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BaseAssembly

Bases: BaseCore

Assembly of layers.

The front layer (front_layer) is the layer the neutron beam starts in, it has an index of 0. The back layer (back_layer) is the final layer from which the unreflected neutron beam is transmitted, its index number depends on the number of finite layers in the system, but it might be accessed at index -1.

Source code in src/easyreflectometry/sample/assemblies/base_assembly.py 
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class BaseAssembly(BaseCore):
    """Assembly of layers.

    The front layer (front_layer) is the layer the neutron beam starts in, it has an index of 0.
    The back layer (back_layer) is the final layer from which the unreflected neutron beam is transmitted,
    its index number depends on the number of finite layers in the system, but it might be accessed at index -1.
    """

    def __init__(
        self,
        name: str,
        type: str,
        interface,
        layers: LayerCollection,
        unique_name: Optional[str] = None,
    ):
        super().__init__(name=name, unique_name=unique_name)
        self._layers = layers

        # Type is needed when fitting in easyscience
        self._type = type
        self._roughness_constraints_setup = False
        self._thickness_constraints_setup = False

        if interface is not None:
            self.interface = interface

    @property
    def layers(self) -> LayerCollection:
        return self._layers

    @layers.setter
    def layers(self, value: LayerCollection) -> None:
        self._layers = value

    @property
    def type(self) -> str:
        """Get type of the assembly.

        Needed by the GUI.
        """
        return self._type

    @property
    def front_layer(self) -> Optional[Layer]:
        """Get the front layer in the assembly."""
        if len(self.layers) == 0:
            return None
        return self.layers[0]

    @front_layer.setter
    def front_layer(self, layer: Layer) -> None:
        """Set the front layer in the assembly.

        Parameters
        ----------
        layer : Layer
            Layer to set as the front layer.
        """
        if len(self.layers) == 0:
            self.layers.append(layer)
        else:
            self.layers[0] = layer

    @property
    def back_layer(self) -> Optional[Layer]:
        """Get the back layer in the assembly."""

        if len(self.layers) < 2:
            return None
        return self.layers[-1]

    @back_layer.setter
    def back_layer(self, layer: Layer) -> None:
        """Set the back layer in the assembly.

        Parameters
        ----------
        layer : Layer
            Layer to set as the back layer.
        """

        if len(self.layers) == 0:
            raise Exception('There is no front layer to add the back layer to. Please add a front layer first.')
        if len(self.layers) == 1:
            self.layers.append(layer)
        else:
            self.layers[-1] = layer

    def _setup_thickness_constraints(self) -> None:
        """Setup thickness constraint, front layer is the deciding layer."""
        independent_param = self.front_layer.thickness
        for i in range(1, len(self.layers)):
            self.layers[i].thickness.make_dependent_on(dependency_expression='a', dependency_map={'a': independent_param})
        self._thickness_constraints_setup = True

    def _enable_thickness_constraints(self):
        """Enable the thickness constraint."""
        if self._thickness_constraints_setup:
            # Make sure that the thickness constraint is enabled
            self._setup_thickness_constraints()
            # Make sure that the thickness parameter is enabled
        else:
            raise Exception('Thickness constraints not setup')

    def _disable_thickness_constraints(self):
        """Disable the thickness constraint."""
        if self._thickness_constraints_setup:
            for i in range(1, len(self.layers)):
                self.layers[i].thickness.make_independent()
        else:
            raise Exception('Thickness constraints not setup')

    def _setup_roughness_constraints(self) -> None:
        """Setup roughness constraint, front layer is the deciding layer."""
        independent_parameter = self.front_layer.roughness
        for i in range(1, len(self.layers)):
            self.layers[i].roughness.make_dependent_on(dependency_expression='a', dependency_map={'a': independent_parameter})
        self._roughness_constraints_setup = True

    def _enable_roughness_constraints(self):
        """Enable the roughness constraint."""
        independent_parameter = self.front_layer.roughness
        for i in range(1, len(self.layers)):
            self.layers[i].roughness.make_dependent_on(dependency_expression='a', dependency_map={'a': independent_parameter})

    def _disable_roughness_constraints(self):
        """Disable the roughness constraint."""
        for i in range(1, len(self.layers)):
            self.layers[i].roughness.make_independent()

type property

Get type of the assembly.

Needed by the GUI.

front_layer property writable

Get the front layer in the assembly.

back_layer property writable

Get the back layer in the assembly.

Multilayer

Bases: BaseAssembly

A multi layer is build from a single or a list of Layer or LayerCollection.

The multi layer will arrange the layers as slabs, allowing the reflectometry to be determined from them. The front layer is where the neutron beam starts in, it has an index of 0.

More information about the usage of this assembly is available in the multilayer documentation_

.. _multilayer documentation: ../sample/assemblies_library.html#multilayer

Source code in src/easyreflectometry/sample/assemblies/multilayer.py 
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class Multilayer(BaseAssembly):
    """A multi layer is build from a single or a list of `Layer` or `LayerCollection`.

    The multi layer will arrange the layers as slabs, allowing the reflectometry to be determined from them.
    The front layer is where the neutron beam starts in, it has an index of 0.

    More information about the usage of this assembly is available in the
    `multilayer documentation`_

    .. _`multilayer documentation`: ../sample/assemblies_library.html#multilayer
    """

    def __init__(
        self,
        layers: Union[Layer, list[Layer], LayerCollection, None] = None,
        name: str = 'EasyMultilayer',
        unique_name: Optional[str] = None,
        interface=None,
        type: str = 'Multi-layer',
        populate_if_none: Optional[bool] = True,
    ):
        """Constructor.

        Parameters
        ----------
        populate_if_none : Optional[bool], optional
            By default, True.
        unique_name : Optional[str], optional
            By default, None.
        layers : Union[Layer, list[Layer], LayerCollection, None], optional
            The layers that make up the multi-layer. By default, None.
        name : str, optional
            Name for multi layer. By default, 'EasyMultilayer'.
        interface :
            Calculator interface. By default, None.
        type : str, optional
            Type of the constructed instance. By default, 'Multi-layer'.
        """
        if layers is None:
            if populate_if_none:
                layers = LayerCollection([Layer(interface=interface)])
            else:
                layers = LayerCollection()
        elif isinstance(layers, Layer):
            layers = LayerCollection(layers, name=layers.name)
        elif isinstance(layers, list):
            layers = LayerCollection(*layers, name='/'.join([layer.name for layer in layers]))
        # Needed to ensure an empty list is created when saving and instatiating the object as_dict -> from_dict
        # Else collisions might occur in global_object.map
        self.populate_if_none = False

        super().__init__(
            name=name,
            type=type,
            interface=interface,
            layers=layers,
            unique_name=unique_name,
        )

    def add_layer(self, *layers: tuple[Layer]) -> None:
        """Add a layer to the multi layer.

        Parameters
        ----------
        *layers : tuple[Layer]
            Layers to add to the multi layer.
        """
        for arg in layers:
            if issubclass(arg.__class__, Layer):
                self.layers.append(arg)
                if self.interface is not None:
                    self.interface().add_layer_to_item(arg.unique_name, self.unique_name)

    def duplicate_layer(self, idx: int) -> None:
        """Duplicate a given layer.

        Parameters
        ----------
        idx : int
            Index of layer to duplicate.
        """
        to_duplicate = self.layers[idx]
        duplicate_layer = Layer(
            material=to_duplicate.material,
            thickness=to_duplicate.thickness.value,
            roughness=to_duplicate.roughness.value,
            name=to_duplicate.name + ' duplicate',
        )
        self.add_layer(duplicate_layer)

    def remove_layer(self, idx: int) -> None:
        """Remove a layer from the item.

        Parameters
        ----------
        idx : int
            Index of layer to remove.
        """
        if self.interface is not None:
            self.interface().remove_layer_from_item(self.layers[idx].unique_name, self.unique_name)
        del self.layers[idx]

    # Representation
    @property
    def _dict_repr(self) -> dict:
        """A simplified dict representation."""
        return {self.name: self.layers._dict_repr}

    @classmethod
    def from_dict(cls, data: dict) -> Multilayer:
        """Create a Multilayer from a dictionary."""
        multilayer = super().from_dict(data)
        return multilayer

__init__(layers=None, name='EasyMultilayer', unique_name=None, interface=None, type='Multi-layer', populate_if_none=True)

Constructor.

Parameters:

Name Type Description Default
populate_if_none Optional[bool]

By default, True.

 True
unique_name Optional[str]

By default, None.

 None
layers Union[Layer, list[Layer], LayerCollection, None]

The layers that make up the multi-layer. By default, None.

 None
name str

Name for multi layer. By default, 'EasyMultilayer'.

 'EasyMultilayer'
interface

Calculator interface. By default, None.

 None
type str

Type of the constructed instance. By default, 'Multi-layer'.

