Unit overhaul 3/6: Store Q as a scipp Variable in 1/angstrom

src/easydynamics/sample_model/diffusion_model/brownian_translational_diffusion.py

@@ -245,6 +245,7 @@ def create_component_collections(
             self._component_collections = []
             return self._component_collections
 
+        Q = Q.values
         component_collection_list = [None] * len(Q)
         # In more complex models, this is used to scale the area of the
         # Lorentzians and the delta function.

src/easydynamics/sample_model/diffusion_model/delta_lorentz.py

@@ -469,6 +469,7 @@ def create_component_collections(
         Q = self.Q
         if Q is None:
             return []
+        Q = Q.values
 
         if self._allow_Q_variation['A_0'] is True:
             A_0_list, A_1_list = self._create_A0_A1_parameter_lists(self.A_0)
@@ -812,7 +813,7 @@ def _create_A0_A1_parameter_lists(
         """
         A_0_list = []
         A_1_list = []
-        for _ in self.Q:
+        for _ in range(len(self.Q)):
             a0 = Parameter(
                 name='A_0',
                 value=float(A_0.value),
@@ -858,7 +859,7 @@ def _create_lorentzian_width_parameter_list(
                 min=MINIMUM_WIDTH,
                 unit=self.unit,
             )
-            for _ in self.Q
+            for _ in range(len(self.Q))
         ]
 
     # ------------------------------------------------------------------

src/easydynamics/sample_model/diffusion_model/diffusion_model_base.py

@@ -146,14 +146,14 @@ def scale(self, scale: Numeric) -> None:
         self._scale.value = float(scale)
 
     @property
-    def Q(self) -> np.ndarray | None:
+    def Q(self) -> sc.Variable | None:
         """
         Get the Q values of the SampleModel.
 
         Returns
         -------
-        np.ndarray | None
-            The Q values of the SampleModel, or None if not set.
+        sc.Variable | None
+            The Q values of the SampleModel in 1/angstrom, or None if not set.
         """
         return self._Q
 
@@ -185,7 +185,7 @@ def Q(self, value: Q_type | None) -> None:
             self._on_Q_change()
             return
 
-        if len(old_Q) != len(new_Q) or not np.allclose(old_Q, new_Q):
+        if len(old_Q) != len(new_Q) or not sc.allclose(old_Q, new_Q):
             raise ValueError(
                 'New Q values are not similar to the old ones. '
                 'To change Q values, first run clear_Q().'
@@ -483,7 +483,7 @@ def _ensure_Q(self, Q: Q_type) -> np.ndarray:
         if Q is None:
             raise ValueError('Q must be provided either as an argument or set in the model.')
 
-        return _validate_and_convert_Q(Q)
+        return _validate_and_convert_Q(Q).values
 
     # ------------------------------------------------------------------
     # dunder methods

src/easydynamics/sample_model/diffusion_model/jump_translational_diffusion.py

@@ -311,6 +311,7 @@ def create_component_collections(
             self._component_collections = []
             return self._component_collections
 
+        Q = Q.values
         component_collection_list = [None] * len(Q)
         # In more complex models, this is used to scale the area of the
         # Lorentzians and the delta function.

src/easydynamics/sample_model/instrument_model.py

@@ -3,7 +3,6 @@
 
 from copy import copy
 
-import numpy as np
 import scipp as sc
 from easyscience.base_classes.new_base import NewBase
 from easyscience.variable import Parameter
@@ -217,14 +216,14 @@ def background_model(self, value: BackgroundModel) -> None:
         self._on_background_model_change()
 
     @property
-    def Q(self) -> np.ndarray | None:
+    def Q(self) -> sc.Variable | None:
         """
         Get the Q values of the InstrumentModel.
 
         Returns
         -------
-        np.ndarray | None
-            The Q values of the InstrumentModel, or None if not set.
+        sc.Variable | None
+            The Q values of the InstrumentModel in 1/angstrom, or None if not set.
         """
         return self._Q
 
@@ -257,7 +256,7 @@ def Q(self, value: Q_type | None) -> None:
             self._on_Q_change()
             return
 
-        if len(old_Q) != len(new_Q) or not np.allclose(old_Q, new_Q):
+        if len(old_Q) != len(new_Q) or not sc.allclose(old_Q, new_Q):
             raise ValueError(
                 'New Q values are not similar to the old ones. '
                 'To change Q values, first run clear_Q().'
@@ -532,7 +531,7 @@ def _generate_energy_offsets(self) -> None:
             self._energy_offsets = []
             return
 
-        self._energy_offsets = [copy(self._energy_offset) for _ in self._Q]
+        self._energy_offsets = [copy(self._energy_offset) for _ in range(len(self._Q))]
 
     def _on_Q_change(self) -> None:
         """Handle changes to the Q values."""

src/easydynamics/sample_model/model_base.py

@@ -187,14 +187,14 @@ def component_collections_is_dirty(self) -> bool:
         return self._component_collections_is_dirty
 
     @property
-    def Q(self) -> np.ndarray | None:
+    def Q(self) -> sc.Variable | None:
         """
         Get the Q values of the SampleModel.
 
