83 clear up classes in sample

EasyReflectometry/calculators/bornagain/calculator.py

@@ -4,10 +4,10 @@
 from easyCore.Objects.Inferface import ItemContainer
 
 from EasyReflectometry.experiment.model import Model
-from EasyReflectometry.sample.items import MultiLayer
-from EasyReflectometry.sample.layer import Layer
-from EasyReflectometry.sample.material import Material
-from EasyReflectometry.sample.material import MaterialMixture
+from EasyReflectometry.sample import Layer
+from EasyReflectometry.sample import Material
+from EasyReflectometry.sample import MaterialMixture
+from EasyReflectometry.sample import Multilayer
 
 from ..calculator_base import CalculatorBase
 from .wrapper import BornAgainWrapper
@@ -55,7 +55,7 @@ def reset_storage(self) -> None:
         """
         self._wrapper.reset_storage()
 
-    def create(self, model: Material | Layer | MultiLayer | Model) -> list[ItemContainer]:
+    def create(self, model: Material | Layer | Multilayer | Model) -> list[ItemContainer]:
         """
         Creation function
 
@@ -103,7 +103,7 @@ def create(self, model: Material | Layer | MultiLayer | Model) -> list[ItemConta
                 )
             )
             self.assign_material_to_layer(model.material.uid, key)
-        elif issubclass(t_, MultiLayer):
+        elif issubclass(t_, Multilayer):
             key = model.uid
             self._wrapper.create_item(key)
             r_list.append(

EasyReflectometry/calculators/bornagain/wrapper.py

@@ -160,7 +160,7 @@ def create_model(self):
         """
         Create a model for analysis
         """
-        self.storage['model'] = ba.MultiLayer()
+        self.storage['model'] = ba.Multilayer()
         self.storage['model'].setRoughnessModel(ba.RoughnessModel.NEVOT_CROCE)
         self.storage['model_items'] = []
         self.storage['model_parameters']['scale'] = 1
@@ -267,7 +267,7 @@ def calculate(self, x_array: np.ndarray) -> np.ndarray:
         simulation = ba.SpecularSimulation()
         simulation.setScan(scan)
 
-        total_model = ba.MultiLayer()
+        total_model = ba.Multilayer()
         for i in self.storage['model_items']:
             for k in range(int(self.storage['item_repeats'][i])):
                 for j in self.storage['item'][i]:

EasyReflectometry/calculators/calculator_base.py

@@ -7,10 +7,10 @@
 from easyCore.Objects.Inferface import ItemContainer
 
 from EasyReflectometry.experiment.model import Model
-from EasyReflectometry.sample.items import MultiLayer
-from EasyReflectometry.sample.layer import Layer
-from EasyReflectometry.sample.material import Material
-from EasyReflectometry.sample.material import MaterialMixture
+from EasyReflectometry.sample import Layer
+from EasyReflectometry.sample import Material
+from EasyReflectometry.sample import MaterialMixture
+from EasyReflectometry.sample import Multilayer
 
 from .wrapper_base import WrapperBase
 
@@ -51,7 +51,7 @@ def reset_storage(self) -> None:
         """
         self._wrapper.reset_storage()
 
-    def create(self, model: Material | Layer | MultiLayer | Model) -> list[ItemContainer]:
+    def create(self, model: Material | Layer | Multilayer | Model) -> list[ItemContainer]:
         """
         Creation function
 
@@ -97,7 +97,7 @@ def create(self, model: Material | Layer | MultiLayer | Model) -> list[ItemConta
                 )
             )
             self.assign_material_to_layer(model.material.uid, key)
-        elif issubclass(t_, MultiLayer):
+        elif issubclass(t_, Multilayer):
             key = model.uid
             self._wrapper.create_item(key)
             r_list.append(
@@ -121,7 +121,7 @@ def create(self, model: Material | Layer | MultiLayer | Model) -> list[ItemConta
                     self._wrapper.update_model,
                 )
             )
-            for i in model.structure:
+            for i in model.sample:
                 self.add_item_to_model(i.uid, key)
         return r_list
 

