diff --git a/.github/workflows/draft-pdf.yml b/.github/workflows/draft-pdf.yml new file mode 100644 index 00000000..a7bce32e --- /dev/null +++ b/.github/workflows/draft-pdf.yml @@ -0,0 +1,28 @@ +name: build JOSS pdf + +on: + push: + branches: + - joss_paper + +jobs: + paper: + runs-on: ubuntu-latest + name: JOSS paper draft + steps: + - name: Checkout + uses: actions/checkout@v4 + - 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: paper/paper.md + - name: Upload + uses: actions/upload-artifact@v4 + 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: paper/paper.pdf \ No newline at end of file diff --git a/.gitignore b/.gitignore index 0e72b548..c62f946a 100644 --- a/.gitignore +++ b/.gitignore @@ -146,4 +146,7 @@ runs # hatch-generated version file src/mpol/mpol_version.py -.ruff_cache \ No newline at end of file +.ruff_cache + +build_joss.sh +prof \ No newline at end of file diff --git a/LICENSE b/LICENSE index 12fd66ef..99ebf233 100644 --- a/LICENSE +++ b/LICENSE @@ -1,6 +1,6 @@ MIT License -Copyright (c) 2019 - 2023 Ian Czekala and contributors +Copyright (c) 2019 - 2025 Ian Czekala and contributors Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal diff --git a/paper/.gitignore b/paper/.gitignore new file mode 100644 index 00000000..2cec151d --- /dev/null +++ b/paper/.gitignore @@ -0,0 +1,2 @@ +jats +paper.pdf \ No newline at end of file diff --git a/paper/fig.pdf b/paper/fig.pdf new file mode 100644 index 00000000..2efd2d9e Binary files /dev/null and b/paper/fig.pdf differ diff --git a/paper/paper.bib b/paper/paper.bib new file mode 100644 index 00000000..0e166ad6 --- /dev/null +++ b/paper/paper.bib @@ -0,0 +1,634 @@ +@article{andrews18, + author = {{Andrews}, Sean M. and {Huang}, Jane and {P{\'e}rez}, Laura M. and {Isella}, Andrea and {Dullemond}, Cornelis P. and {Kurtovic}, Nicol{\'a}s T. and {Guzm{\'a}n}, Viviana V. and {Carpenter}, John M. and {Wilner}, David J. and {Zhang}, Shangjia and {Zhu}, Zhaohuan and {Birnstiel}, Tilman and {Bai}, Xue-Ning and {Benisty}, Myriam and {Hughes}, A. Meredith and {{\"O}berg}, Karin I. and {Ricci}, Luca}, + title = {{The Disk Substructures at High Angular Resolution Project (DSHARP). I. Motivation, Sample, Calibration, and Overview}}, + journal = {Astrophysical Journal Letters}, + keywords = {circumstellar matter, planets and satellites: formation, protoplanetary disks, Astrophysics - Solar and Stellar Astrophysics, Astrophysics - Earth and Planetary Astrophysics}, + year = 2018, + month = dec, + volume = {869}, + number = {2}, + eid = {L41}, + pages = {L41}, + doi = {10.3847/2041-8213/aaf741}, + archiveprefix = {arXiv}, + eprint = {1812.04040}, + primaryclass = {astro-ph.SR}, + adsurl = {https://ui.adsabs.harvard.edu/abs/2018ApJ...869L..41A}, + adsnote = {Provided by the SAO/NASA Astrophysics Data System} +} + +@ARTICLE{hogbom74, + author = {{H{\"o}gbom}, J.~A.}, + title = "{Aperture Synthesis with a Non-Regular Distribution of Interferometer Baselines}", + journal = {Astronomy and Astrophysics Supplement}, + year = 1974, + month = jun, + volume = 15, + pages = {417}, + adsurl = {https://ui.adsabs.harvard.edu/abs/1974A%26AS...15..417H}, + adsnote = {Provided by the SAO/NASA Astrophysics Data System} +} + +@ARTICLE{clark80, + author = {{Clark}, B.~G.}, + title = "{An efficient implementation of the algorithm 'CLEAN'}", + journal = {Astronomy and Astrophysics}, + keywords = {Algorithms, Data Processing, Image Processing, Radio Astronomy, Run Time (Computers), Astronomical Photography, Computer Techniques, Fast Fourier Transformations, Iterative Solution, Very Large Array (Vla)}, + year = 1980, + month = sep, + volume = 89, + pages = {377}, + adsurl = {https://ui.adsabs.harvard.edu/abs/1980A%26A....89..377C}, + adsnote = {Provided by the SAO/NASA Astrophysics Data System} +} + +@INPROCEEDINGS{mcmullin07, + author = {{McMullin}, J.~P. and {Waters}, B. and {Schiebel}, D. and {Young}, W. and + {Golap}, K.}, + title = "{CASA Architecture and Applications}", + booktitle = {Astronomical Data Analysis Software and Systems XVI ASP Conference Series}, + year = "2007", + editor = {{Shaw}, R.~A. and {Hill}, F. and {Bell}, D.~J.}, + volume = {376}, + series = {Astronomical Society of the Pacific Conference Series}, + pages = {127}, + adsurl = {https://ui.adsabs.harvard.edu/abs/2007ASPC..376..127M}, + adsnote = {Provided by the SAO/NASA Astrophysics Data System} +} + +@ARTICLE{casa22, + author = {{CASA Team} and {Bean}, Ben and {Bhatnagar}, Sanjay and {Castro}, Sandra and {Donovan Meyer}, Jennifer and {Emonts}, Bjorn and {Garcia}, Enrique and {Garwood}, Robert and {Golap}, Kumar and {Gonzalez Villalba}, Justo and {Harris}, Pamela and {Hayashi}, Yohei and {Hoskins}, Josh and {Hsieh}, Mingyu and {Jagannathan}, Preshanth and {Kawasaki}, Wataru and {Keimpema}, Aard and {Kettenis}, Mark and {Lopez}, Jorge and {Marvil}, Joshua and {Masters}, Joseph and {McNichols}, Andrew and {Mehringer}, David and {Miel}, Renaud and {Moellenbrock}, George and {Montesino}, Federico and {Nakazato}, Takeshi and {Ott}, Juergen and {Petry}, Dirk and {Pokorny}, Martin and {Raba}, Ryan and {Rau}, Urvashi and {Schiebel}, Darrell and {Schweighart}, Neal and {Sekhar}, Srikrishna and {Shimada}, Kazuhiko and {Small}, Des and {Steeb}, Jan-Willem and {Sugimoto}, Kanako and {Suoranta}, Ville and {Tsutsumi}, Takahiro and {van Bemmel}, Ilse M. and {Verkouter}, Marjolein and {Wells}, Akeem and {Xiong}, Wei and {Szomoru}, Arpad and {Griffith}, Morgan and {Glendenning}, Brian and {Kern}, Jeff}, + title = "{CASA, the Common Astronomy Software Applications for Radio Astronomy}", + journal = {Publications of the Astronomical Society of the Pacific}, + keywords = {Single-dish antennas, Aperture synthesis, Radio astronomy, Radio interferometry, Long baseline interferometry, Astronomy software, Open source software, Software documentation, Astronomy data reduction, Astronomy data analysis, 1460, 53, 1338, 1346, 932, 1855, 1866, 1869, 1861, 1858, Astrophysics - Instrumentation and Methods for Astrophysics, Astrophysics - Astrophysics of Galaxies, Astrophysics - High Energy Astrophysical Phenomena, Astrophysics - Solar and Stellar Astrophysics}, + year = 2022, + month = nov, + volume = {134}, + number = {1041}, + eid = {114501}, + pages = {114501}, + doi = {10.1088/1538-3873/ac9642}, +archivePrefix = {arXiv}, + eprint = {2210.02276}, + primaryClass = {astro-ph.IM}, + adsurl = {https://ui.adsabs.harvard.edu/abs/2022PASP..134k4501C}, + adsnote = {Provided by the SAO/NASA Astrophysics Data System} +} + +@article{zawadzki23, + author = {{Zawadzki}, Brianna and {Czekala}, Ian and {Loomis}, Ryan A. and {Quinn}, Tyler and {Grzybowski}, Hannah and {Frazier}, Robert C. and {Jennings}, Jeff and {Nizam}, Kadri M. and {Jian}, Yina}, + title = {{Regularized