diff --git a/.copier-answers.yml b/.copier-answers.yml
index 7b414c16..5743335a 100644
--- a/.copier-answers.yml
+++ b/.copier-answers.yml
@@ -1,6 +1,6 @@
# WARNING: Do not edit this file manually.
# Any changes will be overwritten by Copier.
-_commit: v0.10.1-25-ga5301e9
+_commit: v0.10.1-41-g508666e
_src_path: gh:easyscience/templates
app_docs_url: https://easyscience.github.io/dynamics-app
app_doi: 10.5281/zenodo.18877180
@@ -12,8 +12,8 @@ home_repo_name: dynamics
lib_docs_url: https://easyscience.github.io/dynamics-lib
lib_doi: 10.5281/zenodo.18877180
lib_package_name: easydynamics
-lib_python_max: '3.12'
-lib_python_min: '3.11'
+lib_python_max: '3.14'
+lib_python_min: '3.12'
lib_repo_name: dynamics-lib
project_contact_email: henrik.jacobsen@ess.eu
project_copyright_years: 2025-2026
diff --git a/.github/workflows/coverage.yml b/.github/workflows/coverage.yml
index cd9ff1e0..e1e44d41 100644
--- a/.github/workflows/coverage.yml
+++ b/.github/workflows/coverage.yml
@@ -1,8 +1,10 @@
name: Coverage checks
on:
- # Trigger the workflow on push
+ # Trigger the workflow on push to develop
push:
+ branches:
+ - develop
# Do not run on version tags (those are handled by other workflows)
tags-ignore: ['v*']
# Trigger the workflow on pull request
@@ -15,11 +17,11 @@ permissions:
actions: write
contents: read
-# Allow only one concurrent workflow, skipping runs queued between the run
-# in-progress and latest queued. And cancel in-progress runs.
+# Allow only one concurrent workflow per PR or branch ref.
+# Cancel in-progress runs only for pull requests, but let branch push runs finish.
concurrency:
group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}
- cancel-in-progress: true
+ cancel-in-progress: ${{ github.event_name == 'pull_request' }}
# Set the environment variables to be used in all jobs defined in this workflow
env:
diff --git a/.github/workflows/issues-labels.yml b/.github/workflows/issues-labels.yml
index 3a60cdd7..df3c55f1 100644
--- a/.github/workflows/issues-labels.yml
+++ b/.github/workflows/issues-labels.yml
@@ -13,9 +13,18 @@ permissions:
jobs:
check-labels:
+ if: github.actor != 'easyscience[bot]'
+
runs-on: ubuntu-latest
+ concurrency:
+ group: issue-labels-${{ github.event.issue.number }}
+ cancel-in-progress: true
+
steps:
+ - name: Checkout repository
+ uses: actions/checkout@v5
+
- name: Setup easyscience[bot]
id: bot
uses: ./.github/actions/setup-easyscience-bot
diff --git a/.github/workflows/lint-format.yml b/.github/workflows/lint-format.yml
index 457d67f4..f1135fa5 100644
--- a/.github/workflows/lint-format.yml
+++ b/.github/workflows/lint-format.yml
@@ -79,12 +79,6 @@ jobs:
shell: bash
run: pixi run docstring-lint-check
- - name: Check formatting of docstrings in Python code
- id: docstring_format
- continue-on-error: true
- shell: bash
- run: pixi run docstring-format-check
-
- name: Check formatting of non-Python files (md, toml, etc.)
id: nonpy_format
continue-on-error: true
@@ -112,7 +106,6 @@ jobs:
echo "| py lint | ${{ steps.py_lint.outcome == 'success' && '✅' || '❌' }} |"
echo "| py format | ${{ steps.py_format.outcome == 'success' && '✅' || '❌' }} |"
echo "| docstring lint | ${{ steps.docstring_lint.outcome == 'success' && '✅' || '❌' }} |"
- echo "| docstring format | ${{ steps.docstring_format.outcome == 'success' && '✅' || '❌' }} |"
echo "| nonpy format | ${{ steps.nonpy_format.outcome == 'success' && '✅' || '❌' }} |"
echo "| notebooks lint | ${{ steps.notebook_lint.outcome == 'success' && '✅' || '❌' }} |"
} >> "$GITHUB_STEP_SUMMARY"
@@ -125,7 +118,6 @@ jobs:
|| steps.py_lint.outcome == 'failure'
|| steps.py_format.outcome == 'failure'
|| steps.docstring_lint.outcome == 'failure'
- || steps.docstring_format.outcome == 'failure'
|| steps.nonpy_format.outcome == 'failure'
|| steps.notebook_lint.outcome == 'failure'
shell: bash
diff --git a/.github/workflows/pypi-test.yml b/.github/workflows/pypi-test.yml
index 117d24d6..7224f1e4 100644
--- a/.github/workflows/pypi-test.yml
+++ b/.github/workflows/pypi-test.yml
@@ -45,30 +45,26 @@ jobs:
- name: Init pixi project
run: pixi init easydynamics
- - name: Add Python 3.12 from Conda
+ - name: Set the minimum system requirements
working-directory: easydynamics
- run: pixi add "python=3.12"
+ run: pixi project system-requirements add macos 14.0
- - name: Add other Conda dependencies
+ - name: Add Python 3.14 from Conda
working-directory: easydynamics
- run: pixi add gsl
+ run: pixi add "python=3.14"
- - name: Add easydynamics from PyPI
+ - name: Add easydynamics (with dev dependencies) from PyPI
working-directory: easydynamics
- run: pixi add --pypi "easydynamics"
-
- - name: Add dev dependencies from PyPI
- working-directory: easydynamics
- run: pixi add --pypi pytest pytest-xdist
-
- - name: Add Pixi task as a shortcut
- working-directory: easydynamics
- run: pixi task add easydynamics "python -m easydynamics"
+ run: pixi add --pypi "easydynamics[dev]"
- name: Run unit tests to verify the installation
working-directory: easydynamics
run: pixi run python -m pytest ../tests/unit/ --color=yes -v
+ - name: Run functional tests to verify the installation
+ working-directory: easydynamics
+ run: pixi run python -m pytest ../tests/functional/ --color=yes -v
+
- name: Run integration tests to verify the installation
working-directory: easydynamics
run: pixi run python -m pytest ../tests/integration/ --color=yes -n auto
diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
index ce03715c..774edf78 100644
--- a/.github/workflows/test.yml
+++ b/.github/workflows/test.yml
@@ -44,8 +44,8 @@ concurrency:
# Set the environment variables to be used in all jobs defined in this workflow
env:
CI_BRANCH: ${{ github.head_ref || github.ref_name }}
- PY_VERSIONS: '3.11 3.12'
- PIXI_ENVS: 'py-311-env py-312-env'
+ PY_VERSIONS: '3.12 3.14'
+ PIXI_ENVS: 'py-312-env py-314-env'
jobs:
# Job 1: Set up environment variables
@@ -96,12 +96,27 @@ jobs:
echo
echo "🔹🔸🔹🔸🔹 Python: $py_ver 🔹🔸🔹🔸🔹"
- env="py-$(echo $py_ver | tr -d .)-env" # Converts 3.11 -> py-311-env
+ env="py-$(echo $py_ver | tr -d .)-env" # Converts 3.XX -> py-3XX-env
echo "Running tests in environment: $env"
pixi run --environment $env unit-tests
done
+ - name: Run functional tests
+ shell: bash
+ run: |
+ set -euo pipefail
+
+ for py_ver in $PY_VERSIONS; do
+ echo
+ echo "🔹🔸🔹🔸🔹 Python: $py_ver 🔹🔸🔹🔸🔹"
+
+ env="py-$(echo $py_ver | tr -d .)-env" # Converts 3.XX -> py-3XX-env
+
+ echo "Running tests in environment: $env"
+ pixi run --environment $env functional-tests
+ done
+
- name: Run integration tests ${{ needs.env-prepare.outputs.pytest-marks }}
shell: bash
run: |
@@ -111,7 +126,7 @@ jobs:
echo
echo "🔹🔸🔹🔸🔹 Python: $py_ver 🔹🔸🔹🔸🔹"
- env="py-$(echo $py_ver | tr -d .)-env" # Converts 3.11 -> py-311-env
+ env="py-$(echo $py_ver | tr -d .)-env" # Converts 3.XX -> py-3XX-env
echo "Running tests in environment: $env"
pixi run --environment $env integration-tests ${{ needs.env-prepare.outputs.pytest-marks }}
@@ -236,7 +251,26 @@ jobs:
cd easydynamics_py$py_ver
echo "Running tests"
- pixi run python -m pytest ../tests/unit/ --color=yes --cov= --cov-report=
+ pixi run python -m pytest ../tests/unit/ --color=yes -v
+
+ echo "Exiting pixi project directory"
+ cd ..
+ done
+
+ - name: Run functional tests
+ shell: bash
+ run: |
+ set -euo pipefail
+
+ for py_ver in $PY_VERSIONS; do
+ echo
+ echo "🔹🔸🔹🔸🔹 Python: $py_ver 🔹🔸🔹🔸🔹"
+
+ echo "Entering pixi project directory easydynamics_py$py_ver"
+ cd easydynamics_py$py_ver
+
+ echo "Running tests"
+ pixi run python -m pytest ../tests/functional/ --color=yes -v
echo "Exiting pixi project directory"
cd ..
diff --git a/.github/workflows/tutorial-tests.yml b/.github/workflows/tutorial-tests.yml
index 4c9244d0..e976e267 100644
--- a/.github/workflows/tutorial-tests.yml
+++ b/.github/workflows/tutorial-tests.yml
@@ -45,10 +45,6 @@ jobs:
- name: Set up pixi
uses: ./.github/actions/setup-pixi
- - name: Test tutorials as python scripts
- shell: bash
- run: pixi run script-tests
-
- name: Prepare notebooks
shell: bash
run: pixi run notebook-prepare
diff --git a/.gitignore b/.gitignore
index 0500ede3..6dc595c7 100644
--- a/.gitignore
+++ b/.gitignore
@@ -41,5 +41,6 @@ CMakeLists.txt.user*
*.dmg
# Misc
+.cache/
*.log
*.zip
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index 5fa0c2cb..9a3855f4 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -39,13 +39,6 @@ repos:
pass_filenames: false
stages: [manual]
- - id: pixi-docstring-format-check
- name: pixi run docstring-format-check
- entry: pixi run docstring-format-check
- language: system
- pass_filenames: false
- stages: [manual]
-
- id: pixi-nonpy-format-check
name: pixi run nonpy-format-check
entry: pixi run nonpy-format-check
diff --git a/.prettierignore b/.prettierignore
index 788ec8fa..a08c3c48 100644
--- a/.prettierignore
+++ b/.prettierignore
@@ -1,3 +1,6 @@
+# Git
+.git/
+
# Copier
.copier-answers*.yml
@@ -14,4 +17,16 @@ docs/docs/assets/
.pytest_cache/
# MyPy
-.mypy_cache
+.mypy_cache/
+
+# Ruff
+.ruff_cache/
+
+# Node
+node_modules
+
+# Misc
+.benchmarks
+.cache
+deps/
+tmp/
diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md
index 85365779..168c5d97 100644
--- a/CONTRIBUTING.md
+++ b/CONTRIBUTING.md
@@ -230,7 +230,6 @@ pixi run license-check.........................Passed
pixi run py-lint-check.........................Passed
pixi run py-format-check.......................Passed
pixi run docstring-lint-check..................Passed
-pixi run docstring-format-check................Passed
pixi run nonpy-format-check....................Passed
pixi run notebook-lint-check...................Passed
pixi run unit-tests............................Passed
diff --git a/docs/docs/installation-and-setup/index.md b/docs/docs/installation-and-setup/index.md
index 6c928741..243d81f8 100644
--- a/docs/docs/installation-and-setup/index.md
+++ b/docs/docs/installation-and-setup/index.md
@@ -5,7 +5,7 @@ icon: material/cog-box
# :material-cog-box: Installation & Setup
**EasyDynamics** is a cross-platform Python library compatible with
-**Python 3.11** through **3.12**.
+**Python 3.12** through **3.14**.
To install and set up EasyDynamics, we recommend using
[**Pixi**](https://pixi.prefix.dev), a modern package manager for
@@ -62,9 +62,9 @@ This section describes the simplest way to set up EasyDynamics using
pixi init easydynamics
cd easydynamics
```
-- Set the Python version for the Pixi environment (e.g., 3.12):
+- Set the Python version for the Pixi environment (e.g., 3.14):
```txt
- pixi add python=3.12
+ pixi add python=3.14
```
- Add EasyDynamics to the Pixi environment from PyPI:
```txt
@@ -231,26 +231,36 @@ first. This can be done individually via the :material-download:
- Navigate to your existing Pixi project, created as described in the
[Installing with Pixi](#installing-with-pixi) section.
-- Launch the Jupyter Lab server:
+- Add JupyterLab and the Pixi kernel for Jupyter:
```txt
- pixi run jupyter lab
+ pixi add --pypi jupyterlab pixi-kernel
+ ```
+- Download the EasyDynamics tutorials to the `tutorials/` directory.
+- Start JupyterLab in the `tutorials/` directory to access the
+ notebooks:
+ ```txt
+ pixi run jupyter lab tutorials/
```
- Your web browser should open automatically. Click on one of the
- `*.ipynb` files downloaded previously and select the `Python (Pixi)`
- kernel to get started.
+ `*.ipynb` files and select the `Python (Pixi)` kernel to get started.
### Classical Run Tutorials Locally
+- Install Jupyter Notebook and IPython kernel:
+ ```txt
+ pip install notebook ipykernel
+ ```
- Add the virtual environment as a Jupyter kernel:
```txt
python -m ipykernel install --user --name=venv --display-name "EasyDynamics Python kernel"
```
-- Launch the Jupyter Notebook server:
+- Download the EasyDynamics tutorials to the `tutorials/` directory.
+- Launch the Jupyter Notebook server (opens browser automatically at
+ `http://localhost:8888/`):
```txt
- jupyter notebook
+ jupyter notebook tutorials/
```
-- Your web browser should open automatically. Click on one of the
- `*.ipynb` files downloaded previously and select the
+- Open one of the `*.ipynb` files and select the
`EasyDynamics Python kernel` to get started.
### Run Tutorials via Google Colab
diff --git a/docs/docs/tutorials/analysis.ipynb b/docs/docs/tutorials/analysis.ipynb
index 623fd942..0d30fd4b 100644
--- a/docs/docs/tutorials/analysis.ipynb
+++ b/docs/docs/tutorials/analysis.ipynb
@@ -213,10 +213,7 @@
" instrument_model=instrument_model,\n",
")\n",
"\n",
- "# We need to hack in the resolution model from the vanadium analysis,\n",
- "# since the setters and getters overwrite the model. This will be fixed\n",
- "# asap.\n",
- "diffusion_analysis.instrument_model._resolution_model = (\n",
+ "diffusion_analysis.instrument_model.resolution_model = (\n",
" vanadium_analysis.instrument_model.resolution_model\n",
")\n",
"\n",
@@ -305,10 +302,7 @@
" instrument_model=instrument_model,\n",
")\n",
"\n",
- "# We again need to hack in the resolution model from the vanadium\n",
- "# analysis, since the setters and getters overwrite the model. This will\n",
- "# be fixed asap.\n",
- "diffusion_model_analysis.instrument_model._resolution_model = (\n",
+ "diffusion_model_analysis.instrument_model.resolution_model = (\n",
" vanadium_analysis.instrument_model.resolution_model\n",
")\n",
"diffusion_model_analysis.instrument_model.resolution_model.fix_all_parameters()\n",
diff --git a/docs/docs/tutorials/convolution.ipynb b/docs/docs/tutorials/convolution.ipynb
index 8b106ebd..04f15cc9 100644
--- a/docs/docs/tutorials/convolution.ipynb
+++ b/docs/docs/tutorials/convolution.ipynb
@@ -120,11 +120,12 @@
" sample_components=sample_components,\n",
" resolution_components=resolution_components,\n",
" energy=energy - energy_offset,\n",
- " upsample_factor=upsample_factor,\n",
- " extension_factor=extension_factor,\n",
" temperature=temperature,\n",
- " normalize_detailed_balance=True,\n",
")\n",
+ "convolver.upsample_factor = upsample_factor\n",
+ "convolver.extension_factor = extension_factor\n",
+ "convolver.normalize_detailed_balance = True\n",
+ "\n",
"y = convolver.convolution()\n",
"\n",
"\n",
@@ -185,11 +186,11 @@
" sample_components=sample_components,\n",
" resolution_components=resolution_components,\n",
" energy=energy,\n",
- " upsample_factor=upsample_factor,\n",
- " extension_factor=extension_factor,\n",
" energy_offset=energy_offset,\n",
" temperature=temperature,\n",
")\n",
+ "convolver.upsample_factor = upsample_factor\n",
+ "convolver.extension_factor = extension_factor\n",
"y = convolver.convolution()\n",
"\n",
"\n",
@@ -213,7 +214,7 @@
],
"metadata": {
"kernelspec": {
- "display_name": "easydynamics_newbase",
+ "display_name": "Python 3",
"language": "python",
"name": "python3"
},
@@ -227,7 +228,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
- "version": "3.12.12"
+ "version": "3.14.4"
}
},
"nbformat": 4,
diff --git a/docs/docs/tutorials/data/create_fake_data.ipynb b/docs/docs/tutorials/data/create_fake_data.ipynb
new file mode 100644
index 00000000..34ddd5f7
--- /dev/null
+++ b/docs/docs/tutorials/data/create_fake_data.ipynb
@@ -0,0 +1,134 @@
+{
+ "cells": [
+ {
+ "cell_type": "markdown",
+ "id": "106d6b6e",
+ "metadata": {},
+ "source": [
+ "This creates the data used in the tutorials."
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "id": "c87bc1c3",
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "import numpy as np\n",
+ "import plopp as pp\n",
+ "import scipp as sc\n",
+ "\n",
+ "import easydynamics.sample_model as sm\n",
+ "from easydynamics.sample_model import ComponentCollection\n",
+ "from easydynamics.sample_model import Gaussian\n",
+ "from easydynamics.sample_model.sample_model import SampleModel\n",
+ "\n",
+ "%matplotlib widget"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "id": "5823f28f",
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "# Create data for tutorial0_basics.ipynb. Data is called fake_simple_data.hdf5.\n",
+ "\n",
+ "Q = sc.linspace(start=0.2, stop=2.1, num=32, unit='1/angstrom', dim='Q')\n",
+ "\n",
+ "component_collection = ComponentCollection()\n",
+ "component_collection.append_component(Gaussian(area=0.45, width=0.1))\n",
+ "\n",
+ "model = SampleModel(components=component_collection, Q=Q)\n",
+ "\n",
+ "for i in range(Q.size):\n",
+ " components = model.get_component_collection(i)\n",
+ " offset = 0.0\n",
+ " components.components[0].area = 3.79 - 0.2 * Q[i].value\n",
+ "\n",
+ "energy = sc.linspace(start=-3.0, stop=3.0, num=756, unit='meV', dim='energy')\n",
+ "\n",
+ "intensity = sc.array(values=model.evaluate(x=energy), dims=['Q', 'energy'])\n",
+ "\n",
+ "intensity_dataarray = sc.DataArray(data=intensity, coords={'Q': Q, 'energy': energy})\n",
+ "\n",
+ "rng = np.random.default_rng()\n",
+ "noise = rng.normal(loc=0.0, scale=1.55, size=intensity_dataarray.shape)\n",
+ "intensity_dataarray.values += noise\n",
+ "intensity_dataarray.variances = noise**2\n",
+ "\n",
+ "sc.io.save_hdf5(intensity_dataarray, 'fake_simple_data.hdf5')\n",
+ "pp.slicer(intensity_dataarray)"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "id": "e8e4c806",
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "# Create data for tutorial0_more_advanced.ipynb. Data is called fake_advanced_data.hdf5.\n",
+ "Q = sc.linspace(start=0.2, stop=2.1, num=32, unit='1/angstrom', dim='Q')\n",
+ "\n",
+ "component_collection = sm.ComponentCollection()\n",
+ "component_collection.append_component(sm.Gaussian(area=0.45, width=0.05))\n",
+ "component_collection.append_component(sm.Lorentzian(area=10.45, width=0.4))\n",
+ "component_collection.append_component(\n",
+ " sm.DampedHarmonicOscillator(area=1.45, width=0.1, center=1.4)\n",
+ ")\n",
+ "component_collection.append_component(sm.Polynomial(coefficients=[1.2, 0.2]))\n",
+ "model = sm.SampleModel(components=component_collection, Q=Q)\n",
+ "\n",
+ "\n",
+ "energy = sc.linspace(start=-3.0, stop=3.0, num=756, unit='meV', dim='energy')\n",
+ "intensity_values = np.zeros((Q.size, energy.size))\n",
+ "rng = np.random.default_rng()\n",
+ "noise = rng.normal(loc=0.0, scale=0.35, size=intensity_dataarray.shape)\n",
+ "\n",
+ "for i in range(Q.size):\n",
+ " components = model.get_component_collection(i)\n",
+ " offset = sc.scalar(value=rng.uniform(0.05, 0.15), unit='meV')\n",
+ " components.components[0].area = 3.79 - 0.2 * Q[i].value\n",
+ " components.components[2].center = 1.4 + Q[i].value / 10.0\n",
+ " components.components[2].area = 2.45 + Q[i].value / 10.0\n",
+ "\n",
+ " intensity_values[i, :] = components.evaluate(x=energy.values - offset.value)\n",
+ "\n",
+ "\n",
+ "intensity = sc.array(values=intensity_values, dims=['Q', 'energy'])\n",
+ "intensity_dataarray = sc.DataArray(data=intensity, coords={'Q': Q, 'energy': energy})\n",
+ "\n",
+ "noise = rng.normal(loc=0.0, scale=0.35, size=intensity_dataarray.shape)\n",
+ "intensity_dataarray.values += noise\n",
+ "intensity_dataarray.variances = noise**2\n",
+ "\n",
+ "sc.io.save_hdf5(intensity_dataarray, 'fake_advanced_data.hdf5')\n",
+ "pp.slicer(intensity_dataarray)"
+ ]
+ }
+ ],
+ "metadata": {
+ "kernelspec": {
+ "display_name": "Python 3",
+ "language": "python",
+ "name": "python3"
+ },
+ "language_info": {
+ "codemirror_mode": {
+ "name": "ipython",
+ "version": 3
+ },
+ "file_extension": ".py",
+ "mimetype": "text/x-python",
+ "name": "python",
+ "nbconvert_exporter": "python",
+ "pygments_lexer": "ipython3",
+ "version": "3.14.4"
+ }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 5
+}
diff --git a/docs/docs/tutorials/data/fake_advanced_data.hdf5 b/docs/docs/tutorials/data/fake_advanced_data.hdf5
new file mode 100644
index 00000000..d83903fb
Binary files /dev/null and b/docs/docs/tutorials/data/fake_advanced_data.hdf5 differ
diff --git a/docs/docs/tutorials/data/fake_simple_data.hdf5 b/docs/docs/tutorials/data/fake_simple_data.hdf5
new file mode 100644
index 00000000..14afb830
Binary files /dev/null and b/docs/docs/tutorials/data/fake_simple_data.hdf5 differ
diff --git a/docs/docs/tutorials/index.md b/docs/docs/tutorials/index.md
index 1038be73..6c4158a3 100644
--- a/docs/docs/tutorials/index.md
+++ b/docs/docs/tutorials/index.md
@@ -21,6 +21,11 @@ We are working on expanding the list of tutorials to include advanced
concept such as interpolating `Parameter`s, sharing `Parameter`s at
multiple `Q` and analysing complex inelastic data.
+- [Tutorial 0: Basics](tutorial0_basics.ipynb) - Get started with
+ EasyDynamics and fit a basic data set.
+- [Tutorial 0: More advanced](tutorial0_more_advanced.ipynb) -
+ Introduction to more advanced features in EasyDynamics, fitting a data
+ set with multiple components and background.
- [Tutorial 1: Brownian Diffusion](tutorial1_brownian.ipynb) - Learn how
to analyse QENS data with elastic incoherent background and Brownian
diffusion.
diff --git a/docs/docs/tutorials/sample_model.ipynb b/docs/docs/tutorials/sample_model.ipynb
index 5371f7df..882048ce 100644
--- a/docs/docs/tutorials/sample_model.ipynb
+++ b/docs/docs/tutorials/sample_model.ipynb
@@ -134,7 +134,7 @@
],
"metadata": {
"kernelspec": {
- "display_name": "easydynamics_newbase",
+ "display_name": "Python 3",
"language": "python",
"name": "python3"
},
@@ -148,7 +148,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
- "version": "3.12.12"
+ "version": "3.14.4"
}
},
"nbformat": 4,
diff --git a/docs/docs/tutorials/tutorial0_basics.ipynb b/docs/docs/tutorials/tutorial0_basics.ipynb
new file mode 100644
index 00000000..44442036
--- /dev/null
+++ b/docs/docs/tutorials/tutorial0_basics.ipynb
@@ -0,0 +1,396 @@
+{
+ "cells": [
+ {
+ "cell_type": "markdown",
+ "id": "8643b10c",
+ "metadata": {},
+ "source": [
+ "# Basic fitting in **EasyDynamics**\n",
+ "We here show how to use **EasyDynamics** to fit a simple synthetic data set. We start with the simplest possible example; later tutorials will be more involved.\n",
+ "\n",
+ "The general procedure is to create an `Experiment` object to hold the data, a `SampleModel` to describe the model, and `Analysis` to fit the model to the data."
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "id": "bca91d3c",
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "# Imports\n",
+ "import pooch\n",
+ "\n",
+ "import easydynamics as edyn\n",
+ "import easydynamics.sample_model as sm\n",
+ "from easydynamics.analysis.analysis import Analysis\n",
+ "\n",
+ "# Make the plots interactive\n",
+ "%matplotlib widget"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "id": "4c8e97b7",
+ "metadata": {},
+ "source": [
+ "We first create an `Experiment` object to contain the data. The data must either be a `hdf5` file or a `scipp.DataArray`; in both cases it must have coordinates `Q` and `energy`. We here use Pooch to download an example data set.\n",
+ "\n",
+ "\n",
+ " 💡 Tip
\n",
+ " \n",
+ " If you have one or more data files that you want to fit using EasyDynamics, you can reach out to us e.g. at henrik.jacobsen@ess.eu for help.\n",
+ "
\n",
+ " \n",
+ "\n",
+ "We give the `Experiment` a `display_name` which is used as the title when plotting the data."
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "id": "7121f9c8",
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "# Load the data\n",
+ "experiment = edyn.Experiment(display_name='Tutorial')\n",
+ "\n",
+ "file_path = pooch.retrieve(\n",
+ " url='https://github.com/easyscience/dynamics-lib/raw/refs/heads/tutorial0/docs/docs/tutorials/data/fake_simple_data.hdf5',\n",
+ " known_hash='b49944c4447e69be4d30d1bed935173c4a1727c25a347285cbb156edc76ee261',\n",
+ ")\n",
+ "\n",
+ "experiment.load_hdf5(filename=file_path)"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "id": "7daa3f64",
+ "metadata": {},
+ "source": [
+ "We can visualize the data in multiple ways, relying on plopp: https://scipp.github.io/plopp/\n",
+ "\n",
+ "For now, let us plot the data using a slicer showing intensity as function of `energy` for various `Q`. You can dragg the slider to choose which $Q$ is displayed. Notice that the title is the `display_name` that we gave the `Experiment`.\n",
+ "\n",
+ "\n",
+ " 💡 Tip
\n",
+ " \n",
+ " You can change the title by running `experiment.display_name=\"new title\"`\n",
+ "
\n",
+ " "
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "id": "fbd31297",
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "experiment.plot_data(slicer=True)"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "id": "6c87b01c",
+ "metadata": {},
+ "source": [
+ "The data looks somewhat noisy. To improve statistics, we can rebin it. The method takes a dictionary of coordinates and the new bins. The new bins can be given as an integer number of bins or as a `scipp.Variable` (https://scipp.github.io/generated/classes/scipp.Variable.html#scipp.Variable) of bin-edges. For now, we just use integers, choosing 16 bins in $Q$ and 256 bins in energy."
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "id": "04644ee2",
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "experiment.rebin({'Q': 16, 'energy': 256})\n",
+ "experiment.plot_data(slicer=True)"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "id": "29b7f6b1",
+ "metadata": {},
+ "source": [
+ "\n",
+ " 💡 Tip
\n",
+ " \n",
+ " You may have noted that the y axis is automatically scaled to include all data for each Q. If you do not want this, use `autoscale=False` in the plot command.\n",
+ "
\n",
+ " \n",
+ "\n",
+ "In this data we see a single Gaussian shaped peak and a background that seems to be zero on average. We now want to fit this data, e.g. to determine how the Gaussian changes with $Q$. We define a `Gaussian` like this:"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "id": "6762faba",
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "gaussian = sm.Gaussian(display_name='Gaussian', area=1, width=0.05)"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "id": "00e2c719",
+ "metadata": {},
+ "source": [
+ "\n",
+ " 💡 Tip
\n",
+ " \n",
+ " You can access and change the values of the parameters of the Gaussian like this:\n",
+ " `gaussian.area=0.5`\n",
+ "
\n",
+ " \n",
+ "\n",
+ "\n",
+ " 💡 Tip
\n",
+ " \n",
+ " The following functions are implemented: Gaussian, Lorentzian, Voigt, Delta Function, Damped Harmonic Oscillator, Polynomial. If you need a different model, you can define your own using ExpressionComponent\n",
+ "
\n",
+ " "
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "id": "088ac17d",
+ "metadata": {},
+ "source": [
+ "We would like to fit this model to our data. However, it would be tedious to copy/paste the model for 16 values of $Q$, especially when the model grows more complicated. Instead, **EasyDynamics** handles this for us; we simply have to create a `SampleModel` and pass it our component."
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "id": "1ec6836f",
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "model = sm.SampleModel(components=gaussian)"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "id": "0b5c3c8b",
+ "metadata": {},
+ "source": [
+ "Our `SampleModel` does not yet have any $Q$ values. We could tell it what $Q$ is by using the `Q` attribute.\n",
+ "```python\n",
+ "Q_values=sc.linspace(start=0.2,stop=2.1,num=16,unit='1/angstrom', dim='Q')\n",
+ "\n",
+ "model.Q=Q_values\n",
+ "```\n",
+ "\n",
+ "This would generate a copy of the model for each of the values of $Q$. \n",
+ "\n",
+ "However, since we want the $Q$ values to match those of the experiment, it is much easier to let **EasyDynamics** handle it. To do this, we make an `Analysis` object and give it out experiment and sample model:"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "id": "b98d63dc",
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "analysis = Analysis(\n",
+ " experiment=experiment,\n",
+ " sample_model=model,\n",
+ ")"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "id": "e220c616",
+ "metadata": {},
+ "source": [
+ "A lot happens under the hood in this step. It automatically extracts the $Q$ values from the experiment and passes them to our `SampleModel`, which in turn generates a copy of the `Gaussian` for each $Q$. We furthermore create an `Analysis1d` object for each $Q$. You will usually not need to think too hard about any of this, since you will mostly interact with your data and model through the `Analysis` object, but it can be good to know what is going on.\n",
+ "\n",
+ "We can access a list of the the `Analysis1d` objects like this:\n"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "id": "fdddd14a",
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "analysis_list = analysis.analysis_list"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "id": "ceb877a5",
+ "metadata": {},
+ "source": [
+ "Let us plot our data and model using the plopp slicer:\n"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "id": "8c13a87a",
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "analysis.plot_data_and_model()"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "id": "a81248a4",
+ "metadata": {},
+ "source": [
+ "The model is of course not yet particularly good, since we didn't try very hard to guess what the parameters should be. However, we can now start fitting it using the `fit` method.\n",
+ "\n",
+ "Let us first fit a single $Q$ index and plot the data and model to see how it looks. We choose an arbitrary $Q$ and plot only that one"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "id": "aec75b7f",
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "fit_result_independent_single_Q = analysis.fit(Q_index=5)\n",
+ "analysis.plot_data_and_model(Q_index=5)"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "id": "af4103fb",
+ "metadata": {},
+ "source": [
+ "The fit looks very good. We can get a list of the parameters for this fit by accesing the corresponding `Analysis1d` object:"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "id": "6d074733",
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "analysis.analysis_list[5].get_all_parameters()"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "id": "c3fe553b",
+ "metadata": {},
+ "source": [
+ "\n",
+ " Note
\n",
+ "\n",
+ "You may note that the center of the Gaussian is fixed, and that we fitted an `energy_offset`. We discuss this in the following tutorial.\n",
+ "
\n",
+ " \n",
+ "\n",
+ "Since the fit looked good, we can now fit all $Q$. We also plot the result, again using the slicer."
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "id": "e98e3d65",
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "fit_result_all_Q = analysis.fit()\n",
+ "analysis.plot_data_and_model()"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "id": "64afbd3c",
+ "metadata": {},
+ "source": [
+ "Information about the fit is stored in the output. It is stored as a list of **EasyScience** `FitResult`s. Here we show a few of the relevant properties:"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "id": "c5a68515",
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "print(f'The reduced chi-squared value for Q_index=5 is: {fit_result_all_Q[5].reduced_chi}')\n",
+ "\n",
+ "print(f'The minimizer engine is: {fit_result_all_Q[5].minimizer_engine}')"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "id": "12936c9d",
+ "metadata": {},
+ "source": [
+ "It can be nice to inspect the fit parameters to look for trends, and sometimes continue working with them. To do this, we convert the parameters to a scipp Dataset (https://scipp.github.io/generated/classes/scipp.Dataset.html#scipp.Dataset)"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "id": "133e682e",
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "analysis.parameters_to_dataset()"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "id": "8acda0e4",
+ "metadata": {},
+ "source": [
+ "We can also plot the parameters as a function of `Q` using the `plot_parameters` method."
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "id": "dfacdf24",
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "analysis.plot_parameters(names=['Gaussian area'])"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "id": "842c1f01",
+ "metadata": {},
+ "source": [
+ "It will soon be possible to use **EasyDynamics** to fit these parameters to e.g. a polynomial."
+ ]
+ }
+ ],
+ "metadata": {
+ "kernelspec": {
+ "display_name": "Python 3",
+ "language": "python",
+ "name": "python3"
+ },
+ "language_info": {
+ "codemirror_mode": {
+ "name": "ipython",
+ "version": 3
+ },
+ "file_extension": ".py",
+ "mimetype": "text/x-python",
+ "name": "python",
+ "nbconvert_exporter": "python",
+ "pygments_lexer": "ipython3",
+ "version": "3.14.4"
+ }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 5
+}
diff --git a/docs/docs/tutorials/tutorial0_more_advanced.ipynb b/docs/docs/tutorials/tutorial0_more_advanced.ipynb
new file mode 100644
index 00000000..49cb8963
--- /dev/null
+++ b/docs/docs/tutorials/tutorial0_more_advanced.ipynb
@@ -0,0 +1,320 @@
+{
+ "cells": [
+ {
+ "cell_type": "markdown",
+ "id": "8643b10c",
+ "metadata": {},
+ "source": [
+ "# Basic fitting in **EasyDynamics**\n",
+ "We here show how to use **EasyDynamics** to fit a more advanced synthetic data set with multiple signals and a background, as well as an energy offset that could from from slight instrument misalignment. \n",
+ "\n",
+ "The general procedure is to create an `Experiment` object to hold the data, a `SampleModel` to describe the model, and `Analysis` to fit the model to the data. The `Analysis` object now also contains an `InstrumentModel`, which describes the background and energy offset."
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "id": "bca91d3c",
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "# Imports\n",
+ "import pooch\n",
+ "\n",
+ "import easydynamics as edyn\n",
+ "import easydynamics.sample_model as sm\n",
+ "\n",
+ "# Make the plots interactive\n",
+ "%matplotlib widget"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "id": "4c8e97b7",
+ "metadata": {},
+ "source": [
+ "As before, we createa an `Experiment` to hold the data, and rebin it."
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "id": "7121f9c8",
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "# Load the data\n",
+ "experiment = edyn.Experiment(display_name='Tutorial')\n",
+ "\n",
+ "file_path = pooch.retrieve(\n",
+ " url='https://github.com/easyscience/dynamics-lib/raw/refs/heads/tutorial0/docs/docs/tutorials/data/fake_advanced_data.hdf5',\n",
+ " known_hash='ee7310249df71a312ebc219f3e16b8da4e9aa37d29df919bbcaa541a38e1c39f',\n",
+ ")\n",
+ "\n",
+ "experiment.load_hdf5(filename=file_path)\n",
+ "experiment.rebin({'Q': 16, 'energy': 256})\n",
+ "experiment.plot_data(slicer=True)"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "id": "29b7f6b1",
+ "metadata": {},
+ "source": [
+ "This time, we see a sharp Gaussian near zero energy transfer, but with broad tails. There is also a pair of symmetrically placed peaks near +-1.5 meV. The background is not zero, and looks like it has a slope. We first focus on the three contributions to the signal: the Gaussian, its tails, which can be described by a Lorentzian, and the peaks near +- 1.5 meV, which can be described by a damped harmonic oscillator.\n",
+ "\n",
+ "We create and place these in a `ComponentCollection` like this:"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "id": "6762faba",
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "gaussian = sm.Gaussian(display_name='Gaussian', area=3, width=0.05)\n",
+ "lorentzian = sm.Lorentzian(display_name='Lorentzian', area=2, width=0.3)\n",
+ "dho = sm.DampedHarmonicOscillator(display_name='DHO', area=1.5, width=0.2, center=1.5)\n",
+ "\n",
+ "collection = sm.ComponentCollection()\n",
+ "collection.append_component(gaussian)\n",
+ "collection.append_component(lorentzian)\n",
+ "collection.append_component(dho)"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "id": "00e2c719",
+ "metadata": {},
+ "source": [
+ "\n",
+ " Note
\n",
+ "\n",
+ "Note that we do not give the Gaussian and Lorentzian a `center` value. In this case, the center is at zero (with a potential offset, see below), and fixed. This is typically what you want when describing elastic (the Gaussian) and quasielastic (the Lorentzian) signals.\n",
+ "
\n",
+ " \n",
+ "We pass this `ComponentCollection` to our `SampleModel`, just like before when we passed only a single component."
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "id": "1ec6836f",
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "model = sm.SampleModel(components=collection)"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "id": "0b5c3c8b",
+ "metadata": {},
+ "source": [
+ "Next, we want to handle the two instrument effects. The first is the small shift in energy: if you zoom in on the peak at the center, you'll see that it is in fact not centered at zero - it is offset. The offset applies to elastic, inelastic and quasielastic scattering. This is very typical in real experiments, and can be caused by slight misalignment or imperfections in the instrument. To handle this, we create an `InstrumentModel`, and give it an `energy_offset`. \n",
+ "\n",
+ "\n",
+ " Note
\n",
+ "\n",
+ "As noted in the previous tutorial, the energy_offset is always present, even when you do not explicitly set an InstrumentModel. This may give problems in two cases: 1) If all peaks are given a center value and allowed to fit it. In the simplest case of a single peak, this is problematic because there are now two parameters determining the center of the peak. The peak center/energy offset are equivalent in this case, and cannot be uniquely determined. 2) If there is no central peak, e.g. if only background scattering is present.\n",
+ "In either case, the energy_offset should be fixed. You can do this in the InstrumentModel using InstrumentModel.fix_energy_offset() or Analysis using Analysis.fix_energy_offset().\n",
+ "
\n",
+ " "
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "id": "8b82f8a4",
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "instrument = sm.InstrumentModel(energy_offset=0.05)"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "id": "0470ce5e",
+ "metadata": {},
+ "source": [
+ "Second, we want to handle the background. We do this with a `BackgroundModel`, which works the same as the `SampleModel`. We give it a `Polynomial` component:\n",
+ "\n",
+ " 💡 Tip
\n",
+ " \n",
+ " SampleModel, BackgroundModel and ResolutionModel (introduced later) all take components in several different ways: you can add a single component like in the previous tutorial, append components using the `append_component` method, or give a ComponentCollection like we do here. \n",
+ "
\n",
+ " \n"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "id": "bdcdc438",
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "background = sm.BackgroundModel(components=sm.Polynomial(coefficients=[1.2, 0.05]))"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "id": "44522a12",
+ "metadata": {},
+ "source": [
+ "We add the background to the instrument model:\n",
+ "\n",
+ " 💡 Tip
\n",
+ " \n",
+ " We could also have created the background model first, and then added it to the InstrumentModel when creating it, i.e. InstrumentModel(energy_offset = 0.05, background_model = background)\n",
+ "
\n",
+ " \n"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "id": "ee677467",
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "instrument.background_model = background"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "id": "02309896",
+ "metadata": {},
+ "source": [
+ "Now we create out `Analysis` object and give it the instrument model:"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "id": "b98d63dc",
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "analysis = edyn.Analysis(\n",
+ " experiment=experiment,\n",
+ " sample_model=model,\n",
+ " instrument_model=instrument,\n",
+ ")"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "id": "ceb877a5",
+ "metadata": {},
+ "source": [
+ "It is always good to check if the model somewhat matches the data."
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "id": "8c13a87a",
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "analysis.plot_data_and_model()"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "id": "a81248a4",
+ "metadata": {},
+ "source": [
+ "As before, let us first fit a single $Q$ index and plot the data and model to see how it looks. We choose an arbitrary $Q$ and plot only that one"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "id": "aec75b7f",
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "fit_result_independent_single_Q = analysis.fit(Q_index=5)\n",
+ "analysis.plot_data_and_model(Q_index=5)"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "id": "af4103fb",
+ "metadata": {},
+ "source": [
+ "The fit looks very good. We can again get a list of the parameters for this fit by accesing the corresponding `Analysis1d` object. Note ethat the Gaussian and Lorentzian centers are both zero, but that the `energy_offset` is non-zero."
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "id": "6d074733",
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "analysis.analysis_list[5].get_all_parameters()"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "id": "c3fe553b",
+ "metadata": {},
+ "source": [
+ "Since the fit looked good, we can now fit all $Q$. We also plot the result, again using the slicer."
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "id": "e98e3d65",
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "fit_result_all_Q = analysis.fit()\n",
+ "analysis.plot_data_and_model()"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "id": "8acda0e4",
+ "metadata": {},
+ "source": [
+ "Let us plot a few parameters as a function of `Q` using the `plot_parameters` method."
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "id": "dfacdf24",
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "analysis.plot_parameters(names=['Gaussian area', 'Lorentzian area', 'DHO area'])"
+ ]
+ }
+ ],
+ "metadata": {
+ "kernelspec": {
+ "display_name": "Python 3",
+ "language": "python",
+ "name": "python3"
+ },
+ "language_info": {
+ "codemirror_mode": {
+ "name": "ipython",
+ "version": 3
+ },
+ "file_extension": ".py",
+ "mimetype": "text/x-python",
+ "name": "python",
+ "nbconvert_exporter": "python",
+ "pygments_lexer": "ipython3",
+ "version": "3.14.4"
+ }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 5
+}
diff --git a/docs/docs/tutorials/tutorial1_brownian.ipynb b/docs/docs/tutorials/tutorial1_brownian.ipynb
index 5562adde..413ce036 100644
--- a/docs/docs/tutorials/tutorial1_brownian.ipynb
+++ b/docs/docs/tutorials/tutorial1_brownian.ipynb
@@ -76,7 +76,9 @@
"source": [
"We can visualize the data in multiple ways, relying on plopp: https://scipp.github.io/plopp/\n",
"\n",
- "We here show two ways to look at the data: as a 2d colormap with intensity as function of `Q` and `energy`, and as a slicer with intensity as function of `energy` for various `Q`."
+ "We here show two ways to look at the data: as a 2d colormap with intensity as function of `Q` and `energy`, and as a slicer with intensity as function of `energy` for various `Q`.\n",
+ "\n",
+ "If you want $Q$ on the x axis, then set `transpose_axes=True`"
]
},
{
@@ -86,7 +88,7 @@
"metadata": {},
"outputs": [],
"source": [
- "vanadium_experiment.plot_data(slicer=False)"
+ "vanadium_experiment.plot_data(slicer=False, transpose_axes=False)"
]
},
{
@@ -396,7 +398,24 @@
"id": "b72a710b",
"metadata": {},
"source": [
- "We don't want to fit our resolution anymore, so we fix all the parameters in it."
+ "We don't want to fit our resolution anymore, so we fix all the parameters in it.\n",
+ "\n",
+ "`Analysis` handles the convolution of the `sample_model` with the `resolution_model`. The calculation is analytical when possible, and otherwise numerical. For numerical convolution, it will give warnings if the result might be inaccurate due to various numerical errors. In that case, two settings can be varied to improve the result.\n",
+ "`upsample_factor` improves accuracy for narrow signals. The default is 5.\n",
+ "`extension_factor` improves accuracy for broad signals. Here, the default is 0.2.\n",
+ "It is furthermore possible to toggle whether detailed balance correction is normalized or not (see next tutorial)"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "id": "0fb0c648",
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "diffusion_analysis.convolution_settings.upsample_factor = 6\n",
+ "diffusion_analysis.convolution_settings.extension_factor = 0.2\n",
+ "diffusion_analysis.convolution_settings.normalize_detailed_balance = True"
]
},
{
@@ -590,9 +609,9 @@
],
"metadata": {
"kernelspec": {
- "display_name": "Python (Pixi)",
+ "display_name": "Python 3",
"language": "python",
- "name": "pixi-kernel-python3"
+ "name": "python3"
},
"language_info": {
"codemirror_mode": {
@@ -604,7 +623,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
- "version": "3.12.13"
+ "version": "3.14.4"
}
},
"nbformat": 4,
diff --git a/docs/docs/tutorials/tutorial2_nanoparticles.ipynb b/docs/docs/tutorials/tutorial2_nanoparticles.ipynb
index e7308dbf..8f4312a1 100644
--- a/docs/docs/tutorials/tutorial2_nanoparticles.ipynb
+++ b/docs/docs/tutorials/tutorial2_nanoparticles.ipynb
@@ -34,7 +34,7 @@
},
{
"cell_type": "code",
- "execution_count": null,
+ "execution_count": 4,
"id": "bca91d3c",
"metadata": {},
"outputs": [],
@@ -70,7 +70,7 @@
},
{
"cell_type": "code",
- "execution_count": null,
+ "execution_count": 6,
"id": "4fbb90da",
"metadata": {},
"outputs": [],
@@ -78,7 +78,7 @@
"resolution_experiment = Experiment(display_name='Nanoparticles, 1.5 K')\n",
"\n",
"file_path = pooch.retrieve(\n",
- " url='https://github.com/easyscience/dynamics-lib/raw/refs/heads/tutorial2/docs/docs/tutorials/data/nano_1p5K.h5',\n",
+ " url='https://github.com/easyscience/dynamics-lib/raw/refs/heads/master/docs/docs/tutorials/data/nano_1p5K.h5',\n",
" known_hash='32935cfaa5e623137ea5f4ba972d0c921bca8d0e067486666cdcf23abf27823e',\n",
")\n",
"\n",
@@ -216,7 +216,7 @@
"resolution_experiment = Experiment(display_name='Nanoparticles, 1.5 K')\n",
"\n",
"file_path = pooch.retrieve(\n",
- " url='https://github.com/easyscience/dynamics-lib/raw/refs/heads/tutorial2/docs/docs/tutorials/data/nano_150K.h5',\n",
+ " url='https://github.com/easyscience/dynamics-lib/raw/refs/heads/master/docs/docs/tutorials/data/nano_150K.h5',\n",
" known_hash='dc3abdaf6d2165f4dbc5df4e0de1890af8d4cd290f2c79ac7b319ccbe44117b8',\n",
")\n",
"\n",
@@ -605,9 +605,9 @@
],
"metadata": {
"kernelspec": {
- "display_name": "Python (Pixi)",
+ "display_name": "Python 3",
"language": "python",
- "name": "pixi-kernel-python3"
+ "name": "python3"
},
"language_info": {
"codemirror_mode": {
@@ -619,7 +619,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
- "version": "3.12.13"
+ "version": "3.14.4"
}
},
"nbformat": 4,
diff --git a/docs/mkdocs.yml b/docs/mkdocs.yml
index bd73822e..a7e2be2b 100644
--- a/docs/mkdocs.yml
+++ b/docs/mkdocs.yml
@@ -148,8 +148,7 @@ plugins:
python:
paths: ['src'] # Change 'src' to your actual sources directory
options:
- docstring_style: google
- render_markdown: true
+ docstring_style: numpy
group_by_category: false
heading_level: 1
show_root_heading: true
@@ -182,7 +181,10 @@ nav:
- Tutorials:
- Tutorials: tutorials/index.md
- Getting Started:
+ - Tutorial 0. Basics: tutorials/tutorial0_basics.ipynb
+ - Tutorial 0. More Advanced: tutorials/tutorial0_more_advanced.ipynb
- Tutorial 1. Brownian Diffusion: tutorials/tutorial1_brownian.ipynb
+ - Tutorial 2. Magnetic nanoparticles: tutorials/tutorial2_nanoparticles.ipynb
- Classes and Methods:
- Components: tutorials/components.ipynb
- Component collection: tutorials/component_collection.ipynb
diff --git a/pixi.lock b/pixi.lock
index cdb11917..0d2efa1f 100644
--- a/pixi.lock
+++ b/pixi.lock
@@ -10,15 +10,74 @@ environments:
packages:
linux-64:
- conda: https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-20_gnu.conda
+ - conda: https://conda.anaconda.org/conda-forge/noarch/_python_abi3_support-1.0-hd8ed1ab_2.conda
+ - conda: https://conda.anaconda.org/conda-forge/noarch/anyio-4.13.0-pyhcf101f3_0.conda
+ - conda: https://conda.anaconda.org/conda-forge/noarch/argon2-cffi-25.1.0-pyhd8ed1ab_0.conda
+ - conda: https://conda.anaconda.org/conda-forge/linux-64/argon2-cffi-bindings-25.1.0-py314h5bd0f2a_2.conda
+ - conda: https://conda.anaconda.org/conda-forge/noarch/arrow-1.4.0-pyhcf101f3_0.conda
+ - conda: https://conda.anaconda.org/conda-forge/noarch/asttokens-3.0.1-pyhd8ed1ab_0.conda
+ - conda: https://conda.anaconda.org/conda-forge/noarch/async-lru-2.3.0-pyhcf101f3_0.conda
+ - conda: https://conda.anaconda.org/conda-forge/noarch/attrs-26.1.0-pyhcf101f3_0.conda
+ - conda: https://conda.anaconda.org/conda-forge/noarch/babel-2.18.0-pyhcf101f3_1.conda
+ - conda: https://conda.anaconda.org/conda-forge/noarch/backports.zstd-1.3.0-py314h680f03e_0.conda
+ - conda: https://conda.anaconda.org/conda-forge/noarch/beautifulsoup4-4.14.3-pyha770c72_0.conda
+ - conda: https://conda.anaconda.org/conda-forge/noarch/bleach-6.3.0-pyhcf101f3_1.conda
+ - conda: https://conda.anaconda.org/conda-forge/noarch/bleach-with-css-6.3.0-hbca2aae_1.conda
+ - conda: https://conda.anaconda.org/conda-forge/linux-64/brotli-python-1.2.0-py314h3de4e8d_1.conda
- conda: https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-hda65f42_9.conda
- conda: https://conda.anaconda.org/conda-forge/linux-64/c-ares-1.34.6-hb03c661_0.conda
- conda: https://conda.anaconda.org/conda-forge/noarch/ca-certificates-2026.2.25-hbd8a1cb_0.conda
+ - conda: https://conda.anaconda.org/conda-forge/noarch/cached-property-1.5.2-hd8ed1ab_1.tar.bz2
+ - conda: https://conda.anaconda.org/conda-forge/noarch/cached_property-1.5.2-pyha770c72_1.tar.bz2
+ - conda: https://conda.anaconda.org/conda-forge/noarch/certifi-2026.2.25-pyhd8ed1ab_0.conda
+ - conda: https://conda.anaconda.org/conda-forge/linux-64/cffi-2.0.0-py314h4a8dc5f_1.conda
+ - conda: https://conda.anaconda.org/conda-forge/noarch/charset-normalizer-3.4.7-pyhd8ed1ab_0.conda
+ - conda: https://conda.anaconda.org/conda-forge/noarch/comm-0.2.3-pyhe01879c_0.conda
+ - conda: https://conda.anaconda.org/conda-forge/noarch/cpython-3.14.4-py314hd8ed1ab_100.conda
+ - conda: https://conda.anaconda.org/conda-forge/linux-64/debugpy-1.8.20-py314h42812f9_0.conda
+ - conda: https://conda.anaconda.org/conda-forge/noarch/decorator-5.2.1-pyhd8ed1ab_0.conda
+ - conda: https://conda.anaconda.org/conda-forge/noarch/defusedxml-0.7.1-pyhd8ed1ab_0.tar.bz2
+ - conda: https://conda.anaconda.org/conda-forge/noarch/exceptiongroup-1.3.1-pyhd8ed1ab_0.conda
+ - conda: https://conda.anaconda.org/conda-forge/noarch/executing-2.2.1-pyhd8ed1ab_0.conda
+ - conda: https://conda.anaconda.org/conda-forge/noarch/fqdn-1.5.1-pyhd8ed1ab_1.conda
+ - conda: https://conda.anaconda.org/conda-forge/noarch/h11-0.16.0-pyhcf101f3_1.conda
+ - conda: https://conda.anaconda.org/conda-forge/noarch/h2-4.3.0-pyhcf101f3_0.conda
+ - conda: https://conda.anaconda.org/conda-forge/noarch/hpack-4.1.0-pyhd8ed1ab_0.conda
+ - conda: https://conda.anaconda.org/conda-forge/noarch/httpcore-1.0.9-pyh29332c3_0.conda
+ - conda: https://conda.anaconda.org/conda-forge/noarch/httpx-0.28.1-pyhd8ed1ab_0.conda
+ - conda: https://conda.anaconda.org/conda-forge/noarch/hyperframe-6.1.0-pyhd8ed1ab_0.conda
- conda: https://conda.anaconda.org/conda-forge/linux-64/icu-78.3-h33c6efd_0.conda
+ - conda: https://conda.anaconda.org/conda-forge/noarch/idna-3.11-pyhd8ed1ab_0.conda
+ - conda: https://conda.anaconda.org/conda-forge/noarch/importlib-metadata-8.8.0-pyhcf101f3_0.conda
+ - conda: https://conda.anaconda.org/conda-forge/noarch/ipykernel-7.2.0-pyha191276_1.conda
+ - conda: https://conda.anaconda.org/conda-forge/noarch/ipython-9.12.0-pyhecfbec7_0.conda
+ - conda: https://conda.anaconda.org/conda-forge/noarch/ipython_pygments_lexers-1.1.1-pyhd8ed1ab_0.conda
+ - conda: https://conda.anaconda.org/conda-forge/noarch/isoduration-20.11.0-pyhd8ed1ab_1.conda
+ - conda: https://conda.anaconda.org/conda-forge/noarch/jedi-0.19.2-pyhd8ed1ab_1.conda
+ - conda: https://conda.anaconda.org/conda-forge/noarch/jinja2-3.1.6-pyhcf101f3_1.conda
+ - conda: https://conda.anaconda.org/conda-forge/noarch/json5-0.14.0-pyhd8ed1ab_0.conda
+ - conda: https://conda.anaconda.org/conda-forge/noarch/jsonpointer-3.1.1-pyhcf101f3_0.conda
+ - conda: https://conda.anaconda.org/conda-forge/noarch/jsonschema-4.26.0-pyhcf101f3_0.conda
+ - conda: https://conda.anaconda.org/conda-forge/noarch/jsonschema-specifications-2025.9.1-pyhcf101f3_0.conda
+ - conda: https://conda.anaconda.org/conda-forge/noarch/jsonschema-with-format-nongpl-4.26.0-hcf101f3_0.conda
+ - conda: https://conda.anaconda.org/conda-forge/noarch/jupyter-lsp-2.3.1-pyhcf101f3_0.conda
+ - conda: https://conda.anaconda.org/conda-forge/noarch/jupyter_client-8.8.0-pyhcf101f3_0.conda
+ - conda: https://conda.anaconda.org/conda-forge/noarch/jupyter_core-5.9.1-pyhc90fa1f_0.conda
+ - conda: https://conda.anaconda.org/conda-forge/noarch/jupyter_events-0.12.0-pyhe01879c_0.conda
+ - conda: https://conda.anaconda.org/conda-forge/noarch/jupyter_server-2.17.0-pyhcf101f3_0.conda
+ - conda: https://conda.anaconda.org/conda-forge/noarch/jupyter_server_terminals-0.5.4-pyhcf101f3_0.conda
+ - conda: https://conda.anaconda.org/conda-forge/noarch/jupyterlab-4.5.6-pyhd8ed1ab_0.conda
+ - conda: https://conda.anaconda.org/conda-forge/noarch/jupyterlab_pygments-0.3.0-pyhd8ed1ab_2.conda
+ - conda: https://conda.anaconda.org/conda-forge/noarch/jupyterlab_server-2.28.0-pyhcf101f3_0.conda
+ - conda: https://conda.anaconda.org/conda-forge/linux-64/keyutils-1.6.3-hb9d3cd8_0.conda
+ - conda: https://conda.anaconda.org/conda-forge/linux-64/krb5-1.22.2-ha1258a1_0.conda
+ - conda: https://conda.anaconda.org/conda-forge/noarch/lark-1.3.1-pyhd8ed1ab_0.conda
- conda: https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.45.1-default_hbd61a6d_102.conda
- conda: https://conda.anaconda.org/conda-forge/linux-64/libabseil-20260107.1-cxx17_h7b12aa8_0.conda
- conda: https://conda.anaconda.org/conda-forge/linux-64/libbrotlicommon-1.2.0-hb03c661_1.conda
- conda: https://conda.anaconda.org/conda-forge/linux-64/libbrotlidec-1.2.0-hb03c661_1.conda
- conda: https://conda.anaconda.org/conda-forge/linux-64/libbrotlienc-1.2.0-hb03c661_1.conda
+ - conda: https://conda.anaconda.org/conda-forge/linux-64/libedit-3.1.20250104-pl5321h7949ede_0.conda
- conda: https://conda.anaconda.org/conda-forge/linux-64/libev-4.33-hd590300_2.conda
- conda: https://conda.anaconda.org/conda-forge/linux-64/libexpat-2.7.5-hecca717_0.conda
- conda: https://conda.anaconda.org/conda-forge/linux-64/libffi-3.5.2-h3435931_0.conda
@@ -26,127 +85,144 @@ environments:
- conda: https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-15.2.0-h69a702a_18.conda
- conda: https://conda.anaconda.org/conda-forge/linux-64/libgomp-15.2.0-he0feb66_18.conda
- conda: https://conda.anaconda.org/conda-forge/linux-64/liblzma-5.8.2-hb03c661_0.conda
+ - conda: https://conda.anaconda.org/conda-forge/linux-64/libmpdec-4.0.0-hb03c661_1.conda
- conda: https://conda.anaconda.org/conda-forge/linux-64/libnghttp2-1.68.1-h877daf1_0.conda
- - conda: https://conda.anaconda.org/conda-forge/linux-64/libnsl-2.0.1-hb9d3cd8_1.conda
+ - conda: https://conda.anaconda.org/conda-forge/linux-64/libsodium-1.0.21-h280c20c_3.conda
- conda: https://conda.anaconda.org/conda-forge/linux-64/libsqlite-3.52.0-hf4e2dac_0.conda
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- conda: https://conda.anaconda.org/conda-forge/linux-64/libuv-1.51.0-hb03c661_1.conda
- - conda: https://conda.anaconda.org/conda-forge/linux-64/libxcrypt-4.4.36-hd590300_1.conda
- conda: https://conda.anaconda.org/conda-forge/linux-64/libzlib-1.3.2-h25fd6f3_2.conda
+ - conda: https://conda.anaconda.org/conda-forge/linux-64/markupsafe-3.0.3-py314h67df5f8_1.conda
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+ md5: 1ab0237036bfb14e923d6107473b0021
+ depends:
+ - vc >=14.3,<15
+ - vc14_runtime >=14.44.35208
+ - ucrt >=10.0.20348.0
+ - libsodium >=1.0.21,<1.0.22.0a0
+ - krb5 >=1.22.2,<1.23.0a0
+ license: MPL-2.0
+ license_family: MOZILLA
+ purls: []
+ size: 265665
+ timestamp: 1772476832995
+- conda: https://conda.anaconda.org/conda-forge/noarch/zipp-3.23.0-pyhcf101f3_1.conda
+ sha256: b4533f7d9efc976511a73ef7d4a2473406d7f4c750884be8e8620b0ce70f4dae
+ md5: 30cd29cb87d819caead4d55184c1d115
+ depends:
+ - python >=3.10
+ - python
+ license: MIT
+ license_family: MIT
+ purls:
+ - pkg:pypi/zipp?source=hash-mapping
+ size: 24194
+ timestamp: 1764460141901
- conda: https://conda.anaconda.org/conda-forge/linux-64/zstd-1.5.7-hb78ec9c_6.conda
sha256: 68f0206ca6e98fea941e5717cec780ed2873ffabc0e1ed34428c061e2c6268c7
md5: 4a13eeac0b5c8e5b8ab496e6c4ddd829
@@ -10369,17 +10147,6 @@ packages:
purls: []
size: 601375
timestamp: 1764777111296
-- conda: https://conda.anaconda.org/conda-forge/osx-64/zstd-1.5.7-h3eecb57_6.conda
- sha256: 47101a4055a70a4876ffc87b750ab2287b67eca793f21c8224be5e1ee6394d3f
- md5: 727109b184d680772e3122f40136d5ca
- depends:
- - __osx >=10.13
- - libzlib >=1.3.1,<2.0a0
- license: BSD-3-Clause
- license_family: BSD
- purls: []
- size: 528148
- timestamp: 1764777156963
- conda: https://conda.anaconda.org/conda-forge/osx-arm64/zstd-1.5.7-hbf9d68e_6.conda
sha256: 9485ba49e8f47d2b597dd399e88f4802e100851b27c21d7525625b0b4025a5d9
md5: ab136e4c34e97f34fb621d2592a393d8
@@ -10391,3 +10158,16 @@ packages:
purls: []
size: 433413
timestamp: 1764777166076
+- conda: https://conda.anaconda.org/conda-forge/win-64/zstd-1.5.7-h534d264_6.conda
+ sha256: 368d8628424966fd8f9c8018326a9c779e06913dd39e646cf331226acc90e5b2
+ md5: 053b84beec00b71ea8ff7a4f84b55207
+ depends:
+ - vc >=14.3,<15
+ - vc14_runtime >=14.44.35208
+ - ucrt >=10.0.20348.0
+ - libzlib >=1.3.1,<2.0a0
+ license: BSD-3-Clause
+ license_family: BSD
+ purls: []
+ size: 388453
+ timestamp: 1764777142545
diff --git a/pixi.toml b/pixi.toml
index ab15262f..c711a178 100644
--- a/pixi.toml
+++ b/pixi.toml
@@ -5,7 +5,7 @@
# Platform-independent
[activation.env]
-PYTHONIOENCODING = "utf-8"
+PYTHONIOENCODING = 'utf-8'
# Platform-specific
@@ -29,13 +29,13 @@ PYTHONPATH = "${PIXI_PROJECT_ROOT}/src;%PYTHONPATH%"
[workspace]
# Supported platforms for the lock file (pixi.lock)
-platforms = ['win-64', 'linux-64', 'osx-64', 'osx-arm64']
+platforms = ['win-64', 'linux-64', 'osx-arm64']
# Channels for fetching packages
channels = ['conda-forge']
#####################
-# System requirements
+# SYSTEM REQUIREMENTS
#####################
[system-requirements]
@@ -53,17 +53,20 @@ macos = '14.0'
# Default feature configuration
[dependencies]
-nodejs = '*' # Required for Prettier (non-Python formatting)
+nodejs = '*' # Required for Prettier (non-Python formatting)
+jupyterlab = '*' # Jupyter notebooks
+pixi-kernel = '*' # Pixi Jupyter kernel
[pypi-dependencies] # == [feature.default.pypi-dependencies]
-easydynamics = { path = ".", editable = true, extras = ['dev'] }
+#pip = '*' # Native package installer
+easydynamics = { path = '.', editable = true, extras = ['dev'] }
# Specific features: Set specific Python versions
[feature.py-min.dependencies]
-python = '3.11.*'
-[feature.py-max.dependencies]
python = '3.12.*'
+[feature.py-max.dependencies]
+python = '3.14.*'
##############
# ENVIRONMENTS
@@ -73,12 +76,12 @@ python = '3.12.*'
# The `default` feature is always included in all environments.
# Additional features can be specified per environment.
-py-311-env = { features = ['default', 'py-min'] }
-py-312-env = { features = ['default', 'py-max'] }
+py-312-env = { features = ['py-min'] }
+py-314-env = { features = ['py-max'] }
# The `default` environment is always created and includes the `default` feature.
# It does not need to be specified explicitly unless non-default features are included.
-default = { features = ['default', 'py-max'] }
+default = { features = ['py-max'] }
#######
# TASKS
@@ -91,9 +94,9 @@ default = { features = ['default', 'py-max'] }
##################
unit-tests = 'python -m pytest tests/unit/ --color=yes -v'
+functional-tests = 'python -m pytest tests/functional/ --color=yes -v'
integration-tests = 'python -m pytest tests/integration/ --color=yes -n auto -v'
-notebook-tests = 'python -m pytest --nbmake docs/docs/tutorials/ --nbmake-timeout=600 --color=yes -n auto -v'
-script-tests = 'python -m pytest tools/test_scripts.py --color=yes -n auto -v'
+notebook-tests = 'python -m pytest --nbmake docs/docs/tutorials/ --nbmake-timeout=1200 --color=yes -n auto -v'
test = { depends-on = ['unit-tests'] }
@@ -103,12 +106,11 @@ test = { depends-on = ['unit-tests'] }
pyproject-check = 'python -m validate_pyproject pyproject.toml'
docstring-lint-check = 'pydoclint --quiet src/'
-docstring-format-check = 'docformatter --check src/'
notebook-lint-check = 'nbqa ruff docs/docs/tutorials/'
py-lint-check = 'ruff check src/ tests/ docs/docs/tutorials/'
-py-format-check = "ruff format --check src/ tests/ docs/docs/tutorials/"
-nonpy-format-check = "npx prettier --list-different --config=prettierrc.toml --ignore-unknown ."
-nonpy-format-check-modified = "python tools/nonpy_prettier_modified.py"
+py-format-check = 'ruff format --check src/ tests/ docs/docs/tutorials/'
+nonpy-format-check = 'npx prettier --list-different --config=prettierrc.toml --ignore-unknown .'
+nonpy-format-check-modified = 'python tools/nonpy_prettier_modified.py'
check = 'pre-commit run --hook-stage manual --all-files'
@@ -116,22 +118,23 @@ check = 'pre-commit run --hook-stage manual --all-files'
# 🛠️ Fixes
##########
-docs-format-fix = 'docformatter --in-place src/ docs/docs/tutorials/'
+docstring-transform = 'pixi run docstripy src/ -s=numpy -w'
+docstring-format-fix = 'format-docstring src/'
notebook-lint-fix = 'nbqa ruff --fix docs/docs/tutorials/'
py-lint-fix = 'ruff check --fix src/ tests/ docs/docs/tutorials/'
py-lint-fix-unsafe = 'ruff check --fix --unsafe-fixes src/ tests/ docs/docs/tutorials/'
-py-format-fix = "ruff format src/ tests/ docs/docs/tutorials/"
+py-format-fix = 'ruff format src/ tests/ docs/docs/tutorials/'
nonpy-format-fix = 'npx prettier --write --list-different --config=prettierrc.toml --ignore-unknown .'
-nonpy-format-fix-modified = "python tools/nonpy_prettier_modified.py --write"
-success-message-fix = 'echo "✅ All auto-formatting steps completed successfully!"'
