joss init

LouisDesdoigts · Feb 9, 2024 · eec9b31 · eec9b31
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diff --git a/.github/workflows/draft-pdf.yml b/.github/workflows/draft-pdf.yml
@@ -0,0 +1,23 @@
+on: [push]
+
+jobs:
+  paper:
+    runs-on: ubuntu-latest
+    name: Paper Draft
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v2
+      - name: Build draft PDF
+        uses: openjournals/openjournals-draft-action@master
+        with:
+          journal: joss
+          # This should be the path to the paper within your repo.
+          paper-path: joss/paper.md
+      - name: Upload
+        uses: actions/upload-artifact@v1
+        with:
+          name: paper
+          # This is the output path where Pandoc will write the compiled
+          # PDF. Note, this should be the same directory as the input
+          # paper.md
+          path: joss/paper.pdf
diff --git a/joss/joss_figure.py b/joss/joss_figure.py
@@ -0,0 +1 @@
+### Script to generate whatever figure we have in the JOSS paper
diff --git a/joss/paper.bib b/joss/paper.bib
@@ -0,0 +1,97 @@
+@software{jax,
+  author = {James Bradbury and Roy Frostig and Peter Hawkins and Matthew James Johnson and Chris Leary and Dougal Maclaurin and Skye Wanderman-Milne},
+  title = {{JAX}: composable transformations of {P}ython+{N}um{P}y programs},
+  url = {http://github.com/google/jax},
+  version = {0.1.55},
+  year = {2018},
+}
+
+@inproceedings{hcipy,
+        author = {Por, E.~H. and Haffert, S.~Y. and Radhakrishnan, V.~M. and Doelman, D.~S. and Van Kooten, M. and Bos, S.~P.},
+        title = "{High Contrast Imaging for Python (HCIPy): an open-source adaptive optics and coronagraph simulator}",
+        booktitle = {Adaptive Optics Systems VI},
+        year = 2018,
+        series = {Proc. {{SPIE}}},
+        volume = 10703,
+        doi = {10.1117/12.2314407},
+        URL = {https://doi.org/10.1117/12.2314407}
+}
+
+@inproceedings{hcipy,
+        author = {Por, E.~H. and Haffert, S.~Y. and Radhakrishnan, V.~M. and Doelman, D.~S. and Van Kooten, M. and Bos, S.~P.},
+        title = "{High Contrast Imaging for Python (HCIPy): an open-source adaptive optics and coronagraph simulator}",
+        booktitle = {Adaptive Optics Systems VI},
+        year = 2018,
+        series = {Proc. {{SPIE}}},
+        volume = 10703,
+        doi = {10.1117/12.2314407},
+        URL = {https://doi.org/10.1117/12.2314407}
+}
+
+@article{prysm, doi = {10.21105/joss.01352}, url = {https://doi.org/10.21105/joss.01352}, year = {2019}, publisher = {The Open Journal}, volume = {4}, number = {37}, pages = {1352}, author = {Brandon Dube}, title = {prysm: A Python optics module}, journal = {Journal of Open Source Software} }
+
+@article{Desdoigts2023,
+  doi = {10.1117/1.jatis.9.2.028007},
+  url = {https://doi.org/10.1117/1.jatis.9.2.028007},
+  year = {2023},
+  month = jun,
+  publisher = {{SPIE}-Intl Soc Optical Eng},
+  volume = {9},
+  number = {02},
+  author = {Louis Desdoigts and Benjamin J. S. Pope and Jordan Dennis and Peter G. Tuthill},
+  title = {Differentiable optics with $\partial$Lux: I{\textemdash}deep calibration of flat field and phase retrieval with automatic differentiation},
+  journal = {Journal of Astronomical Telescopes,  Instruments,  and Systems}
+}
+
+@article{Sitzmann2018,
+  title = {End-to-end optimization of optics and image processing for achromatic extended depth of field and super-resolution imaging},
+  volume = {37},
+  ISSN = {1557-7368},
+  url = {http://dx.doi.org/10.1145/3197517.3201333},
+  DOI = {10.1145/3197517.3201333},
+  number = {4},
+  journal = {ACM Transactions on Graphics},
+  publisher = {Association for Computing Machinery (ACM)},
+  author = {Sitzmann,  Vincent and Diamond,  Steven and Peng,  Yifan and Dun,  Xiong and Boyd,  Stephen and Heidrich,  Wolfgang and Heide,  Felix and Wetzstein,  Gordon},
+  year = {2018},
+  month = jul,
+  pages = {1–13}
+}
+
+@ARTICLE{Page2020,
+       author = {{Page}, Josue and {Favaro}, Paolo},
+        title = "{Learning to Model and Calibrate Optics via a Differentiable Wave Optics Simulator}",
+      journal = {arXiv e-prints},
+     keywords = {Electrical Engineering and Systems Science - Image and Video Processing, Computer Science - Computer Vision and Pattern Recognition},
+         year = 2020,
+        month = may,
+          eid = {arXiv:2005.08562},
+        pages = {arXiv:2005.08562},
+          doi = {10.48550/arXiv.2005.08562},
+archivePrefix = {arXiv},