Maximum Likelihood Image Synthesis and Validation for ALMA Continuum Observations of Protoplanetary Disks}}, + journal = {Publications of the Astronomical Society of the Pacific}, + keywords = {Protoplanetary disks, Submillimeter astronomy, Radio interferometry, Deconvolution, Open source software, 1300, 1647, 1346, 1910, 1866, Astrophysics - Earth and Planetary Astrophysics, Astrophysics - Instrumentation and Methods for Astrophysics}, + year = 2023, + month = jun, + volume = {135}, + number = {1048}, + eid = {064503}, + pages = {064503}, + doi = {10.1088/1538-3873/acdf84}, + archiveprefix = {arXiv}, + eprint = {2209.11813}, + primaryclass = {astro-ph.EP}, + adsurl = {https://ui.adsabs.harvard.edu/abs/2023PASP..135f4503Z}, + adsnote = {Provided by the SAO/NASA Astrophysics Data System} +} + +@article{campagne23, + author = {{Campagne}, Jean-Eric and {Lanusse}, Fran{\c{c}}ois and {Zuntz}, Joe and {Boucaud}, Alexandre and {Casas}, Santiago and {Karamanis}, Minas and {Kirkby}, David and {Lanzieri}, Denise and {Peel}, Austin and {Li}, Yin}, + title = {{JAX-COSMO: An End-to-End Differentiable and GPU Accelerated Cosmology Library}}, + journal = {The Open Journal of Astrophysics}, + keywords = {Astrophysics - Cosmology and Nongalactic Astrophysics, Astrophysics - Instrumentation and Methods for Astrophysics}, + year = 2023, + month = apr, + volume = {6}, + eid = {15}, + pages = {15}, + doi = {10.21105/astro.2302.05163}, + archiveprefix = {arXiv}, + eprint = {2302.05163}, + primaryclass = {astro-ph.CO}, + adsurl = {https://ui.adsabs.harvard.edu/abs/2023OJAp....6E..15C}, + adsnote = {Provided by the SAO/NASA Astrophysics Data System} +} + +@article{bedell19, + author = {{Bedell}, Megan and {Hogg}, David W. and {Foreman-Mackey}, Daniel and {Montet}, Benjamin T. and {Luger}, Rodrigo}, + title = {{WOBBLE: A Data-driven Analysis Technique for Time-series Stellar Spectra}}, + journal = {The Astronomical Journal}, + keywords = {atmospheric effects, methods: data analysis, planets and satellites: detection, stars: individual: 51 Pegasi, Barnard's Star, HD 189733, techniques: radial velocities, Astrophysics - Instrumentation and Methods for Astrophysics, Astrophysics - Earth and Planetary Astrophysics, Astrophysics - Solar and Stellar Astrophysics}, + year = 2019, + month = oct, + volume = {158}, + number = {4}, + eid = {164}, + pages = {164}, + doi = {10.3847/1538-3881/ab40a7}, + archiveprefix = {arXiv}, + eprint = {1901.00503}, + primaryclass = {astro-ph.IM}, + adsurl = {https://ui.adsabs.harvard.edu/abs/2019AJ....158..164B}, + adsnote = {Provided by the SAO/NASA Astrophysics Data System} +} + +@article{dabbech24, + author = {{Dabbech}, Arwa and {Aghabiglou}, Amir and {Chu}, Chung San and {Wiaux}, Yves}, + title = {{CLEANing Cygnus A Deep and Fast with R2D2}}, + journal = {The Astrophysical Journal Letters}, + keywords = {Astronomy image processing, Computational methods, Neural networks, Radio galaxies, Aperture synthesis, Radio interferometry, 2306, 1965, 1933, 1343, 53, 1346, Astrophysics - Instrumentation and Methods for Astrophysics, Computer Science - Machine Learning, Electrical Engineering and Systems Science - Image and Video Processing, Electrical Engineering and Systems Science - Signal Processing}, + year = 2024, + month = may, + volume = {966}, + number = {2}, + eid = {L34}, + pages = {L34}, + doi = {10.3847/2041-8213/ad41df}, + archiveprefix = {arXiv}, + eprint = {2309.03291}, + primaryclass = {astro-ph.IM}, + adsurl = {https://ui.adsabs.harvard.edu/abs/2024ApJ...966L..34D}, + adsnote = {Provided by the SAO/NASA Astrophysics Data System} +} + +@article{wang23, + author = {{Wang}, Ruoqi and {Chen}, Zhuoyang and {Luo}, Qiong and {Wang}, Feng}, + title = {{A Conditional Denoising Diffusion Probabilistic Model for Radio Interferometric Image Reconstruction}}, + journal = {arXiv e-prints}, + keywords = {Astrophysics - Instrumentation and Methods for Astrophysics, Astrophysics - Astrophysics of Galaxies, Computer Science - Computer Vision and Pattern Recognition, Computer Science - Machine Learning, Electrical Engineering and Systems Science - Image and Video Processing}, + year = 2023, + month = may, + eid = {arXiv:2305.09121}, + pages = {arXiv:2305.09121}, + doi = {10.48550/arXiv.2305.09121}, + archiveprefix = {arXiv}, + eprint = {2305.09121}, + primaryclass = {astro-ph.IM}, + adsurl = {https://ui.adsabs.harvard.edu/abs/2023arXiv230509121W}, + adsnote = {Provided by the SAO/NASA Astrophysics Data System} +} + + +@article{dia23, + author = {{Dia}, Noe and {Yantovski-Barth}, M.~J. and {Adam}, Alexandre and {Bowles}, Micah and {Lemos}, Pablo and {Scaife}, Anna M.~M. and {Hezaveh}, Yashar and {Perreault-Levasseur}, Laurence}, + title = {{Bayesian Imaging for Radio Interferometry with Score-Based Priors}}, + journal = {arXiv e-prints}, + keywords = {Astrophysics - Instrumentation and Methods for Astrophysics, Computer Science - Computer Vision and Pattern Recognition}, + year = 2023, + month = nov, + eid = {arXiv:2311.18012}, + pages = {arXiv:2311.18012}, + doi = {10.48550/arXiv.2311.18012}, + archiveprefix = {arXiv}, + eprint = {2311.18012}, + primaryclass = {astro-ph.IM}, + adsurl = {https://ui.adsabs.harvard.edu/abs/2023arXiv231118012D}, + adsnote = {Provided by the SAO/NASA Astrophysics Data System} +} + +@article{jennings20, + author = {{Jennings}, Jeff and {Booth}, Richard A. and {Tazzari}, Marco and {Rosotti}, Giovanni P. and {Clarke}, Cathie J.}, + title = {{frankenstein: protoplanetary disc brightness profile reconstruction at sub-beam resolution with a rapid Gaussian process}}, + journal = {Monthly Notices of the RAS}, + keywords = {methods: data analysis, protoplanetary discs, techniques: interferometric, planets and satellites: detection, submillimetre: general, submillimetre: planetary systems, Astrophysics - Earth and Planetary Astrophysics, Astrophysics - Instrumentation and Methods for Astrophysics}, + year = 2020, + month = jul, + volume = {495}, + number = {3}, + pages = {3209-3232}, + doi = {10.1093/mnras/staa1365}, + archiveprefix = {arXiv}, + eprint = {2005.07709}, + primaryclass = {astro-ph.EP}, + adsurl = {https://ui.adsabs.harvard.edu/abs/2020MNRAS.495.3209J}, + adsnote = {Provided by the SAO/NASA Astrophysics Data System} +} + + + +@article{eht19a, + author = {{Event Horizon Telescope Collaboration} and {Akiyama}, Kazunori and {Alberdi}, Antxon and {Alef}, Walter and {Asada}, Keiichi and {Azulay}, Rebecca and {Baczko}, Anne-Kathrin and {Ball}, David and {Balokovi{\'c}}, Mislav and {Barrett}, John and {Bintley}, Dan and {Blackburn}, Lindy and {Boland}, Wilfred and {Bouman}, Katherine L. and {Bower}, Geoffrey C. and {Bremer}, Michael and {Brinkerink}, Christiaan D. and {Brissenden}, Roger and {Britzen}, Silke and {Broderick}, Avery