+nonpy-format-fix-modified = 'python tools/nonpy_prettier_modified.py --write'
+success-message = 'echo "✅ All auto-formatting steps completed successfully!"'
fix = { depends-on = [
+ 'docstring-format-fix',
'py-format-fix',
- 'docs-format-fix',
'py-lint-fix',
'nonpy-format-fix',
'notebook-lint-fix',
- 'success-message-fix',
+ 'success-message',
] }
####################
@@ -150,6 +153,7 @@ raw-metrics-json = 'radon raw -s -j src/'
#############
unit-tests-coverage = 'pixi run unit-tests --cov=src/easydynamics --cov-report=term-missing'
+functional-tests-coverage = 'pixi run functional-tests --cov=src/easydynamics --cov-report=term-missing'
integration-tests-coverage = 'pixi run integration-tests --cov=src/easydynamics --cov-report=term-missing'
docstring-coverage = 'interrogate -c pyproject.toml src/easydynamics'
@@ -165,8 +169,8 @@ cov = { depends-on = [
notebook-convert = 'jupytext docs/docs/tutorials/*.py --from py:percent --to ipynb'
notebook-strip = 'nbstripout docs/docs/tutorials/*.ipynb'
-notebook-tweak = 'python tools/tweak_notebooks.py tutorials/'
-notebook-exec = 'python -m pytest --nbmake docs/docs/tutorials/ --nbmake-timeout=600 --overwrite --color=yes -n auto -v'
+notebook-tweak = 'python tools/tweak_notebooks.py docs/docs/tutorials/'
+notebook-exec = 'python -m pytest --nbmake docs/docs/tutorials/ --nbmake-timeout=1200 --overwrite --color=yes -n auto -v'
notebook-prepare = { depends-on = [
#'notebook-convert',
@@ -179,11 +183,11 @@ notebook-prepare = { depends-on = [
########################
docs-vars = "JUPYTER_PLATFORM_DIRS=1 PYTHONWARNINGS='ignore::RuntimeWarning'"
-docs-pre = "pixi run docs-vars python -m mkdocs"
-docs-serve = "pixi run docs-pre serve -f docs/mkdocs.yml"
-docs-serve-dirty = "pixi run docs-serve --dirty"
-docs-build = "pixi run docs-pre build -f docs/mkdocs.yml"
-docs-build-local = "pixi run docs-build --no-directory-urls"
+docs-pre = 'pixi run docs-vars python -m mkdocs'
+docs-serve = 'pixi run docs-pre serve -f docs/mkdocs.yml'
+docs-serve-dirty = 'pixi run docs-serve --dirty'
+docs-build = 'pixi run docs-pre build -f docs/mkdocs.yml'
+docs-build-local = 'pixi run docs-build --no-directory-urls'
docs-deploy-pre = 'mike deploy -F docs/mkdocs.yml --push --branch gh-pages --update-aliases --alias-type redirect'
docs-set-default-pre = 'mike set-default -F docs/mkdocs.yml --push --branch gh-pages'
@@ -194,9 +198,9 @@ docs-update-assets = 'python tools/update_docs_assets.py'
# 📦 Template Management Tasks
##############################
-copier-copy = "copier copy gh:easyscience/templates . --data-file ../dynamics/.copier-answers.yml --data template_type=lib"
-copier-recopy = "copier recopy --data-file ../dynamics/.copier-answers.yml --data template_type=lib"
-copier-update = "copier update --data-file ../dynamics/.copier-answers.yml --data template_type=lib"
+copier-copy = 'copier copy gh:easyscience/templates . --data-file ../dynamics/.copier-answers.yml --data template_type=lib'
+copier-recopy = 'copier recopy --data-file ../dynamics/.copier-answers.yml --data template_type=lib'
+copier-update = 'copier update --data-file ../dynamics/.copier-answers.yml --data template_type=lib'
#####################
# 🪝 Pre-commit Hooks
@@ -243,9 +247,9 @@ github-labels = 'python tools/update_github_labels.py'
# ⚖️ SPDX License Headers
#########################
-license-remove = 'python tools/remove_license_headers.py src/ tests/'
-license-add = 'python tools/add_license_headers.py src/ tests/'
-license-check = 'python tools/check_license_headers.py src/ tests/'
+license-remove = 'python tools/license_headers.py remove src/ tests/ --exclude-from-pyproject-toml tool.ruff.exclude'
+license-add = 'python tools/license_headers.py add src/ tests/ --exclude-from-pyproject-toml tool.ruff.exclude'
+license-check = 'python tools/license_headers.py check src/ tests/ --exclude-from-pyproject-toml tool.ruff.exclude'
####################################
# 🚀 Other Development & Build Tasks
diff --git a/pyproject.toml b/pyproject.toml
index bcacdf96..36950e9c 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -17,10 +17,11 @@ classifiers = [
'Operating System :: OS Independent',
'Programming Language :: Python :: 3 :: Only',
'Programming Language :: Python :: 3',
- 'Programming Language :: Python :: 3.11',
'Programming Language :: Python :: 3.12',
+ 'Programming Language :: Python :: 3.13',
+ 'Programming Language :: Python :: 3.14',
]
-requires-python = '>=3.11'
+requires-python = '>=3.12'
dependencies = [
'easyscience', # The base library of the EasyScience framework
'pooch', # Data downloader
@@ -47,7 +48,6 @@ dev = [
'pytest', # Testing
'pytest-cov', # Test coverage
'pytest-xdist', # Enable parallel testing
- 'pytest-forked', # Isolate tests in subprocesses
'ruff', # Linting and formatting code
'radon', # Code complexity and maintainability
'validate-pyproject[all]', # Validate pyproject.toml
@@ -55,7 +55,8 @@ dev = [
'jupytext', # Jupyter notebook text format support
'jupyterquiz', # Quizzes in Jupyter notebooks
'pydoclint', # Docstring linter
- 'docformatter', # Docstring formatter
+ 'format-docstring', # Docstring formatter
+ 'docstripy', # Convert docstrings to other formats
'interrogate', # Docstring coverage checker
'copier', # Template management
'mike', # MkDocs: Versioned documentation support
@@ -177,14 +178,14 @@ testpaths = ['tests']
[tool.ruff]
exclude = ['tmp']
indent-width = 4
-line-length = 99
+line-length = 99 # See also `max-line-length` in [tool.ruff.lint.pycodestyle]
preview = true # Enable new rules that are not yet stable, like DOC
# Formatting options for Ruff
[tool.ruff.format]
docstring-code-format = true # Whether to format code snippets in docstrings
-docstring-code-line-length = 72 # Line length for code snippets in docstrings
+docstring-code-line-length = 99 # Line length for code snippets in docstrings
indent-style = 'space' # PEP 8 recommends using spaces over tabs
line-ending = 'lf' # Line endings will be converted to \n
quote-style = 'single' # But double quotes in docstrings (PEP 8, PEP 257)
@@ -195,16 +196,17 @@ quote-style = 'single' # But double quotes in docstrings (PEP 8, PEP 25
select = [
# Various rules
#'C90', # https://docs.astral.sh/ruff/rules/#mccabe-c90
+ #'D', # https://docs.astral.sh/ruff/rules/#pydocstyle-d
'F', # https://docs.astral.sh/ruff/rules/#pyflakes-f
#'FLY', # https://docs.astral.sh/ruff/rules/#flynt-fly
#'FURB', # https://docs.astral.sh/ruff/rules/#refurb-furb
'I', # https://docs.astral.sh/ruff/rules/#isort-i
#'N', # https://docs.astral.sh/ruff/rules/#pep8-naming-n
- #'NPY', # https://docs.astral.sh/ruff/rules/#numpy-specific-rules-npy
+ 'NPY', # https://docs.astral.sh/ruff/rules/#numpy-specific-rules-npy
#'PGH', # https://docs.astral.sh/ruff/rules/#pygrep-hooks-pgh
- #'PERF', # https://docs.astral.sh/ruff/rules/#perflint-perf
- #'RUF', # https://docs.astral.sh/ruff/rules/#ruff-specific-rules-ruf
- #'TRY', # https://docs.astral.sh/ruff/rules/#tryceratops-try
+ 'PERF', # https://docs.astral.sh/ruff/rules/#perflint-perf
+ 'RUF', # https://docs.astral.sh/ruff/rules/#ruff-specific-rules-ruf
+ #'TRY', # https://docs.astral.sh/ruff/rules/#tryceratops-try # overly restrictive
'UP', # https://docs.astral.sh/ruff/rules/#pyupgrade-up
# pycodestyle (E, W) rules
'E', # https://docs.astral.sh/ruff/rules/#error-e
@@ -213,40 +215,40 @@ select = [
#'PLC', # https://docs.astral.sh/ruff/rules/#convention-plc
#'PLE', # https://docs.astral.sh/ruff/rules/#error-ple
#'PLR', # https://docs.astral.sh/ruff/rules/#refactor-plr
- #'PLW', # https://docs.astral.sh/ruff/rules/#warning-plw
+ #'PLW', # https://docs.astral.sh/ruff/rules/#warning-plw # Good to enable
# flake8 rules
- #'A', # https://docs.astral.sh/ruff/rules/#flake8-builtins-a
- 'ANN', # https://docs.astral.sh/ruff/rules/#flake8-annotations-ann
- 'ARG', # https://docs.astral.sh/ruff/rules/#flake8-unused-arguments-arg
- #'ASYNC', # https://docs.astral.sh/ruff/rules/#flake8-async-async
- 'B', # https://docs.astral.sh/ruff/rules/#flake8-bugbear-b
- #'BLE', # https://docs.astral.sh/ruff/rules/#flake8-blind-except-ble
- 'C4', # https://docs.astral.sh/ruff/rules/#flake8-comprehensions-c4
- #'COM', # https://docs.astral.sh/ruff/rules/#flake8-commas-com
- #'DTZ', # https://docs.astral.sh/ruff/rules/#flake8-datetimez-dtz
- #'EM', # https://docs.astral.sh/ruff/rules/#flake8-errmsg-em
- #'FA', # https://docs.astral.sh/ruff/rules/#flake8-future-annotations-fa
- #'FBT', # https://docs.astral.sh/ruff/rules/#flake8-boolean-trap-fbt
- #'FIX', # https://docs.astral.sh/ruff/rules/#flake8-fixme-fix
- #'G', # https://docs.astral.sh/ruff/rules/#flake8-logging-format-g
- #'ICN', # https://docs.astral.sh/ruff/rules/#flake8-import-conventions-icn
- #'INP', # https://docs.astral.sh/ruff/rules/#flake8-no-pep420-inp
- #'ISC', # https://docs.astral.sh/ruff/rules/#flake8-implicit-str-concat-isc
- #'LOG', # https://docs.astral.sh/ruff/rules/#flake8-logging-log
- #'PIE', # https://docs.astral.sh/ruff/rules/#flake8-pie-pie
- #'PT', # https://docs.astral.sh/ruff/rules/#flake8-pytest-style-pt
- 'PTH', # https://docs.astral.sh/ruff/rules/#flake8-use-pathlib-pth
- #'PYI', # https://docs.astral.sh/ruff/rules/#flake8-pyi-pyi
- 'RET', # https://docs.astral.sh/ruff/rules/#flake8-return-ret
- #'RSE', # https://docs.astral.sh/ruff/rules/#flake8-raise-rse
- 'S', # https://docs.astral.sh/ruff/rules/#flake8-bandit-s
- 'SIM', # https://docs.astral.sh/ruff/rules/#flake8-simplify-sim
- #'SLF', # https://docs.astral.sh/ruff/rules/#flake8-self-slf
- #'SLOT', # https://docs.astral.sh/ruff/rules/#flake8-slots-slot
- #'T20', # https://docs.astral.sh/ruff/rules/#flake8-print-t20
- #'TC', # https://docs.astral.sh/ruff/rules/#flake8-type-checking-tc
- #'TD', # https://docs.astral.sh/ruff/rules/#flake8-todos-td
- #'TID', # https://docs.astral.sh/ruff/rules/#flake8-tidy-imports-tid
+ 'A', # https://docs.astral.sh/ruff/rules/#flake8-builtins-a
+ 'ANN', # https://docs.astral.sh/ruff/rules/#flake8-annotations-ann
+ 'ARG', # https://docs.astral.sh/ruff/rules/#flake8-unused-arguments-arg
+ 'ASYNC', # https://docs.astral.sh/ruff/rules/#flake8-async-async
+ 'B', # https://docs.astral.sh/ruff/rules/#flake8-bugbear-b
+ #'BLE', # https://docs.astral.sh/ruff/rules/#flake8-blind-except-ble # enable when base classes have been merged in
+ 'C4', # https://docs.astral.sh/ruff/rules/#flake8-comprehensions-c4
+ 'COM', # https://docs.astral.sh/ruff/rules/#flake8-commas-com
+ 'DTZ', # https://docs.astral.sh/ruff/rules/#flake8-datetimez-dtz
+ #'EM', # https://docs.astral.sh/ruff/rules/#flake8-errmsg-em # Unsure if I want it - requires all error messages to be rewritten
+ 'FA', # https://docs.astral.sh/ruff/rules/#flake8-future-annotations-fa
+ #'FBT', # https://docs.astral.sh/ruff/rules/#flake8-boolean-trap-fbt # should eventually be enabled, but may break serialization
+ 'FIX', # https://docs.astral.sh/ruff/rules/#flake8-fixme-fix
+ 'G', # https://docs.astral.sh/ruff/rules/#flake8-logging-format-g
+ 'ICN', # https://docs.astral.sh/ruff/rules/#flake8-import-conventions-icn
+ 'INP', # https://docs.astral.sh/ruff/rules/#flake8-no-pep420-inp
+ 'ISC', # https://docs.astral.sh/ruff/rules/#flake8-implicit-str-concat-isc
+ 'LOG', # https://docs.astral.sh/ruff/rules/#flake8-logging-log
+ 'PIE', # https://docs.astral.sh/ruff/rules/#flake8-pie-pie
+ #'PT', # https://docs.astral.sh/ruff/rules/#flake8-pytest-style-pt # Should eventually be enabled, but quite a few errors to fix
+ 'PTH', # https://docs.astral.sh/ruff/rules/#flake8-use-pathlib-pth
+ 'PYI', # https://docs.astral.sh/ruff/rules/#flake8-pyi-pyi
+ 'RET', # https://docs.astral.sh/ruff/rules/#flake8-return-ret
+ 'RSE', # https://docs.astral.sh/ruff/rules/#flake8-raise-rse
+ 'S', # https://docs.astral.sh/ruff/rules/#flake8-bandit-s
+ 'SIM', # https://docs.astral.sh/ruff/rules/#flake8-simplify-sim
+ 'SLF', # https://docs.astral.sh/ruff/rules/#flake8-self-slf
+ 'SLOT', # https://docs.astral.sh/ruff/rules/#flake8-slots-slot
+ 'T20', # https://docs.astral.sh/ruff/rules/#flake8-print-t20
+ 'TC', # https://docs.astral.sh/ruff/rules/#flake8-type-checking-tc
+ 'TD', # https://docs.astral.sh/ruff/rules/#flake8-todos-td
+ 'TID', # https://docs.astral.sh/ruff/rules/#flake8-tidy-imports-tid
]
# Exceptions to the linting rules
@@ -254,18 +256,23 @@ select = [
# Ignore specific rules globally
ignore = [
'COM812', # https://docs.astral.sh/ruff/rules/missing-trailing-comma/
- # The following covered by [tool.pydoclint] section below
- 'D', # https://docs.astral.sh/ruff/rules/#pydocstyle-d
- 'DOC', # https://docs.astral.sh/ruff/rules/#pydoclint-doc
+ # The following is replaced by 'D'/[tool.ruff.lint.pydocstyle] and [tool.pydoclint] 'DOC', # https://docs.astral.sh/ruff/rules/#pydoclint-doc
+ # Disable, as [tool.format_docstring] split one-line docstrings into the canonical multi-line layout
+ 'D200', # https://docs.astral.sh/ruff/rules/unnecessary-multiline-docstring/
]
# Ignore specific rules in certain files or directories
[tool.ruff.lint.per-file-ignores]
+'*/__init__.py' = [
+ 'F401', # re-exports are intentional in __init__.py
+]
'tests/**' = [
'ANN', # https://docs.astral.sh/ruff/rules/#flake8-annotations-ann
+ 'D', # https://docs.astral.sh/ruff/rules/#pydocstyle-d
'DOC', # https://docs.astral.sh/ruff/rules/#pydoclint-doc
'INP001', # https://docs.astral.sh/ruff/rules/implicit-namespace-package/
'S101', # https://docs.astral.sh/ruff/rules/assert/
+ 'SLF', # https://docs.astral.sh/ruff/rules/#flake8-self-slf # may want to eventually enable it, but accessing private methods is quite useful in tests
]
'docs/**' = [
'INP001', # https://docs.astral.sh/ruff/rules/implicit-namespace-package/
@@ -290,18 +297,19 @@ max-complexity = 10
# PEP 8 line length guidance:
# https://peps.python.org/pep-0008/#maximum-line-length
# Use 99 characters as the project-wide maximum for regular code lines.
-max-line-length = 99
-# allow longer lines so that parameter declarations such as
-# `name (Type | Type | None):` remain on a single line. Splitting these
-# lines can prevent tools such as MkDocs and IDEs from correctly
-# parsing and rendering parameter documentation.
-# The descriptive text itself is wrapped more strictly by
-# `docformatter` (see the configuration in [tool.docformatter] below)
-# whenever it is treated as normal paragraph text.
-# The line length for code snippets in docstrings is also more strict,
-# as defined in the [tool.ruff.format] section above.
+# Use 99 characters for docstrings.
+max-line-length = 99 # See also `line-length` in [tool.ruff]
max-doc-length = 99
+[tool.ruff.lint.pydocstyle]
+convention = 'numpy'
+
+[tool.ruff.lint.pylint]
+# Ruff counts `self`/`cls` in max-args; traditional pylint does not.
+# Setting 6 here matches pylint's default of 5 (excluding self).
+max-args = 6
+max-positional-args = 6
+
#############################
# Configuration for pydoclint
#############################
@@ -317,20 +325,22 @@ max-doc-length = 99
# the parameter declarations in the code (in function's signature).
[tool.pydoclint]
-style = "google"
+#exclude = '\.' # Temporarily disable pydoclint until we are ready
+style = 'numpy'
check-style-mismatch = true
check-arg-defaults = true
allow-init-docstring = true
-################################
-# Configuration for docformatter
-################################
+####################################
+# Configuration for format-docstring
+####################################
-# 'docformatter' -- Code formatter for docstrings
-# https://docformatter.readthedocs.io/en/latest/
+# 'format-docstring' -- Code formatter for docstrings
+# https://github.com/jsh9/format-docstring
-[tool.docformatter]
-recursive = true
-wrap-summaries = 72
-wrap-descriptions = 72
-close-quotes-on-newline = true
+[tool.format_docstring]
+#exclude = '\.' # Temporarily disable format-docstring until we are ready
+docstring_style = 'numpy'
+line_length = 99
+fix_rst_backticks = true
+verbose = 'default'
diff --git a/src/easydynamics/__init__.py b/src/easydynamics/__init__.py
index 8173d51c..54557144 100644
--- a/src/easydynamics/__init__.py
+++ b/src/easydynamics/__init__.py
@@ -1,3 +1,13 @@
# SPDX-FileCopyrightText: 2025 EasyScience contributors
# SPDX-License-Identifier: BSD-3-Clause
"""EasyDynamics library."""
+
+from easydynamics.analysis import Analysis
+from easydynamics.experiment import Experiment
+from easydynamics.settings.convolution_settings import ConvolutionSettings
+
+__all__ = [
+ 'Analysis',
+ 'ConvolutionSettings',
+ 'Experiment',
+]
diff --git a/src/easydynamics/analysis/__init__.py b/src/easydynamics/analysis/__init__.py
index 431457ca..a52854bc 100644
--- a/src/easydynamics/analysis/__init__.py
+++ b/src/easydynamics/analysis/__init__.py
@@ -1,7 +1,7 @@
# SPDX-FileCopyrightText: 2026 EasyScience contributors
# SPDX-License-Identifier: BSD-3-Clause
-from .analysis import Analysis
+from easydynamics.analysis.analysis import Analysis
__all__ = [
'Analysis',
diff --git a/src/easydynamics/analysis/analysis.py b/src/easydynamics/analysis/analysis.py
index 23364709..b8493ec9 100644
--- a/src/easydynamics/analysis/analysis.py
+++ b/src/easydynamics/analysis/analysis.py
@@ -16,15 +16,16 @@
from easydynamics.experiment import Experiment
from easydynamics.sample_model import SampleModel
from easydynamics.sample_model.instrument_model import InstrumentModel
+from easydynamics.settings.convolution_settings import ConvolutionSettings
+from easydynamics.settings.detailed_balance_settings import DetailedBalanceSettings
from easydynamics.utils.utils import _in_notebook
class Analysis(AnalysisBase):
- """For analysing two-dimensional data, i.e. intensity as function of
- energy and Q.
+ """
+ For analysing two-dimensional data, i.e. intensity as function of energy and Q.
- Supports independent fits of each Q value and simultaneous fits of
- all Q.
+ Supports independent fits of each Q value and simultaneous fits of all Q.
"""
def __init__(
@@ -34,26 +35,34 @@ def __init__(
experiment: Experiment | None = None,
sample_model: SampleModel | None = None,
instrument_model: InstrumentModel | None = None,
+ convolution_settings: ConvolutionSettings | None = None,
+ detailed_balance_settings: DetailedBalanceSettings | None = None,
extra_parameters: Parameter | list[Parameter] | None = None,
) -> None:
- """Initialize an Analysis object.
-
- Args:
- display_name (str | None, default='MyAnalysis'): Display name of the analysis.
- unique_name (str | None, default=None): Unique name of the analysis. If
- None, a unique name is automatically generated.
- experiment (Experiment | None, default=None): The Experiment associated
- with this Analysis. If None, a default Experiment is
- created.
- sample_model (SampleModel | None, default=None): The SampleModel
- associated with this Analysis. If None, a default
- SampleModel is created.
- instrument_model (InstrumentModel | None, default=None): The
- InstrumentModel associated with this Analysis. If None,
- a default InstrumentModel is created.
- extra_parameters (Parameter | list[Parameter] | None, default=None): Extra
- parameters to be included in the analysis for advanced
- users. If None, no extra parameters are added.
+ """
+ Initialize an Analysis object.
+
+ Parameters
+ ----------
+ display_name : str | None, default='MyAnalysis'
+ Display name of the analysis.
+ unique_name : str | None, default=None
+ Unique name of the analysis. If None, a unique name is automatically generated.
+ experiment : Experiment | None, default=None
+ The Experiment associated with this Analysis. If None, a default Experiment is created.
+ sample_model : SampleModel | None, default=None
+ The SampleModel associated with this Analysis. If None, a default SampleModel is
+ created.
+ instrument_model : InstrumentModel | None, default=None
+ The InstrumentModel associated with this Analysis. If None, a default InstrumentModel
+ is created.
+ convolution_settings : ConvolutionSettings | None, default=None
+ The settings for the convolution. If None, default settings will be used.
+ detailed_balance_settings : DetailedBalanceSettings | None, default=None
+ The settings for detailed balance. If None, default settings will be used.
+ extra_parameters : Parameter | list[Parameter] | None, default=None
+ Extra parameters to be included in the analysis for advanced users. If None, no extra
+ parameters are added.
"""
# Avoid triggering updates before the object is fully
@@ -65,22 +74,15 @@ def __init__(
experiment=experiment,
sample_model=sample_model,
instrument_model=instrument_model,
+ convolution_settings=convolution_settings,
+ detailed_balance_settings=detailed_balance_settings,
extra_parameters=extra_parameters,
)
self._analysis_list = []
if self.Q is not None:
- for Q_index in range(len(self.Q)):
- analysis = Analysis1d(
- display_name=f'{self.display_name}_Q{Q_index}',
- unique_name=(f'{self.unique_name}_Q{Q_index}'),
- experiment=self.experiment,
- sample_model=self.sample_model,
- instrument_model=self.instrument_model,
- extra_parameters=self._extra_parameters,
- Q_index=Q_index,
- )
- self._analysis_list.append(analysis)
+ self._create_analysis_list()
+
# Now we can allow updates to trigger recalculations
self._call_updaters = True
@@ -90,28 +92,33 @@ def __init__(
@property
def analysis_list(self) -> list[Analysis1d]:
- """Get the Analysis1d objects associated with this Analysis.
+ """
+ Get the Analysis1d objects associated with this Analysis.
- Returns:
- list[Analysis1d]: A list of Analysis1d objects, one for
- each Q index.
+ Returns
+ -------
+ list[Analysis1d]
+ A list of Analysis1d objects, one for each Q index.
"""
return self._analysis_list
@analysis_list.setter
def analysis_list(self, _value: list[Analysis1d]) -> None:
- """analysis_list is read-only.
+ """
+ Analysis_list is read-only.
- To change the analysis list, modify the experiment, sample
- model, or instrument model.
+ To change the analysis list, modify the experiment, sample model, or instrument model.
- Args:
- _value (list[Analysis1d]): The new list of Analysis1d objects. This
- argument is ignored, as analysis_list is read-only.
+ Parameters
+ ----------
+ _value : list[Analysis1d]
+ The new list of Analysis1d objects. This argument is ignored, as analysis_list is
+ read-only.
- Raises:
- AttributeError: Always raised, since analysis_list is
- read-only.
+ Raises
+ ------
+ AttributeError
+ Always raised, since analysis_list is read-only.
"""
raise AttributeError(
@@ -128,21 +135,24 @@ def calculate(
Q_index: int | None = None,
energy: sc.Variable | None = None,
) -> list[np.ndarray] | np.ndarray:
- """Calculate model data for a specific Q index. If Q_index is
- None, calculate for all Q indices and return a list of arrays.
-
- Args:
- Q_index (int | None, default=None): Index of the Q value to calculate
- for. If None, calculate for all Q values.
- energy (sc.Variable | None, default=None): The energy values to use for
- calculating the model. If None, uses the energy from the
- experiment.
-
- Returns:
- list[np.ndarray] | np.ndarray: If Q_index is None, returns
- a list of numpy arrays, one for each Q index.
- If Q_index is an integer, returns a single numpy array
- for that Q index.
+ """
+ Calculate model data for a specific Q index.
+
+ If Q_index is None, calculate for all Q indices and return a list of arrays.
+
+ Parameters
+ ----------
+ Q_index : int | None, default=None
+ Index of the Q value to calculate for. If None, calculate for all Q values.
+ energy : sc.Variable | None, default=None
+ The energy values to use for calculating the model. If None, uses the energy from the
+ experiment.
+
+ Returns
+ -------
+ list[np.ndarray] | np.ndarray
+ If Q_index is None, returns a list of numpy arrays, one for each Q index. If Q_index is
+ an integer, returns a single numpy array for that Q index.
"""
if energy is None:
energy = self.energy
@@ -158,25 +168,29 @@ def fit(
fit_method: str = 'independent',
Q_index: int | None = None,
) -> FitResults | list[FitResults]:
- """Fit the model to the experimental data.
-
- Args:
- fit_method (str, default="independent"): Method to use for fitting. Options are
- "independent" (fit each Q index independently, one after
- the other) or "simultaneous" (fit all Q indices
- simultaneously). Default is "independent".
- Q_index (int | None, default=None): If fit_method is "independent",
- specify which Q index to fit. If None, fit all Q indices
- independently. Ignored if fit_method is "simultaneous".
- Default is None.
-
- Returns:
- FitResults | list[FitResults]: a list of FitResults if fitting independently,
- or a single FitResults object if fitting simultaneously.
-
- Raises:
- ValueError: If fit_method is not "independent" or
- "simultaneous" or if there are no Q values available for fitting.
+ """
+ Fit the model to the experimental data.
+
+ Parameters
+ ----------
+ fit_method : str, default='independent'
+ Method to use for fitting. Options are "independent" (fit each Q index independently,
+ one after the other) or "simultaneous" (fit all Q indices simultaneously).
+ Q_index : int | None, default=None
+ If fit_method is "independent", specify which Q index to fit. If None, fit all Q
+ indices independently. Ignored if fit_method is "simultaneous".
+
+ Raises
+ ------
+ ValueError
+ If fit_method is not "independent" or "simultaneous" or if there are no Q values
+ available for fitting.
+
+ Returns
+ -------
+ FitResults | list[FitResults]
+ A list of FitResults if fitting independently, or a single FitResults object if fitting
+ simultaneously.
"""
if self.Q is None:
@@ -202,36 +216,42 @@ def plot_data_and_model(
energy: sc.Variable | None = None,
**kwargs: dict[str, Any],
) -> InteractiveFigure:
- """Plot the experimental data and the model prediction.
+ """
+ Plot the experimental data and the model prediction.
+
Optionally also plot the individual components of the model.
Uses Plopp for plotting: https://scipp.github.io/plopp/
- Args:
- Q_index (int | None, default=None): Index of the Q value to plot. If
- None, plot all Q values. Default is None.
- plot_components (bool, default=True): Whether to plot the individual
- components. Default is True.
- add_background (bool, default=True): Whether to add background components
- to the sample model components when plotting. Default is
- True.
- energy (sc.Variable | None, default=None): The energy values to use for
- calculating the model. If None, uses the energy from the
- experiment.
- **kwargs (dict[str, Any]): Additional keyword arguments passed to plopp
- for customizing the plot.
-
- Raises:
- ValueError: If Q_index is out of bounds, or if there is no
- data to plot, or if there are no Q values available for
- plotting.
- RuntimeError: If not in a Jupyter notebook environment.
- TypeError: If plot_components or add_background is not True
- or False.
-
- Returns:
- InteractiveFigure: A Plopp InteractiveFigure containing the
- plot of the data and model.
+ Parameters
+ ----------
+ Q_index : int | None, default=None
+ Index of the Q value to plot. If None, plot all Q values.
+ plot_components : bool, default=True
+ Whether to plot the individual components.
+ add_background : bool, default=True
+ Whether to add background components to the sample model components when plotting.
+ Default is True.
+ energy : sc.Variable | None, default=None
+ The energy values to use for calculating the model. If None, uses the energy from the
+ experiment.
+ **kwargs : dict[str, Any]
+ Additional keyword arguments passed to plopp for customizing the plot.
+
+ Raises
+ ------
+ ValueError
+ If Q_index is out of bounds, or if there is no data to plot, or if there are no Q
+ values available for plotting.
+ RuntimeError
+ If not in a Jupyter notebook environment.
+ TypeError
+ If plot_components or add_background is not True or False.
+
+ Returns
+ -------
+ InteractiveFigure
+ A Plopp InteractiveFigure containing the plot of the data and model.
"""
if Q_index is not None:
@@ -300,19 +320,21 @@ def plot_data_and_model(
return fig
def parameters_to_dataset(self) -> sc.Dataset:
- """Creates a scipp dataset with copies of the Parameters in the
- model.
+ """
+ Creates a scipp dataset with copies of the Parameters in the model.
Ensures unit consistency across Q.
- Returns:
- sc.Dataset: A dataset where each entry is a parameter, with
- dimensions "Q" and values corresponding to the parameter
- values.
+ Raises
+ ------
+ UnitError
+ If there are inconsistent units for the same parameter across different Q values.
- Raises:
- UnitError: If there are inconsistent units for the same
- parameter across different Q values.
+ Returns
+ -------
+ sc.Dataset
+ A dataset where each entry is a parameter, with dimensions "Q" and values corresponding
+ to the parameter values.
"""
ds = sc.Dataset(coords={'Q': self.Q})
@@ -370,22 +392,28 @@ def plot_parameters(
names: str | list[str] | None = None,
**kwargs: dict[str, Any],
) -> InteractiveFigure:
- """Plot fitted parameters as a function of Q.
-
- Args:
- names (str | list[str] | None, default=None): Name(s) of the parameter(s)
- to plot. If None, plots all parameters.
- **kwargs (dict[str, Any]): Additional keyword arguments passed to
- plopp.slicer for customizing the plot (e.g., title,
- linestyle, marker, color).
-
- Returns:
- InteractiveFigure: A Plopp InteractiveFigure containing the
- plot of the parameters.
-
- Raises:
- TypeError: If names is not a string, list of strings, or None.
- ValueError: If any of the specified parameter names are not found in the dataset.
+ """
+ Plot fitted parameters as a function of Q.
+
+ Parameters
+ ----------
+ names : str | list[str] | None, default=None
+ Name(s) of the parameter(s) to plot. If None, plots all parameters.
+ **kwargs : dict[str, Any]
+ Additional keyword arguments passed to plopp.slicer for customizing the plot (e.g.,
+ title, linestyle, marker, color).
+
+ Raises
+ ------
+ TypeError
+ If names is not a string, list of strings, or None.
+ ValueError
+ If any of the specified parameter names are not found in the dataset.
+
+ Returns
+ -------
+ InteractiveFigure
+ A Plopp InteractiveFigure containing the plot of the parameters.
"""
ds = self.parameters_to_dataset()
@@ -420,13 +448,15 @@ def plot_parameters(
)
def fix_energy_offset(self, Q_index: int | None = None) -> None:
- """Fix the energy offset parameter(s) for a specific Q index, or
- for all Q indices if Q_index is None.
-
- Args:
- Q_index (int | None, default=None): Index of the Q value to
- fix the energy offset for. If None, fixes the energy
- offset for all Q values. Default is None.
+ """
+ Fix the energy offset parameter(s) for a specific Q index, or for all Q indices if Q_index
+ is None.
+
+ Parameters
+ ----------
+ Q_index : int | None, default=None
+ Index of the Q value to fix the energy offset for. If None, fixes the energy offset for
+ all Q values.
"""
if Q_index is not None:
Q_index = self._verify_Q_index(Q_index)
@@ -436,13 +466,15 @@ def fix_energy_offset(self, Q_index: int | None = None) -> None:
analysis.fix_energy_offset()
def free_energy_offset(self, Q_index: int | None = None) -> None:
- """Free the energy offset parameter(s) for a specific Q index,
- or for all Q indices if Q_index is None.
-
- Args:
- Q_index (int | None, default=None): Index of the Q value to
- free the energy offset for. If None, frees the energy
- offset for all Q values. Default is None.
+ """
+ Free the energy offset parameter(s) for a specific Q index, or for all Q indices if Q_index
+ is None.
+
+ Parameters
+ ----------
+ Q_index : int | None, default=None
+ Index of the Q value to free the energy offset for. If None, frees the energy offset
+ for all Q values.
"""
if Q_index is not None:
Q_index = self._verify_Q_index(Q_index)
@@ -456,8 +488,8 @@ def free_energy_offset(self, Q_index: int | None = None) -> None:
#############
def _on_experiment_changed(self) -> None:
- """Update the Q values in the sample and instrument models when
- the experiment changes.
+ """
+ Update the Q values in the sample and instrument models when the experiment changes.
Also update all the Analysis1d objects with the new experiment.
"""
@@ -467,11 +499,10 @@ def _on_experiment_changed(self) -> None:
analysis.experiment = self.experiment
def _on_sample_model_changed(self) -> None:
- """Update the Q values in the sample model when the sample model
- changes.
+ """
+ Update the Q values in the sample model when the sample model changes.
- Also update all the Analysis1d objects with the new sample
- model.
+ Also update all the Analysis1d objects with the new sample model.
"""
if self._call_updaters:
super()._on_sample_model_changed()
@@ -479,30 +510,63 @@ def _on_sample_model_changed(self) -> None:
analysis.sample_model = self.sample_model
def _on_instrument_model_changed(self) -> None:
- """Update the Q values in the instrument model when the
- instrument model changes.
+ """
+ Update the Q values in the instrument model when the instrument model changes.
- Also update all the Analysis1d objects with the new instrument
- model.
+ Also update all the Analysis1d objects with the new instrument model.
"""
if self._call_updaters:
super()._on_instrument_model_changed()
for analysis in self.analysis_list:
analysis.instrument_model = self.instrument_model
+ def _on_convolution_settings_changed(self) -> None:
+ """
+ Update the convolution settings in all Analysis1d objects when the convolution settings
+ change.
+ """
+ if self._call_updaters:
+ super()._on_convolution_settings_changed()
+ for analysis1d in self.analysis_list:
+ analysis1d.convolution_settings = self.convolution_settings
+
+ def _create_analysis_list(self) -> None:
+ """
+ Create the list of Analysis1d objects, one for each Q index, based on the current
+ experiment, sample model, and instrument model.
+ """
+ self._analysis_list = []
+ for Q_index in range(len(self.Q)):
+ analysis = Analysis1d(
+ display_name=f'{self.display_name}_Q{Q_index}',
+ unique_name=(f'{self.unique_name}_Q{Q_index}'),
+ experiment=self.experiment,
+ sample_model=self.sample_model,
+ instrument_model=self.instrument_model,
+ convolution_settings=self.convolution_settings,
+ detailed_balance_settings=self.detailed_balance_settings,
+ extra_parameters=self._extra_parameters,
+ Q_index=Q_index,
+ )
+ self._analysis_list.append(analysis)
+
#############
# Private methods
#############
def _fit_single_Q(self, Q_index: int) -> FitResults:
- """Fit data for a single Q index.
+ """
+ Fit data for a single Q index.
- Args:
- Q_index (int): Index of the Q value to fit.
+ Parameters
+ ----------
+ Q_index : int
+ Index of the Q value to fit.
- Returns:
- FitResults: The results of the fit for the specified
- Q index.
+ Returns
+ -------
+ FitResults
+ The results of the fit for the specified Q index.
"""
Q_index = self._verify_Q_index(Q_index)
@@ -510,34 +574,42 @@ def _fit_single_Q(self, Q_index: int) -> FitResults:
return self.analysis_list[Q_index].fit()
def _fit_all_Q_independently(self) -> list[FitResults]:
- """Fit data for all Q indices independently.
+ """
+ Fit data for all Q indices independently.
- Returns:
- list[FitResults]: A list of FitResults, one for each Q
- index.
+ Returns
+ -------
+ list[FitResults]
+ A list of FitResults, one for each Q index.
"""
return [analysis.fit() for analysis in self.analysis_list]
def _fit_all_Q_simultaneously(self) -> FitResults:
- """Fit data for all Q indices simultaneously.
+ """
+ Fit data for all Q indices simultaneously.
- Returns:
- FitResults: The results of the simultaneous fit across all
- Q indices.
+ Returns
+ -------
+ FitResults
+ The results of the simultaneous fit across all Q indices.
"""
xs = []
ys = []
ws = []
- for analysis in self.analysis_list:
- x, y, weight, _ = self.experiment._extract_x_y_weights_only_finite(analysis.Q_index)
+ for analysis1d in self.analysis_list:
+ x, y, weight, _ = self.experiment._extract_x_y_weights_only_finite( # noqa: SLF001
+ analysis1d.Q_index
+ )
xs.append(x)
ys.append(y)
ws.append(weight)
# Make sure the convolver is up to date for this Q index
- analysis._convolver = analysis._create_convolver(energy=x)
+ analysis1d._convolver = analysis1d._create_convolver( # noqa: SLF001
+ energy=x
+ )
mf = MultiFitter(
fit_objects=self.analysis_list,
@@ -551,26 +623,30 @@ def _fit_all_Q_simultaneously(self) -> FitResults:
)
def get_fit_functions(self) -> list[callable]:
- """Get fit functions for all Q indices, which can be used for
- simultaneous fitting.
+ """
+ Get fit functions for all Q indices, which can be used for simultaneous fitting.
- Returns:
- list[callable]: A list of fit functions, one for each
- Q index.
+ Returns
+ -------
+ list[callable]
+ A list of fit functions, one for each Q index.
"""
return [analysis.as_fit_function() for analysis in self.analysis_list]
def _create_model_array(self, energy: sc.Variable | None = None) -> sc.DataArray:
- """Create a scipp array for the model.
-
- Args:
- energy (sc.Variable | None, default=None): The energy values to use for
- calculating the model. If None, uses the energy from the
- experiment.
-
- Returns:
- sc.DataArray: A DataArray containing the model values, with
- dimensions "Q" and "energy".
+ """
+ Create a scipp array for the model.
+
+ Parameters
+ ----------
+ energy : sc.Variable | None, default=None
+ The energy values to use for calculating the model. If None, uses the energy from the
+ experiment.
+
+ Returns
+ -------
+ sc.DataArray
+ A DataArray containing the model values, with dimensions "Q" and "energy".
"""
if energy is None:
energy = self.energy
@@ -585,23 +661,27 @@ def _create_components_dataset(
add_background: bool = True,
energy: sc.Variable | None = None,
) -> sc.Dataset:
- """Create a scipp dataset containing the individual components
- of the model for plotting.
-
- Args:
- add_background (bool, default=True): Whether to add background components
- to the sample model components when creating the
- dataset.
- energy (sc.Variable | None, default=None): The energy values to use for
- calculating the components. If None, uses the energy from
- the experiment.
-
- Raises:
- TypeError: If add_background is not True or False.
-
- Returns:
- sc.Dataset: A scipp Dataset where each entry is a component
- of the model, with dimensions "Q".
+ """
+ Create a scipp dataset containing the individual components of the model for plotting.
+
+ Parameters
+ ----------
+ add_background : bool, default=True
+ Whether to add background components to the sample model components when creating the
+ dataset.
+ energy : sc.Variable | None, default=None
+ The energy values to use for calculating the components. If None, uses the energy from
+ the experiment.
+
+ Raises
+ ------
+ TypeError
+ If add_background is not True or False.
+
+ Returns
+ -------
+ sc.Dataset
+ A scipp Dataset where each entry is a component of the model, with dimensions "Q".
"""
if not isinstance(add_background, bool):
raise TypeError('add_background must be True or False.')
@@ -610,13 +690,14 @@ def _create_components_dataset(
energy = self.energy
datasets = [
- analysis._create_components_dataset_single_Q(
+ analysis1d._create_components_dataset_single_Q( # noqa: SLF001
add_background=add_background, energy=energy
)
- for analysis in self.analysis_list
+ for analysis1d in self.analysis_list
]
- return sc.concat(datasets, dim='Q')
+ ds = sc.concat(datasets, dim='Q')
+ return ds.assign_coords(Q=self.Q)
#############
# Dunder methods
diff --git a/src/easydynamics/analysis/analysis1d.py b/src/easydynamics/analysis/analysis1d.py
index 81f98f55..489f4381 100644
--- a/src/easydynamics/analysis/analysis1d.py
+++ b/src/easydynamics/analysis/analysis1d.py
@@ -18,14 +18,16 @@
from easydynamics.sample_model import SampleModel
from easydynamics.sample_model.component_collection import ComponentCollection
from easydynamics.sample_model.components.model_component import ModelComponent
+from easydynamics.settings.convolution_settings import ConvolutionSettings
+from easydynamics.settings.detailed_balance_settings import DetailedBalanceSettings
+from easydynamics.utils.detailed_balance import detailed_balance_factor
class Analysis1d(AnalysisBase):
- """For analysing one-dimensional data, i.e. intensity as function of
- energy for a single Q index.
+ """
+ For analysing one-dimensional data, i.e. intensity as function of energy for a single Q index.
- Is used primarily in the Analysis class, but can also be used on its
- own for simpler analyses.
+ Is used primarily in the Analysis class, but can also be used on its own for simpler analyses.
"""
def __init__(
@@ -36,29 +38,37 @@ def __init__(
sample_model: SampleModel | None = None,
instrument_model: InstrumentModel | None = None,
Q_index: int | None = None,
+ convolution_settings: ConvolutionSettings | None = None,
+ detailed_balance_settings: DetailedBalanceSettings | None = None,
extra_parameters: Parameter | list[Parameter] | None = None,
) -> None:
- """Initialize a Analysis1d.
-
- Args:
- display_name (str | None, default='MyAnalysis'): Display name of the analysis.
- unique_name (str | None, default=None): Unique name of the analysis. If
- None, a unique name is automatically generated.
- experiment (Experiment | None, default=None): The Experiment associated
- with this Analysis. If None, a default Experiment is
- created.
- sample_model (SampleModel | None, default=None): The SampleModel
- associated with this Analysis. If None, a default
- SampleModel is created.
- instrument_model (InstrumentModel | None, default=None): The
- InstrumentModel associated with this Analysis. If None,
- a default InstrumentModel is created.
- Q_index (int | None, default=None): The Q index to analyze. If None, the
- analysis will not be able to calculate or fit until a
- Q index is set.
- extra_parameters (Parameter | list[Parameter] | None, default=None): Extra
- parameters to be included in the analysis for advanced
- users. If None, no extra parameters are added.
+ """
+ Initialize a Analysis1d.
+
+ Parameters
+ ----------
+ display_name : str | None, default='MyAnalysis'
+ Display name of the analysis.
+ unique_name : str | None, default=None
+ Unique name of the analysis. If None, a unique name is automatically generated.
+ experiment : Experiment | None, default=None
+ The Experiment associated with this Analysis. If None, a default Experiment is created.
+ sample_model : SampleModel | None, default=None
+ The SampleModel associated with this Analysis. If None, a default SampleModel is
+ created.
+ instrument_model : InstrumentModel | None, default=None
+ The InstrumentModel associated with this Analysis. If None, a default InstrumentModel
+ is created.
+ Q_index : int | None, default=None
+ The Q index to analyze. If None, the analysis will not be able to calculate or fit
+ until a Q index is set.
+ convolution_settings : ConvolutionSettings | None, default=None
+ The settings for the convolution. If None, default settings will be used.
+ detailed_balance_settings : DetailedBalanceSettings | None, default=None
+ The settings for detailed balance. If None, default settings will be used.
+ extra_parameters : Parameter | list[Parameter] | None, default=None
+ Extra parameters to be included in the analysis for advanced users. If None, no extra
+ parameters are added.
"""
super().__init__(
display_name=display_name,
@@ -66,6 +76,8 @@ def __init__(
experiment=experiment,
sample_model=sample_model,
instrument_model=instrument_model,
+ convolution_settings=convolution_settings,
+ detailed_balance_settings=detailed_balance_settings,
extra_parameters=extra_parameters,
)
@@ -89,20 +101,26 @@ def __init__(
@property
def Q_index(self) -> int | None:
- """Get the Q index associated with this Analysis.
+ """
+ Get the Q index associated with this Analysis.
- Returns:
- int | None: The Q index associated with this Analysis.
+ Returns
+ -------
+ int | None
+ The Q index associated with this Analysis.
"""
return self._Q_index
@Q_index.setter
def Q_index(self, value: int | None) -> None:
- """Set the Q index for single Q analysis.
+ """
+ Set the Q index for single Q analysis.
- Args:
- value (int | None): The Q index.
+ Parameters
+ ----------
+ value : int | None
+ The Q index.
"""
self._Q_index = self._verify_Q_index(value)
@@ -113,16 +131,21 @@ def Q_index(self, value: int | None) -> None:
#############
def calculate(self, energy: sc.Variable | None = None) -> np.ndarray:
- """Calculate the model prediction for the chosen Q index. Makes
- sure the convolver is up to date before calculating.
+ """
+ Calculate the model prediction for the chosen Q index.
+
+ Makes sure the convolver is up to date before calculating.
- Args:
- energy (sc.Variable | None, default=None): Optional energy grid to use for
- calculation. If None, the energy grid from the experiment
- is used.
+ Parameters
+ ----------
+ energy : sc.Variable | None, default=None
+ Optional energy grid to use for calculation. If None, the energy grid from the
+ experiment is used.
- Returns:
- np.ndarray: The calculated model prediction.
+ Returns
+ -------
+ np.ndarray
+ The calculated model prediction.
"""
energy = self._verify_energy(energy)
self._convolver = self._create_convolver(energy=energy)
@@ -130,16 +153,21 @@ def calculate(self, energy: sc.Variable | None = None) -> np.ndarray:
return self._calculate(energy=energy)
def _calculate(self, energy: sc.Variable | None = None) -> np.ndarray:
- """Calculate the model prediction for the chosen Q index. Does
- not check if the convolver is up to date.
+ """
+ Calculate the model prediction for the chosen Q index.
+
+ Does not check if the convolver is up to date.
- Args:
- energy (sc.Variable | None, default=None): Optional energy grid to use for
- calculation. If None, the energy grid from the experiment
- is used.
+ Parameters
+ ----------
+ energy : sc.Variable | None, default=None
+ Optional energy grid to use for calculation. If None, the energy grid from the
+ experiment is used.
- Returns:
- np.ndarray: The calculated model prediction.
+ Returns
+ -------
+ np.ndarray
+ The calculated model prediction.
"""
sample_intensity = self._evaluate_sample(energy=energy)
@@ -149,19 +177,21 @@ def _calculate(self, energy: sc.Variable | None = None) -> np.ndarray:
return sample_intensity + background_intensity
def fit(self) -> FitResults:
- """Fit the model to the experimental data for the chosen Q
- index.
+ """
+ Fit the model to the experimental data for the chosen Q index.
- The energy grid is fixed for the duration of the fit.
- Convolution objects are created once and reused during
- parameter optimization for performance reasons.
+ The energy grid is fixed for the duration of the fit. Convolution objects are created once
+ and reused during parameter optimization for performance reasons.
- Returns:
- FitResults: The result of the fit.
+ Raises
+ ------
+ ValueError
+ If no experiment is associated with this Analysis.
- Raises:
- ValueError: If no experiment is associated with this
- Analysis.
+ Returns
+ -------
+ FitResults
+ The result of the fit.
"""
if self._experiment is None:
raise ValueError('No experiment is associated with this Analysis.')
@@ -174,7 +204,7 @@ def fit(self) -> FitResults:
fit_function=self.as_fit_function(),
)
- x, y, weights, _ = self.experiment._extract_x_y_weights_only_finite(
+ x, y, weights, _ = self.experiment._extract_x_y_weights_only_finite( # noqa: SLF001
Q_index=self._require_Q_index()
)
fit_result = fitter.fit(x=x, y=y, weights=weights)
@@ -188,37 +218,43 @@ def as_fit_function(
_x: np.ndarray | sc.Variable | None = None,
**kwargs: dict[str, Any], # noqa: ARG002
) -> callable:
- """Return self._calculate as a fit function.
-
- The EasyScience fitter requires x as input, but
- self._calculate() already uses the correct energy from the
- experiment. So we ignore the x input and just return the
- calculated model.
-
- Args:
- _x (np.ndarray | sc.Variable | None, default=None): Ignored.
- The energy grid is taken from the experiment.
- **kwargs (dict[str, Any]): Ignored. Included for compatibility with the
- EasyScience fitter.
-
- Returns:
- callable: A function that can be used as a fit function in the
- EasyScience fitter, which returns the calculated model.
+ """
+ Return self._calculate as a fit function.
+
+ The EasyScience fitter requires x as input, but self._calculate() already uses the correct
+ energy from the experiment. So we ignore the x input and just return the calculated model.
+
+ Parameters
+ ----------
+ _x : np.ndarray | sc.Variable | None, default=None
+ Ignored. The energy grid is taken from the experiment.
+ **kwargs : dict[str, Any]
+ Ignored. Included for compatibility with the EasyScience fitter.
+
+ Returns
+ -------
+ callable
+ A function that can be used as a fit function in the EasyScience fitter, which returns
+ the calculated model.
"""
def fit_function(
_x: np.ndarray | sc.Variable | None = None,
**kwargs: dict[str, Any], # noqa: ARG001
) -> np.ndarray:
+ """Fit function."""
return self._calculate()
return fit_function
def get_all_variables(self) -> list[DescriptorNumber]:
- """Get all variables used in the analysis.
+ """
+ Get all variables used in the analysis.
- Returns:
- list[DescriptorNumber]: A list of all variables.
+ Returns
+ -------
+ list[DescriptorNumber]
+ A list of all variables.
"""
variables = self.sample_model.get_all_variables(Q_index=self.Q_index)
@@ -236,63 +272,65 @@ def plot_data_and_model(
energy: sc.Variable | None = None,
**kwargs: dict[str, Any],
) -> InteractiveFigure:
- """Plot the experimental data and the model prediction for the
- chosen Q index. Optionally also plot the individual components
- of the model.
+ """
+ Plot the experimental data and the model prediction for the chosen Q index. Optionally also
+ plot the individual components of the model.
Uses Plopp for plotting: https://scipp.github.io/plopp/
- Args:
- plot_components (bool, default=True): Whether to plot the individual
- components of the model.
- add_background (bool, default=True): Whether to add the background to the
- model prediction when plotting individual components.
- energy (sc.Variable | None, default=None): Optional energy grid to use for
- plotting. If None, the energy grid from the experiment
- is used.
- **kwargs (dict[str, Any]): Keyword arguments to pass to the plotting
- function.
-
- Returns:
- InteractiveFigure: A plot of the data and model.
-
- Raises:
- ValueError: If no data is available to plot.
+ Parameters
+ ----------
+ plot_components : bool, default=True
+ Whether to plot the individual components of the model.
+ add_background : bool, default=True
+ Whether to add the background to the model prediction when plotting individual
+ components.
+ energy : sc.Variable | None, default=None
+ Optional energy grid to use for plotting. If None, the energy grid from the experiment
+ is used.
+ **kwargs : dict[str, Any]
+ Keyword arguments to pass to the plotting function.
+
+ Raises
+ ------
+ ValueError
+ If no data is available to plot.
+
+ Returns
+ -------
+ InteractiveFigure
+ A plot of the data and model.
"""
import plopp as pp
- if self.experiment.data is None:
+ plot_kwargs_defaults = {
+ 'title': self.display_name,
+ 'linestyle': {'Data': 'none', 'Model': '-'},
+ 'marker': {'Data': 'o', 'Model': 'none'},
+ 'color': {'Data': 'black', 'Model': 'red'},
+ 'markerfacecolor': {'Data': 'none', 'Model': 'none'},
+ }
+
+ if self.experiment.binned_data is None:
raise ValueError('No data to plot. Please load data first.')
energy = self._verify_energy(energy)
if energy is None:
energy = self._masked_energy
- data = self.experiment.data['Q', self.Q_index]
- model_array = self._create_sample_scipp_array(energy=energy)
-
- component_dataset = self._create_components_dataset_single_Q(
- add_background=add_background, energy=energy
- )
-
# Create a dataset containing the data, model, and individual
# components for plotting.
- data_and_model = sc.Dataset({
- 'Data': data,
- 'Model': model_array,
- })
-
- data_and_model = sc.merge(data_and_model, component_dataset)
- plot_kwargs_defaults = {
- 'title': self.display_name,
- 'linestyle': {'Data': 'none', 'Model': '-'},
- 'marker': {'Data': 'o', 'Model': 'none'},
- 'color': {'Data': 'black', 'Model': 'red'},
- 'markerfacecolor': {'Data': 'none', 'Model': 'none'},
+ data_and_model = {
+ 'Data': self.experiment.binned_data['Q', self.Q_index],
+ 'Model': self._create_model_array(energy=energy),
}
if plot_components:
- for comp_name in component_dataset:
+ components = self._create_components_dataset_single_Q(
+ add_background=add_background, energy=energy
+ )
+ for comp_name in components:
+ data_and_model[comp_name] = components[comp_name]
plot_kwargs_defaults['linestyle'][comp_name] = '--'
plot_kwargs_defaults['marker'][comp_name] = None
@@ -317,42 +355,54 @@ def free_energy_offset(self) -> None:
#############
def _require_Q_index(self) -> int:
- """Get the Q index, ensuring it is set. Raises a ValueError if
- the Q index is not set.
+ """
+ Get the Q index, ensuring it is set.
- Returns:
- int: The Q index.
+ Raises a ValueError if the Q index is not set.
- Raises:
- ValueError: If the Q index is not set.
+ Raises
+ ------
+ ValueError
+ If the Q index is not set.
+
+ Returns
+ -------
+ int
+ The Q index.
"""
if self._Q_index is None:
raise ValueError('Q_index must be set.')
return self._Q_index
def _on_Q_index_changed(self) -> None:
- """Handle changes to the Q index.
+ """
+ Handle changes to the Q index.
- This method is called whenever the Q index is changed. It
- updates the Convolution object for the new Q index and the
- masked energy from the experiment for the new Q index.
+ This method is called whenever the Q index is changed. It updates the Convolution object
+ for the new Q index and the masked energy from the experiment for the new Q index.
"""
masked_energy = self.experiment.get_masked_energy(Q_index=self._Q_index)
self._masked_energy = masked_energy
self._convolver = self._create_convolver()
def _verify_energy(self, energy: sc.Variable | None) -> sc.Variable | None:
- """Verify that the provided energy is the correct type.
-
- Args:
- energy (sc.Variable | None): The energy to verify.
-
- Returns:
- sc.Variable | None: The verified energy, or None if no
- energy is provided.
-
- Raises:
- TypeError: If energy is not a sc.Variable or None.
+ """
+ Verify that the provided energy is the correct type.
+
+ Parameters
+ ----------
+ energy : sc.Variable | None
+ The energy to verify.
+
+ Raises
+ ------
+ TypeError
+ If energy is not a sc.Variable or None.
+
+ Returns
+ -------
+ sc.Variable | None
+ The verified energy, or None if no energy is provided.
"""
if energy is not None and not isinstance(energy, sc.Variable):
@@ -364,18 +414,25 @@ def _calculate_energy_with_offset(
energy: sc.Variable,
energy_offset: Parameter,
) -> sc.Variable:
- """Calculate the energy grid with the energy offset applied.
-
- Args:
- energy (sc.Variable): The energy grid to apply the offset to.
- energy_offset (Parameter): The energy offset to apply.
-
- Returns:
- sc.Variable: The energy grid with the offset applied.
-
- Raises:
- sc.UnitError: If the energy and energy offset have
- incompatible units.
+ """
+ Calculate the energy grid with the energy offset applied.
+
+ Parameters
+ ----------
+ energy : sc.Variable
+ The energy grid to apply the offset to.
+ energy_offset : Parameter
+ The energy offset to apply.
+
+ Raises
+ ------
+ sc.UnitError
+ If the energy and energy offset have incompatible units.
+
+ Returns
+ -------
+ sc.Variable
+ The energy grid with the offset applied.
"""
if energy.unit != energy_offset.unit:
@@ -401,34 +458,38 @@ def _evaluate_components(
convolver: Convolution | None = None,
convolve: bool = True,
energy: sc.Variable | None = None,
+ apply_detailed_balance: bool = False,
) -> np.ndarray:
- """Calculate the contribution of a set of components, optionally
- convolving with the resolution.
-
- If convolve is True and a
- Convolution object is provided (for full model evaluation), we
- use it to perform the convolution of the components with the
+ """
+ Calculate the contribution of a set of components, optionally convolving with the
resolution.
- If convolve is True but no Convolution object is
- provided, create a new Convolution object for the given
- components (for individual components).
- If convolve is False, evaluate the components directly without
- convolution (for background).
-
- Args:
- components (ComponentCollection | ModelComponent): The
- components to evaluate.
- convolver (Convolution | None, default=None): An optional Convolution
- object to use for convolution. If None, a new
- Convolution object will be created if convolve is True.
- convolve (bool, default=True): Whether to perform convolution with the
- resolution. Default is True.
- energy (sc.Variable | None, default=None): Optional energy grid to use for
- evaluation. If None, the energy grid from the experiment
- is used.
-
- Returns:
- np.ndarray: The evaluated contribution of the components.
+
+ If convolve is True and a Convolution object is provided (for full model evaluation), we
+ use it to perform the convolution of the components with the resolution. If convolve is
+ True but no Convolution object is provided, create a new Convolution object for the given
+ components (for individual components). If convolve is False, evaluate the components
+ directly without convolution (for background).
+
+ Parameters
+ ----------
+ components : ComponentCollection | ModelComponent
+ The components to evaluate.
+ convolver : Convolution | None, default=None
+ An optional Convolution object to use for convolution. If None, a new Convolution
+ object will be created if convolve is True.
+ convolve : bool, default=True
+ Whether to perform convolution with the resolution.
+ energy : sc.Variable | None, default=None
+ Optional energy grid to use for evaluation. If None, the energy grid from the
+ experiment is used.
+ apply_detailed_balance : bool, default=False
+ Whether to apply detailed balance correction.
+
+
+ Returns
+ -------
+ np.ndarray
+ The evaluated contribution of the components.
"""
Q_index = self._require_Q_index()
@@ -445,31 +506,51 @@ def _evaluate_components(
if isinstance(components, ComponentCollection) and components.is_empty:
return np.zeros_like(energy.values)
- # No convolution
- if not convolve:
- return components.evaluate(energy_with_offset)
-
- # If a convolver is provided, use it. This allows reusing the
+ # If a convolver is provided, we use it. This allows reusing the
# same convolver for multiple evaluations during fitting for
# performance reasons.
if convolver is not None:
return convolver.convolution()
- # If no convolver is provided, create a new one. This is for
- # evaluating individual components for plotting, where
- # performance is not important.
+ # No convolution can happen for multiple reasons:
+ # Case 1: convolve=False, used for evaluating background components, where we don't want
+ # to convolve with the resolution. In this case, apply_detailed_balance is False,
+ # and we evaluate the components without DBF regardles of the settings
+ # Case 2: convolve=True but there is no resolution_model. In this case,
+ # apply_detailed_balance is True. We apply DBF if temperature is provided and
+ # the settings say to use detailed balance.
- # We don't create a convolver if the resolution is empty.
resolution = self.instrument_model.resolution_model.get_component_collection(Q_index)
- if resolution.is_empty:
- return components.evaluate(energy_with_offset)
+ if not convolve or resolution.is_empty:
+ result_no_convolution = components.evaluate(energy_with_offset)
+ if (
+ apply_detailed_balance
+ and self.temperature is not None
+ and self.detailed_balance_settings.use_detailed_balance
+ ):
+ DBF = detailed_balance_factor(
+ energy=energy_with_offset,
+ temperature=self.temperature,
+ divide_by_temperature=self.detailed_balance_settings.normalize_detailed_balance,
+ energy_unit=self.unit,
+ )
+ result_no_convolution *= DBF
+ return result_no_convolution
+
+ # If no convolver is provided, we create a new one. This is for
+ # evaluating individual components for plotting, where
+ # performance is not important. We already handled the case of
+ # background components above, so we know that this is for sample components,
+ # where detailed balance settings should be applied.
conv = Convolution(
+ energy=energy,
sample_components=components,
resolution_components=resolution,
- energy=energy,
- temperature=self.temperature,
energy_offset=energy_offset,
+ convolution_settings=self.convolution_settings,
+ temperature=self.temperature,
+ detailed_balance_settings=self.detailed_balance_settings,
)
return conv.convolution()
@@ -477,17 +558,21 @@ def _evaluate_sample(
self,
energy: sc.Variable | None = None,
) -> np.ndarray:
- """Evaluate the sample contribution for a given Q index.
+ """
+ Evaluate the sample contribution for a given Q index.
Assumes that self._convolver is up to date.
- Args:
- energy (sc.Variable | None, default=None): Optional energy grid to use for
- evaluation. If None, the energy grid from the experiment
- is used.
+ Parameters
+ ----------
+ energy : sc.Variable | None, default=None
+ Optional energy grid to use for evaluation. If None, the energy grid from the
+ experiment is used.
- Returns:
- np.ndarray: The evaluated sample contribution.
+ Returns
+ -------
+ np.ndarray
+ The evaluated sample contribution.
"""
Q_index = self._require_Q_index()
components = self.sample_model.get_component_collection(Q_index=Q_index)
@@ -496,6 +581,7 @@ def _evaluate_sample(
convolver=self._convolver,
convolve=True,
energy=energy,
+ apply_detailed_balance=True,
)
def _evaluate_sample_component(
@@ -503,35 +589,44 @@ def _evaluate_sample_component(
component: ModelComponent,
energy: sc.Variable | None = None,
) -> np.ndarray:
- """Evaluate a single sample component for the chosen Q index.
-
- Args:
- component (ModelComponent): The sample component to
- evaluate.
- energy (sc.Variable | None, default=None): Optional energy grid to use for
- evaluation. If None, the energy grid from the experiment
- is used.
-
- Returns:
- np.ndarray: The evaluated sample component contribution.
+ """
+ Evaluate a single sample component for the chosen Q index.
+
+ Parameters
+ ----------
+ component : ModelComponent
+ The sample component to evaluate.
+ energy : sc.Variable | None, default=None
+ Optional energy grid to use for evaluation. If None, the energy grid from the
+ experiment is used.
+
+ Returns
+ -------
+ np.ndarray
+ The evaluated sample component contribution.
"""
return self._evaluate_components(
components=component,
convolver=None,
convolve=True,
energy=energy,
+ apply_detailed_balance=True,
)
def _evaluate_background(self, energy: sc.Variable | None = None) -> np.ndarray:
- """Evaluate the background contribution for the chosen Q index.
-
- Args:
- energy (sc.Variable | None, default=None): Optional energy grid to use for
- evaluation. If None, the energy grid from the experiment
- is used.
-
- Returns:
- np.ndarray: The evaluated background contribution.
+ """
+ Evaluate the background contribution for the chosen Q index.
+
+ Parameters
+ ----------
+ energy : sc.Variable | None, default=None
+ Optional energy grid to use for evaluation. If None, the energy grid from the
+ experiment is used.
+
+ Returns
+ -------
+ np.ndarray
+ The evaluated background contribution.
"""
Q_index = self._require_Q_index()
background_components = self.instrument_model.background_model.get_component_collection(
@@ -542,6 +637,7 @@ def _evaluate_background(self, energy: sc.Variable | None = None) -> np.ndarray:
convolver=None,
convolve=False,
energy=energy,
+ apply_detailed_balance=False,
)
def _evaluate_background_component(
@@ -549,18 +645,21 @@ def _evaluate_background_component(
component: ModelComponent,
energy: sc.Variable | None = None,
) -> np.ndarray:
- """Evaluate a single background component for the chosen Q
- index.
-
- Args:
- component (ModelComponent): The background component to
- evaluate.
- energy (sc.Variable | None, default=None): Optional energy grid to use for
- evaluation. If None, the energy grid from the experiment
- is used.
-
- Returns:
- np.ndarray: The evaluated background component contribution.
+ """
+ Evaluate a single background component for the chosen Q index.
+
+ Parameters
+ ----------
+ component : ModelComponent
+ The background component to evaluate.
+ energy : sc.Variable | None, default=None
+ Optional energy grid to use for evaluation. If None, the energy grid from the
+ experiment is used.
+
+ Returns
+ -------
+ np.ndarray
+ The evaluated background component contribution.
"""
return self._evaluate_components(
@@ -568,24 +667,27 @@ def _evaluate_background_component(
convolver=None,
convolve=False,
energy=energy,
+ apply_detailed_balance=False,
)
def _create_convolver(
self,
energy: sc.Variable | None = None,
) -> Convolution | None:
- """Initialize and return a Convolution object for the chosen Q
- index. If the necessary components for convolution are not
- available, return None.
-
- Args:
- energy (sc.Variable | None, default=None): Optional energy grid to use for
- convolution. If None, the energy grid from the experiment
- is used.
-
- Returns:
- Convolution | None: The initialized Convolution object or
- None if not available.
+ """
+ Initialize and return a Convolution object for the chosen Q index. If the necessary
+ components for convolution are not available, return None.
+
+ Parameters
+ ----------
+ energy : sc.Variable | None, default=None
+ Optional energy grid to use for convolution. If None, the energy grid from the
+ experiment is used.
+
+ Returns
+ -------
+ Convolution | None
+ The initialized Convolution object or None if not available.
"""
Q_index = self._require_Q_index()
@@ -602,13 +704,14 @@ def _create_convolver(
if resolution_components.is_empty:
return None
- # TODO: allow convolution options to be set.
return Convolution(
+ energy=energy,
sample_components=sample_components,
resolution_components=resolution_components,
- energy=energy,
- temperature=self.temperature,
energy_offset=self.instrument_model.get_energy_offset(Q_index),
+ convolution_settings=self.convolution_settings,
+ temperature=self.temperature,
+ detailed_balance_settings=self.detailed_balance_settings,
)
#############
@@ -621,19 +724,25 @@ def _create_component_scipp_array(
background: np.ndarray | None = None,
energy: sc.Variable | None = None,
) -> sc.DataArray:
- """Create a scipp DataArray for a single component. Adds the
- background if it is not None.
-
- Args:
- component (ModelComponent): The component to evaluate.
- background (np.ndarray | None, default=None): Optional background to add
- to the component.
- energy (sc.Variable | None, default=None): Optional energy grid to use for
- evaluation. If None, the energy grid from the experiment
- is used.
-
- Returns:
- sc.DataArray: The model calculation of the component.
+ """
+ Create a scipp DataArray for a single component.
+
+ Adds the background if it is not None.
+
+ Parameters
+ ----------
+ component : ModelComponent
+ The component to evaluate.
+ background : np.ndarray | None, default=None
+ Optional background to add to the component.
+ energy : sc.Variable | None, default=None
+ Optional energy grid to use for evaluation. If None, the energy grid from the
+ experiment is used.
+
+ Returns
+ -------
+ sc.DataArray
+ The model calculation of the component.
"""
values = self._evaluate_sample_component(component=component, energy=energy)
@@ -646,16 +755,21 @@ def _create_background_component_scipp_array(
component: ModelComponent,
energy: sc.Variable | None = None,
) -> sc.DataArray:
- """Create a scipp DataArray for a single background component.
-
- Args:
- component (ModelComponent): The component to evaluate.
- energy (sc.Variable | None, default=None): Optional energy grid to use for
- evaluation. If None, the energy grid from the experiment
- is used.
-
- Returns:
- sc.DataArray: The model calculation of the component.
+ """
+ Create a scipp DataArray for a single background component.
+
+ Parameters
+ ----------
+ component : ModelComponent
+ The component to evaluate.
+ energy : sc.Variable | None, default=None
+ Optional energy grid to use for evaluation. If None, the energy grid from the
+ experiment is used.
+
+ Returns
+ -------
+ sc.DataArray
+ The model calculation of the component.
"""
values = self._evaluate_background_component(
@@ -664,18 +778,20 @@ def _create_background_component_scipp_array(
)
return self._to_scipp_array(values=values, energy=energy)
- def _create_sample_scipp_array(self, energy: sc.Variable | None = None) -> sc.DataArray:
- """Create a scipp DataArray for the full sample model including
- background.
-
- Args:
- energy (sc.Variable | None, default=None): Optional energy grid to use for
- evaluation. If None, the energy grid from the experiment
- is used.
-
- Returns:
- sc.DataArray: The model calculation of the full sample
- model.
+ def _create_model_array(self, energy: sc.Variable | None = None) -> sc.DataArray:
+ """
+ Create a scipp DataArray for the full sample model including background.
+
+ Parameters
+ ----------
+ energy : sc.Variable | None, default=None
+ Optional energy grid to use for evaluation. If None, the energy grid from the
+ experiment is used.
+
+ Returns
+ -------
+ sc.DataArray
+ The model calculation of the full sample model.
"""
values = self.calculate(energy=energy)
return self._to_scipp_array(values=values, energy=energy)
@@ -685,18 +801,21 @@ def _create_components_dataset_single_Q(
add_background: bool = True,
energy: sc.Variable | None = None,
) -> dict[str, sc.DataArray]:
- """Create sc.DataArrays for all sample and background
- components.
-
- Args:
- add_background (bool, default=True): Whether to add background components.
- energy (sc.Variable | None, default=None): Optional energy grid to use for
- evaluation. If None, the energy grid from the experiment
- is used.
-
- Returns:
- dict[str, sc.DataArray]: A dictionary of component names to
- their corresponding sc.DataArrays.
+ """
+ Create sc.DataArrays for all sample and background components.
+
+ Parameters
+ ----------
+ add_background : bool, default=True
+ Whether to add background components.
+ energy : sc.Variable | None, default=None
+ Optional energy grid to use for evaluation. If None, the energy grid from the
+ experiment is used.
+
+ Returns
+ -------
+ dict[str, sc.DataArray]
+ A dictionary of component names to their corresponding sc.DataArrays.
"""
scipp_arrays = {}
sample_components = self.sample_model.get_component_collection(
@@ -727,17 +846,22 @@ def _to_scipp_array(
values: np.ndarray,
energy: sc.Variable | None = None,
) -> sc.DataArray:
- """Convert a numpy array of values to a sc.DataArray with the
- correct coordinates for energy and Q.
-
- Args:
- values (np.ndarray): The values to convert.
- energy (sc.Variable | None, default=None): Optional energy grid to use for the
- energy coordinate. If None, the energy grid from the
- experiment is used.
-
- Returns:
- sc.DataArray: The converted sc.DataArray.
+ """
+ Convert a numpy array of values to a sc.DataArray with the correct coordinates for energy
+ and Q.
+
+ Parameters
+ ----------
+ values : np.ndarray
+ The values to convert.
+ energy : sc.Variable | None, default=None
+ Optional energy grid to use for the energy coordinate. If None, the energy grid from
+ the experiment is used.
+
+ Returns
+ -------
+ sc.DataArray
+ The converted sc.DataArray.
"""
if energy is None:
diff --git a/src/easydynamics/analysis/analysis_base.py b/src/easydynamics/analysis/analysis_base.py
index 61247e0e..01f0a20f 100644
--- a/src/easydynamics/analysis/analysis_base.py
+++ b/src/easydynamics/analysis/analysis_base.py
@@ -3,23 +3,25 @@
import numpy as np
import scipp as sc
-from easyscience.base_classes.model_base import ModelBase as EasyScienceModelBase
from easyscience.variable import Parameter
+from easydynamics.base_classes.easydynamics_modelbase import EasyDynamicsModelBase
from easydynamics.experiment import Experiment
from easydynamics.sample_model import InstrumentModel
from easydynamics.sample_model import SampleModel
+from easydynamics.settings.convolution_settings import ConvolutionSettings
+from easydynamics.settings.detailed_balance_settings import DetailedBalanceSettings
-class AnalysisBase(EasyScienceModelBase):
- """Base class for analysis in EasyDynamics. This class is not meant
- to be used directly.
+class AnalysisBase(EasyDynamicsModelBase):
+ """
+ Base class for analysis in EasyDynamics.
+
+ This class is not meant to be used directly.
- An Analysis consists of an Experiment, a SampleModel, and an
- InstrumentModel. The Experiment contains the data to be fitted, the
- SampleModel contains the model for the sample, and the
- InstrumentModel contains the model for the instrument, including
- background and resolution
+ An Analysis consists of an Experiment, a SampleModel, and an InstrumentModel. The Experiment
+ contains the data to be fitted, the SampleModel contains the model for the sample, and the
+ InstrumentModel contains the model for the instrument, including background and resolution
"""
def __init__(
@@ -29,33 +31,44 @@ def __init__(
experiment: Experiment | None = None,
sample_model: SampleModel | None = None,
instrument_model: InstrumentModel | None = None,
+ convolution_settings: ConvolutionSettings | None = None,
+ detailed_balance_settings: DetailedBalanceSettings | None = None,
extra_parameters: Parameter | list[Parameter] | None = None,
) -> None:
- """Initialize the AnalysisBase.
-
- Args:
- display_name (str | None, default='MyAnalysis'): Display name of the analysis.
- unique_name (str | None, default=None): Unique name of the analysis. If
- None, a unique name is automatically generated.
- experiment (Experiment | None, default=None): The Experiment associated
- with this Analysis. If None, a default Experiment is
- created.
- sample_model (SampleModel | None, default=None): The SampleModel
- associated with this Analysis. If None, a default
- SampleModel is created.
- instrument_model (InstrumentModel | None, default=None): The
- InstrumentModel associated with this Analysis. If None,
- a default InstrumentModel is created.
- extra_parameters (Parameter | list[Parameter] | None, default=None): Extra
- parameters to be included in the analysis for advanced
- users. If None, no extra parameters are added.
-
- Raises:
- TypeError: If experiment is not an Experiment or None or
- if sample_model is not a SampleModel or None or if
- instrument_model is not an InstrumentModel or None or if
- extra_parameters is not a Parameter, a list of Parameters,
- or None.
+ """
+ Initialize the AnalysisBase.
+
+ Parameters
+ ----------
+ display_name : str | None, default='MyAnalysis'
+ Display name of the analysis.
+ unique_name : str | None, default=None
+ Unique name of the analysis. If None, a unique name is automatically generated. By
+ default, None.
+ experiment : Experiment | None, default=None
+ The Experiment associated with this Analysis. If None, a default Experiment is created.
+ sample_model : SampleModel | None, default=None
+ The SampleModel associated with this Analysis. If None, a default SampleModel is
+ created.
+ instrument_model : InstrumentModel | None, default=None
+ The InstrumentModel associated with this Analysis. If None, a default InstrumentModel
+ is created.
+ convolution_settings : ConvolutionSettings | None, default=None
+ The settings for the convolution. If None, default settings will be used.
+ detailed_balance_settings : DetailedBalanceSettings | None, default=None
+ The settings for detailed balance. If None, default settings will be used.
+ extra_parameters : Parameter | list[Parameter] | None, default=None
+ Extra parameters to be included in the analysis for advanced users. If None, no extra
+ parameters are added.
+
+ Raises
+ ------
+ TypeError
+ If experiment is not an Experiment or None or if sample_model is not a SampleModel or
+ None or if instrument_model is not an InstrumentModel or None or if
+ convolution_settings is not a ConvolutionSettings or None or if
+ detailed_balance_settings is not a DetailedBalanceSettings or None or if
+ extra_parameters is not a Parameter, a list of Parameters, or None.
"""
super().__init__(display_name=display_name, unique_name=unique_name)
@@ -81,6 +94,15 @@ def __init__(
else:
raise TypeError('instrument_model must be an instance of InstrumentModel or None.')
+ if convolution_settings is None:
+ self.convolution_settings = ConvolutionSettings()
+ elif isinstance(convolution_settings, ConvolutionSettings):
+ self.convolution_settings = convolution_settings
+ else:
+ raise TypeError(
+ 'convolution_settings must be an instance of ConvolutionSettings or None.'
+ )
+
if extra_parameters is not None:
if isinstance(extra_parameters, Parameter):
self._extra_parameters = [extra_parameters]
@@ -93,6 +115,15 @@ def __init__(
else:
self._extra_parameters = []
+ if detailed_balance_settings is None:
+ self._detailed_balance_settings = DetailedBalanceSettings()
+ elif isinstance(detailed_balance_settings, DetailedBalanceSettings):
+ self._detailed_balance_settings = detailed_balance_settings
+ else:
+ raise TypeError(
+ 'detailed_balance_settings must be an instance of DetailedBalanceSettings or None.'
+ )
+
self._on_experiment_changed()
#############
@@ -101,23 +132,31 @@ def __init__(
@property
def experiment(self) -> Experiment:
- """Get the Experiment associated with this Analysis.
+ """
+ Get the Experiment associated with this Analysis.
- Returns:
- Experiment: The Experiment associated with this Analysis.
+ Returns
+ -------
+ Experiment
+ The Experiment associated with this Analysis.
"""
return self._experiment
@experiment.setter
def experiment(self, value: Experiment) -> None:
- """Set the Experiment for this Analysis.
+ """
+ Set the Experiment for this Analysis.
- Args:
- value (Experiment): The Experiment to set for this Analysis.
+ Parameters
+ ----------
+ value : Experiment
+ The Experiment to set for this Analysis.
- Raises:
- TypeError: if value is not an Experiment.
+ Raises
+ ------
+ TypeError
+ If value is not an Experiment.
"""
if not isinstance(value, Experiment):
@@ -127,23 +166,31 @@ def experiment(self, value: Experiment) -> None:
@property
def sample_model(self) -> SampleModel:
- """Get the SampleModel associated with this Analysis.
+ """
+ Get the SampleModel associated with this Analysis.
- Returns:
- SampleModel: The SampleModel associated with this Analysis.
+ Returns
+ -------
+ SampleModel
+ The SampleModel associated with this Analysis.
"""
return self._sample_model
@sample_model.setter
def sample_model(self, value: SampleModel) -> None:
- """Set the SampleModel for this Analysis.
+ """
+ Set the SampleModel for this Analysis.
- Args:
- value (SampleModel): The SampleModel to set for this Analysis.
+ Parameters
+ ----------
+ value : SampleModel
+ The SampleModel to set for this Analysis.
- Raises:
- TypeError: if value is not a SampleModel.
+ Raises
+ ------
+ TypeError
+ If value is not a SampleModel.
"""
if not isinstance(value, SampleModel):
raise TypeError('sample_model must be an instance of SampleModel')
@@ -152,24 +199,30 @@ def sample_model(self, value: SampleModel) -> None:
@property
def instrument_model(self) -> InstrumentModel:
- """Get the InstrumentModel associated with this Analysis.
+ """
+ Get the InstrumentModel associated with this Analysis.
- Returns:
- InstrumentModel: The InstrumentModel associated with this
- Analysis.
+ Returns
+ -------
+ InstrumentModel
+ The InstrumentModel associated with this Analysis.
"""
return self._instrument_model
@instrument_model.setter
def instrument_model(self, value: InstrumentModel) -> None:
- """Set the InstrumentModel for this Analysis.
+ """
+ Set the InstrumentModel for this Analysis.
- Args:
- value (InstrumentModel): The InstrumentModel to set for this
- Analysis.
+ Parameters
+ ----------
+ value : InstrumentModel
+ The InstrumentModel to set for this Analysis.
- Raises:
- TypeError: if value is not an InstrumentModel.
+ Raises
+ ------
+ TypeError
+ If value is not an InstrumentModel.
"""
if not isinstance(value, InstrumentModel):
raise TypeError('instrument_model must be an instance of InstrumentModel')
@@ -178,105 +231,185 @@ def instrument_model(self, value: InstrumentModel) -> None:
@property
def Q(self) -> sc.Variable | None:
- """Get the Q values from the associated Experiment, if
- available.
