joss updates

joss/paper.bib

@@ -105,3 +105,112 @@ @article{Wang2022
   publisher={IEEE}
 }
 
+@ARTICLE{Guyon2018,
+       author = {{Guyon}, Olivier},
+        title = "{Extreme Adaptive Optics}",
+      journal = {\araa},
+         year = 2018,
+        month = sep,
+       volume = {56},
+        pages = {315-355},
+          doi = {10.1146/annurev-astro-081817-052000},
+       adsurl = {https://ui.adsabs.harvard.edu/abs/2018ARA&A..56..315G},
+      adsnote = {Provided by the SAO/NASA Astrophysics Data System}
+}
+
+@ARTICLE{Follette2023,
+       author = {{Follette}, Katherine B.},
+        title = "{An Introduction to High Contrast Differential Imaging of Exoplanets and Disks}",
+      journal = {\pasp},
+     keywords = {Exoplanets, Circumstellar disks, Direct imaging, Coronagraphic imaging, 498, 235, 387, 313, Astrophysics - Instrumentation and Methods for Astrophysics, Astrophysics - Earth and Planetary Astrophysics},
+         year = 2023,
+        month = sep,
+       volume = {135},
+       number = {1051},
+          eid = {093001},
+        pages = {093001},
+          doi = {10.1088/1538-3873/aceb31},
+archivePrefix = {arXiv},
+       eprint = {2308.01354},
+ primaryClass = {astro-ph.IM},
+       adsurl = {https://ui.adsabs.harvard.edu/abs/2023PASP..135i3001F},
+      adsnote = {Provided by the SAO/NASA Astrophysics Data System}
+}
+
+@ARTICLE{Sivaramakrishnan2023,
+       author = {{Sivaramakrishnan}, Anand and {Tuthill}, Peter and {Lloyd}, James P. and {Greenbaum}, Alexandra Z. and {Thatte}, Deepashri and {Cooper}, Rachel A. and {Vandal}, Thomas and {Kammerer}, Jens and {Sanchez-Bermudez}, Joel and {Pope}, Benjamin J.~S. and {Blakely}, Dori and {Albert}, Lo{\"\i}c and {Cook}, Neil J. and {Johnstone}, Doug and {Martel}, Andr{\'e} R. and {Volk}, Kevin and {Soulain}, Anthony and {Artigau}, {\'E}tienne and {Lafreni{\`e}re}, David and {Willott}, Chris J. and {Parmentier}, S{\'e}bastien and {Ford}, K.~E. Saavik and {McKernan}, Barry and {Vila}, M. Bego{\~n}a and {Rowlands}, Neil and {Doyon}, Ren{\'e} and {Beaulieu}, Mathilde and {Desdoigts}, Louis and {Fullerton}, Alexander W. and {De Furio}, Matthew and {Goudfrooij}, Paul and {Holfeltz}, Sherie T. and {LaMassa}, Stephanie and {Maszkiewicz}, Michael and {Meyer}, Michael R. and {Perrin}, Marshall D. and {Pueyo}, Laurent and {Sahlmann}, Johannes and {Sohn}, Sangmo Tony and {Teixeira}, Paula S. and {Zheng}, Sheng-hai},
+        title = "{The Near Infrared Imager and Slitless Spectrograph for the James Webb Space Telescope. IV. Aperture Masking Interferometry}",
+      journal = {\pasp},
+     keywords = {High angular resolution, Interferometers, Direct detection interferometry, Astronomy data reduction, 2167, 805, 386, 1861, Astrophysics - Instrumentation and Methods for Astrophysics},
+         year = 2023,
+        month = jan,
+       volume = {135},
+       number = {1043},
+          eid = {015003},
+        pages = {015003},
+          doi = {10.1088/1538-3873/acaebd},
+archivePrefix = {arXiv},
+       eprint = {2210.17434},
+ primaryClass = {astro-ph.IM},
+       adsurl = {https://ui.adsabs.harvard.edu/abs/2023PASP..135a5003S},
+      adsnote = {Provided by the SAO/NASA Astrophysics Data System}
+}
+
+@INPROCEEDINGS{Girard2022,
+       author = {{Girard}, Julien H. and {Leisenring}, Jarron and {Kammerer}, Jens and {Gennaro}, Mario and {Rieke}, Marcia and {Stansberry}, John and {Rest}, Armin and {Egami}, Eiichi and {Sunnquist}, Ben and {Boyer}, Martha and {Canipe}, Alicia and {Correnti}, Matteo and {Hilbert}, Bryan and {Perrin}, Marshall D. and {Pueyo}, Laurent and {Soummer}, Remi and {Allen}, Marsha and {Bushouse}, Howard and {Aguilar}, Jonathan and {Brooks}, Brian and {Coe}, Dan and {DiFelice}, Audrey and {Golimowski}, David and {Hartig}, George and {Hines}, Dean C. and {Koekemoer}, Anton and {Nickson}, Bryony and {Nikolov}, Nikolay and {Kozhurina-Platais}, Vera and {Pirzkal}, Nor and {Robberto}, Massimo and {Sivaramakrishnan}, Anand and {Sohn}, Sangmo Tony and {Telfer}, Randal and {Wu}, Chi Rai and {Beatty}, Thomas and {Florian}, Michael and {Hainline}, Kevin and {Kelly}, Doug and {Misselt}, Karl and {Schlawin}, Everett and {Sun}, Fengwu and {Williams}, Christina and {Willmer}, Christopher and {Stark}, Christopher and {Ygouf}, Marie and {Carter}, Aarynn and {Beichman}, Charles and {Greene}, Thomas P. and {Roellig}, Thomas and {Krist}, John and {Adams Redai}, J{\'e}a. and {Wang}, Jason and {Clark}, Charles R. and {Lewis}, Dan and {Ferry}, Malcolm},
