easyreflectometry 1.0.0__tar.gz

easyreflectometry-1.0.0/.gitignore

@@ -0,0 +1,49 @@
+# QtCreator
+*.autosave
+
+# QtCreator Qml
+*.qmlproject.user
+*.qmlproject.user.*
+
+# QtCreator Python
+*.pyproject.user
+*.pyproject.user.*
+
+# QtCreator CMake
+CMakeLists.txt.user*
+
+# Python
+__pycache__
+.venv
+.coverage
+.pyc
+
+# Poetry
+dist
+poetry.lock
+*.egg-info
+
+# PyInstaller
+build
+*.spec
+
+# Jupyter
+.ipynb_checkpoints
+
+# macOS
+.DS_Store
+*.app
+*.dmg
+
+# Docs
+docs/_build
+
+# VSCode
+.vscode
+
+# Misc
+..*
+*.log
+*.zip
+.ci/
+.idea/

easyreflectometry-1.0.0/AUTHORS.rst

@@ -0,0 +1,11 @@
+=======
+Credits
+=======
+
+Contributors
+------------
+
+* Andrew R. McCluskey <andrew.mccluskey@ess.eu>
+* Andrew Sazonov <andrew.sazonov@ess.eu>
+* Simon Ward <simon.ward@ess.eu>
+* Andreas Pedersen <andreas.pedersen@ess.eu>

easyreflectometry-1.0.0/LICENSE

@@ -0,0 +1,29 @@
+BSD 3-Clause License
+
+Copyright (c) 2024, Easyscience contributors (https://github.com/EasyScience)
+All rights reserved.
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+
+1. Redistributions of source code must retain the above copyright notice, this
+   list of conditions and the following disclaimer.
+
+2. Redistributions in binary form must reproduce the above copyright notice,
+   this list of conditions and the following disclaimer in the documentation
+   and/or other materials provided with the distribution.
+
+3. Neither the name of the copyright holder nor the names of its
+   contributors may be used to endorse or promote products derived from
+   this software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
+FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