EasyReflectometry/experiment/model.py

@@ -11,10 +11,10 @@
 from easyCore.Objects.ObjectClasses import Parameter
 
 from EasyReflectometry.sample import Layer
-from EasyReflectometry.sample import Layers
-from EasyReflectometry.sample import Structure
-from EasyReflectometry.sample.items import MultiLayer
-from EasyReflectometry.sample.items import RepeatingMultiLayer
+from EasyReflectometry.sample import LayerCollection
+from EasyReflectometry.sample import Multilayer
+from EasyReflectometry.sample import RepeatingMultilayer
+from EasyReflectometry.sample import Sample
 
 LAYER_DETAILS = {
     'scale': {
@@ -47,7 +47,7 @@
 class Model(BaseObj):
     def __init__(
         self,
-        structure: Structure,
+        sample: Sample,
         scale: Parameter,
         background: Parameter,
         resolution: Parameter,
@@ -56,7 +56,7 @@ def __init__(
     ):
         super().__init__(
             name=name,
-            structure=structure,
+            sample=sample,
             scale=scale,
             background=background,
             resolution=resolution,
@@ -72,16 +72,16 @@ def default(cls, interface=None) -> Model:
         :return: Default model container
         :rtype: Model
         """
-        structure = Structure.default()
+        sample = Sample.default()
         scale = Parameter('scale', **LAYER_DETAILS['scale'])
         background = Parameter('background', **LAYER_DETAILS['background'])
         resolution = Parameter('resolution', **LAYER_DETAILS['resolution'])
-        return cls(structure, scale, background, resolution, interface=interface)
+        return cls(sample, scale, background, resolution, interface=interface)
 
     @classmethod
     def from_pars(
         cls,
-        structure: Structure,
+        sample: Sample,
         scale: Parameter,
         background: Parameter,
         resolution: Parameter,
@@ -91,7 +91,7 @@ def from_pars(
         """
         Constructor of a reflectometry experiment model where the parameters are known.
 
-        :param structure: The structure being modelled
+        :param sample: The sample being modelled
         :param scale: Scaling factor of profile
         :param background: Linear background magnitude
         :param background: Constant resolution smearing percentage
@@ -107,33 +107,33 @@ def from_pars(
         resolution = Parameter('resolution', resolution, **default_options['resolution'])
 
         return cls(
-            structure=structure,
+            sample=sample,
             scale=scale,
             background=background,
             resolution=resolution,
             name=name,
             interface=interface,
         )
 
-    def add_item(self, *items: Union[Layer, RepeatingMultiLayer]) -> None:
+    def add_item(self, *items: Union[Layer, RepeatingMultilayer]) -> None:
         """
-        Add a layer or item to the model structure.
+        Add a layer or item to the model sample.
 
-        :param *items: Layers or items to add to model structure
+        :param *items: Layers or items to add to model sample
         """
         for arg in items:
-            if issubclass(arg.__class__, MultiLayer):
-                self.structure.append(arg)
+            if issubclass(arg.__class__, Multilayer):
+                self.sample.append(arg)
                 if self.interface is not None:
                     self.interface().add_item_to_model(arg.uid, self.uid)
 
     def duplicate_item(self, idx: int) -> None:
         """
-        Duplicate a given item or layer in a structure.
+        Duplicate a given item or layer in a sample.
 
