132 add direct initialization as replacement for from pars (#133)

* changing constructor

* constructor

* code cleaning

* tests

* pr response, test dict remains unchanged

* pr response

EasyReflectometry/experiment/model.py

@@ -2,14 +2,16 @@
 
 __author__ = 'github.com/arm61'
 
-from copy import deepcopy
+from numbers import Number
 from typing import Callable
+from typing import Union
 
 import yaml
 from easyCore import np
 from easyCore.Objects.ObjectClasses import BaseObj
 from easyCore.Objects.ObjectClasses import Parameter
 
+from EasyReflectometry.parameter_utils import get_as_parameter
 from EasyReflectometry.sample import BaseAssembly
 from EasyReflectometry.sample import Layer
 from EasyReflectometry.sample import LayerCollection
@@ -53,10 +55,10 @@ class Model(BaseObj):
 
     def __init__(
         self,
-        sample: Sample,
-        scale: Parameter,
-        background: Parameter,
-        resolution_function: Callable[[np.array], float],
+        sample: Union[Sample, None] = None,
+        scale: Union[Parameter, Number, None] = None,
+        background: Union[Parameter, Number, None] = None,
+        resolution_function: Union[Callable[[np.array], float], None] = None,
         name: str = 'EasyModel',
         interface=None,
     ):
@@ -69,6 +71,15 @@ def __init__(
         :param interface: Calculator interface, defaults to `None`.
 
         """
+
+        if sample is None:
+            sample = Sample.default()
+        if resolution_function is None:
+            resolution_function = constant_resolution_function(MODEL_DETAILS['resolution']['value'])
+
+        scale = get_as_parameter(scale, 'scale', MODEL_DETAILS)
+        background = get_as_parameter(background, 'background', MODEL_DETAILS)
+
         super().__init__(
             name=name,
             sample=sample,
@@ -78,60 +89,6 @@ def __init__(
         self.interface = interface
         self._resolution_function = resolution_function
 
-    # Class methods for instance creation
-    @classmethod
-    def default(cls, interface=None) -> Model:
-        """Default instance of the reflectometry experiment model.
-
-        :param interface: Calculator interface, defaults to `None`.
-        """
-        sample = Sample.default()
-        scale = Parameter('scale', **MODEL_DETAILS['scale'])
-        background = Parameter('background', **MODEL_DETAILS['background'])
-        resolution_function = constant_resolution_function(MODEL_DETAILS['resolution']['value'])
-
-        return cls(
-            sample=sample,
-            scale=scale,
-            background=background,
-            resolution_function=resolution_function,
-            interface=interface,
-        )
-
-    @classmethod
-    def from_pars(
-        cls,
-        sample: Sample,
-        scale: float,
-        background: float,
-        resolution_function: Callable[[np.array], float],
-        name: str = 'EasyModel',
-        interface=None,
-    ) -> Model:
-        """Instance of a reflectometry experiment model where the parameters are known.
-
-        :param sample: The sample being modelled.
-        :param scale: Scaling factor of profile.
-        :param background: Linear background magnitude.
-        :param name: Name of the layer, defaults to 'EasyModel'.
-        :param interface: Calculator interface, defaults to `None`.
-        """
-        default_options = deepcopy(MODEL_DETAILS)
-        del default_options['scale']['value']
-        del default_options['background']['value']
-
-        scale = Parameter('scale', scale, **default_options['scale'])
-        background = Parameter('background', background, **default_options['background'])
-
-        return cls(
-            sample=sample,
-            scale=scale,
-            background=background,
-            resolution_function=resolution_function,
-            name=name,
-            interface=interface,
-        )
-
     def add_item(self, *assemblies: list[BaseAssembly]) -> None:
         """Add a layer or item to the model sample.
 