         Returns
         -------
-        np.ndarray | None
-            The Q values of the SampleModel, or None if not set.
+        sc.Variable | None
+            The Q values of the SampleModel in 1/angstrom, or None if not set.
         """
         return self._Q
 
@@ -226,7 +226,7 @@ def Q(self, value: Q_type | None) -> None:
             self._on_Q_change()
             return
 
-        if len(old_Q) != len(new_Q) or not np.allclose(old_Q, new_Q):
+        if len(old_Q) != len(new_Q) or not sc.allclose(old_Q, new_Q):
             raise ValueError(
                 'New Q values are not similar to the old ones. '
                 'To change Q values, first run clear_Q().'
@@ -377,7 +377,7 @@ def _generate_component_collections(self) -> None:
             return
 
         self._component_collections = []
-        for _ in self.Q:
+        for _ in range(len(self.Q)):
             self._component_collections.append(copy(self._components))
 
     def _on_Q_change(self) -> None:
@@ -405,6 +405,6 @@ def __repr__(self) -> str:
             f'{self.__class__.__name__}('
             f'unique_name={self.unique_name!r}, '
             f'unit={self.unit}, '
-            f'Q={self.Q}, '
+            f'Q={None if self.Q is None else self.Q.values}, '
             f'components={self.components})'
         )

src/easydynamics/utils/utils.py

@@ -164,14 +164,17 @@ def energy_to_scipp(energy: np.ndarray, unit: str | sc.Unit) -> sc.Variable:
 
 def _validate_and_convert_Q(
     Q: np.ndarray | Numeric | list | ArrayLike | sc.Variable | None,
-) -> np.ndarray | None:
+) -> sc.Variable | None:
     """
-    Validate and convert Q to a numpy array.
+    Validate and convert Q to a scipp Variable in 1/angstrom.
+
+    Numbers, lists, and numpy arrays are assumed to be in 1/angstrom. Scipp Variables may be in any
+    unit convertible to 1/angstrom and are converted.
 
     Parameters
     ----------
     Q : np.ndarray | Numeric | list | ArrayLike | sc.Variable | None
-        Scattering vector values in 1/angstrom.
+        Scattering vector values.
 
     Raises
     ------
@@ -183,8 +186,8 @@ def _validate_and_convert_Q(
 
     Returns
     -------
-    np.ndarray | None
-        Q as a np.ndarray or None if Q is None.
+    sc.Variable | None
+        Q as a sc.Variable with dimension 'Q' and unit 1/angstrom, or None if Q is None.
     """
     if Q is None:
         return None
@@ -199,13 +202,13 @@ def _validate_and_convert_Q(
         if Q.ndim > 1:
             raise ValueError('Q must be a 1-dimensional array.')
 
-        Q = sc.array(dims=['Q'], values=Q, unit='1/angstrom')
+        Q = sc.array(dims=['Q'], values=Q, unit=CANONICAL_Q_UNIT)
 
     if isinstance(Q, sc.Variable):
         if Q.dims != ('Q',):
             raise ValueError("Q must have a single dimension named 'Q'.")
-        Q = Q.to(unit='1/angstrom')
-    return Q.values
+        Q = Q.to(unit=CANONICAL_Q_UNIT)
+    return Q
 
 
 def _validate_unit(unit: str | sc.Unit | None) -> sc.Unit | None:

tests/unit/easydynamics/analysis/test_analysis_base.py

@@ -501,8 +501,8 @@ def test_on_experiment_changed_updates_Q(self, analysis_base):
             # EXPECT
             # assert that the Q attribute was set
             np.testing.assert_array_equal(analysis_base.Q, fake_Q)
-            np.testing.assert_array_equal(analysis_base.sample_model.Q, fake_Q)
-            np.testing.assert_array_equal(analysis_base.instrument_model.Q, fake_Q)
+            np.testing.assert_array_equal(analysis_base.sample_model.Q.values, fake_Q)
+            np.testing.assert_array_equal(analysis_base.instrument_model.Q.values, fake_Q)
 
     def test_on_sample_model_changed_updates_Q(self, analysis_base):
         # WHEN
@@ -518,7 +518,7 @@ def test_on_sample_model_changed_updates_Q(self, analysis_base):
             analysis_base._on_sample_model_changed()
 
