_warning_emsg = (
"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, set "
"diffraction_object.wavelength = [number], "
"where diffraction_object is the variable name of you Diffraction Object, "
"and number is the wavelength in angstroms."
)

length_mismatch_emsg = "Please ensure {array_name} array and intensity array are of the same length."
non_numeric_value_emsg = "Invalid value found in {array_name} array. Please ensure all values are numeric."
invalid_tth_emsg = "Two theta exceeds 180 degrees. Please check the input values for errors."
invalid_q_or_wavelength_emsg = (
"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."
)


class Diffraction_object:
"""A class to represent and manipulate data associated with diffraction experiments.
Expand Down Expand Up @@ -763,25 +780,35 @@ def q_to_tth(self):

2\theta_n = 2 \arcsin\left(\frac{\lambda q}{4 \pi}\right)

Function adapted from scikit-beam. Thanks to those developers

Parameters
----------
q : array
An array of :math:`q` values
The array of :math:`q` values

wavelength : float
Wavelength of the incoming x-rays

Function adapted from scikit-beam. Thanks to those developers

Returns
-------
two_theta : array
An array of :math:`2\theta` values in radians
The array of :math:`2\theta` values in radians
"""
for i, value in enumerate(self.on_q[0]):
if not isinstance(value, (int, float)):
raise TypeError(non_numeric_value_emsg.format(array_name="q"))
if len(self.on_q[0]) != len(self.on_q[1]):
raise RuntimeError(length_mismatch_emsg.format(array_name="q"))
if self.wavelength is None:
warnings.warn(wavelength_warning_emsg, UserWarning)
return np.empty(0)
q = self.on_q[0]
q = np.asarray(q)
wavelength = float(self.wavelength)
pre_factor = wavelength / (4 * np.pi)
if np.any(np.abs(q * pre_factor) > 1):
raise ValueError(invalid_q_or_wavelength_emsg)
return np.rad2deg(2.0 * np.arcsin(q * pre_factor))

def tth_to_q(self):
Expand All @@ -800,25 +827,33 @@ def tth_to_q(self):

q = \frac{4 \pi \sin\left(\frac{2\theta}{2}\right)}{\lambda}


Function adapted from scikit-beam. Thanks to those developers.

Parameters
----------
two_theta : array
An array of :math:`2\theta` values in units of degrees
The array of :math:`2\theta` values in units of degrees

wavelength : float
Wavelength of the incoming x-rays

Function adapted from scikit-beam. Thanks to those developers.

Returns
-------
q : array
An array of :math:`q` values in the inverse of the units
The array of :math:`q` values in the inverse of the units
of ``wavelength``
"""
for i, value in enumerate(self.on_tth[0]):
if not isinstance(value, (int, float)):
raise TypeError(non_numeric_value_emsg.format(array_name="two theta"))
if len(self.on_tth[0]) != len(self.on_tth[1]):
raise RuntimeError(length_mismatch_emsg.format(array_name="two theta"))
two_theta = np.asarray(np.deg2rad(self.on_tth[0]))
if np.any(two_theta > np.pi):
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as above, I think this isn't doing quite what we want.

raise ValueError(invalid_tth_emsg)
if self.wavelength is None:
warnings.warn(wavelength_warning_emsg, UserWarning)
return np.empty(0)
wavelength = float(self.wavelength)
pre_factor = (4 * np.pi) / wavelength
return pre_factor * np.sin(two_theta / 2)
Expand Down
151 changes: 150 additions & 1 deletion tests/diffpy/utils/scattering_objects/test_diffraction_objects.py
Original file line number Diff line number Diff line change
Expand Up @@ -4,7 +4,7 @@
import pytest
from freezegun import freeze_time

from diffpy.utils.scattering_objects.diffraction_objects import DiffractionObject
from diffpy.utils.scattering_objects.diffraction_objects import DiffractionObject, wavelength_warning_emsg

params = [
( # Default
Expand Down Expand Up @@ -231,6 +231,155 @@ def test_diffraction_objects_equality(inputs1, inputs2, expected):
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. "
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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 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)
Expand Down
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