easyreflectometry-1.0.0/PKG-INFO

@@ -0,0 +1,96 @@
+Metadata-Version: 2.1
+Name: easyreflectometry
+Version: 1.0.0
+Summary: A reflectometry python package built on the EasyScience framework.
+Project-URL: homepage, https://docs.easyreflectometry.org
+Project-URL: documentation, https://docs.easyreflectometry.org
+Author: EasyScience contributors
+License: BSD 3-Clause License
+        
+        Copyright (c) 2024, Easyscience contributors (https://github.com/EasyScience)
+        All rights reserved.
+        
+        Redistribution and use in source and binary forms, with or without
+        modification, are permitted provided that the following conditions are met:
+        
+        1. Redistributions of source code must retain the above copyright notice, this
+           list of conditions and the following disclaimer.
+        
+        2. Redistributions in binary form must reproduce the above copyright notice,
+           this list of conditions and the following disclaimer in the documentation
+           and/or other materials provided with the distribution.
+        
+        3. Neither the name of the copyright holder nor the names of its
+           contributors may be used to endorse or promote products derived from
+           this software without specific prior written permission.
+        
+        THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+        AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+        IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+        DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
+        FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+        DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+        SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+        CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+        OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+        OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+License-File: AUTHORS.rst
+License-File: LICENSE
+Classifier: Development Status :: 3 - Alpha
+Classifier: License :: OSI Approved :: BSD License
+Classifier: Operating System :: OS Independent
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3 :: Only
+Classifier: Programming Language :: Python :: 3.9
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Topic :: Scientific/Engineering
+Requires-Python: <3.12,>=3.9
+Requires-Dist: easyscience>=0.6.0
+Requires-Dist: orsopy>=0.0.4
+Requires-Dist: refl1d>=0.8.14
+Requires-Dist: refnx>=0.1.15
+Requires-Dist: scipp>=23.12.0
+Provides-Extra: dev
+Requires-Dist: build; extra == 'dev'
+Requires-Dist: codecov>=2.1.11; extra == 'dev'
+Requires-Dist: coverage; extra == 'dev'
+Requires-Dist: coveralls; extra == 'dev'
+Requires-Dist: flake8>=6.0.0; extra == 'dev'
+Requires-Dist: ipykernel; extra == 'dev'
+Requires-Dist: jupyter>=1.0.0; extra == 'dev'
+Requires-Dist: jupyterlab; extra == 'dev'
+Requires-Dist: plopp; extra == 'dev'
+Requires-Dist: pytest-cov>=3.0.0; extra == 'dev'
+Requires-Dist: pytest>=5.2; extra == 'dev'
+Requires-Dist: ruff; extra == 'dev'
+Requires-Dist: toml>=0.10; extra == 'dev'
+Requires-Dist: yapf>=0.31.0; extra == 'dev'
+Provides-Extra: docs
+Requires-Dist: myst-parser; extra == 'docs'
+Requires-Dist: nbsphinx; extra == 'docs'
+Requires-Dist: sphinx-autodoc-typehints; extra == 'docs'
+Requires-Dist: sphinx-book-theme; extra == 'docs'
+Requires-Dist: toml; extra == 'docs'
+Description-Content-Type: text/markdown
+
+![Logo](https://github.com/easyScience/EasyReflectometryLib/raw/master/docs/src/_static/logo.png)
+[![CI badge](https://github.com/easyScience/EasyReflectometryLib/actions/workflows/python-ci.yml/badge.svg)](https://github.com/easyScience/easyReflectometryLib/actions/workflows/python-ci.yml)
+[![PyPI badge](http://img.shields.io/pypi/v/EasyReflectometryLib.svg)](https://pypi.python.org/pypi/EasyReflectometryLib)
+[![Coverage badge](https://codecov.io/gh/easyScience/EasyReflectometryLib/branch/master/graph/badge.svg?token=LcnB8AMGkw)](https://codecov.io/gh/easyScience/EasyReflectometryLib)
+[![Quality badge](https://www.codefactor.io/repository/github/easyscience/easyreflectometrylib/badge)](https://www.codefactor.io/repository/github/easyscience/easyreflectometrylib)
+[![Docs badge](https://img.shields.io/badge/docs-built-blue)](http://docs.easyreflectometry.org)
+
+# About
+
+A reflectometry python package and an application.
+
+This repo and documentation is for the `easyreflectometry` Python package that is built on the `easyscience` [framework](https://easyscience.software).
+To get more information about the application visit [`easyreflectometry.org`](https://easyreflectometry.org)
+
+# Installation
+
+```sh
+python -m pip install easyreflectometry
+```

easyreflectometry-1.0.0/README.md

@@ -0,0 +1,19 @@
+![Logo](https://github.com/easyScience/EasyReflectometryLib/raw/master/docs/src/_static/logo.png)
+[![CI badge](https://github.com/easyScience/EasyReflectometryLib/actions/workflows/python-ci.yml/badge.svg)](https://github.com/easyScience/easyReflectometryLib/actions/workflows/python-ci.yml)
+[![PyPI badge](http://img.shields.io/pypi/v/EasyReflectometryLib.svg)](https://pypi.python.org/pypi/EasyReflectometryLib)
+[![Coverage badge](https://codecov.io/gh/easyScience/EasyReflectometryLib/branch/master/graph/badge.svg?token=LcnB8AMGkw)](https://codecov.io/gh/easyScience/EasyReflectometryLib)
+[![Quality badge](https://www.codefactor.io/repository/github/easyscience/easyreflectometrylib/badge)](https://www.codefactor.io/repository/github/easyscience/easyreflectometrylib)
+[![Docs badge](https://img.shields.io/badge/docs-built-blue)](http://docs.easyreflectometry.org)
+
+# About
+
+A reflectometry python package and an application.
+
+This repo and documentation is for the `easyreflectometry` Python package that is built on the `easyscience` [framework](https://easyscience.software).
+To get more information about the application visit [`easyreflectometry.org`](https://easyreflectometry.org)
+
+# Installation
+
+```sh
+python -m pip install easyreflectometry
+```

