Merge pull request #178 from yucongalicechen/q-tth

q_to_tth & tth_to_q

Author: sbillinge

Diff for: doc/source/examples/diffractionobjectsexample.rst

@@ -0,0 +1,34 @@
+.. _Diffraction Objects Example:
+
+:tocdepth: -1
+
+Diffraction Objects Example
+###########################
+
+This example will demonstrate how to use the ``DiffractionObject`` class in the
+``diffpy.utils.scattering_objects.diffraction_objects`` module to process and analyze diffraction data.
+
+1) Assuming we have created a ``DiffractionObject`` called my_diffraction_pattern from a measured diffraction pattern,
+   and we have specified the wavelength (see Section ??, to be added),
+   we can use the ``q_to_tth`` and ``tth_to_q`` functions to convert between q and two-theta. ::
+
+    # Example: convert q to tth
+    my_diffraction_pattern.on_q = [[0, 0.2, 0.4, 0.6, 0.8, 1], [1, 2, 3, 4, 5, 6]]
+    my_diffraction_pattern.q_to_tth()
+
+   This function will convert your provided q array and return a two theta array in degrees.
+   To load the converted array, you can either call ``test.q_to_tth()`` or ``test.on_q[0]``. ::
+
+    # Example: convert tth to q
+    from diffpy.utils.scattering_objects.diffraction_objects import DiffractionObject
+    my_diffraction_pattern.on_tth = [[0, 30, 60, 90, 120, 180], [1, 2, 3, 4, 5, 6]]
+    my_diffraction_pattern.tth_to_q()
+
+   Similarly, to load the converted array, you can either call ``test.tth_to_q()`` or ``test.on_tth[0]``.
+
+2) Both functions require a wavelength to perform conversions. Without a wavelength, they will return empty arrays.
+   Therefore, we strongly encourage you to specify a wavelength when using these functions. ::
+
+    # Example: without wavelength specified
+    my_diffraction_pattern.on_q = [[0, 0.2, 0.4, 0.6, 0.8, 1], [1, 2, 3, 4, 5, 6]]
+    my_diffraction_pattern.q_to_tth()    # returns an empty array

Diff for: doc/source/utilities/diffractionobjectsutility.rst

@@ -0,0 +1,13 @@
+.. _Diffraction Objects Utility:
+
+Diffraction Objects Utility
+===========================
+
+The ``diffpy.utils.scattering_objects.diffraction_objects`` module provides functions
+for managing and analyzing diffraction data, including angle-space conversions
+and interactions between diffraction data.
+
+These functions help developers standardize diffraction data and update the arrays
+in the associated ``DiffractionObject``, enabling easier analysis and further processing.
+
+For a more in-depth tutorial for how to use these functions, click :ref:`here <Diffraction Objects Example>`.

Diff for: news/tth-q.rst

@@ -0,0 +1,23 @@
+**Added:**
+
+* functionality to raise useful warning and error messages during angular conversion between two theta and q
+
+**Changed:**
+
+* <news item>
+
+**Deprecated:**
+
+* <news item>
+
+**Removed:**
+
+* <news item>
+
+**Fixed:**
+
+* <news item>
+
+**Security:**
+
+* <news item>

Diff for: src/diffpy/utils/scattering_objects/diffraction_objects.py

@@ -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.
@@ -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):
@@ -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):
+            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)

Diff for: tests/diffpy/utils/scattering_objects/test_diffraction_objects.py

@@ -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
@@ -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. "
+            "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)