 'Multi-layer'
Source code in src/easyreflectometry/sample/assemblies/multilayer.py 
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def __init__(
    self,
    layers: Union[Layer, list[Layer], LayerCollection, None] = None,
    name: str = 'EasyMultilayer',
    unique_name: Optional[str] = None,
    interface=None,
    type: str = 'Multi-layer',
    populate_if_none: Optional[bool] = True,
):
    """Constructor.

    Parameters
    ----------
    populate_if_none : Optional[bool], optional
        By default, True.
    unique_name : Optional[str], optional
        By default, None.
    layers : Union[Layer, list[Layer], LayerCollection, None], optional
        The layers that make up the multi-layer. By default, None.
    name : str, optional
        Name for multi layer. By default, 'EasyMultilayer'.
    interface :
        Calculator interface. By default, None.
    type : str, optional
        Type of the constructed instance. By default, 'Multi-layer'.
    """
    if layers is None:
        if populate_if_none:
            layers = LayerCollection([Layer(interface=interface)])
        else:
            layers = LayerCollection()
    elif isinstance(layers, Layer):
        layers = LayerCollection(layers, name=layers.name)
    elif isinstance(layers, list):
        layers = LayerCollection(*layers, name='/'.join([layer.name for layer in layers]))
    # Needed to ensure an empty list is created when saving and instatiating the object as_dict -> from_dict
    # Else collisions might occur in global_object.map
    self.populate_if_none = False

    super().__init__(
        name=name,
        type=type,
        interface=interface,
        layers=layers,
        unique_name=unique_name,
    )

add_layer(*layers)

Add a layer to the multi layer.

Parameters:

Name Type Description Default
*layers tuple[Layer]

Layers to add to the multi layer.

 ()
Source code in src/easyreflectometry/sample/assemblies/multilayer.py 
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def add_layer(self, *layers: tuple[Layer]) -> None:
    """Add a layer to the multi layer.

    Parameters
    ----------
    *layers : tuple[Layer]
        Layers to add to the multi layer.
    """
    for arg in layers:
        if issubclass(arg.__class__, Layer):
            self.layers.append(arg)
            if self.interface is not None:
                self.interface().add_layer_to_item(arg.unique_name, self.unique_name)

duplicate_layer(idx)

Duplicate a given layer.

Parameters:

Name Type Description Default
idx int

Index of layer to duplicate.

 required
Source code in src/easyreflectometry/sample/assemblies/multilayer.py 
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def duplicate_layer(self, idx: int) -> None:
    """Duplicate a given layer.

    Parameters
    ----------
    idx : int
        Index of layer to duplicate.
    """
    to_duplicate = self.layers[idx]
    duplicate_layer = Layer(
        material=to_duplicate.material,
        thickness=to_duplicate.thickness.value,
        roughness=to_duplicate.roughness.value,
        name=to_duplicate.name + ' duplicate',
    )
    self.add_layer(duplicate_layer)

remove_layer(idx)

Remove a layer from the item.

Parameters:

Name Type Description Default
idx int

Index of layer to remove.

 required
Source code in src/easyreflectometry/sample/assemblies/multilayer.py 
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def remove_layer(self, idx: int) -> None:
    """Remove a layer from the item.

    Parameters
    ----------
    idx : int
        Index of layer to remove.
    """
    if self.interface is not None:
        self.interface().remove_layer_from_item(self.layers[idx].unique_name, self.unique_name)
    del self.layers[idx]

from_dict(data) classmethod

Create a Multilayer from a dictionary.

Source code in src/easyreflectometry/sample/assemblies/multilayer.py 
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@classmethod
def from_dict(cls, data: dict) -> Multilayer:
    """Create a Multilayer from a dictionary."""
    multilayer = super().from_dict(data)
    return multilayer

RepeatingMultilayer

Bases: Multilayer

A repeating multi layer is build from a Multilayer and which it repeats for a given number of times. This enables a computational efficiency in many reflectometry engines as the operation can be performed for a single Multilayer and cheaply combined for the appropriate number of repetitions.

More information about the usage of this assembly is available in the repeating multilayer documentation_

.. _repeating multilayer documentation: ../sample/assemblies_library.html#repeatingmultilayer

Source code in src/easyreflectometry/sample/assemblies/repeating_multilayer.py 
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class RepeatingMultilayer(Multilayer):
    """A repeating multi layer is build from a `Multilayer` and which it repeats
    for a given number of times. This enables a computational efficiency in many
    reflectometry engines as the operation can be performed for a single
    `Multilayer` and cheaply combined for the appropriate number of
    `repetitions`.

    More information about the usage of this assembly is available in the
    `repeating multilayer documentation`_

    .. _`repeating multilayer documentation`: ../sample/assemblies_library.html#repeatingmultilayer
    """

    def __init__(
        self,
        layers: Union[LayerCollection, Layer, list[Layer], None] = None,
        repetitions: Union[Parameter, int, None] = None,
        name: str = 'EasyRepeatingMultilayer',
        unique_name: Optional[str] = None,
        interface=None,
        populate_if_none: bool = True,
    ):
        """Constructor.

        Parameters
        ----------
        populate_if_none : bool, optional
            By default, True.
        unique_name : Optional[str], optional
            By default, None.
        layers : Union[LayerCollection, Layer, list[Layer], None], optional
            The layers that make up the multi-layer that will be repeated. By default, None.
        repetitions : Union[Parameter, int, None], optional
            Number of repetitions of the given series of layers. By default, None.
        name : str, optional
            Name for the repeating multi layer. By default, 'EasyRepeatingMultilayer'.
        interface :
            Calculator interface. By default, None.
        """
        if unique_name is None:
            unique_name = global_object.generate_unique_name(self.__class__.__name__)

        if layers is None:
            if populate_if_none:
                layers = LayerCollection([Layer(interface=interface)])
            else:
                layers = LayerCollection()
        elif isinstance(layers, Layer):
            layers = LayerCollection(layers, name=layers.name)
        elif isinstance(layers, list):
            layers = LayerCollection(*layers, name='/'.join([layer.name for layer in layers]))

        repetitions = get_as_parameter(
            name='repetitions',
            value=repetitions,
            default_dict=DEFAULTS,
            unique_name_prefix=f'{unique_name}_Repetitions',
        )

        super().__init__(
            layers=layers,
            name=name,
            unique_name=unique_name,
            interface=None,
            type='Repeating Multi-layer',
            populate_if_none=False,
        )
        self._repetitions = repetitions

        if interface is not None:
            self.interface = interface

    @property
    def repetitions(self) -> Parameter:
        return self._repetitions

    @repetitions.setter
    def repetitions(self, value) -> None:
        self._repetitions.value = value

    # Representation
    @property
    def _dict_repr(self) -> dict:
        """A simplified dict representation."""
        d_dict = {self.name: self.layers._dict_repr}
        d_dict[self.name]['repetitions'] = float(self.repetitions.value)
        return d_dict

__init__(layers=None, repetitions=None, name='EasyRepeatingMultilayer', unique_name=None, interface=None, populate_if_none=True)

Constructor.

Parameters:

Name Type Description Default
populate_if_none bool

By default, True.

 True
unique_name Optional[str]

By default, None.

 None
layers Union[LayerCollection, Layer, list[Layer], None]

The layers that make up the multi-layer that will be repeated. By default, None.

 None
repetitions Union[Parameter, int, None]

Number of repetitions of the given series of layers. By default, None.

 None
name str

Name for the repeating multi layer. By default, 'EasyRepeatingMultilayer'.

 'EasyRepeatingMultilayer'
interface

Calculator interface. By default, None.

 None
Source code in src/easyreflectometry/sample/assemblies/repeating_multilayer.py 
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def __init__(
    self,
    layers: Union[LayerCollection, Layer, list[Layer], None] = None,
    repetitions: Union[Parameter, int, None] = None,
    name: str = 'EasyRepeatingMultilayer',
    unique_name: Optional[str] = None,
    interface=None,
    populate_if_none: bool = True,
):
    """Constructor.

