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add documentation
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‎.github/workflows/publish-to-test-pypi.yml

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name: Publish Python 🐍 distributions 📦 to PyPI and TestPyPI
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on: push
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jobs:
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build-n-publish:
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name: Build and publish Python 🐍 distributions 📦 to PyPI and TestPyPI
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@main
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- name: Set up Python 3.8
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uses: actions/setup-python@v3
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with:
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python-version: "3.8"
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- name: Install pypa/build
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run: >-
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python -m
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pip install
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build
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--user
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- name: Build a binary wheel and a source tarball
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run: >-
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python -m
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build
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--sdist
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--wheel
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--outdir dist/
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.
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- name: Publish distribution 📦 to PyPI
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if: startsWith(github.ref, 'refs/tags')
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uses: pypa/gh-action-pypi-publish@release/v1
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with:
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password: ${{ secrets.PYPI_API_TOKEN }}

‎.gitignore

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paper_psf
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*.pdf
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*.png
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paper/jats
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paper/jats
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build

‎docs/Makefile

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# Minimal makefile for Sphinx documentation
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#
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# You can set these variables from the command line, and also
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# from the environment for the first two.
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SPHINXOPTS ?=
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SPHINXBUILD ?= sphinx-build
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SOURCEDIR = source
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BUILDDIR = build
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# Put it first so that "make" without argument is like "make help".
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help:
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@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
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.PHONY: help Makefile
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# Catch-all target: route all unknown targets to Sphinx using the new
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# "make mode" option. $(O) is meant as a shortcut for $(SPHINXOPTS).
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%: Makefile
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@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)

‎docs/make.bat

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@ECHO OFF
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pushd %~dp0
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REM Command file for Sphinx documentation
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if "%SPHINXBUILD%" == "" (
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set SPHINXBUILD=sphinx-build
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)
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set SOURCEDIR=source
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set BUILDDIR=build
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if "%1" == "" goto help
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%SPHINXBUILD% >NUL 2>NUL
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if errorlevel 9009 (
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echo.
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echo.The 'sphinx-build' command was not found. Make sure you have Sphinx
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echo.installed, then set the SPHINXBUILD environment variable to point
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echo.to the full path of the 'sphinx-build' executable. Alternatively you
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echo.may add the Sphinx directory to PATH.
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echo.
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echo.If you don't have Sphinx installed, grab it from
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echo.http://sphinx-doc.org/
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exit /b 1
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)
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%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
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goto end
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:help
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%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
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:end
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popd

‎docs/source/_static/css/custom.css

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html {
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--pst-font-size-base: 22px;
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}

