Merge pull request #206 from EasyScience/develop

Release 1.3.0

docs/src/index.rst

@@ -9,7 +9,7 @@
    usage
    sample/sample
    calculators
-   experiment/experiment
+   model/model
    tutorials/tutorials
    dictionary
    contributing

docs/src/experiment/experiment.rst → docs/src/model/model.rst

@@ -1,5 +1,5 @@
-Experiment
-==========
+Model
+=====
 
 The main component of an experiment in :py:mod:`easyreflectometry` is the :py:class:`Model`. 
 This is a description of the :py:class:`Sample` and the environment in which the experiment is performed. 
@@ -14,19 +14,19 @@ To be able to compute reflectivities it is also necessary to have a :py:class:`C
 
 .. code-block:: python 
 
-   from easyreflectometry.calculators import CalculatorFactory
-   from easyreflectometry.experiment import Model
-   from easyreflectometry.sample import Sample
+      from easyreflectometry.calculators import CalculatorFactory
+      from easyreflectometry.model import Model
+      from easyreflectometry.sample import Sample
 
-   default_sample = Sample()
-   m = Model(
-      sample=default_sample,
-      scale=1.0,
-      background=1e-6
-   )
+      default_sample = Sample()
+      model = Model(
+         sample=default_sample,
+         scale=1.0,
+         background=1e-6
+      )
 
-   interface = CalculatorFactory()
-   model.interface = interface
+      interface = CalculatorFactory()
+      model.interface = interface
 
 This will create a :py:class:`Model` instance with the :py:attr:`default_sample` and the environment variables :py:attr:`scale` factor set to 1.0 and a :py:attr:`background` of 1e-6.
 Following the :py:attr:`interface` is set to the default calculator that is :py:class:`Refnx`.
@@ -39,42 +39,42 @@ In its essence the resolution function controls the smearing to apply when deter
 For a given Q-point the smearing to apply is given as a weighted average of the neighboring Q-point, which weigths are by a normal distribution.
 This normal distribution is then defined by a Q-point dependent Full Width at the Half Maximum (FWHM) that is given by the resolution function.
 
-:py:func:`percentage_fhwm_resolution_function`
+:py:class:`PercentageFwhm`
 Often we rely on a resolution function that has a simple functional dependecy of the Q-point.
 By this is understood that the applied smearing in an Q-point has a FWHM that is simply a percentage of the value of the Q-point.
 
 .. code-block:: python 
 
-   from easyreflectometry.experiment import Model
-   from easyreflectometry.experiment import percentage_fhwm_resolution_function
+      from easyreflectometry.model import Model
+      from easyreflectometry.model import PercentageFwhm
 
-   resolution_function = percentage_fhwm_resolution_function(1.1)
+      resolution_function = PercentageFwhm(1.1)
 
-   m = Model(
-      resolution_function=resolution_function
-   )
+      m = Model(
+         resolution_function=resolution_function
+      )
 
 This will create a :py:class:`Model` instance where the resolution function is defined as 1.1% of the Q-point value, which again is the FWHM for the smearing.
 
 
-:py:func:`linear_spline_resolution_function`
+:py:func:`LinearSpline`
 Alternatively the FWHM value might be determined and declared directly for each measured Q-point.
 When this is the case the provided Q-points and the corresponding FWHM values can be used to declare a linear spline function
 and thereby enable a determination of the reflectivity at an arbitrary point within the provided range of discrete Q-points.
 
 .. code-block:: python 
 
-   from easyreflectometry.experiment import Model
-   from easyreflectometry.experiment import linear_spline_resolution_function
+      from easyreflectometry.model import Model
+      from easyreflectometry.model import LinearSpline
 
-   m = Model()
+      m = Model()
 
-   resolution_function = linear_spline_resolution_function(
-      q_points=[0.01, 0.2, 0.31],
-      fwhm_values=[0.001, 0.043, 0.026]
-   )
+      resolution_function = LinearSpline(
+         q_data_points=[0.01, 0.2, 0.31],
+         fwhm_values=[0.001, 0.043, 0.026]
+      )
 
-   m.resolution_function = resolution_function
+      m.resolution_function = resolution_function
 
 This will create a :py:class:`Model` instance where the resolution function defining the FWHM is determined from a linear interpolation.
 In the present case the provided data Q-points are (`[0.01, 0.2, 0.31]`) and the corresponding FWHM function values are (`[0.001, 0.043, 0.026]`).

