diff --git a/docs/docs/tutorials/tutorial1_brownian.ipynb b/docs/docs/tutorials/tutorial1_brownian.ipynb index 913b72a9..1eaed39c 100644 --- a/docs/docs/tutorials/tutorial1_brownian.ipynb +++ b/docs/docs/tutorials/tutorial1_brownian.ipynb @@ -366,7 +366,7 @@ "id": "927b8fb5", "metadata": {}, "source": [ - "We also create a new instrument_model and attach it to our analysis. We want to use the resolutin that we determined from the vanadium data. Ideally, we'd just attach it to the instrument model like before. However, this is currently not possible due to a small issue in EasyDynamics that will be fixed asap. For now, we need to hack it a bit." + "We also create a new instrument_model and attach it to our analysis, giving it the resolution model determined in the vanadium analysis. " ] }, { @@ -378,20 +378,15 @@ "source": [ "instrument_model = InstrumentModel(\n", " background_model=background_model,\n", + " resolution_model=vanadium_analysis.instrument_model.resolution_model,\n", ")\n", + "instrument_model.resolution_model.fix_all_parameters()\n", "\n", "diffusion_analysis = Analysis(\n", " display_name='Diffusion Analysis',\n", " experiment=diffusion_experiment,\n", " sample_model=sample_model,\n", " instrument_model=instrument_model,\n", - ")\n", - "\n", - "# We need to hack in the resolution model from the vanadium analysis,\n", - "# since the setters and getters overwrite the model. This will be fixed\n", - "# asap.\n", - "diffusion_analysis.instrument_model._resolution_model = (\n", - " vanadium_analysis.instrument_model.resolution_model\n", ")" ] }, @@ -403,17 +398,6 @@ "We don't want to fit our resolution anymore, so we fix all the parameters in it." ] }, - { - "cell_type": "code", - "execution_count": null, - "id": "18e2f0bf", - "metadata": {}, - "outputs": [], - "source": [ - "# We fix all parameters of the resolution model.\n", - "diffusion_analysis.instrument_model.resolution_model.fix_all_parameters()" - ] - }, { "cell_type": "markdown", "id": "e366a05d", @@ -506,10 +490,19 @@ " diffusion_models=diffusion_model,\n", ")\n", "\n", - "background_model = BackgroundModel(components=Polynomial(coefficients=[0.001]))\n", - "\n", + "background_model = BackgroundModel(components=Polynomial(coefficients=[0.001]))" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "48370156", + "metadata": {}, + "outputs": [], + "source": [ "instrument_model = InstrumentModel(\n", " background_model=background_model,\n", + " resolution_model=vanadium_analysis.instrument_model.resolution_model,\n", ")" ] }, @@ -518,7 +511,7 @@ "id": "8bb4abe9", "metadata": {}, "source": [ - "We attach all our models to a new `Analysis` object, again being mindful that we need to hack in the resolution. I promise this will be fixed soon!" + "We attach all our models to a new `Analysis` object." ] }, { @@ -535,12 +528,6 @@ " instrument_model=instrument_model,\n", ")\n", "\n", - "# We again need to hack in the resolution model from the vanadium\n", - "# analysis, since the setters and getters overwrite the model. This will\n", - "# be fixed asap.\n", - "diffusion_model_analysis.instrument_model._resolution_model = (\n", - " vanadium_analysis.instrument_model.resolution_model\n", - ")\n", "diffusion_model_analysis.instrument_model.resolution_model.fix_all_parameters()" ] }, diff --git a/docs/docs/tutorials/tutorial2_nanoparticles.ipynb b/docs/docs/tutorials/tutorial2_nanoparticles.ipynb index f0e01e80..28169b83 100644 --- a/docs/docs/tutorials/tutorial2_nanoparticles.ipynb +++ b/docs/docs/tutorials/tutorial2_nanoparticles.ipynb @@ -275,14 +275,16 @@ "background_model.components = polynomial\n", "\n", "\n", - "instrument_model = InstrumentModel(background_model=background_model)\n", + "instrument_model = InstrumentModel(\n", + " background_model=background_model,\n", + " resolution_model=res_analysis.instrument_model.resolution_model,\n", + ")\n", + "instrument_model.resolution_model.fix_all_parameters()\n", "\n", "\n", "analysis = Analysis(\n", " experiment=experiment, sample_model=sample_model, instrument_model=instrument_model\n", ")\n", - "analysis.instrument_model._resolution_model = res_analysis.instrument_model.resolution_model\n", - "analysis.instrument_model.resolution_model.fix_all_parameters()\n", "\n", "analysis.plot_data_and_model(logy=True)" ] @@ -410,15 +412,16 @@ "polynomial = Polynomial(coefficients=[0.15])\n", "background_model.components = polynomial\n", "\n", - "instrument_model = InstrumentModel(background_model=background_model)\n", - "\n", + "instrument_model = InstrumentModel(\n", + " background_model=background_model,\n", + " resolution_model=res_analysis.instrument_model.resolution_model,\n", + ")\n", + "instrument_model.resolution_model.fix_all_parameters()\n", "\n", "# Create the analysis object\n", "mag_analysis = Analysis(\n", " experiment=experiment, sample_model=mag_sample_model, instrument_model=instrument_model\n", - ")\n", - "mag_analysis.instrument_model._resolution_model = res_analysis.instrument_model.resolution_model\n", - "mag_analysis.instrument_model.resolution_model.fix_all_parameters()" + ")" ] }, { @@ -614,7 +617,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - 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version: 0.15.6 - sha256: 98893c4c0aadc8e448cfa315bd0cc343a5323d740fe5f28ef8a3f9e21b381f7e + version: 0.15.7 + sha256: dce0896488562f09a27b9c91b1f58a097457143931f3c4d519690dea54e624c5 requires_python: '>=3.7' - pypi: https://files.pythonhosted.org/packages/07/d9/5c57a38ebf73df9f1992ce7c6830efc4b341cba8dfbc546e1a40155e922c/scipp-26.3.1-cp312-cp312-macosx_14_0_x86_64.whl name: scipp diff --git a/src/easydynamics/experiment/experiment.py b/src/easydynamics/experiment/experiment.py index a86c8ffd..cfe7dcfb 100644 --- a/src/easydynamics/experiment/experiment.py +++ b/src/easydynamics/experiment/experiment.py @@ -342,6 +342,10 @@ def plot_data(self, slicer: bool = False, **kwargs: dict) -> None: plot_kwargs_defaults = { 'title': self.display_name, } + + if slicer: + plot_kwargs_defaults['keep'] = 'energy' + # Overwrite defaults with any user-provided kwargs plot_kwargs_defaults.update(kwargs) if slicer: diff --git a/src/easydynamics/sample_model/instrument_model.py b/src/easydynamics/sample_model/instrument_model.py index 3f451de9..668e1764 100644 --- a/src/easydynamics/sample_model/instrument_model.py +++ b/src/easydynamics/sample_model/instrument_model.py @@ -173,14 +173,33 @@ def Q(self) -> np.ndarray | None: @Q.setter def Q(self, value: Q_type | None) -> None: - """Set the Q values of the InstrumentModel. + """Set the Q values of the InstrumentModel. If Q is already set, + it raises an error if the new Q values are not similar to the + old ones to prevent accidental changes to the background and + resolution models. To change Q values, first run clear_Q(). Args: - value (Q_type | None): The new Q values for the - InstrumentModel. + value (Q_type | None): The new Q values to set. + + Raises: + ValueError: If the new Q values are not similar to the old + ones when Q is not None """ - self._Q = _validate_and_convert_Q(value) - self._on_Q_change() + if value is None: + return + old_Q = self._Q + new_Q = _validate_and_convert_Q(value) + + if old_Q is None: + self._Q = new_Q + self._on_Q_change() + return + + if len(old_Q) != len(new_Q) or not np.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().' + ) @property def unit(self) -> str | sc.Unit: @@ -242,6 +261,27 @@ def energy_offset(self, value: Numeric) -> None: # Other methods # -------------------------------------------------------------- + def clear_Q(self, confirm: bool = False) -> None: + """Clear the Q values of the InstrumentModel and any associated + ResolutionModel and BackgroundModel, removing all component + collections and their associated Parameters. + + Args: + confirm (bool, default=False): Confirmation to clear Q + values. + + Raises: + ValueError: If confirm is not True. + """ + if not confirm: + raise ValueError( + 'Clearing Q values requires confirmation. Set confirm=True to proceed.' + ) + self._Q = None + self.background_model.clear_Q(confirm=True) + self.resolution_model.clear_Q(confirm=True) + self._on_Q_change() + def convert_unit(self, unit_str: str | sc.Unit) -> None: """Convert the unit of the InstrumentModel. @@ -348,8 +388,8 @@ def _generate_energy_offsets(self) -> None: def _on_Q_change(self) -> None: """Handle