EasyReflectometry/parameter_utils.py

@@ -0,0 +1,30 @@
+from copy import deepcopy
+from numbers import Number
+from typing import Union
+
+from easyCore.Objects.ObjectClasses import Parameter
+
+
+def get_as_parameter(value: Union[Parameter, Number, None], name: str, default_dict: dict[str, str]) -> Parameter:
+    """
+    This function creates a parameter for the variable `name`.  A parameter has a value and metadata.
+    If the value already is a parameter, it is returned.
+    If the value is a number, a parameter is created with this value and metadata from the dictionary.
+    If the value is None, a parameter is created with the default value and metadata from the dictionary.
+
+    param value: The value to use for the parameter.  If None, the default value in the dictionary is used.
+    param name: The name of the parameter
+    param default_dict: Dictionary with entry for `name` containing the default value and metadata for the parameter
+    """
+    # Should leave the passed dictionary unchanged
+    local_dict = deepcopy(default_dict)
+    if value is None:
+        # Create a default parameter using both value and metadata from dictionary
+        return Parameter(name, **local_dict[name])
+    elif isinstance(value, Number):
+        # Create a parameter using provided value and metadata from dictionary
+        del local_dict[name]['value']
+        return Parameter(name, value, **local_dict[name])
+    elif not isinstance(value, Parameter):
+        raise ValueError(f'{name} must be a Parameter, a number, or None.')
+    return value

tests/experiment/test_model.py

@@ -28,7 +28,7 @@
 
 class TestModel(unittest.TestCase):
     def test_default(self):
-        p = Model.default()
+        p = Model()
         assert_equal(p.name, 'EasyModel')
         assert_equal(p.interface, None)
         assert_equal(p.sample.name, 'EasySample')
@@ -58,7 +58,13 @@ def test_from_pars(self):
         o2 = RepeatingMultilayer.from_pars(ls2, 1.0, 'oneLayerItem2')
         d = Sample.from_pars(o1, o2, name='myModel')
         resolution_function = constant_resolution_function(2.0)
-        mod = Model.from_pars(d, 2, 1e-5, resolution_function, 'newModel')
+        mod = Model(
+            sample=d,
+            scale=2,
+            background=1e-5,
+            resolution_function=resolution_function,
+            name='newModel',
+        )
         assert_equal(mod.name, 'newModel')
         assert_equal(mod.interface, None)
         assert_equal(mod.sample.name, 'myModel')
@@ -90,7 +96,7 @@ def test_add_item(self):
         multilayer = Multilayer.default()
         d = Sample.from_pars(o1, name='myModel')
         resolution_function = constant_resolution_function(2.0)
-        mod = Model.from_pars(d, 2, 1e-5, resolution_function, 'newModel')
+        mod = Model(d, 2, 1e-5, resolution_function, 'newModel')
         assert_equal(len(mod.sample), 1)
         mod.add_item(o2)
         assert_equal(len(mod.sample), 2)
@@ -103,7 +109,7 @@ def test_add_item(self):
 
     def test_add_item_exception(self):
         # When
-        mod = Model.default()
+        mod = Model()
 