easyreflectometry-1.0.0/pyproject.toml

@@ -0,0 +1,157 @@
+[build-system]
+requires = [
+    "hatchling<=1.21.0",
+    "setuptools-git-versioning",
+]
+build-backend = "hatchling.build"
+
+[tool.setuptools-git-versioning]
+enabled = true
+
+[project]
+name = "easyreflectometry"
+dynamic = ["version"]
+description = "A reflectometry python package built on the EasyScience framework."
+readme = "README.md"
+authors = [{name = "EasyScience contributors"}]
+license = { file = "LICENSE" }
+classifiers = [
+    "License :: OSI Approved :: BSD License",
+    "Operating System :: OS Independent",
+    "Topic :: Scientific/Engineering",
+    "Programming Language :: Python :: 3",
+    "Programming Language :: Python :: 3 :: Only",
+    "Programming Language :: Python :: 3.9",
+    "Programming Language :: Python :: 3.10",
+    "Programming Language :: Python :: 3.11",
+    "Programming Language :: Python :: 3.12",
+    "Development Status :: 3 - Alpha"
+]
+requires-python = ">=3.9,<3.12"
+dependencies = [
+    "easyscience>=0.6.0",
+    "scipp>=23.12.0",
+    "refnx>=0.1.15",
+    "refl1d>=0.8.14",
+    "orsopy>=0.0.4"
+]
+
+[project.optional-dependencies]
+dev = [
+    "build",
+    "codecov>=2.1.11",
+    "coverage",
+    "coveralls",
+    "flake8>=6.0.0",
+    "ipykernel",
+    "jupyter>=1.0.0",
+    "jupyterlab",
+    "plopp",
+    "pytest>=5.2",
+    "pytest-cov>=3.0.0",
+    "ruff",
+    "toml>=0.10",
+    "yapf>=0.31.0",
+]
+docs = [
+    "myst_parser",
+    "nbsphinx",
+    "sphinx_book_theme",
+    "sphinx_autodoc_typehints",
+    "toml"
+]
+
+[project.urls]
+homepage = "https://docs.easyreflectometry.org"
+documentation = "https://docs.easyreflectometry.org"
+
+[tool.hatch.version]
+path = "src/easyreflectometry/__version__.py"
+
+[tool.hatch.metadata]
+allow-direct-references = true
+
+[tool.hatch.build.targets.sdist]
+packages = ["src"]
+
+[tool.hatch.build.targets.wheel]
+packages = ["src/easyreflectometry"]
+
+[tool.coverage.run]
+source = ["src/easyreflectometry"]
+
+[tool.github.info]
+organization = 'easyScience'
+repo = "easyreflectometry"
+
+[tool.ruff]
+line-length = 127
+exclude = [
+    "docs",
+]
+
+[tool.ruff.format]
+quote-style = "single"
+
+[tool.ruff.per-file-ignores]
+# allow asserts in test files
+"*test_*.py" = ["S101"]
+
+[tool.ruff.lint]
+ignore-init-module-imports = true
+select = [
+    # flake8 settings from existing CI setup
+    "E9", "F63", "F7", "F82",
+    # Code should be polished to fulfill all cases below
+    # https://docs.astral.sh/ruff/rules/
+    # pycodestyle
+    "E",
+    # Pyflakes
+    "F",
+    # pyupgrade
+#    "UP",
+    # flake8-bugbear
+#    "B",
+    # flake8-simplify
+#    "SIM",
+    # isort
+    "I",
+    # flake8-bandit
+    "S",
+]
+
+[tool.ruff.lint.isort]
+force-single-line = true
+
+[tool.tox]
+legacy_tox_ini = """
+[tox]
+isolated_build = True
+envlist = py{3.9,3.10,3.11,3.12}
+[gh-actions]
+python =
+        3.9: py39
+        3.10: py310
+        3.11: py311
+        3.12: py312
+[gh-actions:env]
+PLATFORM =
+    ubuntu-latest: linux
+    macos-latest: macos
+    windows-latest: windows
+[testenv]
+passenv =
+    CI
+    GITHUB_ACTIONS
+    GITHUB_ACTION
+    GITHUB_REF
+    GITHUB_REPOSITORY
+    GITHUB_HEAD_REF
+    GITHUB_RUN_ID
+    GITHUB_SHA
+    COVERAGE_FILE
+deps = coverage
+commands =
+    pip install -e '.[dev]'
+    pytest --cov --cov-report=xml
+"""