+        title = "{JWST/NIRCam coronagraphy: commissioning and first on-sky results}",
+     keywords = {Astrophysics - Instrumentation and Methods for Astrophysics, Astrophysics - Earth and Planetary Astrophysics, Physics - Instrumentation and Detectors, Physics - Optics},
+    booktitle = {Space Telescopes and Instrumentation 2022: Optical, Infrared, and Millimeter Wave},
+         year = 2022,
+       editor = {{Coyle}, Laura E. and {Matsuura}, Shuji and {Perrin}, Marshall D.},
+       series = {Society of Photo-Optical Instrumentation Engineers (SPIE) Conference Series},
+       volume = {12180},
+        month = aug,
+          eid = {121803Q},
+        pages = {121803Q},
+          doi = {10.1117/12.2629636},
+archivePrefix = {arXiv},
+       eprint = {2208.00998},
+ primaryClass = {astro-ph.IM},
+       adsurl = {https://ui.adsabs.harvard.edu/abs/2022SPIE12180E..3QG},
+      adsnote = {Provided by the SAO/NASA Astrophysics Data System}
+}
+
+
+@ARTICLE{Boccaletti2022,
+       author = {{Boccaletti}, A. and {Cossou}, C. and {Baudoz}, P. and {Lagage}, P.~O. and {Dicken}, D. and {Glasse}, A. and {Hines}, D.~C. and {Aguilar}, J. and {Detre}, O. and {Nickson}, B. and {Noriega-Crespo}, A. and {G{\'a}sp{\'a}r}, A. and {Labiano}, A. and {Stark}, C. and {Rouan}, D. and {Reess}, J.~M. and {Wright}, G.~S. and {Rieke}, G. and {Garcia Marin}, M. and {Lajoie}, C. and {Girard}, J. and {Perrin}, M. and {Soummer}, R. and {Pueyo}, L.},
+        title = "{JWST/MIRI coronagraphic performances as measured on-sky}",
+      journal = {\aap},
+     keywords = {instrumentation: high angular resolution, techniques: high angular resolution, techniques: image processing, planetary systems, Astrophysics - Instrumentation and Methods for Astrophysics, Astrophysics - Earth and Planetary Astrophysics},
+         year = 2022,
+        month = nov,
+       volume = {667},
+          eid = {A165},
+        pages = {A165},
+          doi = {10.1051/0004-6361/202244578},
+archivePrefix = {arXiv},
+       eprint = {2207.11080},
+ primaryClass = {astro-ph.IM},
+       adsurl = {https://ui.adsabs.harvard.edu/abs/2022A&A...667A.165B},
+      adsnote = {Provided by the SAO/NASA Astrophysics Data System}
+}
+
+
+@ARTICLE{Cantalloube2021,
+       author = {{Cantalloube}, F. and {Gomez-Gonzalez}, C. and {Absil}, O. and {Cantero}, C. and {Bacher}, R. and {Bonse}, M.~J. and {Bottom}, M. and {Dahlqvist}, C. -H. and {Desgrange}, C. and {Flasseur}, O. and {Fuhrmann}, T. and {Henning}, Th. and {Jensen-Clem}, R. and {Kenworthy}, M. and {Mawet}, D. and {Mesa}, D. and {Meshkat}, T. and {Mouillet}, D. and {Mueller}, A. and {Nasedkin}, E. and {Pairet}, B. and {Pierard}, S. and {Ruffio}, J. -B. and {Samland}, M. and {Stone}, J. and {Van Droogenbroeck}, M.},
+        title = "{Exoplanet Imaging Data Challenge: benchmarking the various image processing methods for exoplanet detection}",
+      journal = {arXiv e-prints},
+     keywords = {Astrophysics - Instrumentation and Methods for Astrophysics, Astrophysics - Earth and Planetary Astrophysics},
+         year = 2021,
+        month = jan,
+          eid = {arXiv:2101.05080},
+        pages = {arXiv:2101.05080},
+          doi = {10.48550/arXiv.2101.05080},
+archivePrefix = {arXiv},
+       eprint = {2101.05080},
+ primaryClass = {astro-ph.IM},
+       adsurl = {https://ui.adsabs.harvard.edu/abs/2021arXiv210105080C},
+      adsnote = {Provided by the SAO/NASA Astrophysics Data System}
+}
+
+