E. and {Broguiere}, Dominique and {Bronzwaer}, Thomas and {Byun}, Do-Young and {Carlstrom}, John E. and {Chael}, Andrew and {Chan}, Chi-kwan and {Chatterjee}, Shami and {Chatterjee}, Koushik and {Chen}, Ming-Tang and {Chen}, Yongjun and {Cho}, Ilje and {Christian}, Pierre and {Conway}, John E. and {Cordes}, James M. and {Crew}, Geoffrey B. and {Cui}, Yuzhu and {Davelaar}, Jordy and {De Laurentis}, Mariafelicia and {Deane}, Roger and {Dempsey}, Jessica and {Desvignes}, Gregory and {Dexter}, Jason and {Doeleman}, Sheperd S. and {Eatough}, Ralph P. and {Falcke}, Heino and {Fish}, Vincent L. and {Fomalont}, Ed and {Fraga-Encinas}, Raquel and {Freeman}, William T. and {Friberg}, Per and {Fromm}, Christian M. and {G{\'o}mez}, Jos{\'e} L. and {Galison}, Peter and {Gammie}, Charles F. and {Garc{\'\i}a}, Roberto and {Gentaz}, Olivier and {Georgiev}, Boris and {Goddi}, Ciriaco and {Gold}, Roman and {Gu}, Minfeng and {Gurwell}, Mark and {Hada}, Kazuhiro and {Hecht}, Michael H. and {Hesper}, Ronald and {Ho}, Luis C. and {Ho}, Paul and {Honma}, Mareki and {Huang}, Chih-Wei L. and {Huang}, Lei and {Hughes}, David H. and {Ikeda}, Shiro and {Inoue}, Makoto and {Issaoun}, Sara and {James}, David J. and {Jannuzi}, Buell T. and {Janssen}, Michael and {Jeter}, Britton and {Jiang}, Wu and {Johnson}, Michael D. and {Jorstad}, Svetlana and {Jung}, Taehyun and {Karami}, Mansour and {Karuppusamy}, Ramesh and {Kawashima}, Tomohisa and {Keating}, Garrett K. and {Kettenis}, Mark and {Kim}, Jae-Young and {Kim}, Junhan and {Kim}, Jongsoo and {Kino}, Motoki and {Koay}, Jun Yi and {Koch}, Patrick M. and {Koyama}, Shoko and {Kramer}, Michael and {Kramer}, Carsten and {Krichbaum}, Thomas P. and {Kuo}, Cheng-Yu and {Lauer}, Tod R. and {Lee}, Sang-Sung and {Li}, Yan-Rong and {Li}, Zhiyuan and {Lindqvist}, Michael and {Liu}, Kuo and {Liuzzo}, Elisabetta and {Lo}, Wen-Ping and {Lobanov}, Andrei P. and {Loinard}, Laurent and {Lonsdale}, Colin and {Lu}, Ru-Sen and {MacDonald}, Nicholas R. and {Mao}, Jirong and {Markoff}, Sera and {Marrone}, Daniel P. and {Marscher}, Alan P. and {Mart{\'\i}-Vidal}, Iv{\'a}n and {Matsushita}, Satoki and {Matthews}, Lynn D. and {Medeiros}, Lia and {Menten}, Karl M. and {Mizuno}, Yosuke and {Mizuno}, Izumi and {Moran}, James M. and {Moriyama}, Kotaro and {Moscibrodzka}, Monika and {M{\"u}ller}, Cornelia and {Nagai}, Hiroshi and {Nagar}, Neil M. and {Nakamura}, Masanori and {Narayan}, Ramesh and {Narayanan}, Gopal and {Natarajan}, Iniyan and {Neri}, Roberto and {Ni}, Chunchong and {Noutsos}, Aristeidis and {Okino}, Hiroki and {Olivares}, H{\'e}ctor and {Ortiz-Le{\'o}n}, Gisela N. and {Oyama}, Tomoaki and {{\"O}zel}, Feryal and {Palumbo}, Daniel C.~M. and {Patel}, Nimesh and {Pen}, Ue-Li and {Pesce}, Dominic W. and {Pi{\'e}tu}, Vincent and {Plambeck}, Richard and {PopStefanija}, Aleksandar and {Porth}, Oliver and {Prather}, Ben and {Preciado-L{\'o}pez}, Jorge A. and {Psaltis}, Dimitrios and {Pu}, Hung-Yi and {Ramakrishnan}, Venkatessh and {Rao}, Ramprasad and {Rawlings}, Mark G. and {Raymond}, Alexander W. and {Rezzolla}, Luciano and {Ripperda}, Bart and {Roelofs}, Freek and {Rogers}, Alan and {Ros}, Eduardo and {Rose}, Mel and {Roshanineshat}, Arash and {Rottmann}, Helge and {Roy}, Alan L. and {Ruszczyk}, Chet and {Ryan}, Benjamin R. and {Rygl}, Kazi L.~J. and {S{\'a}nchez}, Salvador and {S{\'a}nchez-Arguelles}, David and {Sasada}, Mahito and {Savolainen}, Tuomas and {Schloerb}, F. Peter and {Schuster}, Karl-Friedrich and {Shao}, Lijing and {Shen}, Zhiqiang and {Small}, Des and {Sohn}, Bong Won and {SooHoo}, Jason and {Tazaki}, Fumie and {Tiede}, Paul and {Tilanus}, Remo P.~J. and {Titus}, Michael and {Toma}, Kenji and {Torne}, Pablo and {Trent}, Tyler and {Trippe}, Sascha and {Tsuda}, Shuichiro and {van Bemmel}, Ilse and {van Langevelde}, Huib Jan and {van Rossum}, Daniel R. and {Wagner}, Jan and {Wardle}, John and {Weintroub}, Jonathan and {Wex}, Norbert and {Wharton}, Robert and {Wielgus}, Maciek and {Wong}, George N. and {Wu}, Qingwen and {Young}, Ken and {Young}, Andr{\'e} and {Younsi}, Ziri and {Yuan}, Feng and {Yuan}, Ye-Fei and {Zensus}, J. Anton and {Zhao}, Guangyao and {Zhao}, Shan-Shan and {Zhu}, Ziyan and {Algaba}, Juan-Carlos and {Allardi}, Alexander and {Amestica}, Rodrigo and {Anczarski}, Jadyn and {Bach}, Uwe and {Baganoff}, Frederick K. and {Beaudoin}, Christopher and {Benson}, Bradford A. and {Berthold}, Ryan and {Blanchard}, Jay M. and {Blundell}, Ray and {Bustamente}, Sandra and {Cappallo}, Roger and {Castillo-Dom{\'\i}nguez}, Edgar and {Chang}, Chih-Cheng and {Chang}, Shu-Hao and {Chang}, Song-Chu and {Chen}, Chung-Chen and {Chilson}, Ryan and {Chuter}, Tim C. and {C{\'o}rdova Rosado}, Rodrigo and {Coulson}, Iain M. and {Crawford}, Thomas M. and {Crowley}, Joseph and {David}, John and {Derome}, Mark and {Dexter}, Matthew and {Dornbusch}, Sven and {Dudevoir}, Kevin A. and {Dzib}, Sergio A. and {Eckart}, Andreas and {Eckert}, Chris and {Erickson}, Neal R. and {Everett}, Wendeline B. and {Faber}, Aaron and {Farah}, Joseph R. and {Fath}, Vernon and {Folkers}, Thomas W. and {Forbes}, David C. and {Freund}, Robert and {G{\'o}mez-Ruiz}, Arturo I. and {Gale}, David M. and {Gao}, Feng and {Geertsema}, Gertie and {Graham}, David A. and {Greer}, Christopher H. and {Grosslein}, Ronald and {Gueth}, Fr{\'e}d{\'e}ric and {Haggard}, Daryl and {Halverson}, Nils W. and {Han}, Chih-Chiang and {Han}, Kuo-Chang and {Hao}, Jinchi and {Hasegawa}, Yutaka and {Henning}, Jason W. and {Hern{\'a}ndez-G{\'o}mez}, Antonio and {Herrero-Illana}, Rub{\'e}n and {Heyminck}, Stefan and {Hirota}, Akihiko and {Hoge}, James and {Huang}, Yau-De and {Impellizzeri}, C.~M. Violette and {Jiang}, Homin and {Kamble}, Atish and {Keisler}, Ryan and {Kimura}, Kimihiro and {Kono}, Yusuke and {Kubo}, Derek and {Kuroda}, John and {Lacasse}, Richard and {Laing}, Robert A. and {Leitch}, Erik M. and {Li}, Chao-Te and {Lin}, Lupin C. -C. and {Liu}, Ching-Tang and {Liu}, Kuan-Yu and {Lu}, Li-Ming and {Marson}, Ralph G. and {Martin-Cocher}, Pierre L. and {Massingill}, Kyle D. and {Matulonis}, Callie and {McColl}, Martin P. and {McWhirter}, Stephen R. and {Messias}, Hugo and {Meyer-Zhao}, Zheng and {Michalik}, Daniel and {Monta{\~n}a}, Alfredo and {Montgomerie}, William and {Mora-Klein}, Matias and {Muders}, Dirk and {Nadolski}, Andrew and {Navarro}, Santiago and {Neilsen}, Joseph and {Nguyen}, Chi H. and {Nishioka}, Hiroaki and {Norton}, Timothy and {Nowak}, Michael A. and {Nystrom}, George and {Ogawa}, Hideo and {Oshiro}, Peter and {Oyama}, Tomoaki and {Parsons}, Harriet and {Paine}, Scott N. and {Pe{\~n}alver}, Juan and {Phillips}, Neil M. and {Poirier}, Michael and {Pradel}, Nicolas and {Primiani}, Rurik A. and {Raffin}, Philippe A. and {Rahlin}, Alexandra S. and {Reiland}, George and {Risacher}, Christopher and {Ruiz}, Ignacio and {S{\'a}ez-Mada{\'\i}n}, Alejandro F. and {Sassella}, Remi and {Schellart}, Pim and {Shaw}, Paul and {Silva}, Kevin M. and {Shiokawa}, Hotaka and {Smith}, David R. and {Snow}, William and {Souccar}, Kamal and {Sousa}, Don and {Sridharan}, T.