easyreflectometry-1.0.0/src/easyreflectometry/__init__.py

@@ -0,0 +1,6 @@
+from importlib import metadata
+
+try:
+    __version__ = metadata.version(__package__ or __name__)
+except metadata.PackageNotFoundError:
+    __version__ = '0.0.0'

easyreflectometry-1.0.0/src/easyreflectometry/__version__.py

@@ -0,0 +1 @@
+__version__ = '1.0.0'

easyreflectometry-1.0.0/src/easyreflectometry/calculators/__init__.py

@@ -0,0 +1,31 @@
+import traceback
+
+from .calculator_base import CalculatorBase
+from .factory import CalculatorFactory
+
+imported_calculators = []
+
+try:
+    from .refnx.calculator import Refnx
+
+    imported_calculators.append(Refnx)
+except Exception:
+    traceback.print_exc()
+    print('Warning: refnx is not installed')
+
+# try:
+#     from .bornagain.calculator import BornAgain
+#    imported_calculators.append(BornAgain)
+# except Exception:
+#     traceback.print_exc()
+#     print('Warning: BornAgain python is not installed')
+
+try:
+    from .refl1d.calculator import Refl1d  # noqa: F401
+
+    imported_calculators.append(Refl1d)
+except Exception:
+    traceback.print_exc()
+    print('Warning: refl1d is not installed')
+
+__all__ = [CalculatorBase, CalculatorFactory] + imported_calculators

easyreflectometry-1.0.0/src/easyreflectometry/calculators/bornagain/calculator.py