+ """
+ Get the Q values from the associated Experiment, if available.
- Returns:
- sc.Variable | None: The Q values from the associated Experiment,
- if available, and None if not.
+ Returns
+ -------
+ sc.Variable | None
+ The Q values from the associated Experiment, if available, and None if not.
"""
return self.experiment.Q
@Q.setter
def Q(self, _value: sc.Variable) -> None:
- """Q cannot be set, as it is a read-only property derived from
- the Experiment.
+ """
+ Q cannot be set, as it is a read-only property derived from the Experiment.
- Args:
- _value (sc.Variable): The Q values to set. This argument is
- ignored, as Q is a read-only property.
+ Parameters
+ ----------
+ _value : sc.Variable
+ The Q values to set. This argument is ignored, as Q is a read-only property.
- Raises:
- AttributeError: If trying to set Q.
+ Raises
+ ------
+ AttributeError
+ If trying to set Q.
"""
raise AttributeError('Q is a read-only property derived from the Experiment.')
@property
def energy(self) -> sc.Variable | None:
- """Get the energy values from the associated Experiment, if
- available.
+ """
+ Get the energy values from the associated Experiment, if available.
- Returns:
- sc.Variable | None: The energy values from the associated
- Experiment, if available, and None if not.
+ Returns
+ -------
+ sc.Variable | None
+ The energy values from the associated.
"""
return self.experiment.energy
@energy.setter
def energy(self, _value: sc.Variable) -> None:
- """Energy cannot be set, as it is a read-only property derived
- from the Experiment.
+ """
+ Energy cannot be set, as it is a read-only property derived from the Experiment.
- Args:
- _value (sc.Variable): The energy values to set. This argument is
- ignored, as energy is a read-only property.
+ Parameters
+ ----------
+ _value : sc.Variable
+ The energy values to set. This argument is ignored, as energy is a read-only property.
- Raises:
- AttributeError: If trying to set energy.
+ Raises
+ ------
+ AttributeError
+ If trying to set energy.
"""
raise AttributeError('energy is a read-only property derived from the Experiment.')
@property
def temperature(self) -> Parameter | None:
- """Get the temperature from the associated SampleModel, if
- available.
+ """
+ Get the temperature from the associated SampleModel, if available.
- Returns:
- Parameter | None: The temperature from the associated SampleModel,
- if available, and None if not.
+ Returns
+ -------
+ Parameter | None
+ The temperature from the associated SampleModel, if available, and None if not.
"""
return self.sample_model.temperature
@temperature.setter
def temperature(self, _value: np.ndarray | Parameter) -> None:
- """Temperature cannot be set, as it is a read-only property
- derived from the SampleModel.
+ """
+ Temperature cannot be set, as it is a read-only property derived from the SampleModel.
+
+ Parameters
+ ----------
+ _value : np.ndarray | Parameter
+ The temperature to set. This argument is ignored, as temperature is a read-only
+ property.
+
+ Raises
+ ------
+ AttributeError
+ If trying to set temperature.
+ """
- Args:
- _value (np.ndarray | Parameter): The temperature to set.
- This argument is ignored, as temperature is a read-only
- property.
+ raise AttributeError('temperature is a read-only property derived from the SampleModel.')
- Raises:
- AttributeError: If trying to set temperature.
+ @property
+ def convolution_settings(self) -> ConvolutionSettings:
"""
+ Get the convolution settings for this Analysis.
- raise AttributeError('temperature is a read-only property derived from the SampleModel.')
+ Returns
+ -------
+ ConvolutionSettings
+ The convolution settings for this Analysis.
+ """
+ return self._convolution_settings
+
+ @convolution_settings.setter
+ def convolution_settings(self, value: ConvolutionSettings) -> None:
+ """
+ Set the convolution settings for this Analysis.
+
+ Parameters
+ ----------
+ value : ConvolutionSettings
+ The convolution settings to set for this Analysis.
+
+ Raises
+ ------
+ TypeError
+ If value is not an instance of ConvolutionSettings.
+ """
+ if not isinstance(value, ConvolutionSettings):
+ raise TypeError('convolution_settings must be an instance of ConvolutionSettings.')
+ self._convolution_settings = value
+ self._on_convolution_settings_changed()
+
+ @property
+ def detailed_balance_settings(self) -> DetailedBalanceSettings:
+ """
+ Get the DetailedBalanceSettings of the SampleModel.
+
+ Returns
+ -------
+ DetailedBalanceSettings
+ The DetailedBalanceSettings of the SampleModel.
+ """
+ return self._detailed_balance_settings
+
+ @detailed_balance_settings.setter
+ def detailed_balance_settings(self, value: DetailedBalanceSettings) -> None:
+ """
+ Set the DetailedBalanceSettings of the SampleModel.
+
+ Parameters
+ ----------
+ value : DetailedBalanceSettings
+ The DetailedBalanceSettings to set.
+
+ Raises
+ ------
+ TypeError
+ If value is not a DetailedBalanceSettings.
+ """
+ if not isinstance(value, DetailedBalanceSettings):
+ raise TypeError('detailed_balance_settings must be a DetailedBalanceSettings')
+ self._detailed_balance_settings = value
@property
def extra_parameters(self) -> list[Parameter]:
- """Get the extra parameters included in this Analysis.
+ """
+ Get the extra parameters included in this Analysis.
- Returns:
- list[Parameter]: The extra parameters included in this
- Analysis.
+ Returns
+ -------
+ list[Parameter]
+ The extra parameters included in this Analysis.
"""
return self._extra_parameters
@extra_parameters.setter
def extra_parameters(self, value: Parameter | list[Parameter]) -> None:
- """Set the extra parameters for this Analysis.
+ """
+ Set the extra parameters for this Analysis.
- Args:
- value (Parameter | list[Parameter]): The extra parameters to
- include in this Analysis.
+ Parameters
+ ----------
+ value : Parameter | list[Parameter]
+ The extra parameters to include in this Analysis.
- Raises:
- TypeError: If value is not a Parameter, a list of
- Parameters, or None.
+ Raises
+ ------
+ TypeError
+ If value is not a Parameter, a list of Parameters, or None.
"""
if isinstance(value, Parameter):
self._extra_parameters = [value]
@@ -292,11 +425,10 @@ def extra_parameters(self, value: Parameter | list[Parameter]) -> None:
#############
def normalize_resolution(self) -> None:
- """Normalize the resolution in the InstrumentModel to ensure
- that it integrates to 1.
+ """
+ Normalize the resolution in the InstrumentModel to ensure that it integrates to 1.
- This is important for accurate fitting and interpretation of the
- results.
+ This is important for accurate fitting and interpretation of the results.
"""
self.instrument_model.normalize_resolution()
@@ -305,36 +437,49 @@ def normalize_resolution(self) -> None:
#############
def _on_experiment_changed(self) -> None:
- """Update the Q values in the sample and instrument models when
- the experiment changes.
+ """
+ Update the Q values in the sample and instrument models when the experiment changes.
"""
self.sample_model.Q = self.Q
self.instrument_model.Q = self.Q
def _on_sample_model_changed(self) -> None:
- """Update the Q values in the sample model when the sample model
- changes.
+ """
+ Update the Q values in the sample model when the sample model changes.
"""
self.sample_model.Q = self.Q
def _on_instrument_model_changed(self) -> None:
- """Update the Q values in the instrument model when the
- instrument model changes.
+ """
+ Update the Q values in the instrument model when the instrument model changes.
"""
self.instrument_model.Q = self.Q
- def _verify_Q_index(self, Q_index: int | None) -> int | None:
- """Verify that the Q index is valid.
-
- Args:
- Q_index (int | None): The Q index to verify.
-
- Returns:
- int | None: The verified Q index.
+ def _on_convolution_settings_changed(self) -> None:
+ """
+ For subclasses that implement convolution, this method can be overridden
+ """
- Raises:
- TypeError: If Q_index is not an integer or None.
- IndexError: If the Q index is not valid.
+ def _verify_Q_index(self, Q_index: int | None) -> int | None:
+ """
+ Verify that the Q index is valid.
+
+ Parameters
+ ----------
+ Q_index : int | None
+ The Q index to verify.
+
+ Raises
+ ------
+ TypeError
+ If Q_index is not an integer or None.
+ IndexError
+ If the Q index is not valid.
+
+ Returns
+ -------
+ int | None
+ The verified Q index.
"""
if Q_index is None:
return None
@@ -351,10 +496,15 @@ def _verify_Q_index(self, Q_index: int | None) -> int | None:
#############
def __repr__(self) -> str:
- """Return a string representation of the Analysis.
+ """
+ Return a string representation of the Analysis.
- Returns:
- str: A string representation of the Analysis.
+ Returns
+ -------
+ str
+ A string representation of the Analysis.
"""
- return f' {self.__class__.__name__} (display_name={self.display_name}, \
- unique_name={self.unique_name})'
+ return (
+ f' {self.__class__.__name__} (display_name={self.display_name}, '
+ f'unique_name={self.unique_name})'
+ )
diff --git a/src/easydynamics/base_classes/__init__.py b/src/easydynamics/base_classes/__init__.py
new file mode 100644
index 00000000..96d2e045
--- /dev/null
+++ b/src/easydynamics/base_classes/__init__.py
@@ -0,0 +1,10 @@
+# SPDX-FileCopyrightText: 2026 EasyScience contributors
+# SPDX-License-Identifier: BSD-3-Clause
+
+from easydynamics.base_classes.easydynamics_base import EasyDynamicsBase
+from easydynamics.base_classes.easydynamics_modelbase import EasyDynamicsModelBase
+
+__all__ = [
+ 'EasyDynamicsBase',
+ 'EasyDynamicsModelBase',
+]
diff --git a/src/easydynamics/base_classes/easydynamics_base.py b/src/easydynamics/base_classes/easydynamics_base.py
new file mode 100644
index 00000000..1f38c9d3
--- /dev/null
+++ b/src/easydynamics/base_classes/easydynamics_base.py
@@ -0,0 +1,69 @@
+# SPDX-FileCopyrightText: 2026 EasyScience contributors
+# SPDX-License-Identifier: BSD-3-Clause
+
+from easyscience.base_classes.new_base import NewBase
+
+
+class EasyDynamicsBase(NewBase):
+ """Base class for all EasyDynamics classes."""
+
+ def __init__(
+ self,
+ name: str | None = 'MyEasyDynamicsModel',
+ display_name: str | None = 'MyEasyDynamicsModel',
+ unique_name: str | None = None,
+ ) -> None:
+ """
+ Initialize the EasyDynamicsBase.
+
+ Parameters
+ ----------
+ name : str | None, default='MyEasyDynamicsModel'
+ Name of the model.
+ display_name : str | None, default='MyEasyDynamicsModel'
+ Display name of the model.
+ unique_name : str | None, default=None
+ Unique name of the model. If None, a unique name will be generated.
+
+ Raises
+ ------
+ TypeError
+ If name is not a string or None.
+ """
+ super().__init__(display_name=display_name, unique_name=unique_name)
+
+ if name is not None and not isinstance(name, str):
+ raise TypeError('Name must be a string or None.')
+ self._name = name
+
+ @property
+ def name(self) -> str | None:
+ """
+ Get the name of the model.
+
+ Returns
+ -------
+ str | None
+ The name of the model.
+ """
+ return self._name
+
+ @name.setter
+ def name(self, name_str: str | None) -> None:
+ """
+ Set the name of the model.
+
+ Parameters
+ ----------
+ name_str : str | None
+ The new name to set.
+
+ Raises
+ ------
+ TypeError
+ If name_str is not a string or None.
+ """
+
+ if name_str is not None and not isinstance(name_str, str):
+ raise TypeError('Name must be a string or None.')
+ self._name = name_str
diff --git a/src/easydynamics/base_classes/easydynamics_modelbase.py b/src/easydynamics/base_classes/easydynamics_modelbase.py
new file mode 100644
index 00000000..bf266086
--- /dev/null
+++ b/src/easydynamics/base_classes/easydynamics_modelbase.py
@@ -0,0 +1,109 @@
+# SPDX-FileCopyrightText: 2026 EasyScience contributors
+# SPDX-License-Identifier: BSD-3-Clause
+
+import scipp as sc
+from easyscience.base_classes import ModelBase
+
+from easydynamics.utils.utils import _validate_unit
+
+
+class EasyDynamicsModelBase(ModelBase):
+ """Base class for all EasyDynamics models."""
+
+ def __init__(
+ self,
+ unit: str | sc.Unit = 'meV',
+ name: str | None = 'MyEasyDynamicsModel',
+ display_name: str | None = 'MyEasyDynamicsModel',
+ unique_name: str | None = None,
+ ) -> None:
+ """
+ Initialize the EasyDynamicsModelBase.
+
+ Parameters
+ ----------
+ unit : str | sc.Unit, default='meV'
+ Unit of the model.
+ name : str | None, default='MyEasyDynamicsModel'
+ Name of the model.
+ display_name : str | None, default='MyEasyDynamicsModel'
+ Display name of the model.
+ unique_name : str | None, default=None
+ Unique name of the model. If None, a unique name will be generated.
+
+ Raises
+ ------
+ TypeError
+ If name is not a string or None.
+ """
+ super().__init__(display_name=display_name, unique_name=unique_name)
+ self._unit = _validate_unit(unit)
+
+ if name is not None and not isinstance(name, str):
+ raise TypeError('Name must be a string or None.')
+ self._name = name
+
+ @property
+ def unit(self) -> str | sc.Unit | None:
+ """
+ Get the unit of the model.
+
+ Returns
+ -------
+ str | sc.Unit | None
+ The unit of the model.
+ """
+
+ return self._unit
+
+ @unit.setter
+ def unit(self, _unit_str: str) -> None:
+ """
+ Unit is read-only and cannot be set directly.
+
+ Parameters
+ ----------
+ _unit_str : str
+ The new unit to set (ignored).
+
+ Raises
+ ------
+ AttributeError
+ Always raised to indicate that the unit is read-only.
+ """
+ raise AttributeError(
+ f'Unit is read-only. Use convert_unit to change the unit between allowed types '
+ f'or create a new {self.__class__.__name__} with the desired unit.'
+ )
+
+ @property
+ def name(self) -> str | None:
+ """
+ Get the name of the model.
+
+ Returns
+ -------
+ str | None
+ The name of the model.
+ """
+ return self._name
+
+ @name.setter
+ def name(self, name_str: str) -> None:
+ """
+ Set the name of the model.
+
+ Parameters
+ ----------
+ name_str : str
+ The new name to set.
+
+ Raises
+ ------
+ TypeError
+ If name_str is not a string or None.
+ """
+
+ if name_str is not None and not isinstance(name_str, str):
+ raise TypeError('Name must be a string or None.')
+ self._name = name_str
diff --git a/src/easydynamics/convolution/__init__.py b/src/easydynamics/convolution/__init__.py
index 9b023c95..2cbfdcf5 100644
--- a/src/easydynamics/convolution/__init__.py
+++ b/src/easydynamics/convolution/__init__.py
@@ -1,6 +1,6 @@
# SPDX-FileCopyrightText: 2026 EasyScience contributors
# SPDX-License-Identifier: BSD-3-Clause
-from .convolution import Convolution
+from easydynamics.convolution.convolution import Convolution
__all__ = ['Convolution']
diff --git a/src/easydynamics/convolution/analytical_convolution.py b/src/easydynamics/convolution/analytical_convolution.py
index 70ecc318..ce4933b2 100644
--- a/src/easydynamics/convolution/analytical_convolution.py
+++ b/src/easydynamics/convolution/analytical_convolution.py
@@ -1,6 +1,8 @@
# SPDX-FileCopyrightText: 2026 EasyScience contributors
# SPDX-License-Identifier: BSD-3-Clause
+from typing import ClassVar
+
import numpy as np
import scipp as sc
from easyscience.variable import Parameter
@@ -17,16 +19,16 @@
class AnalyticalConvolution(ConvolutionBase):
- """Analytical convolution of a ModelComponent or ComponentCollection
- with a ResolutionModel.
+ """
+ Analytical convolution of a ModelComponent or ComponentCollection with a ResolutionModel.
- Possible analytical convolutions are any combination of delta
- functions, Gaussians, Lorentzians and Voigt profiles.
+ Possible analytical convolutions are any combination of delta functions, Gaussians, Lorentzians
+ and Voigt profiles.
"""
# Mapping of supported component type pairs to convolution methods.
# Delta functions are handled separately.
- _CONVOLUTIONS = {
+ _CONVOLUTIONS: ClassVar[dict[str, object]] = {
('Gaussian', 'Gaussian'): '_convolute_gaussian_gaussian',
('Gaussian', 'Lorentzian'): '_convolute_gaussian_lorentzian',
('Gaussian', 'Voigt'): '_convolute_gaussian_voigt',
@@ -38,44 +40,58 @@ class AnalyticalConvolution(ConvolutionBase):
def __init__(
self,
energy: np.ndarray | sc.Variable,
- energy_unit: str | sc.Unit = 'meV',
+ unit: str | sc.Unit = 'meV',
sample_components: ComponentCollection | ModelComponent | None = None,
resolution_components: ComponentCollection | ModelComponent | None = None,
energy_offset: Numeric | Parameter = 0.0,
+ display_name: str | None = 'MyConvolution',
+ unique_name: str | None = None,
) -> None:
- """Initialize an AnalyticalConvolution.
-
- Args:
- energy (np.ndarray | sc.Variable): 1D array of energy values
- where the convolution is evaluated.
- energy_unit (str | sc.Unit, default='meV'): The unit of the
- energy.
- sample_components (ComponentCollection | ModelComponent | None, default=None):
- The sample model to be convolved.
- resolution_components (ComponentCollection | ModelComponent | None, default=None):
- The resolution model to convolve with.
- energy_offset (Numeric | Parameter, default=0.0): An offset to
- shift the energy values by.
+ """
+ Initialize an AnalyticalConvolution.
+
+ Parameters
+ ----------
+ energy : np.ndarray | sc.Variable
+ 1D array of energy values where the convolution is evaluated.
+ unit : str | sc.Unit, default='meV'
+ The unit of the energy.
+ sample_components : ComponentCollection | ModelComponent | None, default=None
+ The sample model to be convolved.
+ resolution_components : ComponentCollection | ModelComponent | None, default=None
+ The resolution model to convolve with.
+ energy_offset : Numeric | Parameter, default=0.0
+ An offset to shift the energy values by.
+ display_name : str | None, default='MyConvolution'
+ Display name of the model.
+ unique_name : str | None, default=None
+ Unique name of the model. If None, a unique name will be generated.
"""
super().__init__(
energy=energy,
- energy_unit=energy_unit,
+ unit=unit,
sample_components=sample_components,
resolution_components=resolution_components,
energy_offset=energy_offset,
+ display_name=display_name,
+ unique_name=unique_name,
)
def convolution(
self,
) -> np.ndarray:
- """Convolve sample with resolution analytically if possible.
- Accepts ComponentCollection or single ModelComponent for each.
- Possible analytical convolutions are any combination of delta
- functions, Gaussians, Lorentzians and Voigt profiles.
-
- Returns:
- np.ndarray: The convolution of the sample_components and
- resolution_components values evaluated at self.energy.
+ """
+ Convolve sample with resolution analytically if possible.
+
+ Accepts ComponentCollection or single ModelComponent for each. Possible analytical
+ convolutions are any combination of delta functions, Gaussians, Lorentzians and Voigt
+ profiles.
+
+ Returns
+ -------
+ np.ndarray
+ The convolution of the sample_components and resolution_components values evaluated at
+ self.energy.
"""
sample_components = self.sample_components.components
@@ -100,48 +116,47 @@ def _convolute_analytic_pair(
sample_component: ModelComponent,
resolution_component: ModelComponent,
) -> np.ndarray:
- r"""Analytic convolution for component pair (sample_component,
- resolution_component).
+ r"""
+ Analytic convolution for component pair (sample_component, resolution_component).
- The convolution of two Gaussian components results in another
- Gaussian component with width $\sqrt{w_1^2 + w_2^2}$.
+ The convolution of two Gaussian components results in another Gaussian component with width
+ $\sqrt{w_1^2 + w_2^2}$.
- The convolution of two Lorentzian components results in another
- Lorentzian component with width $w_1 + w_2$.
+ The convolution of two Lorentzian components results in another Lorentzian component with
+ width $w_1 + w_2$.
- The convolution of a Gaussian and a Lorentzian results in a
- Voigt profile.
+ The convolution of a Gaussian and a Lorentzian results in a Voigt profile.
- The convolution of a Gaussian and a Voigt profile results in
- another Voigt profile, with the Lorentzian width unchanged and
- the Gaussian widths summed in quadrature.
+ The convolution of a Gaussian and a Voigt profile results in another Voigt profile, with
+ the Lorentzian width unchanged and the Gaussian widths summed in quadrature.
- The convolution of a Lorentzian and a Voigt profile results in
- another Voigt profile, with the Gaussian width unchanged and the
- Lorentzian widths summed.
+ The convolution of a Lorentzian and a Voigt profile results in another Voigt profile, with
+ the Gaussian width unchanged and the Lorentzian widths summed.
- The convolution of two Voigt profiles results in another Voigt
- profile, with the Gaussian widths summed in quadrature and the
- Lorentzian widths summed.
+ The convolution of two Voigt profiles results in another Voigt profile, with the Gaussian
+ widths summed in quadrature and the Lorentzian widths summed.
- The convolution of a delta function with any component or
- ComponentCollection results in the same component or
- ComponentCollection shifted by the delta center.
+ The convolution of a delta function with any component or ComponentCollection results in
+ the same component or ComponentCollection shifted by the delta center.
All areas are multiplied in the convolution.
- Args:
- sample_component (ModelComponent): The sample component to
- be convolved.
- resolution_component (ModelComponent): The resolution
- component to convolve with.
-
- Returns:
- np.ndarray: The convolution result
-
- Raises:
- ValueError: If the component pair cannot be handled
- analytically.
+ Parameters
+ ----------
+ sample_component : ModelComponent
+ The sample component to be convolved.
+ resolution_component : ModelComponent
+ The resolution component to convolve with.
+
+ Raises
+ ------
+ ValueError
+ If the component pair cannot be handled analytically.
+
+ Returns
+ -------
+ np.ndarray
+ The convolution result.
"""
if isinstance(resolution_component, DeltaFunction):
@@ -187,19 +202,22 @@ def _convolute_delta_any(
sample_component: DeltaFunction,
resolution_components: ComponentCollection | ModelComponent,
) -> np.ndarray:
- """Convolution of delta function with any ModelComponent or
- ComponentCollection results in the same component or
- ComponentCollection shifted by the delta center. The areas are
+ """
+ Convolution of delta function with any ModelComponent or ComponentCollection results in the
+ same component or ComponentCollection shifted by the delta center. The areas are
multiplied.
- Args:
- sample_component (DeltaFunction): The sample component to
- be convolved.
- resolution_components (ComponentCollection | ModelComponent)
- : The resolution model to convolve with.
-
- Returns:
- np.ndarray: The evaluated convolution values at self.energy.
+ Parameters
+ ----------
+ sample_component : DeltaFunction
+ The sample component to be convolved.
+ resolution_components : ComponentCollection | ModelComponent
+ : The resolution model to convolve with.
+
+ Returns
+ -------
+ np.ndarray
+ The evaluated convolution values at self.energy.
"""
return sample_component.area.value * resolution_components.evaluate(
self.energy_with_offset.values - sample_component.center.value
@@ -210,18 +228,21 @@ def _convolute_gaussian_gaussian(
sample_component: Gaussian,
resolution_component: Gaussian,
) -> np.ndarray:
- r"""Convolution of two Gaussian components results in another
- Gaussian component with width $\sqrt{w_1^2 + w_2^2}$. The areas
- are multiplied.
-
- Args:
- sample_component (Gaussian): The sample Gaussian component
- to be convolved.
- resolution_component (Gaussian): The resolution Gaussian
- component to convolve with.
-
- Returns:
- np.ndarray: The evaluated convolution values at self.energy.
+ r"""
+ Convolution of two Gaussian components results in another Gaussian component with width
+ $\sqrt{w_1^2 + w_2^2}$. The areas are multiplied.
+
+ Parameters
+ ----------
+ sample_component : Gaussian
+ The sample Gaussian component to be convolved.
+ resolution_component : Gaussian
+ The resolution Gaussian component to convolve with.
+
+ Returns
+ -------
+ np.ndarray
+ The evaluated convolution values at self.energy.
"""
width = np.sqrt(sample_component.width.value**2 + resolution_component.width.value**2)
@@ -237,17 +258,21 @@ def _convolute_gaussian_lorentzian(
sample_component: Gaussian,
resolution_component: Lorentzian,
) -> np.ndarray:
- """Convolution of a Gaussian and a Lorentzian results in a Voigt
- profile. The areas are multiplied.
-
- Args:
- sample_component (Gaussian): The sample Gaussian component
- to be convolved.
- resolution_component (Lorentzian): The resolution Lorentzian
- component to convolve with.
+ """
+ Convolution of a Gaussian and a Lorentzian results in a Voigt profile. The areas are
+ multiplied.
- Returns:
- np.ndarray: The evaluated convolution values at self.energy.
+ Parameters
+ ----------
+ sample_component : Gaussian
+ The sample Gaussian component to be convolved.
+ resolution_component : Lorentzian
+ The resolution Lorentzian component to convolve with.
+
+ Returns
+ -------
+ np.ndarray
+ The evaluated convolution values at self.energy.
"""
center = sample_component.center.value + resolution_component.center.value
area = sample_component.area.value * resolution_component.area.value
@@ -264,19 +289,22 @@ def _convolute_gaussian_voigt(
sample_component: Gaussian,
resolution_component: Voigt,
) -> np.ndarray:
- """Convolution of a Gaussian and a Voigt profile results in
- another Voigt profile. The Lorentzian width remains unchanged,
- while the Gaussian widths are summed in quadrature. The areas
- are multiplied.
-
- Args:
- sample_component (Gaussian): The sample Gaussian component
- to be convolved.
- resolution_component (Voigt): The resolution Voigt component
- to convolve with.
-
- Returns:
- np.ndarray: The evaluated convolution values at self.energy.
+ """
+ Convolution of a Gaussian and a Voigt profile results in another Voigt profile. The
+ Lorentzian width remains unchanged, while the Gaussian widths are summed in quadrature. The
+ areas are multiplied.
+
+ Parameters
+ ----------
+ sample_component : Gaussian
+ The sample Gaussian component to be convolved.
+ resolution_component : Voigt
+ The resolution Voigt component to convolve with.
+
+ Returns
+ -------
+ np.ndarray
+ The evaluated convolution values at self.energy.
"""
area = sample_component.area.value * resolution_component.area.value
@@ -300,18 +328,21 @@ def _convolute_lorentzian_lorentzian(
sample_component: Lorentzian,
resolution_component: Lorentzian,
) -> np.ndarray:
- r"""Convolution of two Lorentzian components results in another
- Lorentzian component with width $w_1 + w_2$. The areas are
- multiplied.
-
- Args:
- sample_component (Lorentzian): The sample Lorentzian
- component to be convolved.
- resolution_component (Lorentzian): The resolution Lorentzian
- component to convolve with.
-
- Returns:
- np.ndarray: The evaluated convolution values at self.energy.
+ r"""
+ Convolution of two Lorentzian components results in another Lorentzian component with width
+ $w_1 + w_2$. The areas are multiplied.
+
+ Parameters
+ ----------
+ sample_component : Lorentzian
+ The sample Lorentzian component to be convolved.
+ resolution_component : Lorentzian
+ The resolution Lorentzian component to convolve with.
+
+ Returns
+ -------
+ np.ndarray
+ The evaluated convolution values at self.energy.
"""
area = sample_component.area.value * resolution_component.area.value
@@ -326,21 +357,24 @@ def _convolute_lorentzian_voigt(
sample_component: Lorentzian,
resolution_component: Voigt,
) -> np.ndarray:
- """Convolution of a Lorentzian and a Voigt profile results in
- another Voigt profile.
+ """
+ Convolution of a Lorentzian and a Voigt profile results in another Voigt profile.
- The Gaussian width remains unchanged, while the Lorentzian
- widths are summed.
+ The Gaussian width remains unchanged, while the Lorentzian widths are summed.
The areas are multiplied.
- Args:
- sample_component (Lorentzian): The sample Lorentzian
- component to be convolved.
- resolution_component (Voigt): The resolution Voigt component
- to convolve with.
- Returns:
- np.ndarray: The evaluated convolution values at self.energy.
+ Parameters
+ ----------
+ sample_component : Lorentzian
+ The sample Lorentzian component to be convolved.
+ resolution_component : Voigt
+ The resolution Voigt component to convolve with.
+
+ Returns
+ -------
+ np.ndarray
+ The evaluated convolution values at self.energy.
"""
area = sample_component.area.value * resolution_component.area.value
@@ -364,21 +398,23 @@ def _convolute_voigt_voigt(
sample_component: Voigt,
resolution_component: Voigt,
) -> np.ndarray:
- """Convolution of two Voigt profiles results in another Voigt
- profile.
-
- The Gaussian widths are summed in quadrature,
- while the Lorentzian widths are summed.
- The areas are multiplied.
-
- Args:
- sample_component (Voigt): The sample Voigt component to be
- convolved.
- resolution_component (Voigt): The resolution Voigt component
- to convolve with.
-
- Returns:
- np.ndarray: The evaluated convolution values at self.energy.
+ """
+ Convolution of two Voigt profiles results in another Voigt profile.
+
+ The Gaussian widths are summed in quadrature, while the Lorentzian widths are summed. The
+ areas are multiplied.
+
+ Parameters
+ ----------
+ sample_component : Voigt
+ The sample Voigt component to be convolved.
+ resolution_component : Voigt
+ The resolution Voigt component to convolve with.
+
+ Returns
+ -------
+ np.ndarray
+ The evaluated convolution values at self.energy.
"""
area = sample_component.area.value * resolution_component.area.value
@@ -404,28 +440,29 @@ def _gaussian_eval(
center: float,
width: float,
) -> np.ndarray:
- r"""Evaluate a Gaussian function.
+ r"""
+ Evaluate a Gaussian function.
- $$
- I(x) = \frac{A}{\sigma \sqrt{2\pi}}
- \exp\left(
- -\frac{1}{2}
- \left(\frac{x - x_0}{\sigma}\right)^2
- \right)
- $$
+ $$ I(x) = \frac{A}{\sigma \sqrt{2\pi}} \exp\left( -\frac{1}{2} \left(\frac{x -
+ x_0}{\sigma}\right)^2 \right) $$
- where $A$ is the area, $x_0$ is the center, and $\sigma$ is the
- width.
+ where $A$ is the area, $x_0$ is the center, and $\sigma$ is the width.
All checks are handled in the calling function.
- Args:
- area (float): The area under the Gaussian curve.
- center (float): The center of the Gaussian.
- width (float): The width (sigma) of the Gaussian.
-
- Returns:
- np.ndarray: The evaluated Gaussian values at self.energy.
+ Parameters
+ ----------
+ area : float
+ The area under the Gaussian curve.
+ center : float
+ The center of the Gaussian.
+ width : float
+ The width (sigma) of the Gaussian.
+
+ Returns
+ -------
+ np.ndarray
+ The evaluated Gaussian values at self.energy.
"""
normalization = 1 / (np.sqrt(2 * np.pi) * width)
@@ -437,22 +474,26 @@ def _lorentzian_eval(self, area: float, center: float, width: float) -> np.ndarr
r"""
Evaluate a Lorentzian function.
- $$
- I(x) = \frac{A}{\\pi} \frac{\Gamma}{(x - x_0)^2 + \Gamma^2},
- $$
+ $$ I(x) = \frac{A}{\\pi} \frac{\Gamma}{(x - x_0)^2 + \Gamma^2}, $$
- where $A$ is the area, $x_0$ is the center, and $\\Gamma$ is
- the half width at half maximum (HWHM).
+ where $A$ is the area, $x_0$ is the center, and $\\Gamma$ is the half width at half maximum
+ (HWHM).
All checks are handled in the calling function.
- Args:
- area (float): The area under the Lorentzian.
- center (float): The center of the Lorentzian.
- width (float): The width (HWHM) of the Lorentzian.
-
- Returns:
- np.ndarray: The evaluated Lorentzian values at self.energy.
+ Parameters
+ ----------
+ area : float
+ The area under the Lorentzian.
+ center : float
+ The center of the Lorentzian.
+ width : float
+ The width (HWHM) of the Lorentzian.
+
+ Returns
+ -------
+ np.ndarray
+ The evaluated Lorentzian values at self.energy.
"""
normalization = width / np.pi
@@ -467,20 +508,24 @@ def _voigt_eval(
gaussian_width: float,
lorentzian_width: float,
) -> np.ndarray:
- """Evaluate a Voigt profile function using scipy's
- voigt_profile.
-
- Args:
- area (float): The area under the Voigt profile.
- center (float): The center of the Voigt profile.
- gaussian_width (float): The Gaussian width (sigma) of the
- Voigt profile.
- lorentzian_width (float): The Lorentzian width (HWHM) of the
- Voigt profile.
-
- Returns:
- np.ndarray: The evaluated Voigt profile values at
- self.energy.
+ """
+ Evaluate a Voigt profile function using scipy's voigt_profile.
+
+ Parameters
+ ----------
+ area : float
+ The area under the Voigt profile.
+ center : float
+ The center of the Voigt profile.
+ gaussian_width : float
+ The Gaussian width (sigma) of the Voigt profile.
+ lorentzian_width : float
+ The Lorentzian width (HWHM) of the Voigt profile.
+
+ Returns
+ -------
+ np.ndarray
+ The evaluated Voigt profile values at self.energy.
"""
return area * voigt_profile(
diff --git a/src/easydynamics/convolution/convolution.py b/src/easydynamics/convolution/convolution.py
index 3f3f1ef3..63bd66c6 100644
--- a/src/easydynamics/convolution/convolution.py
+++ b/src/easydynamics/convolution/convolution.py
@@ -1,6 +1,8 @@
# SPDX-FileCopyrightText: 2026 EasyScience contributors
# SPDX-License-Identifier: BSD-3-Clause
+from typing import ClassVar
+
import numpy as np
import scipp as sc
from easyscience.variable import Parameter
@@ -14,38 +16,37 @@
from easydynamics.sample_model import Lorentzian
from easydynamics.sample_model import Voigt
from easydynamics.sample_model.components.model_component import ModelComponent
+from easydynamics.settings.convolution_settings import ConvolutionSettings
+from easydynamics.settings.detailed_balance_settings import DetailedBalanceSettings
from easydynamics.utils.utils import Numeric
class Convolution(NumericalConvolutionBase):
- """Convolution class that combines analytical and numerical
- convolution methods to efficiently perform convolutions of
- ComponentCollections with ResolutionComponents.
-
- Supports analytical convolution for pairs of analytical model
- components (DeltaFunction, Gaussian, Lorentzian, Voigt), while using
- numerical convolution for other components. If temperature is
- provided, detailed balance correction is applied to the sample
- model. In this case, all convolutions are handled numerically.
- Includes a setting to normalize the detailed balance correction.
- Includes optional upsampling and extended range to improve accuracy
- of the numerical convolutions. Also warns about numerical
- instabilities if peaks are very wide or very narrow.
+ """
+ Convolution class that combines analytical and numerical convolution methods to efficiently
+ perform convolutions of ComponentCollections with ResolutionComponents.
+
+ Supports analytical convolution for pairs of analytical model components (DeltaFunction,
+ Gaussian, Lorentzian, Voigt), while using numerical convolution for other components. If
+ temperature is provided, detailed balance correction is applied to the sample model. In this
+ case, all convolutions are handled numerically. Includes a setting to normalize the detailed
+ balance correction. Includes optional upsampling and extended range to improve accuracy of the
+ numerical convolutions. Also warns about numerical instabilities if peaks are very wide or very
+ narrow.
"""
# When these attributes are changed, the convolution plan
# needs to be rebuilt
- _invalidate_plan_on_change = {
+ _invalidate_plan_on_change: ClassVar[dict[str, object]] = {
'energy',
'_energy',
'_energy_grid',
'_sample_components',
'_resolution_components',
'_temperature',
- '_upsample_factor',
- '_extension_factor',
'_energy_unit',
'_normalize_detailed_balance',
+ '_detailed_balance_settings',
}
def __init__(
@@ -54,75 +55,78 @@ def __init__(
sample_components: ComponentCollection | ModelComponent,
resolution_components: ComponentCollection | ModelComponent,
energy_offset: Numeric | Parameter = 0.0,
- upsample_factor: Numeric | None = 5,
- extension_factor: Numeric | None = 0.2,
+ convolution_settings: ConvolutionSettings | None = None,
temperature: Parameter | Numeric | None = None,
temperature_unit: str | sc.Unit = 'K',
- energy_unit: str | sc.Unit = 'meV',
- normalize_detailed_balance: bool = True,
+ detailed_balance_settings: DetailedBalanceSettings | None = None,
+ unit: str | sc.Unit = 'meV',
+ display_name: str | None = 'MyConvolution',
+ unique_name: str | None = None,
) -> None:
- """Initialize the Convolution class.
-
- Args:
- energy (np.ndarray | sc.Variable): 1D array of energy
- values where the convolution is evaluated.
- sample_components (ComponentCollection | ModelComponent):
- The sample components to be convolved.
- resolution_components (ComponentCollection | ModelComponent):
- The resolution components to convolve with.
- energy_offset (Numeric | Parameter, default=0.0): An energy
- offset to apply to the energy values before convolution.
- upsample_factor (Numeric | None, default=5): The factor by which to
- upsample the input data before convolution. Default is
- 5.
- extension_factor (Numeric | None, default=0.2): The factor by which to
- extend the input data range before convolution. Default
- is 0.2.
- temperature (Parameter | Numeric | None, default=None): The
- temperature to use for detailed balance correction.
- Default is None.
- temperature_unit (str | sc.Unit, default='K'): The unit of the
- temperature parameter. Default is 'K'.
- energy_unit (str | sc.Unit, default='meV'): The unit of the energy.
- Default is 'meV'.
- normalize_detailed_balance (bool, default=True): Whether to
- normalize the detailed balance correction. Default is
- True.
+ """
+ Initialize the Convolution class.
+
+ Parameters
+ ----------
+ energy : np.ndarray | sc.Variable
+ 1D array of energy values where the convolution is evaluated.
+ sample_components : ComponentCollection | ModelComponent
+ The sample components to be convolved.
+ resolution_components : ComponentCollection | ModelComponent
+ The resolution components to convolve with.
+ energy_offset : Numeric | Parameter, default=0.0
+ An energy offset to apply to the energy values before convolution.
+ convolution_settings : ConvolutionSettings | None, default=None
+ The settings for the convolution. If None, default settings will be used.
+ temperature : Parameter | Numeric | None, default=None
+ The temperature to use for detailed balance correction.
+ temperature_unit : str | sc.Unit, default='K'
+ The unit of the temperature parameter.
+ detailed_balance_settings : DetailedBalanceSettings | None, default=None
+ The settings for detailed balance. If None, default settings will be used.
+ unit : str | sc.Unit, default='meV'
+ The unit of the energy.
+ display_name : str | None, default='MyConvolution'
+ Display name of the model.
+ unique_name : str | None, default=None
+ Unique name of the model. If None, a unique name will be generated.
"""
- self._convolution_plan_is_valid = False
self._reactions_enabled = False
super().__init__(
energy=energy,
sample_components=sample_components,
resolution_components=resolution_components,
energy_offset=energy_offset,
- upsample_factor=upsample_factor,
- extension_factor=extension_factor,
+ convolution_settings=convolution_settings,
temperature=temperature,
temperature_unit=temperature_unit,
- energy_unit=energy_unit,
- normalize_detailed_balance=normalize_detailed_balance,
+ detailed_balance_settings=detailed_balance_settings,
+ unit=unit,
+ display_name=display_name,
+ unique_name=unique_name,
)
self._reactions_enabled = True
# Separate sample model components into pairs that can be
# handled analytically, delta functions, and the rest
- # Also initialize analytical and numerical convolvers based on s
- # ample model component
+ # Also initialize analytical and numerical convolvers based on
+ # sample model component
self._build_convolution_plan()
def convolution(
self,
) -> np.ndarray:
- """Perform convolution using analytical convolutions where
- possible, and numerical convolutions for the remaining
- components.
+ """
+ Perform convolution using analytical convolutions where possible, and numerical
+ convolutions for the remaining components.
- Returns:
- np.ndarray: The convolved values evaluated at energy.
+ Returns
+ -------
+ np.ndarray
+ The convolved values evaluated at energy.
"""
- if not self._convolution_plan_is_valid:
+ if not self.convolution_settings.convolution_plan_is_valid:
self._build_convolution_plan()
total = np.zeros_like(self.energy.values, dtype=float)
@@ -141,13 +145,14 @@ def convolution(
return total
def _convolve_delta_functions(self) -> np.ndarray:
- """Convolve delta function components of the sample model with
- the resolution components. No detailed balance correction is
- applied to delta functions.
+ """
+ Convolve delta function components of the sample model with the resolution components. No
+ detailed balance correction is applied to delta functions.
- Returns:
- np.ndarray: The convolved values of the delta function c
- components evaluated at energy.
+ Returns
+ -------
+ np.ndarray
+ The convolved values of the delta function c components evaluated at energy.
"""
return sum(
delta.area.value
@@ -162,22 +167,26 @@ def _check_if_pair_is_analytic(
sample_component: ModelComponent,
resolution_component: ModelComponent,
) -> bool:
- """Check if the convolution of the given component pair can be
- handled analytically.
-
- Args:
- sample_component (ModelComponent): The sample component to
- be convolved.
- resolution_component (ModelComponent): The resolution
- component to convolve with.
-
- Returns:
- bool: True if the component pair can be handled
- analytically, False otherwise.
-
- Raises:
- TypeError: If either component is not a ModelComponent, or if
- the resolution component is a DeltaFunction.
+ """
+ Check if the convolution of the given component pair can be handled analytically.
+
+ Parameters
+ ----------
+ sample_component : ModelComponent
+ The sample component to be convolved.
+ resolution_component : ModelComponent
+ The resolution component to convolve with.
+
+ Raises
+ ------
+ TypeError
+ If either component is not a ModelComponent, or if the resolution component is a
+ DeltaFunction.
+
+ Returns
+ -------
+ bool
+ True if the component pair can be handled analytically, False otherwise.
"""
if not isinstance(sample_component, ModelComponent):
@@ -204,8 +213,8 @@ def _check_if_pair_is_analytic(
)
def _build_convolution_plan(self) -> None:
- """Separate sample model components into analytical pairs, delta
- functions, and the rest.
+ """
+ Separate sample model components into analytical pairs, delta functions, and the rest.
"""
analytical_sample_components = ComponentCollection()
@@ -221,18 +230,20 @@ def _build_convolution_plan(self) -> None:
# If temperature is set, all other components go to
# numerical sample model
- if self.temperature is not None:
+ if (
+ self.temperature is not None
+ and self.detailed_balance_settings.use_detailed_balance
+ ):
numerical_sample_components.append_component(sample_component)
continue
# If temperature is not set, check if all
# resolution components can be convolved analytically with
# this sample component
- pair_is_analytic = []
- for resolution_component in self._resolution_components.components:
- pair_is_analytic.append(
- self._check_if_pair_is_analytic(sample_component, resolution_component)
- )
+ pair_is_analytic = [
+ self._check_if_pair_is_analytic(sample_component, resolution_component)
+ for resolution_component in self._resolution_components.components
+ ]
# If all resolution components can be convolved analytically
# with this sample component, add it to analytical
# sample model. If not, it goes to numerical sample model.
@@ -244,17 +255,17 @@ def _build_convolution_plan(self) -> None:
self._analytical_sample_components = analytical_sample_components
self._delta_sample_components = delta_sample_components
self._numerical_sample_components = numerical_sample_components
- self._convolution_plan_is_valid = True
# Update convolvers
self._set_convolvers()
+ self.convolution_settings.convolution_plan_is_valid = True
def _set_convolvers(self) -> None:
- """Initialize analytical and numerical convolvers based on
- sample model components.
+ """
+ Initialize analytical and numerical convolvers based on sample model components.
- There is no delta function convolver, as delta functions are
- handled directly in the convolution method.
+ There is no delta function convolver, as delta functions are handled directly in the
+ convolution method.
"""
if self._analytical_sample_components.components:
@@ -273,31 +284,34 @@ def _set_convolvers(self) -> None:
energy_offset=self.energy_offset,
sample_components=self._numerical_sample_components,
resolution_components=self._resolution_components,
- upsample_factor=self.upsample_factor,
- extension_factor=self.extension_factor,
+ convolution_settings=self.convolution_settings,
temperature=self.temperature,
temperature_unit=self._temperature_unit,
- normalize_detailed_balance=self.normalize_detailed_balance,
+ detailed_balance_settings=self.detailed_balance_settings,
+ unit=self.unit,
)
else:
self._numerical_convolver = None
# Update some setters so the internal sample models are updated
def __setattr__(self, name: str, value: any) -> None:
- """Custom setattr to invalidate convolution plan on relevant
- attribute changes, and build a new plan.
-
- The new plan is only built after initialization (when
- _reactions_enabled is True) to avoid issues during __init__.
-
- Args:
- name (str): The name of the attribute to set.
- value (any): The value to set the attribute to.
+ """
+ Custom setattr to invalidate convolution plan on relevant attribute changes, and build a
+ new plan.
+
+ The new plan is only built after initialization (when _reactions_enabled is True) to avoid
+ issues during __init__.
+
+ Parameters
+ ----------
+ name : str
+ The name of the attribute to set.
+ value : any
+ The value to set the attribute to.
"""
super().__setattr__(name, value)
- if name in self._invalidate_plan_on_change:
- self._convolution_plan_is_valid = False
-
+ # Only rebuild the convolution plan if reactions are enabled, to
+ # avoid issues during __init__
if getattr(self, '_reactions_enabled', False) and name in self._invalidate_plan_on_change:
- self._build_convolution_plan()
+ self.convolution_settings.convolution_plan_is_valid = False
diff --git a/src/easydynamics/convolution/convolution_base.py b/src/easydynamics/convolution/convolution_base.py
index 3037c649..dd98d5e9 100644
--- a/src/easydynamics/convolution/convolution_base.py
+++ b/src/easydynamics/convolution/convolution_base.py
@@ -5,13 +5,15 @@
import scipp as sc
from easyscience.variable import Parameter
+from easydynamics.base_classes import EasyDynamicsModelBase
from easydynamics.sample_model.component_collection import ComponentCollection
from easydynamics.sample_model.components.model_component import ModelComponent
from easydynamics.utils.utils import Numeric
-class ConvolutionBase:
- """Base class for convolutions of sample and resolution models.
+class ConvolutionBase(EasyDynamicsModelBase):
+ """
+ Base class for convolutions of sample and resolution models.
This base class has no convolution functionality.
"""
@@ -21,52 +23,62 @@ def __init__(
energy: np.ndarray | sc.Variable,
sample_components: ComponentCollection | ModelComponent | None = None,
resolution_components: ComponentCollection | ModelComponent | None = None,
- energy_unit: str | sc.Unit = 'meV',
+ unit: str | sc.Unit = 'meV',
energy_offset: Numeric | Parameter = 0.0,
+ display_name: str | None = 'MyConvolution',
+ unique_name: str | None = None,
) -> None:
- """Initialize the ConvolutionBase.
-
- Args:
- energy (np.ndarray | sc.Variable): 1D array of energy
- values where the convolution is evaluated.
- sample_components (ComponentCollection | ModelComponent | None, default=None):
- The sample model to be convolved.
- resolution_components (ComponentCollection | ModelComponent | None, default=None):
- The resolution model to convolve with.
- energy_unit (str | sc.Unit, default='meV'): The unit of the
- energy.
- energy_offset (Numeric | Parameter, default=0.0): The energy
- offset applied to the convolution. Default is 0.0.
-
- Raises:
- TypeError: If energy is not a numpy ndarray or a scipp
- Variable or if energy_unit is not a string or scipp unit, or if
- energy_offset is not a number or a Parameter, or if
- sample_components is not a ComponentCollection or ModelComponent, or if
- resolution_components is not a ComponentCollection or ModelComponent.
"""
+ Initialize the ConvolutionBase.
+
+ Parameters
+ ----------
+ energy : np.ndarray | sc.Variable
+ 1D array of energy values where the convolution is evaluated.
+ sample_components : ComponentCollection | ModelComponent | None, default=None
+ The sample model to be convolved.
+ resolution_components : ComponentCollection | ModelComponent | None, default=None
+ The resolution model to convolve with.
+ unit : str | sc.Unit, default='meV'
+ The unit of the energy.
+ energy_offset : Numeric | Parameter, default=0.0
+ The energy offset applied to the convolution.
+ display_name : str | None, default='MyConvolution'
+ Display name of the model.
+ unique_name : str | None, default=None
+ Unique name of the model. If None, a unique name will be generated.
+
+ Raises
+ ------
+ TypeError
+ If energy is not a numpy ndarray or a scipp Variable or if energy_unit is not a string
+ or scipp unit, or if energy_offset is not a number or a Parameter, or if
+ sample_components is not a ComponentCollection or ModelComponent, or if
+ resolution_components is not a ComponentCollection or ModelComponent.
+ """
+
+ super().__init__(
+ unit=unit,
+ display_name=display_name,
+ unique_name=unique_name,
+ )
+
if isinstance(energy, Numeric):
energy = np.array([float(energy)])
if not isinstance(energy, (np.ndarray, sc.Variable)):
raise TypeError(f'Energy must be a numpy ndarray or a scipp Variable. Got {energy}')
- if not isinstance(energy_unit, (str, sc.Unit)):
- raise TypeError('Energy_unit must be a string or sc.Unit.')
-
if isinstance(energy, np.ndarray):
- energy = sc.array(dims=['energy'], values=energy, unit=energy_unit)
+ energy = sc.array(dims=['energy'], values=energy, unit=unit)
if isinstance(energy_offset, Numeric):
- energy_offset = Parameter(
- name='energy_offset', value=float(energy_offset), unit=energy_unit
- )
+ energy_offset = Parameter(name='energy_offset', value=float(energy_offset), unit=unit)
if not isinstance(energy_offset, Parameter):
raise TypeError('Energy_offset must be a number or a Parameter.')
self._energy = energy
- self._energy_unit = energy_unit
self._energy_offset = energy_offset
if sample_components is not None and not (
@@ -91,23 +103,30 @@ def __init__(
@property
def energy_offset(self) -> Parameter:
- """Get the energy offset.
+ """
+ Get the energy offset.
- Returns:
- Parameter: The energy offset applied to the convolution.
+ Returns
+ -------
+ Parameter
+ The energy offset applied to the convolution.
"""
return self._energy_offset
@energy_offset.setter
def energy_offset(self, energy_offset: Numeric | Parameter) -> None:
- """Set the energy offset.
+ """
+ Set the energy offset.
- Args:
- energy_offset (Numeric | Parameter): The energy offset to
- apply to the convolution.
+ Parameters
+ ----------
+ energy_offset : Numeric | Parameter
+ The energy offset to apply to the convolution.
- Raises:
- TypeError: If energy_offset is not a number or a Parameter.
+ Raises
+ ------
+ TypeError
+ If energy_offset is not a number or a Parameter.
"""
if not isinstance(energy_offset, Parameter | Numeric):
raise TypeError('Energy_offset must be a number or a Parameter.')
@@ -120,10 +139,13 @@ def energy_offset(self, energy_offset: Numeric | Parameter) -> None:
@property
def energy_with_offset(self) -> sc.Variable:
- """Get the energy with the offset applied.
+ """
+ Get the energy with the offset applied.
- Returns:
- sc.Variable: The energy values with the offset applied.
+ Returns
+ -------
+ sc.Variable
+ The energy values with the offset applied.
"""
energy_with_offset = self.energy.copy()
energy_with_offset.values = self.energy.values - self.energy_offset.value
@@ -131,15 +153,18 @@ def energy_with_offset(self) -> sc.Variable:
@energy_with_offset.setter
def energy_with_offset(self, _value: sc.Variable) -> None:
- """Energy with offset is a read-only property derived from
- energy and energy_offset.
+ """
+ Energy with offset is a read-only property derived from energy and energy_offset.
- Args:
- _value (sc.Variable): The value to set (ignored).
+ Parameters
+ ----------
+ _value : sc.Variable
+ The value to set (ignored).
- Raises:
- AttributeError: Always raised since energy_with_offset is
- read-only.
+ Raises
+ ------
+ AttributeError
+ Always raised since energy_with_offset is read-only.
"""
raise AttributeError(
'Energy with offset is a read-only property derived from energy and energy_offset.'
@@ -147,26 +172,31 @@ def energy_with_offset(self, _value: sc.Variable) -> None:
@property
def energy(self) -> sc.Variable:
- """Get the energy.
+ """
+ Get the energy.
- Returns:
- sc.Variable: The energy values where the convolution is
- evaluated.
+ Returns
+ -------
+ sc.Variable
+ The energy values where the convolution is evaluated.
"""
return self._energy
@energy.setter
def energy(self, energy: np.ndarray | sc.Variable) -> None:
- """Set the energy.
+ """
+ Set the energy.
- Args:
- energy (np.ndarray | sc.Variable): 1D array of energy
- values where the convolution is evaluated.
+ Parameters
+ ----------
+ energy : np.ndarray | sc.Variable
+ 1D array of energy values where the convolution is evaluated.
- Raises:
- TypeError: If energy is not a numpy ndarray or a
- scipp Variable.
+ Raises
+ ------
+ TypeError
+ If energy is not a numpy ndarray or a scipp Variable.
"""
if isinstance(energy, Numeric):
@@ -180,75 +210,69 @@ def energy(self, energy: np.ndarray | sc.Variable) -> None:
if isinstance(energy, sc.Variable):
self._energy = energy
- self._energy_unit = energy.unit
+ self._unit = energy.unit
- @property
- def energy_unit(self) -> str:
- """Get the energy unit.
-
- Returns:
- str: The unit of the energy.
+ def convert_unit(self, unit: str | sc.Unit) -> None:
"""
- return self._energy_unit
-
- @energy_unit.setter
- def energy_unit(self, _unit_str: str) -> None:
- raise AttributeError(
- f'Unit is read-only. Use convert_unit to change the unit between allowed types '
- f'or create a new {self.__class__.__name__} with the desired unit.'
- ) # noqa: E501
-
- def convert_energy_unit(self, energy_unit: str | sc.Unit) -> None:
- """Convert the energy and energy_offset to the specified unit.
-
- Args:
- energy_unit (str | sc.Unit): The unit of the energy.
-
- Raises:
- TypeError: If energy_unit is not a string or scipp unit.
- Exception: If energy cannot be converted to the specified
- unit.
+ Convert the energy and energy_offset to the specified unit.
+
+ Parameters
+ ----------
+ unit : str | sc.Unit
+ The unit of the energy.
+
+ Raises
+ ------
+ TypeError
+ If unit is not a string or scipp unit.
+ Exception
+ If energy cannot be converted to the specified unit.
"""
- if not isinstance(energy_unit, (str, sc.Unit)):
+ if not isinstance(unit, (str, sc.Unit)):
raise TypeError('Energy unit must be a string or scipp unit.')
old_energy = self.energy.copy()
try:
- self.energy = sc.to_unit(self.energy, energy_unit)
+ self.energy = sc.to_unit(self.energy, unit)
except Exception as e:
self.energy = old_energy
raise e
old_energy_offset = self.energy_offset
try:
- self.energy_offset.convert_unit(energy_unit)
+ self.energy_offset.convert_unit(unit)
except Exception as e:
self.energy_offset = old_energy_offset
raise e
- self._energy_unit = energy_unit
+ self._unit = unit
@property
def sample_components(self) -> ComponentCollection | ModelComponent:
- """Get the sample model.
+ """
+ Get the sample model.
- Returns:
- ComponentCollection | ModelComponent: The sample model to
- be convolved.
+ Returns
+ -------
+ ComponentCollection | ModelComponent
+ The sample model to be convolved.
"""
return self._sample_components
@sample_components.setter
def sample_components(self, sample_components: ComponentCollection | ModelComponent) -> None:
- """Set the sample model.
+ """
+ Set the sample model.
- Args:
- sample_components (ComponentCollection | ModelComponent):
- The sample model to be convolved.
+ Parameters
+ ----------
+ sample_components : ComponentCollection | ModelComponent
+ The sample model to be convolved.
- Raises:
- TypeError: If sample_components is not a ComponentCollection
- or ModelComponent.
+ Raises
+ ------
+ TypeError
+ If sample_components is not a ComponentCollection or ModelComponent.
"""
if not isinstance(sample_components, (ComponentCollection, ModelComponent)):
raise TypeError(
@@ -261,11 +285,13 @@ def sample_components(self, sample_components: ComponentCollection | ModelCompon
@property
def resolution_components(self) -> ComponentCollection | ModelComponent:
- """Get the resolution model.
+ """
+ Get the resolution model.
- Returns:
- ComponentCollection | ModelComponent: The resolution model
- to be convolved.
+ Returns
+ -------
+ ComponentCollection | ModelComponent
+ The resolution model to be convolved.
"""
return self._resolution_components
@@ -273,16 +299,19 @@ def resolution_components(self) -> ComponentCollection | ModelComponent:
def resolution_components(
self, resolution_components: ComponentCollection | ModelComponent
) -> None:
- """Set the resolution model.
-
- Args:
- resolution_components (ComponentCollection | ModelComponent):
- The resolution model to be convolved. Can be a
- ComponentCollection or a single ModelComponent
-
- Raises:
- TypeError: If resolution_components is not a
- ComponentCollection or ModelComponent.
+ """
+ Set the resolution model.
+
+ Parameters
+ ----------
+ resolution_components : ComponentCollection | ModelComponent
+ The resolution model to be convolved. Can be a ComponentCollection or a single
+ ModelComponent.
+
+ Raises
+ ------
+ TypeError
+ If resolution_components is not a ComponentCollection or ModelComponent.
"""
if not isinstance(resolution_components, (ComponentCollection, ModelComponent)):
raise TypeError(
diff --git a/src/easydynamics/convolution/energy_grid.py b/src/easydynamics/convolution/energy_grid.py
index 645a605b..0722aa59 100644
--- a/src/easydynamics/convolution/energy_grid.py
+++ b/src/easydynamics/convolution/energy_grid.py
@@ -8,20 +8,21 @@
@dataclass(frozen=True)
class EnergyGrid:
- """Container for the dense energy grid and related metadata.
+ """
+ Container for the dense energy grid and related metadata.
- Attributes:
- energy_dense (np.ndarray): The upsampled and extended energy
- array.
- energy_dense_centered (np.ndarray): The centered version of
- energy_dense (used for resolution evaluation).
- energy_dense_step (float): The spacing of energy_dense
- (used for width checks and normalization).
- energy_span_dense (float): The total span of energy_dense.
- (used for width checks).
- energy_even_length_offset (float): The offset to apply if
- energy_dense has even length (used for convolution
- alignment).
+ Attributes
+ ----------
+ energy_dense : np.ndarray
+ The upsampled and extended energy array.
+ energy_dense_centered : np.ndarray
+ The centered version of energy_dense (used for resolution evaluation).
+ energy_dense_step : float
+ The spacing of energy_dense (used for width checks and normalization).
+ energy_span_dense : float
+ The total span of energy_dense. (used for width checks).
+ energy_even_length_offset : float
+ The offset to apply if energy_dense has even length (used for convolution alignment).
"""
energy_dense: np.ndarray
diff --git a/src/easydynamics/convolution/numerical_convolution.py b/src/easydynamics/convolution/numerical_convolution.py
index 10a55c81..7a990d37 100644
--- a/src/easydynamics/convolution/numerical_convolution.py
+++ b/src/easydynamics/convolution/numerical_convolution.py
@@ -9,18 +9,19 @@
from easydynamics.convolution.numerical_convolution_base import NumericalConvolutionBase
from easydynamics.sample_model.component_collection import ComponentCollection
from easydynamics.sample_model.components.model_component import ModelComponent
+from easydynamics.settings.convolution_settings import ConvolutionSettings
+from easydynamics.settings.detailed_balance_settings import DetailedBalanceSettings
from easydynamics.utils.detailed_balance import detailed_balance_factor
from easydynamics.utils.utils import Numeric
class NumericalConvolution(NumericalConvolutionBase):
- """Numerical convolution of a ComponentCollection with a
- ComponentCollection using FFT.
+ """
+ Numerical convolution of a ComponentCollection with a ComponentCollection using FFT.
- Includes optional upsampling and extended range to improve accuracy.
- Warns about very wide or very narrow peaks in the models. If
- temperature is provided, detailed balance correction is applied to
- the sample model.
+ Includes optional upsampling and extended range to improve accuracy. Warns about very wide or
+ very narrow peaks in the models. If temperature is provided, detailed balance correction is
+ applied to the sample model.
"""
def __init__(
@@ -29,62 +30,72 @@ def __init__(
sample_components: ComponentCollection | ModelComponent,
resolution_components: ComponentCollection | ModelComponent,
energy_offset: Numeric | Parameter = 0.0,
- upsample_factor: Numeric | None = 5,
- extension_factor: Numeric | None = 0.2,
+ convolution_settings: ConvolutionSettings | None = None,
temperature: Parameter | Numeric | None = None,
temperature_unit: str | sc.Unit = 'K',
- energy_unit: str | sc.Unit = 'meV',
- normalize_detailed_balance: bool = True,
+ detailed_balance_settings: DetailedBalanceSettings | None = None,
+ unit: str | sc.Unit = 'meV',
+ display_name: str | None = 'MyConvolution',
+ unique_name: str | None = None,
) -> None:
- """Initialize the NumericalConvolution object.
-
- Args:
- energy (np.ndarray | sc.Variable): 1D array of energy values
- where the convolution is evaluated.
- sample_components (ComponentCollection | ModelComponent):
- The sample model to be convolved.
- resolution_components (ComponentCollection | ModelComponent):
- The resolution model to convolve with.
- energy_offset (Numeric | Parameter, default=0.0): An energy
- offset to apply to the energy values before convolution.
- upsample_factor (Numeric | None, default=5): The factor by which to
- upsample the input data before convolution.
- extension_factor (Numeric | None, default=0.2): The factor by which to
- extend the input data range before convolution.
- temperature (Parameter | Numeric | None, default=None): The
- temperature to use for detailed balance correction.
- Default is None.
- temperature_unit (str | sc.Unit, default='K'): The unit of the
- temperature parameter.
- energy_unit (str | sc.Unit, default='meV'): The unit of the
- energy. Default is 'meV'.
- normalize_detailed_balance (bool, default=True): Whether to
- normalize the detailed balance correction. Default is
- True.
+ """
+ Initialize the NumericalConvolution object.
+
+ Parameters
+ ----------
+ energy : np.ndarray | sc.Variable
+ 1D array of energy values where the convolution is evaluated.
+ sample_components : ComponentCollection | ModelComponent
+ The sample model to be convolved.
+ resolution_components : ComponentCollection | ModelComponent
+ The resolution model to convolve with.
+ energy_offset : Numeric | Parameter, default=0.0
+ An energy offset to apply to the energy values before convolution.
+ convolution_settings : ConvolutionSettings | None, default=None
+ The settings for the convolution.
+ temperature : Parameter | Numeric | None, default=None
+ The temperature to use for detailed balance correction.
+ temperature_unit : str | sc.Unit, default='K'
+ The unit of the temperature parameter.
+ detailed_balance_settings : DetailedBalanceSettings | None, default=None
+ The settings for detailed balance. If None, default settings will be used.
+ unit : str | sc.Unit, default='meV'
+ The unit of the energy.
+ display_name : str | None, default='MyConvolution'
+ Display name of the model.
+ unique_name : str | None, default=None
+ Unique name of the model. If None, a unique name will be generated.
"""
super().__init__(
energy=energy,
sample_components=sample_components,
resolution_components=resolution_components,
energy_offset=energy_offset,
- upsample_factor=upsample_factor,
- extension_factor=extension_factor,
+ convolution_settings=convolution_settings,
temperature=temperature,
temperature_unit=temperature_unit,
- energy_unit=energy_unit,
- normalize_detailed_balance=normalize_detailed_balance,
+ detailed_balance_settings=detailed_balance_settings,
+ unit=unit,
+ display_name=display_name,
+ unique_name=unique_name,
)
def convolution(
self,
) -> np.ndarray:
- """Calculate the convolution of the sample and resolution models
- at the values given in energy. Includes detailed balance
- correction if temperature is provided.
+ """
+ Calculate the convolution of the sample and resolution models at the values given in
+ energy. Includes detailed balance correction if temperature is provided.
- Returns:
- np.ndarray: The convolved values evaluated at energy.
+ Returns
+ -------
+ np.ndarray
+ The convolved values evaluated at energy.
"""
+ # Make sure the convolver is updated with the latest convolution
+ # settings before convolution.
+ if not self.convolution_settings.convolution_plan_is_valid:
+ self._energy_grid = self._create_energy_grid()
# Give warnings if peaks are very wide or very narrow
self._check_width_thresholds(
@@ -105,12 +116,12 @@ def convolution(
)
# Detailed balance correction
- if self.temperature is not None:
+ if self.temperature is not None and self.detailed_balance_settings.use_detailed_balance:
detailed_balance_factor_correction = detailed_balance_factor(
energy=self._energy_grid.energy_dense - self.energy_offset.value,
temperature=self.temperature,
energy_unit=self.energy.unit,
- divide_by_temperature=self.normalize_detailed_balance,
+ divide_by_temperature=self.detailed_balance_settings.normalize_detailed_balance,
)
sample_vals *= detailed_balance_factor_correction
diff --git a/src/easydynamics/convolution/numerical_convolution_base.py b/src/easydynamics/convolution/numerical_convolution_base.py
index ccbdea57..7001e32b 100644
--- a/src/easydynamics/convolution/numerical_convolution_base.py
+++ b/src/easydynamics/convolution/numerical_convolution_base.py
@@ -3,7 +3,6 @@
import warnings
-# from dataclasses import dataclass
import numpy as np
import scipp as sc
from easyscience.variable import Parameter
@@ -12,6 +11,8 @@
from easydynamics.convolution.energy_grid import EnergyGrid
from easydynamics.sample_model.component_collection import ComponentCollection
from easydynamics.sample_model.components.model_component import ModelComponent
+from easydynamics.settings.convolution_settings import ConvolutionSettings
+from easydynamics.settings.detailed_balance_settings import DetailedBalanceSettings
from easydynamics.utils.utils import Numeric
# The thresholds are illustrated in
@@ -25,12 +26,11 @@
class NumericalConvolutionBase(ConvolutionBase):
- """Base class for numerical convolutions of sample and resolution
- models.
+ """
+ Base class for numerical convolutions of sample and resolution models.
- Provides methods to handle upsampling, extension, and detailed
- balance correction. This base class has no convolution
- functionality.
+ Provides methods to handle upsampling, extension, and detailed balance correction. This base
+ class has no convolution functionality.
"""
def __init__(
@@ -39,48 +39,56 @@ def __init__(
sample_components: ComponentCollection | ModelComponent,
resolution_components: ComponentCollection | ModelComponent,
energy_offset: Numeric | Parameter = 0.0,
- upsample_factor: Numeric | None = 5,
- extension_factor: Numeric | None = 0.2,
+ convolution_settings: ConvolutionSettings | None = None,
temperature: Parameter | Numeric | None = None,
temperature_unit: str | sc.Unit = 'K',
- energy_unit: str | sc.Unit = 'meV',
- normalize_detailed_balance: bool = True,
+ detailed_balance_settings: DetailedBalanceSettings | None = None,
+ unit: str | sc.Unit = 'meV',
+ display_name: str | None = 'MyConvolution',
+ unique_name: str | None = None,
) -> None:
- """Initialize the NumericalConvolutionBase.
-
- Args:
- energy (np.ndarray | sc.Variable): 1D array of energy values
- where the convolution is evaluated.
- sample_components (ComponentCollection | ModelComponent):
- The components to be convolved.
- resolution_components (ComponentCollection | ModelComponent):
- The resolution components to convolve with.
- energy_offset (Numeric | Parameter, default=0.0): An energy
- offset to apply to the energy values before convolution.
- upsample_factor (Numeric | None, default=5): The factor by which to
- upsample the input data before convolution.
- extension_factor (Numeric | None, default=0.2): The factor by which to
- extend the input data range before convolution.
- temperature (Parameter | Numeric | None, default=None): The temperature to
- use for detailed balance correction.
- temperature_unit (str | sc.Unit, default='K'): The unit of the
- temperature parameter.
- energy_unit (str | sc.Unit, default='meV'): The unit of the energy.
- normalize_detailed_balance (bool, default=True): Whether to normalize the
- detailed balance correction.
-
- Raises:
- TypeError: If temperature is not None, a number, or a
- Parameter, or if temperature_unit is not a string or sc.Unit, or if
- upsample_factor is not a number or None, or if extension_factor
- is not a number, or if normalize_detailed_balance is not a bool.
+ """
+ Initialize the NumericalConvolutionBase.
+
+ Parameters
+ ----------
+ energy : np.ndarray | sc.Variable
+ 1D array of energy values where the convolution is evaluated.
+ sample_components : ComponentCollection | ModelComponent
+ The components to be convolved.
+ resolution_components : ComponentCollection | ModelComponent
+ The resolution components to convolve with.
+ energy_offset : Numeric | Parameter, default=0.0
+ An energy offset to apply to the energy values before convolution.
+ convolution_settings : ConvolutionSettings | None, default=None
+ The settings for the convolution. If None, default settings will be used.
+ temperature : Parameter | Numeric | None, default=None
+ The temperature to use for detailed balance correction.
+ temperature_unit : str | sc.Unit, default='K'
+ The unit of the temperature parameter.
+ detailed_balance_settings : DetailedBalanceSettings | None, default=None
+ The settings for detailed balance. If None, default settings will be used.
+ unit : str | sc.Unit, default='meV'
+ The unit of the energy.
+ display_name : str | None, default='MyConvolution'
+ Display name of the model.
+ unique_name : str | None, default=None
+ Unique name of the model. If None, a unique name will be generated.
+
+ Raises
+ ------
+ TypeError
+ If temperature is not None, a number, or a Parameter, or if temperature_unit is not a
+ string or sc.Unit.
"""
super().__init__(
energy=energy,
sample_components=sample_components,
resolution_components=resolution_components,
- energy_unit=energy_unit,
+ unit=unit,
energy_offset=energy_offset,
+ display_name=display_name,
+ unique_name=unique_name,
)
if temperature is not None and not isinstance(temperature, (Numeric, Parameter)):
@@ -92,51 +100,101 @@ def __init__(
self._temperature = None
self.temperature = temperature
- self._normalize_detailed_balance = normalize_detailed_balance
+ if convolution_settings is None:
+ convolution_settings = ConvolutionSettings()
+ self._convolution_settings = convolution_settings
- self._upsample_factor = upsample_factor
- self._extension_factor = extension_factor
+ if detailed_balance_settings is None:
+ detailed_balance_settings = DetailedBalanceSettings()
+ if not isinstance(detailed_balance_settings, DetailedBalanceSettings):
+ raise TypeError(
+ 'detailed_balance_settings must be a DetailedBalanceSettings instance.'
+ )
+ self._detailed_balance_settings = detailed_balance_settings
# Create a dense grid to improve accuracy.
# When upsample_factor>1, we evaluate on this grid and
# interpolate back to the original values at the end
self._energy_grid = self._create_energy_grid()
+ @property
+ def convolution_settings(self) -> ConvolutionSettings:
+ """
+ Get the convolution settings.
+
+ Returns
+ -------
+ ConvolutionSettings
+ The convolution settings.
+ """
+
+ return self._convolution_settings
+
+ @convolution_settings.setter
+ def convolution_settings(self, settings: ConvolutionSettings) -> None:
+ """
+ Set the convolution settings and recreate the dense grid.
+
+ Parameters
+ ----------
+ settings : ConvolutionSettings
+ The new convolution settings.
+
+ Raises
+ ------
+ TypeError
+ If settings is not a ConvolutionSettings instance.
+ """
+ if not isinstance(settings, ConvolutionSettings):
+ raise TypeError('settings must be a ConvolutionSettings instance.')
+ self._convolution_settings = settings
+ self._convolution_settings.convolution_plan_is_valid = False
+
@ConvolutionBase.energy.setter
def energy(self, energy: np.ndarray) -> None:
- """Set the energy array and recreate the dense grid.
+ """
+ Set the energy array and recreate the dense grid.
- Args:
- energy (np.ndarray): The new energy array.
+ Parameters
+ ----------
+ energy : np.ndarray
+ The new energy array.
"""
ConvolutionBase.energy.fset(self, energy)
- # Recreate dense grid when energy is updated
- self._energy_grid = self._create_energy_grid()
+ self.convolution_settings.convolution_plan_is_valid = False
@property
def upsample_factor(self) -> Numeric | None:
- """Get the upsample factor.
+ """
+ Get the upsample factor.
- Returns:
- Numeric | None: The upsample factor.
+ Returns
+ -------
+ Numeric | None
+ The upsample factor.
"""
- return self._upsample_factor
+ return self.convolution_settings.upsample_factor
@upsample_factor.setter
def upsample_factor(self, factor: Numeric | None) -> None:
- """Set the upsample factor and recreate the dense grid.
-
- Args:
- factor (Numeric | None): The new upsample factor.
-
- Raises:
- TypeError: If factor is not a number or None.
- ValueError: If factor is not greater than 1.
+ """
+ Set the upsample factor and recreate the dense grid.
+
+ Parameters
+ ----------
+ factor : Numeric | None
+ The new upsample factor.
+
+ Raises
+ ------
+ TypeError
+ If factor is not a number or None.
+ ValueError
+ If factor is not greater than 1.
"""
if factor is None:
- self._upsample_factor = factor
- self._energy_grid = self._create_energy_grid()
+ self.convolution_settings.upsample_factor = factor
return
if not isinstance(factor, Numeric):
@@ -145,41 +203,43 @@ def upsample_factor(self, factor: Numeric | None) -> None:
if factor <= 1.0:
raise ValueError('Upsample factor must be greater than 1.')
- self._upsample_factor = factor
-
- # Recreate dense grid when upsample factor is updated
- self._energy_grid = self._create_energy_grid()
+ self.convolution_settings.upsample_factor = factor
@property
def extension_factor(self) -> float:
- """Get the extension factor.
+ """
+ Get the extension factor.
- The extension factor determines how much the energy range is
- extended on both sides before convolution.
- 0.2 means extending by 20% of the original energy span
- on each side
+ The extension factor determines how much the energy range is extended on both sides before
+ convolution. 0.2 means extending by 20% of the original energy span on each side
- Returns:
- float: The extension factor.
+ Returns
+ -------
+ float
+ The extension factor.