docs/src/tutorials/fitting/repeating.ipynb

@@ -47,7 +47,7 @@
     "from easyreflectometry.sample import RepeatingMultilayer\n",
     "from easyreflectometry.sample import Multilayer\n",
     "from easyreflectometry.model import Model\n",
-    "from easyreflectometry.model import PercentageFhwm\n",
+    "from easyreflectometry.model import PercentageFwhm\n",
     "from easyreflectometry.calculators import CalculatorFactory\n",
     "from easyreflectometry.fitting import Fitter\n",
     "from easyreflectometry.plot import plot\n",
@@ -201,7 +201,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "resolution_function = PercentageFhwm(0)\n",
+    "resolution_function = PercentageFwhm(0)\n",
     "sample = Sample(Multilayer(superphase), rep_multilayer, Multilayer(subphase), name='Multilayer Structure')\n",
     "model = Model(\n",
     "    sample=sample,\n",

docs/src/tutorials/fitting/simple_fitting.ipynb

@@ -40,7 +40,7 @@
     "from easyreflectometry.sample import Material\n",
     "from easyreflectometry.sample import Multilayer\n",
     "from easyreflectometry.model import Model\n",
-    "from easyreflectometry.model import PercentageFhwm\n",
+    "from easyreflectometry.model import PercentageFwhm\n",
     "from easyreflectometry.calculators import CalculatorFactory\n",
     "from easyreflectometry.fitting import Fitter\n",
     "from easyreflectometry.plot import plot"
@@ -306,7 +306,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "resolution_function = PercentageFhwm(0.02)\n",
+    "resolution_function = PercentageFwhm(0.02)\n",
     "model = Model(\n",
     "    sample=sample,\n",
     "    scale=1,\n",

docs/src/tutorials/magnetism.ipynb

@@ -39,7 +39,7 @@
     "\n",
     "from easyreflectometry.calculators import CalculatorFactory\n",
     "from easyreflectometry.model import Model\n",
-    "from easyreflectometry.model import PercentageFhwm\n",
+    "from easyreflectometry.model import PercentageFwhm\n",
     "from easyreflectometry.sample import Layer\n",
     "from easyreflectometry.sample import Material\n",
     "from easyreflectometry.sample import Multilayer\n",
@@ -245,7 +245,7 @@
     "# EasyReflectometry\n",
     "interface.switch('refl1d')\n",
     "model.interface = interface\n",
-    "model.resolution_function = PercentageFhwm(0)\n",
+    "model.resolution_function = PercentageFwhm(0)\n",
     "model_interface = model.interface()\n",
     "model_interface.magnetism = False\n",
     "model_data_no_magnetism_ref1d_easy = model.interface().reflectity_profile(\n",

docs/src/tutorials/sample/material_solvated.ipynb

@@ -46,7 +46,7 @@
     "from easyreflectometry.sample import MaterialSolvated\n",
     "from easyreflectometry.sample import Multilayer\n",
     "from easyreflectometry.model import Model\n",
-    "from easyreflectometry.model import PercentageFhwm\n",
+    "from easyreflectometry.model import PercentageFwhm\n",
     "from easyreflectometry.calculators import CalculatorFactory\n",
     "from easyreflectometry.fitting import Fitter\n",
     "from easyreflectometry.plot import plot"
@@ -191,7 +191,7 @@
     "\n",
     "subphase = Layer(material=d2o, thickness=0, roughness=3, name='D2O Subphase')\n",
     "\n",
-    "resolution_function = PercentageFhwm(0.02)\n",
+    "resolution_function = PercentageFwhm(0.02)\n",
     "sample = Sample(superphase, Multilayer(solvated_film), Multilayer(subphase), name='Film Structure')\n",
     "model = Model(\n",
     "    sample=sample,\n",

docs/src/tutorials/sample/monolayer.ipynb

@@ -44,7 +44,7 @@
     "from easyreflectometry.sample import Multilayer\n",
     "from easyreflectometry.sample import Sample\n",
     "from easyreflectometry.model import Model\n",
-    "from easyreflectometry.model import PercentageFhwm\n",
+    "from easyreflectometry.model import PercentageFwhm\n",
     "from easyreflectometry.fitting import Fitter\n",
     "from easyreflectometry.plot import plot\n",
     "from easyscience.fitting import AvailableMinimizers\n"
@@ -325,7 +325,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "resolution_function = PercentageFhwm(5)\n",
+    "resolution_function = PercentageFwhm(5)\n",
     "sample = Sample(Multilayer(air_layer), dspc, Multilayer(d2o_layer))\n",
     "model = Model(\n",
     "    sample=sample,\n",

