diff --git a/.github/workflows/compile-paper.yaml b/.github/workflows/compile-paper.yaml new file mode 100644 index 0000000..310981b --- /dev/null +++ b/.github/workflows/compile-paper.yaml @@ -0,0 +1,23 @@ +on: [push] + +jobs: + paper: + runs-on: ubuntu-latest + name: 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: joss-paper/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/paper.pdf diff --git a/joss-paper/2dps.pdf b/joss-paper/2dps.pdf new file mode 100644 index 0000000..870263a Binary files /dev/null and b/joss-paper/2dps.pdf differ diff --git a/joss-paper/2dps.png:Zone.Identifier b/joss-paper/2dps.png:Zone.Identifier new file mode 100644 index 0000000..b6cf92b --- /dev/null +++ b/joss-paper/2dps.png:Zone.Identifier @@ -0,0 +1,4 @@ +[ZoneTransfer] +ZoneId=3 +ReferrerUrl=https://21cmsense.readthedocs.io/en/latest/tutorials/understanding_21cmsense.html +HostUrl=https://21cmsense.readthedocs.io/en/latest/_images/tutorials_understanding_21cmsense_75_0.png diff --git a/joss-paper/paper.bib b/joss-paper/paper.bib new file mode 100644 index 0000000..75a451f --- /dev/null +++ b/joss-paper/paper.bib @@ -0,0 +1,382 @@ +@article{ + mwa, + title={The Murchison Widefield Array: The Square Kilometre Array Precursor at Low Radio Frequencies}, + volume={30}, + DOI={10.1017/pasa.2012.007}, + journal={Publications of the Astronomical Society of Australia}, + publisher={Cambridge University Press}, + author={Tingay, S. J. and Goeke, R. and Bowman, J. D. and Emrich, D. and Ord, S. M. and Mitchell, D. A. and Morales, M. F. and Booler, T. and Crosse, B. and Wayth, R. B. and et al.}, + year={2013}, + pages={e007} +} + +@conference{jupyter, + Title = {Jupyter Notebooks -- a publishing format for reproducible computational workflows}, + Author = {Thomas Kluyver and Benjamin Ragan-Kelley and Fernando P{\'e}rez and Brian Granger and Matthias Bussonnier and Jonathan Frederic and Kyle Kelley and Jessica Hamrick and Jason Grout and Sylvain Corlay and Paul Ivanov and Dami{\'a}n Avila and Safia Abdalla and Carol Willing}, + Booktitle = {Positioning and Power in Academic Publishing: Players, Agents and Agendas}, + Editor = {F. Loizides and B. Schmidt}, + Organization = {IOS Press}, + Pages = {87 - 90}, + Year = {2016} +} + +@article{astropy, + title = {The {{Astropy Project}}: {{Building}} an {{Open-science Project}} and {{Status}} of the v2.0 {{Core Package}}}, + shorttitle = {The {{Astropy Project}}}, + author = {{Astropy Collaboration} and {Price-Whelan}, A. M. and Sip{\H o}cz, B. M. and G{\"u}nther, H. M. and Lim, P. L. and Crawford, S. M. and Conseil, S. and Shupe, D. L. and Craig, M. W. and Dencheva, N. and Ginsburg, A. and VanderPlas, J. T. and Bradley, L. D. and {P{\'e}rez-Su{\'a}rez}, D. and {de Val-Borro}, M. and Aldcroft, T. L. and Cruz, K. L. and Robitaille, T. P. and Tollerud, E. J. and Ardelean, C. and Babej, T. and Bach, Y. P. and Bachetti, M. and Bakanov, A. V. and Bamford, S. P. and Barentsen, G. and Barmby, P. and Baumbach, A. and Berry, K. L. and Biscani, F. and Boquien, M. and Bostroem, K. A. and Bouma, L. G. and Brammer, G. B. and Bray, E. M. and Breytenbach, H. and Buddelmeijer, H. and Burke, D. J. and Calderone, G. and Cano Rodr{\'i}guez, J. L. and Cara, M. and Cardoso, J. V. M. and Cheedella, S. and Copin, Y. and Corrales, L. and Crichton, D. and D'Avella, D. and Deil, C. and Depagne, {\'E}. and Dietrich, J. P. and Donath, A. and Droettboom, M. and Earl, N. and Erben, T. and Fabbro, S. and Ferreira, L. A. and Finethy, T. and Fox, R. T. and Garrison, L. H. and Gibbons, S. L. J. and Goldstein, D. A. and Gommers, R. and Greco, J. P. and