~K. and {Srinivasan}, Ranjani and {Stahm}, William and {Stark}, Anthony A. and {Story}, Kyle and {Timmer}, Sjoerd T. and {Vertatschitsch}, Laura and {Walther}, Craig and {Wei}, Ta-Shun and {Whitehorn}, Nathan and {Whitney}, Alan R. and {Woody}, David P. and {Wouterloot}, Jan G.~A. and {Wright}, Melvin and {Yamaguchi}, Paul and {Yu}, Chen-Yu and {Zeballos}, Milagros and {Zhang}, Shuo and {Ziurys}, Lucy}, + title = {{First M87 Event Horizon Telescope Results. I. The Shadow of the Supermassive Black Hole}}, + journal = {The Astrophysical Journal Letters}, + keywords = {accretion, accretion disks, black hole physics, galaxies: active, galaxies: individual: M87, galaxies: jets, gravitation, Astrophysics - Astrophysics of Galaxies, Astrophysics - High Energy Astrophysical Phenomena, General Relativity and Quantum Cosmology}, + year = 2019, + month = apr, + volume = {875}, + number = {1}, + eid = {L1}, + pages = {L1}, + doi = {10.3847/2041-8213/ab0ec7}, + archiveprefix = {arXiv}, + eprint = {1906.11238}, + primaryclass = {astro-ph.GA}, + adsurl = {https://ui.adsabs.harvard.edu/abs/2019ApJ...875L...1E}, + adsnote = {Provided by the SAO/NASA Astrophysics Data System} +} + +@article{eht19d, + author = {{Event Horizon Telescope Collaboration} and {Akiyama}, Kazunori and {Alberdi}, Antxon and {Alef}, Walter and {Asada}, Keiichi and {Azulay}, Rebecca and {Baczko}, Anne-Kathrin and {Ball}, David and {Balokovi{\'c}}, Mislav and {Barrett}, John and {Bintley}, Dan and {Blackburn}, Lindy and {Boland}, Wilfred and {Bouman}, Katherine L. and {Bower}, Geoffrey C. and {Bremer}, Michael and {Brinkerink}, Christiaan D. and {Brissenden}, Roger and {Britzen}, Silke and {Broderick}, Avery E. and {Broguiere}, Dominique and {Bronzwaer}, Thomas and {Byun}, Do-Young and {Carlstrom}, John E. and {Chael}, Andrew and {Chan}, Chi-kwan and {Chatterjee}, Shami and {Chatterjee}, Koushik and {Chen}, Ming-Tang and {Chen}, Yongjun and {Cho}, Ilje and {Christian}, Pierre and {Conway}, John E. and {Cordes}, James M. and {Crew}, Geoffrey B. and {Cui}, Yuzhu and {Davelaar}, Jordy and {De Laurentis}, Mariafelicia and {Deane}, Roger and {Dempsey}, Jessica and {Desvignes}, Gregory and {Dexter}, Jason and {Doeleman}, Sheperd S. and {Eatough}, Ralph P. and {Falcke}, Heino and {Fish}, Vincent L. and {Fomalont}, Ed and {Fraga-Encinas}, Raquel and {Freeman}, William T. and {Friberg}, Per and {Fromm}, Christian M. and {G{\'o}mez}, Jos{\'e} L. and {Galison}, Peter and {Gammie}, Charles F. and {Garc{\'\i}a}, Roberto and {Gentaz}, Olivier and {Georgiev}, Boris and {Goddi}, Ciriaco and {Gold}, Roman and {Gu}, Minfeng and {Gurwell}, Mark and {Hada}, Kazuhiro and {Hecht}, Michael H. and {Hesper}, Ronald and {Ho}, Luis C. and {Ho}, Paul and {Honma}, Mareki and {Huang}, Chih-Wei L. and {Huang}, Lei and {Hughes}, David H. and {Ikeda}, Shiro and {Inoue}, Makoto and {Issaoun}, Sara and {James}, David J. and {Jannuzi}, Buell T. and {Janssen}, Michael and {Jeter}, Britton and {Jiang}, Wu and {Johnson}, Michael D. and {Jorstad}, Svetlana and {Jung}, Taehyun and {Karami}, Mansour and {Karuppusamy}, Ramesh and {Kawashima}, Tomohisa and {Keating}, Garrett K. and {Kettenis}, Mark and {Kim}, Jae-Young and {Kim}, Junhan and {Kim}, Jongsoo and {Kino}, Motoki and {Koay}, Jun Yi and {Koch}, Patrick M. and {Koyama}, Shoko and {Kramer}, Michael and {Kramer}, Carsten and {Krichbaum}, Thomas P. and {Kuo}, Cheng-Yu and {Lauer}, Tod R. and {Lee}, Sang-Sung and {Li}, Yan-Rong and {Li}, Zhiyuan and {Lindqvist}, Michael and {Liu}, Kuo and {Liuzzo}, Elisabetta and {Lo}, Wen-Ping and {Lobanov}, Andrei P. and {Loinard}, Laurent and {Lonsdale}, Colin and {Lu}, Ru-Sen and {MacDonald}, Nicholas R. and {Mao}, Jirong and {Markoff}, Sera and {Marrone}, Daniel P. and {Marscher}, Alan P. and {Mart{\'\i}-Vidal}, Iv{\'a}n and {Matsushita}, Satoki and {Matthews}, Lynn D. and {Medeiros}, Lia and {Menten}, Karl M. and {Mizuno}, Yosuke and {Mizuno}, Izumi and {Moran}, James M. and {Moriyama}, Kotaro and {Moscibrodzka}, Monika and {M{\"u}ller}, Cornelia and {Nagai}, Hiroshi and {Nagar}, Neil M. and {Nakamura}, Masanori and {Narayan}, Ramesh and {Narayanan}, Gopal and {Natarajan}, Iniyan and {Neri}, Roberto and {Ni}, Chunchong and {Noutsos}, Aristeidis and {Okino}, Hiroki and {Olivares}, H{\'e}ctor and {Oyama}, Tomoaki and {{\"O}zel}, Feryal and {Palumbo}, Daniel C.~M. and {Patel}, Nimesh and {Pen}, Ue-Li and {Pesce}, Dominic W. and {Pi{\'e}tu}, Vincent and {Plambeck}, Richard and {PopStefanija}, Aleksandar and {Porth}, Oliver and {Prather}, Ben and {Preciado-L{\'o}pez}, Jorge A. and {Psaltis}, Dimitrios and {Pu}, Hung-Yi and {Ramakrishnan}, Venkatessh and {Rao}, Ramprasad and {Rawlings}, Mark G. and {Raymond}, Alexander W. and {Rezzolla}, Luciano and {Ripperda}, Bart and {Roelofs}, Freek and {Rogers}, Alan and {Ros}, Eduardo and {Rose}, Mel and {Roshanineshat}, Arash and {Rottmann}, Helge and {Roy}, Alan L. and {Ruszczyk}, Chet and {Ryan}, Benjamin R. and {Rygl}, Kazi L.~J. and {S{\'a}nchez}, Salvador and {S{\'a}nchez-Arguelles}, David and {Sasada}, Mahito and {Savolainen}, Tuomas and {Schloerb}, F. Peter and {Schuster}, Karl-Friedrich and {Shao}, Lijing and {Shen}, Zhiqiang and {Small}, Des and {Sohn}, Bong Won and {SooHoo}, Jason and {Tazaki}, Fumie and {Tiede}, Paul and {Tilanus}, Remo P.~J. and {Titus}, Michael and {Toma}, Kenji and {Torne}, Pablo and {Trent}, Tyler and {Trippe}, Sascha and {Tsuda}, Shuichiro and {van Bemmel}, Ilse and {van Langevelde}, Huib Jan and {van Rossum}, Daniel R. and {Wagner}, Jan and {Wardle}, John and {Weintroub}, Jonathan and {Wex}, Norbert and {Wharton}, Robert and {Wielgus}, Maciek and {Wong}, George N. and {Wu}, Qingwen and {Young}, Andr{\'e} and {Young}, Ken and {Younsi}, Ziri and {Yuan}, Feng and {Yuan}, Ye-Fei and {Zensus}, J. Anton and {Zhao}, Guangyao and {Zhao}, Shan-Shan and {Zhu}, Ziyan and {Farah}, Joseph R. and {Meyer-Zhao}, Zheng and {Michalik}, Daniel and {Nadolski}, Andrew and {Nishioka}, Hiroaki and {Pradel}, Nicolas and {Primiani}, Rurik A. and {Souccar}, Kamal and {Vertatschitsch}, Laura and {Yamaguchi}, Paul}, + title = {{First M87 Event Horizon Telescope Results. IV. Imaging the Central Supermassive Black Hole}}, + journal = {The Astrophysical Journal Letters}, + keywords = {black hole physics, galaxies: individual: M87, galaxies: jets, techniques: high angular resolution, techniques: image processing, techniques: interferometric, Astrophysics - Astrophysics of Galaxies, Astrophysics - Instrumentation and Methods for Astrophysics, General Relativity and Quantum Cosmology}, + year = 2019, + month = apr, + volume = {875}, + number = {1}, + eid = {L4}, + pages = {L4}, + doi = {10.3847/2041-8213/ab0e85}, + archiveprefix = {arXiv}, + eprint = {1906.11241}, + primaryclass = {astro-ph.GA}, + adsurl = {https://ui.adsabs.harvard.edu/abs/2019ApJ...875L...4E}, + adsnote = {Provided by the SAO/NASA Astrophysics Data System} +} + + +@article{benisty21, + author = {{Benisty}, Myriam and {Bae}, Jaehan and {Facchini}, Stefano and {Keppler}, Miriam and {Teague}, Richard and {Isella}, Andrea and {Kurtovic}, Nicolas T. and {P{\'e}rez}, Laura M. and {Sierra}, Anibal and {Andrews}, Sean M. and {Carpenter}, John and {Czekala}, Ian and {Dominik}, Carsten and {Henning}, Thomas and {Menard}, Francois and {Pinilla}, Paola and {Zurlo}, Alice}, + title = {{A Circumplanetary Disk around PDS70c}}, + journal = {The Astrophysical Journal Letters}, + keywords = {Protoplanetary disks, 1300, Astrophysics - Earth and Planetary Astrophysics, Astrophysics - Solar and Stellar Astrophysics}, + year = 2021, + month = jul, + volume = {916}, + number = {1}, + eid = {L2}, + pages = {L2}, + doi = {10.3847/2041-8213/ac0f83}, + archiveprefix = {arXiv}, + eprint = {2108.07123}, + primaryclass = {astro-ph.EP}, + adsurl = {https://ui.adsabs.harvard.edu/abs/2021ApJ...916L...2B}, + adsnote = {Provided by the SAO/NASA Astrophysics Data System} +} + +@article{pinte18, + author = {{Pinte}, C. and {Price}, D.~J. and {M{\'e}nard}, F. and {Duch{\^e}ne}, G. and {Dent}, W.~R.~F. and {Hill}, T. and {de Gregorio-Monsalvo}, I. and {Hales}, A. and {Mentiplay}, D.}, + title = {{Kinematic Evidence for an Embedded Protoplanet in a Circumstellar Disk}}, + journal = {The Astrophysical Journal Letters}, + keywords = {protoplanetary disks, radiative transfer, stars: formation, stars: individual: HD 163296, submillimeter: planetary systems, techniques: interferometric, Astrophysics - Solar and Stellar Astrophysics, Astrophysics - Earth and Planetary Astrophysics}, + year = 2018, + month = jun, + volume = {860}, + number = {1}, + eid = {L13}, + pages = {L13}, + doi = {10.3847/2041-8213/aac6dc}, + archiveprefix = {arXiv}, + eprint = {1805.10293}, + primaryclass = {astro-ph.SR}, + adsurl = {https://ui.adsabs.harvard.edu/abs/2018ApJ...860L..13P}, + adsnote = {Provided by the SAO/NASA Astrophysics Data System} +} + +@article{andrews20, + author = {{Andrews}, Sean M.}, + title = {{Observations of Protoplanetary Disk Structures}}, + journal = {Annual Review of Astronomy and Astrophysics}, + keywords = {Astrophysics - Earth and Planetary Astrophysics, Astrophysics - Solar and Stellar Astrophysics}, + year = 2020, + month = aug, + volume = {58}, + pages = {483-528}, + doi = {10.1146/annurev-astro-031220-010302}, + archiveprefix = {arXiv}, + eprint = {2001.05007}, + primaryclass = {astro-ph.EP}, + adsurl = {https://ui.adsabs.harvard.edu/abs/2020ARA&A..58..483A}, + adsnote = {Provided by the SAO/NASA Astrophysics Data System} +} + +@article{dewdney09, + author = {{Dewdney}, P.~E. and {Hall}, P.~J. and {Schilizzi}, R.~T. and {Lazio}, T.~J.~L.~W.}, + title = {{The Square Kilometre Array}}, + journal = {IEEE Proceedings}, + year = 2009, + month = aug, + volume = {97}, + number = {8}, + pages = {1482-1496}, + doi = {10.1109/JPROC.2009.2021005}, + adsurl = {https://ui.adsabs.harvard.edu/abs/2009IEEEP..97.1482D}, + adsnote = {Provided by the SAO/NASA Astrophysics Data System} +} + +@article{narayan86, + author = {{Narayan}, Ramesh and {Nityananda}, Rajaram}, + title = {{Maximum entropy image restoration in astronomy.}}, + journal = {Annual Review of Astronomy and Astrophysics}, + keywords = {Astronomy, Image Reconstruction, Maximum Entropy Method, Atmospheric Effects, Fourier Series, Interferometry, Polarization (Waves), Astronomy, EMISSION SPECTRA, HALLEY'S COMET, INFRARED SPECTROSCOPY, WATER VAPOR, COMETARY ATMOSPHERES, INFRARED ASTRONOMY, SPACE OBSERVATIONS (FROM EARTH), Astrophysics}, + year = 1986, + month = jan, + volume = {24}, + pages = {127-170}, + doi = {10.1146/annurev.aa.24.090186.001015}, + adsurl = {https://ui.adsabs.harvard.edu/abs/1986ARA&A..24..127N}, + adsnote = {Provided by the SAO/NASA Astrophysics Data System} +} + +@article{huang24, + author = {{Huang}, Jane and {Ansdell}, Megan and {Birnstiel}, Tilman and {Czekala}, Ian and {Long}, Feng and {Williams}, Jonathan and {Zhang}, Shangjia and {Zhu}, Zhaohuan}, + title = {{High-resolution ALMA Observations of Richly Structured Protoplanetary Disks in {\ensuremath{\sigma}} Orionis}}, + journal = {The Astrophysical Journal}, + keywords = {Protoplanetary disks, Planet formation, Radio interferometry, 1300, 1241, 1346, Astrophysics - Earth and Planetary Astrophysics, Astrophysics - Solar and Stellar Astrophysics}, + year = 2024, + month = nov, + volume = {976}, + number = {1}, + eid = {132}, + pages = {132}, + doi = {10.3847/1538-4357/ad84df}, + archiveprefix = {arXiv}, + eprint = {2410.03823}, + primaryclass = {astro-ph.EP}, + adsurl = {https://ui.adsabs.harvard.edu/abs/2024ApJ...976..132H}, + adsnote = {Provided by the SAO/NASA Astrophysics Data System} +} + +@book{thompson17, + author = {{Thompson}, A. Richard and {Moran}, James M. and {Swenson}, George W., Jr.}, + title = {{Interferometry and Synthesis in Radio Astronomy, 3rd Edition}}, + year = 2017, + doi = {10.1007/978-3-319-44431-4}, + adsurl = {https://ui.adsabs.harvard.edu/abs/2017isra.book.....T}, + adsnote = {Provided by the SAO/NASA Astrophysics Data System} +} + +@article{disk20, + author = {{Disk Dynamics Collaboration} and {Armitage}, Philip J. and {Bae}, Jaehan and {Benisty}, Myriam and {Bergin}, Edwin A. and {Casassus}, Simon and {Czekala}, Ian and {Facchini}, Stefano and {Fung}, Jeffrey and {Hall}, Cassandra and {Ilee}, John D. and {Keppler}, Miriam and {Kuznetsova}, Aleksandra and {Le Gal}, Romane and {Loomis}, Ryan A. and {Lyra}, Wladimir and {Manger}, Natascha and {Perez}, Sebastian and {Pinte}, Christophe and {Price}, Daniel J. and {Rosotti}, Giovanni and {Szulagyi}, Judit and {Schwarz}, Kamber and {Simon}, Jacob B. and {Teague}, Richard and {Zhang}, Ke}, + title = {{Visualizing the Kinematics of Planet Formation}}, + journal = {arXiv e-prints}, + keywords = {Astrophysics - Earth and Planetary Astrophysics}, + year = 2020, + month = sep, + eid = {arXiv:2009.04345}, + pages = {arXiv:2009.04345}, + doi = {10.48550/arXiv.2009.04345}, + archiveprefix = {arXiv}, + eprint = {2009.04345}, + primaryclass = {astro-ph.EP}, + adsurl = {https://ui.adsabs.harvard.edu/abs/2020arXiv200904345D}, + adsnote = {Provided by the SAO/NASA Astrophysics Data System} +} + +@article{paszke19, + author = {{Paszke}, Adam and {Gross}, Sam and {Massa}, Francisco and {Lerer}, Adam and {Bradbury}, James and {Chanan}, Gregory and {Killeen}, Trevor and {Lin}, Zeming and {Gimelshein}, Natalia and {Antiga}, Luca and {Desmaison}, Alban and {K{\"o}pf}, Andreas and {Yang}, Edward and {DeVito}, Zach and {Raison}, Martin and {Tejani}, Alykhan and {Chilamkurthy}, Sasank and {Steiner}, Benoit and {Fang}, Lu and {Bai}, Junjie and {Chintala}, Soumith}, + title = {{PyTorch: An Imperative Style, High-Performance Deep Learning Library}}, + journal = {arXiv e-prints}, + keywords = {Computer Science - Machine Learning, Computer Science - Mathematical Software, Statistics - Machine Learning}, + year = 2019, + month = dec, + eid = {arXiv:1912.01703}, + pages = {arXiv:1912.01703}, + doi = {10.48550/arXiv.1912.01703}, + archiveprefix = {arXiv}, + eprint = {1912.01703}, + primaryclass = {cs.LG}, + adsurl = {https://ui.adsabs.harvard.edu/abs/2019arXiv191201703P}, + adsnote = {Provided by the SAO/NASA Astrophysics Data System} +} + +@conference{nufft20, + author = {M. J. Muckley and R. Stern and T. Murrell and F. Knoll}, + title = {{TorchKbNufft}: A High-Level, Hardware-Agnostic Non-Uniform Fast {Fourier} Transform}, + booktitle = {ISMRM Workshop on Data Sampling \& Image Reconstruction}, + year = 2020, + note = {Source code available at https://github.com/mmuckley/torchkbnufft} +} + +@article{wootten09, + author = {{Wootten}, Alwyn and {Thompson}, A. Richard}, + title = {{The Atacama Large Millimeter/Submillimeter Array}}, + journal = {IEEE Proceedings}, + keywords = {Astrophysics - Instrumentation and Methods for Astrophysics}, + year = 2009, + month = aug, + volume = {97}, + number = {8}, + pages = {1463-1471}, + doi = {10.1109/JPROC.2009.2020572}, + archiveprefix = {arXiv}, + eprint = {0904.3739}, + primaryclass = {astro-ph.IM}, + adsurl = {https://ui.adsabs.harvard.edu/abs/2009IEEEP..97.1463W}, + adsnote = {Provided by the SAO/NASA Astrophysics Data System} +} + +@article{harris20, + title = {Array programming with {NumPy}}, + author = {Charles R. Harris and K. Jarrod Millman and St{\'{e}}fan J. + van der Walt and Ralf Gommers and Pauli Virtanen and David + Cournapeau and Eric Wieser and Julian Taylor and Sebastian + Berg and Nathaniel J. Smith and Robert Kern and Matti Picus + and Stephan Hoyer and Marten H. van Kerkwijk and Matthew + Brett and Allan Haldane and Jaime Fern{\'{a}}ndez del + R{\'{i}}o and Mark Wiebe and Pearu Peterson and Pierre + G{\'{e}}rard-Marchant and Kevin Sheppard and Tyler Reddy and + Warren Weckesser and Hameer Abbasi and Christoph Gohlke and + Travis E. Oliphant}, + year = {2020}, + month = sep, + journal = {Nature}, + volume = {585}, + number = {7825}, + pages = {357--362}, + doi = {10.1038/s41586-020-2649-2}, + publisher = {Springer Science and Business Media {LLC}}, + url = {https://doi.org/10.1038/s41586-020-2649-2} +} + +@book{condon16, + author = {{Condon}, James J. and {Ransom}, Scott M.}, + title = {{Essential Radio Astronomy}}, + year = 2016, + adsurl = {https://ui.adsabs.harvard.edu/abs/2016era..book.....C}, + adsnote = {Provided by the SAO/NASA Astrophysics Data System} +} + +@article{baydin18, + author = {Atilim Gunes Baydin and Barak A. Pearlmutter and Alexey Andreyevich Radul and Jeffrey Mark Siskind}, + title = {Automatic Differentiation in Machine Learning: a Survey}, + journal = {Journal of Machine Learning Research}, + year = {2018}, + volume = {18}, + number = {153}, + pages = {1--43}, + url = {http://jmlr.org/papers/v18/17-468.html} +} + +@article{loshchilov17, + author = {{Loshchilov}, Ilya and {Hutter}, Frank}, + title = {{Decoupled Weight Decay Regularization}}, + journal = {arXiv e-prints}, + keywords = {Computer Science - Machine Learning, Computer Science - Neural and Evolutionary Computing, Mathematics - Optimization and Control}, + year = 2017, + month = nov, + eid = {arXiv:1711.05101}, + pages = {arXiv:1711.05101}, + doi = {10.48550/arXiv.1711.05101}, + archiveprefix = {arXiv}, + eprint = {1711.05101}, + primaryclass = {cs.LG}, + adsurl = {https://ui.adsabs.harvard.edu/abs/2017arXiv171105101L}, + adsnote = {Provided by the SAO/NASA Astrophysics Data System} +} + +@article{pyro19, + author = {Bingham, Eli and Chen, Jonathan P. and Jankowiak, Martin and Obermeyer, Fritz and Pradhan, Neeraj and Karaletsos, Theofanis and Singh, Rohit and Szerlip, Paul and Horsfall, Paul and Goodman, Noah D.}, + title = {Pyro: deep universal probabilistic programming}, + year = {2019}, + issue_date = {January 2019}, + publisher = {JMLR.org}, + volume = {20}, + number = {1}, + issn = {1532-4435}, + abstract = {Pyro is a probabilistic programming language built on Python as a platform for developing advanced probabilistic models in AI research. To scale to large data sets and high-dimensional models, Pyro uses stochastic variational inference algorithms and probability distributions built on top of PyTorch, a modern GPU-accelerated deep learning framework. To accommodate complex or model-specific algorithmic behavior, Pyro leverages Poutine, a library of composable building blocks for modifying the behavior of probabilistic programs.}, + journal = {J. Mach. Learn. Res.}, + month = {jan}, + pages = {973–978}, + numpages = {6}, + keywords = {probabilistic programming, graphical models, generative models, deep learning, approximate Bayesian inference} +} + +@article{tazzari18, + author = {{Tazzari}, M. and {Beaujean}, F. and {Testi}, L.}, + title = {{GALARIO: a GPU accelerated library for analysing radio interferometer observations}}, + journal = {\mnras}, + archiveprefix = {arXiv}, + eprint = {1709.06999}, + primaryclass = {astro-ph.IM}, + keywords = {methods: numerical, techniques: interferometric, submillimetre: general}, + year = 2018, + month = jun, + volume = 476, + pages = {4527-4542}, + doi = {10.1093/mnras/sty409}, + adsurl = {http://adsabs.harvard.edu/abs/2018MNRAS.476.4527T}, + adsnote = {Provided by the SAO/NASA Astrophysics Data System} +} + + +@article{guzman18, + author = {{Guzm{\'a}n}, Viviana V. and {Huang}, Jane and {Andrews}, Sean M. and {Isella}, Andrea and {P{\'e}rez}, Laura M. and {Carpenter}, John M. and {Dullemond}, Cornelis P. and {Ricci}, Luca and {Birnstiel}, Tilman and {Zhang}, Shangjia and {Zhu}, Zhaohuan and {Bai}, Xue-Ning and {Benisty}, Myriam and {{\"O}berg}, Karin I. and {Wilner}, David J.}, + title = {{The Disk Substructures at High Angular Resolution Program (DSHARP). VIII. The Rich Ringed Substructures in the AS 209 Disk}}, + journal = {\apjl}, + keywords = {dust, extinction, protoplanetary disks, techniques: high angular resolution, Astrophysics - Solar and Stellar Astrophysics, Astrophysics - Earth and Planetary Astrophysics, Astrophysics - Astrophysics of Galaxies}, + year = 2018, + month = dec, + volume = {869}, + number = {2}, + eid = {L48}, + pages = {L48}, + doi = {10.3847/2041-8213/aaedae}, + archiveprefix = {arXiv}, + eprint = {1812.04046}, + primaryclass = {astro-ph.SR}, + adsurl = {https://ui.adsabs.harvard.edu/abs/2018ApJ...869L..48G}, + adsnote = {Provided by the SAO/NASA Astrophysics Data System} +} + + +@article{dia23, + author = {{Dia}, Noe and {Yantovski-Barth}, M.