"""
- return self._extension_factor
+ return self.convolution_settings.extension_factor
@extension_factor.setter
def extension_factor(self, factor: Numeric) -> None:
"""
Set the extension factor and recreate the dense grid.
- The extension factor determines how much the energy range is
- extended on both sides before convolution.
- 0.2 means extending by 20% of the original energy span
- on each side.
- Args:
- factor (Numeric): The new extension factor.
+ The extension factor determines how much the energy range is extended on both sides before
+ convolution. 0.2 means extending by 20% of the original energy span on each side.
+
+ Parameters
+ ----------
+ factor : Numeric
+ The new extension factor.
- Raises:
- TypeError: If factor is not a number.
- ValueError: If factor is negative.
+ Raises
+ ------
+ TypeError
+ If factor is not a number.
+ ValueError
+ If factor is negative.
"""
if not isinstance(factor, Numeric):
@@ -187,35 +247,38 @@ def extension_factor(self, factor: Numeric) -> None:
if factor < 0.0:
raise ValueError('Extension factor must be non-negative.')
- self._extension_factor = float(factor)
- # Recreate dense grid when extension factor is updated
- self._energy_grid = self._create_energy_grid()
+ self.convolution_settings.extension_factor = float(factor)
@property
def temperature(self) -> Parameter | None:
- """Get the temperature.
+ """
+ Get the temperature.
- Returns:
- Parameter | None: The temperature parameter, or None if
- detailed balance correction is disabled.
+ Returns
+ -------
+ Parameter | None
+ The temperature parameter, or None if detailed balance correction is disabled.
"""
return self._temperature
@temperature.setter
def temperature(self, temp: Parameter | Numeric | None) -> None:
- """Set the temperature.
+ """
+ Set the temperature.
- If None, disables detailed balance
- correction and removes the temperature parameter.
+ If None, disables detailed balance correction and removes the temperature parameter.
- Args:
- temp (Parameter | Numeric | None): The temperature to set.
- The unit will be the same as the existing temperature
- parameter if it exists, otherwise 'K'.
+ Parameters
+ ----------
+ temp : Parameter | Numeric | None
+ The temperature to set. The unit will be the same as the existing temperature parameter
+ if it exists, otherwise 'K'.
- Raises:
- TypeError: If temp is not a Numeric, Parameter, or None.
+ Raises
+ ------
+ TypeError
+ If temp is not a Numeric, Parameter, or None.
"""
if temp is None:
@@ -236,53 +299,55 @@ def temperature(self, temp: Parameter | Numeric | None) -> None:
raise TypeError('Temperature must be None, a float or a Parameter.')
@property
- def normalize_detailed_balance(self) -> bool:
- """Get whether to normalize the detailed balance factor.
-
- If True, the detailed balance factor is divided by temperature.
-
- Returns:
- bool: Whether to normalize the detailed balance factor.
+ def detailed_balance_settings(self) -> DetailedBalanceSettings:
"""
+ Get the DetailedBalanceSettings of the Convolution.
- return self._normalize_detailed_balance
-
- @normalize_detailed_balance.setter
- def normalize_detailed_balance(self, normalize: bool) -> None:
- """Set whether to normalize the detailed balance factor.
-
- If True, the detailed balance factor is divided by temperature.
-
- Args:
- normalize (bool): Whether to normalize the detailed balance
- factor.
+ Returns
+ -------
+ DetailedBalanceSettings
+ The DetailedBalanceSettings of the Convolution.
+ """
+ return self._detailed_balance_settings
- Raises:
- TypeError: If normalize is not a bool.
+ @detailed_balance_settings.setter
+ def detailed_balance_settings(self, value: DetailedBalanceSettings) -> None:
"""
+ Set the DetailedBalanceSettings of the Convolution.
- if not isinstance(normalize, bool):
- raise TypeError('normalize_detailed_balance must be True or False.')
+ Parameters
+ ----------
+ value : DetailedBalanceSettings
+ The DetailedBalanceSettings to set.
- self._normalize_detailed_balance = normalize
+ Raises
+ ------
+ TypeError
+ If value is not a DetailedBalanceSettings.
+ """
+ if not isinstance(value, DetailedBalanceSettings):
+ raise TypeError('detailed_balance_settings must be a DetailedBalanceSettings')
+ self._detailed_balance_settings = value
def _create_energy_grid(
self,
) -> EnergyGrid:
- """Create a dense grid by upsampling and extending the energy
- array.
+ """
+ Create a dense grid by upsampling and extending the energy array.
- If upsample_factor is None, no upsampling or extension is
- performed.
- This dense grid is used for convolution to improve accuracy.
+ If upsample_factor is None, no upsampling or extension is performed. This dense grid is
+ used for convolution to improve accuracy.
- Returns:
- EnergyGrid: The dense grid created by upsampling and
- extending energy.
+ Raises
+ ------
+ ValueError
+ If energy array is not uniformly spaced when upsample_factor is None, or if energy
+ array has less than 2 points.
- Raises:
- ValueError: If energy array is not uniformly spaced when
- upsample_factor is None, or if energy array has less than 2 points.
+ Returns
+ -------
+ EnergyGrid
+ The dense grid created by upsampling and extending energy.
"""
if self.upsample_factor is None:
# Check if the array is uniformly spaced.
@@ -332,31 +397,35 @@ def _create_energy_grid(
else:
energy_dense_centered = energy_dense
- return EnergyGrid(
+ energy_grid = EnergyGrid(
energy_dense=energy_dense,
energy_dense_centered=energy_dense_centered,
energy_dense_step=energy_dense_step,
energy_span_dense=energy_span_dense,
energy_even_length_offset=energy_even_length_offset,
)
+ self._energy_grid = energy_grid
+ self.convolution_settings.convolution_plan_is_valid = True
+ return energy_grid
def _check_width_thresholds(
self,
model: ComponentCollection | ModelComponent,
model_name: str,
) -> None:
- """Helper function to check and warn if components are wide
- compared to the span of the data, or narrow compared to the
- spacing.
+ """
+ Helper function to check and warn if components are wide compared to the span of the data,
+ or narrow compared to the spacing.
In both cases, the convolution accuracy may be compromised.
- Args:
- model (ComponentCollection | ModelComponent): The model to
- check
- model_name (str): A string indicating whether the model is a
- 'sample model' or 'resolution model' for warning
- messages.
+ Parameters
+ ----------
+ model : ComponentCollection | ModelComponent
+ The model to check.
+ model_name : str
+ A string indicating whether the model is a 'sample model' or 'resolution model' for
+ warning messages.
"""
# Handle ComponentCollection or ModelComponent
@@ -366,41 +435,46 @@ def _check_width_thresholds(
if hasattr(comp, 'width'):
if comp.width.value > LARGE_WIDTH_THRESHOLD * self._energy_grid.energy_span_dense:
warnings.warn(
- f"The width of the {model_name} component '{comp.unique_name}' \
- ({comp.width.value}) is large compared to the span of the input "
- f'array ({self._energy_grid.energy_span_dense}). \
- This may lead to inaccuracies in the convolution. \
- Increase extension_factor to improve accuracy.',
+ (
+ f"The width of the {model_name} component '{comp.unique_name}' "
+ f'({comp.width.value}) is large compared to the span of the input '
+ f'array ({self._energy_grid.energy_span_dense}). '
+ f'This may lead to inaccuracies in the convolution. '
+ f'Increase extension_factor to improve accuracy.'
+ ),
UserWarning,
stacklevel=3,
)
if comp.width.value < SMALL_WIDTH_THRESHOLD * self._energy_grid.energy_dense_step:
warnings.warn(
- f"The width of the {model_name} component '{comp.unique_name}' \
- ({comp.width.value}) is small compared to the spacing of the input "
- f'array ({self._energy_grid.energy_dense_step}). \
- This may lead to inaccuracies in the convolution. \
- Increase upsample_factor to improve accuracy.',
+ (
+ f"The width of the {model_name} component '{comp.unique_name}' "
+ f'({comp.width.value}) is small compared to the spacing of the input '
+ f'array ({self._energy_grid.energy_dense_step}). '
+ f'This may lead to inaccuracies in the convolution. '
+ f'Increase upsample_factor to improve accuracy.'
+ ),
UserWarning,
stacklevel=3,
)
def __repr__(self) -> str:
- """Return a string representation of the
- NumericalConvolutionBase.
+ """
+ Return a string representation of the NumericalConvolutionBase.
- Returns:
- str: A string representation of the
- NumericalConvolutionBase.
+ Returns
+ -------
+ str
+ A string representation of the NumericalConvolutionBase.
"""
return (
f'{self.__class__.__name__}('
f'energy=array of shape {self.energy.values.shape},\n '
- f'sample_components={repr(self.sample_components)}, \n'
- f'resolution_components={repr(self.resolution_components)},\n '
- f'energy_unit={self._energy_unit}, '
+ f'sample_components={self.sample_components!r}, \n'
+ f'resolution_components={self.resolution_components!r},\n '
+ f'unit={self.unit}, '
f'upsample_factor={self.upsample_factor}, '
f'extension_factor={self.extension_factor}, '
f'temperature={self.temperature}, '
- f'normalize_detailed_balance={self.normalize_detailed_balance})'
+ f'detailed_balance={self.detailed_balance_settings!r})'
)
diff --git a/src/easydynamics/experiment/__init__.py b/src/easydynamics/experiment/__init__.py
index da01800f..f59656ed 100644
--- a/src/easydynamics/experiment/__init__.py
+++ b/src/easydynamics/experiment/__init__.py
@@ -1,7 +1,7 @@
# SPDX-FileCopyrightText: 2026 EasyScience contributors
# SPDX-License-Identifier: BSD-3-Clause
-from .experiment import Experiment
+from easydynamics.experiment.experiment import Experiment
__all__ = [
'Experiment',
diff --git a/src/easydynamics/experiment/experiment.py b/src/easydynamics/experiment/experiment.py
index ad829e37..909fb35a 100644
--- a/src/easydynamics/experiment/experiment.py
+++ b/src/easydynamics/experiment/experiment.py
@@ -7,19 +7,19 @@
import numpy as np
import plopp as pp
import scipp as sc
-from easyscience.base_classes.new_base import NewBase
+from plopp.backends.matplotlib.figure import InteractiveFigure
from scipp.io import load_hdf5 as sc_load_hdf5
from scipp.io import save_hdf5 as sc_save_hdf5
+from easydynamics.base_classes.easydynamics_base import EasyDynamicsBase
from easydynamics.utils.utils import _in_notebook
-class Experiment(NewBase):
- """Holds data from an experiment as a sc.DataArray along with
- metadata.
+class Experiment(EasyDynamicsBase):
+ """
+ Holds data from an experiment as a sc.DataArray along with metadata.
- This is a minimal implementation that will be extended in the
- future.
+ This is a minimal implementation that will be extended in the future.
"""
def __init__(
@@ -28,18 +28,23 @@ def __init__(
unique_name: str | None = None,
data: sc.DataArray | str | None = None,
) -> None:
- """Initialize the Experiment object.
-
- Args:
- display_name (str | None, default="MyExperiment"): Display name of the experiment.
- unique_name (str | None, default=None): Unique name of the experiment. If
- None, a unique name will be generated.
- data (sc.DataArray | str | None, default=None): Dataset associated with
- the experiment. Can be a sc.DataArray or a filename
- string to load from. If None, no data is loaded.
-
- Raises:
- TypeError: If data is not a sc.DataArray, a string, or None.
+ """
+ Initialize the Experiment object.
+
+ Parameters
+ ----------
+ display_name : str | None, default='MyExperiment'
+ Display name of the experiment.
+ unique_name : str | None, default=None
+ Unique name of the experiment. If None, a unique name will be generated. None.
+ data : sc.DataArray | str | None, default=None
+ Dataset associated with the experiment. Can be a sc.DataArray or a filename string to
+ load from. If None, no data is loaded.
+
+ Raises
+ ------
+ TypeError
+ If data is not a sc.DataArray, a string, or None.
"""
super().__init__(
display_name=display_name,
@@ -68,24 +73,30 @@ def __init__(
@property
def data(self) -> sc.DataArray | None:
- """Get the dataset associated with this experiment.
+ """
+ Get the dataset associated with this experiment.
- Returns:
- sc.DataArray | None: The dataset associated with this
- experiment, or None if no data is loaded.
+ Returns
+ -------
+ sc.DataArray | None
+ The dataset associated with this experiment, or None if no data is loaded.
"""
return self._data
@data.setter
def data(self, value: sc.DataArray) -> None:
- """Set the dataset associated with this experiment.
+ """
+ Set the dataset associated with this experiment.
- Args:
- value (sc.DataArray): The new dataset to associate with this
- experiment.
+ Parameters
+ ----------
+ value : sc.DataArray
+ The new dataset to associate with this experiment.
- Raises:
- TypeError: If the value is not a sc.DataArray.
+ Raises
+ ------
+ TypeError
+ If the value is not a sc.DataArray.
"""
if not isinstance(value, sc.DataArray):
raise TypeError(f'Data must be a sc.DataArray, not {type(value).__name__}')
@@ -97,94 +108,122 @@ def data(self, value: sc.DataArray) -> None:
@property
def binned_data(self) -> sc.DataArray | None:
- """Get the binned dataset associated with this experiment.
+ """
+ Get the binned dataset associated with this experiment.
- Returns:
- sc.DataArray | None: The binned dataset associated with this
- experiment, or None if no data is loaded.
+ Returns
+ -------
+ sc.DataArray | None
+ The binned dataset associated with this experiment, or None if no data is loaded.
"""
return self._binned_data
@binned_data.setter
def binned_data(self, _value: sc.DataArray) -> None:
- """Set the binned dataset associated with this experiment. Read-
- only property. Use rebin() to rebin the data instead.
+ """
+ Set the binned dataset associated with this experiment.
+
+ Read- only property. Use rebin() to rebin the data instead.
- Args:
- _value (sc.DataArray): The new binned dataset to associate
- with this experiment (ignored)
+ Parameters
+ ----------
+ _value : sc.DataArray
+ The new binned dataset to associate with this experiment (ignored).
- Raises:
- AttributeError: Always, since binned_data is read-only.
+ Raises
+ ------
+ AttributeError
+ Always, since binned_data is read-only.
"""
raise AttributeError('binned_data is a read-only property. Use rebin() to rebin the data')
@property
def Q(self) -> sc.Variable | None:
- """Get the Q values from the dataset.
+ """
+ Get the Q values from the dataset.
- Returns:
- sc.Variable | None: The Q values from the dataset, or None
- if no data is loaded.
+ Returns
+ -------
+ sc.Variable | None
+ The Q values from the dataset, or None if no data is loaded.
"""
- if self._binned_data is None:
+ if self.binned_data is None:
return None
- return self._binned_data.coords['Q']
+ return self.binned_data.coords['Q']
@Q.setter
def Q(self, _value: sc.Variable) -> None:
- """Set the Q values for the dataset. Q is a read-only property
- derived from the data, so this setter raises an error.
+ """
+ Set the Q values for the dataset.
+
+ Q is a read-only property derived from the data, so this setter raises an error.
- Args:
- _value (sc.Variable): The new Q values to set (ignored)
+ Parameters
+ ----------
+ _value : sc.Variable
+ The new Q values to set (ignored).
- Raises:
- AttributeError: Always, since Q is read-only.
+ Raises
+ ------
+ AttributeError
+ Always, since Q is read-only.
"""
raise AttributeError('Q is a read-only property derived from the data.')
@property
def energy(self) -> sc.Variable | None:
- """Get the energy values from the dataset.
+ """
+ Get the energy values from the dataset.
- Returns:
- sc.Variable | None: The energy values from the dataset, or
- None if no data is loaded.
+ Returns
+ -------
+ sc.Variable | None
+ The energy values from the dataset, or None if no data is loaded.
"""
- if self._binned_data is None:
+ if self.binned_data is None:
return None
- return self._binned_data.coords['energy']
+ return self.binned_data.coords['energy']
@energy.setter
def energy(self, _value: sc.Variable) -> None:
- """Set the energy values for the dataset. Energy is a read-only
- property derived from the data, so this setter raises an error.
+ """
+ Set the energy values for the dataset.
+
+ Energy is a read-only property derived from the data, so this setter raises an error.
- Args:
- _value (sc.Variable): The new energy values to set (ignored)
+ Parameters
+ ----------
+ _value : sc.Variable
+ The new energy values to set (ignored).
- Raises:
- AttributeError: Always, since energy is read-only.
+ Raises
+ ------
+ AttributeError
+ Always, since energy is read-only.
"""
raise AttributeError('energy is a read-only property derived from the data.')
def get_masked_energy(self, Q_index: int) -> sc.Variable | None:
- """Get the energy values from the dataset, removing points where
- the y values or variances are NaN or Inf for the given Q index.
-
- Args:
- Q_index (int): The Q index to get the masked energy values
- for.
-
- Returns:
- sc.Variable | None: The masked energy values from the
- dataset, or None if no data is loaded.
-
- Raises:
- IndexError: If Q_index is not a valid index for the Q values.
"""
- if self._binned_data is None:
+ Get the energy values from the dataset, removing points where the y values or variances are
+ NaN or Inf for the given Q index.
+
+ Parameters
+ ----------
+ Q_index : int
+ The Q index to get the masked energy values for.
+
+ Raises
+ ------
+ IndexError
+ If Q_index is not a valid index for the Q values.
+
+ Returns
+ -------
+ sc.Variable | None
+ The masked energy values from the dataset, or None if no data is loaded.
+ """
+ if self.binned_data is None:
return None
if (
@@ -194,7 +233,7 @@ def get_masked_energy(self, Q_index: int) -> sc.Variable | None:
):
raise IndexError('Q_index must be a valid index for the Q values.')
- energy = self._binned_data.coords['energy']
+ energy = self.binned_data.coords['energy']
_, _, _, mask = self._extract_x_y_weights_only_finite(Q_index=Q_index)
mask_var = sc.array(dims=['energy'], values=mask)
@@ -205,16 +244,21 @@ def get_masked_energy(self, Q_index: int) -> sc.Variable | None:
###########
def load_hdf5(self, filename: str, display_name: str | None = None) -> None:
- """Load data from an HDF5 file.
-
- Args:
- filename (str ): Path to the HDF5 file.
- display_name (str | None, default=None): Optional display name for the
- experiment.
-
- Raises:
- TypeError: If filename is not a string or if display_name is
- not a string or None or if the loaded data is not a sc.DataArray.
+ """
+ Load data from an HDF5 file.
+
+ Parameters
+ ----------
+ filename : str
+ Path to the HDF5 file.
+ display_name : str | None, default=None
+ Optional display name for the experiment.
+
+ Raises
+ ------
+ TypeError
+ If filename is not a string or if display_name is not a string or None or if the loaded
+ data is not a sc.DataArray.
"""
if not isinstance(filename, str):
raise TypeError(f'Filename must be a string, not {type(filename).__name__}')
@@ -235,16 +279,21 @@ def load_hdf5(self, filename: str, display_name: str | None = None) -> None:
self.data = loaded_data
def save_hdf5(self, filename: str | None = None) -> None:
- """Save the dataset to HDF5.
-
- Args:
- filename (str | None, default=None): Path to the output HDF5 file.
- If None, the file will be named after the unique_name of
- the experiment with a .h5 extension.
-
- Raises:
- TypeError: If filename is not a string or None.
- ValueError: If there is no data to save.
+ """
+ Save the dataset to HDF5.
+
+ Parameters
+ ----------
+ filename : str | None, default=None
+ Path to the output HDF5 file. If None, the file will be named after the unique_name of
+ the experiment with a .h5 extension.
+
+ Raises
+ ------
+ TypeError
+ If filename is not a string or None.
+ ValueError
+ If there is no data to save.
"""
if filename is None:
@@ -266,18 +315,23 @@ def remove_data(self) -> None:
self._binned_data = None
def rebin(self, dimensions: dict[str, int | sc.Variable]) -> None:
- """Rebin the dataset along specified dimensions.
-
- Args:
- dimensions (dict[str, int | sc.Variable]): A dictionary
- mapping dimension names to number of bins (int) or bin
- edges (sc.Variable).
-
- Raises:
- TypeError: If dimensions is not a dictionary or if
- keys/values are of incorrect types.
- ValueError: If there is no data to rebin.
- KeyError: If a specified dimension is not in the dataset.
+ """
+ Rebin the dataset along specified dimensions.
+
+ Parameters
+ ----------
+ dimensions : dict[str, int | sc.Variable]
+ A dictionary mapping dimension names to number of bins (int) or bin edges
+ (sc.Variable).
+
+ Raises
+ ------
+ TypeError
+ If dimensions is not a dictionary or if keys/values are of incorrect types.
+ ValueError
+ If there is no data to rebin.
+ KeyError
+ If a specified dimension is not in the dataset.
"""
if not isinstance(dimensions, dict):
@@ -319,24 +373,54 @@ def rebin(self, dimensions: dict[str, int | sc.Variable]) -> None:
# other methods
###########
- def plot_data(self, slicer: bool = False, **kwargs: dict) -> None:
- """Plot the dataset using plopp: https://scipp.github.io/plopp/
-
- Args:
- slicer (bool, default=False): If True, use plopp's slicer instead of plot.
- **kwargs (dict): Additional keyword arguments to pass to plopp.
-
- Raises:
- ValueError: If there is no data to plot.
- RuntimeError: If not in a Jupyter notebook environment.
+ def plot_data(
+ self,
+ slicer: bool = False,
+ transpose_axes: bool = False,
+ **kwargs: dict,
+ ) -> InteractiveFigure:
+ """
+ Plot the dataset using plopp: https://scipp.github.io/plopp/.
+
+ Parameters
+ ----------
+ slicer : bool, default=False
+ If True, use plopp's slicer instead of plot.
+ transpose_axes : bool, default=False
+ If True, transpose the data to have dimensions in the order (energy, Q) before
+ plotting, so that energy is on the x-axis. This only applies when slicer=False.
+ **kwargs : dict
+ Additional keyword arguments to pass to plopp.
+
+ Returns
+ -------
+ InteractiveFigure
+ A plot of the data and model.
+
+ Raises
+ ------
+ ValueError
+ If there is no data to plot.
+ RuntimeError
+ If not in a Jupyter notebook environment.
+ TypeError
+ If slicer or transpose_axes are not True or False.
"""
- if self._binned_data is None:
+ if self.binned_data is None:
raise ValueError('No data to plot. Please load data first.')
if not _in_notebook():
raise RuntimeError('plot_data() can only be used in a Jupyter notebook environment.')
+ if not isinstance(slicer, bool):
+ raise TypeError(f'slicer must be True or False, not {type(slicer).__name__}')
+
+ if not isinstance(transpose_axes, bool):
+ raise TypeError(
+ f'transpose_axes must be True or False, not {type(transpose_axes).__name__}'
+ )
+
plot_kwargs_defaults = {
'title': self.display_name,
}
@@ -348,15 +432,19 @@ def plot_data(self, slicer: bool = False, **kwargs: dict) -> None:
plot_kwargs_defaults.update(kwargs)
if slicer:
fig = pp.slicer(
- self._binned_data,
+ self.binned_data,
**plot_kwargs_defaults,
)
for widget in fig.bottom_bar[0].controls.values():
widget.slider_toggler.value = '-o-'
else:
+ if transpose_axes:
+ data_to_plot = self.binned_data.transpose(dims=['energy', 'Q'])
+ else:
+ data_to_plot = self.binned_data.transpose(dims=['Q', 'energy'])
fig = pp.plot(
- self._binned_data.transpose(dims=['energy', 'Q']),
+ data_to_plot,
**plot_kwargs_defaults,
)
return fig
@@ -367,14 +455,20 @@ def plot_data(self, slicer: bool = False, **kwargs: dict) -> None:
@staticmethod
def _validate_coordinates(data: sc.DataArray) -> None:
- """Validate that required coordinates are present in the data.
-
- Args:
- data (sc.DataArray): The data to validate.
-
- Raises:
- TypeError: If data is not a sc.DataArray.
- ValueError: If required coordinates are missing.
+ """
+ Validate that required coordinates are present in the data.
+
+ Parameters
+ ----------
+ data : sc.DataArray
+ The data to validate.
+
+ Raises
+ ------
+ TypeError
+ If data is not a sc.DataArray.
+ ValueError
+ If required coordinates are missing.
"""
if not isinstance(data, sc.DataArray):
raise TypeError('Data must be a sc.DataArray.')
@@ -385,13 +479,18 @@ def _validate_coordinates(data: sc.DataArray) -> None:
raise ValueError(f"Data is missing required coordinate: '{coord}'")
def _convert_to_bin_centers(self, data: sc.DataArray) -> sc.DataArray:
- """Convert the coordinates of the data to bin centers.
+ """
+ Convert the coordinates of the data to bin centers.
- Args:
- data (sc.DataArray): The data to convert.
+ Parameters
+ ----------
+ data : sc.DataArray
+ The data to convert.
- Returns:
- sc.DataArray: The data with coordinates at bin centers.
+ Returns
+ -------
+ sc.DataArray
+ The data with coordinates at bin centers.
"""
for dim in data.dims:
coord = data.coords[dim]
@@ -401,16 +500,18 @@ def _convert_to_bin_centers(self, data: sc.DataArray) -> sc.DataArray:
return data
def _extract_x_y_var(self, Q_index: int) -> tuple[np.ndarray, np.ndarray, np.ndarray]:
- """Extract the x, y, and weights arrays from the experiment for
- the given Q index.
+ """
+ Extract the x, y, and weights arrays from the experiment for the given Q index.
- Args:
- Q_index (int): The Q index to extract the data for.
+ Parameters
+ ----------
+ Q_index : int
+ The Q index to extract the data for.
- Returns:
- tuple[np.ndarray, np.ndarray, np.ndarray]: The x, y, and
- variances arrays extracted from the experiment for the
- given Q index.
+ Returns
+ -------
+ tuple[np.ndarray, np.ndarray, np.ndarray]
+ The x, y, and variances arrays extracted from the experiment for the given Q index.
"""
data = self.binned_data['Q', Q_index]
x = data.coords['energy'].values
@@ -421,21 +522,26 @@ def _extract_x_y_var(self, Q_index: int) -> tuple[np.ndarray, np.ndarray, np.nda
def _extract_x_y_weights_only_finite(
self, Q_index: int
) -> tuple[np.ndarray, np.ndarray, np.ndarray, np.ndarray]:
- """Extract the x, y, and weights arrays from the experiment for
- the given Q index, removing any NaN and Inf values.
-
- Args:
- Q_index (int): The Q index to extract the data for.
-
- Returns:
- tuple[np.ndarray, np.ndarray, np.ndarray, np.ndarray]: The
- x, y, weights, and mask arrays extracted from the
- experiment for the given Q index, with NaNs and Infs
- removed.
-
- Raises:
- ValueError: If any variances are zero after removing NaNs
- and Infs, since this would lead to infinite weights.
+ """
+ Extract the x, y, and weights arrays from the experiment for the given Q index, removing
+ any NaN and Inf values.
+
+ Parameters
+ ----------
+ Q_index : int
+ The Q index to extract the data for.
+
+ Raises
+ ------
+ ValueError
+ If any variances are zero after removing NaNs and Infs, since this would lead to
+ infinite weights.
+
+ Returns
+ -------
+ tuple[np.ndarray, np.ndarray, np.ndarray, np.ndarray]
+ The x, y, weights, and mask arrays extracted from the experiment for the given Q index,
+ with NaNs and Infs removed.
"""
x, y, var = self._extract_x_y_var(Q_index)
@@ -463,19 +569,25 @@ def _extract_x_y_weights_only_finite(
###########
def __repr__(self) -> str:
- """Return a string representation of the Experiment object.
+ """
+ Return a string representation of the Experiment object.
- Returns:
- str: A string representation of the Experiment object.
+ Returns
+ -------
+ str
+ A string representation of the Experiment object.
"""
return f'Experiment `{self.unique_name}` with data: {self._data}'
def __copy__(self) -> 'Experiment':
- """Return a copy of the object.
+ """
+ Return a copy of the object.
- Returns:
- Experiment: A copy of the Experiment object.
+ Returns
+ -------
+ 'Experiment'
+ A copy of the Experiment object.
"""
temp = self.to_dict(skip=['unique_name'])
new_obj = self.__class__.from_dict(temp)
diff --git a/src/easydynamics/sample_model/__init__.py b/src/easydynamics/sample_model/__init__.py
index 9cb2b108..6f75bafd 100644
--- a/src/easydynamics/sample_model/__init__.py
+++ b/src/easydynamics/sample_model/__init__.py
@@ -1,34 +1,38 @@
# SPDX-FileCopyrightText: 2025 EasyScience contributors
# SPDX-License-Identifier: BSD-3-Clause
-from .background_model import BackgroundModel
-from .component_collection import ComponentCollection
-from .components import DampedHarmonicOscillator
-from .components import DeltaFunction
-from .components import Exponential
-from .components import ExpressionComponent
-from .components import Gaussian
-from .components import Lorentzian
-from .components import Polynomial
-from .components import Voigt
-from .diffusion_model.brownian_translational_diffusion import BrownianTranslationalDiffusion
-from .instrument_model import InstrumentModel
-from .resolution_model import ResolutionModel
-from .sample_model import SampleModel
+from easydynamics.sample_model.background_model import BackgroundModel
+from easydynamics.sample_model.component_collection import ComponentCollection
+from easydynamics.sample_model.components.damped_harmonic_oscillator import (
+ DampedHarmonicOscillator,
+)
+from easydynamics.sample_model.components.delta_function import DeltaFunction
+from easydynamics.sample_model.components.exponential import Exponential
+from easydynamics.sample_model.components.expression_component import ExpressionComponent
+from easydynamics.sample_model.components.gaussian import Gaussian
+from easydynamics.sample_model.components.lorentzian import Lorentzian
+from easydynamics.sample_model.components.polynomial import Polynomial
+from easydynamics.sample_model.components.voigt import Voigt
+from easydynamics.sample_model.diffusion_model.brownian_translational_diffusion import (
+ BrownianTranslationalDiffusion,
+)
+from easydynamics.sample_model.instrument_model import InstrumentModel
+from easydynamics.sample_model.resolution_model import ResolutionModel
+from easydynamics.sample_model.sample_model import SampleModel
__all__ = [
+ 'BackgroundModel',
+ 'BrownianTranslationalDiffusion',
'ComponentCollection',
+ 'DampedHarmonicOscillator',
+ 'DeltaFunction',
+ 'Exponential',
+ 'ExpressionComponent',
'Gaussian',
+ 'InstrumentModel',
'Lorentzian',
- 'Voigt',
- 'DeltaFunction',
- 'DampedHarmonicOscillator',
'Polynomial',
- 'Exponential',
- 'BrownianTranslationalDiffusion',
- 'SampleModel',
'ResolutionModel',
- 'BackgroundModel',
- 'InstrumentModel',
- 'ExpressionComponent',
+ 'SampleModel',
+ 'Voigt',
]
diff --git a/src/easydynamics/sample_model/background_model.py b/src/easydynamics/sample_model/background_model.py
index 2f4645f5..bd403ea2 100644
--- a/src/easydynamics/sample_model/background_model.py
+++ b/src/easydynamics/sample_model/background_model.py
@@ -3,16 +3,15 @@
import scipp as sc
+from easydynamics.sample_model.component_collection import ComponentCollection
+from easydynamics.sample_model.components.model_component import ModelComponent
from easydynamics.sample_model.model_base import ModelBase
from easydynamics.utils.utils import Q_type
-from .component_collection import ComponentCollection
-from .components.model_component import ModelComponent
-
class BackgroundModel(ModelBase):
- """BackgroundModel represents a model of the background in an
- experiment at various Q.
+ """
+ BackgroundModel represents a model of the background in an experiment at various Q.
"""
def __init__(
@@ -23,19 +22,22 @@ def __init__(
components: ModelComponent | ComponentCollection | None = None,
Q: Q_type | None = None,
) -> None:
- """Initialize the BackgroundModel.
+ """
+ Initialize the BackgroundModel.
- Args:
- display_name (str | None, default='MyBackgroundModel'): Display name of the model.
- unique_name (str | None, default=None): Unique name of the model. If None,
- a unique name will be generated.
- unit (str | sc.Unit, default='meV'): Unit of the model.
- components (ModelComponent | ComponentCollection | None, default=None):
- Template components of the model. If None, no components
- are added. These components are copied into
- ComponentCollections for each Q value.
- Q (Q_type | None, default=None): Q values for the model. If None, Q is not
- set.
+ Parameters
+ ----------
+ display_name : str | None, default='MyBackgroundModel'
+ Display name of the model.
+ unique_name : str | None, default=None
+ Unique name of the model. If None, a unique name will be generated.
+ unit : str | sc.Unit, default='meV'
+ Unit of the model.
+ components : ModelComponent | ComponentCollection | None, default=None
+ Template components of the model. If None, no components are added. These components
+ are copied into ComponentCollections for each Q value.
+ Q : Q_type | None, default=None
+ Q values for the model. If None, Q is not set.
"""
super().__init__(
display_name=display_name,
diff --git a/src/easydynamics/sample_model/component_collection.py b/src/easydynamics/sample_model/component_collection.py
index 5f483091..f5f1a45a 100644
--- a/src/easydynamics/sample_model/component_collection.py
+++ b/src/easydynamics/sample_model/component_collection.py
@@ -4,6 +4,7 @@
from __future__ import annotations
import warnings
+from typing import TYPE_CHECKING
import numpy as np
import scipp as sc
@@ -11,14 +12,15 @@
from easyscience.variable import DescriptorBase
from easyscience.variable import Parameter
-from easydynamics.utils.utils import Numeric
+from easydynamics.sample_model.components.model_component import ModelComponent
-from .components.model_component import ModelComponent
+if TYPE_CHECKING:
+ from easydynamics.utils.utils import Numeric
class ComponentCollection(ModelBase):
- """Collection of model components representing a sample, background
- or resolution model.
+ """
+ Collection of model components representing a sample, background or resolution model.
"""
def __init__(
@@ -28,20 +30,24 @@ def __init__(
unique_name: str | None = None,
components: list[ModelComponent] | None = None,
) -> None:
- """Initialize a new ComponentCollection.
-
- Args:
- unit (str | sc.Unit, default='meV'): Unit of the collection.
- display_name (str | None, default="MyComponentCollection"): Display
- name of the collection
- unique_name (str | None, default=None): Unique name of the collection
- Defaults to None.
- components (list[ModelComponent] | None, default=None): Initial model
- components to add to the ComponentCollection.
-
- Raises:
- TypeError: If unit is not a string or sc.Unit,
- or if components is not a list of ModelComponent.
+ """
+ Initialize a new ComponentCollection.
+
+ Parameters
+ ----------
+ unit : str | sc.Unit, default='meV'
+ Unit of the collection.
+ display_name : str | None, default='MyComponentCollection'
+ Display name of the collection.
+ unique_name : str | None, default=None
+ Unique name of the collection.
+ components : list[ModelComponent] | None, default=None
+ Initial model components to add to the ComponentCollection.
+
+ Raises
+ ------
+ TypeError
+ If unit is not a string or sc.Unit, or if components is not a list of ModelComponent.
"""
super().__init__(display_name=display_name, unique_name=unique_name)
@@ -66,24 +72,31 @@ def __init__(
@property
def components(self) -> list[ModelComponent]:
- """Get the list of components in the collection.
+ """
+ Get the list of components in the collection.
- Returns:
- list[ModelComponent]: The components in the collection.
+ Returns
+ -------
+ list[ModelComponent]
+ The components in the collection.
"""
return list(self._components)
@components.setter
def components(self, components: list[ModelComponent]) -> None:
- """Set the list of components in the collection.
+ """
+ Set the list of components in the collection.
- Args:
- components (list[ModelComponent]): The new list of
- components.
+ Parameters
+ ----------
+ components : list[ModelComponent]
+ The new list of components.
- Raises:
- TypeError: If components is not a list of ModelComponent.
+ Raises
+ ------
+ TypeError
+ If components is not a list of ModelComponent.
"""
if not isinstance(components, list):
@@ -99,24 +112,30 @@ def components(self, components: list[ModelComponent]) -> None:
@property
def is_empty(self) -> bool:
- """Check if the ComponentCollection has no components.
+ """
+ Check if the ComponentCollection has no components.
- Returns:
- bool: True if the collection has no components,
- False otherwise.
+ Returns
+ -------
+ bool
+ True if the collection has no components, False otherwise.
"""
return not self._components
@is_empty.setter
def is_empty(self, _value: bool) -> None:
- """is_empty is a read-only property that indicates whether the
- collection has components.
+ """
+ Is_empty is a read-only property that indicates whether the collection has components.
- Args:
- _value (bool): The value to set (ignored).
+ Parameters
+ ----------
+ _value : bool
+ The value to set (ignored).
- Raises:
- AttributeError: Always raised since is_empty is read-only.
+ Raises
+ ------
+ AttributeError
+ Always raised since is_empty is read-only.
"""
raise AttributeError(
'is_empty is a read-only property that indicates '
@@ -125,41 +144,52 @@ def is_empty(self, _value: bool) -> None:
@property
def unit(self) -> str | sc.Unit | None:
- """Get the unit of the ComponentCollection.
+ """
+ Get the unit of the ComponentCollection.
- Returns:
- str | sc.Unit | None: The unit of the ComponentCollection,
- which is the same as the unit of its components.
+ Returns
+ -------
+ str | sc.Unit | None
+ The unit of the ComponentCollection, which is the same as the unit of its components.
"""
return self._unit
@unit.setter
def unit(self, _unit_str: str) -> None:
- """Unit is read-only and cannot be set directly.
+ """
+ Unit is read-only and cannot be set directly.
- Args:
- _unit_str (str): The unit to set (ignored).
+ Parameters
+ ----------
+ _unit_str : str
+ The unit to set (ignored).
- Raises:
- AttributeError: Always raised since unit is read-only.
+ Raises
+ ------
+ AttributeError
+ Always raised since unit is read-only.
"""
raise AttributeError(
f'Unit is read-only. Use convert_unit to change the unit between allowed types '
f'or create a new {self.__class__.__name__} with the desired unit.'
- ) # noqa: E501
+ )
def convert_unit(self, unit: str | sc.Unit) -> None:
- """Convert the unit of the ComponentCollection and all its
- components.
-
- Args:
- unit (str | sc.Unit): The target unit to convert to.
-
- Raises:
- TypeError: If unit is not a string or sc.Unit.
- Exception: If any component cannot be converted to the
- specified unit.
+ """
+ Convert the unit of the ComponentCollection and all its components.
+
+ Parameters
+ ----------
+ unit : str | sc.Unit
+ The target unit to convert to.
+
+ Raises
+ ------
+ TypeError
+ If unit is not a string or sc.Unit.
+ Exception
+ If any component cannot be converted to the specified unit.
"""
if not isinstance(unit, (str, sc.Unit)):
@@ -185,19 +215,22 @@ def convert_unit(self, unit: str | sc.Unit) -> None:
# ------------------------------------------------------------------
def append_component(self, component: ModelComponent | ComponentCollection) -> None:
- """Append a model component or the components from another
- ComponentCollection to this ComponentCollection.
-
- Args:
- component (ModelComponent | "ComponentCollection"): The component
- to append. If a ComponentCollection is provided, all of its
- components will be appended.
-
- Raises:
- TypeError: If component is not a ModelComponent or
- ComponentCollection.
- ValueError: If a component with the same unique name already
- exists in the collection.
+ """
+ Append a model component or the components from another ComponentCollection to this
+ ComponentCollection.
+
+ Parameters
+ ----------
+ component : ModelComponent | ComponentCollection
+ The component to append. If a ComponentCollection is provided, all of its components
+ will be appended.
+
+ Raises
+ ------
+ TypeError
+ If component is not a ModelComponent or ComponentCollection.
+ ValueError
+ If a component with the same unique name already exists in the collection.
"""
if not isinstance(component, (ModelComponent, ComponentCollection)):
raise TypeError(
@@ -219,15 +252,20 @@ def append_component(self, component: ModelComponent | ComponentCollection) -> N
self._components.append(comp)
def remove_component(self, unique_name: str) -> None:
- """Remove a component from the collection by its unique name.
-
- Args:
- unique_name (str): Unique name of the component to remove.
-
- Raises:
- TypeError: If unique_name is not a string.
- KeyError: If no component with the given unique name exists
- in the collection.
+ """
+ Remove a component from the collection by its unique name.
+
+ Parameters
+ ----------
+ unique_name : str
+ Unique name of the component to remove.
+
+ Raises
+ ------
+ TypeError
+ If unique_name is not a string.
+ KeyError
+ If no component with the given unique name exists in the collection.
"""
if not isinstance(unique_name, str):
@@ -246,22 +284,30 @@ def remove_component(self, unique_name: str) -> None:
@property
def components(self) -> list[ModelComponent]:
- """Get the list of components in the collection.
+ """
+ Get the list of components in the collection.
- Returns:
- list[ModelComponent]: The components in the collection.
+ Returns
+ -------
+ list[ModelComponent]
+ The components in the collection.
"""
return list(self._components)
@components.setter
def components(self, components: list[ModelComponent]) -> None:
- """Set the components in the collection.
+ """
+ Set the components in the collection.
- Args:
- components (list[ModelComponent]): The new components in the collection
+ Parameters
+ ----------
+ components : list[ModelComponent]
+ The new components in the collection.
- Raises:
- TypeError: If components is not a list of ModelComponent
+ Raises
+ ------
+ TypeError
+ If components is not a list of ModelComponent.
"""
if not isinstance(components, list):
raise TypeError('components must be a list of ModelComponent instances.')
@@ -276,23 +322,30 @@ def components(self, components: list[ModelComponent]) -> None:
@property
def is_empty(self) -> bool:
- """Returns True if the collection has no components, otherwise
- False.
+ """
+ Returns True if the collection has no components, otherwise False.
- Returns:
- bool: True if the collection has no components, otherwise False
+ Returns
+ -------
+ bool
+ True if the collection has no components, otherwise False.
"""
return not self._components
@is_empty.setter
def is_empty(self, _value: bool) -> None:
- """is_empty is read-only.
+ """
+ Is_empty is read-only.
- Args:
- _value (bool): ignored.
+ Parameters
+ ----------
+ _value : bool
+ Ignored.
- Raises:
- AttributeError: Always raised since is_empty is read-only
+ Raises
+ ------
+ AttributeError
+ Always raised since is_empty is read-only.
"""
raise AttributeError(
'is_empty is a read-only property that indicates '
@@ -300,11 +353,13 @@ def is_empty(self, _value: bool) -> None:
)
def list_component_names(self) -> list[str]:
- """List the names of all components in the model.
+ """
+ List the names of all components in the model.
- Returns:
- list[str]: List of unique names of the components in the
- collection.
+ Returns
+ -------
+ list[str]
+ List of unique names of the components in the collection.
"""
return [component.unique_name for component in self._components]
@@ -314,13 +369,16 @@ def clear_components(self) -> None:
self._components.clear()
def normalize_area(self) -> None:
- """Normalize the areas of all components so they sum to 1. This
- is useful for convolutions.
+ """
+ Normalize the areas of all components so they sum to 1.
- Raises:
- ValueError: If there are no components in the model or
- if the total area is zero or not finite, which
- would prevent normalization.
+ This is useful for convolutions.
+
+ Raises
+ ------
+ ValueError
+ If there are no components in the model or if the total area is zero or not finite,
+ which would prevent normalization.
"""
if not self.components:
raise ValueError('No components in the model to normalize.')
@@ -354,23 +412,30 @@ def normalize_area(self) -> None:
# ------------------------------------------------------------------
def get_all_variables(self) -> list[DescriptorBase]:
- """Get all parameters from the model component.
+ """
+ Get all parameters from the model component.
- Returns:
- list[DescriptorBase]: List of parameters in the component.
+ Returns
+ -------
+ list[DescriptorBase]
+ List of parameters in the component.
"""
return [var for component in self.components for var in component.get_all_variables()]
def evaluate(self, x: Numeric | list | np.ndarray | sc.Variable | sc.DataArray) -> np.ndarray:
- """Evaluate the sum of all components.
+ """
+ Evaluate the sum of all components.
- Args:
- x (Numeric | list | np.ndarray | sc.Variable | sc.DataArray):
- Energy axis.
+ Parameters
+ ----------
+ x : Numeric | list | np.ndarray | sc.Variable | sc.DataArray
+ Energy axis.
- Returns:
- np.ndarray: Evaluated model values.
+ Returns
+ -------
+ np.ndarray
+ Evaluated model values.
"""
if not self.components:
@@ -382,20 +447,29 @@ def evaluate_component(
x: Numeric | list | np.ndarray | sc.Variable | sc.DataArray,
unique_name: str,
) -> np.ndarray:
- """Evaluate a single component by name.
-
- Args:
- x (Numeric | list | np.ndarray | sc.Variable | sc.DataArray):
- Energy axis.
- unique_name (str): Component unique name.
-
- Returns:
- np.ndarray: Evaluated values for the specified component.
- Raises:
- ValueError: If there are no components in the model.
- TypeError: If unique_name is not a string.
- KeyError: If no component with the given unique name exists
- in the collection.
+ """
+ Evaluate a single component by name.
+
+ Parameters
+ ----------
+ x : Numeric | list | np.ndarray | sc.Variable | sc.DataArray
+ Energy axis.
+ unique_name : str
+ Component unique name.
+
+ Raises
+ ------
+ ValueError
+ If there are no components in the model.
+ TypeError
+ If unique_name is not a string.
+ KeyError
+ If no component with the given unique name exists in the collection.
+
+ Returns
+ -------
+ np.ndarray
+ Evaluated values for the specified component.
"""
if not self.components:
raise ValueError('No components in the model to evaluate.')
@@ -428,15 +502,18 @@ def free_all_parameters(self) -> None:
# ------------------------------------------------------------------
def __contains__(self, item: str | ModelComponent) -> bool:
- """Check if a component with the given name or instance exists
- in the ComponentCollection.
+ """
+ Check if a component with the given name or instance exists in the ComponentCollection.
- Args:
- item (str | ModelComponent): The component name or instance
- to check for.
+ Parameters
+ ----------
+ item : str | ModelComponent
+ The component name or instance to check for.
- Returns:
- bool: True if the component exists, False otherwise.
+ Returns
+ -------
+ bool
+ True if the component exists, False otherwise.
"""
if isinstance(item, str):
@@ -448,10 +525,13 @@ def __contains__(self, item: str | ModelComponent) -> bool:
return False
def __repr__(self) -> str:
- """Return a string representation of the ComponentCollection.
+ """
+ Return a string representation of the ComponentCollection.
- Returns:
- str: String representation of the ComponentCollection.
+ Returns
+ -------
+ str
+ String representation of the ComponentCollection.
"""
comp_names = ', '.join(c.unique_name for c in self.components) or 'No components'
diff --git a/src/easydynamics/sample_model/components/__init__.py b/src/easydynamics/sample_model/components/__init__.py
index 54bec057..940f41a7 100644
--- a/src/easydynamics/sample_model/components/__init__.py
+++ b/src/easydynamics/sample_model/components/__init__.py
@@ -1,22 +1,24 @@
# SPDX-FileCopyrightText: 2025 EasyScience contributors
# SPDX-License-Identifier: BSD-3-Clause
-from .damped_harmonic_oscillator import DampedHarmonicOscillator
-from .delta_function import DeltaFunction
-from .exponential import Exponential
-from .expression_component import ExpressionComponent
-from .gaussian import Gaussian
-from .lorentzian import Lorentzian
-from .polynomial import Polynomial
-from .voigt import Voigt
+from easydynamics.sample_model.components.damped_harmonic_oscillator import (
+ DampedHarmonicOscillator,
+)
+from easydynamics.sample_model.components.delta_function import DeltaFunction
+from easydynamics.sample_model.components.exponential import Exponential
+from easydynamics.sample_model.components.expression_component import ExpressionComponent
+from easydynamics.sample_model.components.gaussian import Gaussian
+from easydynamics.sample_model.components.lorentzian import Lorentzian
+from easydynamics.sample_model.components.polynomial import Polynomial
+from easydynamics.sample_model.components.voigt import Voigt
__all__ = [
- 'Gaussian',
- 'Lorentzian',
- 'Voigt',
- 'DeltaFunction',
'DampedHarmonicOscillator',
- 'Polynomial',
+ 'DeltaFunction',
'Exponential',
'ExpressionComponent',
+ 'Gaussian',
+ 'Lorentzian',
+ 'Polynomial',
+ 'Voigt',
]
diff --git a/src/easydynamics/sample_model/components/damped_harmonic_oscillator.py b/src/easydynamics/sample_model/components/damped_harmonic_oscillator.py
index 81a766f7..d74b9116 100644
--- a/src/easydynamics/sample_model/components/damped_harmonic_oscillator.py
+++ b/src/easydynamics/sample_model/components/damped_harmonic_oscillator.py
@@ -3,26 +3,25 @@
from __future__ import annotations
+from typing import TYPE_CHECKING
+
import numpy as np
-import scipp as sc
-from easyscience.variable import Parameter
from easydynamics.sample_model.components.mixins import CreateParametersMixin
+from easydynamics.sample_model.components.model_component import ModelComponent
from easydynamics.utils.utils import Numeric
-from .model_component import ModelComponent
+if TYPE_CHECKING:
+ import scipp as sc
+ from easyscience.variable import Parameter
class DampedHarmonicOscillator(CreateParametersMixin, ModelComponent):
- r"""Model of a Damped Harmonic Oscillator (DHO).
-
- The intensity is given by
- $$
- I(x) = \frac{2 A x_0^2 \gamma}{\pi \left( (x^2 - x_0^2)^2 +
- (2 \gamma x)^2 \right)},
- $$
- where $A$ is the area, $x_0$ is the center, and $\gamma$ is the
- width.
+ r"""
+ Model of a Damped Harmonic Oscillator (DHO).
+
+ The intensity is given by $$ I(x) = \frac{2 A x_0^2 \gamma}{\pi \left( (x^2 - x_0^2)^2 + (2
+ \gamma x)^2 \right)}, $$ where $A$ is the area, $x_0$ is the center, and $\gamma$ is the width.
"""
def __init__(
@@ -34,19 +33,25 @@ def __init__(
display_name: str | None = 'DampedHarmonicOscillator',
unique_name: str | None = None,
) -> None:
- """Initialize the Damped Harmonic Oscillator.
-
- Args:
- area (Numeric | Parameter, default=1.0): Area under the curve.
- center (Numeric | Parameter, default=1.0): Resonance frequency, approximately the
- peak position.
- width (Numeric | Parameter, default=1.0): Damping constant, approximately the
- half width at half max (HWHM) of the peaks.
- unit (str | sc.Unit, default='meV'): Unit of the parameters.
- display_name (str | None, default='DampedHarmonicOscillator'):
- Display name of the component.
- unique_name (str | None, default=None): Unique name of the component.
- If None, a unique_name is automatically generated.
+ """
+ Initialize the Damped Harmonic Oscillator.
+
+ Parameters
+ ----------
+ area : Numeric | Parameter, default=1.0
+ Area under the curve.
+ center : Numeric | Parameter, default=1.0
+ Resonance frequency, approximately the peak position.
+ width : Numeric | Parameter, default=1.0
+ Damping constant, approximately the half width at half max (HWHM) of the peaks. By
+ default, 1.0.
+ unit : str | sc.Unit, default='meV'
+ Unit of the parameters.
+ display_name : str | None, default='DampedHarmonicOscillator'
+ Display name of the component.
+ unique_name : str | None, default=None
+ Unique name of the component. If None, a unique_name is automatically generated. By
+ default, None.
"""
super().__init__(
@@ -73,22 +78,30 @@ def __init__(
@property
def area(self) -> Parameter:
- """Get the area parameter.
+ """
+ Get the area parameter.
- Returns:
- Parameter: The area parameter.
+ Returns
+ -------
+ Parameter
+ The area parameter.
"""
return self._area
@area.setter
def area(self, value: Numeric) -> None:
- """Set the value of the area parameter.
+ """
+ Set the value of the area parameter.
- Args:
- value (Numeric): The new value for the area parameter.
+ Parameters
+ ----------
+ value : Numeric
+ The new value for the area parameter.
- Raises:
- TypeError: If the value is not a number.
+ Raises
+ ------
+ TypeError
+ If the value is not a number.
"""
if not isinstance(value, Numeric):
raise TypeError('area must be a number')
@@ -96,23 +109,32 @@ def area(self, value: Numeric) -> None:
@property
def center(self) -> Parameter:
- """Get the center parameter.
+ """
+ Get the center parameter.
- Returns:
- Parameter: The center parameter.
+ Returns
+ -------
+ Parameter
+ The center parameter.
"""
return self._center
@center.setter
def center(self, value: Numeric) -> None:
- """Set the value of the center parameter.
-
- Args:
- value (Numeric): The new value for the center parameter.
-
- Raises:
- TypeError: If the value is not a number.
- ValueError: If the value is not positive.
+ """
+ Set the value of the center parameter.
+
+ Parameters
+ ----------
+ value : Numeric
+ The new value for the center parameter.
+
+ Raises
+ ------
+ TypeError
+ If the value is not a number.
+ ValueError
+ If the value is not positive.
"""
if not isinstance(value, Numeric):
raise TypeError('center must be a number')
@@ -123,23 +145,32 @@ def center(self, value: Numeric) -> None:
@property
def width(self) -> Parameter:
- """Get the width parameter.
+ """
+ Get the width parameter.
- Returns:
- Parameter: The width parameter.
+ Returns
+ -------
+ Parameter
+ The width parameter.
"""
return self._width
@width.setter
def width(self, value: Numeric) -> None:
- """Set the value of the width parameter.
-
- Args:
- value (Numeric): The new value for the width parameter.
-
- Raises:
- TypeError: If the value is not a number.
- ValueError: If the value is not positive.
+ """
+ Set the value of the width parameter.
+
+ Parameters
+ ----------
+ value : Numeric
+ The new value for the width parameter.
+
+ Raises
+ ------
+ TypeError
+ If the value is not a number.
+ ValueError
+ If the value is not positive.
"""
if not isinstance(value, Numeric):
raise TypeError('width must be a number')
@@ -150,24 +181,22 @@ def width(self, value: Numeric) -> None:
self._width.value = value
def evaluate(self, x: Numeric | list | np.ndarray | sc.Variable | sc.DataArray) -> np.ndarray:
- r"""Evaluate the Damped Harmonic Oscillator at the given x
- values.
-
- If x is a scipp Variable, the unit of the DHO will be converted
- to match x. The intensity is given by
- $$
- I(x) = \frac{2 A x_0^2 \gamma}{\pi \left( (x^2 - x_0^2)^2 +
- (2 \gamma x)^2 \right)},
- $$
- where $A$ is the area, $x_0$ is the center, and $\gamma$ is the
- width.
-
- Args:
- x (Numeric | list | np.ndarray | sc.Variable | sc.DataArray):
- The x values at which to evaluate the DHO.
-
- Returns:
- np.ndarray: The intensity of the DHO at the given x values.
+ r"""
+ Evaluate the Damped Harmonic Oscillator at the given x values.
+
+ If x is a scipp Variable, the unit of the DHO will be converted to match x. The intensity
+ is given by $$ I(x) = \frac{2 A x_0^2 \gamma}{\pi \left( (x^2 - x_0^2)^2 + (2 \gamma x)^2
+ \right)}, $$ where $A$ is the area, $x_0$ is the center, and $\gamma$ is the width.
+
+ Parameters
+ ----------
+ x : Numeric | list | np.ndarray | sc.Variable | sc.DataArray
+ The x values at which to evaluate the DHO.
+
+ Returns
+ -------
+ np.ndarray
+ The intensity of the DHO at the given x values.
"""
x = self._prepare_x_for_evaluate(x)
@@ -179,14 +208,16 @@ def evaluate(self, x: Numeric | list | np.ndarray | sc.Variable | sc.DataArray)
return self.area.value * normalization / (denominator)
def __repr__(self) -> str:
- """Return a string representation of the Damped Harmonic
- Oscillator.
+ """
+ Return a string representation of the Damped Harmonic Oscillator.
- Returns:
- str: A string representation of the Damped Harmonic
- Oscillator.
+ Returns
+ -------
+ str
+ A string representation of the Damped Harmonic Oscillator.
"""
return (
- f'DampedHarmonicOscillator(display_name = {self.display_name}, unit = {self._unit},\n \
- area = {self.area},\n center = {self.center},\n width = {self.width})'
+ f'DampedHarmonicOscillator(display_name = {self.display_name}, '
+ f'unit = {self._unit},\n '
+ f'area = {self.area},\n center = {self.center},\n width = {self.width})'
)
diff --git a/src/easydynamics/sample_model/components/delta_function.py b/src/easydynamics/sample_model/components/delta_function.py
index 820a039b..e3720f8b 100644
--- a/src/easydynamics/sample_model/components/delta_function.py
+++ b/src/easydynamics/sample_model/components/delta_function.py
@@ -3,25 +3,29 @@
from __future__ import annotations
+from typing import TYPE_CHECKING
+
import numpy as np
-import scipp as sc
-from easyscience.variable import Parameter
from easydynamics.sample_model.components.mixins import CreateParametersMixin
+from easydynamics.sample_model.components.model_component import ModelComponent
from easydynamics.utils.utils import Numeric
-from .model_component import ModelComponent
-
EPSILON = 1e-8 # small number to avoid floating point issues
+if TYPE_CHECKING:
+ import scipp as sc
+ from easyscience.variable import Parameter
+
+
class DeltaFunction(CreateParametersMixin, ModelComponent):
- """Delta function.
+ """
+ Delta function.
- Evaluates to zero everywhere, except in convolutions, where it acts
- as an identity. This is handled by the Convolution method. If the
- center is not provided, it will be centered at 0 and fixed, which is
- typically what you want in QENS.
+ Evaluates to zero everywhere, except in convolutions, where it acts as an identity. This is
+ handled by the Convolution method. If the center is not provided, it will be centered at 0 and
+ fixed, which is typically what you want in QENS.
"""
def __init__(
@@ -32,16 +36,22 @@ def __init__(
display_name: str | None = 'DeltaFunction',
unique_name: str | None = None,
) -> None:
- """Initialize the Delta function.
-
- Args:
- center (Numeric | Parameter | None, default=None): Center of the delta function.
- If None, defaults to 0 and is fixed.
- area (Numeric | Parameter, default=1.0): Total area under the curve.
- unit (str | sc.Unit, default='meV'): Unit of the parameters.
- display_name (str | None, default='DeltaFunction'): Name of the component.
- unique_name (str | None, default=None): Unique name of the component.
- If None, a unique_name is automatically generated.
+ """
+ Initialize the Delta function.
+
+ Parameters
+ ----------
+ center : Numeric | Parameter | None, default=None
+ Center of the delta function. If None.
+ area : Numeric | Parameter, default=1.0
+ Total area under the curve.
+ unit : str | sc.Unit, default='meV'
+ Unit of the parameters.
+ display_name : str | None, default='DeltaFunction'
+ Name of the component.
+ unique_name : str | None, default=None
+ Unique name of the component. If None, a unique_name is automatically generated. By
+ default, None.
"""
# Validate inputs and create Parameters if not given
super().__init__(
@@ -61,23 +71,31 @@ def __init__(
@property
def area(self) -> Parameter:
- """Get the area parameter.
+ """
+ Get the area parameter.
- Returns:
- Parameter: The area parameter.
+ Returns
+ -------
+ Parameter
+ The area parameter.
"""
return self._area
@area.setter
def area(self, value: Numeric) -> None:
- """Set the value of the area parameter.
+ """
+ Set the value of the area parameter.
- Args:
- value (Numeric): The new value for the area parameter.
+ Parameters
+ ----------
+ value : Numeric
+ The new value for the area parameter.
- Raises:
- TypeError: If the value is not a number.
+ Raises
+ ------
+ TypeError
+ If the value is not a number.
"""
if not isinstance(value, Numeric):
@@ -86,24 +104,31 @@ def area(self, value: Numeric) -> None:
@property
def center(self) -> Parameter:
- """Get the center parameter.
+ """
+ Get the center parameter.
- Returns:
- Parameter: The center parameter.
+ Returns
+ -------
+ Parameter
+ The center parameter.
"""
return self._center
@center.setter
def center(self, value: Numeric | None) -> None:
- """Set the center parameter value.
+ """
+ Set the center parameter value.
- Args:
- value (Numeric | None): The new value for the center
- parameter. If None, defaults to 0 and is fixed.
+ Parameters
+ ----------
+ value : Numeric | None
+ The new value for the center parameter. If None, defaults to 0 and is fixed.
- Raises:
- TypeError: If the value is not a number or None.
+ Raises
+ ------
+ TypeError
+ If the value is not a number or None.
"""
if value is None:
@@ -114,19 +139,21 @@ def center(self, value: Numeric | None) -> None:
self._center.value = value
def evaluate(self, x: Numeric | list | np.ndarray | sc.Variable | sc.DataArray) -> np.ndarray:
- """Evaluate the Delta function at the given x values.
+ """
+ Evaluate the Delta function at the given x values.
- The Delta function evaluates to zero everywhere, except at the
- center. Its numerical integral is equal to the area. It acts as
- an identity in convolutions.
+ The Delta function evaluates to zero everywhere, except at the center. Its numerical
+ integral is equal to the area. It acts as an identity in convolutions.
- Args:
- x (Numeric | list | np.ndarray | sc.Variable | sc.DataArray):
- The x values at which to evaluate the Delta function.
+ Parameters
+ ----------
+ x : Numeric | list | np.ndarray | sc.Variable | sc.DataArray
+ The x values at which to evaluate the Delta function.
- Returns:
- np.ndarray: The evaluated Delta function at the given x
- values.
+ Returns
+ -------
+ np.ndarray
+ The evaluated Delta function at the given x values.
"""
# x assumed sorted, 1D numpy array
@@ -159,11 +186,16 @@ def evaluate(self, x: Numeric | list | np.ndarray | sc.Variable | sc.DataArray)
return model
def __repr__(self) -> str:
- """Return a string representation of the Delta function.
+ """
+ Return a string representation of the Delta function.
- Returns:
- str: A string representation of the Delta function.
+ Returns
+ -------
+ str
+ A string representation of the Delta function.
"""
- return f'DeltaFunction(unique_name = {self.unique_name}, unit = {self._unit},\n \
- area = {self.area},\n center = {self.center}'
+ return (
+ f'DeltaFunction(unique_name = {self.unique_name}, unit = {self._unit},\n'
+ f'area = {self.area},\n center = {self.center})'
+ )
diff --git a/src/easydynamics/sample_model/components/exponential.py b/src/easydynamics/sample_model/components/exponential.py
index 56a72912..f06e8138 100644
--- a/src/easydynamics/sample_model/components/exponential.py
+++ b/src/easydynamics/sample_model/components/exponential.py
@@ -8,20 +8,19 @@
from easyscience.variable import Parameter
from easydynamics.sample_model.components.mixins import CreateParametersMixin
+from easydynamics.sample_model.components.model_component import ModelComponent
from easydynamics.utils.utils import Numeric
-from .model_component import ModelComponent
-
class Exponential(CreateParametersMixin, ModelComponent):
- r"""Model of an exponential function.
+ r"""
+ Model of an exponential function.
The intensity is given by
$$ I(x) = A e^{B (x-x_0)}, $$
- where $A$ is the amplitude, $x_0$ is the center, and $B$ describes
- the rate of decay or growth.
+ where $A$ is the amplitude, $x_0$ is the center, and $B$ describes the rate of decay or growth.
"""
def __init__(
@@ -33,24 +32,31 @@ def __init__(
display_name: str | None = 'Exponential',
unique_name: str | None = None,
) -> None:
- """Initialize the Exponential component.
-
- Args:
- amplitude (Numeric | Parameter, default=1.0): Amplitude of the
- Exponential.
- center (Numeric | Parameter | None, default=None): Center of the Exponential.
- If None, the center is fixed at 0.
- rate (Numeric | Parameter, default=1.0): Decay or growth
- constant of the Exponential.
- unit (str | sc.Unit, default='meV'): Unit of the parameters.
- display_name (str | None, default='Exponential'): Name of the component.
- unique_name (str | None, default=None): Unique name of the component. if
- None, a unique_name is automatically generated.
-
- Raises:
- TypeError: If amplitude, center, or rate are not numbers or
- Parameters.
- ValueError: If amplitude, center or rate are not finite numbers
+ """
+ Initialize the Exponential component.
+
+ Parameters
+ ----------
+ amplitude : Numeric | Parameter, default=1.0
+ Amplitude of the Exponential.
+ center : Numeric | Parameter | None, default=None
+ Center of the Exponential. If None, the center is fixed at 0.
+ rate : Numeric | Parameter, default=1.0
+ Decay or growth constant of the Exponential.
+ unit : str | sc.Unit, default='meV'
+ Unit of the parameters.
+ display_name : str | None, default='Exponential'
+ Name of the component.
+ unique_name : str | None, default=None
+ Unique name of the component. if None, a unique_name is automatically generated. By
+ default, None.
+
+ Raises
+ ------
+ TypeError
+ If amplitude, center, or rate are not numbers or Parameters.
+ ValueError
+ If amplitude, center or rate are not finite numbers.
"""
# Validate inputs and create Parameters if not given
super().__init__(
@@ -89,23 +95,31 @@ def __init__(
@property
def amplitude(self) -> Parameter:
- """Get the amplitude parameter.
+ """
+ Get the amplitude parameter.
- Returns:
- Parameter: The amplitude parameter.
+ Returns
+ -------
+ Parameter
+ The amplitude parameter.
"""
return self._amplitude
@amplitude.setter
def amplitude(self, value: Numeric) -> None:
- """Set the value of the amplitude parameter.
+ """
+ Set the value of the amplitude parameter.
- Args:
- value (Numeric): The new value for the amplitude parameter.
+ Parameters
+ ----------
+ value : Numeric
+ The new value for the amplitude parameter.
- Raises:
- TypeError: If the value is not a number.
+ Raises
+ ------
+ TypeError
+ If the value is not a number.
"""
if not isinstance(value, Numeric):
@@ -114,24 +128,31 @@ def amplitude(self, value: Numeric) -> None:
@property
def center(self) -> Parameter:
- """Get the center parameter.
+ """
+ Get the center parameter.
- Returns:
- Parameter: The center parameter.
+ Returns
+ -------
+ Parameter
+ The center parameter.
"""
return self._center
@center.setter
def center(self, value: Numeric | None) -> None:
- """Set the center parameter value.
+ """
+ Set the center parameter value.
- Args:
- value (Numeric | None): The new value for the center
- parameter.
+ Parameters
+ ----------
+ value : Numeric | None
+ The new value for the center parameter.
- Raises:
- TypeError: If the value is not a number.
+ Raises
+ ------
+ TypeError
+ If the value is not a number.
"""
if value is None:
@@ -144,23 +165,30 @@ def center(self, value: Numeric | None) -> None:
@property
def rate(self) -> Parameter:
- """Get the rate parameter.
+ """
+ Get the rate parameter.
- Returns:
- Parameter: The rate parameter.
+ Returns
+ -------
+ Parameter
+ The rate parameter.
"""
return self._rate
@rate.setter
def rate(self, value: Numeric) -> None:
- """Set the rate parameter value.
+ """
+ Set the rate parameter value.
- Args:
- value (Numeric): The new value for the rate
- parameter.
+ Parameters
+ ----------
+ value : Numeric
+ The new value for the rate parameter.
- Raises:
- TypeError: If the value is not a number.
+ Raises
+ ------
+ TypeError
+ If the value is not a number.
"""
if not isinstance(value, Numeric):
raise TypeError('rate must be a number')
@@ -171,25 +199,23 @@ def evaluate(
self,
x: Numeric | list | np.ndarray | sc.Variable | sc.DataArray,
) -> np.ndarray:
- r"""Evaluate the Exponential at the given x values.
+ r"""
+ Evaluate the Exponential at the given x values.
- If x is a scipp Variable, the unit of the Exponential will be
- converted to match x.
- The intensity is given by
- $$
- I(x) = A \exp\left( r (x - x_0) \right)
- $$
+ If x is a scipp Variable, the unit of the Exponential will be converted to match x. The
+ intensity is given by $$ I(x) = A \exp\left( r (x - x_0) \right) $$
- where $A$ is the amplitude, $x_0$ is the center, and $r$ is the
- rate.
+ where $A$ is the amplitude, $x_0$ is the center, and $r$ is the rate.
- Args:
- x (Numeric | list | np.ndarray | sc.Variable | sc.DataArray):
- The x values at which to evaluate the Exponential.
+ Parameters
+ ----------
+ x : Numeric | list | np.ndarray | sc.Variable | sc.DataArray
+ The x values at which to evaluate the Exponential.
- Returns:
- np.ndarray: The intensity of the Exponential at the given x
- values.
+ Returns
+ -------
+ np.ndarray
+ The intensity of the Exponential at the given x values.
"""
x = self._prepare_x_for_evaluate(x)
@@ -198,14 +224,20 @@ def evaluate(
return self.amplitude.value * np.exp(exponent)
def convert_unit(self, unit: str | sc.Unit) -> None:
- """Convert the unit of the Parameters in the component.
-
- Args:
- unit (str | sc.Unit): The new unit to convert to.
-
- Raises:
- TypeError: If unit is not a string or sc.Unit.
- Exception: If conversion fails for any parameter.
+ """
+ Convert the unit of the Parameters in the component.
+
+ Parameters
+ ----------
+ unit : str | sc.Unit
+ The new unit to convert to.
+
+ Raises
+ ------
+ TypeError
+ If unit is not a string or sc.Unit.
+ Exception
+ If conversion fails for any parameter.
"""
if not isinstance(unit, (str, sc.Unit)):
@@ -229,10 +261,13 @@ def convert_unit(self, unit: str | sc.Unit) -> None:
raise e
def __repr__(self) -> str:
- """Return a string representation of the Exponential.
+ """
+ Return a string representation of the Exponential.
- Returns:
- str: A string representation of the Exponential.
+ Returns
+ -------
+ str
+ A string representation of the Exponential.
"""
return f'Exponential(unique_name = {self.unique_name}, unit = {self._unit},\n \
diff --git a/src/easydynamics/sample_model/components/expression_component.py b/src/easydynamics/sample_model/components/expression_component.py
index dcc9e445..79ce73ef 100644
--- a/src/easydynamics/sample_model/components/expression_component.py
+++ b/src/easydynamics/sample_model/components/expression_component.py
@@ -3,33 +3,34 @@
from __future__ import annotations
-import numpy as np
-import scipp as sc
+from typing import TYPE_CHECKING
+from typing import ClassVar
+
import sympy as sp
from easyscience.variable import Parameter
+from easydynamics.sample_model.components.model_component import ModelComponent
from easydynamics.utils.utils import Numeric
-from .model_component import ModelComponent
+if TYPE_CHECKING:
+ import numpy as np
+ import scipp as sc
class ExpressionComponent(ModelComponent):
- """Model component defined by a symbolic expression.
+ """
+ Model component defined by a symbolic expression.
- Example:
- expr = ExpressionComponent(
- "A * exp(-(x - x0)**2 / (2*sigma**2))",
- parameters={"A": 10, "x0": 0, "sigma": 1},
- )
+ Example: expr = ExpressionComponent( "A * exp(-(x - x0)**2 / (2*sigma**2))", parameters={"A":
+ 10, "x0": 0, "sigma": 1}, )
- expr.A = 5
- y = expr.evaluate(x)
+ expr.A = 5 y = expr.evaluate(x)
"""
# -------------------------
# Allowed symbolic functions
# -------------------------
- _ALLOWED_FUNCS = {
+ _ALLOWED_FUNCS: ClassVar[dict[str, object]] = {
# Exponentials & logs
'exp': sp.exp,
'log': sp.log,
@@ -62,12 +63,12 @@ class ExpressionComponent(ModelComponent):
# -------------------------
# Allowed constants
# -------------------------
- _ALLOWED_CONSTANTS = {
+ _ALLOWED_CONSTANTS: ClassVar[dict[str, object]] = {
'pi': sp.pi,
'E': sp.E,
}
- _RESERVED_NAMES = {'x'}
+ _RESERVED_NAMES: ClassVar[dict[str, object]] = {'x'}
def __init__(
self,
@@ -77,21 +78,28 @@ def __init__(
display_name: str | None = 'Expression',
unique_name: str | None = None,
) -> None:
- """Initialize the ExpressionComponent.
-
- Args:
- expression (str): The symbolic expression as a string.
- Must contain 'x' as the independent variable.
- parameters (dict[str, Numeric] | None, default=None):
- Dictionary of parameter names and their initial values.
- Defaults to None (no parameters).
- unit (str | sc.Unit, default="meV"): Unit of the output.
- display_name (str | None, default="Expression"): Display name for the component.
- unique_name (str | None, default=None): Unique name for the component.
-
- Raises:
- ValueError: If the expression is invalid or does not contain 'x'.
- TypeError: If any parameter value is not numeric.
+ """
+ Initialize the ExpressionComponent.
+
+ Parameters
+ ----------
+ expression : str
+ The symbolic expression as a string. Must contain 'x' as the independent variable.
+ parameters : dict[str, Numeric] | None, default=None
+ Dictionary of parameter names and their initial values.
+ unit : str | sc.Unit, default='meV'
+ Unit of the output.
+ display_name : str | None, default='Expression'
+ Display name for the component.
+ unique_name : str | None, default=None
+ Unique name for the component.
+
+ Raises
+ ------
+ ValueError
+ If the expression is invalid or does not contain 'x'.
+ TypeError
+ If any parameter value is not numeric.
"""
super().__init__(unit=unit, display_name=display_name, unique_name=unique_name)
@@ -187,13 +195,18 @@ def expression(self) -> str:
@expression.setter
def expression(self, _new_expr: str) -> None:
- """Prevent changing the expression after initialization.
+ """
+ Prevent changing the expression after initialization.
- Args:
- _new_expr (str): New expression string (ignored).
+ Parameters
+ ----------
+ _new_expr : str
+ New expression string (ignored).
- Raises:
- AttributeError: Always raised to prevent changing the expression.
+ Raises
+ ------
+ AttributeError
+ Always raised to prevent changing the expression.
"""
raise AttributeError('Expression cannot be changed after initialization')
@@ -201,14 +214,18 @@ def evaluate(
self,
x: Numeric | list | np.ndarray | sc.Variable | sc.DataArray,
) -> np.ndarray:
- """Evaluate the expression for given x values.
+ """
+ Evaluate the expression for given x values.
- Args:
- x (Numeric | list | np.ndarray | sc.Variable | sc.DataArray):
- Input values for the independent variable.
+ Parameters
+ ----------
+ x : Numeric | list | np.ndarray | sc.Variable | sc.DataArray
+ Input values for the independent variable.
- Returns:
- np.ndarray: Evaluated results.
+ Returns
+ -------
+ np.ndarray
+ Evaluated results.
