191 adjust model and modelcollection to hold functionality from app (#192)

* from materials collection to base collection

* added color to Model

* renaming up and down to be consistent with other code

* adjusted collections

* placeholder for calculated data

* ready to expose data

* datastore and tests

* added functionality

* code cleaning

* explicit clean global obejct for surfactant tests

* unique name in surfactant and layer area per molecule

* code clean

* code cleaning

* code cleaning

* pr response

* pr response and tests

* pr response

Author: andped10

src/easyreflectometry/data/__init__.py

@@ -1,7 +1,9 @@
+from .data_store import DataSet1D
 from .data_store import ProjectData
 from .measurement import load
 
 __all__ = [
     load,
     ProjectData,
+    DataSet1D,
 ]

src/easyreflectometry/data/data_store.py

@@ -81,7 +81,8 @@ def __init__(
         y_label: str = 'y',
     ):
         self._model = model
-        self._model.background = np.min(y)
+        if y is not None and model is not None:
+            self._model.background = np.min(y)
 
         if x is None:
             x = np.array([])
@@ -92,6 +93,9 @@ def __init__(
         if xe is None:
             xe = np.zeros_like(x)
 
+        if len(x) != len(y):
+            raise ValueError('x and y must be the same length')
+
         self.name = name
         if not isinstance(x, np.ndarray):
             x = np.array(x)
@@ -125,5 +129,8 @@ def is_experiment(self) -> bool:
     def is_simulation(self) -> bool:
         return self._model is None
 
+    def data_points(self) -> int:
+        return zip(self.x, self.y)
+
     def __repr__(self) -> str:
         return "1D DataStore of '{:s}' Vs '{:s}' with {} data points".format(self.x_label, self.y_label, len(self.x))

src/easyreflectometry/model/model.py

@@ -60,6 +60,7 @@ def __init__(
         background: Union[Parameter, Number, None] = None,
         resolution_function: Union[ResolutionFunction, None] = None,
         name: str = 'EasyModel',
+        color: str = 'black',
         unique_name: Optional[str] = None,
         interface=None,
     ):
@@ -81,6 +82,7 @@ def __init__(
 
         scale = get_as_parameter('scale', scale, DEFAULTS)
         background = get_as_parameter('background', background, DEFAULTS)
+        self.color = color
 
         super().__init__(
             name=name,
@@ -173,6 +175,7 @@ def _dict_repr(self) -> dict[str, dict[str, str]]:
                 'scale': float(self.scale.value),
                 'background': float(self.background.value),
                 'resolution': resolution,
+                'color': self.color,
                 'sample': self.sample._dict_repr,
             }
         }

src/easyreflectometry/model/model_collection.py

@@ -1,8 +1,7 @@
 from __future__ import annotations
 
-__author__ = 'github.com/arm61'
-
 from typing import List
+from typing import Optional
 from typing import Tuple
 
 from easyreflectometry.sample.collections.base_collection import BaseCollection
@@ -35,21 +34,24 @@ def __init__(
 
         super().__init__(name, interface, *models, **kwargs)
 
-    def add_model(self, new_model: Model):
-        """
-        Add a model to the models.
+    def add_model(self, model: Optional[Model] = None):
+        """Add a model to the collection.
 
-        :param new_model: New model to be added.
+        :param model: Model to add.
         """
-        self.append(new_model)
+        if model is None:
+            model = Model(name='Model new', interface=self.interface)
+        self.append(model)
 
-    def remove_model(self, index: int):
-        """
-        Remove an model from the models.
+    def duplicate_model(self, index: int):
+        """Duplicate a model in the collection.
 
-        :param index: Index of the model to remove
+        :param index: Model to duplicate.
         """
-        self.pop(index)
+        to_be_duplicated = self[index]
+        duplicate = Model.from_dict(to_be_duplicated.as_dict(skip=['unique_name']))
+        duplicate.name = duplicate.name + ' duplicate'
+        self.append(duplicate)
 
     def as_dict(self, skip: List[str] | None = None) -> dict:
         this_dict = super().as_dict(skip=skip)
@@ -62,7 +64,6 @@ def from_dict(cls, this_dict: dict) -> ModelCollection:
         Create an instance of a collection from a dictionary.
 