~J. and {Adam}, Alexandre and {Bowles}, Micah and {Lemos}, Pablo and {Scaife}, Anna M.~M. and {Hezaveh}, Yashar and {Perreault-Levasseur}, Laurence}, + title = {{Bayesian Imaging for Radio Interferometry with Score-Based Priors}}, + journal = {arXiv e-prints}, + keywords = {Astrophysics - Instrumentation and Methods for Astrophysics, Computer Science - Computer Vision and Pattern Recognition}, + year = 2023, + month = nov, + eid = {arXiv:2311.18012}, + pages = {arXiv:2311.18012}, + doi = {10.48550/arXiv.2311.18012}, + archiveprefix = {arXiv}, + eprint = {2311.18012}, + primaryclass = {astro-ph.IM}, + adsurl = {https://ui.adsabs.harvard.edu/abs/2023arXiv231118012D}, + adsnote = {Provided by the SAO/NASA Astrophysics Data System} +} + + +@article{huang18b, + author = {{Huang}, Jane and {Andrews}, Sean M. and {P{\'e}rez}, Laura M. and {Zhu}, Zhaohuan and {Dullemond}, Cornelis P. and {Isella}, Andrea and {Benisty}, Myriam and {Bai}, Xue-Ning and {Birnstiel}, Tilman and {Carpenter}, John M. and {Guzm{\'a}n}, Viviana V. and {Hughes}, A. Meredith and {{\"O}berg}, Karin I. and {Ricci}, Luca and {Wilner}, David J. and {Zhang}, Shangjia}, + title = {{The Disk Substructures at High Angular Resolution Project (DSHARP). III. 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A full-sky Jones formalism}}, + journal = {\aap}, + keywords = {methods: numerical, methods: analytical, methods: data analysis, techniques: interferometric, techniques: polarimetric, Astrophysics - Instrumentation and Methods for Astrophysics}, + year = 2011, + month = mar, + volume = {527}, + eid = {A106}, + pages = {A106}, + doi = {10.1051/0004-6361/201016082}, + archiveprefix = {arXiv}, + eprint = {1101.1764}, + primaryclass = {astro-ph.IM}, + adsurl = {https://ui.adsabs.harvard.edu/abs/2011A&A...527A.106S}, + adsnote = {Provided by the SAO/NASA Astrophysics Data System} +} \ No newline at end of file diff --git a/paper/paper.md b/paper/paper.md new file mode 100644 index 00000000..2cdb63c0 --- /dev/null +++ b/paper/paper.md @@ -0,0 +1,99 @@ +--- +title: 'Million Points of Light (MPoL): a PyTorch library for radio interferometric imaging and inference' +tags: + - Python + - astronomy + - imaging + - fourier + - radio astronomy + - radio interferometry + - machine learning + - neural networks +authors: + - name: Ian Czekala + orcid: 0000-0002-1483-8811 + corresponding: true + affiliation: 1 + - name: co-authors + # - name: Jeff Jennings + # orcid: 0000-0002-7032-2350 + # affiliation: 2 + # - name: Brianna Zawadzki + # orcid: 0000-0001-9319-1296 + # affiliation: 3 + # - name: Kadri Nizam + # orcid: 0000-0002-7217-446X + # affiliation: 2 + # - name: Ryan Loomis + # orcid: 0000-0002-8932-1219 + # affiliation: 4 + # - name: Megan Delamer + # orcid: 0000-0003-1439-2781 + # affiliation: 2 + # - name: Kaylee de Soto + # orcid: 0000-0002-9886-2834 + # affiliation: 2 + # - name: Robert Frazier + # orcid: 0000-0001-6569-3731 + # affiliation: 2 + # - name: Hannah Grzybowski + # # orcid: # can't find + # affiliation: 2 + # - name: Mary Ogborn + # orcid: 0000-0001-9741-2703 + # affiliation: 2 + # - name: Tyler Quinn + # orcid: 0000-0002-8974-8095 + # affiliation: 2 +affiliations: + - name: University of St Andrews, Scotland + index: 1 +# - name: Pennsylvania State University, USA +# index: 2 +# - name: Wesleyan University, USA +# index: 3 +# - name: National Radio Astronomy Observatory, Charlottesville, VA, USA +# index: 4 +date: 16 December 2024 +bibliography: paper.bib +aas-journal: Astrophysical Journal +--- + +# Summary + +Astronomical radio interferometers achieve exquisite angular resolution by cross-correlating signal from a cosmic source simultaneously observed by distant pairs of radio telescopes to produce a Fourier-type measurement called a visibility. *Million Points of Light* (`MPoL`) is a Python library supporting feed-forward modeling of interferometric visibility datasets for synthesis imaging and parametric Bayesian inference, built using the autodifferentiable machine learning framework PyTorch. Neural network components provide a rich set of modular and composable building blocks that can be used to express the physical relationships between latent model parameters and observed data following the radio interferometric measurement equation. Industry-grade optimizers make it straightforward to simultaneously solve for the synthesized image and calibration parameters using stochastic gradient descent. + +# Statement of need + +When an astrophysical source is observed by a radio interferometer, there are typically gaps in the spatial frequency coverage. Therefore, rather than perform a direct Fourier inversion, images must be synthesized from the visibility data using an imaging algorithm; it is common for the incomplete sampling to severely hamper image fidelity [@condon16; @thompson17]. CLEAN is the traditional image synthesis algorithm of the radio interferometry community [@hogbom74], with a modern implementation in the facility software CASA [@mcmullin07; @casa22]. CLEAN excels at the rapid imaging of astronomical fields comprising unresolved point sources (e.g. quasars) and marginally resolved sources, but often struggles to achieve the desired imaging performance for spatially extended sources [@disk20, §3]. + +In the field of planet formation alone, spatially resolved observations from the Atacama Large Millimeter Array (ALMA; @wootten09) have rapidly advanced our understanding of protoplanetary disk structures [@andrews20], kinematic signatures of embedded protoplanets [@pinte18], and circumplanetary disks [@benisty21]. High fidelity imaging algorithms for spatially resolved sources are needed to realize the full scientific potential of groundbreaking observatories like ALMA, the Event Horizon Telescope [@eht19a], and the Square Kilometer Array [@dewdney09] as they deliver significantly improved sensitivity and resolving power compared to previous generation instruments. Moreover, there is an opportunity for a flexible, open-source platform to interface with machine learning algorithms and computational imaging software from non-astronomy fields. + +# The Million Points of Light (MPoL) library + +`MPoL` is a library designed for feed-forward modeling of interferometric datasets using Python, Numpy [@harris20], and the computationally performant machine learning framework PyTorch [@paszke19], which debuted with @zawadzki23. `MPoL` implements a set of foundational interferometry