Greenfield, P. and Groener, A. M. and Grollier, F. and Hagen, A. and Hirst, P. and Homeier, D. and Horton, A. J. and Hosseinzadeh, G. and Hu, L. and Hunkeler, J. S. and Ivezi{\'c}, {\v Z}. and Jain, A. and Jenness, T. and Kanarek, G. and Kendrew, S. and Kern, N. S. and Kerzendorf, W. E. and Khvalko, A. and King, J. and Kirkby, D. and Kulkarni, A. M. and Kumar, A. and Lee, A. and Lenz, D. and Littlefair, S. P. and Ma, Z. and Macleod, D. M. and Mastropietro, M. and McCully, C. and Montagnac, S. and Morris, B. M. and Mueller, M. and Mumford, S. J. and Muna, D. and Murphy, N. A. and Nelson, S. and Nguyen, G. H. and Ninan, J. P. and N{\"o}the, M. and Ogaz, S. and Oh, S. and Parejko, J. K. and Parley, N. and Pascual, S. and Patil, R. and Patil, A. A. and Plunkett, A. L. and Prochaska, J. X. and Rastogi, T. and Reddy Janga, V. and Sabater, J. and Sakurikar, P. and Seifert, M. and Sherbert, L. E. and {Sherwood-Taylor}, H. and Shih, A. Y. and Sick, J. and Silbiger, M. T. and Singanamalla, S. and Singer, L. P. and Sladen, P. H. and Sooley, K. A. and Sornarajah, S. and Streicher, O. and Teuben, P. and Thomas, S. W. and Tremblay, G. R. and Turner, J. E. H. and Terr{\'o}n, V. and {van Kerkwijk}, M. H. and {de la Vega}, A. and Watkins, L. L. and Weaver, B. A. and Whitmore, J. B. and Woillez, J. and Zabalza, V. and {Astropy Contributors}}, + year = {2018}, + month = sep, + journal = {The Astronomical Journal}, + volume = {156}, + pages = {123}, + url = {http://adsabs.harvard.edu/abs/2018AJ....156..123A}, + urldate = {2020-09-28}, + abstract = {The Astropy Project supports and fosters the development of open-source and openly developed Python packages that provide commonly needed functionality to the astronomical community. A key element of the Astropy Project is the core package astropy, which serves as the foundation for more specialized projects and packages. In this article, we provide an overview of the organization of the Astropy project and summarize key features in the core package, as of the recent major release, version 2.0. We then describe the project infrastructure designed to facilitate and support development for a broader ecosystem of interoperable packages. We conclude with a future outlook of planned new features and directions for the broader Astropy Project. .}, + keywords = {methods: data analysis,methods: miscellaneous,methods: statistical,reference systems}, + annotation = {985 citations (Inspire/DOI) [2022-06-01]}, + doi = {10.3847/1538-3881/aabc4f} +} + +@article{fhd, + title = {The {{FHD}}/\${\textbackslash}epsilon\$ppsilon {{Epoch}} of {{Reionisation}} Power Spectrum Pipeline}, + author = {Barry, N. and Beardsley, A. P. and Byrne, R. and Hazelton, B. and Morales, M. F. and Pober, J. C. and Sullivan, I.}, + year = {2019}, + month = jul, + journal = {Publications of the Astronomical Society of Australia}, + volume = {36}, + eprint = {1901.02980}, + pages = {e026}, + url = {http://adsabs.harvard.edu/abs/2019PASA...36...26B}, + urldate = {2020-11-10}, + abstract = {Epoch of Reionisation (EoR) data analysis requires unprecedented levels of accuracy in radio interferometer pipelines. We have developed an imaging power spectrum analysis to meet these requirements and generate robust 21 cm EoR measurements. In this work, we build a signal path framework to mathematically describe each step in the analysis, from data reduction in the Fast Holographic Deconvolution (FHD) package to power spectrum generation in the {$\varepsilon$}ppsilon package. In particular, we focus on the distinguishing characteristics of FHD/{$\varepsilon$}ppsilon: highly accurate spectral