Kidney and visualization changes

.github/workflows/ci.yml

@@ -0,0 +1,31 @@
+name: CI
+
+on:
+  pull_request:
+
+jobs:
+  lint-and-test:
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ["3.10", "3.11"]
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install -e ".[dev,test]"
+
+      - name: Run pre-commit
+        run: pre-commit run --all-files
+
+      - name: Run pytest
+        run: pytest

.github/workflows/test_pypi.yml

@@ -0,0 +1,39 @@
+name: Test PyPI
+
+on:
+  push:
+    branches:
+      - documentation
+  pull_request:
+    branches:
+      - documentation
+
+jobs:
+  build-n-publish:
+    name: Build and publish Python 🐍 distributions 📦 to PyPI and TestPyPI
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@main
+    - name: Set up Python 3.8
+      uses: actions/setup-python@v3
+      with:
+        python-version: "3.8"
+    - name: Install pypa/build
+      run: >-
+        python -m
+        pip install
+        build
+        --user
+    - name: Build a binary wheel and a source tarball
+      run: >-
+        python -m
+        build
+        --sdist
+        --wheel
+        --outdir dist/
+        .
+    - name: Publish distribution 📦 to PyPI
+      if: startsWith(github.ref, 'refs/tags')
+      uses: pypa/gh-action-pypi-publish@release/v1
+      with:
+        password: ${{ secrets.PYPI_API_TOKEN }}

.gitignore

@@ -1,3 +1,4 @@
+
 # Byte-compiled / optimized / DLL files
 __pycache__/
 *.py[cod]
@@ -127,3 +128,13 @@ dmypy.json
 
 # Pyre type checker
 .pyre/
+
+
+# Other
+Notebooks
+xcatPhantom
+pytheranostics/local
+pytheranostics/.vscode
+
+pytheranostics/data/s-values
+pytheranostics/data/ICRP_phantom_masses

.pre-commit-config.yaml

@@ -0,0 +1,58 @@
+repos:
+  - repo: https://github.com/psf/black
+    rev: 25.1.0
+    hooks:
+      - id: black
+        files: '^(pytheranostics/|tests/)|^[^/]+\.py$'
+
+  - repo: https://github.com/pre-commit/mirrors-isort
+    rev: v5.10.1
+    hooks:
+      - id: isort
+        args: ["--profile", "black"]
+        files: '^(pytheranostics/|tests/)|^[^/]+\.py$'
+
+  - repo: https://github.com/PyCQA/flake8
+    rev: 7.3.0
+    hooks:
+      - id: flake8
+        files: '^(pytheranostics/|tests/)|^[^/]+\.py$'
+
+  - repo: https://github.com/PyCQA/pydocstyle
+    rev: 6.3.0
+    hooks:
+      - id: pydocstyle
+        files: '^pytheranostics/.*\.py$'
+        args: ["--convention=numpy"]
+        additional_dependencies: ["tomli"]  # For reading pyproject.toml config
+
+  # Temporarily disabled - mypy follows imports to legacy code with type issues
+  # - repo: https://github.com/pre-commit/mirrors-mypy
+  #   rev: v1.16.1
+  #   hooks:
+  #     - id: mypy
+  #       files: '^(tests/).*\.py$'
+  #       additional_dependencies: [pandas-stubs>=2.0.0, types-requests]
+
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v5.0.0
+    hooks:
+      - id: check-yaml
+      - id: end-of-file-fixer
+        files: '^(pytheranostics/|tests/)|^[^/]+\.(py|md|yml|yaml|toml)$'
+      - id: trailing-whitespace
+        files: '^(pytheranostics/|tests/)|^[^/]+\.(py|md|yml|yaml|toml)$'
+      - id: check-added-large-files
+        args: ['--maxkb=1000']
+
+  - repo: local
+    hooks:
+      - id: pytest-smoke
+        name: pytest (smoke tests only)
+        entry: python
+        language: python
+        args: ["-m", "pytest", "-m", "smoke", "--tb=short"]
+        pass_filenames: false
+        stages: [pre-commit]
+        # NOTE: Keep these dependencies in sync with pyproject.toml [project.dependencies]
+        additional_dependencies: ["pytest>=7.0", "numpy", "matplotlib", "pandas", "pydicom", "openpyxl", "rt-utils", "scikit-image", "simpleitk", "lmfit"]

.readthedocs.yaml

@@ -0,0 +1,35 @@
+# .readthedocs.yaml
+# Read the Docs configuration file
+# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
+
+# Required
+version: 2
+
+# Set the OS, Python version and other tools you might need
+build:
+  os: ubuntu-22.04
+  tools:
+    python: "3.12"
+    # You can also specify other tool versions:
+    # nodejs: "19"
+    # rust: "1.64"
+    # golang: "1.19"
+
+# Build documentation in the "docs/" directory with Sphinx
+sphinx:
+  configuration: docs/source/conf.py
+
+# Optionally build your docs in additional formats such as PDF and ePub
+# formats:
+#    - pdf
+#    - epub
+
+# Optional but recommended, declare the Python requirements required
+# to build your documentation
+# See https://docs.readthedocs.io/en/stable/guides/reproducible-builds.html
+python:
+   install:
+    - method: pip
+      path: .
+      extra_requirements:
+        - docs

.vscode/launch.json

@@ -0,0 +1,15 @@
+{
+    // Use IntelliSense to learn about possible attributes.
+    // Hover to view descriptions of existing attributes.
+    // For more information, visit: https://go.microsoft.com/fwlink/?linkid=830387
+    "version": "0.2.0",
+    "configurations": [
+        {
+            "name": "Python: Current File",
+            "type": "python",
+            "request": "launch",
+            "program": "${file}",
+            "console": "integratedTerminal"
+        }
+    ]
+}

.vscode/settings.json

@@ -0,0 +1,5 @@
+{
+    "python.defaultInterpreterPath": "./.venv/Scripts/python.exe",
+    "python.terminal.activateEnvironment": true,
+    "git.useIntegratedTerminal": true
+}

CHANGES.md

@@ -0,0 +1,27 @@
+# Changelog
+
+All notable changes to this project will be documented in this file.
+
+The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
+and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
+
+## [0.1.0] - 2024-03-19
+
+### Added
+- Initial release of PyTheranostics
+- Basic package structure and modules
+- Core functionality for nuclear medicine image processing
+- Dosimetry calculation tools
+- DICOM handling capabilities
+- Calibration utilities
+- Quality control tools
+- Registration and segmentation modules
+- Visualization and plotting features
+
+### Changed
+- Migrated from doodle to PyTheranostics
+- Updated package name and structure
+- Improved documentation
+
+### Fixed
+- Initial bug fixes and improvements