Append sample

docs/src/api/api.rst

@@ -19,6 +19,15 @@ Sample is build from assemblies.
 
    sample
 
+Project
+=======
+Project provides a higher-level interface for managing models, experiments, and ORSO import.
+
+.. toctree::
+   :maxdepth: 1
+
+   project
+
 Assemblies
 ==========
 Assemblies are collections of layers that are used to represent a specific physical setup.

pyproject.toml

@@ -29,11 +29,11 @@ classifiers = [
 requires-python = ">=3.11,<3.13"
 
 dependencies = [
-    #"easyscience @ git+https://github.com/easyscience/corelib.git@dict_size_changed_bug",
-    "easyscience",
+    "easyscience @ git+https://github.com/easyscience/corelib.git@develop",
+    #"easyscience",
     "scipp",
     "refnx",
-    "refl1d>=1.0.0rc0",
+    "refl1d>=1.0.0",
     "orsopy",
     "svglib<1.6 ; platform_system=='Linux'",
     "xhtml2pdf",

src/easyreflectometry/calculators/calculator_base.py

@@ -7,7 +7,7 @@
 from easyscience.fitting.calculators.interface_factory import ItemContainer
 from easyscience.io import SerializerComponent
 
-#if TYPE_CHECKING:
+# if TYPE_CHECKING:
 from easyreflectometry.model import Model
 from easyreflectometry.sample import BaseAssembly
 from easyreflectometry.sample import Layer

src/easyreflectometry/data/data_store.py

@@ -76,7 +76,7 @@ def __init__(
         y: Optional[Union[np.ndarray, list]] = None,
         ye: Optional[Union[np.ndarray, list]] = None,
         xe: Optional[Union[np.ndarray, list]] = None,
-        model: Optional['Model'] = None, # delay type checking until runtime (quotes)
+        model: Optional['Model'] = None,  # delay type checking until runtime (quotes)
         x_label: str = 'x',
         y_label: str = 'y',
     ):
@@ -117,7 +117,7 @@ def __init__(
         self._color = None
 
     @property
-    def model(self) -> 'Model': # delay type checking until runtime (quotes)
+    def model(self) -> 'Model':  # delay type checking until runtime (quotes)
         return self._model
 
     @model.setter

src/easyreflectometry/fitting.py

@@ -55,13 +55,13 @@ def fit(self, data: sc.DataGroup, id: int = 0) -> sc.DataGroup:
             variances = data['data'][f'R_{i}'].variances
 
             # Find points with non-zero variance
-            zero_variance_mask = (variances == 0.0)
+            zero_variance_mask = variances == 0.0
             num_zero_variance = np.sum(zero_variance_mask)
 
             if num_zero_variance > 0:
                 warnings.warn(
-                    f"Masked {num_zero_variance} data point(s) in reflectivity {i} due to zero variance during fitting.",
-                    UserWarning
+                    f'Masked {num_zero_variance} data point(s) in reflectivity {i} due to zero variance during fitting.',
+                    UserWarning,
                 )
 
             # Keep only points with non-zero variances

src/easyreflectometry/orso_utils.py

@@ -27,14 +27,16 @@
 
     return sample, data
 
+
 def load_data_from_orso_file(fname: str) -> sc.DataGroup:
     """Load data from an ORSO file."""
     try:
         orso_data = orso.load_orso(fname)
     except Exception as e:
-        raise ValueError(f"Error loading ORSO file: {e}")
+        raise ValueError(f'Error loading ORSO file: {e}')
     return load_orso_data(orso_data)
 
+
 def load_orso_model(orso_str: str) -> Sample:
     """
     Load a model from an ORSO file and return a Sample object.
@@ -64,9 +66,9 @@
 
     # Handle case where layers are not resolved correctly
     if not orso_layers:
-        raise ValueError("Could not resolve ORSO layers.")
+        raise ValueError('Could not resolve ORSO layers.')
 
-    logger.debug(f"Resolved layers: {orso_layers}")
+    logger.debug(f'Resolved layers: {orso_layers}')
 
     # Convert ORSO layers to EasyReflectometry layers
     erl_layers = []
@@ -98,7 +100,7 @@
         material=Material(sld=m_sld, isld=m_isld, name=m_name),
         thickness=layer.thickness.magnitude if layer.thickness is not None else 0.0,
         roughness=layer.roughness.magnitude if layer.roughness is not None else 0.0,
-        name=layer.original_name if layer.original_name is not None else m_name
+        name=layer.original_name if layer.original_name is not None else m_name,
     )
 