joss/paper.md

@@ -37,10 +37,10 @@ bibliography: paper.bib
 # Summary
 
 <!-- why physical optics in astronomy  -->
-One of the foundational problems in optical astronomy is that of imaging scenes at resolutions close to the diffraction limit of a telescope. This is important both in ground-based astronomy, where the turbulent atmosphere blurs the 
+One of the foundational problems in optical astronomy is that of imaging scenes at resolutions close to the diffraction limit of a telescope. One of the most stringent cases for high-dynamic-range, high-resolution imaging is exoplanet direct imaging [@Follette2023], whether with adaptive optics systems on large telescopes on Earth [@Guyon2018], or with space-based imagers such as the James Webb Space Telescope coronagraphs [@Boccaletti2022,@Girard2022] and interferometer [@Sivaramakrishnan2023]. In each case, a central issue is in accurately modelling the point spread function (PSF) of the telescope: the diffraction pattern by which light from a point source is spread out over the detector, which is affected by wavelength-scale irregularities at each optical surface the light encounters, and which can drown out the signals of faint planets and circumstellar material. While there are many data-driven approaches to nonparametrically inferring and subtracting this PSF [@Cantalloube2021], the motivation for our work here is to use principled deterministic physics to model optical systems; to perform high-dimensional inferences from data, jointly about telescopes and the scenes they observe; to train neural networks to model electronics together with optics; and to produce principled, high-dimensional designs for telescope hardware. These problems necessitate a physical optics model which is fast and differentiable.
 
 <!-- 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. 
+In this paper we introduce `dLux`[^dlux], an open-source Python package for differentiable physical optics simulation. Leveraging `jax` [@jax] for automatic differentiation and vectorization, it 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 -->