         :param data: The dictionary for the collection
-        :return: An instance of the collection
         """
         collection_dict = this_dict.copy()
         # We neeed to call from_dict on the base class to get the models

src/easyreflectometry/project.py

@@ -6,10 +6,11 @@
 from typing import Optional
 from typing import Union
 
+import numpy as np
 from easyscience import global_object
 from easyscience.fitting import AvailableMinimizers
 
-from easyreflectometry.data.data_store import DataSet1D
+from easyreflectometry.data import DataSet1D
 from easyreflectometry.model import Model
 from easyreflectometry.model import ModelCollection
 from easyreflectometry.sample import Layer
@@ -18,6 +19,29 @@
 from easyreflectometry.sample import Sample
 from easyreflectometry.sample.collections.base_collection import BaseCollection
 
+MODELS_SAMPLE_DATA = [
+    DataSet1D(
+        name='Sample Data 0',
+        x=np.array([1, 2, 3, 4, 5, 6, 7, 8, 9, 10]),
+        y=np.array([1, 2, 3, 4, 5, 6, 7, 8, 9, 10]),
+    )
+]
+MODELS_MODEL_DATA = [
+    DataSet1D(
+        name='Model Data 0',
+        x=np.array([1, 2, 3, 4, 5, 6, 7, 8, 9, 10]),
+        y=np.array([1.5, 2.5, 3.5, 4.5, 5.5, 6.5, 7.5, 8.5, 9.5, 10.5]),
+    )
+]
+EXPERIMENTAL_DATA = [
+    DataSet1D(
+        name='Example Data 0',
+        x=np.array([1, 2, 3, 4, 5, 6, 7, 8, 9, 10]),
+        y=np.array([0.5, 1.5, 2.5, 3.5, 4.5, 5.5, 6.5, 7.5, 8.5, 9.5]),
+        ye=np.array([0.1, 0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8, 0.9, 1.0]),
+    )
+]
+
 
 class Project:
     def __init__(self):
@@ -95,6 +119,15 @@ def experiments(self, experiments: List[DataSet1D]) -> None:
     def path_json(self):
         return self.path / 'project.json'
 
+    def sample_data_for_model_at_index(self, index: int = 0) -> DataSet1D:
+        return MODELS_SAMPLE_DATA[index]
+
+    def model_data_for_model_at_index(self, index: int = 0) -> DataSet1D:
+        return MODELS_MODEL_DATA[index]
+
+    def experimental_data_for_model_at_index(self, index: int = 0) -> DataSet1D:
+        return EXPERIMENTAL_DATA[index]
+
     def default_model(self):
         self._replace_collection(MaterialCollection(), self._materials)
 

src/easyreflectometry/sample/assemblies/surfactant_layer.py

@@ -2,6 +2,7 @@
 
 from typing import Optional
 
+from easyscience import global_object
 from easyscience.Constraints import ObjConstraint
 from easyscience.Objects.new_variable import Parameter
 
@@ -44,8 +45,17 @@ def __init__(
         :param conformal_roughness: Constrain the roughness to be the same for both layers, defaults to `False`.
         :param interface: Calculator interface, defaults to `None`.
         """
+        if unique_name is None:
+            unique_name = global_object.generate_unique_name(self.__class__.__name__)
+
         if tail_layer is None:
-            air = Material(0, 0, 'Air')
+            air = Material(
+                sld=0,
+                isld=0,
+                name='Air',
+                unique_name=unique_name + '_MaterialTail',
+                interface=interface,
+            )
             tail_layer = LayerAreaPerMolecule(
                 molecular_formula='C32D64',
                 thickness=16,
@@ -54,9 +64,17 @@ def __init__(
                 area_per_molecule=48.2,
                 roughness=3,
                 name='DPPC Tail',
+                unique_name=unique_name + '_LayerAreaPerMoleculeTail',
+                interface=interface,
             )
         if head_layer is None:
-            d2o = Material(6.36, 0, 'D2O')
+            d2o = Material(
+                sld=6.36,
+                isld=0,
+                name='D2O',
+                unique_name=unique_name + '_MaterialHead',
+                interface=interface,
+            )
             head_layer = LayerAreaPerMolecule(
                 molecular_formula='C10H18NO8P',
                 thickness=10.0,
@@ -65,8 +83,16 @@ def __init__(
                 area_per_molecule=48.2,
                 roughness=3.0,
                 name='DPPC Head',
+                unique_name=unique_name + '_LayerAreaPerMoleculeHead',
+                interface=interface,
             )
-        surfactant = LayerCollection(tail_layer, head_layer, name=name)
+        surfactant = LayerCollection(
+            tail_layer,
+            head_layer,
+            name='Layers',
+            unique_name=unique_name + '_LayerCollection',
+            interface=interface,
+        )
         super().__init__(
             name=name,
             unique_name=unique_name,

src/easyreflectometry/sample/collections/base_collection.py

@@ -37,6 +37,32 @@ def names(self) -> list:
         """
         return [i.name for i in self]
 