changes to the Q values.""" self._generate_energy_offsets() - self._resolution_model.Q = self._Q - self._background_model.Q = self._Q + self.resolution_model.Q = self.Q + self.background_model.Q = self.Q def _on_energy_offset_change(self) -> None: """Handle changes to the energy offset.""" @@ -358,11 +398,11 @@ def _on_energy_offset_change(self) -> None: def _on_resolution_model_change(self) -> None: """Handle changes to the resolution model.""" - self._resolution_model.Q = self._Q + self.resolution_model.Q = self.Q def _on_background_model_change(self) -> None: """Handle changes to the background model.""" - self._background_model.Q = self._Q + self.background_model.Q = self.Q # ------------------------------------------------------------- # Dunder methods diff --git a/src/easydynamics/sample_model/model_base.py b/src/easydynamics/sample_model/model_base.py index e92e5861..89ebb1f5 100644 --- a/src/easydynamics/sample_model/model_base.py +++ b/src/easydynamics/sample_model/model_base.py @@ -231,23 +231,48 @@ def Q(self) -> np.ndarray | None: @Q.setter def Q(self, value: Q_type | None) -> None: - """Set the Q values of the SampleModel. + """Set the Q values of the SampleModel. If Q is already set, it + throws an error if the new Q values are not similar to the old + ones. To change Q values, first run clear_Q(). Args: - value (Q_type | None): The new Q values to set. If None, Q - will be unset. + value (Q_type | None): The new Q values to set. + + Raises: + ValueError: If the new Q values are not similar to the old + ones when Q is already set. """ + if value is None: + return old_Q = self._Q new_Q = _validate_and_convert_Q(value) - if ( - old_Q is not None - and new_Q is not None - and len(old_Q) == len(new_Q) - and all(np.isclose(old_Q, new_Q)) - ): - return # No change in Q, so do nothing - self._Q = new_Q + if old_Q is None: + self._Q = new_Q + self._on_Q_change() + return + + if len(old_Q) != len(new_Q) or not np.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().' + ) + + def clear_Q(self, confirm: bool = False) -> None: + """Clear the Q values of the SampleModel, removing all component + collections and their associated Parameters. + + Args: + confirm (bool, default=False): Confirmation to clear Q values. + + Raises: + ValueError: If confirm is not True. + """ + if not confirm: + raise ValueError( + 'Clearing Q values requires confirmation. Set confirm=True to proceed.' + ) + self._Q = None self._on_Q_change() # ------------------------------------------------------------------ diff --git a/tests/unit/easydynamics/analysis/test_analysis.py b/tests/unit/easydynamics/analysis/test_analysis.py index 6fafc09a..b62dc2b6 100644 --- a/tests/unit/easydynamics/analysis/test_analysis.py +++ b/tests/unit/easydynamics/analysis/test_analysis.py @@ -476,10 +476,10 @@ def test_plot_parameters(self, analysis): # and that we return the figure assert result is fake_fig - def test_on_experiment_changed(self, analysis): + def test_on_experiment_changed_similar_Q(self, analysis): # WHEN # Create a new experiment. - Q = sc.array(dims=['Q'], values=[2, 3, 4], unit='1/Angstrom') + Q = sc.array(dims=['Q'], values=[1, 2, 3], unit='1/Angstrom') energy = sc.array(dims=['energy'], values=[20.0, 30.0, 40.0], unit='meV') data = sc.array( dims=['Q', 'energy'], @@ -491,15 +491,37 @@ def test_on_experiment_changed(self, analysis): new_experiment = Experiment(data=data_array) - # THEN (this call _on_experiment_changed internally) + # THEN (this calls _on_experiment_changed internally) analysis.experiment = new_experiment # EXPECT - assert np.array_equal(analysis.Q.values, [2, 3, 4]) + assert np.array_equal(analysis.Q.values, [1, 2, 3]) assert len(analysis.analysis_list) == 3 for analysis1d in analysis.analysis_list: assert analysis1d.experiment is new_experiment + def test_on_experiment_changed_different_Q_raises(self, analysis): + # WHEN + # Create a new experiment with different Q values. + Q = sc.array(dims=['Q'], values=[4, 5, 6], unit='1/Angstrom') + energy = sc.array(dims=['energy'], values=[20.0, 30.0, 40.0], unit='meV') + data = sc.array( + dims=['Q', 'energy'], + values=[[2.0, 3.0, 4.0], [5.0, 6.0, 7.0], [8.0, 9.0, 