"""
x = self._prepare_x_for_evaluate(x)
@@ -222,23 +239,31 @@ def evaluate(
return self._func(*args)
def get_all_variables(self) -> list[Parameter]:
- """Return all parameters.
+ """
+ Return all parameters.
- Returns:
- list[Parameter]: List of all parameters in the expression.
+ Returns
+ -------
+ list[Parameter]
+ List of all parameters in the expression.
"""
return list(self._parameters.values())
def convert_unit(self, _new_unit: str | sc.Unit) -> None:
- """Convert the unit of the expression.
+ """
+ Convert the unit of the expression.
Unit conversion is not implemented for ExpressionComponent.
- Args:
- _new_unit (str | sc.Unit): The new unit to convert to (ignored).
+ Parameters
+ ----------
+ _new_unit : str | sc.Unit
+ The new unit to convert to (ignored).
- Raises:
- NotImplementedError: Always raised to indicate unit conversion is not supported.
+ Raises
+ ------
+ NotImplementedError
+ Always raised to indicate unit conversion is not supported.
"""
raise NotImplementedError('Unit conversion is not implemented for ExpressionComponent')
@@ -248,30 +273,43 @@ def convert_unit(self, _new_unit: str | sc.Unit) -> None:
# -------------------------
def __getattr__(self, name: str) -> Parameter:
- """Allow access to parameters as attributes.
-
- Args:
- name (str): Name of the parameter to access.
-
- Returns:
- Parameter: The parameter with the given name.
-
- Raises:
- AttributeError: If the parameter does not exist.
+ """
+ Allow access to parameters as attributes.
+
+ Parameters
+ ----------
+ name : str
+ Name of the parameter to access.
+
+ Raises
+ ------
+ AttributeError
+ If the parameter does not exist.
+
+ Returns
+ -------
+ Parameter
+ The parameter with the given name.
"""
if '_parameters' in self.__dict__ and name in self._parameters:
return self._parameters[name]
raise AttributeError(f"{self.__class__.__name__} has no attribute '{name}'")
def __setattr__(self, name: str, value: Numeric) -> None:
- """Allow setting parameter values as attributes.
-
- Args:
- name (str): Name of the parameter to set.
- value (Numeric): New value for the parameter.
-
- Raises:
- TypeError: If the value is not numeric.
+ """
+ Allow setting parameter values as attributes.
+
+ Parameters
+ ----------
+ name : str
+ Name of the parameter to set.
+ value : Numeric
+ New value for the parameter.
+
+ Raises
+ ------
+ TypeError
+ If the value is not numeric.
"""
if '_parameters' in self.__dict__ and name in self._parameters:
param = self._parameters[name]
@@ -285,15 +323,18 @@ def __setattr__(self, name: str, value: Numeric) -> None:
super().__setattr__(name, value)
def __dir__(self) -> list[str]:
- """Include parameter names in dir() output for better IDE
- support.
+ """
+ Include parameter names in dir() output for better IDE support.
- Returns:
- list[str]: List of attribute names, including parameters.
+ Returns
+ -------
+ list[str]
+ List of attribute names, including parameters.
"""
return super().__dir__() + list(self._parameters.keys())
def __repr__(self) -> str:
+ """Repr function."""
param_str = ', '.join(f'{k}={v.value}' for k, v in self._parameters.items())
return (
f'{self.__class__.__name__}(\n'
diff --git a/src/easydynamics/sample_model/components/gaussian.py b/src/easydynamics/sample_model/components/gaussian.py
index 892577e1..4e9629c1 100644
--- a/src/easydynamics/sample_model/components/gaussian.py
+++ b/src/easydynamics/sample_model/components/gaussian.py
@@ -3,34 +3,32 @@
from __future__ import annotations
+from typing import TYPE_CHECKING
+
import numpy as np
-import scipp as sc
-from easyscience.variable import Parameter
from easydynamics.sample_model.components.mixins import CreateParametersMixin
+from easydynamics.sample_model.components.model_component import ModelComponent
from easydynamics.utils.utils import Numeric
-from .model_component import ModelComponent
+if TYPE_CHECKING:
+ import scipp as sc
+ from easyscience.variable import Parameter
class Gaussian(CreateParametersMixin, ModelComponent):
- r"""Model of a Gaussian function.
+ r"""
+ Model of a Gaussian function.
The intensity is given by
- $$
- I(x) = \frac{A}{\sigma \sqrt{2\pi}}
- \exp\left(
- -\frac{1}{2}
- \left(\frac{x - x_0}{\sigma}\right)^2
- \right)
- $$
+ $$ I(x) = \frac{A}{\sigma \sqrt{2\pi}} \exp\left( -\frac{1}{2} \left(\frac{x -
+ x_0}{\sigma}\right)^2 \right) $$
- where $A$ is the area, $x_0$ is the center, and $\sigma$ is the
- width.
+ where $A$ is the area, $x_0$ is the center, and $\sigma$ is the width.
- If the center is not provided, it will be centered at 0 and
- fixed, which is typically what you want in QENS.
+ If the center is not provided, it will be centered at 0 and fixed, which is typically what you
+ want in QENS.
"""
def __init__(
@@ -42,17 +40,24 @@ def __init__(
display_name: str | None = 'Gaussian',
unique_name: str | None = None,
) -> None:
- """Initialize the Gaussian component.
-
- Args:
- area (Numeric | Parameter, default=1.0): Area of the Gaussian.
- center (Numeric | Parameter | None, default=None): Center of the
- Gaussian. If None, defaults to 0 and is fixed.
- width (Numeric | Parameter, default=1.0): Standard deviation.
- unit (str | sc.Unit, default='meV'): Unit of the parameters.
- display_name (str | None, default='Gaussian'): Name of the component.
- unique_name (str | None, default=None): Unique name of the component.
- if None, a unique_name is automatically generated.
+ """
+ Initialize the Gaussian component.
+
+ Parameters
+ ----------
+ area : Numeric | Parameter, default=1.0
+ Area of the Gaussian.
+ center : Numeric | Parameter | None, default=None
+ Center of the Gaussian. If None.
+ width : Numeric | Parameter, default=1.0
+ Standard deviation.
+ unit : str | sc.Unit, default='meV'
+ Unit of the parameters.
+ display_name : str | None, default='Gaussian'
+ Name of the component.
+ unique_name : str | None, default=None
+ Unique name of the component. if None, a unique_name is automatically generated. By
+ default, None.
"""
# Validate inputs and create Parameters if not given
super().__init__(
@@ -74,23 +79,31 @@ def __init__(
@property
def area(self) -> Parameter:
- """Get the area parameter.
+ """
+ Get the area parameter.
- Returns:
- Parameter: The area parameter.
+ Returns
+ -------
+ Parameter
+ The area parameter.
"""
return self._area
@area.setter
def area(self, value: Numeric) -> None:
- """Set the value of the area parameter.
+ """
+ Set the value of the area parameter.
- Args:
- value (Numeric): The new value for the area parameter.
+ Parameters
+ ----------
+ value : Numeric
+ The new value for the area parameter.
- Raises:
- TypeError: If the value is not a number.
+ Raises
+ ------
+ TypeError
+ If the value is not a number.
"""
if not isinstance(value, Numeric):
@@ -99,24 +112,31 @@ def area(self, value: Numeric) -> None:
@property
def center(self) -> Parameter:
- """Get the center parameter.
+ """
+ Get the center parameter.
- Returns:
- Parameter: The center parameter.
+ Returns
+ -------
+ Parameter
+ The center parameter.
"""
return self._center
@center.setter
def center(self, value: Numeric | None) -> None:
- """Set the center parameter value.
+ """
+ Set the center parameter value.
- Args:
- value (Numeric | None): The new value for the center
- parameter. If None, defaults to 0 and is fixed.
+ Parameters
+ ----------
+ value : Numeric | None
+ The new value for the center parameter. If None, defaults to 0 and is fixed.
- Raises:
- TypeError: If the value is not a number or None.
+ Raises
+ ------
+ TypeError
+ If the value is not a number or None.
"""
if value is None:
@@ -128,24 +148,32 @@ def center(self, value: Numeric | None) -> None:
@property
def width(self) -> Parameter:
- """Get the width parameter (standard deviation).
+ """
+ Get the width parameter (standard deviation).
- Returns:
- Parameter: The width parameter.
+ Returns
+ -------
+ Parameter
+ The width parameter.
"""
return self._width
@width.setter
def width(self, value: Numeric) -> None:
- """Set the width parameter value.
-
- Args:
- value (Numeric): The new value for the width
- parameter.
-
- Raises:
- TypeError: If the value is not a number or None.
- ValueError: If the value is not positive.
+ """
+ Set the width parameter value.
+
+ Parameters
+ ----------
+ value : Numeric
+ The new value for the width parameter.
+
+ Raises
+ ------
+ TypeError
+ If the value is not a number or None.
+ ValueError
+ If the value is not positive.
"""
if not isinstance(value, Numeric):
raise TypeError('width must be a number')
@@ -159,30 +187,24 @@ def evaluate(
self,
x: Numeric | list | np.ndarray | sc.Variable | sc.DataArray,
) -> np.ndarray:
- r"""Evaluate the Gaussian at the given x values.
+ r"""
+ Evaluate the Gaussian at the given x values.
- If x is a scipp Variable, the unit of the Gaussian will be
- converted to match x.
- The intensity is given by
- $$
- I(x) = \frac{A}{\sigma \sqrt{2\pi}}
- \exp\left(
- -\frac{1}{2}
- \left(\frac{x - x_0}{\sigma}\right)^2
- \right)
- $$
+ If x is a scipp Variable, the unit of the Gaussian will be converted to match x. The
+ intensity is given by $$ I(x) = \frac{A}{\sigma \sqrt{2\pi}} \exp\left( -\frac{1}{2}
+ \left(\frac{x - x_0}{\sigma}\right)^2 \right) $$
- where $A$ is the area, $x_0$ is the center, and $\sigma$ is the
- width.
+ where $A$ is the area, $x_0$ is the center, and $\sigma$ is the width.
+ Parameters
+ ----------
+ x : Numeric | list | np.ndarray | sc.Variable | sc.DataArray
+ The x values at which to evaluate the Gaussian.
- Args:
- x (Numeric | list | np.ndarray | sc.Variable | sc.DataArray):
- The x values at which to evaluate the Gaussian.
-
- Returns:
- np.ndarray: The intensity of the Gaussian at the given x
- values.
+ Returns
+ -------
+ np.ndarray
+ The intensity of the Gaussian at the given x values.
"""
x = self._prepare_x_for_evaluate(x)
@@ -193,11 +215,16 @@ def evaluate(
return self.area.value * normalization * np.exp(exponent)
def __repr__(self) -> str:
- """Return a string representation of the Gaussian.
+ """
+ Return a string representation of the Gaussian.
- Returns:
- str: A string representation of the Gaussian.
+ Returns
+ -------
+ str
+ A string representation of the Gaussian.
"""
- return f'Gaussian(unique_name = {self.unique_name}, unit = {self._unit},\n \
- area = {self.area},\n center = {self.center},\n width = {self.width})'
+ return (
+ f'Gaussian(unique_name = {self.unique_name}, unit = {self._unit},\n'
+ f'area = {self.area},\n center = {self.center},\n width = {self.width})'
+ )
diff --git a/src/easydynamics/sample_model/components/lorentzian.py b/src/easydynamics/sample_model/components/lorentzian.py
index 8f5697bd..d86b1ed6 100644
--- a/src/easydynamics/sample_model/components/lorentzian.py
+++ b/src/easydynamics/sample_model/components/lorentzian.py
@@ -3,28 +3,29 @@
from __future__ import annotations
+from typing import TYPE_CHECKING
+
import numpy as np
-import scipp as sc
-from easyscience.variable import Parameter
from easydynamics.sample_model.components.mixins import CreateParametersMixin
+from easydynamics.sample_model.components.model_component import ModelComponent
from easydynamics.utils.utils import Numeric
-from .model_component import ModelComponent
+if TYPE_CHECKING:
+ import scipp as sc
+ from easyscience.variable import Parameter
class Lorentzian(CreateParametersMixin, ModelComponent):
- r"""Model of a Lorentzian function.
+ r"""
+ Model of a Lorentzian function.
- The intensity is given by
- $$
- I(x) = \frac{A}{\pi} \frac{\Gamma}{(x - x_0)^2 + \Gamma^2},
- $$
- where $A$ is the area, $x_0$ is the center, and $\Gamma$ is the
- half width at half maximum (HWHM).
+ The intensity is given by $$ I(x) = \frac{A}{\pi} \frac{\Gamma}{(x - x_0)^2 + \Gamma^2}, $$
+ where $A$ is the area, $x_0$ is the center, and $\Gamma$ is the half width at half maximum
+ (HWHM).
- If the center is not provided, it will be centered at 0
- and fixed, which is typically what you want in QENS.
+ If the center is not provided, it will be centered at 0 and fixed, which is typically what you
+ want in QENS.
"""
def __init__(
@@ -36,18 +37,24 @@ def __init__(
display_name: str | None = 'Lorentzian',
unique_name: str | None = None,
) -> None:
- """Initialize the Lorentzian component.
-
- Args:
- area (Numeric | Parameter, default=1.0): Area of the Lorentzian.
- center (Numeric | Parameter | None, default=None): Center of the
- Lorentzian. If None, defaults to 0 and is fixed.
- width (Numeric | Parameter, default=1.0): Half width at half maximum
- (HWHM).
- unit (str | sc.Unit, default='meV'): Unit of the parameters.
- display_name (str | None, default='Lorentzian'): Name of the component.
- unique_name (str | None, default=None): Unique name of the component. If
- None, a unique_name is automatically generated.
+ """
+ Initialize the Lorentzian component.
+
+ Parameters
+ ----------
+ area : Numeric | Parameter, default=1.0
+ Area of the Lorentzian.
+ center : Numeric | Parameter | None, default=None
+ Center of the Lorentzian. If None.
+ width : Numeric | Parameter, default=1.0
+ Half width at half maximum (HWHM).
+ unit : str | sc.Unit, default='meV'
+ Unit of the parameters.
+ display_name : str | None, default='Lorentzian'
+ Name of the component.
+ unique_name : str | None, default=None
+ Unique name of the component. If None, a unique_name is automatically generated. By
+ default, None.
"""
super().__init__(
@@ -69,22 +76,30 @@ def __init__(
@property
def area(self) -> Parameter:
- """Get the area parameter.
+ """
+ Get the area parameter.
- Returns:
- Parameter: The area parameter.
+ Returns
+ -------
+ Parameter
+ The area parameter.
"""
return self._area
@area.setter
def area(self, value: Numeric) -> None:
- """Set the value of the area parameter.
+ """
+ Set the value of the area parameter.
- Args:
- value (Numeric): The new value for the area parameter.
+ Parameters
+ ----------
+ value : Numeric
+ The new value for the area parameter.
- Raises:
- TypeError: If the value is not a number.
+ Raises
+ ------
+ TypeError
+ If the value is not a number.
"""
if not isinstance(value, Numeric):
raise TypeError('area must be a number')
@@ -92,23 +107,30 @@ def area(self, value: Numeric) -> None:
@property
def center(self) -> Parameter:
- """Get the center parameter.
+ """
+ Get the center parameter.
- Returns:
- Parameter: The center parameter.
+ Returns
+ -------
+ Parameter
+ The center parameter.
"""
return self._center
@center.setter
def center(self, value: Numeric | None) -> None:
- """Set the value of the center parameter.
+ """
+ Set the value of the center parameter.
- Args:
- value (Numeric | None): The new value for the center
- parameter. If None, defaults to 0 and is fixed.
+ Parameters
+ ----------
+ value : Numeric | None
+ The new value for the center parameter. If None, defaults to 0 and is fixed.
- Raises:
- TypeError: If the value is not a number or None.
+ Raises
+ ------
+ TypeError
+ If the value is not a number or None.
"""
if value is None:
@@ -120,24 +142,32 @@ def center(self, value: Numeric | None) -> None:
@property
def width(self) -> Parameter:
- """Get the width parameter (HWHM).
+ """
+ Get the width parameter (HWHM).
- Returns:
- Parameter: The width parameter.
+ Returns
+ -------
+ Parameter
+ The width parameter.
"""
return self._width
@width.setter
def width(self, value: Numeric) -> None:
- """Set the width parameter value (HWHM).
-
- Args:
- value (Numeric): The new value for the width
- parameter.
-
- Raises:
- TypeError: If the value is not a number.
- ValueError: If the value is not positive.
+ """
+ Set the width parameter value (HWHM).
+
+ Parameters
+ ----------
+ value : Numeric
+ The new value for the width parameter.
+
+ Raises
+ ------
+ TypeError
+ If the value is not a number.
+ ValueError
+ If the value is not positive.
"""
if not isinstance(value, Numeric):
raise TypeError('width must be a number')
@@ -147,26 +177,26 @@ def width(self, value: Numeric) -> None:
self._width.value = value
def evaluate(self, x: Numeric | list | np.ndarray | sc.Variable | sc.DataArray) -> np.ndarray:
- r"""Evaluate the Lorentzian at the given x values.
+ r"""
+ Evaluate the Lorentzian at the given x values.
- If x is a scipp Variable, the unit of the Lorentzian will be
- converted to match x. The intensity is given by
+ If x is a scipp Variable, the unit of the Lorentzian will be converted to match x. The
+ intensity is given by
- $$
- I(x) = \frac{A}{\pi} \frac{\Gamma}{(x -
- x_0)^2 + \Gamma^2},
- $$
+ $$ I(x) = \frac{A}{\pi} \frac{\Gamma}{(x - x_0)^2 + \Gamma^2}, $$
- where $A$ is the area, $x_0$ is the center, and $\Gamma$ is
- the half width at half maximum (HWHM).
+ where $A$ is the area, $x_0$ is the center, and $\Gamma$ is the half width at half maximum
+ (HWHM).
- Args:
- x (Numeric | list | np.ndarray | sc.Variable | sc.DataArray):
- The x values at which to evaluate the Lorentzian.
+ Parameters
+ ----------
+ x : Numeric | list | np.ndarray | sc.Variable | sc.DataArray
+ The x values at which to evaluate the Lorentzian.
- Returns:
- np.ndarray: The intensity of the Lorentzian at the given x
- values.
+ Returns
+ -------
+ np.ndarray
+ The intensity of the Lorentzian at the given x values.
"""
x = self._prepare_x_for_evaluate(x)
@@ -177,10 +207,15 @@ def evaluate(self, x: Numeric | list | np.ndarray | sc.Variable | sc.DataArray)
return self.area.value * normalization / denominator
def __repr__(self) -> str:
- """Return a string representation of the Lorentzian.
+ """
+ Return a string representation of the Lorentzian.
- Returns:
- str: A string representation of the Lorentzian.
+ Returns
+ -------
+ str
+ A string representation of the Lorentzian.
"""
- return f'Lorentzian(unique_name = {self.unique_name}, unit = {self._unit},\n \
- area = {self.area},\n center = {self.center},\n width = {self.width})'
+ return (
+ f'Lorentzian(unique_name = {self.unique_name}, unit = {self._unit},\n'
+ f'area = {self.area},\n center = {self.center},\n width = {self.width})'
+ )
diff --git a/src/easydynamics/sample_model/components/mixins.py b/src/easydynamics/sample_model/components/mixins.py
index b5125767..a80a7200 100644
--- a/src/easydynamics/sample_model/components/mixins.py
+++ b/src/easydynamics/sample_model/components/mixins.py
@@ -15,12 +15,11 @@
class CreateParametersMixin:
- """Provides parameter creation and validation methods for model
- components.
+ """
+ Provides parameter creation and validation methods for model components.
- This mixin provides methods to create and validate common physics
- parameters (area, center, width) with appropriate bounds and type
- checking.
+ This mixin provides methods to create and validate common physics parameters (area, center,
+ width) with appropriate bounds and type checking.
"""
def _create_area_parameter(
@@ -30,26 +29,34 @@ def _create_area_parameter(
unit: str | sc.Unit = 'meV',
minimum_area: float = MINIMUM_AREA,
) -> Parameter:
- """Validate and convert a number to a Parameter describing the
- area of a function.
-
- If the area is negative, a warning is raised.
- If the area is non-negative, its minimum is set to 0 to avoid it
- accidentally becoming negative during fitting.
-
- Args:
- area (Numeric | Parameter): The area value or Parameter.
- name (str): The name of the model component.
- unit (str | sc.Unit, default='meV'): The unit of the area Parameter.
- minimum_area (float, default=MINIMUM_AREA): The minimum allowed area.
-
- Returns:
- Parameter: The validated area Parameter.
-
- Raises:
- TypeError: If area is not a number or a Parameter.
- ValueError: If area is not a finite number or if the area
- Parameter has a non-finite value.
+ """
+ Validate and convert a number to a Parameter describing the area of a function.
+
+ If the area is negative, a warning is raised. If the area is non-negative, its minimum is
+ set to 0 to avoid it accidentally becoming negative during fitting.
+
+ Parameters
+ ----------
+ area : Numeric | Parameter
+ The area value or Parameter.
+ name : str
+ The name of the model component.
+ unit : str | sc.Unit, default='meV'
+ The unit of the area Parameter.
+ minimum_area : float, default=MINIMUM_AREA
+ The minimum allowed area.
+
+ Raises
+ ------
+ TypeError
+ If area is not a number or a Parameter.
+ ValueError
+ If area is not a finite number or if the area Parameter has a non-finite value.
+
+ Returns
+ -------
+ Parameter
+ The validated area Parameter.
"""
if not isinstance(area, (Parameter, Numeric)):
raise TypeError('area must be a number or a Parameter.')
@@ -79,28 +86,34 @@ def _create_center_parameter(
unit: str | sc.Unit = 'meV',
enforce_minimum_center: bool = False,
) -> Parameter:
- """Validate and convert a number to a Parameter describing the
- center of a function.
-
- Args:
- center (Numeric | Parameter | None): The center value or
- Parameter.
- name (str): The name of the model component.
- fix_if_none (bool): Whether to fix the center Parameter
- if center is None.
- unit (str | sc.Unit, default='meV'): The unit of the center
- Parameter.
- enforce_minimum_center (bool, default=False): Whether to
- enforce a minimum center value to avoid zero center in
- DHO.
-
- Returns:
- Parameter: The validated center Parameter.
-
- Raises:
- TypeError: If center is not None, a number, or a Parameter.
- ValueError: If center is a number but not finite, or if
- center is a Parameter but has a non-finite value.
+ """
+ Validate and convert a number to a Parameter describing the center of a function.
+
+ Parameters
+ ----------
+ center : Numeric | Parameter | None
+ The center value or Parameter.
+ name : str
+ The name of the model component.
+ fix_if_none : bool
+ Whether to fix the center Parameter if center is None.
+ unit : str | sc.Unit, default='meV'
+ The unit of the center Parameter.
+ enforce_minimum_center : bool, default=False
+ Whether to enforce a minimum center value to avoid zero center in DHO.
+
+ Raises
+ ------
+ TypeError
+ If center is not None, a number, or a Parameter.
+ ValueError
+ If center is a number but not finite, or if center is a Parameter but has a non-finite
+ value.
+
+ Returns
+ -------
+ Parameter
+ The validated center Parameter.
"""
if center is not None and not isinstance(center, (Numeric, Parameter)):
raise TypeError('center must be None, a number, or a Parameter.')
@@ -129,23 +142,33 @@ def _create_width_parameter(
unit: str | sc.Unit = 'meV',
minimum_width: float = MINIMUM_WIDTH,
) -> Parameter:
- """Validate and convert a number to a Parameter describing the
- width of a function.
-
- Args:
- width (Numeric | Parameter): The width value or Parameter.
- name (str): The name of the model component.
- param_name (str, default='width'): The name of the width parameter.
- unit (str | sc.Unit, default='meV'): The unit of the width Parameter.
- minimum_width (float, default=MINIMUM_WIDTH): The minimum
- allowed width.
-
- Returns:
- Parameter: The validated width Parameter.
-
- Raises:
- TypeError: If width is not a number or a Parameter.
- ValueError: If width is non-positive.
+ """
+ Validate and convert a number to a Parameter describing the width of a function.
+
+ Parameters
+ ----------
+ width : Numeric | Parameter
+ The width value or Parameter.
+ name : str
+ The name of the model component.
+ param_name : str, default='width'
+ The name of the width parameter.
+ unit : str | sc.Unit, default='meV'
+ The unit of the width Parameter.
+ minimum_width : float, default=MINIMUM_WIDTH
+ The minimum allowed width.
+
+ Raises
+ ------
+ TypeError
+ If width is not a number or a Parameter.
+ ValueError
+ If width is non-positive.
+
+ Returns
+ -------
+ Parameter
+ The validated width Parameter.
"""
if not isinstance(width, (Numeric, Parameter)):
raise TypeError(f'{param_name} must be a number or a Parameter.')
diff --git a/src/easydynamics/sample_model/components/model_component.py b/src/easydynamics/sample_model/components/model_component.py
index bfbd7384..6d0f9a0e 100644
--- a/src/easydynamics/sample_model/components/model_component.py
+++ b/src/easydynamics/sample_model/components/model_component.py
@@ -8,13 +8,13 @@
import numpy as np
import scipp as sc
-from easyscience.base_classes.model_base import ModelBase
from scipp import UnitError
+from easydynamics.base_classes.easydynamics_modelbase import EasyDynamicsModelBase
from easydynamics.utils.utils import Numeric
-class ModelComponent(ModelBase):
+class ModelComponent(EasyDynamicsModelBase):
"""Abstract base class for all model components."""
def __init__(
@@ -23,44 +23,55 @@ def __init__(
display_name: str | None = None,
unique_name: str | None = None,
) -> None:
- """Initialize the ModelComponent.
-
- Args:
- unit (str | sc.Unit, default="meV"): The unit of the model component.
- display_name (str | None, default=None): A human-readable name for the
- component.
- unique_name (str | None, default=None): A unique identifier for the
- component.
"""
- self.validate_unit(unit)
- super().__init__(display_name=display_name, unique_name=unique_name)
+ Initialize the ModelComponent.
+
+ Parameters
+ ----------
+ unit : str | sc.Unit, default='meV'
+ The unit of the model component.
+ display_name : str | None, default=None
+ A human-readable name for the component.
+ unique_name : str | None, default=None
+ A unique identifier for the component.
+ """
+ super().__init__(unit=unit, display_name=display_name, unique_name=unique_name)
self._unit = unit
@property
def unit(self) -> str:
- """Get the unit.
+ """
+ Get the unit.
- Returns:
- str: The unit of the model component.
+ Returns
+ -------
+ str
+ The unit of the model component.
"""
return str(self._unit)
@unit.setter
def unit(self, _unit_str: str) -> None:
- """Unit is read-only. Use convert_unit to change the unit
- between allowed types or create a new ModelComponent with the
- desired unit.
+ """
+ Unit is read-only.
- Args:
- _unit_str (str): The new unit to set.
+ Use convert_unit to change the unit between allowed types or create a new ModelComponent
+ with the desired unit.
- Raises:
- AttributeError: Always raised since unit is read-only.
+ Parameters
+ ----------
+ _unit_str : str
+ The new unit to set.
+
+ Raises
+ ------
+ AttributeError
+ Always raised since unit is read-only.
"""
raise AttributeError(
f'Unit is read-only. Use convert_unit to change the unit between allowed types '
f'or create a new {self.__class__.__name__} with the desired unit.'
- ) # noqa: E501
+ )
def fix_all_parameters(self) -> None:
"""Fix all parameters in the model component."""
@@ -77,21 +88,26 @@ def free_all_parameters(self) -> None:
def _prepare_x_for_evaluate(
self, x: Numeric | list | np.ndarray | sc.Variable | sc.DataArray
) -> np.ndarray:
- """Prepare the input x for evaluation by handling units and
- converting to a numpy array.
-
- Args:
- x (Numeric | list | np.ndarray | sc.Variable | sc.DataArray):
- The input data to prepare.
-
- Returns:
- np.ndarray: The prepared input data as a numpy array.
-
- Raises:
- ValueError: If x contains NaN or infinite values, or if a
- sc.DataArray has more than one coordinate.
- UnitError: If x has incompatible units that cannot be
- converted to the component's unit.
+ """
+ Prepare the input x for evaluation by handling units and converting to a numpy array.
+
+ Parameters
+ ----------
+ x : Numeric | list | np.ndarray | sc.Variable | sc.DataArray
+ The input data to prepare.
+
+ Raises
+ ------
+ ValueError
+ If x contains NaN or infinite values, or if a sc.DataArray has more than one
+ coordinate.
+ UnitError
+ If x has incompatible units that cannot be converted to the component's unit.
+
+ Returns
+ -------
+ np.ndarray
+ The prepared input data as a numpy array.
"""
# Handle units
@@ -106,7 +122,7 @@ def _prepare_x_for_evaluate(
f'Found {ncoords} coordinates: {coord_names}.'
)
# get the coordinate, it's a sc.Variable
- coord_name, coord_obj = next(iter(coords.items()))
+ _, coord_obj = next(iter(coords.items()))
x = coord_obj
if isinstance(x, sc.Variable):
# Need to check if the units are consistent,
@@ -146,31 +162,21 @@ def _prepare_x_for_evaluate(
return np.sort(x_in)
- @staticmethod
- def validate_unit(unit: str | sc.Unit | None) -> None:
- """Validate that the unit is either a string or a scipp Unit.
-
- Args:
- unit (str | sc.Unit | None): The unit to validate.
-
- Raises:
- TypeError: If unit is not a string or scipp Unit.
- """
- if unit is not None and not isinstance(unit, (str, sc.Unit)):
- raise TypeError(
- f'unit must be None, a string, or a scipp Unit, got {type(unit).__name__}'
- )
-
def convert_unit(self, unit: str | sc.Unit) -> None:
- """Convert the unit of the Parameters in the component.
-
- Args:
- unit (str | sc.Unit): The new unit to convert to.
-
- Raises:
- TypeError: If the provided unit is not a str or sc.Unit
- Exception: If the provided unit is invalid or incompatible
- with the component's parameters.
+ """
+ Convert the unit of the Parameters in the component.
+
+ Parameters
+ ----------
+ unit : str | sc.Unit
+ The new unit to convert to.
+
+ Raises
+ ------
+ TypeError
+ If the provided unit is not a str or sc.Unit.
+ Exception
+ If the provided unit is invalid or incompatible with the component's parameters.
"""
if not isinstance(unit, (str, sc.Unit)):
raise TypeError(f'Unit must be a string or sc.Unit, got {type(unit).__name__}')
@@ -193,23 +199,30 @@ def convert_unit(self, unit: str | sc.Unit) -> None:
@abstractmethod
def evaluate(self, x: Numeric | list | np.ndarray | sc.Variable | sc.DataArray) -> np.ndarray:
- """Abstract method to evaluate the model component at input x.
+ """
+ Abstract method to evaluate the model component at input x.
+
Must be implemented by subclasses.
- Args:
- x (Numeric | list | np.ndarray | sc.Variable | sc.DataArray):
- The x values at which to evaluate the component.
+ Parameters
+ ----------
+ x : Numeric | list | np.ndarray | sc.Variable | sc.DataArray
+ The x values at which to evaluate the component.
- Returns:
- np.ndarray: Evaluated function values.
+ Returns
+ -------
+ np.ndarray
+ Evaluated function values.
"""
- pass
def __repr__(self) -> str:
- """Return a string representation of the ModelComponent.
+ """
+ Return a string representation of the ModelComponent.
- Returns:
- str: A string representation of the ModelComponent.
+ Returns
+ -------
+ str
+ A string representation of the ModelComponent.
"""
return f'{self.__class__.__name__}(unique_name={self.unique_name}, unit={self._unit})'
diff --git a/src/easydynamics/sample_model/components/polynomial.py b/src/easydynamics/sample_model/components/polynomial.py
index 340ca537..cd3cd997 100644
--- a/src/easydynamics/sample_model/components/polynomial.py
+++ b/src/easydynamics/sample_model/components/polynomial.py
@@ -4,7 +4,7 @@
from __future__ import annotations
import warnings
-from collections.abc import Sequence
+from typing import TYPE_CHECKING
import numpy as np
import scipp as sc
@@ -12,19 +12,19 @@
from easyscience.variable import Parameter
from scipp import UnitError
+from easydynamics.sample_model.components.model_component import ModelComponent
from easydynamics.utils.utils import Numeric
-from .model_component import ModelComponent
+if TYPE_CHECKING:
+ from collections.abc import Sequence
class Polynomial(ModelComponent):
- r"""Polynomial function component.
+ r"""
+ Polynomial function component.
- The intensity is given by
- $$
- I(x) = c_0 + c_1 x + c_2 x^2 + ... + c_N x^N,
- $$
- where $C_i$ are the coefficients.
+ The intensity is given by $$ I(x) = c_0 + c_1 x + c_2 x^2 + ... + c_N x^N, $$ where $C_i$ are
+ the coefficients.
"""
def __init__(
@@ -34,24 +34,28 @@ def __init__(
display_name: str | None = 'Polynomial',
unique_name: str | None = None,
) -> None:
- """Initialize the Polynomial component.
-
- Args:
- coefficients (Sequence[Numeric | Parameter], default=(0.0,)):
- Coefficients c0, c1, ..., cN
- unit (str | sc.Unit, default='meV'): Unit of the Polynomial
- component.
- display_name (str | None, default='Polynomial'): Display
- name of the Polynomial component.
- unique_name (str | None, default=None): Unique name of the
- component. If None, a unique_name is automatically
- generated.
-
- Raises:
- TypeError: If coefficients is not a sequence of numbers or
- Parameters or if any item in coefficients is not a
- number or Parameter.
- ValueError: If coefficients is an empty sequence.
+ """
+ Initialize the Polynomial component.
+
+ Parameters
+ ----------
+ coefficients : Sequence[Numeric | Parameter], default=(0.0,)
+ Coefficients c0, c1, ..., cN.
+ unit : str | sc.Unit, default='meV'
+ Unit of the Polynomial component.
+ display_name : str | None, default='Polynomial'
+ Display name of the Polynomial component.
+ unique_name : str | None, default=None
+ Unique name of the component. If None, a unique_name is automatically generated. By
+ default, None.
+
+ Raises
+ ------
+ TypeError
+ If coefficients is not a sequence of numbers or Parameters or if any item in
+ coefficients is not a number or Parameter.
+ ValueError
+ If coefficients is an empty sequence.
"""
super().__init__(display_name=display_name, unit=unit, unique_name=unique_name)
@@ -84,29 +88,35 @@ def __init__(
@property
def coefficients(self) -> list[Parameter]:
- """Get the coefficients of the polynomial as a list of
- Parameters.
+ """
+ Get the coefficients of the polynomial as a list of Parameters.
- Returns:
- list[Parameter]: The coefficients of the polynomial.
+ Returns
+ -------
+ list[Parameter]
+ The coefficients of the polynomial.
"""
return list(self._coefficients)
@coefficients.setter
def coefficients(self, coeffs: Sequence[Numeric | Parameter]) -> None:
- """Set the coefficients of the polynomial.
+ """
+ Set the coefficients of the polynomial.
Length must match current number of coefficients.
- Args:
- coeffs (Sequence[Numeric | Parameter]): New coefficients as
- a sequence of numbers or Parameters.
-
- Raises:
- TypeError: If coeffs is not a sequence of numbers or
- Parameters or if any item in coeffs is not a number or Parameter.
- ValueError: If the length of coeffs does not match the
- existing number of coefficients.
+ Parameters
+ ----------
+ coeffs : Sequence[Numeric | Parameter]
+ New coefficients as a sequence of numbers or Parameters.
+
+ Raises
+ ------
+ TypeError
+ If coeffs is not a sequence of numbers or Parameters or if any item in coeffs is not a
+ number or Parameter.
+ ValueError
+ If the length of coeffs does not match the existing number of coefficients.
"""
if not isinstance(coeffs, (list, tuple, np.ndarray)):
raise TypeError(
@@ -126,29 +136,32 @@ def coefficients(self, coeffs: Sequence[Numeric | Parameter]) -> None:
raise TypeError('Each coefficient must be either a numeric value or a Parameter.')
def coefficient_values(self) -> list[float]:
- """Get the coefficients of the polynomial as a list.
+ """
+ Get the coefficients of the polynomial as a list.
- Returns:
- list[float]: The coefficient values of the polynomial.
+ Returns
+ -------
+ list[float]
+ The coefficient values of the polynomial.
"""
return [param.value for param in self._coefficients]
def evaluate(self, x: Numeric | list | np.ndarray | sc.Variable | sc.DataArray) -> np.ndarray:
- r"""Evaluate the Polynomial at the given x values.
+ r"""
+ Evaluate the Polynomial at the given x values.
- The intensity is given by
- $$
- I(x) = c_0 + c_1 x + c_2 x^2 + ... + c_N x^N,
- $$
- where $C_i$ are the coefficients.
+ The intensity is given by $$ I(x) = c_0 + c_1 x + c_2 x^2 + ...
+ + c_N x^N, $$ where $C_i$ are the coefficients.
- Args:
- x (Numeric | list | np.ndarray | sc.Variable | sc.DataArray):
- The x values at which to evaluate the Polynomial.
+ Parameters
+ ----------
+ x : Numeric | list | np.ndarray | sc.Variable | sc.DataArray
+ The x values at which to evaluate the Polynomial.
- Returns:
- np.ndarray: The evaluated Polynomial at the given x
- values.
+ Returns
+ -------
+ np.ndarray
+ The evaluated Polynomial at the given x values.
"""
x = self._prepare_x_for_evaluate(x)
@@ -168,24 +181,30 @@ def evaluate(self, x: Numeric | list | np.ndarray | sc.Variable | sc.DataArray)
@property
def degree(self) -> int:
- """Get the degree of the polynomial.
+ """
+ Get the degree of the polynomial.
- Returns:
- int: The degree of the polynomial.
+ Returns
+ -------
+ int
+ The degree of the polynomial.
"""
return len(self._coefficients) - 1
@degree.setter
def degree(self, _value: int) -> None:
- """The degree is determined by the number of coefficients and
- cannot be set directly.
+ """
+ The degree is determined by the number of coefficients and cannot be set directly.
- Args:
- _value (int): The new degree of the polynomial.
+ Parameters
+ ----------
+ _value : int
+ The new degree of the polynomial.
- Raises:
- AttributeError: Always raised since degree cannot be set
- directly.
+ Raises
+ ------
+ AttributeError
+ Always raised since degree cannot be set directly.
"""
raise AttributeError(
'The degree of the polynomial is determined by the number of coefficients '
@@ -193,21 +212,29 @@ def degree(self, _value: int) -> None:
)
def get_all_variables(self) -> list[DescriptorBase]:
- """Get all variables from the model component.
+ """
+ Get all variables from the model component.
- Returns:
- list[DescriptorBase]: List of variables in the component.
+ Returns
+ -------
+ list[DescriptorBase]
+ List of variables in the component.
"""
return list(self._coefficients)
def convert_unit(self, unit: str | sc.Unit) -> None:
- """Convert the unit of the polynomial.
+ """
+ Convert the unit of the polynomial.
- Args:
- unit (str | sc.Unit): The target unit to convert to.
+ Parameters
+ ----------
+ unit : str | sc.Unit
+ The target unit to convert to.
- Raises:
- UnitError: If the provided unit is not a string or sc.Unit.
+ Raises
+ ------
+ UnitError
+ If the provided unit is not a string or sc.Unit.
"""
if not isinstance(unit, (str, sc.Unit)):
@@ -226,10 +253,13 @@ def convert_unit(self, unit: str | sc.Unit) -> None:
self._unit = unit
def __repr__(self) -> str:
- """Return a string representation of the Polynomial.
+ """
+ Return a string representation of the Polynomial.
- Returns:
- str: A string representation of the Polynomial.
+ Returns
+ -------
+ str
+ A string representation of the Polynomial.
"""
coeffs_str = ', '.join(f'{param.name}={param.value}' for param in self._coefficients)
@@ -237,26 +267,3 @@ def __repr__(self) -> str:
f'Polynomial(unique_name = {self.unique_name}, '
f'unit = {self._unit},\n coefficients = [{coeffs_str}])'
)
-
-
-# from typing import Callable, Dict
-# class UserDefinedComponent(ModelComponent):
-# """
-# User-defined model component, defined via a custom function.
-
-# Args:
-# func (Callable): Function accepting (x, params) and returning
-# np.ndarray.
-# params (dict): Parameters passed to the function.
-# """
-
-# def __init__(
-# self, name, func: Callable[[np.ndarray, Dict], np.ndarray],
-# params: Dict
-# ):
-# super().__init__(name=name)
-# self.func = func
-# self.params = params
-
-# def evaluate(self, x):
-# return self.func(x, self.params)
diff --git a/src/easydynamics/sample_model/components/voigt.py b/src/easydynamics/sample_model/components/voigt.py
index d57c91bc..4aafd03b 100644
--- a/src/easydynamics/sample_model/components/voigt.py
+++ b/src/easydynamics/sample_model/components/voigt.py
@@ -3,21 +3,26 @@
from __future__ import annotations
-import numpy as np
-import scipp as sc
-from easyscience.variable import Parameter
+from typing import TYPE_CHECKING
+
from scipy.special import voigt_profile
from easydynamics.sample_model.components.mixins import CreateParametersMixin
+from easydynamics.sample_model.components.model_component import ModelComponent
from easydynamics.utils.utils import Numeric
-from .model_component import ModelComponent
+if TYPE_CHECKING:
+ import numpy as np
+ import scipp as sc
+ from easyscience.variable import Parameter
class Voigt(CreateParametersMixin, ModelComponent):
- r"""Voigt profile, a convolution of Gaussian and Lorentzian. If the
- center is not provided, it will be centered at 0 and fixed, which is
- typically what you want in QENS.
+ r"""
+ Voigt profile, a convolution of Gaussian and Lorentzian.
+
+ If the center is not provided, it will be centered at 0 and fixed, which is typically what you
+ want in QENS.
Use scipy.special.voigt_profile to evaluate the Voigt profile.
"""
@@ -32,19 +37,26 @@ def __init__(
display_name: str | None = 'Voigt',
unique_name: str | None = None,
) -> None:
- """Initialize a Voigt component.
-
- Args:
- area (Numeric | Parameter, default=1.0): Total area under the curve.
- center (Numeric | Parameter | None, default=None): Center of the Voigt profile.
- gaussian_width (Numeric | Parameter, default=1.0): Standard deviation of the
- Gaussian part.
- lorentzian_width (Numeric | Parameter, default=1.0): Half width at half max
- (HWHM) of the Lorentzian part.
- unit (str | sc.Unit, default='meV'): Unit of the parameters.
- display_name (str | None, default='Voigt'): Display name of the component.
- unique_name (str | None, default=None): Unique name of the component.
- If None, a unique_name is automatically generated.
+ """
+ Initialize a Voigt component.
+
+ Parameters
+ ----------
+ area : Numeric | Parameter, default=1.0
+ Total area under the curve.
+ center : Numeric | Parameter | None, default=None
+ Center of the Voigt profile.
+ gaussian_width : Numeric | Parameter, default=1.0
+ Standard deviation of the Gaussian part.
+ lorentzian_width : Numeric | Parameter, default=1.0
+ Half width at half max (HWHM) of the Lorentzian part.
+ unit : str | sc.Unit, default='meV'
+ Unit of the parameters.
+ display_name : str | None, default='Voigt'
+ Display name of the component.
+ unique_name : str | None, default=None
+ Unique name of the component. If None, a unique_name is automatically generated. By
+ default, None.
"""
super().__init__(
@@ -78,22 +90,30 @@ def __init__(
@property
def area(self) -> Parameter:
- """Get the area parameter.
+ """
+ Get the area parameter.
- Returns:
- Parameter: The area parameter.
+ Returns
+ -------
+ Parameter
+ The area parameter.
"""
return self._area
@area.setter
def area(self, value: Numeric) -> None:
- """Set the value of the area parameter.
+ """
+ Set the value of the area parameter.
- Args:
- value (Numeric): The new value for the area parameter.
+ Parameters
+ ----------
+ value : Numeric
+ The new value for the area parameter.
- Raises:
- TypeError: If the value is not a number.
+ Raises
+ ------
+ TypeError
+ If the value is not a number.
"""
if not isinstance(value, Numeric):
raise TypeError('area must be a number')
@@ -101,23 +121,30 @@ def area(self, value: Numeric) -> None:
@property
def center(self) -> Parameter:
- """Get the center parameter.
+ """
+ Get the center parameter.
- Returns:
- Parameter: The center parameter.
+ Returns
+ -------
+ Parameter
+ The center parameter.
"""
return self._center
@center.setter
def center(self, value: Numeric | None) -> None:
- """Set the value of the center parameter.
+ """
+ Set the value of the center parameter.
- Args:
- value (Numeric | None): The new value for the center
- parameter. If None, defaults to 0 and is fixed.
+ Parameters
+ ----------
+ value : Numeric | None
+ The new value for the center parameter. If None, defaults to 0 and is fixed.
- Raises:
- TypeError: If the value is not a number.
+ Raises
+ ------
+ TypeError
+ If the value is not a number.
"""
if value is None:
value = 0.0
@@ -128,24 +155,32 @@ def center(self, value: Numeric | None) -> None:
@property
def gaussian_width(self) -> Parameter:
- """Get the Gaussian width parameter.
+ """
+ Get the Gaussian width parameter.
- Returns:
- Parameter: The Gaussian width parameter.
+ Returns
+ -------
+ Parameter
+ The Gaussian width parameter.
"""
return self._gaussian_width
@gaussian_width.setter
def gaussian_width(self, value: Numeric) -> None:
- """Set the width parameter value.
-
- Args:
- value (Numeric): The new value for the width
- parameter.
-
- Raises:
- TypeError: If the value is not a number.
- ValueError: If the value is not positive.
+ """
+ Set the width parameter value.
+
+ Parameters
+ ----------
+ value : Numeric
+ The new value for the width parameter.
+
+ Raises
+ ------
+ TypeError
+ If the value is not a number.
+ ValueError
+ If the value is not positive.
"""
if not isinstance(value, Numeric):
raise TypeError('gaussian_width must be a number')
@@ -155,24 +190,32 @@ def gaussian_width(self, value: Numeric) -> None:
@property
def lorentzian_width(self) -> Parameter:
- """Get the Lorentzian width parameter (HWHM).
+ """
+ Get the Lorentzian width parameter (HWHM).
- Returns:
- Parameter: The Lorentzian width parameter.
+ Returns
+ -------
+ Parameter
+ The Lorentzian width parameter.
"""
return self._lorentzian_width
@lorentzian_width.setter
def lorentzian_width(self, value: Numeric) -> None:
- """Set the value of the Lorentzian width parameter.
-
- Args:
- value (Numeric): The new value for the Lorentzian width
- parameter.
-
- Raises:
- TypeError: If the value is not a number.
- ValueError: If the value is not positive.
+ """
+ Set the value of the Lorentzian width parameter.
+
+ Parameters
+ ----------
+ value : Numeric
+ The new value for the Lorentzian width parameter.
+
+ Raises
+ ------
+ TypeError
+ If the value is not a number.
+ ValueError
+ If the value is not positive.
"""
if not isinstance(value, Numeric):
raise TypeError('lorentzian_width must be a number')
@@ -181,22 +224,22 @@ def lorentzian_width(self, value: Numeric) -> None:
self._lorentzian_width.value = value
def evaluate(self, x: Numeric | list | np.ndarray | sc.Variable | sc.DataArray) -> np.ndarray:
- r"""Evaluate the Voigt at the given x values.
-
- If x is a scipp Variable, the unit of the Voigt will be
- converted to match x. The Voigt evaluates to the convolution of
- a Gaussian with sigma gaussian_width and a Lorentzian with half
- width at half max lorentzian_width, centered at center, with
- area equal to area.
-
-
- Args:
- x (Numeric | list | np.ndarray | sc.Variable | sc.DataArray):
- The x values at which to evaluate the Voigt.
-
- Returns:
- np.ndarray: The intensity of the Voigt at the given x
- values.
+ r"""
+ Evaluate the Voigt at the given x values.
+
+ If x is a scipp Variable, the unit of the Voigt will be converted to match x. The Voigt
+ evaluates to the convolution of a Gaussian with sigma gaussian_width and a Lorentzian with
+ half width at half max lorentzian_width, centered at center, with area equal to area.
+
+ Parameters
+ ----------
+ x : Numeric | list | np.ndarray | sc.Variable | sc.DataArray
+ The x values at which to evaluate the Voigt.
+
+ Returns
+ -------
+ np.ndarray
+ The intensity of the Voigt at the given x values.
"""
x = self._prepare_x_for_evaluate(x)
@@ -208,14 +251,19 @@ def evaluate(self, x: Numeric | list | np.ndarray | sc.Variable | sc.DataArray)
)
def __repr__(self) -> str:
- """Return a string representation of the Voigt.
+ """
+ Return a string representation of the Voigt.
- Returns:
- str: A string representation of the Voigt.
+ Returns
+ -------
+ str
+ A string representation of the Voigt.
"""
- return f'Voigt(unique_name = {self.unique_name}, unit = {self._unit},\n \
- area = {self.area},\n \
- center = {self.center},\n \
- gaussian_width = {self.gaussian_width},\n \
- lorentzian_width = {self.lorentzian_width})'
+ return (
+ f'Voigt(unique_name = {self.unique_name}, unit = {self._unit},\n'
+ f'area = {self.area},\n'
+ f'center = {self.center},\n'
+ f'gaussian_width = {self.gaussian_width},\n'
+ f'lorentzian_width = {self.lorentzian_width})'
+ )
diff --git a/src/easydynamics/sample_model/diffusion_model/__init__.py b/src/easydynamics/sample_model/diffusion_model/__init__.py
index 7291f83e..ceee6588 100644
--- a/src/easydynamics/sample_model/diffusion_model/__init__.py
+++ b/src/easydynamics/sample_model/diffusion_model/__init__.py
@@ -1,8 +1,12 @@
# SPDX-FileCopyrightText: 2026 EasyScience contributors
# SPDX-License-Identifier: BSD-3-Clause
-from .brownian_translational_diffusion import BrownianTranslationalDiffusion
-from .jump_translational_diffusion import JumpTranslationalDiffusion
+from easydynamics.sample_model.diffusion_model.brownian_translational_diffusion import (
+ BrownianTranslationalDiffusion,
+)
+from easydynamics.sample_model.diffusion_model.jump_translational_diffusion import (
+ JumpTranslationalDiffusion,
+)
__all__ = [
'BrownianTranslationalDiffusion',
diff --git a/src/easydynamics/sample_model/diffusion_model/brownian_translational_diffusion.py b/src/easydynamics/sample_model/diffusion_model/brownian_translational_diffusion.py
index f9aa17d3..b3872d9a 100644
--- a/src/easydynamics/sample_model/diffusion_model/brownian_translational_diffusion.py
+++ b/src/easydynamics/sample_model/diffusion_model/brownian_translational_diffusion.py
@@ -18,24 +18,20 @@
class BrownianTranslationalDiffusion(DiffusionModelBase):
- r"""Model of Brownian translational diffusion, consisting of a
- Lorentzian function for each Q-value, where the width is given by $D
- Q^2$, where $D$ is the diffusion coefficient. The area of the
- Lorentzians is given by the scale parameter multiplied by the QISF,
- which is 1 for this model. The EISF is 0 for this model, so there is
- no delta function component. Q is assumed to have units of
- 1/angstrom. Creates ComponentCollections with Lorentzian components
- for given Q-values.
-
- Example:
- >>>Q=np.linspace(0.5,2,7)
- >>>energy=np.linspace(-2, 2, 501)
- >>>scale=1.0
+ r"""
+ Model of Brownian translational diffusion, consisting of a Lorentzian function for each
+ Q-value, where the width is given by $D Q^2$, where $D$ is the diffusion coefficient. The area
+ of the Lorentzians is given by the scale parameter multiplied by the QISF, which is 1 for this
+ model. The EISF is 0 for this model, so there is no delta function component. Q is assumed to
+ have units of 1/angstrom. Creates ComponentCollections with Lorentzian components for given
+ Q-values.
+
+ Example: >>>Q=np.linspace(0.5,2,7) >>>energy=np.linspace(-2, 2, 501) >>>scale=1.0
>>>diffusion_coefficient = 2.4e-9 # m^2/s
>>>diffusion_model=BrownianTranslationalDiffusion(display_name="DiffusionModel",
>>>scale=scale, diffusion_coefficient= diffusion_coefficient)
- >>>component_collections=diffusion_model.create_component_collections(Q)
- See also the tutorials.
+ >>>component_collections=diffusion_model.create_component_collections(Q) See also the
+ tutorials.
"""
def __init__(
@@ -46,23 +42,27 @@ def __init__(
scale: Numeric = 1.0,
diffusion_coefficient: Numeric = 1.0,
) -> None:
- """Initialize a new BrownianTranslationalDiffusion model.
-
- Args:
- display_name (str | None, default='BrownianTranslationalDiffusion'):
- Display name of the diffusion model.
- unique_name (str | None, default=None): Unique name of the diffusion
- model. If None, a unique name will be generated.
- unit (str | sc.Unit, default='meV'): Unit of the diffusion model. Must be
- convertible to meV.
- scale (Numeric, default=1.0): Scale factor for the diffusion model. Must
- be a non-negative number.
- diffusion_coefficient (Numeric, default=1.0): Diffusion coefficient D in
- m^2/s.
-
- Raises:
- TypeError: If scale or diffusion_coefficient is not a
- number.
+ """
+ Initialize a new BrownianTranslationalDiffusion model.
+
+ Parameters
+ ----------
+ display_name : str | None, default='BrownianTranslationalDiffusion'
+ Display name of the diffusion model.
+ unique_name : str | None, default=None
+ Unique name of the diffusion model. If None, a unique name will be generated. By
+ default, None.
+ unit : str | sc.Unit, default='meV'
+ Unit of the diffusion model. Must be convertible to meV.
+ scale : Numeric, default=1.0
+ Scale factor for the diffusion model. Must be a non-negative number.
+ diffusion_coefficient : Numeric, default=1.0
+ Diffusion coefficient D in m^2/s.
+
+ Raises
+ ------
+ TypeError
+ If scale or diffusion_coefficient is not a number.
"""
if not isinstance(scale, Numeric):
raise TypeError('scale must be a number.')
@@ -93,24 +93,32 @@ def __init__(
@property
def diffusion_coefficient(self) -> Parameter:
- """Get the diffusion coefficient parameter D.
+ """
+ Get the diffusion coefficient parameter D.
- Returns:
- Parameter: Diffusion coefficient D in m^2/s.
+ Returns
+ -------
+ Parameter
+ Diffusion coefficient D in m^2/s.
"""
return self._diffusion_coefficient
@diffusion_coefficient.setter
def diffusion_coefficient(self, diffusion_coefficient: Numeric) -> None:
- """Set the diffusion coefficient parameter D.
-
- Args:
- diffusion_coefficient (Numeric): The new value for the
- diffusion coefficient D in m^2/s.
-
- Raises:
- TypeError: If diffusion_coefficient is not a number.
- ValueError: If diffusion_coefficient is negative.
+ """
+ Set the diffusion coefficient parameter D.
+
+ Parameters
+ ----------
+ diffusion_coefficient : Numeric
+ The new value for the diffusion coefficient D in m^2/s.
+
+ Raises
+ ------
+ TypeError
+ If diffusion_coefficient is not a number.
+ ValueError
+ If diffusion_coefficient is negative.
"""
if not isinstance(diffusion_coefficient, Numeric):
raise TypeError('diffusion_coefficient must be a number.')
@@ -124,15 +132,18 @@ def diffusion_coefficient(self, diffusion_coefficient: Numeric) -> None:
# ------------------------------------------------------------------
def calculate_width(self, Q: Q_type) -> np.ndarray:
- """Calculate the half-width at half-maximum (HWHM) for the
- diffusion model.
+ """
+ Calculate the half-width at half-maximum (HWHM) for the diffusion model.
- Args:
- Q (Q_type): Scattering vector in 1/angstrom
+ Parameters
+ ----------
+ Q : Q_type
+ Scattering vector in 1/angstrom.
- Returns:
- np.ndarray: HWHM values in the unit of the model
- (e.g., meV).
+ Returns
+ -------
+ np.ndarray
+ HWHM values in the unit of the model (e.g., meV).
"""
Q = _validate_and_convert_Q(Q)
@@ -142,28 +153,36 @@ def calculate_width(self, Q: Q_type) -> np.ndarray:
return Q**2 * unit_conversion_factor.value
def calculate_EISF(self, Q: Q_type) -> np.ndarray:
- """Calculate the Elastic Incoherent Structure Factor (EISF) for
- the Brownian translational diffusion model.
+ """
+ Calculate the Elastic Incoherent Structure Factor (EISF) for the Brownian translational
+ diffusion model.
- Args:
- Q (Q_type): Scattering
- vector in 1/angstrom
+ Parameters
+ ----------
+ Q : Q_type
+ Scattering vector in 1/angstrom.
- Returns:
- np.ndarray: EISF values (dimensionless).
+ Returns
+ -------
+ np.ndarray
+ EISF values (dimensionless).
"""
Q = _validate_and_convert_Q(Q)
return np.zeros_like(Q)
def calculate_QISF(self, Q: Q_type) -> np.ndarray:
- """Calculate the Quasi-Elastic Incoherent Structure Factor
- (QISF).
+ """
+ Calculate the Quasi-Elastic Incoherent Structure Factor (QISF).
- Args:
- Q (Q_type): Scattering vector in 1/angstrom
+ Parameters
+ ----------
+ Q : Q_type
+ Scattering vector in 1/angstrom.
- Returns:
- np.ndarray: QISF values (dimensionless).
+ Returns
+ -------
+ np.ndarray
+ QISF values (dimensionless).
"""
Q = _validate_and_convert_Q(Q)
@@ -174,23 +193,28 @@ def create_component_collections(
Q: Q_type,
component_display_name: str = 'Brownian diffusion',
) -> list[ComponentCollection]:
- r"""Create ComponentCollection components for the Brownian
- translational diffusion model at given Q values.
-
- Args:
- Q (Q_type): Scattering vector values.
- component_display_name (str, default="Brownian diffusion"):
- Name of the Lorentzian component.
-
- Returns:
- list[ComponentCollection]: List of ComponentCollections with
- Lorentzian components for each Q value. Each Lorentzian
- has a width given by $D*Q^2$ and an area given by the
- scale parameter multiplied by the QISF (which is 1 for
- this model).
-
- Raises:
- TypeError: If component_display_name is not a string.
+ r"""
+ Create ComponentCollection components for the Brownian translational diffusion model at
+ given Q values.
+
+ Parameters
+ ----------
+ Q : Q_type
+ Scattering vector values.
+ component_display_name : str, default='Brownian diffusion'
+ Name of the Lorentzian component.
+
+ Raises
+ ------
+ TypeError
+ If component_display_name is not a string.
+
+ Returns
+ -------
+ list[ComponentCollection]
+ List of ComponentCollections with Lorentzian components for each Q value. Each
+ Lorentzian has a width given by $D*Q^2$ and an area given by the scale parameter
+ multiplied by the QISF (which is 1 for this model).
"""
Q = _validate_and_convert_Q(Q)
@@ -241,17 +265,24 @@ def create_component_collections(
# ------------------------------------------------------------------
def _write_width_dependency_expression(self, Q: float) -> str:
- """Write the dependency expression for the width as a function
- of Q to make dependent Parameters.
+ """
+ Write the dependency expression for the width as a function of Q to make dependent
+ Parameters.
- Args:
- Q (float): Scattering vector in 1/angstrom.
+ Parameters
+ ----------
+ Q : float
+ Scattering vector in 1/angstrom.
- Returns:
- str: Dependency expression for the width.
+ Raises
+ ------
+ TypeError
+ If Q is not a float.
- Raises:
- TypeError: If Q is not a float.
+ Returns
+ -------
+ str
+ Dependency expression for the width.
"""
if not isinstance(Q, (float)):
raise TypeError('Q must be a float.')
@@ -260,11 +291,13 @@ def _write_width_dependency_expression(self, Q: float) -> str:
return f'hbar * D* {Q} **2*1/(angstrom**2)'
def _write_width_dependency_map_expression(self) -> dict[str, DescriptorNumber]:
- """Write the dependency map expression to make dependent
- Parameters.
+ """
+ Write the dependency map expression to make dependent Parameters.
- Returns:
- dict[str, DescriptorNumber]: Dependency map for the width.
+ Returns
+ -------
+ dict[str, DescriptorNumber]
+ Dependency map for the width.
"""
return {
'D': self.diffusion_coefficient,
@@ -273,17 +306,23 @@ def _write_width_dependency_map_expression(self) -> dict[str, DescriptorNumber]:
}
def _write_area_dependency_expression(self, QISF: float) -> str:
- """Write the dependency expression for the area to make
- dependent Parameters.
-
- Args:
- QISF (float): Quasielastic Incoherent Scattering Function.
-
- Returns:
- str: Dependency expression for the area.
-
- Raises:
- TypeError: If QISF is not a float.
+ """
+ Write the dependency expression for the area to make dependent Parameters.
+
+ Parameters
+ ----------
+ QISF : float
+ Quasielastic Incoherent Scattering Function.
+
+ Raises
+ ------
+ TypeError
+ If QISF is not a float.
+
+ Returns
+ -------
+ str
+ Dependency expression for the area.
"""
if not isinstance(QISF, (float)):
raise TypeError('QISF must be a float.')
@@ -291,11 +330,13 @@ def _write_area_dependency_expression(self, QISF: float) -> str:
return f'{QISF} * scale'
def _write_area_dependency_map_expression(self) -> dict[str, DescriptorNumber]:
- """Write the dependency map expression to make dependent
- Parameters.
+ """
+ Write the dependency map expression to make dependent Parameters.
- Returns:
- dict[str, DescriptorNumber]: Dependency map for the area.
+ Returns
+ -------
+ dict[str, DescriptorNumber]
+ Dependency map for the area.
"""
return {
'scale': self.scale,
@@ -306,12 +347,13 @@ def _write_area_dependency_map_expression(self) -> dict[str, DescriptorNumber]:
# ------------------------------------------------------------------
def __repr__(self) -> str:
- """String representation of the BrownianTranslationalDiffusion
- model.
+ """
+ String representation of the BrownianTranslationalDiffusion model.
- Returns:
- str: String representation of the
- BrownianTranslationalDiffusion model.
+ Returns
+ -------
+ str
+ String representation of the BrownianTranslationalDiffusion model.
"""
return (
f'BrownianTranslationalDiffusion(display_name={self.display_name},'
diff --git a/src/easydynamics/sample_model/diffusion_model/diffusion_model_base.py b/src/easydynamics/sample_model/diffusion_model/diffusion_model_base.py
index 6360ca52..0e83351e 100644
--- a/src/easydynamics/sample_model/diffusion_model/diffusion_model_base.py
+++ b/src/easydynamics/sample_model/diffusion_model/diffusion_model_base.py
@@ -2,15 +2,15 @@
# SPDX-License-Identifier: BSD-3-Clause
import scipp as sc
-from easyscience.base_classes.model_base import ModelBase
from easyscience.variable import DescriptorNumber
from easyscience.variable import Parameter
from scipp import UnitError
+from easydynamics.base_classes.easydynamics_modelbase import EasyDynamicsModelBase
from easydynamics.utils.utils import Numeric
-class DiffusionModelBase(ModelBase):
+class DiffusionModelBase(EasyDynamicsModelBase):
"""Base class for constructing diffusion models."""
def __init__(
@@ -20,22 +20,27 @@ def __init__(
scale: Numeric = 1.0,
unit: str | sc.Unit = 'meV',
) -> None:
- """Initialize a new DiffusionModel.
-
- Args:
- display_name (str | None, default='MyDiffusionModel'):
- Display name of the diffusion model.
- unique_name (str | None, default=None): Unique name of the diffusion
- model. If None, a unique name will be generated.
- scale (Numeric, default=1.0): Scale factor for the diffusion model. Must
- be a non-negative number.
- unit (str | sc.Unit, default='meV'): Unit of the diffusion model. Must be
- convertible to meV.
-
- Raises:
- TypeError: If scale is not a number.
- UnitError: If unit is not a string or scipp Unit, or if it
- cannot be converted to meV.
+ """
+ Initialize a new DiffusionModel.
+
+ Parameters
+ ----------
+ display_name : str | None, default='MyDiffusionModel'
+ Display name of the diffusion model.
+ unique_name : str | None, default=None
+ Unique name of the diffusion model. If None, a unique name will be generated. By
+ default, None.
+ scale : Numeric, default=1.0
+ Scale factor for the diffusion model. Must be a non-negative number.
+ unit : str | sc.Unit, default='meV'
+ Unit of the diffusion model. Must be convertible to meV.
+
+ Raises
+ ------
+ TypeError
+ If scale is not a number.
+ UnitError
+ If unit is not a string or scipp Unit, or if it cannot be converted to meV.
"""
try:
@@ -51,60 +56,41 @@ def __init__(
scale = Parameter(name='scale', value=float(scale), fixed=False, min=0.0, unit=unit)
- super().__init__(display_name=display_name, unique_name=unique_name)
- self._unit = unit
+ super().__init__(display_name=display_name, unique_name=unique_name, unit=unit)
self._scale = scale
# ------------------------------------------------------------------
# Properties
# ------------------------------------------------------------------
- @property
- def unit(self) -> str | sc.Unit | None:
- """Get the unit of the energy axis of the DiffusionModel.
-
- Returns:
- str | sc.Unit | None: Unit of the DiffusionModel.
- """
- return str(self._unit)
-
- @unit.setter
- def unit(self, _unit_str: str) -> None:
- """The unit of the energy axis is read-only. To change the unit,
- use convert_unit or create a new DiffusionModel with the desired
- unit.
-
- Args:
- _unit_str (str): The new unit to set (ignored)
-
- Raises:
- AttributeError: Always, since the unit is read-only.
- """
- raise AttributeError(
- f'Unit is read-only. Use convert_unit to change the unit between allowed types '
- f'or create a new {self.__class__.__name__} with the desired unit.'
- ) # noqa: E501
-
@property
def scale(self) -> Parameter:
- """Get the scale parameter of the diffusion model.
+ """
+ Get the scale parameter of the diffusion model.
- Returns:
- Parameter: scale parameter of the diffusion model
+ Returns
+ -------
+ Parameter
+ Scale parameter of the diffusion model.
"""
return self._scale
@scale.setter
def scale(self, scale: Numeric) -> None:
- """Set the scale parameter of the diffusion model.
-
- Args:
- scale (Numeric): The new value for the scale parameter. Must
- be a non-negative number.
-
- Raises:
- TypeError: If scale is not a number.
- ValueError: If scale is negative.
+ """
+ Set the scale parameter of the diffusion model.
+
+ Parameters
+ ----------
+ scale : Numeric
+ The new value for the scale parameter. Must be a non-negative number.
+
+ Raises
+ ------
+ TypeError
+ If scale is not a number.
+ ValueError
+ If scale is negative.
"""
if not isinstance(scale, Numeric):
raise TypeError('scale must be a number.')
@@ -118,9 +104,12 @@ def scale(self, scale: Numeric) -> None:
# ------------------------------------------------------------------
def __repr__(self) -> str:
- """String representation of the Diffusion model.
+ """
+ String representation of the Diffusion model.
- Returns:
- str: String representation of the DiffusionModel.
+ Returns
+ -------
+ str
+ String representation of the DiffusionModel.
"""
return f'{self.__class__.__name__}(display_name={self.display_name}, unit={self.unit})'
diff --git a/src/easydynamics/sample_model/diffusion_model/jump_translational_diffusion.py b/src/easydynamics/sample_model/diffusion_model/jump_translational_diffusion.py
index 888a0ad5..346ce152 100644
--- a/src/easydynamics/sample_model/diffusion_model/jump_translational_diffusion.py
+++ b/src/easydynamics/sample_model/diffusion_model/jump_translational_diffusion.py
@@ -18,29 +18,22 @@
class JumpTranslationalDiffusion(DiffusionModelBase):
- r"""Model of Jump translational diffusion. The model consists of a
- Lorentzian function for each Q-value, where the width is given by
-
- $$
- \Gamma(Q) = \frac{Q^2}{1+D t Q^2}.
- $$
-
- where $D$ is the diffusion coefficient and $t$ is the relaxation
- time. Q is assumed to have units of 1/angstrom. Creates
- ComponentCollections with Lorentzian components for given Q-values.
-
- Example:
- >>> Q = np.linspace(0.5, 2, 7)
- >>> energy = np.linspace(-2, 2, 501)
- >>> scale = 1.0
- >>> diffusion_coefficient = 2.4e-9 # m^2/s
- >>> relaxation_time = 1.0 # ps
- >>> diffusion_model=JumpTranslationalDiffusion(
- >>> scale = scale, diffusion_coefficient = (diffusion_coefficient,)
- >>> relaxation_time=relaxation_time)
- >>> component_collections=
- >>> diffusion_model.create_component_collections(Q)
- See also the tutorials..
+ r"""
+ Model of Jump translational diffusion.
+
+ The model consists of a Lorentzian function for each Q-value, where the width is given by
+
+ $$ \Gamma(Q) = \frac{Q^2}{1+D t Q^2}. $$
+
+ where $D$ is the diffusion coefficient and $t$ is the relaxation time. Q is assumed to have
+ units of 1/angstrom. Creates ComponentCollections with Lorentzian components for given
+ Q-values.
+
+ Example: >>> Q = np.linspace(0.5, 2, 7) >>> energy = np.linspace(-2, 2, 501) >>> scale = 1.0
+ >>> diffusion_coefficient = 2.4e-9 # m^2/s >>> relaxation_time = 1.0 # ps >>>
+ diffusion_model=JumpTranslationalDiffusion( >>> scale = scale, diffusion_coefficient =
+ (diffusion_coefficient,) >>> relaxation_time=relaxation_time) >>> component_collections= >>>
+ diffusion_model.create_component_collections(Q) See also the tutorials..
"""
def __init__(
@@ -52,24 +45,29 @@ def __init__(
diffusion_coefficient: Numeric = 1.0,
relaxation_time: Numeric = 1.0,
) -> None:
- """Initialize a new JumpTranslationalDiffusion model.
-
- Args:
- display_name (str | None, default="JumpTranslationalDiffusion"):
- Display name of the diffusion model.
- unique_name (str | None, default=None): Unique name of the diffusion
- model. If None, a unique name will be generated.
- unit (str | sc.Unit, default="meV"): Unit of the diffusion model. Must be
- convertible to meV.
- scale (Numeric, default=1.0): Scale factor for the diffusion model. Must
- be a non-negative number.
- diffusion_coefficient (Numeric, default=1.0): Diffusion coefficient D in
- m^2/s.
- relaxation_time (Numeric, default=1.0): Relaxation time t in ps.
-
- Raises:
- TypeError: If scale, diffusion_coefficient, or
- relaxation_time are not numbers.
+ """
+ Initialize a new JumpTranslationalDiffusion model.
+
+ Parameters
+ ----------
+ display_name : str | None, default='JumpTranslationalDiffusion'
+ Display name of the diffusion model.
+ unique_name : str | None, default=None
+ Unique name of the diffusion model. If None, a unique name will be generated. By
+ default, None.
+ unit : str | sc.Unit, default='meV'
+ Unit of the diffusion model. Must be convertible to meV.
+ scale : Numeric, default=1.0
+ Scale factor for the diffusion model. Must be a non-negative number.
+ diffusion_coefficient : Numeric, default=1.0
+ Diffusion coefficient D in m^2/s.
+ relaxation_time : Numeric, default=1.0
+ Relaxation time t in ps.
+
+ Raises
+ ------
+ TypeError
+ If scale, diffusion_coefficient, or relaxation_time are not numbers.
"""
super().__init__(
display_name=display_name,
@@ -109,24 +107,32 @@ def __init__(
@property
def diffusion_coefficient(self) -> Parameter:
- """Get the diffusion coefficient parameter D.
+ """
+ Get the diffusion coefficient parameter D.
- Returns:
- Parameter: Diffusion coefficient D.
+ Returns
+ -------
+ Parameter
+ Diffusion coefficient D.
"""
return self._diffusion_coefficient
@diffusion_coefficient.setter
def diffusion_coefficient(self, diffusion_coefficient: Numeric) -> None:
- """Set the diffusion coefficient parameter D.
-
- Args:
- diffusion_coefficient (Numeric): Diffusion coefficient D in
- m^2/s.
-
- Raises:
- TypeError: If diffusion_coefficient is not a number.
- ValueError: If diffusion_coefficient is negative.
+ """
+ Set the diffusion coefficient parameter D.
+
+ Parameters
+ ----------
+ diffusion_coefficient : Numeric
+ Diffusion coefficient D in m^2/s.
+
+ Raises
+ ------
+ TypeError
+ If diffusion_coefficient is not a number.
+ ValueError
+ If diffusion_coefficient is negative.
"""
if not isinstance(diffusion_coefficient, Numeric):
raise TypeError('diffusion_coefficient must be a number.')
@@ -136,23 +142,32 @@ def diffusion_coefficient(self, diffusion_coefficient: Numeric) -> None:
@property
def relaxation_time(self) -> Parameter:
- """Get the relaxation time parameter t.
+ """
+ Get the relaxation time parameter t.
- Returns:
- Parameter: Relaxation time t in ps.
+ Returns
+ -------
+ Parameter
+ Relaxation time t in ps.
"""
return self._relaxation_time
@relaxation_time.setter
def relaxation_time(self, relaxation_time: Numeric) -> None:
- """Set the relaxation time parameter t.
-
- Args:
- relaxation_time (Numeric): Relaxation time t in ps.
-
- Raises:
- TypeError: If relaxation_time is not a number.
- ValueError: If relaxation_time is negative.
+ """
+ Set the relaxation time parameter t.
+
+ Parameters
+ ----------
+ relaxation_time : Numeric
+ Relaxation time t in ps.
+
+ Raises
+ ------
+ TypeError
+ If relaxation_time is not a number.
+ ValueError
+ If relaxation_time is negative.
"""
if not isinstance(relaxation_time, Numeric):
raise TypeError('relaxation_time must be a number.')
@@ -166,17 +181,19 @@ def relaxation_time(self, relaxation_time: Numeric) -> None:
################################
def calculate_width(self, Q: Q_type) -> np.ndarray:
- r"""Calculate the half-width at half-maximum (HWHM) for the
- diffusion model. $\Gamma(Q) = Q^2/(1+D t Q^2)$, where $D$ is the
- diffusion coefficient and $t$ is the relaxation time.
-
- Args:
- Q (Q_type): Scattering vector in 1/angstrom. Can be a single
- value or an array of values.
-
- Returns:
- np.ndarray: HWHM values in the unit of the model (e.g.,
- meV).