docs/src/tutorials/sample/multi_contrast.ipynb

@@ -43,7 +43,7 @@
     "from easyreflectometry.sample import LayerAreaPerMolecule\n",
     "from easyreflectometry.sample import Sample\n",
     "from easyreflectometry.model import Model\n",
-    "from easyreflectometry.model import PercentageFhwm\n",
+    "from easyreflectometry.model import PercentageFwhm\n",
     "from easyreflectometry.calculators import CalculatorFactory\n",
     "from easyreflectometry.fitting import Fitter\n",
     "from easyscience.fitting import AvailableMinimizers\n",
@@ -417,7 +417,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "resolution_function = PercentageFhwm(5)\n",
+    "resolution_function = PercentageFwhm(5)\n",
     "\n",
     "d13d2o_sample = Sample(Multilayer(air_layer), d13d2o, Multilayer(d2o_layer))\n",
     "d70d2o_sample = Sample(Multilayer(air_layer), d70d2o, Multilayer(d2o_layer))\n",

src/easyreflectometry/calculators/refl1d/wrapper.py

@@ -6,7 +6,7 @@
 from refl1d import model
 from refl1d import names
 
-from easyreflectometry.model import PercentageFhwm
+from easyreflectometry.model import PercentageFwhm
 
 from ..wrapper_base import WrapperBase
 
@@ -157,7 +157,7 @@ def calculate(self, q_array: np.ndarray, model_name: str) -> np.ndarray:
         sample = _build_sample(self.storage, model_name)
         dq_array = self._resolution_function.smearing(q_array)
 
-        if isinstance(self._resolution_function, PercentageFhwm):
+        if isinstance(self._resolution_function, PercentageFwhm):
             # Get percentage of Q and change from sigma to FWHM
             dq_array = dq_array * q_array / 100 / (2 * np.sqrt(2 * np.log(2)))
 

src/easyreflectometry/calculators/refnx/wrapper.py

@@ -5,7 +5,7 @@
 import numpy as np
 from refnx import reflect
 
-from easyreflectometry.model import PercentageFhwm
+from easyreflectometry.model import PercentageFwhm
 
 from ..wrapper_base import WrapperBase
 
@@ -143,7 +143,7 @@ def calculate(self, q_array: np.ndarray, model_name: str) -> np.ndarray:
         )
 
         dq_vector = self._resolution_function.smearing(q_array)
-        if isinstance(self._resolution_function, PercentageFhwm):
+        if isinstance(self._resolution_function, PercentageFwhm):
             # FWHM Percentage resolution is constant given as
             # For a constant resolution percentage refnx supports to pass a scalar value rather than a vector
             dq_vector = dq_vector[0]

src/easyreflectometry/calculators/wrapper_base.py

@@ -2,7 +2,7 @@
 
 import numpy as np
 
-from easyreflectometry.model import PercentageFhwm
+from easyreflectometry.model import PercentageFwhm
 from easyreflectometry.model import ResolutionFunction
 
 
@@ -16,7 +16,7 @@ def __init__(self):
             'item': {},
             'model': {},
         }
-        self._resolution_function = PercentageFhwm()
+        self._resolution_function = PercentageFwhm()
 
     def reset_storage(self):
         """Reset the storage area to blank."""

src/easyreflectometry/model/__init__.py

@@ -1,12 +1,12 @@
 from .model import Model
 from .model_collection import ModelCollection
 from .resolution_functions import LinearSpline
-from .resolution_functions import PercentageFhwm
+from .resolution_functions import PercentageFwhm
 from .resolution_functions import ResolutionFunction
 
 __all__ = (
     LinearSpline,
-    PercentageFhwm,
+    PercentageFwhm,
     ResolutionFunction,
     Model,
     ModelCollection,

src/easyreflectometry/model/model.py

@@ -17,7 +17,7 @@
 from easyreflectometry.utils import get_as_parameter
 from easyreflectometry.utils import yaml_dump
 
-from .resolution_functions import PercentageFhwm
+from .resolution_functions import PercentageFwhm
 from .resolution_functions import ResolutionFunction
 
 DEFAULTS = {
@@ -71,7 +71,7 @@ def __init__(
         :param scale: Scaling factor of profile.
         :param background: Linear background magnitude.
         :param name: Name of the model, defaults to 'EasyModel'.
-        :param resolution_function: Resolution function, defaults to PercentageFhwm.
+        :param resolution_function: Resolution function, defaults to PercentageFwhm.
         :param interface: Calculator interface, defaults to `None`.
 