    Parameters
    ----------
    populate_if_none : bool, optional
        By default, True.
    unique_name : Optional[str], optional
        By default, None.
    layers : Union[LayerCollection, Layer, list[Layer], None], optional
        The layers that make up the multi-layer that will be repeated. By default, None.
    repetitions : Union[Parameter, int, None], optional
        Number of repetitions of the given series of layers. By default, None.
    name : str, optional
        Name for the repeating multi layer. By default, 'EasyRepeatingMultilayer'.
    interface :
        Calculator interface. By default, None.
    """
    if unique_name is None:
        unique_name = global_object.generate_unique_name(self.__class__.__name__)

    if layers is None:
        if populate_if_none:
            layers = LayerCollection([Layer(interface=interface)])
        else:
            layers = LayerCollection()
    elif isinstance(layers, Layer):
        layers = LayerCollection(layers, name=layers.name)
    elif isinstance(layers, list):
        layers = LayerCollection(*layers, name='/'.join([layer.name for layer in layers]))

    repetitions = get_as_parameter(
        name='repetitions',
        value=repetitions,
        default_dict=DEFAULTS,
        unique_name_prefix=f'{unique_name}_Repetitions',
    )

    super().__init__(
        layers=layers,
        name=name,
        unique_name=unique_name,
        interface=None,
        type='Repeating Multi-layer',
        populate_if_none=False,
    )
    self._repetitions = repetitions

    if interface is not None:
        self.interface = interface

SurfactantLayer

Bases: BaseAssembly

A surfactant layer constructs a series of layers representing the head and tail groups of a surfactant. This assembly allows the definition of a surfactant or lipid using the chemistry of the head (head_layer) and tail (tail_layer) regions, additionally this approach will make the application of constraints such as conformal roughness or area per molecule more straight forward.

More information about the usage of this assembly is available in the surfactant documentation_

.. _surfactant documentation: ../sample/assemblies_library.html#surfactantlayer

Source code in src/easyreflectometry/sample/assemblies/surfactant_layer.py 
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class SurfactantLayer(BaseAssembly):
    """A surfactant layer constructs a series of layers representing the
    head and tail groups of a surfactant.
    This assembly allows the definition of a surfactant or lipid using the chemistry
    of the head (head_layer) and tail (tail_layer) regions, additionally
    this approach will make the application of constraints such as conformal roughness
    or area per molecule more straight forward.

    More information about the usage of this assembly is available in the
    `surfactant documentation`_

    .. _`surfactant documentation`: ../sample/assemblies_library.html#surfactantlayer
    """

    def __init__(
        self,
        tail_layer: Optional[LayerAreaPerMolecule] = None,
        head_layer: Optional[LayerAreaPerMolecule] = None,
        name: str = 'EasySurfactantLayer',
        unique_name: Optional[str] = None,
        constrain_area_per_molecule: bool = False,
        conformal_roughness: bool = False,
        interface=None,
    ):
        """Constructor.

        Parameters
        ----------
        unique_name : Optional[str], optional
            By default, None.
        tail_layer : Optional[LayerAreaPerMolecule], optional
            Layer representing the tail part of the surfactant layer. By default, None.
        head_layer : Optional[LayerAreaPerMolecule], optional
            Layer representing the head part of the surfactant layer. By default, None.
        name : str, optional
            Name for surfactant layer. By default, 'EasySurfactantLayer'.
        constrain_area_per_molecule : bool, optional
            Constrain the area per molecule. By default, False.
        conformal_roughness : bool, optional
            Constrain the roughness to be the same for both layers. By default, False.
        interface :
            Calculator interface. By default, None.
        """
        if unique_name is None:
            unique_name = global_object.generate_unique_name(self.__class__.__name__)

        if tail_layer is None:
            air = Material(
                sld=0,
                isld=0,
                name='Air',
                unique_name=unique_name + '_MaterialTail',
                interface=interface,
            )
            tail_layer = LayerAreaPerMolecule(
                molecular_formula='C32D64',
                thickness=16,
                solvent=air,
                solvent_fraction=0.0,
                area_per_molecule=48.2,
                roughness=3,
                name='DPPC Tail',
                unique_name=unique_name + '_LayerAreaPerMoleculeTail',
                interface=interface,
            )
        if head_layer is None:
            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,
                solvent=d2o,
                solvent_fraction=0.2,
                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='Layers',
            unique_name=unique_name + '_LayerCollection',
            interface=interface,
        )
        super().__init__(
            name=name,
            unique_name=unique_name,
            type='Surfactant Layer',
            layers=surfactant,
            interface=interface,
        )

        self.conformal = False

        if constrain_area_per_molecule:
            self.constrain_area_per_molecule = True
        if conformal_roughness:
            self._enable_roughness_constraints()
            self.conformal = True

    @property
    def tail_layer(self) -> Optional[LayerAreaPerMolecule]:
        """Get the tail layer of the surfactant surface."""
        return self.front_layer

    @tail_layer.setter
    def tail_layer(self, layer: LayerAreaPerMolecule) -> None:
        """Set the tail layer of the surfactant surface."""
        self.front_layer = layer

    @property
    def head_layer(self) -> Optional[LayerAreaPerMolecule]:
        """Get the head layer of the surfactant surface."""
        return self.back_layer

    @head_layer.setter
    def head_layer(self, layer: LayerAreaPerMolecule) -> None:
        """Set the head layer of the surfactant surface."""
        self.back_layer = layer

    @property
    def constrain_area_per_molecule(self) -> bool:
        """Get the area per molecule constraint status."""
        constrained = not self.head_layer._area_per_molecule.independent
        return constrained

    @constrain_area_per_molecule.setter
    def constrain_area_per_molecule(self, status: bool):
        """Set the status for the area per molecule constraint such that the head and tail layers have the
        same area per molecule.

        Parameters
        ----------
        status : bool
            Boolean description the wanted of the constraint.
        """
        if status:
            independent_param = self.tail_layer._area_per_molecule
            self.head_layer._area_per_molecule.make_dependent_on(
                dependency_expression='a', dependency_map={'a': independent_param}
            )
        else:
            self.head_layer._area_per_molecule.make_independent()
        return

    @property
    def conformal_roughness(self) -> bool:
        """Get the roughness constraint status."""
        return self.conformal

    @conformal_roughness.setter
    def conformal_roughness(self, status: bool):
        """Set the status for the roughness to be the same for both layers.

        Parameters
        ----------
        status : bool
            Boolean description the wanted of the constraint.
        """
        if status:
            self._enable_roughness_constraints()
            self.conformal = True
        else:
            self._disable_roughness_constraints()
            self.conformal = False

    def constrain_solvent_roughness(self, solvent_roughness: Parameter):
        """Add the constraint to the solvent roughness.

        Parameters
        ----------
        solvent_roughness : Parameter
            The solvent roughness parameter.
        """
        if not self.conformal_roughness:
            raise ValueError('Roughness must be conformal to use this function.')
        solvent_roughness.value = self.tail_layer.roughness.value
        solvent_roughness.make_dependent_on(dependency_expression='a', dependency_map={'a': self.tail_layer.roughness})

    def constrain_multiple_contrast(
        self,
        another_contrast: SurfactantLayer,
        head_layer_thickness: bool = True,
        tail_layer_thickness: bool = True,
        head_layer_area_per_molecule: bool = True,
        tail_layer_area_per_molecule: bool = True,
        head_layer_fraction: bool = True,
        tail_layer_fraction: bool = True,
    ):
        """Constrain structural parameters between surfactant layer objects.

        Parameters
        ----------
        tail_layer_fraction : bool, optional
            By default, True.
        head_layer_fraction : bool, optional
            By default, True.
        tail_layer_area_per_molecule : bool, optional
            By default, True.
        head_layer_area_per_molecule : bool, optional
            By default, True.
        tail_layer_thickness : bool, optional
            By default, True.
        head_layer_thickness : bool, optional
            By default, True.
        another_contrast : SurfactantLayer
            The surfactant layer to constrain.
        """
        if head_layer_thickness:
            self.head_layer.thickness.make_dependent_on(
                dependency_expression='a',
                dependency_map={'a': another_contrast.head_layer.thickness},
            )

        if tail_layer_thickness:
            self.tail_layer.thickness.make_dependent_on(
                dependency_expression='a',
                dependency_map={'a': another_contrast.tail_layer.thickness},
            )

        if head_layer_area_per_molecule:
            self.head_layer._area_per_molecule.make_dependent_on(
                dependency_expression='a',
                dependency_map={'a': another_contrast.head_layer._area_per_molecule},
            )

        if tail_layer_area_per_molecule:
            self.tail_layer._area_per_molecule.make_dependent_on(
                dependency_expression='a',
                dependency_map={'a': another_contrast.tail_layer._area_per_molecule},
            )

        if head_layer_fraction:
            self.head_layer.material._fraction.make_dependent_on(
                dependency_expression='a',
                dependency_map={'a': another_contrast.head_layer.material._fraction},
            )

        if tail_layer_fraction:
            self.tail_layer.material._fraction.make_dependent_on(
                dependency_expression='a',
                dependency_map={'a': another_contrast.tail_layer.material._fraction},
            )

    @property
    def _dict_repr(self) -> dict:
        """A simplified dict representation."""
        return {
            self.name: {
                'head_layer': self.head_layer._dict_repr,
                'tail_layer': self.tail_layer._dict_repr,
                'area per molecule constrained': self.constrain_area_per_molecule,
                'conformal roughness': self.conformal_roughness,
            }
        }

    def to_dict(self, skip: Optional[list[str]] = None) -> dict:
        """Serialize, dropping the derived ``layers`` field (it is rebuilt
        from ``tail_layer`` and ``head_layer`` in ``__init__``).
        """
        this_dict = super().to_dict(skip=skip)
        this_dict.pop('layers', None)
        return this_dict

    def as_dict(self, skip: Optional[list[str]] = None) -> dict:
        return self.to_dict(skip=skip)

constrain_area_per_molecule property writable

Get the area per molecule constraint status.

tail_layer property writable

Get the tail layer of the surfactant surface.

head_layer property writable

Get the head layer of the surfactant surface.

conformal_roughness property writable

Get the roughness constraint status.