components using PyTorch `nn.module`, which can be easily combined to build a forward-model of the interferometric dataset(s) at hand. We strive to seamlessly integrate with the PyTorch ecosystem so that users can easily leverage well-established machine learning workflows: optimization with stochastic gradient descent, straightforward acceleration with GPU(s), and integration with common neural network architectures. + +In a typical feed-forward workflow, `MPoL` users will use foundational components like `BaseCube` and `ImageCube` to define the true-sky model, Fourier layers like `FourierCube` or `NuFFT` [wrapping `torchkbnufft`; @nufft20] to apply the Fourier transform and sample the visibility function at the location of the array baselines, and the negative log likelihood to calculate a data loss. Backpropagation [see @baydin18 for a review] and stochastic gradient descent [e.g., AdamW; @loshchilov17] are used to find the true-sky model that minimizes the loss function. However, because of the aforementioned gaps in spatial frequency coverage, there is technically an infinite number of true-sky images fully consistent with the data likelihood, so regularization loss terms are required. `MPoL` supports Regularized Maximum Likelihood (RML) imaging with common regularizers like maximum entropy, sparsity, and others [e.g., as used in @eht19d]; users can also implement custom regularizers with PyTorch. + +`MPoL` also provides several other workflows relevant to astrophysical research. First, by seamlessly coupling with the probabilistic programming language Pyro [@pyro19], `MPoL` supports Bayesian parametric inference of astronomical sources. Second, users can implement additional data calibration components as their data requires, enabling fine-scale, residual calibration physics to be parameterized and optimized simultaneously with image synthesis [following the radio interferometric measurement equation @hamaker96; @smirnov11a]. Finally, the library also provides convenience utilities like `DirtyImager` (with Briggs robust and UV taper) to confirm the data has been loaded correctly. + +# Documentation, examples, and scientific results + +MPoL is freely available, open-source software licensed via the MIT license and is developed on GitHub at [MPoL-dev/MPoL](https://github.com/MPoL-dev/MPoL). Installation and API documentation is hosted at [https://mpol-dev.github.io/MPoL/](https://mpol-dev.github.io/MPoL/), and is continuously built with each commit to the `main` branch. As a library, `MPoL` expects researchers to write short scripts using use `MPoL` and PyTorch primitives, in much the same way that PyTorch users write scripts for machine learning workflows (e.g., as in the [official PyTorch examples](https://github.com/pytorch/examples)). `MPoL` example projects are hosted on GitHub at [MPoL-dev/examples](https://github.com/MPoL-dev/examples). These include an introduction to generating mock data, a quickstart using stochastic gradient descent, and a Pyro workflow using SVI to replicate the parametric inference done in @guzman18, among others. In Figure \ref{imlup}, we compare an image obtained with CLEAN to that using `MPoL` and RML, synthesized from the data presented in @huang18b, highlighting the improvement in resolution offered by feed-forward modeling technologies. + +`MPoL` has already been used in a number of scientific publications. @zawadzki23 introduced `MPoL` and explored RML imaging for ALMA observations of protoplanetary disks, finding a 3x improvement in spatial resolution at comparable sensitivity. @dia23 used `MPoL` as a reference imaging implementation to evaluate the performance of their score-based prior algorithm. @huang24 used the parametric inference capabilities of `MPoL` to analyze radial dust substructures in a suite of eight protoplanetary disks in $\sigma$ Orionis stellar cluster. `MPoL` was selected as an imaging technology of the exoALMA large program, where Zawadzki et al. 2024 *submitted* used RML imaging to obtain high resolution image cubes of non-Keplerian features in protoplanetary disks. + +![Left: the synthesized image produced by the DSHARP ALMA Large Program [@andrews18] using `CASA/tclean`. Right: The regularized maximum likelihood image produced using `MPoL` on the same data. Both images are displayed using a `sqrt` stretch, with upper limit truncated to 70\% and 40\% of max value for CLEAN and `MPoL`, respectively, to emphasize faint features. The CLEAN algorithm permits negative intensity values, while the `MPoL` algorithm enforces image positivity by construction. Each side of the image is 3 arcseconds. Intensity units are shown in units of Jy/arcsec^2^. \label{imlup}](fig.pdf) + +# Similar tools + +Recently, there has been significant work to design robust algorithms to image spatially resolved sources. A non-exhaustive list includes the `RESOLVE` family of algorithms, which impose Gaussian random field image priors, the multi-algorithm approach of the Event Horizon Telescope Collaboration [@eht19d] including regularized maximum likelihood techniques, and domain-specific non-parametric 1D approaches like `frank` [@jennings20]. Several approaches have leveraged deep-learning, such as score-based priors [@dia23], denoising diffusion probabilistic models [@wang23], and residual-to-residual deep neural networks [@dabbech24]. By contrast to many imaging software programs, `MPoL` is designed as a library, and so in theory can support a variety of forward-modeling workflows. The MPoL-dev organization also develops the [MPoL-dev/visread](https://mpol-dev.github.io/visread/) package, which is designed to facilitate the extraction of visibility data from CASA's Measurement Set format for use in alternative imaging workflows. + +The parametric modeling capabilities of `MPoL`, provided by integration with `Pyro`, are similar to the `emcee` [@foreman-mackey13] + synthetic visibility workflow provided by the Galario software [@tazzari18]. Since PyTorch enables automatic differentiation, `Pyro` users can utilize HMC/NUTS sampling [@neal12; @hoffman14], which offers significant benefits in high dimensional spaces compared to ensemble MCMC samplers. + + +# Acknowledgements + +We acknowledge funding from an ALMA Development Cycle 8 grant number AST-1519126. ALMA is a partnership of ESO (representing its member states), NSF (USA) and NINS (Japan), together with NRC (Canada), MOST and ASIAA (Taiwan), and KASI (Republic of Korea), in cooperation with the Republic of Chile. The Joint ALMA Observatory is operated by ESO, AUI/NRAO and NAOJ. The National Radio Astronomy Observatory is a facility of the National Science Foundation operated under cooperative agreement by Associated Universities, Inc. + +# References