10.0]], + variances=[[0.1, 0.2, 0.3], [0.4, 0.5, 0.6], [0.7, 0.8, 0.9]], + ) + + data_array = sc.DataArray(data=data, coords={'Q': Q, 'energy': energy}) + + new_experiment = Experiment(data=data_array) + + # THEN / EXPECT + with pytest.raises( + ValueError, + match='New Q values are not similar to the old ones', + ): + analysis.experiment = new_experiment + def test_on_sample_model_changed(self, analysis): # WHEN # Create a new sample model. diff --git a/tests/unit/easydynamics/experiment/test_experiment.py b/tests/unit/easydynamics/experiment/test_experiment.py index 84d09059..b6efee97 100644 --- a/tests/unit/easydynamics/experiment/test_experiment.py +++ b/tests/unit/easydynamics/experiment/test_experiment.py @@ -351,10 +351,31 @@ def test_plot_data_success(self, experiment): # EXPECT mock_plot.assert_called_once() args, kwargs = mock_plot.call_args - assert sc.identical(args[0], experiment._data.transpose()) + assert sc.identical(args[0], experiment.data.transpose()) assert kwargs['title'] == f'{experiment.display_name}' assert result == mock_fig + def test_plot_data_slicer_success(self, experiment): + "Test plotting data successfully when in notebook environment" + # WHEN + with ( + patch(f'{Experiment.__module__}._in_notebook', return_value=True), + patch('plopp.slicer') as mock_plot, + ): + mock_fig = MagicMock() + mock_plot.return_value = mock_fig + + # THEN + result = experiment.plot_data(slicer=True) + + # EXPECT + mock_plot.assert_called_once() + args, kwargs = mock_plot.call_args + assert sc.identical(args[0], experiment.data) + assert kwargs['title'] == f'{experiment.display_name}' + assert kwargs['keep'] == 'energy' + assert result == mock_fig + def test_plot_data_no_data_raises(self): "Test plotting data raises ValueError when no data is present" # WHEN diff --git a/tests/unit/easydynamics/sample_model/test_instrument_model.py b/tests/unit/easydynamics/sample_model/test_instrument_model.py index 69c46879..634dea8a 100644 --- a/tests/unit/easydynamics/sample_model/test_instrument_model.py +++ b/tests/unit/easydynamics/sample_model/test_instrument_model.py @@ -6,6 +6,7 @@ import numpy as np import pytest +import scipp as sc from easydynamics.sample_model import Gaussian from easydynamics.sample_model import Polynomial @@ -33,6 +34,21 @@ def instrument_model(self): return instrument_model + @pytest.fixture + def instrument_model_without_Q(self): + component1 = Polynomial(coefficients=[1.0, 2.0]) + background_model = BackgroundModel(components=component1) + + component2 = Gaussian() + resolution_model = ResolutionModel(components=component2) + + instrument_model_without_Q = InstrumentModel( + display_name='TestInstrumentModel', + background_model=background_model, + resolution_model=resolution_model, + ) + return instrument_model_without_Q + @pytest.fixture def resolution_model(self): component = Gaussian() @@ -143,23 +159,19 @@ def test_background_model_setter_raises(self, instrument_model): ): instrument_model.background_model = 123 - def test_Q_setter(self, instrument_model): - "Test that Q setter calls the appropriate methods." + def test_clear_Q(self, instrument_model): # WHEN - new_Q = np.array([4.0, 5.0, 6.0]) - - instrument_model._on_Q_change = MagicMock() + instrument_model.clear_Q(confirm=True) - # THEN EXPECT - with patch( - 'easydynamics.sample_model.instrument_model._validate_and_convert_Q', - return_value=new_Q, - ) as mock_validate: - instrument_model.Q = new_Q + # THEN / EXPECT + assert instrument_model.Q is None + assert instrument_model.background_model.Q is None + assert instrument_model.resolution_model.Q is None - np.testing.assert_array_equal(instrument_model.Q, new_Q) - mock_validate.assert_called_once_with(new_Q) - instrument_model._on_Q_change.assert_called_once() + def test_clear_Q_raises_without_confirm(self, instrument_model): + # WHEN / THEN / EXPECT + with pytest.raises(ValueError, match='Clearing Q values requires confirmation'): + instrument_model.clear_Q() def test_unit_setter_raises(self, instrument_model): # WHEN / THEN / EXPECT @@ -207,7 +219,7 @@ def test_get_energy_offset_at_Q_invalid_index_raises(self, instrument_model): def test_get_energy_offset_at_Q_no_Q_raises(self, instrument_model): # WHEN - instrument_model.Q = None + instrument_model.clear_Q(confirm=True) # THEN / EXPECT with pytest.raises( @@ -296,7 +308,7 @@ def test_get_all_variables(self, instrument_model): def test_get_all_variables_no_Q(self, instrument_model): # WHEN - instrument_model.Q = None + instrument_model.clear_Q(confirm=True) # THEN all_vars = instrument_model.get_all_variables() @@ -363,19 +375,44 @@ def test_generate_energy_offsets(self, instrument_model): assert offset.unit == instrument_model.unit assert offset.value == instrument_model.energy_offset.value - def test_on_Q_change(self, instrument_model): + def test_Q_setter(self, instrument_model_without_Q): # WHEN - instrument_model._generate_energy_offsets = MagicMock() - new_Q = np.array([1.0, 2.0, 3.0, 4.0]) + instrument_model_without_Q._generate_energy_offsets = MagicMock() + first_new_Q = np.array([1.0, 2.0, 3.0]) + + # THEN + instrument_model_without_Q.Q = first_new_Q + + # EXPECT + instrument_model_without_Q._generate_energy_offsets.assert_called_once() + 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) + + # THEN + new_Q = np.array([4.0, 5.0, 6.0]) + + # EXPECT + with pytest.raises(ValueError, match='New Q values are not similar to the old ones'): + instrument_model_without_Q.Q = new_Q + + # THEN + new_Q = None + instrument_model_without_Q.Q = new_Q + + # EXPECT + # No new calls to _generate_energy_offsets, and Q values remain unchanged + instrument_model_without_Q._generate_energy_offsets.assert_called_once() + 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) # THEN - instrument_model._Q = new_Q - instrument_model._on_Q_change() + new_Q = sc.Variable(dims=['Q'], values=[1.0, 2.0, 3.0], unit='1/angstrom') # EXPECT - instrument_model._generate_energy_offsets.assert_called_once() - instrument_model._background_model.Q = new_Q - instrument_model._resolution_model.Q = new_Q + # No new calls to _generate_energy_offsets, and Q values remain unchanged + instrument_model_without_Q._generate_energy_offsets.assert_called_once() + 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) def test_on_energy_offset_change(self, instrument_model): # WHEN diff --git a/tests/unit/easydynamics/sample_model/test_model_base.py b/tests/unit/easydynamics/sample_model/test_model_base.py index 9de4c138..d1ade1e3 100644 --- a/tests/unit/easydynamics/sample_model/test_model_base.py +++ b/tests/unit/easydynamics/sample_model/test_model_base.py @@ -5,6 +5,7 @@ import numpy as np import pytest +import scipp as sc from scipp import UnitError from easydynamics.sample_model import ComponentCollection @@ -304,14 +305,61 @@ def test_components_setter_invalid_raises(self, model_base): ): model_base.components = 'invalid_component' - def test_Q_setter(self, model_base): + def test_Q_setter_raises_if_Q_is_not_similar(self, model_base): + # WHEN / THEN / EXPECT + with pytest.raises(ValueError, match='New Q values are not similar to'): + model_base.Q = [10.0, 20.0, 30.0] + + @pytest.mark.parametrize( + 'new_Q', + [ + [1.0, 2.0, 3.0], + np.array([1.0, 2.0, 3.0]), + sc.Variable(dims=['Q'], values=[1.0, 2.0, 3.0], unit='1/angstrom'), + ], + ids=['list', 'numpy_array', 'scipp_variable'], + ) + def test_Q_setter_with_similar_Q(self, model_base, new_Q): # WHEN - new_Q = [0.5, 1.5, 2.5] + old_Q = model_base.Q + + # THEN model_base.Q = new_Q + # EXPECT + np.testing.assert_array_equal(model_base.Q, old_Q) + + def test_Q_setter_with_none(self, model_base): + # WHEN + model_base.Q = None + old_Q = model_base.Q + # THEN / EXPECT + assert model_base.Q is old_Q + + def test_Q_setter_when_current_Q_is_none(self, model_base): + # WHEN + model_base._Q = None + new_Q = [0.5, 1.5, 2.5] + + # THEN + model_base.Q = new_Q + + # EXPECT np.testing.assert_array_equal(model_base.Q, np.array(new_Q)) + def test_clear_Q(self, model_base): + # WHEN + model_base.clear_Q(confirm=True) + + # THEN / EXPECT + assert model_base.Q is None + + def test_clear_Q_raises_without_confirm(self, model_base): + # WHEN / THEN / EXPECT + with pytest.raises(ValueError, match='Clearing Q values requires confirmation'): + model_base.clear_Q() + def test_repr(self, model_base): # WHEN repr_str = repr(model_base)