Allow normalising the resolution function

docs/docs/tutorials/tutorial1_brownian.ipynb

@@ -330,7 +330,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "diffusion_experiment.plot_data(slicer=True)"
+    "diffusion_experiment.plot_data(slicer=True, ymax=4)"
    ]
   },
   {
@@ -366,7 +366,7 @@
    "id": "927b8fb5",
    "metadata": {},
    "source": [
-    "We also create a new instrument_model and attach it to our analysis, giving it the resolution model determined in the vanadium analysis. "
+    "We also create a new instrument_model and attach it to our analysis, giving it the resolution model determined in the vanadium analysis. We further fix all parameters in the resolution model and normalize it."
    ]
   },
   {
@@ -381,6 +381,7 @@
     "    resolution_model=vanadium_analysis.instrument_model.resolution_model,\n",
     ")\n",
     "instrument_model.resolution_model.fix_all_parameters()\n",
+    "instrument_model.normalize_resolution()\n",
     "\n",
     "diffusion_analysis = Analysis(\n",
     "    display_name='Diffusion Analysis',\n",
@@ -565,7 +566,7 @@
    "outputs": [],
    "source": [
     "diffusion_model_analysis.fit(fit_method='simultaneous')\n",
-    "diffusion_model_analysis.plot_data_and_model()"
+    "diffusion_model_analysis.plot_data_and_model(ymax=2)"
    ]
   },
   {

docs/docs/tutorials/tutorial2_nanoparticles.ipynb

@@ -280,6 +280,7 @@
     "    resolution_model=res_analysis.instrument_model.resolution_model,\n",
     ")\n",
     "instrument_model.resolution_model.fix_all_parameters()\n",
+    "instrument_model.normalize_resolution()\n",
     "\n",
     "\n",
     "analysis = Analysis(\n",
@@ -417,6 +418,7 @@
     "    resolution_model=res_analysis.instrument_model.resolution_model,\n",
     ")\n",
     "instrument_model.resolution_model.fix_all_parameters()\n",
+    "instrument_model.normalize_resolution()\n",
     "\n",
     "# Create the analysis object\n",
     "mag_analysis = Analysis(\n",

src/easydynamics/analysis/analysis_base.py

@@ -290,6 +290,15 @@ def extra_parameters(self, value: Parameter | list[Parameter]) -> None:
     # Other methods
     #############
 
+    def normalize_resolution(self) -> None:
+        """Normalize the resolution in the InstrumentModel to ensure
+        that it integrates to 1.
+
+        This is important for accurate fitting and interpretation of the
+        results.
+        """
+        self.instrument_model.normalize_resolution()
+
     #############
     # Private methods
     #############

src/easydynamics/sample_model/instrument_model.py

@@ -351,6 +351,10 @@ def free_resolution_parameters(self) -> None:
         """Free all parameters in the resolution model."""
         self.resolution_model.free_all_parameters()
 
+    def normalize_resolution(self) -> None:
+        """Normalize the resolution model to have area 1."""
+        self.resolution_model.normalize_area()
+
     def get_energy_offset_at_Q(self, Q_index: int) -> Parameter:
         """Get the energy offset Parameter at a specific Q index.
 

src/easydynamics/sample_model/model_base.py

@@ -351,6 +351,11 @@ def get_component_collection(self, Q_index: int) -> ComponentCollection:
             )
         return self._component_collections[Q_index]
 
+    def normalize_area(self) -> None:
+        """Normalize the area of the model across all Q values."""
+        for collection in self._component_collections:
+            collection.normalize_area()
+
     # ------------------------------------------------------------------
     # Private methods
     # ------------------------------------------------------------------

tests/unit/easydynamics/analysis/test_analysis_base.py

@@ -265,6 +265,21 @@ def test_extra_parameters_setter_invalid_type(self, analysis_base, invalid_extra
         ):
             analysis_base.extra_parameters = invalid_extra_parameters
 
+    #############
+    # Other methods
+    #############
+
+    def test_normalize_resolution_calls_instrument_model(self, analysis_base):
+        with patch.object(
+            analysis_base.instrument_model, 'normalize_resolution'
+        ) as mock_normalize_resolution:
+            analysis_base.normalize_resolution()
+            mock_normalize_resolution.assert_called_once()
+
+    #############
+    # Private methods
+    #############
+
     def test_on_experiment_changed_updates_Q(self, analysis_base):
         # WHEN
         fake_Q = [1, 2, 3]

tests/unit/easydynamics/sample_model/test_instrument_model.py

@@ -351,6 +351,16 @@ def test_get_all_variables_with_nonint_Q_index_raises(self, instrument_model):
         ):
             instrument_model.get_all_variables(Q_index='invalid_index')
 
+    def test_normalize_resolution(self, instrument_model):
+        # WHEN
+        instrument_model.resolution_model.normalize_area = MagicMock()
+
+        # THEN
+        instrument_model.normalize_resolution()
+
+        # EXPECT
+        instrument_model.resolution_model.normalize_area.assert_called_once()
+
     def test_generate_energy_offsets_Q_none(self, instrument_model):
         # WHEN
         instrument_model._Q = None

tests/unit/easydynamics/sample_model/test_model_base.py

@@ -360,6 +360,17 @@ def test_clear_Q_raises_without_confirm(self, model_base):
         with pytest.raises(ValueError, match='Clearing Q values requires confirmation'):
             model_base.clear_Q()
 
+    def test_normalize_area(self, model_base):
+        # WHEN
+
+        # THEN
+        model_base.normalize_area()
+
+        # EXPECT
+        for collection in model_base._component_collections:
+            total_area = sum(component.area.value for component in collection.components)
+            assert total_area == pytest.approx(1.0)
+
     def test_repr(self, model_base):
         # WHEN
         repr_str = repr(model_base)