__init__(tail_layer=None, head_layer=None, name='EasySurfactantLayer', unique_name=None, constrain_area_per_molecule=False, conformal_roughness=False, interface=None)

Constructor.

Parameters:

Name Type Description Default
unique_name Optional[str]

By default, None.

 None
tail_layer Optional[LayerAreaPerMolecule]

Layer representing the tail part of the surfactant layer. By default, None.

 None
head_layer Optional[LayerAreaPerMolecule]

Layer representing the head part of the surfactant layer. By default, None.

 None
name str

Name for surfactant layer. By default, 'EasySurfactantLayer'.

 'EasySurfactantLayer'
constrain_area_per_molecule bool

Constrain the area per molecule. By default, False.

 False
conformal_roughness bool

Constrain the roughness to be the same for both layers. By default, False.

 False
interface

Calculator interface. By default, None.

 None
Source code in src/easyreflectometry/sample/assemblies/surfactant_layer.py 
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def __init__(
    self,
    tail_layer: Optional[LayerAreaPerMolecule] = None,
    head_layer: Optional[LayerAreaPerMolecule] = None,
    name: str = 'EasySurfactantLayer',
    unique_name: Optional[str] = None,
    constrain_area_per_molecule: bool = False,
    conformal_roughness: bool = False,
    interface=None,
):
    """Constructor.

    Parameters
    ----------
    unique_name : Optional[str], optional
        By default, None.
    tail_layer : Optional[LayerAreaPerMolecule], optional
        Layer representing the tail part of the surfactant layer. By default, None.
    head_layer : Optional[LayerAreaPerMolecule], optional
        Layer representing the head part of the surfactant layer. By default, None.
    name : str, optional
        Name for surfactant layer. By default, 'EasySurfactantLayer'.
    constrain_area_per_molecule : bool, optional
        Constrain the area per molecule. By default, False.
    conformal_roughness : bool, optional
        Constrain the roughness to be the same for both layers. By default, False.
    interface :
        Calculator interface. By default, None.
    """
    if unique_name is None:
        unique_name = global_object.generate_unique_name(self.__class__.__name__)

    if tail_layer is None:
        air = Material(
            sld=0,
            isld=0,
            name='Air',
            unique_name=unique_name + '_MaterialTail',
            interface=interface,
        )
        tail_layer = LayerAreaPerMolecule(
            molecular_formula='C32D64',
            thickness=16,
            solvent=air,
            solvent_fraction=0.0,
            area_per_molecule=48.2,
            roughness=3,
            name='DPPC Tail',
            unique_name=unique_name + '_LayerAreaPerMoleculeTail',
            interface=interface,
        )
    if head_layer is None:
        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,
            solvent=d2o,
            solvent_fraction=0.2,
            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='Layers',
        unique_name=unique_name + '_LayerCollection',
        interface=interface,
    )
    super().__init__(
        name=name,
        unique_name=unique_name,
        type='Surfactant Layer',
        layers=surfactant,
        interface=interface,
    )

    self.conformal = False

    if constrain_area_per_molecule:
        self.constrain_area_per_molecule = True
    if conformal_roughness:
        self._enable_roughness_constraints()
        self.conformal = True

constrain_solvent_roughness(solvent_roughness)

Add the constraint to the solvent roughness.

Parameters:

Name Type Description Default
solvent_roughness Parameter

The solvent roughness parameter.

 required
Source code in src/easyreflectometry/sample/assemblies/surfactant_layer.py 
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def constrain_solvent_roughness(self, solvent_roughness: Parameter):
    """Add the constraint to the solvent roughness.

    Parameters
    ----------
    solvent_roughness : Parameter
        The solvent roughness parameter.
    """
    if not self.conformal_roughness:
        raise ValueError('Roughness must be conformal to use this function.')
    solvent_roughness.value = self.tail_layer.roughness.value
    solvent_roughness.make_dependent_on(dependency_expression='a', dependency_map={'a': self.tail_layer.roughness})

constrain_multiple_contrast(another_contrast, head_layer_thickness=True, tail_layer_thickness=True, head_layer_area_per_molecule=True, tail_layer_area_per_molecule=True, head_layer_fraction=True, tail_layer_fraction=True)

Constrain structural parameters between surfactant layer objects.

Parameters:

Name Type Description Default
tail_layer_fraction bool

By default, True.

 True
head_layer_fraction bool

By default, True.

 True
tail_layer_area_per_molecule bool

By default, True.

 True
head_layer_area_per_molecule bool

By default, True.

 True
tail_layer_thickness bool

By default, True.

 True
head_layer_thickness bool

By default, True.

 True
another_contrast SurfactantLayer

The surfactant layer to constrain.

 required
Source code in src/easyreflectometry/sample/assemblies/surfactant_layer.py 
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def constrain_multiple_contrast(
    self,
    another_contrast: SurfactantLayer,
    head_layer_thickness: bool = True,
    tail_layer_thickness: bool = True,
    head_layer_area_per_molecule: bool = True,
    tail_layer_area_per_molecule: bool = True,
    head_layer_fraction: bool = True,
    tail_layer_fraction: bool = True,
):
    """Constrain structural parameters between surfactant layer objects.

    Parameters
    ----------
    tail_layer_fraction : bool, optional
        By default, True.
    head_layer_fraction : bool, optional
        By default, True.
    tail_layer_area_per_molecule : bool, optional
        By default, True.
    head_layer_area_per_molecule : bool, optional
        By default, True.
    tail_layer_thickness : bool, optional
        By default, True.
    head_layer_thickness : bool, optional
        By default, True.
    another_contrast : SurfactantLayer
        The surfactant layer to constrain.
    """
    if head_layer_thickness:
        self.head_layer.thickness.make_dependent_on(
            dependency_expression='a',
            dependency_map={'a': another_contrast.head_layer.thickness},
        )

    if tail_layer_thickness:
        self.tail_layer.thickness.make_dependent_on(
            dependency_expression='a',
            dependency_map={'a': another_contrast.tail_layer.thickness},
        )

    if head_layer_area_per_molecule:
        self.head_layer._area_per_molecule.make_dependent_on(
            dependency_expression='a',
            dependency_map={'a': another_contrast.head_layer._area_per_molecule},
        )

    if tail_layer_area_per_molecule:
        self.tail_layer._area_per_molecule.make_dependent_on(
            dependency_expression='a',
            dependency_map={'a': another_contrast.tail_layer._area_per_molecule},
        )

    if head_layer_fraction:
        self.head_layer.material._fraction.make_dependent_on(
            dependency_expression='a',
            dependency_map={'a': another_contrast.head_layer.material._fraction},
        )

    if tail_layer_fraction:
        self.tail_layer.material._fraction.make_dependent_on(
            dependency_expression='a',
            dependency_map={'a': another_contrast.tail_layer.material._fraction},
        )

to_dict(skip=None)

Serialize, dropping the derived layers field (it is rebuilt from tail_layer and head_layer in __init__).

Source code in src/easyreflectometry/sample/assemblies/surfactant_layer.py 
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def to_dict(self, skip: Optional[list[str]] = None) -> dict:
    """Serialize, dropping the derived ``layers`` field (it is rebuilt
    from ``tail_layer`` and ``head_layer`` in ``__init__``).
    """
    this_dict = super().to_dict(skip=skip)
    this_dict.pop('layers', None)
    return this_dict

Layer

Bases: BaseCore

Source code in src/easyreflectometry/sample/elements/layers/layer.py 
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class Layer(BaseCore):
    def __init__(
        self,
        material: Union[Material, None] = None,
        thickness: Union[Parameter, float, None] = None,
        roughness: Union[Parameter, float, None] = None,
        name: str = 'EasyLayer',
        unique_name: Optional[str] = None,
        interface=None,
    ):
        """Constructor.