calibration, extensive data verification products, and end-to-end error propagation. We present our key data analysis products in detail to facilitate understanding of the prominent systematics in image-based power spectrum analyses. As a verification to our analysis, we also highlight a full-pipeline analysis simulation to demonstrate signal preservation and lack of signal loss. This careful treatment ensures that the FHD/{$\varepsilon$}ppsilon power spectrum pipeline can reduce radio interferometric data to produce credible 21 cm EoR measurements.}, + archiveprefix = {arxiv}, + keywords = {Astrophysics - Instrumentation and Methods for Astrophysics,cosmology: dark ages,data analysis,first stars,instrumentation,interferometers,interferometric,methods,reionisation,techniques}, + file = {C:\Users\steve\Zotero\storage\MB6SV4BT\1901.html}, + doi = {10.1017/pasa.2019.21} +} + +@article{Breitman2024, + title = {{{21CMEMU}}: An Emulator of {{21CMFAST}} Summary Observables}, + shorttitle = {{{21CMEMU}}}, + author = {Breitman, Daniela and Mesinger, Andrei and Murray, Steven G. and Prelogovi{\'c}, David and Qin, Yuxiang and Trotta, Roberto}, + year = {2024}, + month = feb, + journal = {Monthly Notices of the Royal Astronomical Society}, + volume = {527}, + pages = {9833--9852}, + issn = {0035-8711}, + url = {https://ui.adsabs.harvard.edu/abs/2024MNRAS.527.9833B}, + urldate = {2024-01-18}, + abstract = {Recent years have witnessed rapid progress in observations of the epoch of reionization (EoR). These have enabled high-dimensional inference of galaxy and intergalactic medium (IGM) properties during the first billion years of our Universe. However, even using efficient, seminumerical simulations, traditional inference approaches that compute 3D lightcones on-the-fly can take 105 core hours. Here we present 21CMEMU: an emulator of several summary observables from the popular 21CMFAST simulation code. 21CMEMU takes as input nine parameters characterizing EoR galaxies, and outputs the following summary statistics: (i) the IGM mean neutral fraction; (ii) the 21-cm power spectrum; (iii) the mean 21-cm spin temperature; (iv) the sky-averaged (global) 21-cm signal; (vi) the ultraviolet (UV) luminosity functions (LFs); and (vii) the Thomson scattering optical depth to the cosmic microwave background (CMB). All observables are predicted with sub- per cent median accuracy, with a reduction of the computational cost by a factor of over 104. After validating inference results, we showcase a few applications, including: (i) quantifying the relative constraining power of different observational data sets; (ii) seeing how recent claims of a late EoR impact previous inferences; and (iii) forecasting upcoming constraints from the sixth observing season of the Hydrogen Epoch of Reionization Array (HERA) telescope. 21CMEMU is publicly available, and is included as an alternative simulator in the public 21CMMC sampler.}, + keywords = {Astrophysics - Astrophysics of Galaxies,Astrophysics - Cosmology and Nongalactic Astrophysics,cosmology: theory,dark ages,first stars,methods: data analysis,methods: statistical,reionization,Statistics - Machine Learning}, + annotation = {ADS Bibcode: 2024MNRAS.527.9833B}, + file = {C:\Users\steve\Zotero\storage\NT4VDXN4\Breitman et al. - 2024 - 21CMEMU an emulator of 21CMFAST summary observabl.pdf}, + doi = {10.1093/mnras/stad3849} +} + +@article{hera, + title = {Hydrogen {{Epoch}} of {{Reionization Array}} ({{HERA}})}, + author = {DeBoer, David R. and Parsons, Aaron R. and Aguirre, James E. and Alexander, Paul and Ali, Zaki S. and Beardsley, Adam