             # EXPECT
-            np.testing.assert_array_equal(analysis_base.sample_model.Q, fake_Q)
+            np.testing.assert_array_equal(analysis_base.sample_model.Q.values, fake_Q)
 
     def test_on_instrument_model_changed_updates_Q(self, analysis_base):
         fake_Q = [1, 2, 3]
@@ -530,7 +530,7 @@ def test_on_instrument_model_changed_updates_Q(self, analysis_base):
             mock_Q.return_value = fake_Q
 
             analysis_base._on_instrument_model_changed()
-            np.testing.assert_array_equal(analysis_base.instrument_model.Q, fake_Q)
+            np.testing.assert_array_equal(analysis_base.instrument_model.Q.values, fake_Q)
 
     def test_repr(self, analysis_base):
         # WHEN

tests/unit/easydynamics/sample_model/diffusion_model/test_delta_lorentz.py

@@ -404,7 +404,7 @@ def test_calculate_EISF_with_Q(self, delta_lorentz_model_with_Q):
         for i in range(len(eisf)):
             expected = delta_lorentz_model_with_Q._A_0_list[i].value * np.exp(
                 -delta_lorentz_model_with_Q.mean_u_squared.value
-                * delta_lorentz_model_with_Q.Q[i] ** 2
+                * delta_lorentz_model_with_Q.Q.values[i] ** 2
             )
             assert eisf[i] == pytest.approx(expected)
 
@@ -428,7 +428,7 @@ def test_calculate_QISF_with_Q(self, delta_lorentz_model_with_Q):
         for i in range(len(qisf)):
             expected = delta_lorentz_model_with_Q._A_1_list[i].value * np.exp(
                 -delta_lorentz_model_with_Q.mean_u_squared.value
-                * delta_lorentz_model_with_Q.Q[i] ** 2
+                * delta_lorentz_model_with_Q.Q.values[i] ** 2
             )
 
             assert qisf[i] == pytest.approx(expected)

tests/unit/easydynamics/sample_model/diffusion_model/test_diffusion_model_base.py

@@ -3,6 +3,7 @@
 
 import numpy as np
 import pytest
+import scipp as sc
 from easyscience.variable.parameter import Parameter
 
 from easydynamics.sample_model.diffusion_model.diffusion_model_base import DiffusionModelBase
@@ -131,7 +132,9 @@ def test_Q_property(self, diffusion_model):
         diffusion_model.Q = [1.0, 2.0, 3.0]
 
         # EXPECT
-        np.testing.assert_allclose(diffusion_model.Q, [1.0, 2.0, 3.0])
+        assert isinstance(diffusion_model.Q, sc.Variable)
+        assert diffusion_model.Q.unit == sc.Unit('1/angstrom')
+        np.testing.assert_allclose(diffusion_model.Q.values, [1.0, 2.0, 3.0])
 
         # THEN EXPECT
         with pytest.raises(ValueError, match=r'New Q values are not similar to the old ones'):
@@ -147,6 +150,16 @@ def test_Q_property(self, diffusion_model):
         # EXPECT
         assert diffusion_model.Q is None
 
+    def test_Q_setter_accepts_equivalent_scipp_Q_in_other_unit(self, diffusion_model):
+        # WHEN
+        diffusion_model.Q = [1.0, 2.0, 3.0]
+
+        # THEN: the same Q in 1/nm is equivalent after conversion, so no error is raised
+        diffusion_model.Q = sc.Variable(dims=['Q'], values=[10.0, 20.0, 30.0], unit='1/nm')
+
+        # EXPECT
+        np.testing.assert_allclose(diffusion_model.Q.values, [1.0, 2.0, 3.0])
+
     def test_repr(self, diffusion_model):
         # WHEN THEN
         repr_str = repr(diffusion_model)

tests/unit/easydynamics/sample_model/test_background_model.py

@@ -45,7 +45,7 @@ def test_init(self, background_model):
         assert model.display_name == 'InitModel'
         assert model.unit == 'meV'
         assert len(model.components) == 2
-        np.testing.assert_array_equal(model.Q, np.array([1.0, 2.0, 3.0]))
+        np.testing.assert_array_equal(model.Q.values, np.array([1.0, 2.0, 3.0]))
 