        Parameters
        ----------
        unique_name : Optional[str], optional
            By default, None.
        material : Union[Material, None], optional
            The material for the layer. By default, None.
        thickness : Union[Parameter, float, None], optional
            Layer thickness in Angstrom. By default, None.
        roughness : Union[Parameter, float, None], optional
            Upper roughness on the layer in Angstrom. By default, None.
        name : str, optional
            Name of the layer. By default, 'EasyLayer'.
        interface :
            Interface object. By default, None.
        """
        if material is None:
            material = Material(interface=interface)

        if unique_name is None:
            unique_name = global_object.generate_unique_name(self.__class__.__name__)

        thickness_value = thickness
        thickness = get_as_parameter(
            name='thickness',
            value=thickness,
            default_dict=DEFAULTS,
            unique_name_prefix=f'{unique_name}_Thickness',
        )
        thickness.default_limits_pending = not isinstance(thickness_value, Parameter)

        roughness_value = roughness
        roughness = get_as_parameter(
            name='roughness',
            value=roughness,
            default_dict=DEFAULTS,
            unique_name_prefix=f'{unique_name}_Roughness',
        )
        roughness.default_limits_pending = not isinstance(roughness_value, Parameter)

        super().__init__(name=name, unique_name=unique_name)
        self._material = material
        self._thickness = thickness
        self._roughness = roughness

        if interface is not None:
            self.interface = interface

    @property
    def material(self) -> Material:
        return self._material

    @material.setter
    def material(self, value: Material) -> None:
        self._material = value

    @property
    def thickness(self) -> Parameter:
        return self._thickness

    @thickness.setter
    def thickness(self, value: float) -> None:
        self._thickness.value = value

    @property
    def roughness(self) -> Parameter:
        return self._roughness

    @roughness.setter
    def roughness(self, value: float) -> None:
        self._roughness.value = value

    def assign_material(self, material: Material) -> None:
        """Assign a material to the layer interface.

        Parameters
        ----------
        material : Material
            The material to assign to the layer.
        """
        self._material = material
        if self.interface is not None:
            self.interface().assign_material_to_layer(self.material.unique_name, self.unique_name)

    # Representation
    @property
    def _dict_repr(self) -> dict[str, str]:
        """A simplified dict representation."""
        return {
            self.name: {
                'material': self.material._dict_repr,
                'thickness': f'{self.thickness.value:.3f} {self.thickness.unit}',
                'roughness': f'{self.roughness.value:.3f} {self.roughness.unit}',
            }
        }

__init__(material=None, thickness=None, roughness=None, name='EasyLayer', unique_name=None, interface=None)

Constructor.

Parameters:

Name Type Description Default
unique_name Optional[str]

By default, None.

 None
material Union[Material, None]

The material for the layer. By default, None.

 None
thickness Union[Parameter, float, None]

Layer thickness in Angstrom. By default, None.

 None
roughness Union[Parameter, float, None]

Upper roughness on the layer in Angstrom. By default, None.

 None
name str

Name of the layer. By default, 'EasyLayer'.

 'EasyLayer'
interface

Interface object. By default, None.

 None
Source code in src/easyreflectometry/sample/elements/layers/layer.py 
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def __init__(
    self,
    material: Union[Material, None] = None,
    thickness: Union[Parameter, float, None] = None,
    roughness: Union[Parameter, float, None] = None,
    name: str = 'EasyLayer',
    unique_name: Optional[str] = None,
    interface=None,
):
    """Constructor.

    Parameters
    ----------
    unique_name : Optional[str], optional
        By default, None.
    material : Union[Material, None], optional
        The material for the layer. By default, None.
    thickness : Union[Parameter, float, None], optional
        Layer thickness in Angstrom. By default, None.
    roughness : Union[Parameter, float, None], optional
        Upper roughness on the layer in Angstrom. By default, None.
    name : str, optional
        Name of the layer. By default, 'EasyLayer'.
    interface :
        Interface object. By default, None.
    """
    if material is None:
        material = Material(interface=interface)

    if unique_name is None:
        unique_name = global_object.generate_unique_name(self.__class__.__name__)

    thickness_value = thickness
    thickness = get_as_parameter(
        name='thickness',
        value=thickness,
        default_dict=DEFAULTS,
        unique_name_prefix=f'{unique_name}_Thickness',
    )
    thickness.default_limits_pending = not isinstance(thickness_value, Parameter)

    roughness_value = roughness
    roughness = get_as_parameter(
        name='roughness',
        value=roughness,
        default_dict=DEFAULTS,
        unique_name_prefix=f'{unique_name}_Roughness',
    )
    roughness.default_limits_pending = not isinstance(roughness_value, Parameter)

    super().__init__(name=name, unique_name=unique_name)
    self._material = material
    self._thickness = thickness
    self._roughness = roughness

    if interface is not None:
        self.interface = interface

assign_material(material)

Assign a material to the layer interface.

Parameters:

Name Type Description Default
material Material

The material to assign to the layer.

 required
Source code in src/easyreflectometry/sample/elements/layers/layer.py 
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def assign_material(self, material: Material) -> None:
    """Assign a material to the layer interface.

    Parameters
    ----------
    material : Material
        The material to assign to the layer.
    """
    self._material = material
    if self.interface is not None:
        self.interface().assign_material_to_layer(self.material.unique_name, self.unique_name)

BaseCollection

Bases: EasyList

Local base for sample-tree collections (Material/Layer/Assembly/Model collections).

Built on top of easyscience.base_classes.EasyList (the replacement for the deprecated CollectionBase). On top of EasyList this class adds:

  • a name property
  • an interface property whose setter propagates the calculator interface to every contained item
  • propagation of the current interface to newly inserted items
  • a populate_if_none flag preserved for serialization round-trip
  • convenience helpers names, move_up, move_down, remove_at
  • a yaml-formatted __repr__ driven by _dict_repr
  • an as_dict alias for to_dict with skip= support and interface excluded by default

Subclasses (LayerCollection, MaterialCollection, Sample, ModelCollection) keep their existing constructor shape — they pass name and interface positionally to this class, items as *args, and additional configuration as kwargs.

Source code in src/easyreflectometry/sample/collections/base_collection.py 
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class BaseCollection(EasyList):
    """Local base for sample-tree collections (Material/Layer/Assembly/Model collections).

    Built on top of `easyscience.base_classes.EasyList` (the replacement for
    the deprecated `CollectionBase`). On top of `EasyList` this class adds:

    - a `name` property
    - an `interface` property whose setter propagates the calculator interface
      to every contained item
    - propagation of the current `interface` to newly inserted items
    - a `populate_if_none` flag preserved for serialization round-trip
    - convenience helpers `names`, `move_up`, `move_down`, `remove_at`
    - a yaml-formatted `__repr__` driven by `_dict_repr`
    - an `as_dict` alias for `to_dict` with `skip=` support and `interface`
      excluded by default

    Subclasses (`LayerCollection`, `MaterialCollection`, `Sample`,
    `ModelCollection`) keep their existing constructor shape — they pass
    `name` and `interface` positionally to this class, items as `*args`, and
    additional configuration as kwargs.
    """

    def __init__(
        self,
        name: str,
        interface: Any = None,
        *args: Any,
        unique_name: Optional[str] = None,
        populate_if_none: bool = False,
        **kwargs: Any,
    ):
        # `_interface` must exist before `super().__init__` because `EasyList`
        # calls `self.append(item)` for each positional arg, which routes
        # through our `insert` override and reads `self._interface`.
        self._interface = None
        self._name = name
        # Legacy `CollectionBase` accepted items either positionally or as a
        # list-valued keyword (e.g. ``LayerCollection(layers=[a, b])``). Pull
        # any list-valued kwarg into the positional stream so callers using
        # that older pattern keep working.
        extra_items = []
        for key in list(kwargs.keys()):
            if isinstance(kwargs[key], list) and kwargs[key] and key != 'data':
                extra_items.extend(kwargs.pop(key))
        if extra_items:
            args = tuple(args) + tuple(extra_items)
        super().__init__(*args, unique_name=unique_name, **kwargs)
        # `populate_if_none` is a control flag, not state. It is serialized so
        # `from_dict` knows whether the original construction filled in
        # defaults; the value should be `False` once the data is restored.
        self.populate_if_none = populate_if_none

        # Assign interface LAST — propagates to all contained items.
        if interface is not None:
            self.interface = interface

    # ----- name -----

    @property
    def name(self) -> str:
        return self._name

    @name.setter
    def name(self, value: str) -> None:
        self._name = value

    # ----- interface -----

    @property
    def interface(self) -> Any:
        return self._interface

    @interface.setter
    def interface(self, new_interface: Any) -> None:
        self._interface = new_interface
        if new_interface is None:
            return
        # Propagate to existing items.
        for item in self._data:
            if self._has_interface_setter(type(item)):
                item.interface = new_interface
        # Tell the calculator to bind to self (matches the legacy CollectionBase
        # behavior which called `interface.generate_bindings(self)` once per
        # collection).
        if hasattr(new_interface, 'generate_bindings'):
            new_interface.generate_bindings(self)

    def _get_key(self, obj):
        """Use the item's `name` for string-indexed lookups.