P. and Bernardi, Gianni and Bowman, Judd D. and Bradley, Richard F. and Carilli, Chris L. and Cheng, Carina and Acedo, Eloy de Lera and Dillon, Joshua S. and {Ewall-Wice}, Aaron and Fadana, Gcobisa and Fagnoni, Nicolas and Fritz, Randall and Furlanetto, Steve R. and Glendenning, Brian and Greig, Bradley and Grobbelaar, Jasper and Hazelton, Bryna J. and Hewitt, Jacqueline N. and Hickish, Jack and Jacobs, Daniel C. and Julius, Austin and Kariseb, MacCalvin and Kohn, Saul A. and {Telalo Lekalake} and Liu, Adrian and Loots, Anita and MacMahon, David and Malan, Lourence and Malgas, Cresshim and Maree, Matthys and {Zachary Martinot} and Mathison, Nathan and Matsetela, Eunice and Mesinger, Andrei and Morales, Miguel F. and Neben, Abraham R. and Patra, Nipanjana and Pieterse, Samantha and Pober, Jonathan C. and {Razavi-Ghods}, Nima and Ringuette, Jon and {James Robnett} and Rosie, Kathryn and Sell, Raddwine and Smith, Craig and Syce, Angelo and Tegmark, Max and {Nithyanandan Thyagarajan} and Williams, Peter K. G. and Zheng, Haoxuan}, + year = {2017}, + journal = {Publications of the Astronomical Society of the Pacific}, + volume = {129}, + number = {974}, + pages = {045001}, + issn = {1538-3873}, + url = {http://stacks.iop.org/1538-3873/129/i=974/a=045001}, + urldate = {2018-11-20}, + abstract = {The Hydrogen Epoch of Reionization Array (HERA) is a staged experiment to measure 21 cm emission from the primordial intergalactic medium (IGM) throughout cosmic reionization ( z = 6{\textendash}12), and to explore earlier epochs of our Cosmic Dawn ( z {$\sim$} 30). During these epochs, early stars and black holes heated and ionized the IGM, introducing fluctuations in 21 cm emission. HERA is designed to characterize the evolution of the 21 cm power spectrum to constrain the timing and morphology of reionization, the properties of the first galaxies, the evolution of large-scale structure, and the early sources of heating. The full HERA instrument will be a 350-element interferometer in South Africa consisting of 14 m parabolic dishes observing from 50 to 250 MHz. Currently, 19 dishes have been deployed on site and the next 18 are under construction. HERA has been designated as an SKA Precursor instrument. In this paper, we summarize HERA's scientific context and provide forecasts for its key science results. After reviewing the current state of the art in foreground mitigation, we use the delay-spectrum technique to motivate high-level performance requirements for the HERA instrument. Next, we present the HERA instrument design, along with the subsystem specifications that ensure that HERA meets its performance requirements. Finally, we summarize the schedule and status of the project. We conclude by suggesting that, given the realities of foreground contamination, current-generation 21 cm instruments are approaching their sensitivity limits. HERA is designed to bring both the sensitivity and the precision to deliver its primary science on the basis of proven foreground filtering techniques, while developing new subtraction techniques to unlock new capabilities. The result will be a major step toward realizing the widely recognized scientific potential of 21 cm cosmology.