‎docs/source/conf.py

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# Configuration file for the Sphinx documentation builder.
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#
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# This file only contains a selection of the most common options. For a full
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# list see the documentation:
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# https://www.sphinx-doc.org/en/master/usage/configuration.html
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# -- Path setup --------------------------------------------------------------
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# If extensions (or modules to document with autodoc) are in another directory,
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# add these directories to sys.path here. If the directory is relative to the
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# documentation root, use os.path.abspath to make it absolute, like shown here.
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#
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import os
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import sys
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import toml
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sys.path.insert(0, os.path.abspath('../../src'))
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# -- Project information -----------------------------------------------------
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project = 'SPECTPSFToolbox'
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copyright = '2024, Luke Polson'
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author = 'Luke Polson'
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# The full version, including alpha/beta/rc tags
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with open('../../pyproject.toml', 'r') as f:
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release = toml.load(f)['project']['version']
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# -- General configuration ---------------------------------------------------
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# Add any Sphinx extension module names here, as strings. They can be
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# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
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# ones.
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extensions = [
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"myst_parser",
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"sphinx.ext.autosectionlabel",
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"sphinx.ext.autodoc",
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'sphinx.ext.viewcode',
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"sphinx.ext.napoleon",
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"sphinx_design",
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"nbsphinx",
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"autoapi.extension",
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"IPython.sphinxext.ipython_console_highlighting"
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]
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# Where to autogen API
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autoapi_dirs = ['../../src/spectpsftoolbox']
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autoapi_options = [ 'members', 'undoc-members', 'private-members', 'show-inheritance', 'show-module-summary', 'special-members', 'imported-members', 'recursive']
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autoapi_template_dir = "_templates/autoapi"
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# Add any paths that contain templates here, relative to this directory.
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templates_path = ['_templates']
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# List of patterns, relative to source directory, that match files and
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# directories to ignore when looking for source files.
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# This pattern also affects html_static_path and html_extra_path.
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exclude_patterns = []
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# -- Options for HTML output -------------------------------------------------
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# The theme to use for HTML and HTML Help pages. See the documentation for
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# a list of builtin themes.
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#
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html_theme = 'pydata_sphinx_theme'
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#html_logo = 'images/PT1.png'
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# Add any paths that contain custom static files (such as style sheets) here,
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# relative to this directory. They are copied after the builtin static files,
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# so a file named "default.css" will overwrite the builtin "default.css".
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html_static_path = ['_static']
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html_css_files = [
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'css/custom.css',
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]
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# typehints
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autodoc_typehints = "description"
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autodoc_inherit_docstrings=True
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# Add link to github
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html_theme_options = {
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"icon_links": [
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{
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"name": "GitHub",
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"url": "https://github.com/lukepolson/SPECTPSFToolbox",
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"icon": "fa-brands fa-github",
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"type": "fontawesome",
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},
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],
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'fixed_sidebar': True,
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'sidebar_width': '220px',
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}
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linkcheck_anchors = False

‎docs/source/index.rst

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.. SPECTPSFToolbox documentation master file, created by
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sphinx-quickstart on Fri Aug 2 21:56:39 2024.
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You can adapt this file completely to your liking, but it should at least
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contain the root `toctree` directive.
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SPECTPSFToolbox Documentation
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===========================================
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The ``SPECTPSFToolbox`` is a collection of python functions and classes that can be used for modeling the point spread functions (PSFs) of gamma cameras. The PSF models developed by the toolbox can be saved and used in `PyTomography <https://pytomography.readthedocs.io/en/latest/>`_ for SPECT image reconstruction.
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In traditional SPECT reconstruction, only the geometric component of the PSF is considered; this library provides a means for modeling the septal scatter and septal penetration components, permitting more accurate image reconstruction when these components are significant.
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.. grid:: 1 3 3 3
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:gutter: 2
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.. grid-item-card:: Tutorials
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:link: tutorials
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:link-type: doc
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:link-alt: Tutorials
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:text-align: center
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:material-outlined:`psychology;8em;sd-text-secondary`
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These tutorials show how to construct operators, fit them to real/Monte Carlo PSF data, and use them in image reconstruction.
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.. grid-item-card:: API Reference
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:link: autoapi/index
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:link-type: doc
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:link-alt: API
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:text-align: center
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:material-outlined:`computer;8em;sd-text-secondary`
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View the application programming interface of the library
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.. grid-item-card:: Get Help
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:text-align: center
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:material-outlined:`live_help;8em;sd-text-secondary`
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.. button-link:: https://github.com/lukepolson/SPECTPSFToolbox/issues
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:shadow:
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:expand:
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:color: warning
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**Report an issue**
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.. button-link:: https://pytomography.discourse.group/
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:shadow:
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:expand:
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:color: warning
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**Ask questions on PyTomography discourse**