        Matches the legacy `CollectionBase.__getitem__` behaviour which
        searched by `item.name`. `EasyList` defaults to `unique_name`; the
        existing `Project` code (and callers) look items up by their pretty
        name (e.g. `materials['Air']`).
        """
        return getattr(obj, 'name', None) or obj.unique_name

    @staticmethod
    def _has_interface_setter(obj_type: type) -> bool:
        for klass in obj_type.__mro__:
            prop = klass.__dict__.get('interface')
            if isinstance(prop, property):
                return prop.fset is not None
        return False

    # ----- mutable-sequence overrides that propagate interface -----

    def insert(self, index: int, value: Any) -> None:
        """Insert and (if an interface is set) propagate it to the new item.

        Legacy `CollectionBase.insert` did `value.interface = self.interface`
        after registering the item; we replicate the same behaviour here so
        downstream calculator state stays in sync when items are appended
        after the collection's interface was already set.

        The type check from `EasyList.insert` is bypassed: each subclass
        accepts a single item type (Layer / Material / BaseAssembly / Model)
        and enforces it elsewhere, while the EasyList check would require
        every item to be a `NewBase` subclass — which was historically not
        guaranteed and forces an extra coupling we don't need.
        """
        if not isinstance(index, int):
            raise TypeError('Index must be an integer')
        # Skip the EasyList protected-types check; mimic the rest of its insert
        # (duplicate-name warning + append-to-_data).
        import warnings as _warnings

        if value in self:
            _warnings.warn(f'Item with unique name "{self._get_key(value)}" already in collection, it will be ignored')
            return
        self._data.insert(index, value)
        if self._interface is not None and self._has_interface_setter(type(value)):
            value.interface = self._interface

    # ----- helpers -----

    @property
    def names(self) -> list:
        """List of item names."""
        return [getattr(item, 'name', None) for item in self._data]

    @property
    def data(self) -> list:
        """Read-only view of the underlying item list.

        Provided for compatibility with code (and tests) written against the
        legacy `CollectionBase` shape, which exposed items via `.data`.
        """
        return list(self._data)

    def move_up(self, index: int) -> None:
        """Move the element at the given index up in the collection."""
        if index == 0:
            return
        self.insert(index - 1, self.pop(index))

    def move_down(self, index: int) -> None:
        """Move the element at the given index down in the collection."""
        if index == len(self) - 1:
            return
        self.insert(index + 1, self.pop(index))

    def remove_at(self, index: int) -> None:
        """Remove the item at *index* from the collection.

        Renamed from the legacy `BaseCollection.remove(index)` which shadowed
        `MutableSequence.remove(value)` (remove-by-value, inherited from
        `EasyList`). Callers that meant "remove by index" should use this; the
        standard `remove(value)` is still available with its usual semantics.
        """
        self.pop(index)

    # ----- compatibility shims (kept until call sites migrate) -----

    def get_parameters(self) -> List[Parameter]:
        """Compatibility alias for legacy callers; prefer `get_all_parameters`."""
        return self.get_all_parameters()

    def get_all_variables(self) -> List:
        """Flat list of every Parameter/Descriptor across all items.

        Walks each item in the collection and unions whatever each item
        exposes via its own `get_all_variables` (for `ModelBase` /
        `BaseCore` children) or, for objects that lack that hook,
        unions any direct `DescriptorBase` attributes.
        """
        from easyscience.variable.descriptor_base import DescriptorBase

        out: list = []
        seen: set[int] = set()
        for item in self._data:
            if hasattr(item, 'get_all_variables'):
                for v in item.get_all_variables():
                    if id(v) not in seen:
                        seen.add(id(v))
                        out.append(v)
            elif isinstance(item, DescriptorBase):
                if id(item) not in seen:
                    seen.add(id(item))
                    out.append(item)
        return out

    def get_all_parameters(self) -> List[Parameter]:
        return [v for v in self.get_all_variables() if isinstance(v, Parameter)]

    def get_free_parameters(self) -> List[Parameter]:
        return [p for p in self.get_all_parameters() if p.independent and not p.fixed]

    def get_fit_parameters(self) -> List[Parameter]:
        """Alias kept for the minimizer; matches `ModelBase.get_fit_parameters`."""
        return self.get_free_parameters()

    def _get_linkable_attributes(self) -> List[Parameter]:
        """Bridge for `easyscience.fitting.calculators.interface_factory.generate_bindings`."""
        return self.get_all_variables()

    # ----- repr -----

    @property
    def _dict_repr(self) -> dict:
        """A simplified dict representation."""
        return {self.name: [getattr(i, '_dict_repr', repr(i)) for i in self._data]}

    def __repr__(self) -> str:
        try:
            return yaml_dump(self._dict_repr)
        except Exception:
            return super().__repr__()

    # ----- serialization -----

    def _convert_to_dict(self, d: dict, encoder=None, skip: Optional[List[str]] = None, **kwargs) -> dict:
        """Serializer hook used when this collection is encoded as a *child*
        attribute (e.g. `Multilayer.layers`).

        `SerializerBase._convert_to_dict` iterates `_arg_spec` to populate the
        base dict and then calls `obj._convert_to_dict(d, ...)` if defined.
        Because `data` is supplied via `*args` (VAR_POSITIONAL — not part of
        `_arg_spec`), without this hook the nested encoding would miss the
        items entirely and round-trip would reconstruct an empty collection.
        """
        if skip is None:
            skip = []
        if self._protected_types != [NewBase] and 'protected_types' not in d:
            d['protected_types'] = [{'@module': c.__module__, '@class': c.__name__} for c in self._protected_types]
        # Encode each item. Defer to the encoder's recursive walk so nested
        # ModelBase / NewBase items get properly serialized.
        item_skip = list(skip)
        items: list = []
        for item in self._data:
            if encoder is not None and hasattr(encoder, '_recursive_encoder'):
                items.append(encoder._recursive_encoder(item, skip=item_skip, encoder=encoder, full_encode=False))
            elif hasattr(item, 'to_dict'):
                try:
                    items.append(item.to_dict(skip=list(item_skip)))
                except TypeError:
                    items.append(item.to_dict())
            else:
                items.append(item)
        d['data'] = items
        return d

    def to_dict(self, skip: Optional[List[str]] = None) -> dict:
        """Serialize with `skip` support; `interface` excluded by default.

        `EasyList.to_dict` doesn't accept a `skip` argument and is hard-wired
        to dump `data` plus the parent's `_arg_spec` view. We reimplement here
        so existing callers (`Project`, `Model.as_dict`, etc.) can keep
        passing `skip=['unique_name']` or similar.

        ``NewBase.to_dict`` mutates the ``skip`` list in-place (e.g. it
        appends ``'unique_name'`` when the collection's own unique_name is
        default-generated). We therefore pass a *copy* to it, otherwise the
        mutation would leak into the per-item serialization below and force
        every item Parameter dict to drop its ``unique_name`` — breaking the
        from_dict round-trip.
        """
        skip = list(skip or [])
        if 'interface' not in skip:
            skip.append('interface')
        # Matches legacy `BasedBase.as_dict`: drop unique_name from the
        # serialized form so nested Parameters don't get explicit names that
        # would collide with the auto-generated names produced when the global
        # counter restarts during reconstruction.
        if 'unique_name' not in skip:
            skip.append('unique_name')
        dict_repr = NewBase.to_dict(self, skip=list(skip))
        if self._protected_types != [NewBase]:
            dict_repr['protected_types'] = [{'@module': c.__module__, '@class': c.__name__} for c in self._protected_types]
        dict_repr['data'] = []
        for item in self._data:
            # Items that are ModelBase / BaseCore subclasses accept `skip`;
            # other shapes use their no-arg `to_dict`/`as_dict`.
            if hasattr(item, 'to_dict'):
                try:
                    dict_repr['data'].append(item.to_dict(skip=list(skip)))
                except TypeError:
                    dict_repr['data'].append(item.to_dict())
            else:
                dict_repr['data'].append(item.as_dict(skip=list(skip)))
        return dict_repr

    def as_dict(self, skip: Optional[List[str]] = None) -> dict:
        """Compatibility alias for :meth:`to_dict`."""
        return self.to_dict(skip=skip)

    def __deepcopy__(self, memo):
        """Round-trip via dict-skip-unique to get a fresh copy.

        `NewBase.__copy__` already does this; the override is kept (rather
        than deleted) to mirror the legacy `BaseCollection.__deepcopy__`
        semantics — callers that relied on `copy.deepcopy(collection)` still
        get a clone built from `from_dict(as_dict(skip=['unique_name']))`.
        """
        return self.from_dict(self.as_dict(skip=['unique_name']))

names property

List of item names.

data property

Read-only view of the underlying item list.

Provided for compatibility with code (and tests) written against the legacy CollectionBase shape, which exposed items via .data.

insert(index, value)

Insert and (if an interface is set) propagate it to the new item.

Legacy CollectionBase.insert did value.interface = self.interface after registering the item; we replicate the same behaviour here so downstream calculator state stays in sync when items are appended after the collection's interface was already set.