@@ -0,0 +1,200 @@
+__author__ = 'github.com/arm61'
+
+import numpy as np
+from easyreflectometry.experiment import Model
+from easyreflectometry.sample import Layer
+from easyreflectometry.sample import Material
+from easyreflectometry.sample import MaterialMixture
+from easyreflectometry.sample import Multilayer
+from easyscience.Objects.Inferface import ItemContainer
+
+from ..calculator_base import CalculatorBase
+from .wrapper import BornAgainWrapper
+
+"""
+THIS CODE IS NOT FUNCTIONAL
+PLEASE CONSULT ONE OF THE OTHER CALCULATORS FOR A FUNCTIONAL EXAMPLE
+"""
+
+
+class BornAgain(CalculatorBase):
+    """
+    Calculator for BornAgain
+    """
+
+    name = 'BornAgain'
+
+    _material_link = {
+        'sld': 'real',
+        'isld': 'imag',
+    }
+
+    _layer_link = {
+        'thickness': 'thickness',
+        'roughness': 'sigma',
+    }
+
+    _item_link = {
+        'repetitions': 'repeats',
+    }
+
+    _model_link = {
+        'scale': 'scale',
+        'background': 'background',
+        'resolution': 'resolution',
+    }
+
+    def __init__(self):
+        super().__init__()
+        self._wrapper = BornAgainWrapper()
+
+    def reset_storage(self) -> None:
+        """
+        Reset the storage area of the calculator
+        """
+        self._wrapper.reset_storage()
+
+    def create(self, model: Material | Layer | Multilayer | Model) -> list[ItemContainer]:
+        """
+        Creation function
+
+        :param model: Object to be created
+        :type model: Union[Material, Layer, Item, Model]
+        :return: Item containers of the objects
+        :rtype: List[ItemContainer]
+        """
+        r_list = []
+        t_ = type(model)
+        if issubclass(t_, Material):
+            key = model.uid
+            if key not in self._wrapper.storage['material'].keys():
+                self._wrapper.create_material(key)
+            r_list.append(
+                ItemContainer(
+                    key,
+                    self._material_link,
+                    self._wrapper.get_material_value,
+                    self._wrapper.update_material,
+                )
+            )
+        elif issubclass(t_, MaterialMixture):
+            key = model.uid
+            if key not in self._wrapper.storage['material'].keys():
+                self._wrapper.create_material(key)
+            r_list.append(
+                ItemContainer(
+                    key,
+                    self._material_link,
+                    self._wrapper.get_material_value,
+                    self._wrapper.update_material,
+                )
+            )
+        elif issubclass(t_, Layer):
+            key = model.uid
+            if key not in self._wrapper.storage['layer'].keys():
+                self._wrapper.create_layer(key)
+            r_list.append(
+                ItemContainer(
+                    key,
+                    self._layer_link,
+                    self._wrapper.get_layer_value,
+                    self._wrapper.update_layer,
+                )
+            )
+            self.assign_material_to_layer(model.material.uid, key)
+        elif issubclass(t_, Multilayer):
+            key = model.uid
+            self._wrapper.create_item(key)
+            r_list.append(
+                ItemContainer(
+                    key,
+                    self._item_link,
+                    self._wrapper.get_item_value,
+                    self._wrapper.update_item,
+                )
+            )
+            for i in model.layers:
+                self.add_layer_to_item(i.uid, model.uid)
+        elif issubclass(t_, Model):
+            self._wrapper.create_model()
+            r_list.append(
+                ItemContainer(
+                    'model',
+                    self._model_link,
+                    self._wrapper.get_model_value,
+                    self._wrapper.update_model,
+                )
+            )
+            for i in model.structure:
+                self.add_item_to_model(i.uid)
+        return r_list
+
+    def assign_material_to_layer(self, material_id: int, layer_id: int) -> None:
+        """
+        Assign a material to a layer.
+
+        :param material_name: The material name
+        :type material_name: str
+        :param layer_name: The layer name
+        :type layer_name: str
+        """
+        self._wrapper.assign_material_to_layer(material_id, layer_id)
+
+    def add_layer_to_item(self, layer_id: int, item_id: int) -> None:
+        """
+        Add a layer to the item stack
+
+        :param item_id: The item id
+        :type item_id: int
+        :param layer_id: The layer id
+        :type layer_id: int
+        """
+        self._wrapper.add_layer_to_item(layer_id, item_id)
+
+    def remove_layer_from_item(self, layer_id: int, item_id: int) -> None:
+        """
+        Remove a layer from an item stack
+
+        :param item_id: The item id
+        :param layer_id: The layer id
+        """
+        self._wrapper.remove_layer_from_item(layer_id, item_id)
+
+    def add_item_to_model(self, item_id: int) -> None:
+        """
+        Add a layer to the item stack
+
+        :param item_id: The item id
+        :type item_id: int
+        """
+        self._wrapper.add_item(item_id)
+
+    def remove_item_from_model(self, item_id: int) -> None:
+        """
+        Remove a layer from the item stack
+
+        :param item_id: The item id
+        :type item_id: int
+        :param layer_id: The layer id
+        :type layer_id: int
+        """
+        self._wrapper.remove_item(item_id)
+
+    def fit_func(self, x_array: np.ndarray) -> np.ndarray:
+        """
+        Function to perform a fit
+        :param x_array: points to be calculated at
+        :type x_array: np.ndarray
+        :return: calculated points
+        :rtype: np.ndarray
+        """
+        return self._wrapper.calculate(x_array)
+
+    def sld_profile(self) -> tuple([np.ndarray, np.ndarray]):
+        """
+        Return the scattering length density profile.
+
+        :return: z and sld(z)
+        :rtype: tuple[np.ndarray, np.ndarray]
+        """
+        return self._wrapper.sld_profile()