         """
@@ -81,7 +81,7 @@ def __init__(
         if sample is None:
             sample = Sample(interface=interface)
         if resolution_function is None:
-            resolution_function = PercentageFhwm(DEFAULTS['resolution']['value'])
+            resolution_function = PercentageFwhm(DEFAULTS['resolution']['value'])
 
         scale = get_as_parameter('scale', scale, DEFAULTS)
         background = get_as_parameter('background', background, DEFAULTS)
@@ -168,7 +168,7 @@ def interface(self, new_interface) -> None:
     @property
     def _dict_repr(self) -> dict[str, dict[str, str]]:
         """A simplified dict representation."""
-        if isinstance(self._resolution_function, PercentageFhwm):
+        if isinstance(self._resolution_function, PercentageFwhm):
             resolution_value = self._resolution_function.as_dict()['constant']
             resolution = f'{resolution_value} %'
         else:

src/easyreflectometry/model/resolution_functions.py

@@ -26,14 +26,14 @@ def as_dict(self, skip: Optional[List[str]] = None) -> dict: ...
 
     @classmethod
     def from_dict(cls, data: dict) -> ResolutionFunction:
-        if data['smearing'] == 'PercentageFhwm':
-            return PercentageFhwm(data['constant'])
+        if data['smearing'] == 'PercentageFwhm':
+            return PercentageFwhm(data['constant'])
         if data['smearing'] == 'LinearSpline':
             return LinearSpline(data['q_data_points'], data['fwhm_values'])
         raise ValueError('Unknown resolution function type')
 
 
-class PercentageFhwm(ResolutionFunction):
+class PercentageFwhm(ResolutionFunction):
     def __init__(self, constant: Union[None, float] = None):
         if constant is None:
             constant = DEFAULT_RESOLUTION_FWHM_PERCENTAGE
@@ -45,7 +45,7 @@ def smearing(self, q: Union[np.array, float]) -> np.array:
     def as_dict(
         self, skip: Optional[List[str]] = None
     ) -> dict[str, str]:  # skip is kept for consistency of the as_dict signature
-        return {'smearing': 'PercentageFhwm', 'constant': self.constant}
+        return {'smearing': 'PercentageFwhm', 'constant': self.constant}
 
 
 class LinearSpline(ResolutionFunction):

src/easyreflectometry/project.py

@@ -21,7 +21,7 @@
 from easyreflectometry.model import LinearSpline
 from easyreflectometry.model import Model
 from easyreflectometry.model import ModelCollection
-from easyreflectometry.model import PercentageFhwm
+from easyreflectometry.model import PercentageFwhm
 from easyreflectometry.sample import Layer
 from easyreflectometry.sample import Material
 from easyreflectometry.sample import MaterialCollection
@@ -266,7 +266,7 @@ def sld_data_for_model_at_index(self, index: int = 0) -> DataSet1D:
 
     def sample_data_for_model_at_index(self, index: int = 0, q_range: Optional[np.array] = None) -> DataSet1D:
         original_resolution_function = self.models[index].resolution_function
-        self.models[index].resolution_function = PercentageFhwm(0)
+        self.models[index].resolution_function = PercentageFwhm(0)
         reflectivity_data = self.model_data_for_model_at_index(index, q_range)
         self.models[index].resolution_function = original_resolution_function
 

src/easyreflectometry/summary/summary.py

@@ -144,7 +144,7 @@ def _experiments_section(self) -> str:
             experiment_name = experiment.name
             num_data_points = len(experiment.x)
             resolution_function = self._project.models[idx].resolution_function.as_dict()['smearing']
-            if resolution_function == 'PercentageFhwm':
+            if resolution_function == 'PercentageFwhm':
                 precentage = self._project.models[idx].resolution_function.as_dict()['constant']
                 resolution_function = f'{resolution_function} {precentage}%'
             range_min = min(experiment.y)