         :param idx: Index of the item or layer to duplicate
         """
-        to_duplicate = self.structure[idx]
+        to_duplicate = self.sample[idx]
         duplicate_layers = []
         for i in to_duplicate.layers:
             duplicate_layers.append(
@@ -145,7 +145,7 @@ def duplicate_item(self, idx: int) -> None:
                 )
             )
         duplicate = to_duplicate.__class__.from_pars(
-            Layers.from_pars(*duplicate_layers, name=to_duplicate.layers.name + ' duplicate'),
+            LayerCollection.from_pars(*duplicate_layers, name=to_duplicate.layers.name + ' duplicate'),
             name=to_duplicate.name + ' duplicate',
         )
         self.add_item(duplicate)
@@ -158,8 +158,8 @@ def remove_item(self, idx) -> None:
         :type idx: int
         """
         if self.interface is not None:
-            self.interface().remove_item_from_model(self.structure[idx].uid, self.uid)
-        del self.structure[idx]
+            self.interface().remove_item_from_model(self.sample[idx].uid, self.uid)
+        del self.sample[idx]
 
     @property
     def uid(self) -> int:
@@ -181,7 +181,7 @@ def _dict_repr(self) -> dict[str, dict[str, str]]:
                 'scale': self.scale.raw_value,
                 'background': self.background.raw_value,
                 'resolution': f'{self.resolution.raw_value} %',
-                'structure': self.structure._dict_repr,
+                'sample': self.sample._dict_repr,
             }
         }
 

EasyReflectometry/sample/__init__.py

@@ -1,6 +1,25 @@
-from .layer import Layer
-from .layers import Layers
-from .materials import Materials
-from .structure import Structure
+from .assemblies.gradient_layer import GradientLayer
+from .assemblies.multilayer import Multilayer
+from .assemblies.repeating_multilayer import RepeatingMultilayer
+from .assemblies.surfactant_layer import SurfactantLayer
+from .elements.layer_collection import LayerCollection
+from .elements.layers.layer import Layer
+from .elements.layers.layer_apm import LayerApm
+from .elements.material_collection import MaterialCollection
+from .elements.materials.material import Material
+from .elements.materials.material_mixture import MaterialMixture
+from .sample import Sample
 
-_ = (Layer, Layers, Materials, Structure)
+__all__ = (
+    GradientLayer,
+    Multilayer,
+    RepeatingMultilayer,
+    SurfactantLayer,
+    Layer,
+    LayerApm,
+    LayerCollection,
+    Material,
+    MaterialMixture,
+    MaterialCollection,
+    Sample,
+)

EasyReflectometry/sample/assemblies/base_assembly.py

@@ -0,0 +1,40 @@
+from abc import abstractmethod
+from typing import Any
+
+import yaml
+from easyCore.Objects.ObjectClasses import BaseObj
+
+
+class BaseAssembly(BaseObj):
+    def __init__(
+        self,
+        name: str,
+        interface,
+        **kwargs,
+    ):
+        super().__init__(name=name, **kwargs)
+        self.interface = interface
+
+    @abstractmethod
+    def default(cls, interface=None) -> Any:
+        ...
+
+    @abstractmethod
+    def _dict_repr(self) -> dict[str, str]:
+        ...
+
+    @property
+    def uid(self) -> int:
+        """
+        :return: UID from the borg map
+        """
+        return self._borg.map.convert_id_to_key(self)
+
+    def __repr__(self) -> str:
+        """
+        String representation of the layer.
+
+        :return: a string representation of the layer
+        :rtype: str
+        """
+        return yaml.dump(self._dict_repr, sort_keys=False)

EasyReflectometry/sample/items/gradient_layer.py → EasyReflectometry/sample/assemblies/gradient_layer.py

@@ -3,13 +3,12 @@
 from easyCore.Fitting.Constraints import ObjConstraint
 from numpy import arange
 
-from EasyReflectometry.sample.layer import Layer
-from EasyReflectometry.sample.material import Material
+from ..elements.layers.layer import Layer
+from ..elements.materials.material import Material
+from .multilayer import Multilayer
 
-from .multilayer import MultiLayer
 
-
-class GradientLayer(MultiLayer):
+class GradientLayer(Multilayer):
     """
     A :py:class:`GradientLayer` constructs a gradient multilayer for the
     provided initial and final material.