 
@@ -107,10 +109,7 @@
     if material.sld is None and material.mass_density is not None:
         # Calculate SLD from mass density
         m_density = material.mass_density.magnitude
-        density = MaterialDensity(
-            chemical_structure=material_name,
-            density=m_density
-        )
+        density = MaterialDensity(chemical_structure=material_name, density=m_density)
         m_sld = density.sld.value
         m_isld = density.isld.value
     else:
@@ -123,6 +122,7 @@
 
     return m_sld, m_isld
 
+
 def load_orso_data(orso_str: str) -> DataSet1D:
     data = {}
     coords = {}

src/easyreflectometry/project.py

@@ -18,6 +18,8 @@
 from easyreflectometry.data import DataSet1D
 from easyreflectometry.data import load_as_dataset
 from easyreflectometry.fitting import MultiFitter
+
+# from easyreflectometry.model import LinearSpline
 from easyreflectometry.model import Model
 from easyreflectometry.model import ModelCollection
 from easyreflectometry.model import PercentageFwhm
@@ -268,10 +270,53 @@ def load_orso_file(self, path: Union[Path, str]) -> None:
             self._with_experiments = True
         pass
 
-    def set_sample_from_orso(self, sample) -> None:
+    def set_sample_from_orso(self, sample: Sample) -> None:
+        """Replace the current project model collection with a single model built from an ORSO-parsed sample.
+
+        This is a convenience helper for the ORSO import pipeline where a complete
+        :class:`~easyreflectometry.sample.Sample` is constructed elsewhere.
+
+        :param sample: Sample to set as the project's (single) model.
+        :type sample: easyreflectometry.sample.Sample
+        :return: ``None``.
+        :rtype: None
+        """
         model = Model(sample=sample)
         self.models = ModelCollection([model])
 
+    def add_sample_from_orso(self, sample: Sample) -> None:
+        """Add a new model with the given sample to the existing model collection.
+
+        The created model is appended to :attr:`models`, its calculator interface is
+        set to the project's current calculator, and any materials referenced in the
+        sample are added to the project's material collection.
+
+        After adding the model, :attr:`current_model_index` is updated to point to
+        the newly added model.
+
+        :param sample: Sample to add as a new model.
+        :type sample: easyreflectometry.sample.Sample
+        :return: ``None``.
+        :rtype: None
+        """
+        model = Model(sample=sample)
+        self.models.add_model(model)
+        # Set interface after adding to collection
+        model.interface = self._calculator
+        # Extract materials from the new model and add to project materials
+        self._materials.extend(self._get_materials_from_model(model))
+        # Switch to the newly added model so its data is visible in the UI
+        self.current_model_index = len(self._models) - 1
+
+    def _get_materials_from_model(self, model: Model) -> 'MaterialCollection':
+        """Get all materials from a single model's sample."""
+        materials_in_model = MaterialCollection(populate_if_none=False)
+        for assembly in model.sample:
+            for layer in assembly.layers:
+                if layer.material not in materials_in_model:
+                    materials_in_model.append(layer.material)
+        return materials_in_model
+
     def load_new_experiment(self, path: Union[Path, str]) -> None:
         new_experiment = load_as_dataset(str(path))
         new_index = len(self._experiments)
@@ -291,6 +336,10 @@ def load_new_experiment(self, path: Union[Path, str]) -> None:
             q_error = new_experiment.xe
             # TODO: set resolution function based on value of control in GUI
             resolution_function = Pointwise(q_data_points=[q, reflectivity, q_error])
+            # resolution_function = LinearSpline(
+            #     q_data_points=self._experiments[new_index].y,
+            #     fwhm_values=np.sqrt(self._experiments[new_index].ye),
+            # )
             self.models[model_index].resolution_function = resolution_function
 
     def load_experiment_for_model_at_index(self, path: Union[Path, str], index: Optional[int] = 0) -> None:

tests/calculators/refl1d/test_refl1d_calculator.py

@@ -61,7 +61,7 @@ def test_reflectity_profile(self):
             5.7605e-07,
             2.3775e-07,
             1.3093e-07,
-            1.0520e-07
+            1.0520e-07,
         ]
         assert_almost_equal(p.reflectity_profile(q, 'MyModel'), expected, decimal=4)
 
@@ -106,7 +106,7 @@ def test_calculate2(self):
             1.0968e-06,
             4.5635e-07,
             3.4120e-07,
-            2.7505e-07
+            2.7505e-07,
         ]
         assert_almost_equal(actual, expected, decimal=4)
 

tests/calculators/refl1d/test_refl1d_wrapper.py

@@ -232,7 +232,7 @@ def test_calculate(self):
             5.7605e-07,
             2.3775e-07,
             1.3093e-07,
-            1.0520e-07
+            1.0520e-07,
         ]
         assert_almost_equal(p.calculate(q, 'MyModel'), expected, decimal=4)
 