     @pytest.mark.parametrize(
         'invalid_component, expected_error_msg',

tests/unit/easydynamics/sample_model/test_instrument_model.py

@@ -68,12 +68,12 @@ def test_init(self, instrument_model):
 
         # EXPECT
         assert model.display_name == 'TestInstrumentModel'
-        np.testing.assert_array_equal(model.Q, np.array([1.0, 2.0, 3.0]))
+        np.testing.assert_array_equal(model.Q.values, np.array([1.0, 2.0, 3.0]))
         assert isinstance(model.background_model, BackgroundModel)
         assert isinstance(model.resolution_model, ResolutionModel)
-        np.testing.assert_array_equal(model.background_model.Q, np.array([1.0, 2.0, 3.0]))
-        np.testing.assert_array_equal(model.resolution_model.Q, np.array([1.0, 2.0, 3.0]))
-        np.testing.assert_array_equal(model.Q, np.array([1.0, 2.0, 3.0]))
+        np.testing.assert_array_equal(model.background_model.Q.values, np.array([1.0, 2.0, 3.0]))
+        np.testing.assert_array_equal(model.resolution_model.Q.values, np.array([1.0, 2.0, 3.0]))
+        np.testing.assert_array_equal(model.Q.values, np.array([1.0, 2.0, 3.0]))
 
     def test_init_defaults(self):
         # WHEN THEN
@@ -441,8 +441,12 @@ def test_Q_setter(self, instrument_model_without_Q):
 
         # EXPECT
         assert instrument_model_without_Q._energy_offsets_is_dirty is True
-        np.testing.assert_array_equal(instrument_model_without_Q.background_model.Q, first_new_Q)
-        np.testing.assert_array_equal(instrument_model_without_Q.resolution_model.Q, first_new_Q)
+        np.testing.assert_array_equal(
+            instrument_model_without_Q.background_model.Q.values, first_new_Q
+        )
+        np.testing.assert_array_equal(
+            instrument_model_without_Q.resolution_model.Q.values, first_new_Q
+        )
 
         # THEN
         new_Q = np.array([4.0, 5.0, 6.0])
@@ -457,17 +461,25 @@ def test_Q_setter(self, instrument_model_without_Q):
 
         # EXPECT
         # Q values remain unchanged
-        np.testing.assert_array_equal(instrument_model_without_Q.background_model.Q, first_new_Q)
-        np.testing.assert_array_equal(instrument_model_without_Q.resolution_model.Q, first_new_Q)
+        np.testing.assert_array_equal(
+            instrument_model_without_Q.background_model.Q.values, first_new_Q
+        )
+        np.testing.assert_array_equal(
+            instrument_model_without_Q.resolution_model.Q.values, first_new_Q
+        )
 
         # THEN - set Q to an equivalent scipp Variable; values match so should be accepted
         new_Q = sc.Variable(dims=['Q'], values=[1.0, 2.0, 3.0], unit='1/angstrom')
         instrument_model_without_Q.Q = new_Q
 
         # EXPECT - Q propagated to child models, offsets marked dirty again
         assert instrument_model_without_Q._energy_offsets_is_dirty is True
-        np.testing.assert_array_equal(instrument_model_without_Q.background_model.Q, first_new_Q)
-        np.testing.assert_array_equal(instrument_model_without_Q.resolution_model.Q, first_new_Q)
+        np.testing.assert_array_equal(
+            instrument_model_without_Q.background_model.Q.values, first_new_Q
+        )
+        np.testing.assert_array_equal(
+            instrument_model_without_Q.resolution_model.Q.values, first_new_Q
+        )
 
     def test_fix_and_free_offset(self, instrument_model):
         # WHEN

tests/unit/easydynamics/sample_model/test_model_base.py

@@ -51,7 +51,7 @@ def test_init(self, model_base):
         assert model.display_name == 'InitModel'
         assert model.unit == 'meV'
         assert len(model.components) == 2
-        np.testing.assert_array_equal(model.Q, np.array([1.0, 2.0, 3.0]))
+        np.testing.assert_array_equal(model.Q.values, np.array([1.0, 2.0, 3.0]))
 
     def test_init_raises_with_invalid_components(self):
         # WHEN / THEN / EXPECT
@@ -352,7 +352,7 @@ def test_Q_setter_when_current_Q_is_none(self, model_base):
         model_base.Q = new_Q
 
         # EXPECT
-        np.testing.assert_array_equal(model_base.Q, np.array(new_Q))
+        np.testing.assert_array_equal(model_base.Q.values, np.array(new_Q))
 
     def test_clear_Q(self, model_base):
         # WHEN