The type check from EasyList.insert is bypassed: each subclass accepts a single item type (Layer / Material / BaseAssembly / Model) and enforces it elsewhere, while the EasyList check would require every item to be a NewBase subclass — which was historically not guaranteed and forces an extra coupling we don't need.

Source code in src/easyreflectometry/sample/collections/base_collection.py 
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def insert(self, index: int, value: Any) -> None:
    """Insert and (if an interface is set) propagate it to the new item.

    Legacy `CollectionBase.insert` did `value.interface = self.interface`
    after registering the item; we replicate the same behaviour here so
    downstream calculator state stays in sync when items are appended
    after the collection's interface was already set.

    The type check from `EasyList.insert` is bypassed: each subclass
    accepts a single item type (Layer / Material / BaseAssembly / Model)
    and enforces it elsewhere, while the EasyList check would require
    every item to be a `NewBase` subclass — which was historically not
    guaranteed and forces an extra coupling we don't need.
    """
    if not isinstance(index, int):
        raise TypeError('Index must be an integer')
    # Skip the EasyList protected-types check; mimic the rest of its insert
    # (duplicate-name warning + append-to-_data).
    import warnings as _warnings

    if value in self:
        _warnings.warn(f'Item with unique name "{self._get_key(value)}" already in collection, it will be ignored')
        return
    self._data.insert(index, value)
    if self._interface is not None and self._has_interface_setter(type(value)):
        value.interface = self._interface

move_up(index)

Move the element at the given index up in the collection.

Source code in src/easyreflectometry/sample/collections/base_collection.py 
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def move_up(self, index: int) -> None:
    """Move the element at the given index up in the collection."""
    if index == 0:
        return
    self.insert(index - 1, self.pop(index))

move_down(index)

Move the element at the given index down in the collection.

Source code in src/easyreflectometry/sample/collections/base_collection.py 
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def move_down(self, index: int) -> None:
    """Move the element at the given index down in the collection."""
    if index == len(self) - 1:
        return
    self.insert(index + 1, self.pop(index))

remove_at(index)

Remove the item at index from the collection.

Renamed from the legacy BaseCollection.remove(index) which shadowed MutableSequence.remove(value) (remove-by-value, inherited from EasyList). Callers that meant "remove by index" should use this; the standard remove(value) is still available with its usual semantics.

Source code in src/easyreflectometry/sample/collections/base_collection.py 
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def remove_at(self, index: int) -> None:
    """Remove the item at *index* from the collection.

    Renamed from the legacy `BaseCollection.remove(index)` which shadowed
    `MutableSequence.remove(value)` (remove-by-value, inherited from
    `EasyList`). Callers that meant "remove by index" should use this; the
    standard `remove(value)` is still available with its usual semantics.
    """
    self.pop(index)

get_parameters()

Compatibility alias for legacy callers; prefer get_all_parameters.

Source code in src/easyreflectometry/sample/collections/base_collection.py 
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def get_parameters(self) -> List[Parameter]:
    """Compatibility alias for legacy callers; prefer `get_all_parameters`."""
    return self.get_all_parameters()

get_all_variables()

Flat list of every Parameter/Descriptor across all items.

Walks each item in the collection and unions whatever each item exposes via its own get_all_variables (for ModelBase / BaseCore children) or, for objects that lack that hook, unions any direct DescriptorBase attributes.

Source code in src/easyreflectometry/sample/collections/base_collection.py 
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def get_all_variables(self) -> List:
    """Flat list of every Parameter/Descriptor across all items.

    Walks each item in the collection and unions whatever each item
    exposes via its own `get_all_variables` (for `ModelBase` /
    `BaseCore` children) or, for objects that lack that hook,
    unions any direct `DescriptorBase` attributes.
    """
    from easyscience.variable.descriptor_base import DescriptorBase

    out: list = []
    seen: set[int] = set()
    for item in self._data:
        if hasattr(item, 'get_all_variables'):
            for v in item.get_all_variables():
                if id(v) not in seen:
                    seen.add(id(v))
                    out.append(v)
        elif isinstance(item, DescriptorBase):
            if id(item) not in seen:
                seen.add(id(item))
                out.append(item)
    return out

get_fit_parameters()

Alias kept for the minimizer; matches ModelBase.get_fit_parameters.

Source code in src/easyreflectometry/sample/collections/base_collection.py 
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def get_fit_parameters(self) -> List[Parameter]:
    """Alias kept for the minimizer; matches `ModelBase.get_fit_parameters`."""
    return self.get_free_parameters()

to_dict(skip=None)

Serialize with skip support; interface excluded by default.

EasyList.to_dict doesn't accept a skip argument and is hard-wired to dump data plus the parent's _arg_spec view. We reimplement here so existing callers (Project, Model.as_dict, etc.) can keep passing skip=['unique_name'] or similar.

NewBase.to_dict mutates the skip list in-place (e.g. it appends 'unique_name' when the collection's own unique_name is default-generated). We therefore pass a copy to it, otherwise the mutation would leak into the per-item serialization below and force every item Parameter dict to drop its unique_name — breaking the from_dict round-trip.

Source code in src/easyreflectometry/sample/collections/base_collection.py 
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def to_dict(self, skip: Optional[List[str]] = None) -> dict:
    """Serialize with `skip` support; `interface` excluded by default.

    `EasyList.to_dict` doesn't accept a `skip` argument and is hard-wired
    to dump `data` plus the parent's `_arg_spec` view. We reimplement here
    so existing callers (`Project`, `Model.as_dict`, etc.) can keep
    passing `skip=['unique_name']` or similar.

    ``NewBase.to_dict`` mutates the ``skip`` list in-place (e.g. it
    appends ``'unique_name'`` when the collection's own unique_name is
    default-generated). We therefore pass a *copy* to it, otherwise the
    mutation would leak into the per-item serialization below and force
    every item Parameter dict to drop its ``unique_name`` — breaking the
    from_dict round-trip.
    """
    skip = list(skip or [])
    if 'interface' not in skip:
        skip.append('interface')
    # Matches legacy `BasedBase.as_dict`: drop unique_name from the
    # serialized form so nested Parameters don't get explicit names that
    # would collide with the auto-generated names produced when the global
    # counter restarts during reconstruction.
    if 'unique_name' not in skip:
        skip.append('unique_name')
    dict_repr = NewBase.to_dict(self, skip=list(skip))
    if self._protected_types != [NewBase]:
        dict_repr['protected_types'] = [{'@module': c.__module__, '@class': c.__name__} for c in self._protected_types]
    dict_repr['data'] = []
    for item in self._data:
        # Items that are ModelBase / BaseCore subclasses accept `skip`;
        # other shapes use their no-arg `to_dict`/`as_dict`.
        if hasattr(item, 'to_dict'):
            try:
                dict_repr['data'].append(item.to_dict(skip=list(skip)))
            except TypeError:
                dict_repr['data'].append(item.to_dict())
        else:
            dict_repr['data'].append(item.as_dict(skip=list(skip)))
    return dict_repr

as_dict(skip=None)

Compatibility alias for :meth:to_dict.

Source code in src/easyreflectometry/sample/collections/base_collection.py 
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def as_dict(self, skip: Optional[List[str]] = None) -> dict:
    """Compatibility alias for :meth:`to_dict`."""
    return self.to_dict(skip=skip)

__deepcopy__(memo)

Round-trip via dict-skip-unique to get a fresh copy.

NewBase.__copy__ already does this; the override is kept (rather than deleted) to mirror the legacy BaseCollection.__deepcopy__ semantics — callers that relied on copy.deepcopy(collection) still get a clone built from from_dict(as_dict(skip=['unique_name'])).

Source code in src/easyreflectometry/sample/collections/base_collection.py 
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def __deepcopy__(self, memo):
    """Round-trip via dict-skip-unique to get a fresh copy.

    `NewBase.__copy__` already does this; the override is kept (rather
    than deleted) to mirror the legacy `BaseCollection.__deepcopy__`
    semantics — callers that relied on `copy.deepcopy(collection)` still
    get a clone built from `from_dict(as_dict(skip=['unique_name']))`.
    """
    return self.from_dict(self.as_dict(skip=['unique_name']))

Sample

Bases: BaseCollection

A sample is a collection of assemblies that represent the structure for which experimental measurements exist.

Source code in src/easyreflectometry/sample/collections/sample.py 
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class Sample(BaseCollection):
    """A sample is a collection of assemblies that represent the structure for which experimental measurements exist."""

    def __init__(
        self,
        *assemblies: Optional[List[BaseAssembly]],
        name: str = 'EasySample',
        interface=None,
        unique_name: Optional[str] = None,
        populate_if_none: bool = True,
        **kwargs,
    ):
        """Constructor.