}, + langid = {english}, + annotation = {352 citations (Inspire/DOI) [2022-06-01]}, + doi = {10.1088/1538-3873/129/974/045001} +} + +@article{Greig2015, + title = {{{21CMMC}}: An {{MCMC}} Analysis Tool Enabling Astrophysical Parameter Studies of the Cosmic 21 Cm Signal}, + shorttitle = {{{21CMMC}}}, + author = {Greig, Bradley and Mesinger, Andrei}, + year = {2015}, + month = jun, + journal = {Monthly Notices of the Royal Astronomical Society}, + volume = {449}, + number = {4}, + eprint = {1501.06576}, + pages = {4246--4263}, + issn = {0035-8711, 1365-2966}, + url = {http://arxiv.org/abs/1501.06576}, + urldate = {2018-05-16}, + abstract = {We introduce 21CMMC: a parallelized, Monte Carlo Markov Chain analysis tool, incorporating the epoch of reionization (EoR) seminumerical simulation 21CMFAST. 21CMMC estimates astrophysical parameter constraints from 21 cm EoR experiments, accommodating a variety of EoR models, as well as priors on model parameters and the reionization history. To illustrate its utility, we consider two different EoR scenarios, one with a single population of galaxies (with a mass-independent ionizing efficiency) and a second, more general model with two different, feedback-regulated populations (each with mass-dependent ionizing efficiencies). As an example, combining three observations (z=8, 9 and 10) of the 21 cm power spectrum with a conservative noise estimate and uniform model priors, we find that interferometers with specifications like the Low Frequency Array/Hydrogen Epoch of Reionization Array (HERA)/Square Kilometre Array 1 (SKA1) can constrain common reionization parameters: the ionizing efficiency (or similarly the escape fraction), the mean free path of ionizing photons and the log of the minimum virial temperature of star-forming haloes to within 45.3/22.0/16.7, 33.5/18.4/17.8 and 6.3/3.3/2.4 per cent, {\textasciitilde}\$1{\textbackslash}sigma\$ fractional uncertainty, respectively. Instead, if we optimistically assume that we can perfectly characterize the EoR modelling uncertainties, we can improve on these constraints by up to a factor of {\textasciitilde}few. Similarly, the fractional uncertainty on the average neutral fraction can be constrained to within \${\textbackslash}lesssim10\$ per cent for HERA and SKA1. By studying the resulting impact on astrophysical constraints, 21CMMC can be used to optimize (i) interferometer designs; (ii) foreground cleaning algorithms; (iii) observing strategies; (iv) alternative statistics characterizing the 21 cm signal; and (v) synergies with other observational programs.}, + archiveprefix = {arxiv}, + keywords = {Astrophysics - Cosmology and Nongalactic Astrophysics,cosmology: theory,dark ages,diffuse radiation,early Universe,first stars,galaxies: high-redshift,intergalactic medium,reionization}, + annotation = {140 citations (Inspire/arXiv) [2022-06-01] 140 citations (Inspire/DOI) [2022-06-01]}, + file = {C:\Users\steve\Zotero\storage\AI3HIJNV\1501.html}, + doi = {10.1093/mnras/stv571} +} + +@article{Greig2017, + title = {Simultaneously Constraining the Astrophysics of Reionization and the Epoch of Heating with {{21CMMC}}}, + author = {Greig, Bradley and Mesinger, Andrei}, + year = {2017}, + month = dec, + journal = {Monthly Notices of the Royal Astronomical Society}, + volume = {472}, + pages = {2651--2669}, + url = {http://adsabs.harvard.edu/abs/2017MNRAS.472.2651G}, + urldate = {2020-10-21}, + abstract = {The cosmic 21 cm signal is set to revolutionize our understanding of the early Universe, allowing us to probe the 3D temperature and ionization structure of the intergalactic medium (IGM). It will open a window on to the unseen first galaxies, showing us how their UV and X-ray photons drove the cosmic milestones of the epoch of reionization (EoR) and epoch of heating (EoH). To facilitate parameter inference from the 21 cm signal, we previously developed 21CMMC: a Monte Carlo Markov Chain sampler of 3D EoR simulations. Here, we extend 21CMMC to include simultaneous