+ r"""
+ Calculate the half-width at half-maximum (HWHM) for the diffusion model. $\Gamma(Q) =
+ Q^2/(1+D t Q^2)$, where $D$ is the diffusion coefficient and $t$ is the relaxation time.
+
+ Parameters
+ ----------
+ Q : Q_type
+ Scattering vector in 1/angstrom. Can be a single value or an array of values.
+
+ Returns
+ -------
+ np.ndarray
+ HWHM values in the unit of the model (e.g., meV).
"""
Q = _validate_and_convert_Q(Q)
@@ -198,27 +215,35 @@ def calculate_width(self, Q: Q_type) -> np.ndarray:
return numerator / denominator
def calculate_EISF(self, Q: Q_type) -> np.ndarray:
- """Calculate the Elastic Incoherent Structure Factor (EISF).
+ """
+ Calculate the Elastic Incoherent Structure Factor (EISF).
- Args:
- Q (Q_type): Scattering vector in 1/angstrom. Can be a single
- value or an array of values.
+ Parameters
+ ----------
+ Q : Q_type
+ Scattering vector in 1/angstrom. Can be a single value or an array of values.
- Returns:
- np.ndarray: EISF values (dimensionless).
+ Returns
+ -------
+ np.ndarray
+ EISF values (dimensionless).
"""
Q = _validate_and_convert_Q(Q)
return np.zeros_like(Q)
def calculate_QISF(self, Q: Q_type) -> np.ndarray:
- """Calculate the Quasi-Elastic Incoherent Structure Factor
- (QISF).
-
- Args:
- Q (Q_type): Scattering vector in 1/angstrom. Can be a single
- value or an array of values.
- Returns:
- np.ndarray: QISF values (dimensionless).
+ """
+ Calculate the Quasi-Elastic Incoherent Structure Factor (QISF).
+
+ Parameters
+ ----------
+ Q : Q_type
+ Scattering vector in 1/angstrom. Can be a single value or an array of values.
+
+ Returns
+ -------
+ np.ndarray
+ QISF values (dimensionless).
"""
Q = _validate_and_convert_Q(Q)
return np.ones_like(Q)
@@ -228,21 +253,25 @@ def create_component_collections(
Q: Q_type,
component_display_name: str = 'Jump translational diffusion',
) -> list[ComponentCollection]:
- """Create ComponentCollection components for the diffusion model
- at given Q values.
-
- Args:
- Q (Q_type): Scattering vector in 1/angstrom. Can be a single
- value or an array of values.
- component_display_name (str, default="Jump translational diffusion"):
- Name of the Jump Diffusion Lorentzian component.
-
- Returns:
- list[ComponentCollection]: List of ComponentCollections with
- Jump Diffusion Lorentzian components.
-
- Raises:
- TypeError: If component_display_name is not a string.
+ """
+ Create ComponentCollection components for the diffusion model at given Q values.
+
+ Parameters
+ ----------
+ Q : Q_type
+ Scattering vector in 1/angstrom. Can be a single value or an array of values.
+ component_display_name : str, default='Jump translational diffusion'
+ Name of the Jump Diffusion Lorentzian component.
+
+ Raises
+ ------
+ TypeError
+ If component_display_name is not a string.
+
+ Returns
+ -------
+ list[ComponentCollection]
+ List of ComponentCollections with Jump Diffusion Lorentzian components.
"""
Q = _validate_and_convert_Q(Q)
@@ -293,17 +322,24 @@ def create_component_collections(
################################
def _write_width_dependency_expression(self, Q: float) -> str:
- """Write the dependency expression for the width as a function
- of Q to make dependent Parameters.
+ """
+ Write the dependency expression for the width as a function of Q to make dependent
+ Parameters.
- Args:
- Q (float): Scattering vector in 1/angstrom
+ Parameters
+ ----------
+ Q : float
+ Scattering vector in 1/angstrom.
- Returns:
- str: Dependency expression for the width.
+ Raises
+ ------
+ TypeError
+ If Q is not a float.
- Raises:
- TypeError: If Q is not a float.
+ Returns
+ -------
+ str
+ Dependency expression for the width.
"""
if not isinstance(Q, (float)):
raise TypeError('Q must be a float.')
@@ -312,11 +348,13 @@ def _write_width_dependency_expression(self, Q: float) -> str:
return f'hbar * D* {Q} **2/(angstrom**2)/(1 + (D * t* {Q} **2/(angstrom**2)))'
def _write_width_dependency_map_expression(self) -> dict[str, DescriptorNumber]:
- """Write the dependency map expression to make dependent
- Parameters.
+ """
+ Write the dependency map expression to make dependent Parameters.
- Returns:
- dict[str, DescriptorNumber]: Dependency map for the width.
+ Returns
+ -------
+ dict[str, DescriptorNumber]
+ Dependency map for the width.
"""
return {
'D': self._diffusion_coefficient,
@@ -326,17 +364,23 @@ def _write_width_dependency_map_expression(self) -> dict[str, DescriptorNumber]:
}
def _write_area_dependency_expression(self, QISF: float) -> str:
- """Write the dependency expression for the area to make
- dependent Parameters.
-
- Args:
- QISF (float): Q-dependent intermediate scattering function.
-
- Returns:
- str: Dependency expression for the area.
-
- Raises:
- TypeError: If QISF is not a float.
+ """
+ Write the dependency expression for the area to make dependent Parameters.
+
+ Parameters
+ ----------
+ QISF : float
+ Q-dependent intermediate scattering function.
+
+ Raises
+ ------
+ TypeError
+ If QISF is not a float.
+
+ Returns
+ -------
+ str
+ Dependency expression for the area.
"""
if not isinstance(QISF, (float)):
@@ -345,11 +389,13 @@ def _write_area_dependency_expression(self, QISF: float) -> str:
return f'{QISF} * scale'
def _write_area_dependency_map_expression(self) -> dict[str, DescriptorNumber]:
- """Write the dependency map expression to make dependent
- Parameters.
+ """
+ Write the dependency map expression to make dependent Parameters.
- Returns:
- dict[str, DescriptorNumber]: Dependency map for the area.
+ Returns
+ -------
+ dict[str, DescriptorNumber]
+ Dependency map for the area.
"""
return {
'scale': self._scale,
@@ -360,12 +406,13 @@ def _write_area_dependency_map_expression(self) -> dict[str, DescriptorNumber]:
################################
def __repr__(self) -> str:
- """String representation of the JumpTranslationalDiffusion
- model.
+ """
+ String representation of the JumpTranslationalDiffusion model.
- Returns:
- str: String representation of the JumpTranslationalDiffusion
- model.
+ Returns
+ -------
+ str
+ String representation of the JumpTranslationalDiffusion model.
"""
return (
f'JumpTranslationalDiffusion(display_name={self.display_name}, '
diff --git a/src/easydynamics/sample_model/instrument_model.py b/src/easydynamics/sample_model/instrument_model.py
index 78815553..6468cd3b 100644
--- a/src/easydynamics/sample_model/instrument_model.py
+++ b/src/easydynamics/sample_model/instrument_model.py
@@ -17,11 +17,11 @@
class InstrumentModel(NewBase):
- """InstrumentModel represents a model of the instrument in an
- experiment at various Q.
+ """
+ InstrumentModel represents a model of the instrument in an experiment at various Q.
- It can contain a model of the resolution function for convolutions,
- of the background and an offset in the energy axis.
+ It can contain a model of the resolution function for convolutions, of the background and an
+ offset in the energy axis.
"""
def __init__(
@@ -34,30 +34,34 @@ def __init__(
energy_offset: Numeric | None = None,
unit: str | sc.Unit = 'meV',
) -> None:
- """Initialize an InstrumentModel.
-
- Args:
- display_name (str, default="MyInstrumentModel"): The display name of the
- InstrumentModel. Default is "MyInstrumentModel".
- unique_name (str | None, default=None): The unique name of the
- InstrumentModel.
- Q (Q_type | None, default=None): The Q values where the instrument is modelled.
- resolution_model (ResolutionModel | None, default=None): The resolution
- model of the instrument. If None, an empty resolution
- model is created and no resolution convolution is
- carried out.
- background_model (BackgroundModel | None, default=None): The background
- model of the instrument. If None, an empty background
- model is created, and the background evaluates to 0.
- energy_offset (Numeric | None, default=None): Template energy offset
- of the instrument. Will be copied to each Q value. If
- None, the energy offset will be 0.
- unit (str | sc.Unit, default="meV"): The unit of the energy axis.
-
- Raises:
- TypeError: If resolution_model is not a ResolutionModel or
- None, or if background_model is not a BackgroundModel or None, or
- if energy_offset is not a number or None.
+ """
+ Initialize an InstrumentModel.
+
+ Parameters
+ ----------
+ display_name : str, default='MyInstrumentModel'
+ The display name of the InstrumentModel.
+ unique_name : str | None, default=None
+ The unique name of the InstrumentModel.
+ Q : Q_type | None, default=None
+ The Q values where the instrument is modelled.
+ resolution_model : ResolutionModel | None, default=None
+ The resolution model of the instrument. If None, an empty resolution model is created
+ and no resolution convolution is carried out.
+ background_model : BackgroundModel | None, default=None
+ The background model of the instrument. If None, an empty background model is created,
+ and the background evaluates to 0.
+ energy_offset : Numeric | None, default=None
+ Template energy offset of the instrument. Will be copied to each Q value. If None, the
+ energy offset will be 0.
+ unit : str | sc.Unit, default='meV'
+ The unit of the energy axis.
+
+ Raises
+ ------
+ TypeError
+ If resolution_model is not a ResolutionModel or None, or if background_model is not a
+ BackgroundModel or None, or if energy_offset is not a number or None.
"""
super().__init__(
display_name=display_name,
@@ -107,23 +111,30 @@ def __init__(
@property
def resolution_model(self) -> ResolutionModel:
- """Get the resolution model of the instrument.
+ """
+ Get the resolution model of the instrument.
- Returns:
- ResolutionModel: The resolution model of the instrument.
+ Returns
+ -------
+ ResolutionModel
+ The resolution model of the instrument.
"""
return self._resolution_model
@resolution_model.setter
def resolution_model(self, value: ResolutionModel) -> None:
- """Set the resolution model of the instrument.
+ """
+ Set the resolution model of the instrument.
- Args:
- value (ResolutionModel): The new resolution model of the
- instrument.
+ Parameters
+ ----------
+ value : ResolutionModel
+ The new resolution model of the instrument.
- Raises:
- TypeError: If value is not a ResolutionModel.
+ Raises
+ ------
+ TypeError
+ If value is not a ResolutionModel.
"""
if not isinstance(value, ResolutionModel):
raise TypeError(
@@ -134,24 +145,31 @@ def resolution_model(self, value: ResolutionModel) -> None:
@property
def background_model(self) -> BackgroundModel:
- """Get the background model of the instrument.
+ """
+ Get the background model of the instrument.
- Returns:
- BackgroundModel: The background model of the instrument.
+ Returns
+ -------
+ BackgroundModel
+ The background model of the instrument.
"""
return self._background_model
@background_model.setter
def background_model(self, value: BackgroundModel) -> None:
- """Set the background model of the instrument.
+ """
+ Set the background model of the instrument.
- Args:
- value (BackgroundModel): The new background model of the
- instrument.
+ Parameters
+ ----------
+ value : BackgroundModel
+ The new background model of the instrument.
- Raises:
- TypeError: If value is not a BackgroundModel.
+ Raises
+ ------
+ TypeError
+ If value is not a BackgroundModel.
"""
if not isinstance(value, BackgroundModel):
@@ -163,28 +181,34 @@ def background_model(self, value: BackgroundModel) -> None:
@property
def Q(self) -> np.ndarray | None:
- """Get the Q values of the InstrumentModel.
+ """
+ Get the Q values of the InstrumentModel.
- Returns:
- np.ndarray | None: The Q values of the InstrumentModel, or
- None if not set
+ Returns
+ -------
+ np.ndarray | None
+ The Q values of the InstrumentModel, or None if not set.
"""
return self._Q
@Q.setter
def Q(self, value: Q_type | None) -> None:
- """Set the Q values of the InstrumentModel. If Q is already set,
- it raises an error if the new Q values are not similar to the
- old ones to prevent accidental changes to the background and
- resolution models. To change Q values, first run clear_Q().
+ """
+ Set the Q values of the InstrumentModel.
+
+ If Q is already set, it raises an error if the new Q values are not similar to the old ones
+ to prevent accidental changes to the background and resolution models. To change Q values,
+ first run clear_Q().
- Args:
- value (Q_type | None): The new Q values to set.
- If None, Q values are not changed.
+ Parameters
+ ----------
+ value : Q_type | None
+ The new Q values to set. If None, Q values are not changed.
- Raises:
- ValueError: If the new Q values are not similar to the old
- ones when Q is not None
+ Raises
+ ------
+ ValueError
+ If the new Q values are not similar to the old ones when Q is not None.
"""
if value is None:
return
@@ -204,53 +228,65 @@ def Q(self, value: Q_type | None) -> None:
@property
def unit(self) -> str | sc.Unit:
- """Get the unit of the InstrumentModel.
+ """
+ Get the unit of the InstrumentModel.
- Returns:
- str | sc.Unit: The unit of the InstrumentModel.
+ Returns
+ -------
+ str | sc.Unit
+ The unit of the InstrumentModel.
"""
return self._unit
@unit.setter
def unit(self, _unit_str: str) -> None:
- """Set the unit of the InstrumentModel. The unit is read-only
- and cannot be set directly. Use convert_unit to change the unit
- between allowed types or create a new InstrumentModel with the
- desired unit.
+ """
+ Set the unit of the InstrumentModel.
+
+ The unit is read-only and cannot be set directly. Use convert_unit to change the unit
+ between allowed types or create a new InstrumentModel with the desired unit.
- Args:
- _unit_str (str): The new unit for the InstrumentModel
- (ignored)
+ Parameters
+ ----------
+ _unit_str : str
+ The new unit for the InstrumentModel (ignored).
- Raises:
- AttributeError: Always, as the unit is read-only.
+ Raises
+ ------
+ AttributeError
+ Always, as the unit is read-only.
"""
raise AttributeError(
f'Unit is read-only. Use convert_unit to change the unit between allowed types '
f'or create a new {self.__class__.__name__} with the desired unit.'
- ) # noqa: E501
+ )
@property
def energy_offset(self) -> Parameter:
- """Get the energy offset template parameter of the instrument
- model.
+ """
+ Get the energy offset template parameter of the instrument model.
- Returns:
- Parameter: The energy offset template parameter of the
- instrument model.
+ Returns
+ -------
+ Parameter
+ The energy offset template parameter of the instrument model.
"""
return self._energy_offset
@energy_offset.setter
def energy_offset(self, value: Numeric) -> None:
- """Set the offset parameter of the instrument model.
+ """
+ Set the offset parameter of the instrument model.
- Args:
- value (Numeric): The new value for the energy offset
- parameter. Will be copied to all Q values.
+ Parameters
+ ----------
+ value : Numeric
+ The new value for the energy offset parameter. Will be copied to all Q values.
- Raises:
- TypeError: If value is not a number.
+ Raises
+ ------
+ TypeError
+ If value is not a number.
"""
if not isinstance(value, Numeric):
raise TypeError(f'energy_offset must be a number, got {type(value).__name__}')
@@ -263,16 +299,19 @@ def energy_offset(self, value: Numeric) -> None:
# --------------------------------------------------------------
def clear_Q(self, confirm: bool = False) -> None:
- """Clear the Q values of the InstrumentModel and any associated
- ResolutionModel and BackgroundModel, removing all component
- collections and their associated Parameters.
-
- Args:
- confirm (bool, default=False): Confirmation to clear Q
- values.
-
- Raises:
- ValueError: If confirm is not True.
+ """
+ Clear the Q values of the InstrumentModel and any associated ResolutionModel and
+ BackgroundModel, removing all component collections and their associated Parameters.
+
+ Parameters
+ ----------
+ confirm : bool, default=False
+ Confirmation to clear Q values.
+
+ Raises
+ ------
+ ValueError
+ If confirm is not True.
"""
if not confirm:
raise ValueError(
@@ -284,14 +323,18 @@ def clear_Q(self, confirm: bool = False) -> None:
self._on_Q_change()
def convert_unit(self, unit_str: str | sc.Unit) -> None:
- """Convert the unit of the InstrumentModel.
+ """
+ Convert the unit of the InstrumentModel.
- Args:
- unit_str (str | sc.Unit): The unit to convert to.
+ Parameters
+ ----------
+ unit_str : str | sc.Unit
+ The unit to convert to.
- Raises:
- ValueError: If unit_str is not a valid unit string or
- scipp Unit.
+ Raises
+ ------
+ ValueError
+ If unit_str is not a valid unit string or scipp Unit.
"""
unit = _validate_unit(unit_str)
if unit is None:
@@ -306,23 +349,28 @@ def convert_unit(self, unit_str: str | sc.Unit) -> None:
self._unit = unit
def get_all_variables(self, Q_index: int | None = None) -> list[Parameter]:
- """Get all variables in the InstrumentModel.
-
- Args:
- Q_index (int | None, default=None): The index of the Q value to get
- variables for. If None, get variables for all Q values.
-
- Returns:
- list[Parameter]: A list of all variables in the
- InstrumentModel. If Q_index is specified, only variables
- from the ComponentCollection at the given Q index are
- included. Otherwise, all variables in the
- InstrumentModel are included.
-
- Raises:
- TypeError: If Q_index is not an int or None.
- IndexError: If Q_index is out of bounds for the Q values in
- the InstrumentModel.
+ """
+ Get all variables in the InstrumentModel.
+
+ Parameters
+ ----------
+ Q_index : int | None, default=None
+ The index of the Q value to get variables for. If None, get variables for all Q values.
+
+
+ Raises
+ ------
+ TypeError
+ If Q_index is not an int or None.
+ IndexError
+ If Q_index is out of bounds for the Q values in the InstrumentModel.
+
+ Returns
+ -------
+ list[Parameter]
+ A list of all variables in the InstrumentModel. If Q_index is specified, only variables
+ from the ComponentCollection at the given Q index are included. Otherwise, all
+ variables in the InstrumentModel are included.
"""
if self._Q is None:
return []
@@ -359,20 +407,29 @@ def get_energy_offset(
self,
Q_index: int | None = None,
) -> Parameter | list[Parameter]:
- """Get the energy offset Parameter at a specific Q index.
-
- Args:
- Q_index (int | None, default=None): The index of the Q value to get the energy
- offset for. If None, get the energy offset for all Q values.
-
- Returns:
- Parameter | list[Parameter]: The energy offset Parameter at the specified Q
- index, or a list of Parameters if Q_index is None.
-
- Raises:
- ValueError: If no Q values are set in the InstrumentModel.
- IndexError: If Q_index is out of bounds.
- TypeError: If Q_index is not an int or None.
+ """
+ Get the energy offset Parameter at a specific Q index.
+
+ Parameters
+ ----------
+ Q_index : int | None, default=None
+ The index of the Q value to get the energy offset for. If None, get the energy offset
+ for all Q values.
+
+ Raises
+ ------
+ ValueError
+ If no Q values are set in the InstrumentModel.
+ IndexError
+ If Q_index is out of bounds.
+ TypeError
+ If Q_index is not an int or None.
+
+ Returns
+ -------
+ Parameter | list[Parameter]
+ The energy offset Parameter at the specified Q index, or a list of Parameters if
+ Q_index is None.
"""
if self._Q is None:
raise ValueError('No Q values are set in the InstrumentModel.')
@@ -389,26 +446,32 @@ def get_energy_offset(
return self._energy_offsets[Q_index]
def fix_energy_offset(self, Q_index: int | None = None) -> None:
- """Fix energy offset parameters. If Q_index is specified, only
- fix the energy offset for that Q value. If Q_index is None, fix
- energy offsets for all Q values.
+ """
+ Fix energy offset parameters.
+
+ If Q_index is specified, only fix the energy offset for that Q value. If Q_index is None,
+ fix energy offsets for all Q values.
- Args:
- Q_index (int | None, default=None): The index of the Q value
- to fix the energy offset for. If None, fix energy
- offsets for all Q values.
+ Parameters
+ ----------
+ Q_index : int | None, default=None
+ The index of the Q value to fix the energy offset for. If None, fix energy offsets for
+ all Q values.
"""
self._fix_or_free_energy_offset(Q_index, fixed=True)
def free_energy_offset(self, Q_index: int | None = None) -> None:
- """Free energy offset parameters. If Q_index is specified, only
- free the energy offset for that Q value. If Q_index is None,
+ """
+ Free energy offset parameters.
+
+ If Q_index is specified, only free the energy offset for that Q value. If Q_index is None,
free energy offsets for all Q values.
- Args:
- Q_index (int | None, default=None): The index of the Q value
- to free the energy offset for. If None, free energy
- offsets for all Q values.
+ Parameters
+ ----------
+ Q_index : int | None, default=None
+ The index of the Q value to free the energy offset for. If None, free energy offsets
+ for all Q values.
"""
self._fix_or_free_energy_offset(Q_index, fixed=False)
@@ -416,21 +479,26 @@ def free_energy_offset(self, Q_index: int | None = None) -> None:
# Private methods
# --------------------------------------------------------------
def _fix_or_free_energy_offset(self, Q_index: int | None = None, fixed: bool = True) -> None:
- """Fix or free energy offset parameters. If Q_index is
- specified, only fix or free the energy offset for that Q value.
- If Q_index is None, fix or free energy offsets for all Q values.
-
- Args:
- Q_index (int | None, default=None): The index of the Q value
- to fix or free the energy offset for. If None, fix or
- free energy offsets for all Q values.
- fixed (bool, default=True): Whether to fix (True) or free
- (False) the energy offset.
-
- Raises:
- TypeError: If Q_index is not an int or None.
- IndexError: If Q_index is out of bounds for the Q values in
- the InstrumentModel.
+ """
+ Fix or free energy offset parameters.
+
+ If Q_index is specified, only fix or free the energy offset for that Q value. If Q_index is
+ None, fix or free energy offsets for all Q values.
+
+ Parameters
+ ----------
+ Q_index : int | None, default=None
+ The index of the Q value to fix or free the energy offset for. If None, fix or free
+ energy offsets for all Q values.
+ fixed : bool, default=True
+ Whether to fix (True) or free (False) the energy offset.
+
+ Raises
+ ------
+ TypeError
+ If Q_index is not an int or None.
+ IndexError
+ If Q_index is out of bounds for the Q values in the InstrumentModel.
"""
if Q_index is None:
@@ -478,10 +546,13 @@ def _on_background_model_change(self) -> None:
# -------------------------------------------------------------
def __repr__(self) -> str:
- """Return a string representation of the InstrumentModel.
+ """
+ Return a string representation of the InstrumentModel.
- Returns:
- str: A string representation of the InstrumentModel.
+ Returns
+ -------
+ str
+ A string representation of the InstrumentModel.
"""
return (
diff --git a/src/easydynamics/sample_model/model_base.py b/src/easydynamics/sample_model/model_base.py
index 0bb95860..e76d4370 100644
--- a/src/easydynamics/sample_model/model_base.py
+++ b/src/easydynamics/sample_model/model_base.py
@@ -5,22 +5,21 @@
import numpy as np
import scipp as sc
-from easyscience.base_classes.model_base import ModelBase as EasyScienceModelBase
from easyscience.variable import Parameter
+from easydynamics.base_classes.easydynamics_modelbase import EasyDynamicsModelBase
from easydynamics.sample_model.component_collection import ComponentCollection
from easydynamics.sample_model.components.model_component import ModelComponent
from easydynamics.utils.utils import Numeric
from easydynamics.utils.utils import Q_type
from easydynamics.utils.utils import _validate_and_convert_Q
-from easydynamics.utils.utils import _validate_unit
-class ModelBase(EasyScienceModelBase):
- """Base class for Sample Models.
+class ModelBase(EasyDynamicsModelBase):
+ """
+ Base class for Sample Models.
- Contains common functionality for models with components and Q
- dependence.
+ Contains common functionality for models with components and Q dependence.
"""
def __init__(
@@ -31,28 +30,33 @@ def __init__(
components: ModelComponent | ComponentCollection | None = None,
Q: Q_type | None = None,
) -> None:
- """Initialize the ModelBase.
-
- Args:
- display_name (str, default="MyModelBase"): Display name of the model.
- unique_name (str | None, default=None): Unique name of the model. If None,
- a unique name will be generated.
- unit (str | sc.Unit | None, default="meV"): Unit of the model.
- components (ModelComponent | ComponentCollection | None, default=None):
- Template components of the model. If None, no components
- are added. These components are copied into
- ComponentCollections for each Q value.
- Q (Q_type | None, default=None): Q values for the model.
- If None, Q is not set.
-
- Raises:
- TypeError: If components is not a ModelComponent or ComponentCollection.
+ """
+ Initialize the ModelBase.
+
+ Parameters
+ ----------
+ display_name : str, default='MyModelBase'
+ Display name of the model.
+ unique_name : str | None, default=None
+ Unique name of the model. If None, a unique name will be generated.
+ unit : str | sc.Unit | None, default='meV'
+ Unit of the model.
+ components : ModelComponent | ComponentCollection | None, default=None
+ Template components of the model. If None, no components are added. These components
+ are copied into ComponentCollections for each Q value.
+ Q : Q_type | None, default=None
+ Q values for the model. If None, Q is not set.
+
+ Raises
+ ------
+ TypeError
+ If components is not a ModelComponent or ComponentCollection.
"""
super().__init__(
+ unit=unit,
display_name=display_name,
unique_name=unique_name,
)
- self._unit = _validate_unit(unit)
self._Q = _validate_and_convert_Q(Q)
if components is not None and not isinstance(
@@ -72,23 +76,26 @@ def __init__(
def evaluate(
self, x: Numeric | list | np.ndarray | sc.Variable | sc.DataArray
) -> list[np.ndarray]:
- """Evaluate the sample model at all Q for the given x values.
-
- Args:
- x (Numeric | list | np.ndarray | sc.Variable | sc.DataArray):
- Energy axis values to evaluate the model at. If a scipp
- Variable or DataArray is provided, the unit of the model
- will be converted to match the unit of x for evaluation, and
- the result will be returned in the same unit as x.
-
- Returns:
- list[np.ndarray]: A list of numpy arrays containing the
- evaluated model values for each Q. The length of the
- list will match the number of Q values in the model.
-
- Raises:
- ValueError: If there are no components in the model to
- evaluate.
+ """
+ Evaluate the sample model at all Q for the given x values.
+
+ Parameters
+ ----------
+ x : Numeric | list | np.ndarray | sc.Variable | sc.DataArray
+ Energy axis values to evaluate the model at. If a scipp Variable or DataArray is
+ provided, the unit of the model will be converted to match the unit of x for
+ evaluation, and the result will be returned in the same unit as x.
+
+ Raises
+ ------
+ ValueError
+ If there are no components in the model to evaluate.
+
+ Returns
+ -------
+ list[np.ndarray]
+ A list of numpy arrays containing the evaluated model values for each Q. The length of
+ the list will match the number of Q values in the model.
"""
if not self._component_collections:
@@ -102,23 +109,25 @@ def evaluate(
# Component management
# ------------------------------------------------------------------
def append_component(self, component: ModelComponent | ComponentCollection) -> None:
- """Append a ModelComponent or ComponentCollection to the
- SampleModel.
+ """
+ Append a ModelComponent or ComponentCollection to the SampleModel.
- Args:
- component (ModelComponent | ComponentCollection): The
- ModelComponent or ComponentCollection to append.
+ Parameters
+ ----------
+ component : ModelComponent | ComponentCollection
+ The ModelComponent or ComponentCollection to append.
"""
self._components.append_component(component)
self._on_components_change()
def remove_component(self, unique_name: str) -> None:
- """Remove a ModelComponent from the SampleModel by its unique
- name.
+ """
+ Remove a ModelComponent from the SampleModel by its unique name.
- Args:
- unique_name (str): The unique name of the ModelComponent
- to remove.
+ Parameters
+ ----------
+ unique_name : str
+ The unique name of the ModelComponent to remove.
"""
self._components.remove_component(unique_name)
self._on_components_change()
@@ -134,81 +143,63 @@ def clear_components(self) -> None:
@property
def unit(self) -> str | sc.Unit | None:
- """Get the unit of the ComponentCollection.
+ """
+ Get the unit of the SampleModel.
- Returns:
- str | sc.Unit | None: The unit of the ComponentCollection.
+ Returns
+ -------
+ str | sc.Unit | None
+ The unit of the SampleModel.
"""
return self._unit
@unit.setter
def unit(self, _unit_str: str) -> None:
- """Unit is read-only and cannot be set directly.
+ """
+ Unit is read-only and cannot be set directly.
- Args:
- _unit_str (str): The new unit to set (ignored).
+ Parameters
+ ----------
+ _unit_str : str
+ The new unit to set (ignored).
- Raises:
- AttributeError: Always raised to indicate that the unit is
- read-only.
+ Raises
+ ------
+ AttributeError
+ Always raised to indicate that the unit is read-only.
"""
raise AttributeError(
f'Unit is read-only. Use convert_unit to change the unit between allowed types '
f'or create a new {self.__class__.__name__} with the desired unit.'
- ) # noqa: E501
-
- def convert_unit(self, unit: str | sc.Unit) -> None:
- """Convert the unit of the ComponentCollection and all its
- components.
-
- Args:
- unit (str | sc.Unit): The new unit to convert to.
-
- Raises:
- TypeError: If the provided unit is not a string or sc.Unit.
- Exception: If the provided unit is not compatible with the
- current unit.
- """
-
- old_unit = self._unit
-
- if not isinstance(unit, (str, sc.Unit)):
- raise TypeError(f'Unit must be a string or sc.Unit, got {type(unit).__name__}')
- try:
- for component in self.components:
- component.convert_unit(unit)
- self._unit = unit
- except Exception as e:
- # Attempt to rollback on failure
- try:
- for component in self.components:
- component.convert_unit(old_unit)
- except Exception: # noqa: S110
- pass # Best effort rollback
- raise e
- self._on_components_change()
+ )
@property
def components(self) -> list[ModelComponent]:
- """Get the components of the SampleModel.
+ """
+ Get the components of the SampleModel.
- Returns:
- list[ModelComponent]: The components of the SampleModel.
+ Returns
+ -------
+ list[ModelComponent]
+ The components of the SampleModel.
"""
return self._components.components
@components.setter
def components(self, value: ModelComponent | ComponentCollection | None) -> None:
- """Set the components of the SampleModel.
+ """
+ Set the components of the SampleModel.
- Args:
- value (ModelComponent | ComponentCollection | None): The new
- components to set. If None, all components will be cleared.
+ Parameters
+ ----------
+ value : ModelComponent | ComponentCollection | None
+ The new components to set. If None, all components will be cleared.
- Raises:
- TypeError: If value is not a ModelComponent,
- ComponentCollection, or None.
+ Raises
+ ------
+ TypeError
+ If value is not a ModelComponent, ComponentCollection, or None.
"""
if not isinstance(value, (ModelComponent, ComponentCollection, type(None))):
raise TypeError('Components must be a ModelComponent or a ComponentCollection')
@@ -219,27 +210,33 @@ def components(self, value: ModelComponent | ComponentCollection | None) -> None
@property
def Q(self) -> np.ndarray | None:
- """Get the Q values of the SampleModel.
+ """
+ Get the Q values of the SampleModel.
- Returns:
- np.ndarray | None: The Q values of the SampleModel, or None
- if not set.
+ Returns
+ -------
+ np.ndarray | None
+ The Q values of the SampleModel, or None if not set.
"""
return self._Q
@Q.setter
def Q(self, value: Q_type | None) -> None:
- """Set the Q values of the SampleModel. If Q is already set, it
- throws an error if the new Q values are not similar to the old
+ """
+ Set the Q values of the SampleModel.
+
+ If Q is already set, it throws an error if the new Q values are not similar to the old
ones. To change Q values, first run clear_Q().
- Args:
- value (Q_type | None): The new Q values to set.
- If None, Q values are not changed.
+ Parameters
+ ----------
+ value : Q_type | None
+ The new Q values to set. If None, Q values are not changed.
- Raises:
- ValueError: If the new Q values are not similar to the old
- ones when Q is already set.
+ Raises
+ ------
+ ValueError
+ If the new Q values are not similar to the old ones when Q is already set.
"""
if value is None:
return
@@ -258,14 +255,19 @@ def Q(self, value: Q_type | None) -> None:
)
def clear_Q(self, confirm: bool = False) -> None:
- """Clear the Q values of the SampleModel, removing all component
- collections and their associated Parameters.
-
- Args:
- confirm (bool, default=False): Confirmation to clear Q values.
-
- Raises:
- ValueError: If confirm is not True.
+ """
+ Clear the Q values of the SampleModel, removing all component collections and their
+ associated Parameters.
+
+ Parameters
+ ----------
+ confirm : bool, default=False
+ Confirmation to clear Q values.
+
+ Raises
+ ------
+ ValueError
+ If confirm is not True.
"""
if not confirm:
raise ValueError(
@@ -277,6 +279,42 @@ def clear_Q(self, confirm: bool = False) -> None:
# ------------------------------------------------------------------
# Other methods
# ------------------------------------------------------------------
+
+ def convert_unit(self, unit: str | sc.Unit) -> None:
+ """
+ Convert the unit of the ComponentCollection and all its components.
+
+ Parameters
+ ----------
+ unit : str | sc.Unit
+ The new unit to convert to.
+
+ Raises
+ ------
+ TypeError
+ If the provided unit is not a string or sc.Unit.
+ Exception
+ If the provided unit is not compatible with the current unit.
+ """
+
+ old_unit = self._unit
+
+ if not isinstance(unit, (str, sc.Unit)):
+ raise TypeError(f'Unit must be a string or sc.Unit, got {type(unit).__name__}')
+ try:
+ for component in self.components:
+ component.convert_unit(unit)
+ self._unit = unit
+ except Exception as e:
+ # Attempt to rollback on failure
+ try:
+ for component in self.components:
+ component.convert_unit(old_unit)
+ except Exception: # noqa: S110
+ pass # Best effort rollback
+ raise e
+ self._on_components_change()
+
def fix_all_parameters(self) -> None:
"""Fix all Parameters in all ComponentCollections."""
for par in self.get_all_variables():
@@ -288,24 +326,29 @@ def free_all_parameters(self) -> None:
par.fixed = False
def get_all_variables(self, Q_index: int | None = None) -> list[Parameter]:
- """Get all Parameters and Descriptors from all
- ComponentCollections in the ModelBase. Parameters Ignores the
- Parameters and Descriptors in self._components as these are just
+ """
+ Get all Parameters and Descriptors from all ComponentCollections in the ModelBase.
+ Parameters Ignores the Parameters and Descriptors in self._components as these are just
templates.
- Args:
- Q_index (int | None, default=None): If None, get variables for all
- ComponentCollections. If int, get variables for the
- ComponentCollection at this index. Defaults to None.
-
- Returns:
- list[Parameter]: A list of all Parameters and Descriptors
- from the ComponentCollections in the ModelBase.
-
- Raises:
- TypeError: If Q_index is not an int or None.
- IndexError: If Q_index is out of bounds for the number of
- ComponentCollections.
+ Parameters
+ ----------
+ Q_index : int | None, default=None
+ If None, get variables for all ComponentCollections. If int, get variables for the
+ ComponentCollection at this index.
+
+ Raises
+ ------
+ TypeError
+ If Q_index is not an int or None.
+ IndexError
+ If Q_index is out of bounds for the number of ComponentCollections.
+
+ Returns
+ -------
+ list[Parameter]
+ A list of all Parameters and Descriptors from the ComponentCollections in the
+ ModelBase.
"""
if Q_index is None:
@@ -326,19 +369,25 @@ def get_all_variables(self, Q_index: int | None = None) -> list[Parameter]:
return all_vars
def get_component_collection(self, Q_index: int) -> ComponentCollection:
- """Get the ComponentCollection at the given Q index.
-
- Args:
- Q_index (int): The index of the desired ComponentCollection.
-
- Returns:
- ComponentCollection: The ComponentCollection at the
- specified Q index.
-
- Raises:
- TypeError: If Q_index is not an int.
- IndexError: If Q_index is out of bounds for the number of
- ComponentCollections.
+ """
+ Get the ComponentCollection at the given Q index.
+
+ Parameters
+ ----------
+ Q_index : int
+ The index of the desired ComponentCollection.
+
+ Raises
+ ------
+ TypeError
+ If Q_index is not an int.
+ IndexError
+ If Q_index is out of bounds for the number of ComponentCollections.
+
+ Returns
+ -------
+ ComponentCollection
+ The ComponentCollection at the.
"""
if not isinstance(Q_index, int):
raise TypeError(f'Q_index must be an int, got {type(Q_index).__name__}')
@@ -382,10 +431,13 @@ def _on_components_change(self) -> None:
# ------------------------------------------------------------------
def __repr__(self) -> str:
- """Return a string representation of the ModelBase.
+ """
+ Return a string representation of the ModelBase.
- Returns:
- str: A string representation of the ModelBase.
+ Returns
+ -------
+ str
+ A string representation of the ModelBase.
"""
return (
f'{self.__class__.__name__}(unique_name={self.unique_name}, '
diff --git a/src/easydynamics/sample_model/resolution_model.py b/src/easydynamics/sample_model/resolution_model.py
index 639bf8f8..3d2385e7 100644
--- a/src/easydynamics/sample_model/resolution_model.py
+++ b/src/easydynamics/sample_model/resolution_model.py
@@ -3,18 +3,17 @@
import scipp as sc
+from easydynamics.sample_model.component_collection import ComponentCollection
+from easydynamics.sample_model.components import DeltaFunction
+from easydynamics.sample_model.components import Polynomial
+from easydynamics.sample_model.components.model_component import ModelComponent
from easydynamics.sample_model.model_base import ModelBase
from easydynamics.utils.utils import Q_type
-from .component_collection import ComponentCollection
-from .components import DeltaFunction
-from .components import Polynomial
-from .components.model_component import ModelComponent
-
class ResolutionModel(ModelBase):
- """ResolutionModel represents a model of the instrment resolution in
- an experiment at various Q.
+ """
+ ResolutionModel represents a model of the instrment resolution in an experiment at various Q.
"""
def __init__(
@@ -25,19 +24,22 @@ def __init__(
components: ModelComponent | ComponentCollection | None = None,
Q: Q_type | None = None,
) -> None:
- """Initialize a ResolutionModel.
+ """
+ Initialize a ResolutionModel.
- Args:
- display_name (str, default="MyResolutionModel"): Display name of the model.
- unique_name (str | None, default=None): Unique name of the model. If None,
- a unique name will be generated.
- unit (str | sc.Unit, default="meV"): Unit of the model.
- components (ModelComponent | ComponentCollection | None, default=None):
- Template components of the model. If None, no components
- are added. These components are copied into
- ComponentCollections for each Q value.
- Q (Q_type | None, default=None): Q values for the model. If None, Q is not
- set.
+ Parameters
+ ----------
+ display_name : str, default='MyResolutionModel'
+ Display name of the model.
+ unique_name : str | None, default=None
+ Unique name of the model. If None, a unique name will be generated.
+ unit : str | sc.Unit, default='meV'
+ Unit of the model.
+ components : ModelComponent | ComponentCollection | None, default=None
+ Template components of the model. If None, no components are added. These components
+ are copied into ComponentCollections for each Q value.
+ Q : Q_type | None, default=None
+ Q values for the model. If None, Q is not set.
"""
super().__init__(
@@ -49,17 +51,21 @@ def __init__(
)
def append_component(self, component: ModelComponent | ComponentCollection) -> None:
- """Append a component to the ResolutionModel.
+ """
+ Append a component to the ResolutionModel.
- Does not allow DeltaFunction or Polynomial components, as these
- are not physical resolution components.
+ Does not allow DeltaFunction or Polynomial components, as these are not physical resolution
+ components.
- Args:
- component (ModelComponent | ComponentCollection):
- Component(s) to append.
+ Parameters
+ ----------
+ component : ModelComponent | ComponentCollection
+ Component(s) to append.
- Raises:
- TypeError: If the component is a DeltaFunction or Polynomial
+ Raises
+ ------
+ TypeError
+ If the component is a DeltaFunction or Polynomial.
"""
if isinstance(component, ComponentCollection):
components = component.components
diff --git a/src/easydynamics/sample_model/sample_model.py b/src/easydynamics/sample_model/sample_model.py
index d6c63492..fdf8eb09 100644
--- a/src/easydynamics/sample_model/sample_model.py
+++ b/src/easydynamics/sample_model/sample_model.py
@@ -7,20 +7,20 @@
import scipp as sc
from easyscience.variable import Parameter
+from easydynamics.sample_model.component_collection import ComponentCollection
+from easydynamics.sample_model.components.model_component import ModelComponent
from easydynamics.sample_model.diffusion_model.diffusion_model_base import DiffusionModelBase
from easydynamics.sample_model.model_base import ModelBase
+from easydynamics.settings.detailed_balance_settings import DetailedBalanceSettings
from easydynamics.utils import detailed_balance_factor
from easydynamics.utils.utils import Numeric
from easydynamics.utils.utils import Q_type
-from .component_collection import ComponentCollection
-from .components.model_component import ModelComponent
-
class SampleModel(ModelBase):
- """SampleModel represents a model of a sample with components and
- diffusion models, parameterized by Q and optionally temperature.
- Generates ComponentCollections for each Q value, combining
+ """
+ SampleModel represents a model of a sample with components and diffusion models, parameterized
+ by Q and optionally temperature. Generates ComponentCollections for each Q value, combining
components from the base model and diffusion models.
Applies detailed balancing based on temperature if provided.
@@ -36,38 +36,42 @@ def __init__(
diffusion_models: DiffusionModelBase | list[DiffusionModelBase] | None = None,
temperature: float | None = None,
temperature_unit: str | sc.Unit = 'K',
- divide_by_temperature: bool = True,
+ detailed_balance_settings: DetailedBalanceSettings | None = None,
) -> None:
- """Initialize the SampleModel.
-
- Args:
- display_name (str, default="MySampleModel"): Display name of the model.
- unique_name (str | None, default=None): Unique name of the model. If None,
- a unique name will be generated.
- unit (str | sc.Unit, default="meV"): Unit of the model. If None,
- defaults to "meV".
- components (ModelComponent | ComponentCollection | None, default=None):
- Template components of the model. If None, no components
- are added. These components are copied into
- ComponentCollections for each Q value.
- Q (Q_type | None, default=None):
- Q values for the model. If None, Q is not set.
- diffusion_models (DiffusionModelBase | list[DiffusionModelBase] | None, default=None):
- Diffusion models to include in the SampleModel. If None,
- no diffusion models are added.
- temperature (float | None, default=None): Temperature for detailed
- balancing. If None, no detailed balancing is applied.
- temperature_unit (str | sc.Unit, default="K"): Unit of the temperature.
- Defaults to "K".
- divide_by_temperature (bool, default=True): Whether to divide the detailed
- balance factor by temperature. Defaults to True.
-
- Raises:
- TypeError: If diffusion_models is not a DiffusionModelBase,
- a list of DiffusionModelBase, or None, or if temperature
- is not a number or None, or if divide_by_temperature is
- not a bool.
- ValueError: If temperature is negative.
+ """
+ Initialize the SampleModel.
+
+ Parameters
+ ----------
+ display_name : str, default='MySampleModel'
+ Display name of the model.
+ unique_name : str | None, default=None
+ Unique name of the model. If None, a unique name will be generated.
+ unit : str | sc.Unit, default='meV'
+ Unit of the model. If None,.
+ components : ModelComponent | ComponentCollection | None, default=None
+ Template components of the model. If None, no components are added. These components
+ are copied into ComponentCollections for each Q value.
+ Q : Q_type | None, default=None
+ Q values for the model. If None, Q is not set.
+ diffusion_models : DiffusionModelBase | list[DiffusionModelBase] | None, default=None
+ Diffusion models to include in the SampleModel. If None, no diffusion models are added.
+ temperature : float | None, default=None
+ Temperature for detailed balancing. If None, no detailed balancing is applied. By
+ default, None.
+ temperature_unit : str | sc.Unit, default='K'
+ Unit of the temperature.
+ detailed_balance_settings : DetailedBalanceSettings | None, default=None
+ Settings for detailed balancing.
+
+ Raises
+ ------
+ TypeError
+ If diffusion_models is not a DiffusionModelBase, a list of DiffusionModelBase, or None,
+ or if temperature is not a number or None, or if detailed_balance_settings is not a
+ DetailedBalanceSettings instance.
+ ValueError
+ If temperature is negative.
"""
if diffusion_models is None:
self._diffusion_models = []
@@ -108,24 +112,30 @@ def __init__(
)
self._temperature_unit = temperature_unit
- if not isinstance(divide_by_temperature, bool):
- raise TypeError('divide_by_temperature must be True or False')
- self._divide_by_temperature = divide_by_temperature
+ if detailed_balance_settings is None:
+ self._detailed_balance_settings = DetailedBalanceSettings()
+ elif isinstance(detailed_balance_settings, DetailedBalanceSettings):
+ self._detailed_balance_settings = detailed_balance_settings
+ else:
+ raise TypeError('detailed_balance_settings must be a DetailedBalanceSettings or None')
# ------------------------------------------------------------------
# Component management
# ------------------------------------------------------------------
def append_diffusion_model(self, diffusion_model: DiffusionModelBase) -> None:
- """Append a DiffusionModel to the SampleModel.
+ """
+ Append a DiffusionModel to the SampleModel.
- Args:
- diffusion_model (DiffusionModelBase): The DiffusionModel
- to append.
+ Parameters
+ ----------
+ diffusion_model : DiffusionModelBase
+ The DiffusionModel to append.
- Raises:
- TypeError: If the diffusion_model is not a
- DiffusionModelBase
+ Raises
+ ------
+ TypeError
+ If the diffusion_model is not a DiffusionModelBase.
"""
if not isinstance(diffusion_model, DiffusionModelBase):
@@ -137,14 +147,18 @@ def append_diffusion_model(self, diffusion_model: DiffusionModelBase) -> None:
self._generate_component_collections()
def remove_diffusion_model(self, name: 'str') -> None:
- """Remove a DiffusionModel from the SampleModel by unique name.
+ """
+ Remove a DiffusionModel from the SampleModel by unique name.
- Args:
- name (str): The unique name of the DiffusionModel to remove.
+ Parameters
+ ----------
+ name : 'str'
+ The unique name of the DiffusionModel to remove.
- Raises:
- ValueError: If no DiffusionModel with the given unique name
- is found.
+ Raises
+ ------
+ ValueError
+ If no DiffusionModel with the given unique name is found.
"""
for i, dm in enumerate(self._diffusion_models):
if dm.unique_name == name:
@@ -167,11 +181,13 @@ def clear_diffusion_models(self) -> None:
@property
def diffusion_models(self) -> list[DiffusionModelBase]:
- """Get the diffusion models of the SampleModel.
+ """
+ Get the diffusion models of the SampleModel.
- Returns:
- list[DiffusionModelBase]: The diffusion models of the
- SampleModel.
+ Returns
+ -------
+ list[DiffusionModelBase]
+ The diffusion models of the SampleModel.
"""
return self._diffusion_models
@@ -179,17 +195,19 @@ def diffusion_models(self) -> list[DiffusionModelBase]:
def diffusion_models(
self, value: DiffusionModelBase | list[DiffusionModelBase] | None
) -> None:
- """Set the diffusion models of the SampleModel.
-
- Args:
- value (DiffusionModelBase | list[DiffusionModelBase] | None):
- The diffusion model(s) to set. Can be a single
- DiffusionModelBase, a list of DiffusionModelBase, or
- None to clear all diffusion models.
-
- Raises:
- TypeError: If value is not a DiffusionModelBase, a list of
- DiffusionModelBase, or None.
+ """
+ Set the diffusion models of the SampleModel.
+
+ Parameters
+ ----------
+ value : DiffusionModelBase | list[DiffusionModelBase] | None
+ The diffusion model(s) to set. Can be a single DiffusionModelBase, a list of
+ DiffusionModelBase, or None to clear all diffusion models.
+
+ Raises
+ ------
+ TypeError
+ If value is not a DiffusionModelBase, a list of DiffusionModelBase, or None.
"""
if value is None:
@@ -210,25 +228,32 @@ def diffusion_models(
@property
def temperature(self) -> Parameter | None:
- """Get the temperature of the SampleModel.
+ """
+ Get the temperature of the SampleModel.
- Returns:
- Parameter | None: The temperature Parameter of the
- SampleModel, or None if not set.
+ Returns
+ -------
+ Parameter | None
+ The temperature Parameter of the SampleModel, or None if not set.
"""
return self._temperature
@temperature.setter
def temperature(self, value: Numeric | None) -> None:
- """Set the temperature of the SampleModel.
-
- Args:
- value (Numeric | None): The temperature value to set. Can be
- a number or None to unset the temperature.
-
- Raises:
- TypeError: If value is not a number or None.
- ValueError: If value is negative.
+ """
+ Set the temperature of the SampleModel.
+
+ Parameters
+ ----------
+ value : Numeric | None
+ The temperature value to set. Can be a number or None to unset the temperature.
+
+ Raises
+ ------
+ TypeError
+ If value is not a number or None.
+ ValueError
+ If value is negative.
"""
if value is None:
self._temperature = None
@@ -253,82 +278,160 @@ def temperature(self, value: Numeric | None) -> None:
@property
def temperature_unit(self) -> str | sc.Unit:
- """Get the temperature unit of the SampleModel.
+ """
+ Get the temperature unit of the SampleModel.
- Returns:
- str | sc.Unit: The unit of the temperature Parameter.
+ Returns
+ -------
+ str | sc.Unit
+ The unit of the temperature Parameter.
"""
return self._temperature_unit
@temperature_unit.setter
def temperature_unit(self, _value: str | sc.Unit) -> None:
- """The temperature unit of the SampleModel is read-only.
+ """
+ The temperature unit of the SampleModel is read-only.
- Args:
- _value (str | sc.Unit): The unit to set for the temperature
- Parameter.
+ Parameters
+ ----------
+ _value : str | sc.Unit
+ The unit to set for the temperature Parameter.
- Raises:
- AttributeError: Always, as temperature_unit is read-only.
+ Raises
+ ------
+ AttributeError
+ Always, as temperature_unit is read-only.
"""
raise AttributeError(
f'Temperature_unit is read-only. Use convert_temperature_unit to change the unit between allowed types ' # noqa: E501
f'or create a new {self.__class__.__name__} with the desired unit.'
- ) # noqa: E501
+ )
def convert_temperature_unit(self, unit: str | sc.Unit) -> None:
- """Convert the unit of the temperature Parameter.
-
- Args:
- unit (str | sc.Unit): The unit to convert the temperature
- Parameter to.
-
- Raises:
- ValueError: If temperature is not set or conversion fails.
- Exception: If the provided unit is invalid or cannot be converted.
+ """
+ Convert the unit of the temperature Parameter.
+
+ Parameters
+ ----------
+ unit : str | sc.Unit
+ The unit to convert the temperature Parameter to.
+
+ Raises
+ ------
+ ValueError
+ If temperature is not set or conversion fails.
+ Exception
+ If the provided unit is invalid or cannot be converted.
"""
- if self._temperature is None:
+ if self.temperature is None:
raise ValueError('Temperature is not set, cannot convert unit.')
- old_unit = self._temperature.unit
+ old_unit = self.temperature.unit
try:
- self._temperature.convert_unit(unit)
+ self.temperature.convert_unit(unit)
self._temperature_unit = unit
except Exception:
# Attempt to rollback on failure
with suppress(Exception):
- self._temperature.convert_unit(old_unit)
+ self.temperature.convert_unit(old_unit)
raise
@property
- def divide_by_temperature(self) -> bool:
- """Get whether to divide the detailed balance factor by
- temperature.
+ def normalize_detailed_balance(self) -> bool:
+ """
+ Get whether to divide the detailed balance factor by temperature.
- Returns:
- bool: True if the detailed balance factor is divided by
- temperature, False otherwise.
+ Returns
+ -------
+ bool
+ True if the detailed balance factor is divided by temperature, False otherwise.
"""
- return self._divide_by_temperature
+ return self.detailed_balance_settings.normalize_detailed_balance
- @divide_by_temperature.setter
- def divide_by_temperature(self, value: bool) -> None:
- """Set whether to divide the detailed balance factor by
- temperature.
+ @normalize_detailed_balance.setter
+ def normalize_detailed_balance(self, value: bool) -> None:
+ """
+ Set whether to divide the detailed balance factor by temperature.
- Args:
- value (bool): True to divide the detailed balance factor by
- temperature, False otherwise.
+ Parameters
+ ----------
+ value : bool
+ True to divide the detailed balance factor by temperature, False otherwise.
- Raises:
- TypeError: If value is not a bool.
+ Raises
+ ------
+ TypeError
+ If value is not a bool.
"""
if not isinstance(value, bool):
- raise TypeError('divide_by_temperature must be True or False')
- self._divide_by_temperature = value
+ raise TypeError('normalize_detailed_balance must be True or False')
+ self.detailed_balance_settings.normalize_detailed_balance = value
+
+ @property
+ def use_detailed_balance(self) -> bool:
+ """
+ Get whether to apply detailed balance to the model.
+
+ Returns
+ -------
+ bool
+ True if detailed balance is applied, False otherwise.
+ """
+ return self.detailed_balance_settings.use_detailed_balance
+
+ @use_detailed_balance.setter
+ def use_detailed_balance(self, value: bool) -> None:
+ """
+ Set whether to apply detailed balance to the model.
+
+ Parameters
+ ----------
+ value : bool
+ True to apply detailed balance, False otherwise.
+
+ Raises
+ ------
+ TypeError
+ If value is not a bool.
+ """
+ if not isinstance(value, bool):
+ raise TypeError('use_detailed_balance must be True or False')
+ self.detailed_balance_settings.use_detailed_balance = value
+
+ @property
+ def detailed_balance_settings(self) -> DetailedBalanceSettings:
+ """
+ Get the DetailedBalanceSettings of the SampleModel.
+
+ Returns
+ -------
+ DetailedBalanceSettings
+ The DetailedBalanceSettings of the SampleModel.
+ """
+ return self._detailed_balance_settings
+
+ @detailed_balance_settings.setter
+ def detailed_balance_settings(self, value: DetailedBalanceSettings) -> None:
+ """
+ Set the DetailedBalanceSettings of the SampleModel.
+
+ Parameters
+ ----------
+ value : DetailedBalanceSettings
+ The DetailedBalanceSettings to set.
+
+ Raises
+ ------
+ TypeError
+ If value is not a DetailedBalanceSettings.
+ """
+ if not isinstance(value, DetailedBalanceSettings):
+ raise TypeError('detailed_balance_settings must be a DetailedBalanceSettings')
+ self._detailed_balance_settings = value
# ------------------------------------------------------------------
# Other methods
@@ -337,52 +440,57 @@ def divide_by_temperature(self, value: bool) -> None:
def evaluate(
self, x: Numeric | list | np.ndarray | sc.Variable | sc.DataArray
) -> list[np.ndarray]:
- """Evaluate the sample model at all Q for the given x values.
-
- Args:
- x (Numeric | list | np.ndarray | sc.Variable | sc.DataArray):
- The x values to evaluate the model at. Can be a number,
- list, numpy array, scipp Variable, or scipp DataArray.
-
- Returns:
- list[np.ndarray]: List of evaluated model values for each Q.
+ """
+ Evaluate the sample model at all Q for the given x values.
+
+ Parameters
+ ----------
+ x : Numeric | list | np.ndarray | sc.Variable | sc.DataArray
+ The x values to evaluate the model at. Can be a number, list, numpy array, scipp
+ Variable, or scipp DataArray.
+
+ Returns
+ -------
+ list[np.ndarray]
+ List of evaluated model values for each Q.
"""
y = super().evaluate(x)
- if self._temperature is not None:
+ if self.temperature is not None and self.detailed_balance_settings.use_detailed_balance:
DBF = detailed_balance_factor(
energy=x,
- temperature=self._temperature,
- divide_by_temperature=self._divide_by_temperature,
- energy_unit=self._unit,
+ temperature=self.temperature,
+ divide_by_temperature=self.detailed_balance_settings.normalize_detailed_balance,
+ energy_unit=self.unit,
)
y = [yi * DBF for yi in y]
return y
def get_all_variables(self, Q_index: int | None = None) -> list[Parameter]:
- """Get all Parameters and Descriptors from all
- ComponentCollections in the SampleModel.
-
- Also includes temperature if set and all variables from
- diffusion models. Ignores the Parameters and Descriptors in
- self._components as these are just templates.
-
- Args:
- Q_index (int | None, default=None): If specified, only get variables from
- the ComponentCollection at the given Q index. If None,
- get variables from all ComponentCollections.
-
- Returns:
- list[Parameter]: List of all Parameters and Descriptors,
- including temperature if set and all variables from
- diffusion models.
+ """
+ Get all Parameters and Descriptors from all ComponentCollections in the SampleModel.
+
+ Also includes temperature if set and all variables from diffusion models. Ignores the
+ Parameters and Descriptors in self._components as these are just templates.
+
+ Parameters
+ ----------
+ Q_index : int | None, default=None
+ If specified, only get variables from the ComponentCollection at the given Q index. If
+ None, get variables from all ComponentCollections.
+
+ Returns
+ -------
+ list[Parameter]
+ List of all Parameters and Descriptors, including temperature if set and all variables
+ from diffusion models.
"""
all_vars = super().get_all_variables(Q_index=Q_index)
- if self._temperature is not None:
- all_vars.append(self._temperature)
+ if self.temperature is not None:
+ all_vars.append(self.temperature)
for diffusion_model in self._diffusion_models:
all_vars.extend(diffusion_model.get_all_variables())
@@ -394,11 +502,10 @@ def get_all_variables(self, Q_index: int | None = None) -> list[Parameter]:
# ------------------------------------------------------------------
def _generate_component_collections(self) -> None:
- """Generate ComponentCollections from the DiffusionModels for
- each Q and add the components from self._components.
"""
- # TODO regenerate automatically if Q, diffusion models
- # or components have changed
+ Generate ComponentCollections from the DiffusionModels for each Q and add the components
+ from self._components.
+ """
super()._generate_component_collections()
if self._Q is None:
@@ -422,16 +529,19 @@ def _on_diffusion_models_change(self) -> None:
# ------------------------------------------------------------------
def __repr__(self) -> str:
- """Return a string representation of the SampleModel.
+ """
+ Return a string representation of the SampleModel.
- Returns:
- str: A string representation of the SampleModel.
+ Returns
+ -------
+ str
+ A string representation of the SampleModel.
"""
return (
- f'{self.__class__.__name__}(unique_name={self.unique_name}, unit={self._unit}), '
- f'Q = {self._Q}, '
- f'components = {self._components}, diffusion_models = {self._diffusion_models}, '
- f'temperature = {self._temperature}, '
- f'divide_by_temperature = {self._divide_by_temperature}'
+ f'{self.__class__.__name__}(unique_name={self.unique_name}, unit={self.unit}), '
+ f'Q = {self.Q}, '
+ f'components = {self.components}, diffusion_models = {self.diffusion_models}, '
+ f'temperature = {self.temperature}, '
+ f'detailed_balance_settings = {self.detailed_balance_settings}'
)
diff --git a/src/easydynamics/settings/__init__.py b/src/easydynamics/settings/__init__.py
new file mode 100644
index 00000000..c401fbce
--- /dev/null
+++ b/src/easydynamics/settings/__init__.py
@@ -0,0 +1,10 @@
+# SPDX-FileCopyrightText: 2025 EasyScience contributors
+# SPDX-License-Identifier: BSD-3-Clause
+
+from easydynamics.settings.convolution_settings import ConvolutionSettings
+from easydynamics.settings.detailed_balance_settings import DetailedBalanceSettings
+
+__all__ = [
+ 'ConvolutionSettings',
+ 'DetailedBalanceSettings',
+]
diff --git a/src/easydynamics/settings/convolution_settings.py b/src/easydynamics/settings/convolution_settings.py
new file mode 100644
index 00000000..a845fc91
--- /dev/null
+++ b/src/easydynamics/settings/convolution_settings.py
@@ -0,0 +1,200 @@
+# SPDX-FileCopyrightText: 2026 EasyScience contributors
+# SPDX-License-Identifier: BSD-3-Clause
+
+
+from easydynamics.base_classes.easydynamics_base import EasyDynamicsBase
+from easydynamics.utils.utils import Numeric
+
+
+class ConvolutionSettings(EasyDynamicsBase):
+ """
+ Settings for numerical convolutions.
+ """
+
+ def __init__(
+ self,
+ upsample_factor: Numeric | None = 5,
+ extension_factor: Numeric | None = 0.2,
+ display_name: str | None = 'MyConvolutionSettings',
+ unique_name: str | None = None,
+ ) -> None:
+ """
+ Initialize the ConvolutionSettings.
+
+ Parameters
+ ----------
+ upsample_factor : Numeric | None, default=5
+ The factor by which to upsample the input data before convolution.
+ extension_factor : Numeric | None, default=0.2
+ The factor by which to extend the input data range before convolution.
+ display_name : str | None, default='MyConvolutionSettings'
+ Display name of the model.
+ unique_name : str | None, default=None
+ Unique name of the model. If None, a unique name will be generated.
+
+ Raises
+ ------
+ TypeError
+ If upsample_factor is not a number or None. If extension_factor is not a number or
+ None.
+ ValueError
+ If upsample_factor is not greater than 1. If extension_factor is negative.
+ """
+ super().__init__(
+ display_name=display_name,
+ unique_name=unique_name,
+ )
+
+ if extension_factor is not None:
+ if not isinstance(extension_factor, Numeric):
+ raise TypeError('Extension factor must be a number.')
+ extension_factor = float(extension_factor)
+ if extension_factor < 0.0:
+ raise ValueError('Extension factor must be non-negative.')
+ self._extension_factor = extension_factor
+
+ if upsample_factor is not None:
+ if not isinstance(upsample_factor, Numeric):
+ raise TypeError('Upsample factor must be a numerical value or None.')
+ upsample_factor = float(upsample_factor)
+ if upsample_factor <= 1.0:
+ raise ValueError('Upsample factor must be greater than 1.')
+ self._upsample_factor = upsample_factor
+
+ self._convolution_plan_is_valid = False
+
+ @property
+ def upsample_factor(self) -> Numeric | None:
+ """
+ Get the upsample factor.
+
+ Returns
+ -------
+ Numeric | None
+ The upsample factor.
+ """
+
+ return self._upsample_factor
+
+ @upsample_factor.setter
+ def upsample_factor(self, factor: Numeric | None) -> None:
+ """
+ Set the upsample factor and recreate the dense grid.
+
+ Parameters
+ ----------
+ factor : Numeric | None
+ The new upsample factor.
+
+ Raises
+ ------
+ TypeError
+ If factor is not a number or None.
+ ValueError
+ If factor is not greater than 1.
+ """
+ if factor is None:
+ self._upsample_factor = factor
+ self.convolution_plan_is_valid = False
+ return
+
+ if not isinstance(factor, Numeric):
+ raise TypeError('Upsample factor must be a numerical value or None.')
+ factor = float(factor)
+ if factor <= 1.0:
+ raise ValueError('Upsample factor must be greater than 1.')
+
+ self._upsample_factor = factor
+
+ self.convolution_plan_is_valid = False
+
+ @property
+ def extension_factor(self) -> float:
+ """
+ Get the extension factor.
+
+ The extension factor determines how much the energy range is extended on both sides before
+ convolution. 0.2 means extending by 20% of the original energy span on each side
+
+ Returns
+ -------
+ float
+ The extension factor.
+ """
+
+ return self._extension_factor
+
+ @extension_factor.setter
+ def extension_factor(self, factor: Numeric) -> None:
+ """
+ Set the extension factor and recreate the dense grid.
+
+ The extension factor determines how much the energy range is extended on both sides before
+ convolution. 0.2 means extending by 20% of the original energy span on each side.
+
+ Parameters
+ ----------
+ factor : Numeric
+ The new extension factor.
+
+ Raises
+ ------
+ TypeError
+ If factor is not a number.
+ ValueError
+ If factor is negative.
+ """
+
+ if not isinstance(factor, Numeric):
+ raise TypeError('Extension factor must be a number.')
+ if factor < 0.0:
+ raise ValueError('Extension factor must be non-negative.')
+
+ self._extension_factor = float(factor)
+ self.convolution_plan_is_valid = False
+
+ @property
+ def convolution_plan_is_valid(self) -> bool:
+ """
+ Get whether the convolution plan is valid.
+
+ Returns
+ -------
+ bool
+ Whether the convolution plan is valid.
+ """
+ return self._convolution_plan_is_valid
+
+ @convolution_plan_is_valid.setter
+ def convolution_plan_is_valid(self, is_valid: bool) -> None:
+ """
+ Set whether the convolution plan is valid.
+
+ Parameters
+ ----------
+ is_valid : bool
+ Whether the convolution plan is valid.
+
+ Raises
+ ------
+ TypeError
+ If is_valid is not a bool.
+ """
+ if not isinstance(is_valid, bool):
+ raise TypeError('convolution_plan_is_valid must be True or False.')
+ self._convolution_plan_is_valid = is_valid
+
+ def __repr__(self) -> str:
+ """
+ Return a string representation of the ConvolutionSettings.
+
+ Returns
+ -------
+ str
+ A string representation of the ConvolutionSettings.
+ """
+ return (
+ f'{self.__class__.__name__}('
+ f'upsample_factor={self.upsample_factor}, '
+ f'extension_factor={self.extension_factor})'
+ )
diff --git a/src/easydynamics/settings/detailed_balance_settings.py b/src/easydynamics/settings/detailed_balance_settings.py
new file mode 100644
index 00000000..75cfce1f
--- /dev/null
+++ b/src/easydynamics/settings/detailed_balance_settings.py
@@ -0,0 +1,134 @@
+# SPDX-FileCopyrightText: 2026 EasyScience contributors
+# SPDX-License-Identifier: BSD-3-Clause
+
+
+from easydynamics.base_classes.easydynamics_base import EasyDynamicsBase
+
+
+class DetailedBalanceSettings(EasyDynamicsBase):
+ """
+ Class to manage detailed balance settings for a SampleModel or Analysis.
+ """
+
+ def __init__(
+ self,
+ use_detailed_balance: bool = True,
+ normalize_detailed_balance: bool = True,
+ display_name: str = 'DetailedBalanceSettings',
+ unique_name: str | None = None,
+ ) -> None:
+ """
+ Initialize the DetailedBalanceSettings.
+
+ Parameters
+ ----------
+ use_detailed_balance : bool, default=True
+ Whether to apply detailed balance to the model. If False, no detailed balance is
+ applied.
+ normalize_detailed_balance : bool, default=True
+ Whether to normalize the detailed balance factor by dividing with temperature.
+ display_name : str, default='DetailedBalanceSettings'
+ Display name of the model.
+ unique_name : str | None, default=None
+ Unique name of the model. If None, a unique name will be generated.
+
+
+ Raises
+ ------
+ TypeError
+ If use_detailed_balance or normalize_detailed_balance is not a bool.
+ """
+ if not isinstance(use_detailed_balance, bool):
+ raise TypeError('use_detailed_balance must be True or False')
+ self._use_detailed_balance = use_detailed_balance
+
+ if not isinstance(normalize_detailed_balance, bool):
+ raise TypeError('normalize_detailed_balance must be True or False')
+ self._normalize_detailed_balance = normalize_detailed_balance
+
+ super().__init__(
+ display_name=display_name,
+ unique_name=unique_name,
+ )
+
+ # ------------------------------------------------------------------
+ # Properties
+ # ------------------------------------------------------------------
+
+ @property
+ def use_detailed_balance(self) -> bool:
+ """
+ Get whether to apply detailed balance to the model.
+
+ Returns
+ -------
+ bool
+ True if detailed balance is applied, False otherwise.
+ """
+ return self._use_detailed_balance
+
+ @use_detailed_balance.setter
+ def use_detailed_balance(self, value: bool) -> None:
+ """
+ Set whether to apply detailed balance to the model.
+
+ Parameters
+ ----------
+ value : bool
+ True to apply detailed balance, False otherwise.
+
+ Raises
+ ------
+ TypeError
+ If value is not a bool.
+ """
+ if not isinstance(value, bool):
+ raise TypeError('use_detailed_balance must be True or False')
+ self._use_detailed_balance = value
+
+ @property
+ def normalize_detailed_balance(self) -> bool:
+ """
+ Get whether to divide the detailed balance factor by temperature.
+
+ Returns
+ -------
+ bool
+ True if the detailed balance factor should be normalized by dividing with temperature,
+ False otherwise.
+ """
+ return self._normalize_detailed_balance
+
+ @normalize_detailed_balance.setter
+ def normalize_detailed_balance(self, value: bool) -> None:
+ """
+ Set whether to normalize the detailed balance factor by dividing with temperature.
+
+ Parameters
+ ----------
+ value : bool
+ True to normalize the detailed balance factor by dividing with temperature, False
+ otherwise.
+
+ Raises
+ ------
+ TypeError
+ If value is not a bool.
+ """
+ if not isinstance(value, bool):
+ raise TypeError('normalize_detailed_balance must be True or False')
+ self._normalize_detailed_balance = value
+
+ def __repr__(self) -> str:
+ """
+ Return a string representation of the DetailedBalanceSettings.
+
+ Returns
+ -------
+ str
+ A string representation of the DetailedBalanceSettings.
+ """
+ return (
+ f'DetailedBalanceSettings(use_detailed_balance={self.use_detailed_balance}, '
+ f'normalize_detailed_balance={self.normalize_detailed_balance})'
+ )
diff --git a/src/easydynamics/utils/__init__.py b/src/easydynamics/utils/__init__.py
index 6792d72e..18e7bee5 100644
--- a/src/easydynamics/utils/__init__.py
+++ b/src/easydynamics/utils/__init__.py
@@ -1,6 +1,6 @@
# SPDX-FileCopyrightText: 2025 EasyScience contributors
# SPDX-License-Identifier: BSD-3-Clause
-from .detailed_balance import detailed_balance_factor
+from easydynamics.utils.detailed_balance import detailed_balance_factor
__all__ = ['detailed_balance_factor']
diff --git a/src/easydynamics/utils/detailed_balance.py b/src/easydynamics/utils/detailed_balance.py
index cd8ff347..6ee9e19f 100644
--- a/src/easydynamics/utils/detailed_balance.py
+++ b/src/easydynamics/utils/detailed_balance.py
@@ -23,58 +23,55 @@
def detailed_balance_factor(
- energy: int | float | list | np.ndarray | sc.Variable,
- temperature: int | float | sc.Variable | Parameter,
+ energy: float | list | np.ndarray | sc.Variable,
+ temperature: float | sc.Variable | Parameter,
energy_unit: str | sc.Unit = 'meV',
temperature_unit: str | sc.Unit = 'K',
divide_by_temperature: bool = True,
) -> np.ndarray:
r"""
- Compute the detailed balance factor (DBF):
- $$
- DBF(E, T) = E(n(E)+1)=\frac{E}{(1 - e^{-E / (k_B*T)})}},
- $$
- where $n(E)$ is the Bose-Einstein distribution, $E$ is the energy
- transfer, and $T$ is the temperature. $k_B$ is the Boltzmann
- constant.
- If divide_by_temperature is True, the result is normalized by
- $k_B*T$ to have value 1 at $E=0$.
-
- Args:
- energy (int | float | list | np.ndarray | sc.Variable): The energy
- transfer. If number, assumed to be in meV unless energy_unit
- is set.
- temperature (int | float | sc.Variable | Parameter): The
- temperature. If number, assumed to be in K unless
- temperature_unit is set.
- energy_unit (str | sc.Unit, default='meV'): Unit for energy if energy is
- given as a number or list. Default is 'meV'
- temperature_unit (str | sc.Unit, default='K'): Unit for temperature if
- temperature is given as a number. Default is 'K'
- divide_by_temperature (bool, default=True): If True, divide the result
- by $k_B*T$ to make it dimensionless and have value 1 at E=0.
- Default is True.
-
- Returns:
- np.ndarray: Detailed balance factor evaluated at the
- given energy and temperature.
-
- Raises:
- TypeError: If energy or temperature is not a number, list,
- numpy array, or scipp Variable, or if energy_unit or
- temperature_unit is not a string or scipp Unit,
- or if divide_by_temperature is not a boolean.
- ValueError: If temperature is negative, or if energy is a numpy
- array with more than 1 dimension, or if temperature is a
- scipp Variable that does not have a single dimension named
- 'temperature', or if energy is a scipp Variable that does
- not have a single dimension named 'energy'.
- UnitError: If the provided energy_unit or temperature_unit is
- invalid, or if the units of energy or temperature cannot be
- converted to the expected units.
- ZeroDivisionError: If divide_by_temperature is True and temperature is zero.
-
- Examples:
+ Compute the detailed balance factor (DBF): $$ DBF(E, T) = E(n(E)+1)=\frac{E}{(1 - e^{-E /
+ (k_B*T)})}}, $$ where $n(E)$ is the Bose-Einstein distribution, $E$ is the energy transfer, and
+ $T$ is the temperature. $k_B$ is the Boltzmann constant. If divide_by_temperature is True, the
+ result is normalized by $k_B*T$ to have value 1 at $E=0$.
+
+ Parameters
+ ----------
+ energy : float | list | np.ndarray | sc.Variable
+ The energy transfer. If number, assumed to be in meV unless energy_unit is set.
+ temperature : float | sc.Variable | Parameter
+ The temperature. If number, assumed to be in K unless temperature_unit is set.
+ energy_unit : str | sc.Unit, default='meV'
+ Unit for energy if energy is given as a number or list.
+ temperature_unit : str | sc.Unit, default='K'
+ Unit for temperature if temperature is given as a number.
+ divide_by_temperature : bool, default=True
+ If True, divide the result by $k_B*T$ to make it dimensionless and have value 1 at E=0. By
+ default, True.
+
+ Raises
+ ------
+ TypeError
+ If energy or temperature is not a number, list, numpy array, or scipp Variable, or if
+ energy_unit or temperature_unit is not a string or scipp Unit, or if divide_by_temperature
+ is not a boolean.
+ ValueError
+ If temperature is negative, or if energy is a numpy array with more than 1 dimension, or if
+ temperature is a scipp Variable that does not have a single dimension named 'temperature',
+ or if energy is a scipp Variable that does not have a single dimension named 'energy'.
+ UnitError
+ If the provided energy_unit or temperature_unit is invalid, or if the units of energy or
+ temperature cannot be converted to the expected units.
+ ZeroDivisionError
+ If divide_by_temperature is True and temperature is zero.
+
+ Returns
+ -------
+ np.ndarray
+ Detailed balance factor evaluated at the given energy and temperature.