+    def move_up(self, index: int):
+        """Move the element at the given index up in the collection.
+
+        :param index: Index of the element to move up.
+        """
+        if index == 0:
+            return
+        self.insert(index - 1, self.pop(index))
+
+    def move_down(self, index: int):
+        """Move the element at the given index down in the collection.
+
+        :param index: Index of the element to move down.
+        """
+        if index == len(self) - 1:
+            return
+        self.insert(index + 1, self.pop(index))
+
+    def remove(self, index: int):
+        """
+        Remove an element from the elements.
+
+        :param index: Index of the element to remove
+        """
+        self.pop(index)
+
     @property
     def _dict_repr(self) -> dict:
         """

src/easyreflectometry/sample/collections/layer_collection.py

@@ -20,3 +20,25 @@ def __init__(
             layers = []
 
         super().__init__(name, interface, unique_name=unique_name, *layers, **kwargs)
+
+    def add_layer(self, layer: Optional[Layer] = None):
+        """Add a layer to the collection.
+
+        :param layer: Layer to add.
+        """
+        if layer is None:
+            layer = Layer(
+                name='New EasyLayer',
+                interface=self.interface,
+            )
+        self.append(layer)
+
+    def duplicate_layer(self, index: int):
+        """Duplicate a layer in the collection.
+
+        :param layer: Assembly to add.
+        """
+        to_be_duplicated = self[index]
+        duplicate = Layer.from_dict(to_be_duplicated.as_dict(skip=['unique_name']))
+        duplicate.name = duplicate.name + ' duplicate'
+        self.append(duplicate)

src/easyreflectometry/sample/collections/material_collection.py

@@ -45,7 +45,8 @@ def add_material(self, material: Optional[Material] = None):
         :param material: Material to add.
         """
         if material is None:
-            material = Material(sld=2.074, isld=0.000, name='Si new', interface=self.interface)
+            material = Material(sld=2.074, isld=0.000, name='Si new')
+        material.interface = self.interface
         self.append(material)
 
     def duplicate_material(self, index: int):
@@ -57,28 +58,3 @@ def duplicate_material(self, index: int):
         duplicate = Material.from_dict(to_be_duplicated.as_dict(skip=['unique_name']))
         duplicate.name = duplicate.name + ' duplicate'
         self.append(duplicate)
-
-    def move_material_up(self, index: int):
-        """Move the material at the given index up in the collection.
-
-        :param index: Index of the material to move up.
-        """
-        if index == 0:
-            return
-        self.insert(index - 1, self.pop(index))
-
-    def move_material_down(self, index: int):
-        """Move the material at the given index down in the collection.
-
-        :param index: Index of the material to move down.
-        """
-        if index == len(self) - 1:
-            return
-        self.insert(index + 1, self.pop(index))
-
-    def remove_material(self, index: int):
-        """Remove the material at the given index from the collection.
-
-        :param index: Index of the material to remove.
-        """
-        self.pop(index)

src/easyreflectometry/sample/collections/sample.py

@@ -56,7 +56,10 @@ def add_assembly(self, assembly: Optional[BaseAssembly] = None):
         :param assembly: Assembly to add.
         """
         if assembly is None:
-            assembly = Multilayer(name='New EasyMultilayer', interface=self.interface)
+            assembly = Multilayer(
+                name='New EasyMultilayer',
+                interface=self.interface,
+            )
         self._enable_changes_to_outermost_layers()
         self.append(assembly)
         self._disable_changes_to_outermost_layers()
@@ -78,26 +81,22 @@ def duplicate_assembly(self, index: int):
         self.append(duplicate)
         self._disable_changes_to_outermost_layers()
 
-    def move_assembly_up(self, index: int):
+    def move_up(self, index: int):
         """Move the assembly at the given index up in the sample.
 
         :param index: Index of the assembly to move up.
         """
-        if index == 0:
-            return
         self._enable_changes_to_outermost_layers()
-        self.insert(index - 1, self.pop(index))
+        super().move_up(index)
         self._disable_changes_to_outermost_layers()
 
-    def move_assembly_down(self, index: int):
+    def move_down(self, index: int):
         """Move the assembly at the given index down in the sample.
 
         :param index: Index of the assembly to move down.
         """
-        if index == len(self) - 1:
-            return
         self._enable_changes_to_outermost_layers()
-        self.insert(index + 1, self.pop(index))
+        super().move_down(index)
         self._disable_changes_to_outermost_layers()
 
     def remove_assembly(self, index: int):