PAROS 0.1.0__tar.gz

paros-0.1.0/.github/workflows/ci.yml

@@ -0,0 +1,59 @@
+name: Continuous Integration
+
+on:
+  - push
+  - pull_request
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python: ["3.9", "3.10", "3.11", "3.12"]
+    steps:
+      - uses: actions/checkout@v4
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python }}
+          cache: pip
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install hatch
+      - name: Build PAROS
+        run: hatch build
+
+  format:
+    name: Format and lint
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python }}
+          cache: pip
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install hatch
+      - name: Format and lint
+        run: hatch fmt --check
+
+  jupyter:
+    name: Test Jupyter notebooks
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python }}
+          cache: pip
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install hatch
+      - name: Format and lint
+        run: hatch run jupyter:run-all

paros-0.1.0/.github/workflows/release.yml

@@ -0,0 +1,79 @@
+name: Publish to PyPI
+
+on:
+  release:
+    types: [released]
+
+permissions:
+  contents: read
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    
+    permissions:
+      contents: read
+
+    steps:
+      - uses: actions/checkout@v4
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.12"
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install build
+      - name: Build package
+        run: python -m build
+      - name: Upload dist
+        uses: actions/upload-artifact@v4
+        with:
+          name: paros_dist
+          path: "dist/"
+        
+  publish_to_pypi:
+    name: Publish to PyPI
+    runs-on: ubuntu-latest
+    environment: PyPI
+    needs: build
+
+    permissions:
+      id-token: write
+
+    steps:
+      - name: Download dist
+        uses: actions/download-artifact@v4
+        with:
+          name: paros_dist
+          path: dist
+      - name: Publish package
+        uses: pypa/gh-action-pypi-publish@v1.8.11
+        
+  upload_to_github:
+    name: Upload to GitHub
+    runs-on: ubuntu-latest
+    if: github.event_name == 'release'
+    needs: build
+    
+    permissions:
+      contents: write
+
+    steps:
+      - name: Download dist
+        uses: actions/download-artifact@v4
+        with:
+          name: paros_dist
+          path: dist
+      - name: Upload wheels to GitHub release
+        uses: svenstaro/upload-release-action@2.7.0
+        with:
+          tag: ${{ github.ref }}
+          file: "dist/*.whl"
+          file_glob: true
+      - name: Upload dist to GitHub release
+        uses: svenstaro/upload-release-action@2.7.0
+        with:
+          tag: ${{ github.ref }}
+          file: "dist/*.tar.gz"
+          file_glob: true

paros-0.1.0/.github/workflows/test-release.yml

@@ -0,0 +1,53 @@
+name: Publish to TestPyPI
+
+on:
+  # Manual trigger
+  workflow_dispatch:
+
+permissions:
+  contents: read
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    
+    permissions:
+      contents: read
+
+    steps:
+      - uses: actions/checkout@v4
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.12"
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install build
+      - name: Build package
+        run: python -m build
+      - name: Upload dist
+        uses: actions/upload-artifact@v4
+        with:
+          name: paros_dist
+          path: "dist/"
+        
+  publish_to_testpypi:
+    name: Publish to TestPyPI
+    runs-on: ubuntu-latest
+    environment: TestPyPI
+    needs: build
+
+    permissions:
+      id-token: write
+
+    steps:
+      - name: Download dist
+        uses: actions/download-artifact@v4
+        with:
+          name: paros_dist
+          path: dist
+      - name: Publish package
+        uses: pypa/gh-action-pypi-publish@v1.8.11
+        with:
+          repository-url: https://test.pypi.org/legacy/

paros-0.1.0/.github/workflows/voici.yml

@@ -0,0 +1,53 @@
+name: Build and Deploy
+
+on:
+  push:
+    branches:
+      - main
+  pull_request:
+    branches:
+      - '*'
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+
+      - name: Setup Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.10"
+
+      - name: Install mamba
+        uses: mamba-org/setup-micromamba@v1
+        with:
+          micromamba-version: "1.5.6-0"
+          environment-file: "voici/build-environment.yml"
+
+      - name: Build the JupyterLite site
+        shell: bash -l {0}
+        run: cd voici && voici build --contents simple_example.ipynb --output-dir dist
+
+      - name: Upload artifact
+        uses: actions/upload-pages-artifact@v3
+        with:
+          path: ./voici/dist
+
+  deploy:
+    needs: build
+    if: github.ref == 'refs/heads/main'
+    permissions:
+      pages: write
+      id-token: write
+
+    environment:
+      name: github-pages
+      url: ${{ steps.deployment.outputs.page_url }}
+
+    runs-on: ubuntu-latest
+    steps:
+      - name: Deploy to GitHub Pages
+        id: deployment
+        uses: actions/deploy-pages@v4