        Parameters
        ----------
        **kwargs :
        populate_if_none : bool, optional
            By default, True.
        unique_name : Optional[str], optional
            By default, None.
        *assemblies : Optional[List[BaseAssembly]]
        args :
            The assemblies in the sample.
        name : str, optional
            Name of the sample. By default, 'EasySample'.
        interface :
            Calculator interface. By default, None.
        """
        # `from_dict` (via `EasyList.from_dict`) passes the items as a single
        # list-positional arg; unpack that so validation and super() agree.
        if len(assemblies) == 1 and isinstance(assemblies[0], list):
            assemblies = tuple(assemblies[0])

        if not assemblies:
            if populate_if_none:
                assemblies = DEFAULT_ELEMENTS(interface)
            else:
                assemblies = []

        for assembly in assemblies:
            if not issubclass(type(assembly), BaseAssembly):
                raise ValueError('The elements must be an Assembly.')
        super().__init__(
            name,
            interface,
            *assemblies,
            unique_name=unique_name,
            populate_if_none=populate_if_none,
            **kwargs,
        )

    def add_assembly(self, assembly: Optional[BaseAssembly] = None):
        """Add an assembly to the sample.

        Parameters
        ----------
        assembly : Optional[BaseAssembly], optional
            Assembly to add. By default, None.
        """
        if assembly is None:
            assembly = Multilayer(
                name='EasyMultilayer added',
                interface=self.interface,
            )
        self.append(assembly)

    def duplicate_assembly(self, index: int):
        """Add an assembly to the sample.

        Parameters
        ----------
        index : int
        assembly :
            Assembly to add.
        """
        # Order matters: RepeatingMultilayer and SurfactantLayer are subclasses of
        # BaseAssembly but not Multilayer; however a RepeatingMultilayer IS a
        # Multilayer, so the most-specific check must come first to avoid
        # serialising it through the wrong `from_dict`.
        to_be_duplicated = self[index]
        if isinstance(to_be_duplicated, RepeatingMultilayer):
            duplicate = RepeatingMultilayer.from_dict(to_be_duplicated.as_dict(skip=['unique_name']))
        elif isinstance(to_be_duplicated, SurfactantLayer):
            duplicate = SurfactantLayer.from_dict(to_be_duplicated.as_dict(skip=['unique_name']))
        elif isinstance(to_be_duplicated, Multilayer):
            duplicate = Multilayer.from_dict(to_be_duplicated.as_dict(skip=['unique_name']))
        else:
            raise TypeError(f'Cannot duplicate assembly of type {type(to_be_duplicated).__name__}')
        duplicate.name = duplicate.name + ' duplicate'
        self.append(duplicate)

    def move_up(self, index: int):
        """Move the assembly at the given index up in the sample.

        Parameters
        ----------
        index : int
            Index of the assembly to move up.
        """
        super().move_up(index)

    def move_down(self, index: int):
        """Move the assembly at the given index down in the sample.

        Parameters
        ----------
        index : int
            Index of the assembly to move down.
        """
        super().move_down(index)

    def remove_assembly(self, index: int):
        """Remove the assembly at the given index from the sample.

        Parameters
        ----------
        index : int
            Index of the assembly to remove.
        """
        self.pop(index)

    @property
    def superphase(self) -> Layer:
        """The superphase of the sample."""
        return self[0].front_layer

    @property
    def subphase(self) -> Layer:
        """The subphase of the sample."""
        # This assembly only got one layer
        if self[-1].back_layer is None:
            return self[-1].front_layer
        else:
            return self[-1].back_layer

superphase property

The superphase of the sample.

subphase property

The subphase of the sample.

__init__(*assemblies, name='EasySample', interface=None, unique_name=None, populate_if_none=True, **kwargs)

Constructor.

Parameters:

Name Type Description Default
**kwargs
{}
populate_if_none bool

By default, True.

 True
unique_name Optional[str]

By default, None.

 None
*assemblies Optional[List[BaseAssembly]]
()
args

The assemblies in the sample.

 required
name str

Name of the sample. By default, 'EasySample'.

 'EasySample'
interface

Calculator interface. By default, None.

 None
Source code in src/easyreflectometry/sample/collections/sample.py 
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def __init__(
    self,
    *assemblies: Optional[List[BaseAssembly]],
    name: str = 'EasySample',
    interface=None,
    unique_name: Optional[str] = None,
    populate_if_none: bool = True,
    **kwargs,
):
    """Constructor.

    Parameters
    ----------
    **kwargs :
    populate_if_none : bool, optional
        By default, True.
    unique_name : Optional[str], optional
        By default, None.
    *assemblies : Optional[List[BaseAssembly]]
    args :
        The assemblies in the sample.
    name : str, optional
        Name of the sample. By default, 'EasySample'.
    interface :
        Calculator interface. By default, None.
    """
    # `from_dict` (via `EasyList.from_dict`) passes the items as a single
    # list-positional arg; unpack that so validation and super() agree.
    if len(assemblies) == 1 and isinstance(assemblies[0], list):
        assemblies = tuple(assemblies[0])

    if not assemblies:
        if populate_if_none:
            assemblies = DEFAULT_ELEMENTS(interface)
        else:
            assemblies = []

    for assembly in assemblies:
        if not issubclass(type(assembly), BaseAssembly):
            raise ValueError('The elements must be an Assembly.')
    super().__init__(
        name,
        interface,
        *assemblies,
        unique_name=unique_name,
        populate_if_none=populate_if_none,
        **kwargs,
    )

add_assembly(assembly=None)

Add an assembly to the sample.

Parameters:

Name Type Description Default
assembly Optional[BaseAssembly]

Assembly to add. By default, None.

 None
Source code in src/easyreflectometry/sample/collections/sample.py 
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def add_assembly(self, assembly: Optional[BaseAssembly] = None):
    """Add an assembly to the sample.

    Parameters
    ----------
    assembly : Optional[BaseAssembly], optional
        Assembly to add. By default, None.
    """
    if assembly is None:
        assembly = Multilayer(
            name='EasyMultilayer added',
            interface=self.interface,
        )
    self.append(assembly)

duplicate_assembly(index)

Add an assembly to the sample.

Parameters:

Name Type Description Default
index int
required
assembly

Assembly to add.

 required
Source code in src/easyreflectometry/sample/collections/sample.py 
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def duplicate_assembly(self, index: int):
    """Add an assembly to the sample.

    Parameters
    ----------
    index : int
    assembly :
        Assembly to add.
    """
    # Order matters: RepeatingMultilayer and SurfactantLayer are subclasses of
    # BaseAssembly but not Multilayer; however a RepeatingMultilayer IS a
    # Multilayer, so the most-specific check must come first to avoid
    # serialising it through the wrong `from_dict`.
    to_be_duplicated = self[index]
    if isinstance(to_be_duplicated, RepeatingMultilayer):
        duplicate = RepeatingMultilayer.from_dict(to_be_duplicated.as_dict(skip=['unique_name']))
    elif isinstance(to_be_duplicated, SurfactantLayer):
        duplicate = SurfactantLayer.from_dict(to_be_duplicated.as_dict(skip=['unique_name']))
    elif isinstance(to_be_duplicated, Multilayer):
        duplicate = Multilayer.from_dict(to_be_duplicated.as_dict(skip=['unique_name']))
    else:
        raise TypeError(f'Cannot duplicate assembly of type {type(to_be_duplicated).__name__}')
    duplicate.name = duplicate.name + ' duplicate'
    self.append(duplicate)

move_up(index)

Move the assembly at the given index up in the sample.

Parameters:

Name Type Description Default
index int

Index of the assembly to move up.

 required
Source code in src/easyreflectometry/sample/collections/sample.py 
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def move_up(self, index: int):
    """Move the assembly at the given index up in the sample.

    Parameters
    ----------
    index : int
        Index of the assembly to move up.
    """
    super().move_up(index)

move_down(index)

Move the assembly at the given index down in the sample.

Parameters:

Name Type Description Default
index int

Index of the assembly to move down.

 required
Source code in src/easyreflectometry/sample/collections/sample.py 
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def move_down(self, index: int):
    """Move the assembly at the given index down in the sample.

    Parameters
    ----------
    index : int
        Index of the assembly to move down.
    """
    super().move_down(index)

remove_assembly(index)

Remove the assembly at the given index from the sample.

Parameters:

Name Type Description Default
index int

Index of the assembly to remove.

 required
Source code in src/easyreflectometry/sample/collections/sample.py 
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def remove_assembly(self, index: int):
    """Remove the assembly at the given index from the sample.

    Parameters
    ----------
    index : int
        Index of the assembly to remove.
    """
    self.pop(index)

DEFAULT_ELEMENTS(interface)

:meta private:.

Source code in src/easyreflectometry/sample/collections/sample.py 
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def DEFAULT_ELEMENTS(interface):
    """:meta private:."""
    return (
        Multilayer(interface=interface),
        Multilayer(interface=interface),
    )