         # Then Expect
         with pytest.raises(ValueError):
@@ -121,7 +127,7 @@ def test_add_item_with_interface_refnx(self):
         o2 = RepeatingMultilayer.from_pars(ls2, 1.0, 'oneLayerItem2')
         d = Sample.from_pars(o1, name='myModel')
         resolution_function = constant_resolution_function(2.0)
-        mod = Model.from_pars(d, 2, 1e-5, resolution_function, 'newModel', interface=interface)
+        mod = Model(d, 2, 1e-5, resolution_function, 'newModel', interface=interface)
         assert_equal(len(mod.interface()._wrapper.storage['item']), 1)
         assert_equal(len(mod.interface()._wrapper.storage['layer']), 2)
         mod.add_item(o2)
@@ -141,7 +147,7 @@ def test_add_item_with_interface_refl1d(self):
         o2 = RepeatingMultilayer.from_pars(ls2, 1.0, 'oneLayerItem2')
         d = Sample.from_pars(o1, name='myModel')
         resolution_function = constant_resolution_function(2.0)
-        mod = Model.from_pars(d, 2, 1e-5, resolution_function, 'newModel', interface=interface)
+        mod = Model(d, 2, 1e-5, resolution_function, 'newModel', interface=interface)
         assert_equal(len(mod.interface()._wrapper.storage['item']), 1)
         assert_equal(len(mod.interface()._wrapper.storage['layer']), 2)
         mod.add_item(o2)
@@ -160,7 +166,7 @@ def test_add_item_with_interface_refl1d(self):
     #     o1 = RepeatingMultilayer.from_pars(ls1, 2.0, 'twoLayerItem1')
     #     o2 = RepeatingMultilayer.from_pars(ls2, 1.0, 'oneLayerItem2')
     #     d = Sample.from_pars(o1, name='myModel')
-    #     mod = Model.from_pars(d, 2, 1e-5, 2.0, 'newModel', interface=interface)
+    #     mod = Model(d, 2, 1e-5, 2.0, 'newModel', interface=interface)
     #     assert_equal(len(mod.interface()._wrapper.storage['item']), 1)
     #     assert_equal(len(mod.interface()._wrapper.storage['layer']), 2)
     #     mod.add_item(o2)
@@ -178,7 +184,7 @@ def test_duplicate_item(self):
         o2 = RepeatingMultilayer.from_pars(ls2, 1.0, 'oneLayerItem2')
         d = Sample.from_pars(o1, name='myModel')
         resolution_function = constant_resolution_function(2.0)
-        mod = Model.from_pars(d, 2, 1e-5, resolution_function, 'newModel')
+        mod = Model(d, 2, 1e-5, resolution_function, 'newModel')
         assert_equal(len(mod.sample), 1)
         mod.add_item(o2)
         assert_equal(len(mod.sample), 2)
@@ -199,7 +205,7 @@ def test_duplicate_item_with_interface_refnx(self):
         o2 = RepeatingMultilayer.from_pars(ls2, 1.0, 'oneLayerItem2')
         d = Sample.from_pars(o1, name='myModel')
         resolution_function = constant_resolution_function(2.0)
-        mod = Model.from_pars(d, 2, 1e-5, resolution_function, 'newModel', interface=interface)
+        mod = Model(d, 2, 1e-5, resolution_function, 'newModel', interface=interface)
         assert_equal(len(mod.interface()._wrapper.storage['item']), 1)
         mod.add_item(o2)
         assert_equal(len(mod.interface()._wrapper.storage['item']), 2)
@@ -219,7 +225,7 @@ def test_duplicate_item_with_interface_refl1d(self):
         o2 = RepeatingMultilayer.from_pars(ls2, 1.0, 'oneLayerItem2')
         d = Sample.from_pars(o1, name='myModel')
         resolution_function = constant_resolution_function(2.0)
-        mod = Model.from_pars(d, 2, 1e-5, resolution_function, 'newModel', interface=interface)
+        mod = Model(d, 2, 1e-5, resolution_function, 'newModel', interface=interface)
         assert_equal(len(mod.interface()._wrapper.storage['item']), 1)
         mod.add_item(o2)
         assert_equal(len(mod.interface()._wrapper.storage['item']), 2)
@@ -238,7 +244,7 @@ def test_duplicate_item_with_interface_refl1d(self):
     #     o1 = RepeatingMultilayer.from_pars(ls1, 2.0, 'twoLayerItem1')
     #     o2 = RepeatingMultilayer.from_pars(ls2, 1.0, 'oneLayerItem2')
     #     d = Sample.from_pars(o1, name='myModel')
-    #     mod = Model.from_pars(d, 2, 1e-5, 2.0, 'newModel', interface=interface)
+    #     mod = Model(d, 2, 1e-5, 2.0, 'newModel', interface=interface)
     #     assert_equal(len(mod.interface()._wrapper.storage['item']), 1)
     #     mod.add_item(o2)
     #     assert_equal(len(mod.interface()._wrapper.storage['item']), 2)
@@ -256,7 +262,7 @@ def test_remove_item(self):
         o2 = RepeatingMultilayer.from_pars(ls2, 1.0, 'oneLayerItem2')
         d = Sample.from_pars(o1, name='myModel')
         resolution_function = constant_resolution_function(2.0)
-        mod = Model.from_pars(d, 2, 1e-5, resolution_function, 'newModel')
+        mod = Model(d, 2, 1e-5, resolution_function, 'newModel')
         assert_equal(len(mod.sample), 1)
         mod.add_item(o2)
         assert_equal(len(mod.sample), 2)
@@ -275,7 +281,7 @@ def test_remove_item_with_interface_refnx(self):
         o2 = RepeatingMultilayer.from_pars(ls2, 1.0, 'oneLayerItem2')
         d = Sample.from_pars(o1, name='myModel')
         resolution_function = constant_resolution_function(2.0)
-        mod = Model.from_pars(d, 2, 1e-5, resolution_function, 'newModel', interface=interface)
+        mod = Model(d, 2, 1e-5, resolution_function, 'newModel', interface=interface)
         assert_equal(len(mod.interface()._wrapper.storage['item']), 1)
         assert_equal(len(mod.interface()._wrapper.storage['layer']), 2)
         mod.add_item(o2)
@@ -296,9 +302,9 @@ def test_remove_item_with_interface_refl1d(self):
         ls2 = LayerCollection.from_pars(l2, l1, name='twoLayer2')
         o1 = RepeatingMultilayer.from_pars(ls1, 2.0, 'twoLayerItem1')
         o2 = RepeatingMultilayer.from_pars(ls2, 1.0, 'oneLayerItem2')
-        d = Sample.from_pars(o1, name='myModel')
+        d = Sample(o1, name='myModel')
         resolution_function = constant_resolution_function(2.0)
-        mod = Model.from_pars(d, 2, 1e-5, resolution_function, 'newModel', interface=interface)
+        mod = Model(d, 2, 1e-5, resolution_function, 'newModel', interface=interface)
         assert_equal(len(mod.interface()._wrapper.storage['item']), 1)
         assert_equal(len(mod.interface()._wrapper.storage['layer']), 2)
         mod.add_item(o2)
@@ -320,7 +326,7 @@ def test_remove_item_with_interface_refl1d(self):
     #     o1 = RepeatingMultilayer.from_pars(ls1, 2.0, 'twoLayerItem1')
     #     o2 = RepeatingMultilayer.from_pars(ls2, 1.0, 'oneLayerItem2')
     #     d = Sample.from_pars(o1, name='myModel')
-    #     mod = Model.from_pars(d, 2, 1e-5, 2.0, 'newModel', interface=interface)
+    #     mod = Model(d, 2, 1e-5, 2.0, 'newModel', interface=interface)
     #     assert_equal(len(mod.interface()._wrapper.storage['item']), 1)
     #     assert_equal(len(mod.interface()._wrapper.storage['layer']), 2)
     #     mod.add_item(o2)
@@ -331,17 +337,17 @@ def test_remove_item_with_interface_refl1d(self):
     #     assert_equal(len(mod.interface()._wrapper.storage['layer']), 2)
 