+       eprint = {2005.08562},
+ primaryClass = {eess.IV},
+       adsurl = {https://ui.adsabs.harvard.edu/abs/2020arXiv200508562P},
+      adsnote = {Provided by the SAO/NASA Astrophysics Data System}
+}
+
+
+@ARTICLE{Liaudat2023,
+       author = {{Liaudat}, Tobias and {Starck}, Jean-Luc and {Kilbinger}, Martin and {Frugier}, Pierre-Antoine},
+        title = "{Rethinking data-driven point spread function modeling with a differentiable optical model}",
+      journal = {Inverse Problems},
+     keywords = {point spread function modeling, automatic differentiation, super-resolution, chromatic variations, matrix factorization, Astrophysics - Instrumentation and Methods for Astrophysics, Computer Science - Computer Vision and Pattern Recognition},
+         year = 2023,
+        month = mar,
+       volume = {39},
+       number = {3},
+          eid = {035008},
+        pages = {035008},
+          doi = {10.1088/1361-6420/acb664},
+archivePrefix = {arXiv},
+       eprint = {2203.04908},
+ primaryClass = {astro-ph.IM},
+       adsurl = {https://ui.adsabs.harvard.edu/abs/2023InvPr..39c5008L},
+      adsnote = {Provided by the SAO/NASA Astrophysics Data System}
+}
+
diff --git a/joss/paper.md b/joss/paper.md
@@ -0,0 +1,83 @@
+---
+title: 'dLux: Differentiable Physical Optics in Jax'
+tags:
+  - Python
+  - Physical Optics
+  - Telescopes
+  - Exoplanet Science
+
+authors:
+  - name: Louis Desdoigts
+    orcid: 0000-0002-1015-9029
+    affiliation: 1 # (Multiple affiliations must be quoted)
+    corresponding: true
+  - name: Benjamin J. S. PopeS
+    affiliation: "2,3"
+    orcid: 0000-0003-2595-9114
+  - name: Jordan Dennis 
+    affiliation: 2
+    orcid: 0000-0001-8125-6494
+affiliations:
+ - name: School of Physics, University of Sydney, Cammperdown, NSW 2006, Australia
+   index: 1
+ - name: School of Mathematics and Physics, University of Queensland, St Lucia, QLD 4072, Australia
+   index: 2
+ - name: Centre for Astrophysics, University of Southern Queensland, West Street, Toowoomba, QLD 4350, Australia
+   index: 3
+date: 9 Feb 2024
+bibliography: paper.bib
+---
+
+# Summary
+
+<!-- why physical optics in astronomy  -->
+
+<!-- what is dLux -->
+`dLux`[^dlux] is an first open-source Python package for physical optics simulation. Using `jax` [@jax] it is differentiable and deploys natively on CPU, GPU, and parallelized HPC environments. `dLux` can perform Fourier optical simulations using matrix and FFT based propagation, as well as simulate linear and nonlinear detector effects. 
+
+<!-- more here -->
+
+<!-- something about zodiax? -->
+
+# Statement of need
+
+<!-- describe problem and relevant citations -->
+
+<!-- describe what has to happen in physical optics etc -->
+
+<!-- alternative packages for astronomy: poppy, prysm, xaosim, hcipy, whatever liaudat has -->
+Non-differentiable open-source physical optics packages used in astronomy include `poppy` [@poppy], `prysm` [@prysm], and in `WaveOpticsPropagation.jl`.
+
+Differentiable alternatives to `dLux` used in astronomy so far include `WaveDiff` [@Liaudat2023] and recent versions of `hcipy` [@hcipy]...
+
+<!-- alternative packages outside of astronomy -->
+Similar approaches using differentiable optical models have been applied in the `DeepOptics` project [@Sitzmann2018] for general cameras and `WaveBlocks` [@Page2020] in microscopy... etc
+
+<!-- dLux is open source: briefly explain its use -->
+We introduce a new open-source physical optics package, `dLux` (named for taking *partial derivatives of light*), written in Python and using `jax`. It inherits an object oriented framework from `equinox`... etc
+
+- class or feature 1
+- class or feature 2, etc
+
+<!-- cite Desdoigts papers it has been used in  -->
+
+# Documentation & Case Studies
+<!-- briefly summarize tutorials  -->
+
+In the accompanying [documentation](https://louisdesdoigts.github.io/dLux), we have produced several notebooks illustrating use cases...
+
+- [example 1](https://louisdesdoigts.github.io/dLux/notebooks/whatever/);
+
+Figures produced for... are shown in \autoref{fig1}. 
+<!-- also ref joss_figure.py to make figure, or do similar with notebook, so that it is reproducible -->
+
+![Figure Caption. \label{fig1}](joss_figure.png)
+
+# Acknowledgements
+
+<!-- whoever we acknowledge  -->
+
+# References
+<!-- you are only supposed to put refs in the .bib if they are actually used -->
+
+[^dlux]: [https://github.com/louisdesdoigts/dLux](https://github.com/louisdesdoigts/dLux)