+
+ Examples
+ --------
>>> detailed_balance_factor(1.0, 300) # 1 meV at 300 K
>>> detailed_balance_factor(
... energy=[1.0, 2.0],
@@ -182,32 +179,36 @@ def detailed_balance_factor(
def _convert_to_scipp_variable(
- value: int | float | list | np.ndarray | Parameter | sc.Variable,
+ value: float | list | np.ndarray | Parameter | sc.Variable,
name: str,
unit: str | None = None,
) -> sc.Variable:
- """Convert various input types to a scipp Variable with proper
- units.
-
- Args:
- value (int | float | list | np.ndarray | Parameter | sc.Variable):
- The value to convert. Can be a number, list, numpy array,
- Parameter, or scipp Variable. If a number or list, the unit
- must be specified in the unit argument.
- name (str): The name of the variable, used for error messages.
- unit (str | None, default=None): The unit to use if value is a number or list.
- Must be specified if value is a number or list. Ignored if
- value is a Parameter or sc.Variable, which have their own
- units.
-
- Raises:
- TypeError: If value is not one of the accepted types, or if unit
- is not a string when needed.
- UnitError: If the provided unit is invalid.
-
- Returns:
- sc.Variable: The input value converted to a scipp Variable with
- appropriate units.
+ """
+ Convert various input types to a scipp Variable with proper units.
+
+ Parameters
+ ----------
+ value : float | list | np.ndarray | Parameter | sc.Variable
+ The value to convert. Can be a number, list, numpy array, Parameter, or scipp Variable. If
+ a number or list, the unit must be specified in the unit argument.
+ name : str
+ The name of the variable, used for error messages.
+ unit : str | None, default=None
+ The unit to use if value is a number or list. Must be specified if value is a number or
+ list. Ignored if value is a Parameter or sc.Variable, which have their own units. By
+ default, None.
+
+ Raises
+ ------
+ TypeError
+ If value is not one of the accepted types, or if unit is not a string when needed.
+ UnitError
+ If the provided unit is invalid.
+
+ Returns
+ -------
+ sc.Variable
+ The input value converted to a scipp Variable with appropriate units.
"""
if isinstance(value, sc.Variable):
return value
diff --git a/src/easydynamics/utils/utils.py b/src/easydynamics/utils/utils.py
index 7b9134bc..d9fc27c0 100644
--- a/src/easydynamics/utils/utils.py
+++ b/src/easydynamics/utils/utils.py
@@ -19,20 +19,26 @@
def _validate_and_convert_Q(
Q: np.ndarray | Numeric | list | ArrayLike | sc.Variable | None,
) -> np.ndarray | None:
- """Validate and convert Q to a numpy array.
-
- Args:
- Q (np.ndarray | Numeric | list | ArrayLike | sc.Variable | None):
- Scattering vector values in 1/angstrom.
-
- Returns:
- np.ndarray | None: Q as a np.ndarray or None if Q is None.
-
- Raises:
- TypeError: If Q is not a number, list, numpy array, or scipp
- Variable.
- ValueError: If Q is a numpy array with more than 1 dimension, or
- if Q is a scipp Variable that does not have a single dimension named 'Q'.
+ """
+ Validate and convert Q to a numpy array.
+
+ Parameters
+ ----------
+ Q : np.ndarray | Numeric | list | ArrayLike | sc.Variable | None
+ Scattering vector values in 1/angstrom.
+
+ Raises
+ ------
+ TypeError
+ If Q is not a number, list, numpy array, or scipp Variable.
+ ValueError
+ If Q is a numpy array with more than 1 dimension, or if Q is a scipp Variable that does not
+ have a single dimension named 'Q'.
+
+ Returns
+ -------
+ np.ndarray | None
+ Q as a np.ndarray or None if Q is None.
"""
if Q is None:
return None
@@ -57,30 +63,43 @@ def _validate_and_convert_Q(
def _validate_unit(unit: str | sc.Unit | None) -> sc.Unit | None:
- """Validate that the unit is a string or scipp Unit.
-
- Args:
- unit (str | sc.Unit | None): Unit to validate.
-
- Returns:
- sc.Unit | None: Validated unit or None.
-
- Raises:
- TypeError: If unit is not None, a string, or a scipp Unit.
+ """
+ Validate that the unit is a string or scipp Unit.
+
+ Parameters
+ ----------
+ unit : str | sc.Unit | None
+ Unit to validate.
+
+ Raises
+ ------
+ TypeError
+ If unit is not None, a string, or a scipp Unit.
+
+ Returns
+ -------
+ sc.Unit | None
+ Validated unit or None.
"""
if unit is not None and not isinstance(unit, (str, sc.Unit)):
raise TypeError(f'unit must be None, a string, or a scipp Unit, got {type(unit).__name__}')
- if isinstance(unit, str):
- unit = sc.Unit(unit)
+ # if isinstance(unit, str):
+ # unit = sc.Unit(unit)
+
+ if isinstance(unit, sc.Unit):
+ unit = str(unit)
return unit
def _in_notebook() -> bool:
- """Check if the code is running in a Jupyter notebook.
+ """
+ Check if the code is running in a Jupyter notebook.
- Returns:
- bool: True if in a Jupyter notebook, False otherwise.
+ Returns
+ -------
+ bool
+ True if in a Jupyter notebook, False otherwise.
"""
try:
from IPython import get_ipython
diff --git a/tests/functional/test_dummy.py b/tests/functional/test_dummy.py
new file mode 100644
index 00000000..b45b191f
--- /dev/null
+++ b/tests/functional/test_dummy.py
@@ -0,0 +1,8 @@
+# SPDX-FileCopyrightText: 2025-2026 EasyDynamics contributors
+# SPDX-License-Identifier: BSD-3-Clause
+
+
+def test_dummy():
+ calculated = 2 + 2
+ expected = 4
+ assert calculated == expected
diff --git a/tests/unit/easydynamics/analysis/test_analysis.py b/tests/unit/easydynamics/analysis/test_analysis.py
index 291e1811..91e8f795 100644
--- a/tests/unit/easydynamics/analysis/test_analysis.py
+++ b/tests/unit/easydynamics/analysis/test_analysis.py
@@ -14,6 +14,7 @@
from easydynamics.sample_model import InstrumentModel
from easydynamics.sample_model import SampleModel
from easydynamics.sample_model.components.gaussian import Gaussian
+from easydynamics.settings.convolution_settings import ConvolutionSettings
class TestAnalysis:
@@ -41,6 +42,31 @@ def analysis(self):
extra_parameters=None,
)
+ @pytest.fixture
+ def analysis_single_Q(self):
+ Q = sc.array(dims=['Q'], values=[1, 2, 3], unit='1/Angstrom')
+ energy = sc.array(dims=['energy'], values=[10.0, 20.0, 30.0], unit='meV')
+ data = sc.array(
+ dims=['Q', 'energy'],
+ values=[[1.0, 2.0, 3.0], [4.0, 5.0, 6.0], [7.0, 8.0, 9.0]],
+ variances=[[0.1, 0.2, 0.3], [0.4, 0.5, 0.6], [0.7, 0.8, 0.9]],
+ )
+
+ data_array = sc.DataArray(data=data, coords={'Q': Q, 'energy': energy})
+
+ experiment = Experiment(data=data_array)
+ experiment.rebin({'Q': 1})
+ sample_model = SampleModel(components=Gaussian(), display_name='Gaussian')
+ instrument_model = InstrumentModel()
+
+ return Analysis(
+ display_name='TestAnalysis',
+ experiment=experiment,
+ sample_model=sample_model,
+ instrument_model=instrument_model,
+ extra_parameters=None,
+ )
+
def test_init(self, analysis):
# WHEN THEN
@@ -177,7 +203,7 @@ def test_fit_with_invalid_fit_method(self, analysis):
# WHEN / THEN / EXPECT
with pytest.raises(
ValueError,
- match="Invalid fit method. Choose 'independent' or 'simultaneous'.",
+ match=r"Invalid fit method. Choose 'independent' or 'simultaneous'.",
):
analysis.fit(fit_method='invalid_fit_method')
@@ -260,6 +286,9 @@ def test_plot_data_and_model_defaults(self, analysis):
fake_fig.bottom_bar = [MagicMock()]
fake_fig.bottom_bar[0].controls = {'test': fake_widget}
+ fake_data = MagicMock()
+ fake_data.coords = {'Q': 'Q_VALUES', 'energy': 'ENERGY_VALUES'}
+
analysis._create_model_array = MagicMock(return_value='MODEL')
with (
patch('plopp.slicer', return_value=fake_fig) as mock_slicer,
@@ -270,7 +299,7 @@ def test_plot_data_and_model_defaults(self, analysis):
) as mock_binned,
patch('easydynamics.analysis.analysis._in_notebook', return_value=True),
):
- mock_binned.return_value = 'DATA'
+ mock_binned.return_value = fake_data
# THEN
fig = analysis.plot_data_and_model(plot_components=False)
@@ -284,7 +313,7 @@ def test_plot_data_and_model_defaults(self, analysis):
assert 'Data' in data_passed
assert 'Model' in data_passed
- assert data_passed['Data'] == 'DATA'
+ assert data_passed['Data'] == fake_data
assert data_passed['Model'] == 'MODEL'
# Check the default kwargs
@@ -310,6 +339,9 @@ def test_plot_data_and_model_plot_components_true(self, analysis):
fake_fig.bottom_bar = [MagicMock()]
fake_fig.bottom_bar[0].controls = {'test': fake_widget}
+ fake_data = MagicMock()
+ fake_data.coords = {'Q': 'Q_VALUES', 'energy': 'ENERGY_VALUES'}
+
analysis._create_model_array = MagicMock(return_value='MODEL')
analysis._create_components_dataset = MagicMock(return_value={'Gaussian': 'GAUSS'})
with (
@@ -321,7 +353,7 @@ def test_plot_data_and_model_plot_components_true(self, analysis):
) as mock_binned,
patch('easydynamics.analysis.analysis._in_notebook', return_value=True),
):
- mock_binned.return_value = 'DATA'
+ mock_binned.return_value = fake_data
# THEN
fig = analysis.plot_data_and_model(plot_components=True)
@@ -335,7 +367,7 @@ def test_plot_data_and_model_plot_components_true(self, analysis):
assert 'Data' in data_passed
assert 'Model' in data_passed
- assert data_passed['Data'] == 'DATA'
+ assert data_passed['Data'] == fake_data
assert data_passed['Model'] == 'MODEL'
# Check the default kwargs
assert kwargs['title'] == 'TestAnalysis'
@@ -583,6 +615,18 @@ def test_on_instrument_model_changed(self, analysis):
for analysis1d in analysis.analysis_list:
assert analysis1d.instrument_model is new_instrument_model
+ def test_on_convolution_settings_changed(self, analysis):
+ # WHEN
+ new_convolution_settings = ConvolutionSettings()
+
+ # THEN (this calls _on_convolution_settings_changed internally)
+ analysis.convolution_settings = new_convolution_settings
+
+ # EXPECT
+ assert analysis.convolution_settings is new_convolution_settings
+ for analysis1d in analysis.analysis_list:
+ assert analysis1d.convolution_settings is new_convolution_settings
+
def test_fit_single_Q_valid(self, analysis):
# WHEN
analysis.analysis_list[1].fit = MagicMock(return_value='fit_result_Q1')
@@ -640,7 +684,7 @@ def test_fit_all_Q_simultaneously(self, analysis):
expected_fit_objects = analysis.analysis_list
expected_fit_functions = analysis.get_fit_functions()
mock_fitter.assert_called_once()
- args, kwargs = mock_fitter.call_args
+ _, kwargs = mock_fitter.call_args
assert kwargs['fit_objects'] == expected_fit_objects
assert kwargs['fit_functions'] == expected_fit_functions
@@ -657,7 +701,7 @@ def test_fit_all_Q_simultaneously(self, analysis):
expected_ws.append(1.0 / np.sqrt(data.variances))
fake_fitter_instance.fit.assert_called_once()
- args, kwargs = fake_fitter_instance.fit.call_args
+ _, kwargs = fake_fitter_instance.fit.call_args
np.testing.assert_array_equal(kwargs['x'], expected_xs)
np.testing.assert_array_equal(kwargs['y'], expected_ys)
np.testing.assert_array_equal(kwargs['weights'], expected_ws)
@@ -723,3 +767,27 @@ def test_create_components_dataset(self, analysis):
assert component_name in components_dataset
assert 'Q' in components_dataset[component_name].dims
assert 'energy' in components_dataset[component_name].dims
+ assert components_dataset.sizes['Q'] == analysis.Q.sizes['Q']
+
+ def test_create_components_dataset_single_Q(self, analysis_single_Q):
+ # WHEN
+
+ # Add another component so that there are two components
+ analysis_single_Q.sample_model.append_component(
+ Gaussian(display_name='Gaussian2', area=0.5)
+ )
+
+ # THEN
+ components_dataset = analysis_single_Q._create_components_dataset(add_background=True)
+
+ # THEN EXPECT
+ assert isinstance(components_dataset, sc.Dataset)
+ component_names = [comp.display_name for comp in analysis_single_Q.sample_model.components]
+ for component_name in component_names:
+ assert component_name in components_dataset
+ assert 'Q' in components_dataset[component_name].dims
+ assert 'energy' in components_dataset[component_name].dims
+
+ assert components_dataset.coords['Q'].dims == ('Q',)
+ assert components_dataset.sizes['Q'] == 1
+ assert components_dataset.coords['Q'].ndim == 1
diff --git a/tests/unit/easydynamics/analysis/test_analysis1d.py b/tests/unit/easydynamics/analysis/test_analysis1d.py
index 43763011..234e166c 100644
--- a/tests/unit/easydynamics/analysis/test_analysis1d.py
+++ b/tests/unit/easydynamics/analysis/test_analysis1d.py
@@ -230,8 +230,11 @@ def test_get_all_variables(self, analysis1d):
assert Counter(variables) == Counter(expected_vars)
def test_plot_raises_if_no_data(self, analysis1d):
- analysis1d.experiment._data = None
+ # WHEN THEN
+ # override the binned data with None to simulate no data available for plotting
+ analysis1d.experiment._binned_data = None
+ # EXPECT
with pytest.raises(ValueError, match='No data'):
analysis1d.plot_data_and_model()
@@ -240,7 +243,7 @@ def test_plot_calls_plopp_with_correct_arguments(self, analysis1d):
# Mock the data and model components to be plotted
fake_model = sc.DataArray(data=sc.array(dims=['energy'], values=[1, 2, 3]))
- analysis1d._create_sample_scipp_array = MagicMock(return_value=fake_model)
+ analysis1d._create_model_array = MagicMock(return_value=fake_model)
fake_components = sc.Dataset({
'Component1': sc.DataArray(data=sc.array(dims=['energy'], values=[0.1, 0.2, 0.3]))
@@ -262,7 +265,7 @@ def test_plot_calls_plopp_with_correct_arguments(self, analysis1d):
mock_plot.assert_called_once()
# Inspect arguments
- args, kwargs = mock_plot.call_args
+ args, _ = mock_plot.call_args
dataset_passed = args[0]
@@ -344,7 +347,7 @@ def test_verify_energy_raises(self, analysis1d):
energy = np.array([10.0, 20.0])
# THEN / EXPECT
- with pytest.raises(TypeError, match='Energy must be a sc.Variable or None'):
+ with pytest.raises(TypeError, match=r'Energy must be a sc.Variable or None'):
analysis1d._verify_energy(energy)
def test_calculate_energy_with_offset(self, analysis1d):
@@ -399,7 +402,7 @@ def test_evaluate_components_no_components(self, analysis1d):
# EXPECT
assert isinstance(result, np.ndarray)
assert result.shape == (len(analysis1d.experiment.energy),)
- assert np.all(result == 0.0)
+ assert np.all(result == pytest.approx(0.0))
def test_evaluate_components_no_convolution(self, analysis1d):
# WHEN
@@ -443,6 +446,38 @@ def test_evaluate_components_empty_resolution(self, analysis1d):
components.evaluate.assert_called_once()
assert np.array_equal(result, np.array([1.0, 2.0, 3.0]))
+ def test_evaluate_components_empty_resolution_DBF(self, analysis1d):
+ # WHEN
+ components = MagicMock()
+ components.evaluate = MagicMock(return_value=np.array([1.0, 2.0, 3.0]))
+
+ # Set temperature so DBF will be applied
+ analysis1d.sample_model.temperature = 10
+ mock_dbf = np.array([10.0, 10.0, 10.0])
+
+ # The default analysis1d has no resolution model components, so
+ # no convolution should be applied even if convolve=True
+
+ with patch(
+ 'easydynamics.analysis.analysis1d.detailed_balance_factor',
+ return_value=mock_dbf,
+ ) as dbf_mock:
+ # WHEN
+ result = analysis1d._evaluate_components(
+ components=components,
+ convolver=None,
+ convolve=True,
+ apply_detailed_balance=True,
+ )
+
+ # EXPECT
+ components.evaluate.assert_called_once()
+ dbf_mock.assert_called_once()
+
+ # EXPECT multiplication applied
+ expected = np.array([1.0, 2.0, 3.0]) * mock_dbf
+ assert np.array_equal(result, expected)
+
def test_evaluate_with_resolution(self, analysis1d):
# WHEN (set up the resolution model and create a component to
# evaluate)
@@ -508,6 +543,7 @@ def test_evaluate_sample(self, analysis1d):
convolver=analysis1d._convolver,
convolve=True,
energy=None,
+ apply_detailed_balance=True,
)
def test_evaluate_sample_component(self, analysis1d):
@@ -527,6 +563,7 @@ def test_evaluate_sample_component(self, analysis1d):
convolver=None,
convolve=True,
energy=None,
+ apply_detailed_balance=True,
)
def test_evaluate_background(self, analysis1d):
@@ -552,6 +589,7 @@ def test_evaluate_background(self, analysis1d):
convolver=None,
convolve=False,
energy=None,
+ apply_detailed_balance=False,
)
def test_evaluate_background_component(self, analysis1d):
@@ -571,6 +609,7 @@ def test_evaluate_background_component(self, analysis1d):
convolver=None,
convolve=False,
energy=None,
+ apply_detailed_balance=False,
)
def test_create_convolver(self, analysis1d):
@@ -608,7 +647,7 @@ def test_create_convolver(self, analysis1d):
assert kwargs['resolution_components'] is resolution_components
assert sc.identical(kwargs['energy'], analysis1d.energy)
assert kwargs['temperature'] is analysis1d.temperature
- assert kwargs['energy_offset'] == 123.0
+ assert kwargs['energy_offset'] == pytest.approx(123.0)
assert result == MockConvolution.return_value
@@ -718,8 +757,8 @@ def test_create_background_component_scipp_array(self, analysis1d):
np.array([1.0, 2.0, 3.0]),
)
- def test_create_sample_scipp_array(self, analysis1d):
- """Test that _create_sample_scipp_array correctly
+ def test_create_model_array(self, analysis1d):
+ """Test that _create_model_array correctly
evaluates the full model and calls _to_scipp_array with the
correct values."""
@@ -730,7 +769,7 @@ def test_create_sample_scipp_array(self, analysis1d):
analysis1d._to_scipp_array = MagicMock()
# THEN
- analysis1d._create_sample_scipp_array()
+ analysis1d._create_model_array()
# EXPECT
analysis1d._calculate.assert_called_once()
diff --git a/tests/unit/easydynamics/analysis/test_analysis_base.py b/tests/unit/easydynamics/analysis/test_analysis_base.py
index 4b47c59e..a7241831 100644
--- a/tests/unit/easydynamics/analysis/test_analysis_base.py
+++ b/tests/unit/easydynamics/analysis/test_analysis_base.py
@@ -12,6 +12,8 @@
from easydynamics.experiment import Experiment
from easydynamics.sample_model import InstrumentModel
from easydynamics.sample_model import SampleModel
+from easydynamics.settings.convolution_settings import ConvolutionSettings
+from easydynamics.settings.detailed_balance_settings import DetailedBalanceSettings
class TestAnalysisBase:
@@ -37,6 +39,29 @@ def test_init(self, analysis_base):
assert isinstance(analysis_base.instrument_model, InstrumentModel)
assert analysis_base._extra_parameters == []
+ def test_init_convolution_settings(self):
+ # WHEN
+ convolution_settings = ConvolutionSettings(upsample_factor=2, extension_factor=0.5)
+
+ # THEN
+ analysis = AnalysisBase(convolution_settings=convolution_settings)
+
+ # EXPECT
+ assert analysis.convolution_settings is convolution_settings
+
+ def test_init_detailed_balance_settings(self):
+ # WHEN
+ detailed_balance_settings = DetailedBalanceSettings(
+ use_detailed_balance=False,
+ normalize_detailed_balance=False,
+ )
+
+ # THEN
+ analysis = AnalysisBase(detailed_balance_settings=detailed_balance_settings)
+
+ # EXPECT
+ assert analysis.detailed_balance_settings is detailed_balance_settings
+
def test_init_extra_parameter(self):
extra_parameter = Parameter(name='param1', value=1.0)
analysis = AnalysisBase(extra_parameters=extra_parameter)
@@ -73,6 +98,16 @@ def test_init_calls_on_experiment_changed(self):
TypeError,
'instrument_model must be an instance of InstrumentModel',
),
+ (
+ {'convolution_settings': 'not convolution settings'},
+ TypeError,
+ 'convolution_settings must be an instance of ConvolutionSettings',
+ ),
+ (
+ {'detailed_balance_settings': 'not detailed balance settings'},
+ TypeError,
+ 'detailed_balance_settings must be an instance of DetailedBalanceSettings',
+ ),
(
{'extra_parameters': 123},
TypeError,
@@ -88,6 +123,8 @@ def test_init_calls_on_experiment_changed(self):
'invalid experiment',
'invalid sample_model',
'invalid instrument_model',
+ 'invalid convolution_settings',
+ 'invalid detailed_balance_settings',
'invalid extra_parameters',
'invalid extra_parameters list',
],
@@ -163,7 +200,7 @@ def test_Q_property(self, analysis_base):
def test_Q_setter_raises(self, analysis_base):
with pytest.raises(
AttributeError,
- match='Q is a read-only property derived from the Experiment.',
+ match=r'Q is a read-only property derived from the Experiment.',
):
analysis_base.Q = [1, 2, 3]
@@ -183,7 +220,7 @@ def test_energy_property(self, analysis_base):
def test_energy_setter_raises(self, analysis_base):
with pytest.raises(
AttributeError,
- match='energy is a read-only property derived from the Experiment.',
+ match=r'energy is a read-only property derived from the Experiment.',
):
analysis_base.energy = [10, 20, 30]
@@ -218,6 +255,63 @@ def test_temperature_setter_raises(self, analysis_base):
):
analysis_base.temperature = 300
+ def test_convolution_settings_property(self, analysis_base):
+ # WHEN
+ convolution_settings = ConvolutionSettings(
+ upsample_factor=2,
+ extension_factor=0.5,
+ )
+
+ # THEN
+ analysis_base.convolution_settings = convolution_settings
+
+ # EXPECT
+ assert analysis_base.convolution_settings is convolution_settings
+
+ def test_convolution_settings_setter_invalid_type(self, analysis_base):
+
+ # WHEN THEN EXPECT
+ with pytest.raises(
+ TypeError,
+ match='convolution_settings must be an instance of ConvolutionSettings',
+ ):
+ analysis_base.convolution_settings = 'not convolution settings'
+
+ def test_convolution_settings_calls_on_convolution_settings_changed(self, analysis_base):
+ # WHEN
+ convolution_settings = ConvolutionSettings(
+ upsample_factor=2,
+ extension_factor=0.5,
+ )
+ with patch.object(
+ analysis_base, '_on_convolution_settings_changed'
+ ) as mock_on_convolution_settings_changed:
+ # THEN
+ analysis_base.convolution_settings = convolution_settings
+
+ # EXPECT
+ mock_on_convolution_settings_changed.assert_called_once()
+
+ def test_detailed_balance_settings_property(self, analysis_base):
+ # WHEN
+ new_settings = DetailedBalanceSettings(
+ use_detailed_balance=False, normalize_detailed_balance=False
+ )
+
+ # THEN
+ analysis_base.detailed_balance_settings = new_settings
+
+ # EXPECT
+ assert analysis_base.detailed_balance_settings is new_settings
+
+ def test_detailed_balance_settings_setter_invalid(self, analysis_base):
+ # WHEN / THEN / EXPECT
+ with pytest.raises(
+ TypeError,
+ match='detailed_balance_settings must be a DetailedBalanceSettings',
+ ):
+ analysis_base.detailed_balance_settings = 'invalid_settings'
+
@pytest.mark.parametrize(
'extra_parameters',
[
diff --git a/tests/unit/easydynamics/base_classes/test_easydynamics_base.py b/tests/unit/easydynamics/base_classes/test_easydynamics_base.py
new file mode 100644
index 00000000..90d62c1a
--- /dev/null
+++ b/tests/unit/easydynamics/base_classes/test_easydynamics_base.py
@@ -0,0 +1,70 @@
+# SPDX-FileCopyrightText: 2026 EasyScience contributors
+# SPDX-License-Identifier: BSD-3-Clause
+
+import pytest
+
+from easydynamics.base_classes import EasyDynamicsBase
+
+
+class TestEasyDynamicsBase:
+ """Tests for the EasyDynamicsBase class."""
+
+ @pytest.fixture
+ def easy_dynamics_base(self):
+ """Fixture for creating an instance of EasyDynamicsBase."""
+
+ return EasyDynamicsBase(name='TestModel')
+
+ def test_initialization(self, easy_dynamics_base):
+ """Test that the EasyDynamicsBase is initialized correctly."""
+
+ # WHEN THEN EXPECT
+ assert easy_dynamics_base.name == 'TestModel'
+ assert easy_dynamics_base.display_name == 'MyEasyDynamicsModel'
+ assert easy_dynamics_base.unique_name is not None
+
+ def test_init_raises_type_error_for_invalid_name(self):
+ """Test that initializing with an invalid name raises a TypeError."""
+ # WHEN THEN EXPECT
+ with pytest.raises(TypeError, match=r'Name must be a string or None.'):
+ EasyDynamicsBase(name=123) # Not a string
+
+ def test_init_name_can_be_none(self):
+ """Test that initializing with name as None works correctly."""
+ # WHEN THEN EXPECT
+ model = EasyDynamicsBase(name=None)
+
+ # THEN EXPECT
+ assert model.name is None
+
+ def test_name_setter_and_getter(self, easy_dynamics_base):
+ """Test that the name setter and getter work correctly."""
+ # WHEN THEN EXPECT
+ assert easy_dynamics_base.name == 'TestModel'
+
+ # THEN
+ easy_dynamics_base.name = 'NewName'
+
+ # EXPECT
+ assert easy_dynamics_base.name == 'NewName'
+
+ # THEN
+ easy_dynamics_base.name = None
+
+ # EXPECT
+ assert easy_dynamics_base.name is None
+
+ @pytest.mark.parametrize(
+ 'invalid_name',
+ [
+ 123, # Not a string
+ [1, 2, 3], # Not a string
+ {'name': 'Test'}, # Not a string
+ ],
+ ids=['integer', 'list', 'dict'],
+ )
+ def test_name_setter_invalid_type(self, easy_dynamics_base, invalid_name):
+ """Test that setting the name to an invalid type raises a TypeError."""
+ # WHEN THEN EXPECT
+ with pytest.raises(TypeError, match=r'Name must be a string or None.'):
+ easy_dynamics_base.name = invalid_name
diff --git a/tests/unit/easydynamics/base_classes/test_easydynamics_modelbase.py b/tests/unit/easydynamics/base_classes/test_easydynamics_modelbase.py
new file mode 100644
index 00000000..c2d30f71
--- /dev/null
+++ b/tests/unit/easydynamics/base_classes/test_easydynamics_modelbase.py
@@ -0,0 +1,80 @@
+# SPDX-FileCopyrightText: 2026 EasyScience contributors
+# SPDX-License-Identifier: BSD-3-Clause
+
+import pytest
+
+from easydynamics.base_classes import EasyDynamicsModelBase
+
+
+class TestEasyDynamicsModelBase:
+ """Tests for the EasyDynamicsModelBase class."""
+
+ @pytest.fixture
+ def easy_dynamics_modelbase(self):
+ """Fixture for creating an instance of EasyDynamicsModelBase."""
+
+ return EasyDynamicsModelBase(name='TestModel', unit='meV')
+
+ def test_initialization(self, easy_dynamics_modelbase):
+ """Test that the EasyDynamicsModelBase is initialized correctly."""
+
+ # WHEN THEN EXPECT
+ assert easy_dynamics_modelbase.name == 'TestModel'
+ assert easy_dynamics_modelbase.display_name == 'MyEasyDynamicsModel'
+ assert easy_dynamics_modelbase.unique_name is not None
+
+ def test_init_raises_type_error_for_invalid_name(self):
+ """Test that initializing with an invalid name raises a TypeError."""
+ # WHEN THEN EXPECT
+ with pytest.raises(TypeError, match=r'Name must be a string or None.'):
+ EasyDynamicsModelBase(name=123) # Not a string
+
+ def test_init_name_can_be_none(self):
+ """Test that initializing with name as None works correctly."""
+ # WHEN THEN EXPECT
+ model = EasyDynamicsModelBase(name=None)
+
+ # THEN EXPECT
+ assert model.name is None
+
+ def test_name_setter_and_getter(self, easy_dynamics_modelbase):
+ """Test that the name setter and getter work correctly."""
+ # WHEN THEN EXPECT
+ assert easy_dynamics_modelbase.name == 'TestModel'
+
+ # THEN
+ easy_dynamics_modelbase.name = 'NewName'
+
+ # EXPECT
+ assert easy_dynamics_modelbase.name == 'NewName'
+
+ # THEN
+ easy_dynamics_modelbase.name = None
+
+ # EXPECT
+ assert easy_dynamics_modelbase.name is None
+
+ @pytest.mark.parametrize(
+ 'invalid_name',
+ [
+ 123, # Not a string
+ [1, 2, 3], # Not a string
+ {'name': 'Test'}, # Not a string
+ ],
+ ids=['integer', 'list', 'dict'],
+ )
+ def test_name_setter_invalid_type(self, easy_dynamics_modelbase, invalid_name):
+ """Test that setting the name to an invalid type raises a TypeError."""
+ # WHEN THEN EXPECT
+ with pytest.raises(TypeError, match=r'Name must be a string or None.'):
+ easy_dynamics_modelbase.name = invalid_name
+
+ def test_unit_property(self, easy_dynamics_modelbase):
+ # WHEN THEN EXPECT
+
+ assert easy_dynamics_modelbase.unit == 'meV'
+
+ def test_unit_setter_raises(self, easy_dynamics_modelbase):
+ # WHEN / THEN / EXPECT
+ with pytest.raises(AttributeError, match='Use convert_unit to change '):
+ easy_dynamics_modelbase.unit = 'K'
diff --git a/tests/unit/easydynamics/convolution/test_analytical_convolution.py b/tests/unit/easydynamics/convolution/test_analytical_convolution.py
index 162a920b..c9d3f46e 100644
--- a/tests/unit/easydynamics/convolution/test_analytical_convolution.py
+++ b/tests/unit/easydynamics/convolution/test_analytical_convolution.py
@@ -126,7 +126,7 @@ def mock_convolute_analytic_pair(sample_component, resolution_component): # noq
# EXPECT
# 2 sample components x 2 resolution components
- assert np.all(result == 4.0)
+ assert np.all(result == pytest.approx(4.0))
assert mocked_pair.call_count == 4
# Gather the actual calls to verify correct pairs
@@ -178,7 +178,7 @@ def mock_convolute_analytic_pair(sample_component, resolution_component): # noq
# EXPECT
# 1 sample component x 1 resolution component
- assert np.all(result == 1.0)
+ assert np.all(result == pytest.approx(1.0))
assert mocked_pair.call_count == 1
# Gather the actual calls to verify correct pairs
diff --git a/tests/unit/easydynamics/convolution/test_convolution.py b/tests/unit/easydynamics/convolution/test_convolution.py
index 468df680..f3aff801 100644
--- a/tests/unit/easydynamics/convolution/test_convolution.py
+++ b/tests/unit/easydynamics/convolution/test_convolution.py
@@ -2,6 +2,7 @@
# SPDX-License-Identifier: BSD-3-Clause
from contextlib import nullcontext
+from typing import ClassVar
from unittest.mock import patch
import numpy as np
@@ -74,10 +75,10 @@ def test_init(self, default_convolution):
assert isinstance(default_convolution._sample_components, ComponentCollection)
assert isinstance(default_convolution._resolution_components, ComponentCollection)
assert default_convolution.upsample_factor == 5
- assert default_convolution.extension_factor == 0.2
+ assert default_convolution.extension_factor == pytest.approx(0.2)
assert default_convolution.temperature is None
- assert default_convolution.energy_unit == 'meV'
- assert default_convolution.normalize_detailed_balance is True
+ assert default_convolution.unit == 'meV'
+ assert default_convolution.detailed_balance_settings.normalize_detailed_balance is True
assert isinstance(default_convolution._energy_grid, EnergyGrid)
assert isinstance(default_convolution._analytical_sample_components, ComponentCollection)
@@ -96,7 +97,7 @@ def test_init(self, default_convolution):
default_convolution._delta_sample_components.components[0]
is default_convolution.sample_components.components[2]
)
- assert default_convolution._convolution_plan_is_valid is True
+ assert default_convolution.convolution_settings.convolution_plan_is_valid is True
assert default_convolution._reactions_enabled is True
def test_init_components(self, convolution_with_components):
@@ -108,10 +109,13 @@ def test_init_components(self, convolution_with_components):
assert isinstance(convolution_with_components._sample_components, ComponentCollection)
assert isinstance(convolution_with_components._resolution_components, ComponentCollection)
assert convolution_with_components.upsample_factor == 5
- assert convolution_with_components.extension_factor == 0.2
+ assert convolution_with_components.extension_factor == pytest.approx(0.2)
assert convolution_with_components.temperature is None
- assert convolution_with_components.energy_unit == 'meV'
- assert convolution_with_components.normalize_detailed_balance is True
+ assert convolution_with_components.unit == 'meV'
+ assert (
+ convolution_with_components.detailed_balance_settings.normalize_detailed_balance
+ is True
+ )
assert isinstance(convolution_with_components._energy_grid, EnergyGrid)
assert isinstance(
@@ -132,7 +136,7 @@ def test_init_components(self, convolution_with_components):
convolution_with_components._delta_sample_components, ComponentCollection
)
assert convolution_with_components._delta_sample_components.is_empty
- assert convolution_with_components._convolution_plan_is_valid is True
+ assert convolution_with_components.convolution_settings.convolution_plan_is_valid is True
assert convolution_with_components._reactions_enabled is True
def test_convolution_plan_is_built_when_invalid(self, default_convolution):
@@ -141,7 +145,7 @@ def test_convolution_plan_is_built_when_invalid(self, default_convolution):
"""
# WHEN
conv = default_convolution
- conv._convolution_plan_is_valid = False
+ conv.convolution_settings.convolution_plan_is_valid = False
# THEN EXPECT
with patch.object(conv, '_build_convolution_plan') as build_plan:
@@ -243,6 +247,7 @@ def test_convolution_calls_correct_methods(
)
conv.sample_components = sample_components # This updates the internal sample models
+ conv._build_convolution_plan() # Ensure the plan is built with the new components
# THEN
# Mock the methods to be tested. Use nullcontext if the
@@ -275,7 +280,7 @@ def test_convolution_calls_correct_methods(
patch_numerical as mock_numerical_method,
patch_delta as mock_delta_method,
):
- conv._convolution_plan_is_valid = True
+ conv.convolution_settings._convolution_plan_is_valid = True
conv.convolution()
if analytical_component:
@@ -317,7 +322,7 @@ def test_convolve_delta_functions(self, default_convolution):
assert np.allclose(result, expected_values)
# List of analytic functions
- analytic_functions = [
+ analytic_functions: ClassVar[list[object]] = [
Gaussian(display_name='G', area=1.0, center=0.0, width=0.1),
Lorentzian(display_name='L', area=1.0, center=0.0, width=0.1),
Voigt(
@@ -330,14 +335,19 @@ def test_convolve_delta_functions(self, default_convolution):
]
# List of non-analytic functions
- non_analytic_functions = [
+ non_analytic_functions: ClassVar[list[object]] = [
DampedHarmonicOscillator(display_name='DHO', area=1.0, center=1.0, width=0.1),
Polynomial(display_name='P', coefficients=[1.0, 0.0, 0.0]),
]
- all_functions_except_delta = analytic_functions + non_analytic_functions
- all_functions = all_functions_except_delta + [
- DeltaFunction(display_name='Delta', area=1.0, center=0.0)
+ all_functions_except_delta: ClassVar[list[object]] = [
+ *analytic_functions,
+ *non_analytic_functions,
+ ]
+
+ all_functions: ClassVar[list[object]] = [
+ *all_functions_except_delta,
+ DeltaFunction(display_name='Delta', area=1.0, center=0.0),
]
@pytest.mark.parametrize('function1', all_functions, ids=lambda f: f.__class__.__name__)
@@ -474,8 +484,6 @@ def test_build_convolution_plan(
conv.sample_components = sample_components # This updates the internal sample models
if temperature is not None:
conv.temperature = temperature
- # It is already called by sample_components setter, but we now
- # call it explicitly
conv._build_convolution_plan()
# EXPECT
@@ -514,7 +522,7 @@ def test_build_convolution_plan(
expected_numerical_count += 1
assert len(conv._numerical_sample_components.components) == expected_numerical_count
- assert conv._convolution_plan_is_valid is True
+ assert conv.convolution_settings.convolution_plan_is_valid is True
@pytest.mark.parametrize(
'analytical_component',
@@ -557,9 +565,10 @@ def test_set_convolvers(
)
# THEN
- conv.sample_components = sample_components # This updates the internal sample models
- # Should already have been called by sample_components setter,
+ conv.sample_components = sample_components
+ # Should already have been called by _build_convolution_plan,
# but we now call it explicitly
+ conv._build_convolution_plan() # Ensure the plan is built with the new components
conv._set_convolvers()
# EXPECT
@@ -572,3 +581,40 @@ def test_set_convolvers(
assert isinstance(conv._numerical_convolver, NumericalConvolution)
else:
assert conv._numerical_convolver is None
+
+ def test_setattr_does_not_invalidate_plan_for_non_tracked_attribute(
+ self,
+ default_convolution,
+ ):
+ # WHEN
+ conv = default_convolution
+ conv.convolution_settings.convolution_plan_is_valid = True
+
+ # Capture current identity of internal state to ensure no rebuild
+ old_plan_id = id(conv._analytical_sample_components)
+ old_numerical_id = id(conv._numerical_sample_components)
+ old_delta_id = id(conv._delta_sample_components)
+
+ # THEN (NOT in _invalidate_plan_on_change)
+ conv.display_name = 'new_name'
+
+ # EXPECT
+ assert conv.convolution_settings.convolution_plan_is_valid is True
+ assert id(conv._analytical_sample_components) == old_plan_id
+ assert id(conv._numerical_sample_components) == old_numerical_id
+ assert id(conv._delta_sample_components) == old_delta_id
+ assert conv.display_name == 'new_name'
+
+ def test_setattr_invalidates_plan_for_tracked_attribute(
+ self,
+ default_convolution,
+ ):
+ # WHEN
+ conv = default_convolution
+ conv.convolution_settings.convolution_plan_is_valid = True
+
+ # THEN
+ conv.upsample_factor = 10
+
+ # EXPECT
+ assert conv.convolution_settings.convolution_plan_is_valid is False
diff --git a/tests/unit/easydynamics/convolution/test_convolution_base.py b/tests/unit/easydynamics/convolution/test_convolution_base.py
index 44ae133c..eceb8d7d 100644
--- a/tests/unit/easydynamics/convolution/test_convolution_base.py
+++ b/tests/unit/easydynamics/convolution/test_convolution_base.py
@@ -78,7 +78,7 @@ def test_init_energy_numerical_none_offset(self):
'energy': 'invalid',
'sample_components': ComponentCollection(),
'resolution_components': ComponentCollection(),
- 'energy_unit': 'meV',
+ 'unit': 'meV',
'energy_offset': 0,
},
'Energy must be',
@@ -88,7 +88,7 @@ def test_init_energy_numerical_none_offset(self):
'energy': np.linspace(-10, 10, 100),
'sample_components': 'invalid',
'resolution_components': ComponentCollection(),
- 'energy_unit': 'meV',
+ 'unit': 'meV',
'energy_offset': 0,
},
(
@@ -101,7 +101,7 @@ def test_init_energy_numerical_none_offset(self):
'energy': np.linspace(-10, 10, 100),
'sample_components': ComponentCollection(),
'resolution_components': 'invalid',
- 'energy_unit': 'meV',
+ 'unit': 'meV',
'energy_offset': 0,
},
(
@@ -114,17 +114,17 @@ def test_init_energy_numerical_none_offset(self):
'energy': np.linspace(-10, 10, 100),
'sample_components': ComponentCollection(),
'resolution_components': ComponentCollection(),
- 'energy_unit': 123,
+ 'unit': 123,
'energy_offset': 0,
},
- 'Energy_unit must be ',
+ 'unit must be ',
),
(
{
'energy': np.linspace(-10, 10, 100),
'sample_components': ComponentCollection(),
'resolution_components': ComponentCollection(),
- 'energy_unit': 'meV',
+ 'unit': 'meV',
'energy_offset': 'invalid',
},
'Energy_offset must be ',
@@ -169,64 +169,64 @@ def test_energy_setter_invalid_type_raises(self, convolution_base):
# WHEN THEN EXPECT
with pytest.raises(
TypeError,
- match='Energy must be a Number, a numpy ndarray or a scipp Variable.',
+ match=r'Energy must be a Number, a numpy ndarray or a scipp Variable.',
):
convolution_base.energy = 'invalid'
- def test_energy_unit_property(self, convolution_base):
+ def test_unit_property(self, convolution_base):
# WHEN THEN EXPECT
assert convolution_base.energy.unit == 'meV'
- def test_energy_unit_setter_raises(self, convolution_base):
+ def test_unit_setter_raises(self, convolution_base):
# WHEN THEN EXPECT
with pytest.raises(
AttributeError,
- match='Use convert_unit to change the unit between allowed types ',
+ match=r'Use convert_unit to change the unit between allowed types ',
):
- convolution_base.energy_unit = 'K'
+ convolution_base.unit = 'K'
- def test_convert_energy_unit(self, convolution_base):
+ def test_convert_unit(self, convolution_base):
# WHEN THEN
- convolution_base.convert_energy_unit('eV')
+ convolution_base.convert_unit('eV')
# EXPECT
assert convolution_base.energy.unit == 'eV'
- assert convolution_base.energy_unit == 'eV'
+ assert convolution_base.unit == 'eV'
assert np.allclose(convolution_base.energy.values, np.linspace(-0.01, 0.01, 100))
- def test_convert_energy_unit_invalid_type_raises(self, convolution_base):
+ def test_convert_unit_invalid_type_raises(self, convolution_base):
# WHEN THEN EXPECT
with pytest.raises(
TypeError,
- match='Energy unit must be a string or scipp unit.',
+ match=r'Energy unit must be a string or scipp unit.',
):
- convolution_base.convert_energy_unit(123)
+ convolution_base.convert_unit(123)
- def test_convert_energy_unit_invalid_unit_rollback(self, convolution_base):
+ def test_convert_unit_invalid_unit_rollback(self, convolution_base):
# WHEN THEN
with pytest.raises(
UnitError,
- match='Conversion from `meV` to `s` is not valid.',
+ match=r'Conversion from `meV` to `s` is not valid.',
):
- convolution_base.convert_energy_unit('s')
+ convolution_base.convert_unit('s')
# EXPECT
- assert convolution_base.energy_unit == 'meV'
+ assert convolution_base.unit == 'meV'
assert np.allclose(convolution_base.energy.values, np.linspace(-10, 10, 100))
- def test_convert_energy_unit_invalid_offset_unit_rollback(self, convolution_base):
+ def test_convert_unit_invalid_offset_unit_rollback(self, convolution_base):
# WHEN
convolution_base.energy_offset = Parameter(name='energy_offset', value=5, unit='s')
# THEN
with pytest.raises(
UnitError,
- match='Conversion from `s` to `meV` is not valid.',
+ match=r'Conversion from `s` to `meV` is not valid.',
):
- convolution_base.convert_energy_unit('meV')
+ convolution_base.convert_unit('meV')
# EXPECT
- assert convolution_base.energy_unit == 'meV'
+ assert convolution_base.unit == 'meV'
assert convolution_base.energy_offset.unit == 's'
def test_energy_offset_property(self, convolution_base):
@@ -246,7 +246,7 @@ def test_energy_offset_setter_invalid_type_raises(self, convolution_base):
# WHEN THEN EXPECT
with pytest.raises(
TypeError,
- match='Energy_offset must be a number or a Parameter.',
+ match=r'Energy_offset must be a number or a Parameter.',
):
convolution_base.energy_offset = 'invalid'
@@ -277,8 +277,8 @@ def test_sample_components_setter_invalid_type_raises(self, convolution_base):
with pytest.raises(
TypeError,
match=(
- '`sample_components` is an instance of str, '
- 'but must be a ComponentCollection or ModelComponent.'
+ r'`sample_components` is an instance of str, '
+ r'but must be a ComponentCollection or ModelComponent.'
),
):
convolution_base.sample_components = 'invalid'
@@ -301,8 +301,8 @@ def test_resolution_components_setter_invalid_type_raises(self, convolution_base
with pytest.raises(
TypeError,
match=(
- '`resolution_components` is an instance of str, '
- 'but must be a ComponentCollection or ModelComponent.'
+ r'`resolution_components` is an instance of str, '
+ r'but must be a ComponentCollection or ModelComponent.'
),
):
convolution_base.resolution_components = 'invalid'
diff --git a/tests/unit/easydynamics/convolution/test_numerical_convolution.py b/tests/unit/easydynamics/convolution/test_numerical_convolution.py
index 29e5dfd6..8b015355 100644
--- a/tests/unit/easydynamics/convolution/test_numerical_convolution.py
+++ b/tests/unit/easydynamics/convolution/test_numerical_convolution.py
@@ -46,10 +46,13 @@ def test_init(self, default_numerical_convolution):
default_numerical_convolution._resolution_components, ComponentCollection
)
assert default_numerical_convolution.upsample_factor == 5
- assert default_numerical_convolution.extension_factor == 0.2
+ assert default_numerical_convolution.extension_factor == pytest.approx(0.2)
assert default_numerical_convolution.temperature is None
- assert default_numerical_convolution.energy_unit == 'meV'
- assert default_numerical_convolution.normalize_detailed_balance is True
+ assert default_numerical_convolution.unit == 'meV'
+ assert (
+ default_numerical_convolution.detailed_balance_settings.normalize_detailed_balance
+ is True
+ )
assert isinstance(default_numerical_convolution._energy_grid, EnergyGrid)
@pytest.mark.parametrize('upsample_factor', [None, 5])
diff --git a/tests/unit/easydynamics/convolution/test_numerical_convolution_base.py b/tests/unit/easydynamics/convolution/test_numerical_convolution_base.py
index 3934eefb..d349d591 100644
--- a/tests/unit/easydynamics/convolution/test_numerical_convolution_base.py
+++ b/tests/unit/easydynamics/convolution/test_numerical_convolution_base.py
@@ -10,6 +10,8 @@
from easydynamics.convolution.numerical_convolution_base import NumericalConvolutionBase
from easydynamics.sample_model import Gaussian
from easydynamics.sample_model.component_collection import ComponentCollection
+from easydynamics.settings.convolution_settings import ConvolutionSettings
+from easydynamics.settings.detailed_balance_settings import DetailedBalanceSettings
class TestNumericalConvolutionBase:
@@ -44,10 +46,13 @@ def test_init(self, default_numerical_convolution_base):
ComponentCollection,
)
assert default_numerical_convolution_base.upsample_factor == 5
- assert default_numerical_convolution_base.extension_factor == 0.2
+ assert default_numerical_convolution_base.extension_factor == pytest.approx(0.2)
assert default_numerical_convolution_base.temperature is None
- assert default_numerical_convolution_base.energy_unit == 'meV'
- assert default_numerical_convolution_base.normalize_detailed_balance is True
+ assert default_numerical_convolution_base.unit == 'meV'
+ assert (
+ default_numerical_convolution_base.detailed_balance_settings.normalize_detailed_balance
+ is True
+ )
assert isinstance(default_numerical_convolution_base._energy_grid, EnergyGrid)
def test_init_with_custom_parameters(self):
@@ -59,74 +64,87 @@ def test_init_with_custom_parameters(self):
energy = np.linspace(-5, 5, 50)
sample_components = ComponentCollection(display_name='ComponentCollection')
resolution_components = ComponentCollection(display_name='ResolutionModel')
- upsample_factor = 10
- extension_factor = 0.5
+ resolution_settings = ConvolutionSettings(upsample_factor=10, extension_factor=0.5)
temperature = 300.0
temperature_unit = 'K'
- energy_unit = 'meV'
- normalize_detailed_balance = False
+ detailed_balance_settings = DetailedBalanceSettings(normalize_detailed_balance=False)
+ unit = 'meV'
# THEN
numerical_convolution_base = NumericalConvolutionBase(
energy=energy,
sample_components=sample_components,
resolution_components=resolution_components,
- upsample_factor=upsample_factor,
- extension_factor=extension_factor,
+ convolution_settings=resolution_settings,
+ detailed_balance_settings=detailed_balance_settings,
temperature=temperature,
temperature_unit=temperature_unit,
- energy_unit=energy_unit,
- normalize_detailed_balance=normalize_detailed_balance,
+ unit=unit,
)
# EXPECT
- assert numerical_convolution_base.upsample_factor == upsample_factor
- assert numerical_convolution_base.extension_factor == extension_factor
+ assert numerical_convolution_base.upsample_factor == 10
+ assert numerical_convolution_base.extension_factor == pytest.approx(0.5)
assert numerical_convolution_base.temperature.value == temperature
assert numerical_convolution_base.temperature.unit == temperature_unit
- assert numerical_convolution_base.energy_unit == energy_unit
- assert numerical_convolution_base.normalize_detailed_balance == normalize_detailed_balance
+ assert numerical_convolution_base.unit == unit
+ assert (
+ numerical_convolution_base.detailed_balance_settings.normalize_detailed_balance
+ is False
+ )
+ assert numerical_convolution_base.detailed_balance_settings is detailed_balance_settings
assert isinstance(numerical_convolution_base._energy_grid, EnergyGrid)
- def test_init_raises_type_error_for_invalid_temperature(self):
+ @pytest.mark.parametrize(
+ 'invalid_input, expected_exception, match',
+ [
+ # temperature
+ (
+ {'temperature': 'invalid_temperature'},
+ TypeError,
+ r'Temperature must be None, a number or a Parameter.',
+ ),
+ # temperature_unit
+ (
+ {'temperature_unit': 123},
+ TypeError,
+ r'Temperature_unit must be a string or sc.Unit.',
+ ),
+ # detailed_balance_settings
+ (
+ {'detailed_balance_settings': 'invalid_settings'},
+ TypeError,
+ r'detailed_balance_settings must be a DetailedBalanceSettings instance.',
+ ),
+ ],
+ ids=[
+ 'temperature_invalid_type',
+ 'temperature_unit_invalid_type',
+ 'detailed_balance_settings_invalid_type',
+ ],
+ )
+ def test_init_raises_for_invalid_input(self, invalid_input, expected_exception, match):
"""
- Test that initialization raises TypeError for invalid
- temperature.
+ Test that initialization raises appropriate exceptions for
+ invalid input parameters.
"""
# WHEN
energy = np.linspace(-5, 5, 50)
sample_components = ComponentCollection(display_name='ComponentCollection')
resolution_components = ComponentCollection(display_name='ResolutionModel')
- invalid_temperature = 'invalid_temperature'
# THEN EXPECT
- with pytest.raises(TypeError, match='Temperature must be None, a number or a Parameter.'):
+ with pytest.raises(expected_exception, match=match):
NumericalConvolutionBase(
energy=energy,
sample_components=sample_components,
resolution_components=resolution_components,
- temperature=invalid_temperature,
+ **invalid_input,
)
- def test_init_raises_type_error_for_invalid_temperature_unit(self):
- """
- Test that initialization raises TypeError for invalid
- temperature_unit.
- """
- # WHEN
- energy = np.linspace(-5, 5, 50)
- sample_components = ComponentCollection(display_name='ComponentCollection')
- resolution_components = ComponentCollection(display_name='ResolutionModel')
- invalid_temperature_unit = 123 # Not a string or sc.Unit
-
- # THEN EXPECT
- with pytest.raises(TypeError, match='Temperature_unit must be a string or sc.Unit.'):
- NumericalConvolutionBase(
- energy=energy,
- sample_components=sample_components,
- resolution_components=resolution_components,
- temperature_unit=invalid_temperature_unit,
- )
+ ####################
+ # Test properties
+ ###################
def test_energy_setter(self, default_numerical_convolution_base):
"""
@@ -135,41 +153,64 @@ def test_energy_setter(self, default_numerical_convolution_base):
"""
# WHEN
new_energy = np.linspace(-20, 20, 201)
+
+ # THEN
default_numerical_convolution_base.energy = new_energy
- # THEN EXPECT
+ # EXPECT
assert isinstance(default_numerical_convolution_base.energy, sc.Variable)
assert np.allclose(default_numerical_convolution_base.energy.values, new_energy)
+
+ # EXPECT: plan invalidated
+ assert (
+ default_numerical_convolution_base.convolution_settings.convolution_plan_is_valid
+ is False
+ )
+
+ # THEN
+ # Force regeneration of energy grid
+ default_numerical_convolution_base._create_energy_grid()
+
+ # EXPECT
assert default_numerical_convolution_base._energy_grid.energy_dense.shape[0] == round(
201 * default_numerical_convolution_base.upsample_factor
)
- def test_upsample_factor_setter(self, default_numerical_convolution_base):
+ @pytest.mark.parametrize(
+ 'new_upsample_factor, expected_size',
+ [
+ (10, (101 * 10)),
+ (None, 101),
+ ],
+ ids=['upsample_10', 'no_upsampling'],
+ )
+ def test_upsample_factor_setter(
+ self,
+ default_numerical_convolution_base,
+ new_upsample_factor,
+ expected_size,
+ ):
"""
- Test setting a new upsample factor updates the energy grid
- accordingly.
+ Test setting upsample factor updates the energy grid correctly,
+ including disabling upsampling when set to None.
"""
# WHEN
- new_upsample_factor = 10
default_numerical_convolution_base.upsample_factor = new_upsample_factor
- # THEN EXPECT
- assert default_numerical_convolution_base.upsample_factor == new_upsample_factor
- assert default_numerical_convolution_base._energy_grid.energy_dense.shape[0] == round(
- 101 * new_upsample_factor
+ # EXPECT: plan invalidated
+ assert (
+ default_numerical_convolution_base.convolution_settings.convolution_plan_is_valid
+ is False
)
- def test_upsample_factor_setter_none(self, default_numerical_convolution_base):
- """
- Test setting upsample factor to None disables upsampling.
- """
- # WHEN
- new_upsample_factor = None
- default_numerical_convolution_base.upsample_factor = new_upsample_factor
+ # Force regeneration of energy grid
+ default_numerical_convolution_base._create_energy_grid()
- # THEN EXPECT
+ # EXPECT: correct factor + grid size
assert default_numerical_convolution_base.upsample_factor == new_upsample_factor
- assert default_numerical_convolution_base._energy_grid.energy_dense.shape[0] == 101
+ assert (
+ default_numerical_convolution_base._energy_grid.energy_dense.shape[0] == expected_size
+ )
@pytest.mark.parametrize(
'invalid_upsample_factor, expected_exception',
@@ -204,9 +245,21 @@ def test_extension_factor_setter(self, default_numerical_convolution_base):
"""
# WHEN
new_extension_factor = 0.5
+
+ # THEN
default_numerical_convolution_base.extension_factor = new_extension_factor
- # THEN EXPECT
+ # EXPECT: plan invalidated
+ assert (
+ default_numerical_convolution_base.convolution_settings.convolution_plan_is_valid
+ is False
+ )
+
+ # THEN
+ # Force regeneration of energy grid
+ default_numerical_convolution_base._create_energy_grid()
+
+ # EXPECT
assert default_numerical_convolution_base.extension_factor == new_extension_factor
expected_span = 20 + (0.5 * 20) # original span + extension
assert np.isclose(
@@ -287,7 +340,7 @@ def test_temperature_setter_does_not_replace_parameter(
# EXPECT
assert default_numerical_convolution_base.temperature is temp_param
- assert default_numerical_convolution_base.temperature.value == 350.0
+ assert default_numerical_convolution_base.temperature.value == pytest.approx(350.0)
def test_temperature_setter_raises(self, default_numerical_convolution_base):
"""
@@ -302,10 +355,15 @@ def test_normalize_detailed_balance_setter(self, default_numerical_convolution_b
Test setting normalize_detailed_balance to False.
"""
# WHEN
- default_numerical_convolution_base.normalize_detailed_balance = False
+ default_numerical_convolution_base.detailed_balance_settings.normalize_detailed_balance = (
+ False
+ )
# THEN EXPECT
- assert default_numerical_convolution_base.normalize_detailed_balance is False
+ assert (
+ default_numerical_convolution_base.detailed_balance_settings.normalize_detailed_balance
+ is False
+ )
def test_normalize_detailed_balance_setter_raises(self, default_numerical_convolution_base):
"""
@@ -314,7 +372,87 @@ def test_normalize_detailed_balance_setter_raises(self, default_numerical_convol
"""
# WHEN THEN EXPECT
with pytest.raises(TypeError, match='normalize_detailed_balance must be'):
- default_numerical_convolution_base.normalize_detailed_balance = 'invalid'
+ default_numerical_convolution_base.detailed_balance_settings.normalize_detailed_balance = ( # noqa: E501
+ 'invalid'
+ )
+
+ def test_detailed_balance_settings_property(self, default_numerical_convolution_base):
+ # WHEN
+ new_settings = DetailedBalanceSettings(
+ use_detailed_balance=False, normalize_detailed_balance=False
+ )
+
+ # THEN
+ default_numerical_convolution_base.detailed_balance_settings = new_settings
+
+ # EXPECT
+ assert default_numerical_convolution_base.detailed_balance_settings is new_settings
+
+ def test_detailed_balance_settings_setter_invalid(self, default_numerical_convolution_base):
+ # WHEN / THEN / EXPECT
+ with pytest.raises(
+ TypeError,
+ match='detailed_balance_settings must be a DetailedBalanceSettings',
+ ):
+ default_numerical_convolution_base.detailed_balance_settings = 'invalid_settings'
+
+ def test_convolution_settings_setter_valid(
+ self,
+ default_numerical_convolution_base,
+ ):
+ new_settings = ConvolutionSettings()
+
+ # WHEN
+ new_settings.convolution_plan_is_valid = True
+
+ # THEN
+ default_numerical_convolution_base.convolution_settings = new_settings
+
+ # EXPECT
+ assert default_numerical_convolution_base.convolution_settings is new_settings
+ assert new_settings.convolution_plan_is_valid is False
+
+ @pytest.mark.parametrize(
+ 'value, expected_exception, match',
+ [
+ (None, TypeError, 'must be a ConvolutionSettings instance'),
+ ('settings', TypeError, 'must be a ConvolutionSettings instance'),
+ (123, TypeError, 'must be a ConvolutionSettings instance'),
+ ],
+ ids=[
+ 'none',
+ 'string',
+ 'int',
+ ],
+ )
+ def test_convolution_settings_setter_invalid(
+ self,
+ default_numerical_convolution_base,
+ value,
+ expected_exception,
+ match,
+ ):
+ # WHEN / THEN / EXPECT
+ with pytest.raises(expected_exception, match=match):
+ default_numerical_convolution_base.convolution_settings = value
+
+ def test_convolution_settings_overwrites_existing(
+ self,
+ default_numerical_convolution_base,
+ ):
+ first = ConvolutionSettings()
+ second = ConvolutionSettings()
+
+ # WHEN
+ default_numerical_convolution_base.convolution_settings = first
+ default_numerical_convolution_base.convolution_settings = second
+
+ # EXPECT
+ assert default_numerical_convolution_base.convolution_settings is second
+
+ ####################
+ # Other tests
+ ###################
def test_create_energy_grid_upsample_none(self, default_numerical_convolution_base):
"""
@@ -347,11 +485,12 @@ def test_create_energy_grid_upsample_none_non_uniform_raises(
"""
# WHEN
default_numerical_convolution_base.energy = np.array([0, 1, 3, 6, 10])
+ default_numerical_convolution_base.upsample_factor = None
with pytest.raises(
ValueError,
match='Input array `energy` must be uniformly spaced if upsample_factor is not given',
):
- default_numerical_convolution_base.upsample_factor = None
+ default_numerical_convolution_base._create_energy_grid()
@pytest.mark.parametrize('num_points', [100, 101], ids=['even', 'odd'])
def test_create_energy_grid_upsample_and_extension(
@@ -502,7 +641,7 @@ def test_repr(self, default_numerical_convolution_base):
assert 'resolution_components=' in repr_str
# Important parameters
- assert 'energy_unit=meV' in repr_str
+ assert 'unit=meV' in repr_str
assert 'upsample_factor=5' in repr_str
assert 'extension_factor=0.2' in repr_str
assert 'temperature=None' in repr_str
diff --git a/tests/unit/easydynamics/experiment/test_experiment.py b/tests/unit/easydynamics/experiment/test_experiment.py
index 4568580e..7ffc83c8 100644
--- a/tests/unit/easydynamics/experiment/test_experiment.py
+++ b/tests/unit/easydynamics/experiment/test_experiment.py
@@ -305,7 +305,7 @@ def test_get_masked_energy(self, experiment_with_data):
# EXPECT
assert len(masked_energy) == 1
- assert masked_energy.values == 30.0
+ assert masked_energy.values == pytest.approx(30.0)
def test_get_masked_energy_no_data_returns_None(self):
"Test getting masked energy returns zero when no data is present"
@@ -332,7 +332,15 @@ def test_get_masked_energy_invalid_Q_index_raises(self, experiment_with_data, Q_
# test plotting
##############
- def test_plot_data_success(self, experiment):
+ @pytest.mark.parametrize(
+ 'transpose_axes, expected_dims',
+ [
+ (False, ['Q', 'energy']),
+ (True, ['energy', 'Q']),
+ ],
+ ids=['no_transpose', 'transpose'],
+ )
+ def test_plot_data_success(self, experiment, transpose_axes, expected_dims):
"Test plotting data successfully when in notebook environment"
# WHEN
with (
@@ -343,12 +351,12 @@ def test_plot_data_success(self, experiment):
mock_plot.return_value = mock_fig
# THEN
- result = experiment.plot_data()
+ result = experiment.plot_data(transpose_axes=transpose_axes)
# EXPECT
mock_plot.assert_called_once()
args, kwargs = mock_plot.call_args
- assert sc.identical(args[0], experiment.data.transpose())
+ assert sc.identical(args[0], experiment.data.transpose(dims=expected_dims))
assert kwargs['title'] == f'{experiment.display_name}'
assert result == mock_fig
@@ -395,6 +403,25 @@ def test_plot_data_not_in_notebook_raises(self, experiment):
):
experiment.plot_data()
+ def test_plot_data_invalid_slicer_type_raises(self, experiment):
+ "Test plotting data raises TypeError when slicer argument is invalid"
+ # WHEN THEN EXPECT
+
+ with (
+ patch(f'{Experiment.__module__}._in_notebook', return_value=True),
+ pytest.raises(TypeError, match='slicer must be True or False'),
+ ):
+ experiment.plot_data(slicer='not_a_boolean')
+
+ def test_plot_data_invalid_transpose_type_raises(self, experiment):
+ "Test plotting data raises TypeError when transpose argument is invalid"
+ # WHEN THEN EXPECT
+ with (
+ patch(f'{Experiment.__module__}._in_notebook', return_value=True),
+ pytest.raises(TypeError, match='transpose_axes must be True or False'),
+ ):
+ experiment.plot_data(transpose_axes='not_a_boolean')
+
##############
# test private methods
##############
@@ -499,7 +526,9 @@ def test_extract_x_y_weights_only_finite(self, experiment_with_data):
assert np.isfinite(x).all()
assert np.isfinite(y).all()
assert np.isfinite(weights).all()
- assert weights[0] == 1.0 / (experiment_with_data.data.variances[Q_index][2] ** 0.5)
+ assert weights[0] == pytest.approx(
+ 1.0 / (experiment_with_data.data.variances[Q_index][2] ** 0.5)
+ )
assert len(x) == len(y) == len(weights) == 1 # 2 values should be removed
# Mask should indicate which values were removed
assert np.array_equal(mask, [False, False, True])
diff --git a/tests/unit/easydynamics/sample_model/components/test_damped_harmonic_oscillator.py b/tests/unit/easydynamics/sample_model/components/test_damped_harmonic_oscillator.py
index 702c0bfc..79e1913f 100644
--- a/tests/unit/easydynamics/sample_model/components/test_damped_harmonic_oscillator.py
+++ b/tests/unit/easydynamics/sample_model/components/test_damped_harmonic_oscillator.py
@@ -24,17 +24,17 @@ def test_init_no_inputs(self):
# EXPECT
assert dho.display_name == 'DampedHarmonicOscillator'
- assert dho.area.value == 1.0
- assert dho.center.value == 1.0
- assert dho.width.value == 1.0
+ assert dho.area.value == pytest.approx(1.0)
+ assert dho.center.value == pytest.approx(1.0)
+ assert dho.width.value == pytest.approx(1.0)
assert dho.unit == 'meV'
def test_initialization(self, dho: DampedHarmonicOscillator):
# WHEN THEN EXPECT
assert dho.display_name == 'TestDHO'
- assert dho.area.value == 2.0
- assert dho.center.value == 1.5
- assert dho.width.value == 0.3
+ assert dho.area.value == pytest.approx(2.0)
+ assert dho.center.value == pytest.approx(1.5)
+ assert dho.width.value == pytest.approx(0.3)
assert dho.unit == 'meV'
def test_init_with_parameters(self):
@@ -88,7 +88,7 @@ def test_negative_width_raises(self):
# WHEN THEN EXPECT
with pytest.raises(
ValueError,
- match='The width of a DampedHarmonicOscillator must be greater than zero.',
+ match=r'The width of a DampedHarmonicOscillator must be greater than zero.',
):
DampedHarmonicOscillator(
display_name='TestDampedHarmonicOscillator',
@@ -190,9 +190,9 @@ def test_convert_unit(self, dho: DampedHarmonicOscillator):
# EXPECT
assert dho.unit == 'microeV'
- assert dho.area.value == 2 * 1e3
- assert dho.center.value == 1.5 * 1e3
- assert dho.width.value == 0.3 * 1e3
+ assert dho.area.value == pytest.approx(2 * 1e3)
+ assert dho.center.value == pytest.approx(1.5 * 1e3)
+ assert dho.width.value == pytest.approx(0.3 * 1e3)
def test_copy(self, dho: DampedHarmonicOscillator):
# WHEN THEN
diff --git a/tests/unit/easydynamics/sample_model/components/test_delta_function.py b/tests/unit/easydynamics/sample_model/components/test_delta_function.py
index b5c4bc11..be1e33a0 100644
--- a/tests/unit/easydynamics/sample_model/components/test_delta_function.py
+++ b/tests/unit/easydynamics/sample_model/components/test_delta_function.py
@@ -23,16 +23,16 @@ def test_init_no_inputs(self):
# EXPECT
assert delta_function.display_name == 'DeltaFunction'
- assert delta_function.area.value == 1.0
- assert delta_function.center.value == 0.0
+ assert delta_function.area.value == pytest.approx(1.0)
+ assert delta_function.center.value == pytest.approx(0.0)
assert delta_function.unit == 'meV'
assert delta_function.center.fixed is True
def test_initialization(self, delta_function: DeltaFunction):
# WHEN THEN EXPECT
assert delta_function.display_name == 'TestDeltaFunction'
- assert delta_function.area.value == 2.0
- assert delta_function.center.value == 0.5
+ assert delta_function.area.value == pytest.approx(2.0)
+ assert delta_function.center.value == pytest.approx(0.5)
assert delta_function.unit == 'meV'
@pytest.mark.parametrize(
@@ -167,7 +167,7 @@ def test_center_is_fixed_if_set_to_None(self, delta_function: DeltaFunction):
delta_function.center = None
# EXPECT
- assert delta_function.center.value == 0.0
+ assert delta_function.center.value == pytest.approx(0.0)
assert delta_function.center.fixed is True
def test_get_all_parameters(self, delta_function: DeltaFunction):
@@ -190,8 +190,8 @@ def test_convert_unit(self, delta_function: DeltaFunction):
# EXPECT
assert delta_function.unit == 'microeV'
- assert delta_function.area.value == 2 * 1e3
- assert delta_function.center.value == 0.5 * 1e3
+ assert delta_function.area.value == pytest.approx(2 * 1e3)
+ assert delta_function.center.value == pytest.approx(0.5 * 1e3)
def test_copy(self, delta_function: DeltaFunction):
# WHEN THEN
diff --git a/tests/unit/easydynamics/sample_model/components/test_exponential.py b/tests/unit/easydynamics/sample_model/components/test_exponential.py
index d61be76e..2a824532 100644
--- a/tests/unit/easydynamics/sample_model/components/test_exponential.py
+++ b/tests/unit/easydynamics/sample_model/components/test_exponential.py
@@ -28,17 +28,17 @@ def test_init_no_inputs(self):
# THEN EXPECT
assert exponential.display_name == 'Exponential'
- assert exponential.amplitude.value == 1.0
- assert exponential.center.value == 0.0
- assert exponential.rate.value == 1.0
+ assert exponential.amplitude.value == pytest.approx(1.0)
+ assert exponential.center.value == pytest.approx(0.0)
+ assert exponential.rate.value == pytest.approx(1.0)
assert exponential.unit == 'meV'
def test_initialization(self, exponential: Exponential):
# WHEN THEN EXPECT
assert exponential.display_name == 'TestExponential'
- assert exponential.amplitude.value == 2.0
- assert exponential.center.value == 0.5
- assert exponential.rate.value == 1.2
+ assert exponential.amplitude.value == pytest.approx(2.0)
+ assert exponential.center.value == pytest.approx(0.5)
+ assert exponential.rate.value == pytest.approx(1.2)
assert exponential.unit == 'meV'
def test_init_with_parameters(self):
@@ -133,7 +133,7 @@ def test_center_is_fixed_if_set_to_None(self, exponential: Exponential):
exponential.center = None
# EXPECT
- assert exponential.center.value == 0.0
+ assert exponential.center.value == pytest.approx(0.0)
assert exponential.center.fixed is True
def test_evaluate(self, exponential: Exponential):
@@ -172,33 +172,33 @@ def test_convert_unit(self, exponential: Exponential):
# THEN EXPECT
assert exponential.unit == 'microeV'
- assert exponential.amplitude.value == 2.0 * 1e3
- assert exponential.center.value == 0.5 * 1e3
+ assert exponential.amplitude.value == pytest.approx(2.0 * 1e3)
+ assert exponential.center.value == pytest.approx(0.5 * 1e3)
# rate should scale inversely
- assert exponential.rate.value == 1.2 / 1e3
+ assert exponential.rate.value == pytest.approx(1.2 / 1e3)
assert str(exponential.rate.unit) == '1/ueV'
def test_convert_unit_incorrect_unit_raises(self, exponential: Exponential):
# WHEN THEN EXPECT
- with pytest.raises(TypeError, match='unit must be a string or sc.Unit'):
+ with pytest.raises(TypeError, match=r'unit must be a string or sc.Unit'):
exponential.convert_unit(123)
def test_convert_unit_rollback(self, exponential: Exponential):
# WHEN
with pytest.raises(
UnitError,
- match='Failed to convert unit: Conversion from `meV` to `m` is not valid.',
+ match=r'Failed to convert unit: Conversion from `meV` to `m` is not valid.',
):
exponential.convert_unit('m')
# THEN EXPECT - values should be unchanged
assert exponential.unit == 'meV'
- assert exponential.amplitude.value == 2.0
+ assert exponential.amplitude.value == pytest.approx(2.0)
assert exponential.amplitude.unit == 'meV'
- assert exponential.center.value == 0.5
+ assert exponential.center.value == pytest.approx(0.5)
assert exponential.center.unit == 'meV'
- assert exponential.rate.value == 1.2
+ assert exponential.rate.value == pytest.approx(1.2)
assert exponential.rate.unit == '1/meV'
def test_copy(self, exponential: Exponential):
diff --git a/tests/unit/easydynamics/sample_model/components/test_expression_component.py b/tests/unit/easydynamics/sample_model/components/test_expression_component.py
index 4a7a43fd..27399844 100644
--- a/tests/unit/easydynamics/sample_model/components/test_expression_component.py
+++ b/tests/unit/easydynamics/sample_model/components/test_expression_component.py
@@ -23,16 +23,16 @@ def test_init_valid(self, expr: ExpressionComponent):
assert expr.display_name == 'TestExpression'
assert expr.unit == 'meV'
- assert expr.A.value == 2.0
- assert expr.x0.value == 0.5
- assert expr.sigma.value == 0.6
+ assert expr.A.value == pytest.approx(2.0)
+ assert expr.x0.value == pytest.approx(0.5)
+ assert expr.sigma.value == pytest.approx(0.6)
def test_init_without_parameters(self):
# WHEN THEN
expr = ExpressionComponent('A * x', parameters=None)
# EXPECT
- assert expr.A.value == 1.0 # default
+ assert expr.A.value == pytest.approx(1.0) # default
def test_invalid_expression_raises(self):
# WHEN THEN EXPECT
@@ -88,7 +88,7 @@ def test_parameter_setter(self, expr: ExpressionComponent):
expr.A = 3.0
# EXPECT
- assert expr.A.value == 3.0
+ assert expr.A.value == pytest.approx(3.0)
assert isinstance(expr.A, Parameter)
def test_parameter_getter_invalid_name(self, expr: ExpressionComponent):
@@ -131,8 +131,8 @@ def test_missing_parameter_defaults(self):
expr = ExpressionComponent('A * x + B', parameters={'A': 2.0})
# EXPECT
- assert expr.A.value == 2.0
- assert expr.B.value == 1.0 # default
+ assert expr.A.value == pytest.approx(2.0)
+ assert expr.B.value == pytest.approx(1.0) # default
def test_dir_includes_parameters(self, expr: ExpressionComponent):
# WHEN THEN
diff --git a/tests/unit/easydynamics/sample_model/components/test_gaussian.py b/tests/unit/easydynamics/sample_model/components/test_gaussian.py
index b1ad6f92..7119852a 100644
--- a/tests/unit/easydynamics/sample_model/components/test_gaussian.py
+++ b/tests/unit/easydynamics/sample_model/components/test_gaussian.py
@@ -22,18 +22,18 @@ def test_init_no_inputs(self):
# EXPECT
assert gaussian.display_name == 'Gaussian'
- assert gaussian.area.value == 1.0
- assert gaussian.center.value == 0.0
- assert gaussian.width.value == 1.0
+ assert gaussian.area.value == pytest.approx(1.0)
+ assert gaussian.center.value == pytest.approx(0.0)
+ assert gaussian.width.value == pytest.approx(1.0)
assert gaussian.unit == 'meV'
assert gaussian.center.fixed is True
def test_initialization(self, gaussian: Gaussian):
# WHEN THEN EXPECT
assert gaussian.display_name == 'TestGaussian'
- assert gaussian.area.value == 2.0
- assert gaussian.center.value == 0.5
- assert gaussian.width.value == 0.6
+ assert gaussian.area.value == pytest.approx(2.0)
+ assert gaussian.center.value == pytest.approx(0.5)
+ assert gaussian.width.value == pytest.approx(0.6)
assert gaussian.unit == 'meV'
def test_init_with_parameters(self):
@@ -85,7 +85,9 @@ def test_input_type_validation_raises(self, kwargs, expected_message):
def test_negative_width_raises(self):
# WHEN THEN EXPECT
- with pytest.raises(ValueError, match='The width of a Gaussian must be greater than zero.'):
+ with pytest.raises(
+ ValueError, match=r'The width of a Gaussian must be greater than zero.'