     def test_uid(self):
-        p = Model.default()
+        p = Model()
         assert_equal(p.uid, p._borg.map.convert_id_to_key(p))
 
     def test_set_resolution_function(self):
         mock_resolution_function = MagicMock()
-        model = Model.default()
+        model = Model()
         model.set_resolution_function(mock_resolution_function)
         assert model._resolution_function == mock_resolution_function
 
     def test_repr(self):
-        model = Model.default()
+        model = Model()
 
         assert (
             model.__repr__()
@@ -350,7 +356,7 @@ def test_repr(self):
 
     def test_repr_resolution_function(self):
         resolution_function = linear_spline_resolution_function([0, 10], [0, 10])
-        model = Model.default()
+        model = Model()
         model.set_resolution_function(resolution_function)
         assert (
             model.__repr__()
@@ -360,7 +366,7 @@ def test_repr_resolution_function(self):
     def test_dict_round_trip(self):
         resolution_function = linear_spline_resolution_function([0, 10], [0, 10])
         interface = CalculatorFactory()
-        model = Model.default(interface)
+        model = Model(interface=interface)
         model.set_resolution_function(resolution_function)
         surfactant = SurfactantLayer.default()
         model.add_item(surfactant)

tests/test_fitting.py

@@ -35,7 +35,7 @@ def test_fitting(self):
             superphase,
             name='Film Structure',
         )
-        model = Model.from_pars(sample, 1, 1e-6, 0.02, 'Film Model')
+        model = Model(sample, 1, 1e-6, 0.02, 'Film Model')
         # Thicknesses
         sio2_layer.thickness.bounds = (15, 50)
         film_layer.thickness.bounds = (200, 300)