paros-0.1.0/.gitignore

@@ -0,0 +1,165 @@
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+cover/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+.pybuilder/
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# Voici
+voici/_output/
+.jupyterlite.doit.db
+
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+#   For a library or package, you might want to ignore these files since the code is
+#   intended to run in multiple environments; otherwise, check them in:
+# .python-version
+
+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   having no cross-platform support, pipenv may install dependencies that don't work, or not
+#   install all needed dependencies.
+#Pipfile.lock
+
+# poetry
+#   Similar to Pipfile.lock, it is generally recommended to include poetry.lock in version control.
+#   This is especially recommended for binary packages to ensure reproducibility, and is more
+#   commonly ignored for libraries.
+#   https://python-poetry.org/docs/basic-usage/#commit-your-poetrylock-file-to-version-control
+#poetry.lock
+
+# pdm
+#   Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control.
+#pdm.lock
+#   pdm stores project-wide configurations in .pdm.toml, but it is recommended to not include it
+#   in version control.
+#   https://pdm.fming.dev/#use-with-ide
+.pdm.toml
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
+
+# pytype static type analyzer
+.pytype/
+
+# Cython debug symbols
+cython_debug/
+
+# PyCharm
+#  JetBrains specific template is maintained in a separate JetBrains.gitignore that can
+#  be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore
+#  and can be added to the global gitignore or merged into this file.  For a more nuclear
+#  option (not recommended) you can uncomment the following to ignore the entire idea folder.
+.idea/

paros-0.1.0/CONTRIBUTING.md

@@ -0,0 +1,22 @@
+# Contributing to PAROS
+
+Thank you for considering contributing to PAROS! Before contributing, please read these guidelines, so we can process
+your contribution as quickly as possible.
+
+## Contribution ideas
+
+We aim to make usage of the PAROS method as easy as possible by providing the code open-source in our Git repository. Any contributions serving this goal are welcome. For example, the addition of calibration experiments for other cameras than already provided could be added.
+
+## Code style
+
+- Please format your docstrings according to [numpydoc](https://numpydoc.readthedocs.io/en/latest/format.html).
+
+## Workflow
+
+### 1. Add your new feature
+
+Add your contribution in a new feature branch. 
+
+### 2. Open a Pull Request
+
+Open a Pull Request, wait for our suggestions, and get your contribution merged!

paros-0.1.0/LICENSE

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2024 Lennart Pors
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

paros-0.1.0/PAROS/__init__.py

@@ -0,0 +1,10 @@
+"""PARaxial Optical fundus Scaling (PAROS)
+
+Paros is a method to calculate the magnification of fundus images based on the optical characteristics of the patient's
+eye. The full method and validation are described in (article reference to be added upon acceptance).
+"""
+
+from PAROS import data, eyephantom, fundscale
+
+__all__ = ("data", "eyephantom", "fundscale")
+__version__ = "0.1.0"

paros-0.1.0/PAROS/data/__init__.py

@@ -0,0 +1,70 @@
+"""Calibration and lens data files."""
+
+import importlib.resources
+from pathlib import Path
+from typing import cast
+
+import pandas as pd
+
+__all__ = ("get_camera_calibration_data", "get_lens_data")
+
+calibration = importlib.resources.files("PAROS.data.calibration")
+lenses = importlib.resources.files("PAROS.data.lenses")
+
+
+def _find_available_manufacturers():
+    return [i.name for i in calibration.iterdir() if i.is_dir()]
+
+
+_camera_manufacturers = _find_available_manufacturers()
+
+
+def get_camera_calibration_data(manufacturer: str, camera: str) -> pd.DataFrame:
+    """Get camera calibration data for a given manufacturer and camera.
+
+    Reads the data file at `PAROS/data/calibration/{manufacturer}/{camera}.csv` and
+    returns it as a pandas DataFrame.
+
+    Parameters
+    ----------
+    manufacturer : str
+        Camera manufacturer name.
+    camera : str
+        Camera model name.
+
+    Returns
+    -------
+    pandas.DataFrame
+        Dataframe containing the camera calibration data.
+    """
+    if manufacturer not in _camera_manufacturers:
+        raise KeyError(f"Manufacturer {manufacturer} does not exist.")
+
+    try:
+        camera_data_file = cast(Path, calibration.joinpath(manufacturer, camera + ".csv"))
+
+        return pd.read_csv(camera_data_file)
+    except FileNotFoundError as e:
+        raise KeyError(f"Camera {camera} does not exist for manufacturer {manufacturer}.") from e
+
+
+def get_lens_data(name: str) -> pd.DataFrame:
+    """Get lens data.
+
+    Reads the data file at `PAROS/data/lenses/{name}.csv` and returns it as a pandas DataFrame.
+
+    Parameters
+    ----------
+    name : str
+        Name of the lens data set.
+
+    Returns
+    -------
+    pandas.DataFrame
+        Dataframe containing the lens data.
+    """
+    try:
+        lens_data_file = cast(Path, lenses.joinpath(name + ".csv"))
+        return pd.read_csv(lens_data_file)
+    except FileNotFoundError as e:
+        raise KeyError(f"Lens data does not exist for name {name}.") from e