‎docs/source/tutorials.rst

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.. _tutorial-index:
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************************
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Tutorials
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************************
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The tutorials use data that can be downloaded `here <https://drive.google.com/drive/folders/1dUBC1EbUgEH-Cug-oWIS7Yy_tpAqhe4j?usp=sharing>`_.
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.. grid:: 1 2 4 4
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:gutter: 2
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.. grid-item-card:: 1: Kernel1D
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:link: tutorials/1_kernel1d_intro
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:link-type: doc
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:link-alt: Tutorial 1
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:text-align: center
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:material-outlined:`psychology;4em;sd-text-secondary`
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.. grid-item-card:: 2: Kernel2D
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:link: tutorials/2_kernel2d_intro
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:link-type: doc
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:link-alt: Tutorial 2
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:text-align: center
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:material-outlined:`psychology;4em;sd-text-secondary`
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.. grid-item-card:: 3: Operators
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:link: tutorials/3_operators
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:link-type: doc
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:link-alt: Tutorial 3
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:text-align: center
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:material-outlined:`psychology;4em;sd-text-secondary`
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.. grid-item-card:: 4: Optimization Intro
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:link: tutorials/4_optimization_intro
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:link-type: doc
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:link-alt: Tutorial 4
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:text-align: center
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:material-outlined:`psychology;4em;sd-text-secondary`
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.. grid-item-card:: 5: Optimization Ac225
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:link: tutorials/5_optimization_ac225
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:link-type: doc
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:link-alt: Tutorial 5
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:text-align: center
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:material-outlined:`psychology;4em;sd-text-secondary`
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.. grid-item-card:: 6: NearestKernel Ac225
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:link: tutorials/6_nearestkernel_ac225
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:link-type: doc
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:link-alt: Tutorial 6
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:text-align: center
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:material-outlined:`psychology;4em;sd-text-secondary`
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.. grid-item-card:: 7: Ac225 Reconstruction
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:link: tutorials/7_pytomography_ac225_recon
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:link-type: doc
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:link-alt: Tutorial 7
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:text-align: center
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:material-outlined:`psychology;4em;sd-text-secondary`
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.. grid-item-card:: 8: Lu177 Low Energy Collimator
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:link: tutorials/8_pytomography_lu177_le_recon
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:link-type: doc
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:link-alt: Tutorial 8
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:text-align: center
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:material-outlined:`psychology;4em;sd-text-secondary`
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.. grid-item-card:: 9: Lu177 Medium Energy Collimator
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:link: tutorials/9_lu177_me_modeling_and_recon
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:link-type: doc
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:link-alt: Tutorial 9
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:text-align: center
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:material-outlined:`psychology;4em;sd-text-secondary`

‎tutorials/1_kernel1d_intro.ipynb ‎docs/source/tutorials/1_kernel1d_intro.ipynb

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‎tutorials/2_kernel2d_intro.ipynb ‎docs/source/tutorials/2_kernel2d_intro.ipynb

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‎tutorials/3_operators.ipynb ‎docs/source/tutorials/3_operators.ipynb

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‎tutorials/4_optimization_intro.ipynb ‎docs/source/tutorials/4_optimization_intro.ipynb

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‎tutorials/5_optimization_ac225.ipynb ‎docs/source/tutorials/5_optimization_ac225.ipynb

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‎tutorials/6_nearestkernel_ac225.ipynb ‎docs/source/tutorials/6_nearestkernel_ac225.ipynb

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‎tutorials/7_pytomography_ac225recon.ipynb ‎docs/source/tutorials/7_pytomography_ac225recon.ipynb

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‎tutorials/8_pytomography_lu177_le_recon.ipynb ‎docs/source/tutorials/8_pytomography_lu177_le_recon.ipynb

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‎tutorials/9_lu177_me_modeling_and_recon.ipynb ‎docs/source/tutorials/9_lu177_me_modeling_and_recon.ipynb

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‎tutorials/paper_plots.ipynb ‎docs/source/tutorials/paper_plots.ipynb

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‎tutorials/sample_simind_script/positions.txt ‎docs/source/tutorials/sample_simind_script/positions.txt

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‎tutorials/sample_simind_script/run_multi_lu177.sh ‎docs/source/tutorials/sample_simind_script/run_multi_lu177.sh

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‎tutorials/sample_simind_script/simind128_shift.smc ‎docs/source/tutorials/sample_simind_script/simind128_shift.smc

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