+ ):
Gaussian(
display_name='TestGaussian',
area=2.0,
@@ -150,7 +152,7 @@ def test_center_is_fixed_if_set_to_None(self, gaussian: Gaussian):
gaussian.center = None
# EXPECT
- assert gaussian.center.value == 0.0
+ assert gaussian.center.value == pytest.approx(0.0)
assert gaussian.center.fixed is True
def test_get_all_parameters(self, gaussian: Gaussian):
@@ -190,9 +192,9 @@ def test_convert_unit(self, gaussian: Gaussian):
# EXPECT
assert gaussian.unit == 'microeV'
- assert gaussian.area.value == 2 * 1e3
- assert gaussian.center.value == 0.5 * 1e3
- assert gaussian.width.value == 0.6 * 1e3
+ assert gaussian.area.value == pytest.approx(2 * 1e3)
+ assert gaussian.center.value == pytest.approx(0.5 * 1e3)
+ assert gaussian.width.value == pytest.approx(0.6 * 1e3)
def test_copy(self, gaussian: Gaussian):
# WHEN THEN
diff --git a/tests/unit/easydynamics/sample_model/components/test_lorentzian.py b/tests/unit/easydynamics/sample_model/components/test_lorentzian.py
index 5f87032d..4ce1e1db 100644
--- a/tests/unit/easydynamics/sample_model/components/test_lorentzian.py
+++ b/tests/unit/easydynamics/sample_model/components/test_lorentzian.py
@@ -24,18 +24,18 @@ def test_init_no_inputs(self):
# EXPECT
assert lorentzian.display_name == 'Lorentzian'
- assert lorentzian.area.value == 1.0
- assert lorentzian.center.value == 0.0
- assert lorentzian.width.value == 1.0
+ assert lorentzian.area.value == pytest.approx(1.0)
+ assert lorentzian.center.value == pytest.approx(0.0)
+ assert lorentzian.width.value == pytest.approx(1.0)
assert lorentzian.unit == 'meV'
assert lorentzian.center.fixed is True
def test_initialization(self, lorentzian: Lorentzian):
# WHEN THEN EXPECT
assert lorentzian.display_name == 'TestLorentzian'
- assert lorentzian.area.value == 2.0
- assert lorentzian.center.value == 0.5
- assert lorentzian.width.value == 0.6
+ assert lorentzian.area.value == pytest.approx(2.0)
+ assert lorentzian.center.value == pytest.approx(0.5)
+ assert lorentzian.width.value == pytest.approx(0.6)
assert lorentzian.unit == 'meV'
def test_init_with_parameters(self):
@@ -88,7 +88,7 @@ def test_input_type_validation_raises(self, kwargs, expected_message):
def test_negative_width_raises(self):
# WHEN THEN EXPECT
with pytest.raises(
- ValueError, match='The width of a Lorentzian must be greater than zero.'
+ ValueError, match=r'The width of a Lorentzian must be greater than zero.'
):
Lorentzian(
display_name='TestLorentzian',
@@ -152,7 +152,7 @@ def test_center_is_fixed_if_set_to_None(self, lorentzian: Lorentzian):
lorentzian.center = None
# EXPECT
- assert lorentzian.center.value == 0.0
+ assert lorentzian.center.value == pytest.approx(0.0)
assert lorentzian.center.fixed is True
def test_get_all_parameters(self, lorentzian: Lorentzian):
@@ -189,9 +189,9 @@ def test_convert_unit(self, lorentzian: Lorentzian):
# EXPECT
assert lorentzian.unit == 'microeV'
- assert lorentzian.area.value == 2 * 1e3
- assert lorentzian.center.value == 0.5 * 1e3
- assert lorentzian.width.value == 0.6 * 1e3
+ assert lorentzian.area.value == pytest.approx(2 * 1e3)
+ assert lorentzian.center.value == pytest.approx(0.5 * 1e3)
+ assert lorentzian.width.value == pytest.approx(0.6 * 1e3)
def test_copy(self, lorentzian: Lorentzian):
# WHEN THEN
diff --git a/tests/unit/easydynamics/sample_model/components/test_mixins.py b/tests/unit/easydynamics/sample_model/components/test_mixins.py
index 7c5160ae..4989f76e 100644
--- a/tests/unit/easydynamics/sample_model/components/test_mixins.py
+++ b/tests/unit/easydynamics/sample_model/components/test_mixins.py
@@ -23,10 +23,10 @@ def test_create_area_parameter_from_numeric(self, dummy_model, area_input, unit)
# EXPECT
assert isinstance(area_param, Parameter)
assert area_param.name == 'TestModel area'
- assert area_param.value == float(area_input)
+ assert area_param.value == pytest.approx(area_input)
assert area_param.unit == unit
assert not area_param.fixed
- assert area_param.min == 0.0
+ assert area_param.min == pytest.approx(0.0)
def test_create_area_parameter_from_parameter(self, dummy_model):
# WHEN
@@ -37,7 +37,7 @@ def test_create_area_parameter_from_parameter(self, dummy_model):
# EXPECT
assert area_param is area_input # Should be the same object
- assert area_param.min == 0.0
+ assert area_param.min == pytest.approx(0.0)
def test_create_area_parameter_invalid_type_raises(self, dummy_model):
# WHEN THEN EXPECT
@@ -75,7 +75,7 @@ def test_create_center_parameter_from_numeric(self, dummy_model, center_input, u
# EXPECT
assert isinstance(center_param, Parameter)
assert center_param.name == 'TestModel center'
- assert center_param.value == float(center_input)
+ assert center_param.value == pytest.approx(center_input)
assert center_param.unit == unit
assert not center_param.fixed
@@ -88,7 +88,7 @@ def test_create_center_parameter_from_None(self, dummy_model, fix_if_none):
# EXPECT
assert isinstance(center_param, Parameter)
assert center_param.name == 'TestModel center'
- assert center_param.value == 0.0
+ assert center_param.value == pytest.approx(0.0)
assert center_param.unit == 'meV'
assert center_param.fixed == fix_if_none
@@ -134,7 +134,7 @@ def test_create_width_parameter_from_numeric(self, dummy_model, width_input, uni
# EXPECT
assert isinstance(width_param, Parameter)
assert width_param.name == 'TestModel width'
- assert width_param.value == float(width_input)
+ assert width_param.value == pytest.approx(width_input)
assert width_param.unit == unit
assert not width_param.fixed
diff --git a/tests/unit/easydynamics/sample_model/components/test_model_component.py b/tests/unit/easydynamics/sample_model/components/test_model_component.py
index 9e47d4e9..514ced73 100644
--- a/tests/unit/easydynamics/sample_model/components/test_model_component.py
+++ b/tests/unit/easydynamics/sample_model/components/test_model_component.py
@@ -8,8 +8,6 @@
from easydynamics.sample_model.components.model_component import ModelComponent
-Numeric = float | int
-
class DummyComponent(ModelComponent):
def __init__(self):
@@ -42,13 +40,13 @@ def test_convert_unit(self, dummy: DummyComponent):
# EXPECT
assert dummy.unit == 'microeV'
- assert dummy.area.value == 1 * 1e3
- assert dummy.center.value == 2 * 1e3
- assert dummy.width.value == 3 * 1e3
+ assert dummy.area.value == pytest.approx(1 * 1e3)
+ assert dummy.center.value == pytest.approx(2 * 1e3)
+ assert dummy.width.value == pytest.approx(3 * 1e3)
def test_convert_unit_incorrect_unit_raises(self, dummy: DummyComponent):
# WHEN THEN EXPECT
- with pytest.raises(TypeError, match='Unit must be a string or sc.Unit'):
+ with pytest.raises(TypeError, match=r'Unit must be a string or sc.Unit'):
dummy.convert_unit(123)
def test_free_and_fix_all_parameters(self, dummy):
@@ -150,7 +148,7 @@ def test_prepare_x_for_evaluate_with_different_unit_warns(self, dummy):
# THEN EXPECT
with pytest.warns(
UserWarning,
- match='Input x has unit µeV, but DummyComponent component ',
+ match='Input x has unit [µμ]eV, but DummyComponent component ',
):
x_prepared = dummy._prepare_x_for_evaluate(x)
@@ -158,7 +156,7 @@ def test_prepare_x_for_evaluate_with_different_unit_warns(self, dummy):
assert isinstance(x_prepared, np.ndarray)
assert x_prepared.shape == (3,)
np.testing.assert_array_equal(x_prepared, [1.0, 2.0, 3.0])
- assert dummy.unit == 'µeV'
- assert dummy.area.value == 1.0 * 1e3
- assert dummy.center.value == 2.0 * 1e3
- assert dummy.width.value == 3.0 * 1e3
+ assert dummy.unit == 'µeV' # noqa: RUF001
+ assert dummy.area.value == pytest.approx(1.0 * 1e3)
+ assert dummy.center.value == pytest.approx(2.0 * 1e3)
+ assert dummy.width.value == pytest.approx(3.0 * 1e3)
diff --git a/tests/unit/easydynamics/sample_model/components/test_polynomial.py b/tests/unit/easydynamics/sample_model/components/test_polynomial.py
index aa7790d2..5e42e677 100644
--- a/tests/unit/easydynamics/sample_model/components/test_polynomial.py
+++ b/tests/unit/easydynamics/sample_model/components/test_polynomial.py
@@ -22,15 +22,15 @@ def test_init_no_inputs(self):
# EXPECT
assert polynomial.display_name == 'Polynomial'
- assert polynomial.coefficients[0].value == 0.0
+ assert polynomial.coefficients[0].value == pytest.approx(0.0)
assert polynomial.unit == 'meV'
def test_initialization(self, polynomial: Polynomial):
# WHEN THEN EXPECT
assert polynomial.display_name == 'TestPolynomial'
- assert polynomial.coefficients[0].value == 1.0
- assert polynomial.coefficients[1].value == -2.0
- assert polynomial.coefficients[2].value == 3.0
+ assert polynomial.coefficients[0].value == pytest.approx(1.0)
+ assert polynomial.coefficients[1].value == pytest.approx(-2.0)
+ assert polynomial.coefficients[2].value == pytest.approx(3.0)
@pytest.mark.parametrize(
'kwargs, expected_message',
@@ -60,7 +60,7 @@ def test_input_type_validation_raises(self, kwargs, expected_message):
def test_init_no_coefficients_raises(self):
# WHEN THEN EXPECT
- with pytest.raises(ValueError, match='At least one coefficient must be provided.'):
+ with pytest.raises(ValueError, match=r'At least one coefficient must be provided.'):
Polynomial(display_name='TestPolynomial', coefficients=[])
def test_negative_value_warns_in_evaluate(self):
diff --git a/tests/unit/easydynamics/sample_model/components/test_voigt.py b/tests/unit/easydynamics/sample_model/components/test_voigt.py
index f4ea949d..5bf866d8 100644
--- a/tests/unit/easydynamics/sample_model/components/test_voigt.py
+++ b/tests/unit/easydynamics/sample_model/components/test_voigt.py
@@ -30,20 +30,20 @@ def test_init_no_inputs(self):
# EXPECT
assert voigt.display_name == 'Voigt'
- assert voigt.area.value == 1.0
- assert voigt.center.value == 0.0
- assert voigt.gaussian_width.value == 1.0
- assert voigt.lorentzian_width.value == 1.0
+ assert voigt.area.value == pytest.approx(1.0)
+ assert voigt.center.value == pytest.approx(0.0)
+ assert voigt.gaussian_width.value == pytest.approx(1.0)
+ assert voigt.lorentzian_width.value == pytest.approx(1.0)
assert voigt.unit == 'meV'
assert voigt.center.fixed is True
def test_initialization(self, voigt: Voigt):
# WHEN THEN EXPECT
assert voigt.display_name == 'TestVoigt'
- assert voigt.area.value == 2.0
- assert voigt.center.value == 0.5
- assert voigt.gaussian_width.value == 0.6
- assert voigt.lorentzian_width.value == 0.7
+ assert voigt.area.value == pytest.approx(2.0)
+ assert voigt.center.value == pytest.approx(0.5)
+ assert voigt.gaussian_width.value == pytest.approx(0.6)
+ assert voigt.lorentzian_width.value == pytest.approx(0.7)
assert voigt.unit == 'meV'
def test_init_with_parameters(self):
@@ -133,7 +133,7 @@ def test_input_type_validation_raises(self, kwargs, expected_message):
def test_negative_gaussian_width_raises(self):
# WHEN THEN EXPECT
with pytest.raises(
- ValueError, match='The gaussian_width of a Voigt must be greater than.'
+ ValueError, match=r'The gaussian_width of a Voigt must be greater than.'
):
Voigt(
display_name='TestVoigt',
@@ -148,7 +148,7 @@ def test_negative_lorentzian_width_raises(self):
# WHEN THEN EXPECT
with pytest.raises(
ValueError,
- match='The lorentzian_width of a Voigt must be greater than zero.',
+ match=r'The lorentzian_width of a Voigt must be greater than zero.',
):
Voigt(
display_name='TestVoigt',
@@ -217,7 +217,7 @@ def test_center_is_fixed_if_set_to_None(self, voigt: Voigt):
voigt.center = None
# EXPECT
- assert voigt.center.value == 0.0
+ assert voigt.center.value == pytest.approx(0.0)
assert voigt.center.fixed is True
def test_evaluate(self, voigt: Voigt):
@@ -243,7 +243,7 @@ def test_center_is_fixed_if_init_to_None(self):
)
# EXPECT
- assert test_voigt.center.value == 0.0
+ assert test_voigt.center.value == pytest.approx(0.0)
assert test_voigt.center.fixed is True
def test_convert_unit(self, voigt: Voigt):
@@ -252,10 +252,10 @@ def test_convert_unit(self, voigt: Voigt):
# EXPECT
assert voigt.unit == 'microeV'
- assert voigt.area.value == 2 * 1e3
- assert voigt.center.value == 0.5 * 1e3
- assert voigt.gaussian_width.value == 0.6 * 1e3
- assert voigt.lorentzian_width.value == 0.7 * 1e3
+ assert voigt.area.value == pytest.approx(2 * 1e3)
+ assert voigt.center.value == pytest.approx(0.5 * 1e3)
+ assert voigt.gaussian_width.value == pytest.approx(0.6 * 1e3)
+ assert voigt.lorentzian_width.value == pytest.approx(0.7 * 1e3)
def test_get_all_parameters(self, voigt: Voigt):
# WHEN THEN
diff --git a/tests/unit/easydynamics/sample_model/diffusion_model/test_brownian_translational_diffusion.py b/tests/unit/easydynamics/sample_model/diffusion_model/test_brownian_translational_diffusion.py
index 80ec766f..be25890e 100644
--- a/tests/unit/easydynamics/sample_model/diffusion_model/test_brownian_translational_diffusion.py
+++ b/tests/unit/easydynamics/sample_model/diffusion_model/test_brownian_translational_diffusion.py
@@ -26,8 +26,8 @@ def test_init_default(self, brownian_diffusion_model):
# WHEN THEN EXPECT
assert brownian_diffusion_model.display_name == 'BrownianTranslationalDiffusion'
assert brownian_diffusion_model.unit == 'meV'
- assert brownian_diffusion_model.scale.value == 1.0
- assert brownian_diffusion_model.diffusion_coefficient.value == 1.0
+ assert brownian_diffusion_model.scale.value == pytest.approx(1.0)
+ assert brownian_diffusion_model.diffusion_coefficient.value == pytest.approx(1.0)
@pytest.mark.parametrize(
'kwargs,expected_exception, expected_message',
@@ -70,16 +70,16 @@ def test_diffusion_coefficient_setter(self, brownian_diffusion_model):
brownian_diffusion_model.diffusion_coefficient = 3.0
# THEN EXPECT
- assert brownian_diffusion_model.diffusion_coefficient.value == 3.0
+ assert brownian_diffusion_model.diffusion_coefficient.value == pytest.approx(3.0)
def test_diffusion_coefficient_setter_raises(self, brownian_diffusion_model):
# WHEN THEN EXPECT
- with pytest.raises(TypeError, match='diffusion_coefficient must be a number.'):
+ with pytest.raises(TypeError, match=r'diffusion_coefficient must be a number.'):
brownian_diffusion_model.diffusion_coefficient = 'invalid' # Invalid type
def test_diffusion_coefficient_setter_negative_raises(self, brownian_diffusion_model):
# WHEN THEN EXPECT
- with pytest.raises(ValueError, match='diffusion_coefficient must be non-negative.'):
+ with pytest.raises(ValueError, match=r'diffusion_coefficient must be non-negative.'):
brownian_diffusion_model.diffusion_coefficient = -1.0 # Invalid negative value
def test_calculate_width_type_error(self, brownian_diffusion_model):
@@ -170,7 +170,7 @@ def test_create_component_collections_component_name_must_be_string(
self, brownian_diffusion_model
):
# WHEN THEN EXPECT
- with pytest.raises(TypeError, match='component_name must be a string.'):
+ with pytest.raises(TypeError, match=r'component_name must be a string.'):
brownian_diffusion_model.create_component_collections(
Q=np.array([0.1, 0.2, 0.3]), component_display_name=123
)
@@ -182,7 +182,7 @@ def test_create_component_collections_Q_type_error(self, brownian_diffusion_mode
def test_create_component_collections_Q_1dimensional_error(self, brownian_diffusion_model):
# WHEN THEN EXPECT
- with pytest.raises(ValueError, match='Q must be a 1-dimensional array.'):
+ with pytest.raises(ValueError, match=r'Q must be a 1-dimensional array.'):
brownian_diffusion_model.create_component_collections(
Q=np.array([[0.1, 0.2], [0.3, 0.4]])
) # Invalid shape
diff --git a/tests/unit/easydynamics/sample_model/diffusion_model/test_diffusion_model.py b/tests/unit/easydynamics/sample_model/diffusion_model/test_diffusion_model.py
index 67f654b2..c46dc561 100644
--- a/tests/unit/easydynamics/sample_model/diffusion_model/test_diffusion_model.py
+++ b/tests/unit/easydynamics/sample_model/diffusion_model/test_diffusion_model.py
@@ -20,7 +20,7 @@ def test_unit_setter_raises(self, diffusion_model):
# WHEN THEN EXPECT
with pytest.raises(
AttributeError,
- match='Unit is read-only. Use convert_unit to change the unit between allowed types',
+ match=r'Unit is read-only. Use convert_unit to change the unit between allowed types',
):
diffusion_model.unit = 'eV'
@@ -29,16 +29,16 @@ def test_scale_setter(self, diffusion_model):
diffusion_model.scale = 2.0
# THEN EXPECT
- assert diffusion_model.scale.value == 2.0
+ assert diffusion_model.scale.value == pytest.approx(2.0)
def test_scale_setter_negative_raises(self, diffusion_model):
# WHEN THEN EXPECT
- with pytest.raises(ValueError, match='scale must be non-negative.'):
+ with pytest.raises(ValueError, match=r'scale must be non-negative.'):
diffusion_model.scale = -1.0 # Invalid negative value
def test_scale_setter_raises(self, diffusion_model):
# WHEN THEN EXPECT
- with pytest.raises(TypeError, match='scale must be a number.'):
+ with pytest.raises(TypeError, match=r'scale must be a number.'):
diffusion_model.scale = 'invalid' # Invalid type
def test_repr(self, diffusion_model):
diff --git a/tests/unit/easydynamics/sample_model/diffusion_model/test_jump_translational_diffusion.py b/tests/unit/easydynamics/sample_model/diffusion_model/test_jump_translational_diffusion.py
index 756d422f..9388a2db 100644
--- a/tests/unit/easydynamics/sample_model/diffusion_model/test_jump_translational_diffusion.py
+++ b/tests/unit/easydynamics/sample_model/diffusion_model/test_jump_translational_diffusion.py
@@ -26,9 +26,9 @@ def test_init_default(self, jump_diffusion_model):
# WHEN THEN EXPECT
assert jump_diffusion_model.display_name == 'JumpTranslationalDiffusion'
assert jump_diffusion_model.unit == 'meV'
- assert jump_diffusion_model.scale.value == 1.0
- assert jump_diffusion_model.diffusion_coefficient.value == 1.0
- assert jump_diffusion_model.relaxation_time.value == 1.0
+ assert jump_diffusion_model.scale.value == pytest.approx(1.0)
+ assert jump_diffusion_model.diffusion_coefficient.value == pytest.approx(1.0)
+ assert jump_diffusion_model.relaxation_time.value == pytest.approx(1.0)
@pytest.mark.parametrize(
'kwargs,expected_exception, expected_message',
@@ -84,16 +84,16 @@ def test_diffusion_coefficient_setter(self, jump_diffusion_model):
jump_diffusion_model.diffusion_coefficient = 3.0
# THEN EXPECT
- assert jump_diffusion_model.diffusion_coefficient.value == 3.0
+ assert jump_diffusion_model.diffusion_coefficient.value == pytest.approx(3.0)
def test_diffusion_coefficient_setter_raises(self, jump_diffusion_model):
# WHEN THEN EXPECT
- with pytest.raises(TypeError, match='diffusion_coefficient must be a number.'):
+ with pytest.raises(TypeError, match=r'diffusion_coefficient must be a number.'):
jump_diffusion_model.diffusion_coefficient = 'invalid' # Invalid type
def test_diffusion_coefficient_setter_negative_raises(self, jump_diffusion_model):
# WHEN THEN EXPECT
- with pytest.raises(ValueError, match='diffusion_coefficient must be non-negative.'):
+ with pytest.raises(ValueError, match=r'diffusion_coefficient must be non-negative.'):
jump_diffusion_model.diffusion_coefficient = -1.0 # Invalid negative value
def test_relaxation_time_setter(self, jump_diffusion_model):
@@ -101,16 +101,16 @@ def test_relaxation_time_setter(self, jump_diffusion_model):
jump_diffusion_model.relaxation_time = 2.5
# THEN EXPECT
- assert jump_diffusion_model.relaxation_time.value == 2.5
+ assert jump_diffusion_model.relaxation_time.value == pytest.approx(2.5)
def test_relaxation_time_setter_raises(self, jump_diffusion_model):
# WHEN THEN EXPECT
- with pytest.raises(TypeError, match='relaxation_time must be a number.'):
+ with pytest.raises(TypeError, match=r'relaxation_time must be a number.'):
jump_diffusion_model.relaxation_time = 'invalid' # Invalid type
def test_relaxation_time_setter_negative_raises(self, jump_diffusion_model):
# WHEN THEN EXPECT
- with pytest.raises(ValueError, match='relaxation_time must be non-negative.'):
+ with pytest.raises(ValueError, match=r'relaxation_time must be non-negative.'):
jump_diffusion_model.relaxation_time = -1.0 # Invalid negative value
def test_calculate_width_type_error(self, jump_diffusion_model):
@@ -208,7 +208,7 @@ def test_create_component_collections_component_name_must_be_string(
self, jump_diffusion_model
):
# WHEN THEN EXPECT
- with pytest.raises(TypeError, match='component_name must be a string.'):
+ with pytest.raises(TypeError, match=r'component_name must be a string.'):
jump_diffusion_model.create_component_collections(
Q=np.array([0.1, 0.2, 0.3]), component_display_name=123
)
@@ -220,7 +220,7 @@ def test_create_component_collections_Q_type_error(self, jump_diffusion_model):
def test_create_component_collections_Q_1dimensional_error(self, jump_diffusion_model):
# WHEN THEN EXPECT
- with pytest.raises(ValueError, match='Q must be a 1-dimensional array.'):
+ with pytest.raises(ValueError, match=r'Q must be a 1-dimensional array.'):
jump_diffusion_model.create_component_collections(
Q=np.array([[0.1, 0.2], [0.3, 0.4]])
) # Invalid shape
diff --git a/tests/unit/easydynamics/sample_model/test_component_collection.py b/tests/unit/easydynamics/sample_model/test_component_collection.py
index 15ea38ba..c7d41aa1 100644
--- a/tests/unit/easydynamics/sample_model/test_component_collection.py
+++ b/tests/unit/easydynamics/sample_model/test_component_collection.py
@@ -66,7 +66,7 @@ def test_init_with_components(self):
def test_init_with_invalid_components_raises(self):
# WHEN THEN EXPECT
- with pytest.raises(TypeError, match='Component must be.'):
+ with pytest.raises(TypeError, match='Component must be'):
ComponentCollection(components=['NotAComponent'])
def test_init_with_invalid_list_of_components_raises(self):
@@ -152,7 +152,7 @@ def test_component_setter(self, component_collection):
def test_component_setter_invalid_raises(self, component_collection):
# WHEN THEN EXPECT
- with pytest.raises(TypeError, match=' must be instances of ModelComponent.'):
+ with pytest.raises(TypeError, match=r' must be instances of ModelComponent.'):
component_collection.components = ['NotAComponent']
with pytest.raises(TypeError, match='components must be a list of'):
@@ -174,7 +174,7 @@ def test_is_empty(self):
def test_is_empty_setter(self, component_collection):
# WHEN THEN EXPECT
- with pytest.raises(AttributeError, match='is_empty is a read-only property.'):
+ with pytest.raises(AttributeError, match=r'is_empty is a read-only property.'):
component_collection.is_empty = True
def test_component_setter_empty_list(self, component_collection):
@@ -204,7 +204,7 @@ def test_convert_unit(self, component_collection):
def test_convert_unit_incorrect_unit_raises(self, component_collection):
# WHEN THEN EXPECT
- with pytest.raises(TypeError, match='Unit must be a string or sc.Unit'):
+ with pytest.raises(TypeError, match=r'Unit must be a string or sc.Unit'):
component_collection.convert_unit(123)
def test_convert_unit_failure_rolls_back(self, component_collection):
@@ -224,7 +224,7 @@ def convert_unit(self, _unit: str) -> None:
}
# EXPECT
- with pytest.raises(RuntimeError, match='Conversion failed.'):
+ with pytest.raises(RuntimeError, match=r'Conversion failed.'):
component_collection.convert_unit('eV')
# Check that all components have their original units
@@ -235,7 +235,7 @@ def test_set_unit(self, component_collection):
# WHEN THEN EXPECT
with pytest.raises(
AttributeError,
- match='Unit is read-only. Use convert_unit to change the unit',
+ match=r'Unit is read-only. Use convert_unit to change the unit',
):
component_collection.unit = 'eV'
@@ -255,7 +255,7 @@ def test_evaluate_no_components_returns_zero(self):
x = np.linspace(-5, 5, 100)
# EXPECT
result = component_collection.evaluate(x)
- assert np.all(result == 0.0)
+ assert np.all(result == pytest.approx(0.0))
assert result.shape == x.shape
def test_evaluate_component(self, component_collection):
@@ -283,7 +283,7 @@ def test_evaluate_component_no_components_raises(self):
component_collection = ComponentCollection(display_name='EmptyModel')
x = np.linspace(-5, 5, 100)
# EXPECT
- with pytest.raises(ValueError, match='No components in the model to evaluate.'):
+ with pytest.raises(ValueError, match=r'No components in the model to evaluate.'):
component_collection.evaluate_component(x, 'AnyComponent')
def test_evaluate_component_invalid_name_type_raises(self, component_collection):
@@ -293,7 +293,7 @@ def test_evaluate_component_invalid_name_type_raises(self, component_collection)
# THEN EXPECT
with pytest.raises(
TypeError,
- match="Component unique name must be a string, got instead.",
+ match=r"Component unique name must be a string, got instead.",
):
component_collection.evaluate_component(x, 123)
@@ -312,7 +312,7 @@ def test_normalize_area_no_components_raises(self):
# WHEN THEN
component_collection = ComponentCollection(display_name='EmptyModel')
# EXPECT
- with pytest.raises(ValueError, match='No components in the model to normalize.'):
+ with pytest.raises(ValueError, match=r'No components in the model to normalize.'):
component_collection.normalize_area()
@pytest.mark.parametrize(
@@ -326,7 +326,7 @@ def test_normalize_area_not_finite_area_raises(self, component_collection, area_
component_collection.components[1].area = area_value
# EXPECT
- with pytest.raises(ValueError, match='cannot normalize.'):
+ with pytest.raises(ValueError, match=r'cannot normalize'):
component_collection.normalize_area()
def test_normalize_area_non_area_component_warns(self, component_collection):
diff --git a/tests/unit/easydynamics/sample_model/test_instrument_model.py b/tests/unit/easydynamics/sample_model/test_instrument_model.py
index dad4ae9f..e8983b0d 100644
--- a/tests/unit/easydynamics/sample_model/test_instrument_model.py
+++ b/tests/unit/easydynamics/sample_model/test_instrument_model.py
@@ -172,7 +172,7 @@ def test_unit_setter_raises(self, instrument_model):
# WHEN / THEN / EXPECT
with pytest.raises(
AttributeError,
- match='Unit is read-only. Use convert_unit to change the unit between allowed types ',
+ match=r'Unit is read-only. Use convert_unit to change the unit between allowed types ',
):
instrument_model.unit = 'meV'
@@ -184,7 +184,7 @@ def test_energy_offset_setter(self, instrument_model):
instrument_model.energy_offset = 1.0
# EXPECT
- assert instrument_model.energy_offset.value == 1.0
+ assert instrument_model.energy_offset.value == pytest.approx(1.0)
instrument_model._on_energy_offset_change.assert_called_once()
def test_energy_offset_setter_raises(self, instrument_model):
diff --git a/tests/unit/easydynamics/sample_model/test_model_base.py b/tests/unit/easydynamics/sample_model/test_model_base.py
index 41f1cf59..5ad066a2 100644
--- a/tests/unit/easydynamics/sample_model/test_model_base.py
+++ b/tests/unit/easydynamics/sample_model/test_model_base.py
@@ -268,7 +268,7 @@ def test_convert_unit_invalid_raises(self, model_base):
def test_convert_unit_incorrect_unit_raises(self, model_base):
# WHEN THEN EXPECT
- with pytest.raises(TypeError, match='Unit must be a string or sc.Unit'):
+ with pytest.raises(TypeError, match=r'Unit must be a string or sc.Unit'):
model_base.convert_unit(123)
def test_components_setter(self, model_base):
diff --git a/tests/unit/easydynamics/sample_model/test_sample_model.py b/tests/unit/easydynamics/sample_model/test_sample_model.py
index 6c20f0b0..712dfa8b 100644
--- a/tests/unit/easydynamics/sample_model/test_sample_model.py
+++ b/tests/unit/easydynamics/sample_model/test_sample_model.py
@@ -15,6 +15,7 @@
BrownianTranslationalDiffusion,
)
from easydynamics.sample_model.sample_model import SampleModel
+from easydynamics.settings.detailed_balance_settings import DetailedBalanceSettings
class TestSampleModel:
@@ -65,52 +66,76 @@ def test_init(self, sample_model):
assert isinstance(model.diffusion_models, list)
assert len(model.diffusion_models) == 1
assert isinstance(model.diffusion_models[0], BrownianTranslationalDiffusion)
- assert model.temperature.value == 10.0
- assert model.divide_by_temperature is True
+ assert model.temperature.value == pytest.approx(10.0)
+ assert model.normalize_detailed_balance is True
+ assert model.use_detailed_balance is True
+ assert isinstance(model.detailed_balance_settings, DetailedBalanceSettings)
np.testing.assert_array_equal(model.Q, np.array([1.0, 2.0, 3.0]))
- def test_init_list_of_diffusion_model(self):
+ def test_init_custom_input(self):
# WHEN THEN
diffusion_model1 = BrownianTranslationalDiffusion()
diffusion_model2 = BrownianTranslationalDiffusion()
- sample_model = SampleModel(diffusion_models=[diffusion_model1, diffusion_model2])
+
+ detailed_balance_settings = DetailedBalanceSettings(
+ use_detailed_balance=False,
+ normalize_detailed_balance=False,
+ )
+ sample_model = SampleModel(
+ diffusion_models=[diffusion_model1, diffusion_model2],
+ detailed_balance_settings=detailed_balance_settings,
+ )
# EXPECT
assert len(sample_model.diffusion_models) == 2
assert sample_model.diffusion_models[0] is diffusion_model1
assert sample_model.diffusion_models[1] is diffusion_model2
+ assert sample_model.use_detailed_balance is False
+ assert sample_model.normalize_detailed_balance is False
+ assert sample_model.detailed_balance_settings is detailed_balance_settings
- def test_init_raises_with_invalid_diffusion_model(self):
- # WHEN / THEN / EXPECT
- with pytest.raises(
- TypeError,
- match='diffusion_models must be ',
- ):
- SampleModel(diffusion_models='invalid_diffusion_model')
-
- def test_init_raises_with_invalid_temperature(self):
- # WHEN / THEN / EXPECT
- with pytest.raises(
- TypeError,
- match='temperature must be a number or None',
- ):
- SampleModel(temperature='invalid_temperature')
-
- def test_init_raises_with_negative_temperature(self):
- # WHEN / THEN / EXPECT
- with pytest.raises(
- ValueError,
- match='temperature must be non-negative',
- ):
- SampleModel(temperature=-5.0)
-
- def test_init_raises_with_invalid_divide_by_temperature(self):
- # WHEN / THEN / EXPECT
- with pytest.raises(
- TypeError,
- match='divide_by_temperature must be True or False',
- ):
- SampleModel(divide_by_temperature='invalid_value')
+ @pytest.mark.parametrize(
+ 'invalid_input, expected_exception, match',
+ [
+ # diffusion_models
+ (
+ {'diffusion_models': 'invalid_diffusion_model'},
+ TypeError,
+ 'diffusion_models must be a DiffusionModelBase',
+ ),
+ # temperature
+ (
+ {'temperature': 'invalid_temperature'},
+ TypeError,
+ 'temperature must be a number or None',
+ ),
+ (
+ {'temperature': -5.0},
+ ValueError,
+ 'temperature must be non-negative',
+ ),
+ # detailed_balance_settings
+ (
+ {'detailed_balance_settings': 'invalid_settings'},
+ TypeError,
+ 'detailed_balance_settings must be a DetailedBalanceSettings or None',
+ ),
+ ],
+ ids=[
+ 'diffusion_models_invalid_type',
+ 'temperature_not_numeric',
+ 'temperature_negative',
+ 'detailed_balance_settings_invalid_type',
+ ],
+ )
+ def test_init_raises_for_invalid_input(self, invalid_input, expected_exception, match):
+ """
+ Test that initialization raises appropriate exceptions for
+ invalid input parameters.
+ """
+ # WHEN THEN EXPECT
+ with pytest.raises(expected_exception, match=match):
+ SampleModel(**invalid_input)
def test_append_and_remove_and_clear_diffusion_model(self, sample_model):
# WHEN
@@ -205,7 +230,7 @@ def test_temperature_setter(self, sample_model):
model.temperature = 20.0
# EXPECT
- assert model.temperature.value == 20.0
+ assert model.temperature.value == pytest.approx(20.0)
# THEN
model.temperature = None
@@ -217,7 +242,7 @@ def test_temperature_setter(self, sample_model):
model.temperature = 0.0
# EXPECT
- assert model.temperature.value == 0.0
+ assert model.temperature.value == pytest.approx(0.0)
@pytest.mark.parametrize(
'invalid_value',
@@ -233,7 +258,7 @@ def test_temperature_setter_raises_with_invalid_type(self, invalid_value, sample
# WHEN / THEN / EXPECT
with pytest.raises(
(TypeError, ValueError),
- match='temperature must be a number or None|temperature must be non-negative',
+ match=r'temperature must be a number or None|temperature must be non-negative',
):
sample_model.temperature = invalid_value
@@ -279,29 +304,75 @@ def test_convert_temperature_unit_raises_with_invalid_unit(self, sample_model):
):
model.convert_temperature_unit('invalid_unit')
- def test_divide_by_temperature_setter(self, sample_model):
+ def test_normalize_detailed_balance_setter(self, sample_model):
# WHEN
model = sample_model
# THEN
- model.divide_by_temperature = False
+ model.normalize_detailed_balance = False
# EXPECT
- assert model.divide_by_temperature is False
+ assert model.normalize_detailed_balance is False
# THEN
- model.divide_by_temperature = True
+ model.normalize_detailed_balance = True
# EXPECT
- assert model.divide_by_temperature is True
+ assert model.normalize_detailed_balance is True
- def test_divide_by_temperature_setter_raises_with_invalid_type(self, sample_model):
+ def test_normalize_detailed_balance_setter_raises_with_invalid_type(self, sample_model):
# WHEN / THEN / EXPECT
with pytest.raises(
TypeError,
- match='divide_by_temperature must be True or False',
+ match='normalize_detailed_balance must be True or False',
):
- sample_model.divide_by_temperature = 'invalid_value'
+ sample_model.normalize_detailed_balance = 'invalid_value'
+
+ def test_use_detailed_balance_setter(self, sample_model):
+ # WHEN
+ model = sample_model
+
+ # THEN
+ model.use_detailed_balance = False
+
+ # EXPECT
+ assert model.use_detailed_balance is False
+
+ # THEN
+ model.use_detailed_balance = True
+
+ # EXPECT
+ assert model.use_detailed_balance is True
+
+ def test_use_detailed_balance_setter_raises_with_invalid_type(self, sample_model):
+ # WHEN / THEN / EXPECT
+ with pytest.raises(
+ TypeError,
+ match='use_detailed_balance must be True or False',
+ ):
+ sample_model.use_detailed_balance = 'invalid_value'
+
+ def test_detailed_balance_settings_property(self, sample_model):
+ # WHEN
+ new_settings = DetailedBalanceSettings(
+ use_detailed_balance=False, normalize_detailed_balance=False
+ )
+
+ # THEN
+ sample_model.detailed_balance_settings = new_settings
+
+ # EXPECT
+ assert sample_model.detailed_balance_settings is new_settings
+ assert sample_model.use_detailed_balance is False
+ assert sample_model.normalize_detailed_balance is False
+
+ def test_detailed_balance_settings_setter_invalid(self, sample_model):
+ # WHEN / THEN / EXPECT
+ with pytest.raises(
+ TypeError,
+ match='detailed_balance_settings must be a DetailedBalanceSettings',
+ ):
+ sample_model.detailed_balance_settings = 'invalid_settings'
def test_evaluate_calls_dbf(self, sample_model):
# WHEN
@@ -325,7 +396,7 @@ def test_evaluate_calls_dbf(self, sample_model):
mock_dbf.assert_called_once_with(
energy=x,
temperature=sample_model.temperature,
- divide_by_temperature=sample_model.divide_by_temperature,
+ divide_by_temperature=sample_model.normalize_detailed_balance,
energy_unit=sample_model.unit,
)
@@ -337,6 +408,51 @@ def test_evaluate_calls_dbf(self, sample_model):
np.testing.assert_allclose(result[0], np.array([1.0, 2.0, 3.0]) * 10.0)
np.testing.assert_allclose(result[1], np.array([4.0, 5.0, 6.0]) * 10.0)
+ @pytest.mark.parametrize(
+ 'temperature, use_detailed_balance',
+ [
+ (None, True), # DB disabled because temperature is None
+ (300.0, False), # DB disabled explicitly
+ ],
+ ids=[
+ 'temperature_none',
+ 'use_detailed_balance_false',
+ ],
+ )
+ def test_evaluate_doesnt_call_dbf_when_disabled(
+ self, sample_model, temperature, use_detailed_balance
+ ):
+ # WHEN
+ x = np.array([0.0, 1.0, 2.0])
+
+ collection1 = Mock()
+ collection2 = Mock()
+
+ collection1.evaluate.return_value = np.array([1.0, 2.0, 3.0])
+ collection2.evaluate.return_value = np.array([4.0, 5.0, 6.0])
+
+ sample_model._component_collections = [collection1, collection2]
+
+ sample_model.temperature = temperature
+ sample_model.use_detailed_balance = use_detailed_balance
+
+ with patch('easydynamics.sample_model.sample_model.detailed_balance_factor') as mock_dbf:
+ mock_dbf.return_value = np.array([10.0, 10.0, 10.0]) # simplified DBF
+ # THEN
+ result = sample_model.evaluate(x)
+
+ # EXPECT
+ # Check that DBF was not called since detailed balance is disabled
+ mock_dbf.assert_not_called()
+
+ # Check that evaluate was called on each component
+ collection1.evaluate.assert_called_once_with(x)
+ collection2.evaluate.assert_called_once_with(x)
+
+ # Check that results were not modified by DBF
+ np.testing.assert_allclose(result[0], np.array([1.0, 2.0, 3.0]))
+ np.testing.assert_allclose(result[1], np.array([4.0, 5.0, 6.0]))
+
def test_generate_component_collections(self, sample_model):
# WHEN THEN
sample_model._generate_component_collections()
@@ -347,9 +463,9 @@ def test_generate_component_collections(self, sample_model):
assert isinstance(collection, ComponentCollection)
assert len(collection.components) == 3 # 3 components
assert collection.components[0].display_name == 'TestGaussian1'
- assert collection.components[0].area.value == 1.0
+ assert collection.components[0].area.value == pytest.approx(1.0)
assert collection.components[1].display_name == 'TestLorentzian1'
- assert collection.components[1].area.value == 2.0
+ assert collection.components[1].area.value == pytest.approx(2.0)
assert collection.components[2].display_name == 'Brownian diffusion'
assert isinstance(collection.components[2], Lorentzian)
@@ -389,4 +505,4 @@ def test_repr(self, sample_model):
assert 'components' in repr_str
assert 'diffusion_models' in repr_str
assert 'temperature' in repr_str
- assert 'divide_by_temperature' in repr_str
+ assert 'normalize_detailed_balance' in repr_str
diff --git a/tests/unit/easydynamics/settings/test_convolution_settings.py b/tests/unit/easydynamics/settings/test_convolution_settings.py
new file mode 100644
index 00000000..60e70bdf
--- /dev/null
+++ b/tests/unit/easydynamics/settings/test_convolution_settings.py
@@ -0,0 +1,237 @@
+# SPDX-FileCopyrightText: 2026 EasyScience contributors
+# SPDX-License-Identifier: BSD-3-Clause
+
+import pytest
+
+from easydynamics.settings.convolution_settings import ConvolutionSettings
+
+
+class TestConvolutionSettings:
+ @pytest.fixture
+ def default_convolution_settings(self):
+ return ConvolutionSettings()
+
+ def test_init(self, default_convolution_settings):
+ """
+ Test initialization of ConvolutionSettings with default
+ parameters.
+ """
+ # WHEN THEN EXPECT
+ assert isinstance(default_convolution_settings, ConvolutionSettings)
+ assert default_convolution_settings.upsample_factor == 5
+ assert default_convolution_settings.extension_factor == pytest.approx(0.2)
+ assert default_convolution_settings.convolution_plan_is_valid is False
+
+ def test_init_with_custom_parameters(self):
+ """
+ Test initialization of ConvolutionSettings with custom
+ parameters.
+ """
+ # WHEN
+ convolution_settings = ConvolutionSettings(
+ upsample_factor=10,
+ extension_factor=0.5,
+ )
+
+ # THEN EXPECT
+ assert convolution_settings.upsample_factor == 10
+ assert convolution_settings.extension_factor == pytest.approx(0.5)
+ assert convolution_settings.convolution_plan_is_valid is False
+
+ def test_init_with_None(self):
+ """
+ Test initialization of ConvolutionSettings with custom
+ parameters.
+ """
+ # WHEN
+ convolution_settings = ConvolutionSettings(
+ upsample_factor=None,
+ extension_factor=None,
+ )
+
+ # THEN EXPECT
+ assert convolution_settings.upsample_factor is None
+ assert convolution_settings.extension_factor is None
+ assert convolution_settings.convolution_plan_is_valid is False
+
+ @pytest.mark.parametrize(
+ 'invalid_input, expected_exception, match',
+ [
+ ({'extension_factor': '0.2'}, TypeError, 'must be a number'),
+ ({'extension_factor': -0.1}, ValueError, 'must be non-negative'),
+ ({'upsample_factor': '5'}, TypeError, 'must be a numerical value or None'),
+ ({'upsample_factor': 1.0}, ValueError, 'must be greater than 1'),
+ ({'upsample_factor': 0.5}, ValueError, 'must be greater than 1'),
+ ],
+ ids=[
+ 'extension_factor_not_numeric',
+ 'extension_factor_negative',
+ 'upsample_factor_not_numeric',
+ 'upsample_factor_equal_1',
+ 'upsample_factor_less_than_1',
+ ],
+ )
+ def test_init_raises_for_invalid_input(self, invalid_input, expected_exception, match):
+ """
+ Test that initialization raises appropriate exceptions for
+ invalid input parameters.
+ """
+ # WHEN THEN EXPECT
+ with pytest.raises(expected_exception, match=match):
+ ConvolutionSettings(**invalid_input)
+
+ @pytest.mark.parametrize(
+ 'value',
+ [2, 5.0, None],
+ ids=[
+ 'integer_valid',
+ 'float_valid',
+ 'none_valid',
+ ],
+ )
+ def test_upsample_factor_setter_valid(self, default_convolution_settings, value):
+ settings = default_convolution_settings
+
+ # WHEN
+ # Ensure it's True first so we can test the reset
+ settings.convolution_plan_is_valid = True
+
+ # THEN
+ settings.upsample_factor = value
+
+ # EXPECT
+ expected = pytest.approx(float(value)) if value is not None else None
+ assert settings.upsample_factor == expected
+ assert settings.convolution_plan_is_valid is False
+
+ @pytest.mark.parametrize(
+ 'value, expected_exception, match',
+ [
+ ('5', TypeError, 'must be a numerical value or None'),
+ (1.0, ValueError, 'must be greater than 1'),
+ (0.5, ValueError, 'must be greater than 1'),
+ ],
+ ids=[
+ 'not_numeric',
+ 'equal_1',
+ 'less_than_1',
+ ],
+ )
+ def test_upsample_factor_setter_invalid(
+ self,
+ default_convolution_settings,
+ value,
+ expected_exception,
+ match,
+ ):
+ # WHEN THEN EXPECT
+ with pytest.raises(expected_exception, match=match):
+ default_convolution_settings.upsample_factor = value
+
+ @pytest.mark.parametrize(
+ 'value',
+ [0.0, 0.2, 1, 5.5],
+ ids=[
+ 'zero',
+ 'typical_fraction',
+ 'integer',
+ 'float',
+ ],
+ )
+ def test_extension_factor_setter_valid(self, default_convolution_settings, value):
+
+ # WHEN
+ default_convolution_settings.convolution_plan_is_valid = True
+
+ # THEN
+ default_convolution_settings.extension_factor = value
+
+ # EXPECT
+ assert default_convolution_settings.extension_factor == pytest.approx(float(value))
+ assert default_convolution_settings.convolution_plan_is_valid is False
+
+ @pytest.mark.parametrize(
+ 'value, expected_exception, match',
+ [
+ ('0.2', TypeError, 'must be a number'),
+ (-0.1, ValueError, 'must be non-negative'),
+ ],
+ ids=[
+ 'not_numeric',
+ 'negative',
+ ],
+ )
+ def test_extension_factor_setter_invalid(
+ self,
+ default_convolution_settings,
+ value,
+ expected_exception,
+ match,
+ ):
+
+ # WHEN / THEN / EXPECT
+ with pytest.raises(expected_exception, match=match):
+ default_convolution_settings.extension_factor = value
+
+ @pytest.mark.parametrize(
+ 'value',
+ [True, False],
+ ids=[
+ 'true',
+ 'false',
+ ],
+ )
+ def test_convolution_plan_is_valid_setter_valid(
+ self,
+ default_convolution_settings,
+ value,
+ ):
+ # WHEN
+ default_convolution_settings.convolution_plan_is_valid = not value
+
+ # THEN
+ default_convolution_settings.convolution_plan_is_valid = value
+
+ # EXPECT
+ assert default_convolution_settings.convolution_plan_is_valid is value
+
+ @pytest.mark.parametrize(
+ 'value, expected_exception, match',
+ [
+ ('True', TypeError, 'must be True or False'),
+ (1, TypeError, 'must be True or False'),
+ (None, TypeError, 'must be True or False'),
+ ],
+ ids=[
+ 'string',
+ 'int',
+ 'none',
+ ],
+ )
+ def test_convolution_plan_is_valid_setter_invalid(
+ self,
+ default_convolution_settings,
+ value,
+ expected_exception,
+ match,
+ ):
+ # WHEN / THEN / EXPECT
+ with pytest.raises(expected_exception, match=match):
+ default_convolution_settings.convolution_plan_is_valid = value
+
+ def test_repr_default(self, default_convolution_settings):
+ # WHEN
+ repr_str = repr(default_convolution_settings)
+
+ # EXPECT
+ assert repr_str == ('ConvolutionSettings(upsample_factor=5.0, extension_factor=0.2)')
+
+ def test_repr_reflects_updated_values(self, default_convolution_settings):
+ # WHEN
+ default_convolution_settings.upsample_factor = 3
+ default_convolution_settings.extension_factor = 0.5
+
+ repr_str = repr(default_convolution_settings)
+
+ # EXPECT
+ assert repr_str == ('ConvolutionSettings(upsample_factor=3.0, extension_factor=0.5)')
diff --git a/tests/unit/easydynamics/settings/test_detailed_balance_settings.py b/tests/unit/easydynamics/settings/test_detailed_balance_settings.py
new file mode 100644
index 00000000..dba4d9d6
--- /dev/null
+++ b/tests/unit/easydynamics/settings/test_detailed_balance_settings.py
@@ -0,0 +1,131 @@
+# SPDX-FileCopyrightText: 2026 EasyScience contributors
+# SPDX-License-Identifier: BSD-3-Clause
+
+import pytest
+
+from easydynamics.settings.detailed_balance_settings import DetailedBalanceSettings
+
+
+class TestDetailedBalanceSettings:
+ @pytest.fixture
+ def default_detailed_balance_settings(self):
+ return DetailedBalanceSettings()
+
+ def test_init(self, default_detailed_balance_settings):
+ """
+ Test initialization of DetailedBalanceSettings with default
+ parameters.
+ """
+ # WHEN THEN EXPECT
+ assert isinstance(default_detailed_balance_settings, DetailedBalanceSettings)
+ assert default_detailed_balance_settings.use_detailed_balance is True
+ assert default_detailed_balance_settings.normalize_detailed_balance is True
+ assert default_detailed_balance_settings.display_name == 'DetailedBalanceSettings'
+
+ def test_init_with_custom_parameters(self):
+ """
+ Test initialization of DetailedBalanceSettings with custom
+ parameters.
+ """
+ # WHEN
+ detailed_balance_settings = DetailedBalanceSettings(
+ use_detailed_balance=False,
+ normalize_detailed_balance=False,
+ )
+
+ # THEN EXPECT
+ assert detailed_balance_settings.use_detailed_balance is False
+ assert detailed_balance_settings.normalize_detailed_balance is False
+ assert detailed_balance_settings.display_name == 'DetailedBalanceSettings'
+
+ @pytest.mark.parametrize(
+ 'invalid_input, expected_exception, match',
+ [
+ (
+ {'use_detailed_balance': 'not_a_boolean'},
+ TypeError,
+ 'must be True or False',
+ ),
+ (
+ {'normalize_detailed_balance': 'not_a_boolean'},
+ TypeError,
+ 'must be True or False',
+ ),
+ ],
+ ids=[
+ 'use_detailed_balance_not_boolean',
+ 'normalize_detailed_balance_not_boolean',
+ ],
+ )
+ def test_init_raises_for_invalid_input(self, invalid_input, expected_exception, match):
+ """
+ Test that initialization raises appropriate exceptions for
+ invalid input parameters.
+ """
+ # WHEN THEN EXPECT
+ with pytest.raises(expected_exception, match=match):
+ DetailedBalanceSettings(**invalid_input)
+
+ def test_setters_valid(self, default_detailed_balance_settings):
+
+ # WHEN
+ # Ensure it's True first so we can test the reset
+ assert default_detailed_balance_settings.use_detailed_balance is True
+ assert default_detailed_balance_settings.normalize_detailed_balance is True
+
+ # THEN
+ default_detailed_balance_settings.use_detailed_balance = False
+ default_detailed_balance_settings.normalize_detailed_balance = False
+
+ # EXPECT
+ assert default_detailed_balance_settings.use_detailed_balance is False
+ assert default_detailed_balance_settings.normalize_detailed_balance is False
+
+ @pytest.mark.parametrize(
+ 'value, expected_exception, match',
+ [
+ ('5', TypeError, 'must be True or False'),
+ (1, TypeError, 'must be True or False'),
+ (None, TypeError, 'must be True or False'),
+ ],
+ ids=[
+ 'string',
+ 'integer',
+ 'none',
+ ],
+ )
+ def test_setters_invalid(
+ self,
+ default_detailed_balance_settings,
+ value,
+ expected_exception,
+ match,
+ ):
+ # WHEN THEN EXPECT
+ with pytest.raises(expected_exception, match=match):
+ default_detailed_balance_settings.use_detailed_balance = value
+
+ # WHEN THEN EXPECT
+ with pytest.raises(expected_exception, match=match):
+ default_detailed_balance_settings.normalize_detailed_balance = value
+
+ def test_repr_default(self, default_detailed_balance_settings):
+ # WHEN
+ repr_str = repr(default_detailed_balance_settings)
+
+ # EXPECT
+ assert repr_str == (
+ 'DetailedBalanceSettings(use_detailed_balance=True, normalize_detailed_balance=True)'
+ )
+
+ def test_repr_reflects_updated_values(self, default_detailed_balance_settings):
+ # WHEN
+ default_detailed_balance_settings.use_detailed_balance = False
+ default_detailed_balance_settings.normalize_detailed_balance = False
+
+ repr_str = repr(default_detailed_balance_settings)
+
+ # EXPECT
+ assert repr_str == (
+ 'DetailedBalanceSettings(use_detailed_balance=False, normalize_detailed_balance=False)'
+ )
diff --git a/tests/unit/easydynamics/utils/test_detailed_balance.py b/tests/unit/easydynamics/utils/test_detailed_balance.py
index 7662dff3..bebf5407 100644
--- a/tests/unit/easydynamics/utils/test_detailed_balance.py
+++ b/tests/unit/easydynamics/utils/test_detailed_balance.py
@@ -21,7 +21,7 @@ def test_energy_unit_not_string_error(self):
T = 100
energy_unit = 5
# Then Expect
- with pytest.raises(TypeError, match='energy_unit must be a string.'):
+ with pytest.raises(TypeError, match=r'energy_unit must be a string.'):
detailed_balance_factor(energy, T, energy_unit=energy_unit)
@pytest.mark.parametrize('temperature_unit', [5, 5.0, {}, []])
@@ -30,7 +30,7 @@ def test_temperature_unit_not_string_error(self, temperature_unit):
energy = 2.0
T = 100
# Then Expect
- with pytest.raises(TypeError, match='temperature_unit must be a string.'):
+ with pytest.raises(TypeError, match=r'temperature_unit must be a string.'):
detailed_balance_factor(energy, T, temperature_unit=temperature_unit)
def test_divide_by_temperature_not_bool_error(self):
@@ -39,7 +39,7 @@ def test_divide_by_temperature_not_bool_error(self):
T = 100
divide_by_temperature = 'yes'
# Then Expect
- with pytest.raises(TypeError, match='divide_by_temperature must be True or False.'):
+ with pytest.raises(TypeError, match=r'divide_by_temperature must be True or False.'):
detailed_balance_factor(energy, T, divide_by_temperature=divide_by_temperature)
@pytest.mark.parametrize(
@@ -219,7 +219,7 @@ def test_energy_unit_warning(self):
# Then
with pytest.warns(
UserWarning,
- match='Input energy has unit µeV, but energy_unit was set to meV. Using µeV.',
+ match='Input energy has unit [µμ]eV, but energy_unit was set to meV. Using [µμ]eV.',
):
result = detailed_balance_factor(
energy=energy,
diff --git a/tests/unit/easydynamics/utils/test_utils.py b/tests/unit/easydynamics/utils/test_utils.py
index 7aa72a78..680d2a28 100644
--- a/tests/unit/easydynamics/utils/test_utils.py
+++ b/tests/unit/easydynamics/utils/test_utils.py
@@ -92,13 +92,13 @@ def test_validate_unit_valid(self, unit_input):
if unit_input is None:
assert unit is None
else:
- assert isinstance(unit, sc.Unit)
+ assert isinstance(unit, str)
def test_validate_unit_string_conversion(self):
- unit = _validate_unit('meV')
+ unit = _validate_unit(sc.Unit('meV'))
- assert isinstance(unit, sc.Unit)
- assert unit == sc.Unit('meV')
+ assert isinstance(unit, str)
+ assert unit == 'meV'
@pytest.mark.parametrize(
'unit_input',
diff --git a/tools/add_license_headers.py b/tools/add_license_headers.py
deleted file mode 100644
index 28febde7..00000000
--- a/tools/add_license_headers.py
+++ /dev/null
@@ -1,151 +0,0 @@
-# SPDX-FileCopyrightText: 2026 EasyScience contributors
-# SPDX-License-Identifier: BSD-3-Clause
-"""Add SPDX headers to Python files.
-
-- SPDX-FileCopyrightText with the license holder name and organization
- URL from ``pyproject.toml`` as well as the file's creation year.
-- SPDX-License-Identifier is taken from the project license value in
- ``pyproject.toml``.
-"""
-
-from __future__ import annotations
-
-import argparse
-import tomllib
-from datetime import datetime
-from pathlib import Path
-from typing import Optional
-from typing import Union
-
-from git import Repo
-from spdx_headers.core import find_repository_root
-from spdx_headers.core import get_copyright_info
-from spdx_headers.data import load_license_data
-from spdx_headers.operations import add_header_to_single_file
-
-LICENSE_DATABASE = load_license_data()
-
-
-def load_pyproject(repo_path: Union[str, Path]) -> dict:
- """Load and return parsed ``pyproject.toml`` data for the
- repository.
- """
- repo_root = find_repository_root(repo_path)
- pyproject_path = repo_root / 'pyproject.toml'
-
- with open(pyproject_path, 'rb') as file_handle:
- return tomllib.load(file_handle)
-
-
-def get_file_creation_year(file_path: Union[str, Path]) -> str:
- """Return the year the file was first added to Git history.
-
- If the year cannot be determined, fall back to the current year.
- """
- file_path = Path(file_path)
-
- repo = Repo(file_path, search_parent_directories=True)
- root = Path(repo.working_tree_dir).resolve()
- rel_path = file_path.resolve().relative_to(root)
-
- rel_path_git = rel_path.as_posix() # IMPORTANT for git pathspec
-
- # Get the year when the file was first added to Git history.
- # NOTE: Do not combine `--reverse` with `--max-count=1` here, as it can
- # yield an empty result with some Git versions. Instead, get the full
- # filtered output and take the first line.
- log_output = repo.git.log(
- '--follow',
- '--diff-filter=A',
- '--reverse',
- '--format=%ad',
- '--date=format:%Y',
- '--',
- rel_path_git,
- ).strip()
-
- year = log_output.splitlines()[0].strip() if log_output else ''
-
- return year or str(datetime.now().year)
-
-
-def get_org_url(repo_path: Union[str, Path]) -> str:
- """Return the organization URL derived from the repository source
- URL.
- """
- pyproject_data = load_pyproject(repo_path)
- repo_url = pyproject_data['project']['urls']['Source Code']
- return repo_url.rsplit('/', 1)[0]
-
-
-def get_project_license(repo_path: Union[str, Path]) -> str:
- """Return the project license value from ``pyproject.toml``."""
- pyproject_data = load_pyproject(repo_path)
- return pyproject_data['project']['license']
-
-
-def get_copyright_holder(repo_path: Union[str, Path]) -> str:
- """Return the repository copyright holder name."""
- _, name, _ = get_copyright_info(repo_path)
- return name
-
-
-def add_spdx_header(
- target_file: Union[str, Path],
- *,
- license_key: str,
- copyright_holder: str,
- org_url: str,
-) -> None:
- """Add SPDX headers."""
- year = get_file_creation_year(target_file)
-
- add_header_to_single_file(
- filepath=target_file,
- license_key=license_key,
- license_data=LICENSE_DATABASE,
- year=year,
- name=copyright_holder,
- email=org_url,
- )
-
-
-def build_parser() -> argparse.ArgumentParser:
- parser = argparse.ArgumentParser(
- description='Add SPDX headers to Python files under the given paths.',
- )
- parser.add_argument(
- 'paths',
- nargs='+',
- help='Relative paths to scan (e.g. src tests)',
- )
- return parser
-
-
-def main(argv: Optional[list[str]] = None) -> int:
- parser = build_parser()
- args = parser.parse_args(argv)
-
- repo_path = Path('.').resolve()
- license_key = get_project_license(repo_path)
- copyright_holder = get_copyright_holder(repo_path)
- org_url = get_org_url(repo_path)
-
- for base_dir in args.paths:
- base_path = Path(base_dir)
- if not base_path.exists():
- parser.error(f'Path does not exist: {base_dir}')
-
- for py_file in base_path.rglob('*.py'):
- add_spdx_header(
- py_file,
- license_key=license_key,
- copyright_holder=copyright_holder,
- org_url=org_url,
- )
-
- return 0
-
-
-if __name__ == '__main__':
- raise SystemExit(main())
diff --git a/tools/check_license_headers.py b/tools/check_license_headers.py
deleted file mode 100644
index c8a4df21..00000000
--- a/tools/check_license_headers.py
+++ /dev/null
@@ -1,45 +0,0 @@
-# SPDX-FileCopyrightText: 2026 EasyScience contributors
-# SPDX-License-Identifier: BSD-3-Clause
-"""Check SPDX headers in Python files."""
-
-from __future__ import annotations
-
-import argparse
-from pathlib import Path
-from typing import Optional
-
-from spdx_headers.operations import check_headers
-
-
-def build_parser() -> argparse.ArgumentParser:
- parser = argparse.ArgumentParser(
- description='Check SPDX headers in Python files under the given paths.',
- )
- parser.add_argument(
- 'paths',
- nargs='+',
- help='Relative paths to scan (e.g. src tests)',
- )
- return parser
-
-
-def main(argv: Optional[list[str]] = None) -> int:
- parser = build_parser()
- args = parser.parse_args(argv)
-
- exit_codes = []
-
- for base_dir in args.paths:
- base_path = Path(base_dir)
- if not base_path.exists():
- parser.error(f'Path does not exist: {base_dir}')
-
- print('=' * 50)
- print(f'Checking SPDX headers in: {base_dir}')
- exit_codes.append(check_headers(base_dir))
-
- return 0 if all(code == 0 for code in exit_codes) else 1
-
-
-if __name__ == '__main__':
- raise SystemExit(main())
diff --git a/tools/license_headers.py b/tools/license_headers.py
new file mode 100644
index 00000000..47d23524
--- /dev/null
+++ b/tools/license_headers.py
@@ -0,0 +1,315 @@
+# SPDX-FileCopyrightText: 2026 EasyScience contributors
+# SPDX-License-Identifier: BSD-3-Clause
+"""Add, remove, or check SPDX headers in Python files."""
+
+from __future__ import annotations
+
+import argparse
+import fnmatch
+import tomllib
+from datetime import datetime
+from pathlib import Path
+from typing import Any
+from typing import Optional
+from typing import Union
+
+from git import Repo
+from spdx_headers.core import find_repository_root
+from spdx_headers.core import get_copyright_info
+from spdx_headers.core import has_spdx_header
+from spdx_headers.data import load_license_data
+from spdx_headers.operations import add_header_to_single_file
+from spdx_headers.operations import remove_header_from_single_file
+
+LICENSE_DATABASE = load_license_data()
+
+
+def load_pyproject(repo_path: Union[str, Path]) -> dict[str, Any]:
+ """Load and return parsed ``pyproject.toml`` data for the repository."""
+ repo_root = find_repository_root(repo_path)
+ pyproject_path = repo_root / 'pyproject.toml'
+
+ with pyproject_path.open('rb') as file_handle:
+ return tomllib.load(file_handle)
+
+
+def get_pyproject_value(pyproject_data: dict[str, Any], dotted_key: str) -> Any:
+ """Return a nested ``pyproject.toml`` value from a dotted key."""
+ value: Any = pyproject_data
+ for part in dotted_key.split('.'):
+ if not isinstance(value, dict) or part not in value:
+ raise KeyError(dotted_key)
+ value = value[part]
+ return value
+
+
+def normalize_pattern(pattern: str) -> str:
+ """Normalize an exclude pattern to a POSIX-style relative path."""
+ normalized = Path(pattern).as_posix()
+ if normalized.startswith('./'):
+ normalized = normalized[2:]
+ return normalized.rstrip('/')
+
+
+def get_exclude_patterns(
+ repo_path: Union[str, Path],
+ exclude_values: list[str],
+ exclude_from_pyproject_toml: Optional[str],
+) -> list[str]:
+ """Return normalized exclude patterns from CLI and ``pyproject.toml``."""
+ pyproject_data = load_pyproject(repo_path)
+ patterns: list[str] = []
+
+ if exclude_from_pyproject_toml:
+ value = get_pyproject_value(pyproject_data, exclude_from_pyproject_toml)
+ if not isinstance(value, list) or not all(isinstance(item, str) for item in value):
+ raise ValueError(
+ f'{exclude_from_pyproject_toml} in pyproject.toml must be a list of strings.',
+ )
+ patterns.extend(value)
+
+ for item in exclude_values:
+ try:
+ value = get_pyproject_value(pyproject_data, item)
+ except KeyError:
+ patterns.append(item)
+ continue
+
+ if not isinstance(value, list) or not all(isinstance(entry, str) for entry in value):
+ raise ValueError(f'{item} in pyproject.toml must be a list of strings.')
+ patterns.extend(value)
+
+ normalized_patterns: list[str] = []
+ seen: set[str] = set()
+ for pattern in patterns:
+ normalized = normalize_pattern(pattern)
+ if normalized and normalized not in seen:
+ normalized_patterns.append(normalized)
+ seen.add(normalized)
+
+ return normalized_patterns
+
+
+def get_file_creation_year(file_path: Union[str, Path]) -> str:
+ """Return the year the file was first added to Git history.
+
+ If the year cannot be determined, fall back to the current year.
+ """
+ file_path = Path(file_path)
+
+ repo = Repo(file_path, search_parent_directories=True)
+ root = Path(repo.working_tree_dir).resolve()
+ rel_path = file_path.resolve().relative_to(root)
+
+ rel_path_git = rel_path.as_posix()
+
+ log_output = repo.git.log(
+ '--follow',
+ '--diff-filter=A',
+ '--reverse',
+ '--format=%ad',
+ '--date=format:%Y',
+ '--',
+ rel_path_git,
+ ).strip()
+
+ year = log_output.splitlines()[0].strip() if log_output else ''
+
+ return year or str(datetime.now().year)
+
+
+def get_org_url(repo_path: Union[str, Path]) -> str:
+ """Return the organization URL derived from the repository source URL."""
+ pyproject_data = load_pyproject(repo_path)
+ repo_url = pyproject_data['project']['urls']['Source Code']
+ return repo_url.rsplit('/', 1)[0]
+
+
+def get_project_license(repo_path: Union[str, Path]) -> str:
+ """Return the project license value from ``pyproject.toml``."""
+ pyproject_data = load_pyproject(repo_path)
+ return pyproject_data['project']['license']
+
+
+def get_copyright_holder(repo_path: Union[str, Path]) -> str:
+ """Return the repository copyright holder name."""
+ _, name, _ = get_copyright_info(repo_path)
+ return name
+
+
+def add_spdx_header(
+ target_file: Union[str, Path],
+ *,
+ license_key: str,
+ copyright_holder: str,
+ org_url: str,
+) -> None:
+ """Add SPDX headers to one file."""
+ year = get_file_creation_year(target_file)
+
+ add_header_to_single_file(
+ filepath=target_file,
+ license_key=license_key,
+ license_data=LICENSE_DATABASE,
+ year=year,
+ name=copyright_holder,
+ email=org_url,
+ )
+
+
+def is_excluded(relative_path: str, exclude_patterns: list[str]) -> bool:
+ """Return whether a relative path should be excluded."""
+ for pattern in exclude_patterns:
+ if fnmatch.fnmatch(relative_path, pattern):
+ return True
+ if relative_path == pattern:
+ return True
+ if relative_path.startswith(f'{pattern}/'):
+ return True
+ return False
+
+
+def iter_python_files(
+ paths: list[str],
+ *,
+ repo_root: Path,
+ exclude_patterns: list[str],
+ parser: argparse.ArgumentParser,
+) -> list[Path]:
+ """Collect Python files under the given paths after exclusions."""
+ files: list[Path] = []
+ seen: set[Path] = set()
+
+ for base_dir in paths:
+ base_path = Path(base_dir)
+ if not base_path.exists():
+ parser.error(f'Path does not exist: {base_dir}')
+
+ if base_path.is_file():
+ candidates = [base_path] if base_path.suffix == '.py' else []
+ else:
+ candidates = sorted(base_path.rglob('*.py'))
+
+ for py_file in candidates:
+ resolved = py_file.resolve()
+ try:
+ relative_path = resolved.relative_to(repo_root).as_posix()
+ except ValueError:
+ relative_path = py_file.as_posix()
+
+ if is_excluded(relative_path, exclude_patterns):
+ continue
+
+ if resolved not in seen:
+ files.append(py_file)
+ seen.add(resolved)
+
+ return files
+
+
+def run_add(
+ files: list[Path],
+ *,
+ license_key: str,
+ copyright_holder: str,
+ org_url: str,
+) -> int:
+ """Add SPDX headers to all selected files."""
+ for py_file in files:
+ add_spdx_header(
+ py_file,
+ license_key=license_key,
+ copyright_holder=copyright_holder,
+ org_url=org_url,
+ )
+ return 0
+
+
+def run_remove(files: list[Path]) -> int:
+ """Remove SPDX headers from all selected files."""
+ for py_file in files:
+ remove_header_from_single_file(py_file)
+ return 0
+
+
+def run_check(files: list[Path]) -> int:
+ """Check SPDX headers in all selected files."""
+ missing_files = [py_file for py_file in files if not has_spdx_header(py_file)]
+
+ if not missing_files:
+ print('✓ All Python files have valid SPDX headers.')
+ return 0
+
+ print('✗ The following files are missing SPDX headers:')
+ for py_file in missing_files:
+ print(f' - {py_file.as_posix()}')
+ print(f'\nFound {len(missing_files)} files without SPDX headers.')
+ return 1
+
+
+def build_parser() -> argparse.ArgumentParser:
+ """Build the CLI argument parser."""
+ parser = argparse.ArgumentParser(
+ description='Add, remove, or check SPDX headers in Python files.',
+ )
+ subparsers = parser.add_subparsers(dest='command', required=True)
+
+ for command_name in ('check', 'remove', 'add'):
+ command_parser = subparsers.add_parser(command_name)
+ command_parser.add_argument(
+ 'paths',
+ nargs='+',
+ help='Relative paths to scan (e.g. src tests)',
+ )
+ command_parser.add_argument(
+ '--exclude',
+ nargs='*',
+ default=[],
+ help='Exclude paths, glob patterns, or pyproject dotted keys.',
+ )
+ command_parser.add_argument(
+ '--exclude-from-pyproject-toml',
+ help='Read exclude patterns from a dotted key in pyproject.toml.',
+ )
+
+ return parser
+
+
+def main(argv: Optional[list[str]] = None) -> int:
+ """Run the SPDX header CLI."""
+ parser = build_parser()
+ args = parser.parse_args(argv)
+
+ repo_path = Path('.').resolve()
+ repo_root = find_repository_root(repo_path).resolve()
+ exclude_patterns = get_exclude_patterns(
+ repo_path,
+ args.exclude,
+ args.exclude_from_pyproject_toml,
+ )
+ files = iter_python_files(
+ args.paths,
+ repo_root=repo_root,
+ exclude_patterns=exclude_patterns,
+ parser=parser,
+ )
+
+ if args.command == 'check':
+ return run_check(files)
+
+ if args.command == 'remove':
+ return run_remove(files)
+
+ license_key = get_project_license(repo_path)
+ copyright_holder = get_copyright_holder(repo_path)
+ org_url = get_org_url(repo_path)
+ return run_add(
+ files,
+ license_key=license_key,
+ copyright_holder=copyright_holder,
+ org_url=org_url,
+ )
+
+
+if __name__ == '__main__':
+ raise SystemExit(main())
diff --git a/tools/remove_license_headers.py b/tools/remove_license_headers.py
deleted file mode 100644
index f5d09da5..00000000
--- a/tools/remove_license_headers.py
+++ /dev/null
@@ -1,41 +0,0 @@
-# SPDX-FileCopyrightText: 2026 EasyScience contributors
-# SPDX-License-Identifier: BSD-3-Clause
-"""Remove SPDX headers from Python files."""
-
-from __future__ import annotations
-
-import argparse
-from pathlib import Path
-from typing import Optional
-
-from spdx_headers.operations import remove_header_from_py_files
-
-
-def build_parser() -> argparse.ArgumentParser:
- parser = argparse.ArgumentParser(
- description='Remove SPDX headers from Python files under the given paths.',
- )
- parser.add_argument(
- 'paths',
- nargs='+',
- help='Relative paths to scan (e.g. src tests)',
- )
- return parser
-
-
-def main(argv: Optional[list[str]] = None) -> int:
- parser = build_parser()
- args = parser.parse_args(argv)
-
- for base_dir in args.paths:
- base_path = Path(base_dir)
- if not base_path.exists():
- parser.error(f'Path does not exist: {base_dir}')
-
- remove_header_from_py_files(base_dir)
-
- return 0
-
-
-if __name__ == '__main__':
- raise SystemExit(main())