paros-0.1.0/PAROS/data/calibration/Topcon/TRC_50DX.csv

@@ -0,0 +1,10 @@
+experiment_number,lens_1,lens_2,uncorrected_measurement,distance_camera_eye_mm,distance_camera_pinhole_mm,distance_pinhole_lens1_mm,distance_lens1_lens2_mm,distance_lens2_grid_mm,axial_length
+0,LB_1471,LB_1945,6.966666667,5.5,49.61969784,2.880302163,3.027080745,29.69261709,40.71969784
+1,LB_1471,LB_1945,6.726666667,5.5,49.61969784,2.880302163,3.027080745,31.69261709,42.71969784
+2,LB_1471,LB_1945,6.6,5.5,49.61969784,2.880302163,3.027080745,33.69261709,44.71969784
+3,LB_1471,LB_1945,6.37,5.5,49.61969784,2.880302163,3.027080745,35.69261709,46.71969784
+4,LB_1471,LB_1945,6.25,5.5,49.61969784,2.880302163,3.027080745,37.69261709,48.71969784
+5,LB_1471,LB_1945,6.086666667,5.5,49.61969784,2.880302163,3.027080745,39.69261709,50.71969784
+6,LB_1471,LB_1945,5.973333333,5.5,49.61969784,2.880302163,3.027080745,41.69261709,52.71969784
+7,LB_1471,LB_1945,5.746666667,5.5,49.61969784,2.880302163,3.027080745,43.69261709,54.71969784
+8,LB_1471,LB_1945,5.613333333,5.5,49.61969784,2.880302163,3.027080745,45.39261709,56.41969784

paros-0.1.0/PAROS/data/calibration/Topcon/TRC_50IX.csv

@@ -0,0 +1,11 @@
+lens_1,lens_2,axial_length,distance_camera_eye_mm,uncorrected_measurement,distance_camera_pinhole_mm,distance_pinhole_lens1_mm,distance_lens1_lens2_mm,distance_lens2_grid_mm,experiment_number
+LE_1156,LB_1945,83.9874534,5.5,3.31,50.2374534,2.262546596,6.344836312,71.54261709,0
+LE_1156,LB_1945,90.7374534,5.5,3.13,50.2374534,2.262546596,6.344836312,78.29261709,1
+LE_1156,LB_1945,78.0374534,5.5,3.46,50.2374534,2.262546596,6.344836312,65.59261709,2
+LE_1156,LB_1945,134.6374534,5.5,2.24,50.2374534,2.262546596,6.344836312,122.1926171,3
+LE_1156,LB_1945,107.9374534,5.5,2.69,50.2374534,2.262546596,6.344836312,95.49261709,4
+LE_1156,LB_1945,72.0374534,5.5,3.71,50.2374534,2.262546596,6.344836312,59.59261709,5
+LE_1156,LB_1945,63.6374534,5.5,4.08,50.2374534,2.262546596,6.344836312,51.19261709,6
+LE_1234,LB_1056,62.51915876,5,4.28,45.31915876,2.180841236,5.205295461,51.1138633,7
+LE_1234,LB_1056,75.91915876,5,3.66,45.31915876,2.180841236,5.205295461,64.5138633,8
+LE_1234,LB_1056,96.51915876,5,2.98,45.31915876,2.180841236,5.205295461,85.1138633,9

paros-0.1.0/PAROS/data/calibration/__init__.py

@@ -0,0 +1 @@
+"""Camera calibration data files."""

paros-0.1.0/PAROS/data/lenses/__init__.py

@@ -0,0 +1 @@
+"""Lens data files."""

paros-0.1.0/PAROS/data/lenses/phantom.csv

@@ -0,0 +1,13 @@
+name,lens_type,thickness_centre,thickness_edge,diameter,power,front_radius,back_radius,refractive_index,power_calculated
+LB_1409,biconvex,2.2,2.0,25.6,1.0,1029.8,-1029.8,1.515,1.0001942124684402
+LB_1869,biconvex,2.3,2.0,25.6,2.0,514.7,-514.7,1.515,2.001165727608315
+LB_1056_1,biconvex,2.6,2.0,25.6,4.0,257.1,-257.1,1.515,4.006223259432127
+LE_1234,convex-concave,3.6,2.0,25.6,10.0,-82.2,-32.1,1.515,9.77840689451304
+LE_1156,convex-concave,3.3,2.0,25.6,8.0,-106.9,-40.6,1.515,7.867142534572616
+LE_1104,convex-concave,3.1,2.0,25.6,6.7,-131.6,-49.1,1.515,6.575424510489725
+LE_1202,convex-concave,2.8,2.0,25.6,5.0,-182.2,-66.2,1.515,4.952891978205283
+LB_1945,biconvex,2.8,2.0,25.6,5.0,205.6,-205.6,1.515,5.009727626459142
+LB_1056,biconvex,2.6,2.0,25.6,4.0,257.1,-257.1,1.515,4.006223259432127
+LB_1779,biconvex,2.5,2.0,25.6,3.3,308.6,-308.6,1.515,3.3376539209332456
+LB_1471,biconvex,5.2,2.0,25.6,20.0,50.6,-50.6,1.515,20.355731225296400
+LB_1757,biconvex,7.7,2.0,25.6,33.3,29.5,-29.5,1.515,34.91525423728813