@@ -276,7 +276,7 @@ def test_calculate_three_items(self):
             1.0968e-06,
             4.5635e-07,
             3.4120e-07,
-            2.7505e-07
+            2.7505e-07,
         ]
         assert_almost_equal(p.calculate(q, 'MyModel'), expected, decimal=4)
 
@@ -396,7 +396,7 @@ def test_get_polarized_probe_oversampling():
     probe = _get_polarized_probe(q_array=q, dq_array=dq, model_name=model_name, storage=storage, oversampling_factor=2)
 
     # Then
-    assert len(probe.xs[0].calc_Qo) == 2*len(q)
+    assert len(probe.xs[0].calc_Qo) == 2 * len(q)
 
 
 def test_get_polarized_probe_polarization():

tests/data/test_data_store.py

@@ -29,13 +29,7 @@ def test_constructor_default_values(self):
     def test_constructor_with_values(self):
         # When
         data = DataSet1D(
-            x=[1, 2, 3], 
-            y=[4, 5, 6], 
-            ye=[7, 8, 9], 
-            xe=[10, 11, 12], 
-            x_label='label_x', 
-            y_label='label_y', 
-            name='MyDataSet1D'
+            x=[1, 2, 3], y=[4, 5, 6], ye=[7, 8, 9], xe=[10, 11, 12], x_label='label_x', y_label='label_y', name='MyDataSet1D'
         )
 
         # Then
@@ -116,19 +110,15 @@ def test_is_simulation_property(self):
 
     def test_data_points(self):
         # When
-        data = DataSet1D(
-            x=[1, 2, 3], y=[4, 5, 6], ye=[7, 8, 9], xe=[10, 11, 12]
-        )
+        data = DataSet1D(x=[1, 2, 3], y=[4, 5, 6], ye=[7, 8, 9], xe=[10, 11, 12])
 
         # Then
         points = list(data.data_points())
         assert points == [(1, 4, 7, 10), (2, 5, 8, 11), (3, 6, 9, 12)]
 
     def test_repr(self):
         # When
-        data = DataSet1D(
-            x=[1, 2, 3], y=[4, 5, 6], x_label='Q', y_label='R'
-        )
+        data = DataSet1D(x=[1, 2, 3], y=[4, 5, 6], x_label='Q', y_label='R')
 
         # Then
         expected = "1D DataStore of 'Q' Vs 'R' with 3 data points"
@@ -194,7 +184,7 @@ def test_setitem(self):
         item1 = DataSet1D(name='item1')
         item2 = DataSet1D(name='item2')
         store = DataStore(item1)
-        
+
         # When
         store[0] = item2
 
@@ -314,4 +304,3 @@ def test_constructor_with_custom_datastores(self):
         assert project.sim_data == sim_store
         assert project.exp_data.name == 'CustomExp'
         assert project.sim_data.name == 'CustomSim'
-

tests/summary/test_summary.py

@@ -177,7 +177,7 @@ def test_save_sld_plot(self, project: Project, tmp_path) -> None:
         # Expect
         assert os.path.exists(file_path)
 
-    @pytest.mark.skip(reason="Matplotlib issue with headless CI environments")
+    @pytest.mark.skip(reason='Matplotlib issue with headless CI environments')
     def test_save_fit_experiment_plot(self, project: Project, tmp_path) -> None:
         # When
         summary = Summary(project)

tests/test_data.py

@@ -224,8 +224,7 @@ def test_load_txt_three_columns(self):
         assert coords_name in er_data['coords']
 
         # xe should be zeros for 3-column file
-        assert_almost_equal(er_data['coords'][coords_name].variances,
-                           np.zeros_like(er_data['coords'][coords_name].values))
+        assert_almost_equal(er_data['coords'][coords_name].variances, np.zeros_like(er_data['coords'][coords_name].values))
 
     def test_load_txt_with_zero_errors(self):
         fpath = os.path.join(PATH_STATIC, 'ref_zero_var.txt')
@@ -246,6 +245,7 @@ def test_load_txt_file_not_found(self):
     def test_load_txt_insufficient_columns(self):
         # Create a temporary file with insufficient columns
         import tempfile
+
         with tempfile.NamedTemporaryFile(mode='w', suffix='.txt', delete=False) as f:
             f.write('1.0 2.0\n')  # Only 2 columns
             temp_path = f.name
@@ -272,7 +272,7 @@ def test_load_orso_multiple_datasets(self):
                 if data_key.replace('R_', '') in coord_key:
                     coord_key_found = True
                     break
-            assert coord_key_found, f"No corresponding coord found for {data_key}"
+            assert coord_key_found, f'No corresponding coord found for {data_key}'
 
     def test_load_orso_with_attrs(self):
         fpath = os.path.join(PATH_STATIC, 'test_example1.ort')