modelling of the EoH, resulting in a complete Bayesian inference framework for the astrophysics dominating the observable epochs of the cosmic 21 cm signal. We demonstrate that second-generation interferometers, the Hydrogen Epoch of Reionization Array and Square Kilometre Array will be able to constrain ionizing and X-ray source properties of the first galaxies with a fractional precision of the order of {$\sim$}1-10 per cent (1{$\sigma$}). The ionization history of the Universe can be constrained to within a few percent. Using our extended framework, we quantify the bias in EoR parameter recovery incurred by the common simplification of a saturated spin temperature in the IGM. Depending on the extent of overlap between the EoR and the EoH, the recovered astrophysical parameters can be biased by {$\sim$}3{$\sigma$}-10{$\sigma$}.}, + keywords = {cosmology: theory,dark ages,diffuse radiation,early Universe,first stars,galaxies: high-redshift,intergalactic medium,reionization}, + annotation = {78 citations (Inspire/DOI) [2022-06-01]}, + doi = {10.1093/mnras/stx2118} +} + +@article{Greig2018, + title = {{{21CMMC}} with a {{3D}} Light-Cone: The Impact of the Co-Evolution Approximation on the Astrophysics of Reionisation and Cosmic Dawn}, + shorttitle = {{{21CMMC}} with a {{3D}} Light-Cone}, + author = {Greig, Bradley and Mesinger, Andrei}, + year = {2018}, + month = jul, + journal = {Monthly Notices of the Royal Astronomical Society}, + volume = {477}, + number = {3}, + pages = {3217--3229}, + issn = {0035-8711, 1365-2966}, + url = {http://arxiv.org/abs/1801.01592}, + urldate = {2018-08-28}, + abstract = {We extend 21CMMC, a Monte Carlo Markov Chain sampler of 3D reionisation simulations, to perform parameter estimation directly on 3D light-cones of the cosmic 21cm signal. This brings theoretical analysis closer to the tomographic 21-cm observations achievable with next generation interferometers like HERA and the SKA. Parameter recovery can therefore account for modes which evolve with redshift/frequency. Additionally, simulated data can be more easily corrupted to resemble real data. Using the light-cone version of 21CMMC, we quantify the biases in the recovered astrophysical parameters if we use the 21cm power spectrum from the co-evolution approximation to fit a 3D light-cone mock observation. While ignoring the light-cone effect under most assumptions will not significantly bias the recovered astrophysical parameters, it can lead to an underestimation of the associated uncertainty. However significant biases (\${\textbackslash}sim\$few -- 10 \${\textbackslash}sigma\$) can occur if the 21cm signal evolves rapidly (i.e. the epochs of reionisation and heating overlap significantly) and: (i) foreground removal is very efficient, allowing large physical scales (\$k{\textbackslash}lesssim0.1\${\textasciitilde}Mpc\$\^\{-1\}\$) to be used in the analysis or (ii) theoretical modelling is accurate to within \${\textbackslash}sim10\$ per cent in the power spectrum amplitude.}, + keywords = {Astrophysics - Cosmology and Nongalactic Astrophysics}, + annotation = {45 citations (Inspire/arXiv) [2022-06-01] 45 citations (Inspire/DOI) [2022-06-01]}, + file = {C:\Users\steve\Zotero\storage\GLX5S3XA\1801.html}, + doi = {10.1093/mnras/sty796} +} + +@article{Greig2020, + ids = {Greig2019}, + title = {Reionization and Cosmic Dawn Astrophysics from the {{Square Kilometre Array}}: Impact of Observing Strategies}, + shorttitle = {Reionization and Cosmic Dawn Astrophysics from the {{Square Kilometre Array}}}, + author = {Greig, Bradley and Mesinger, Andrei and Koopmans, L{\'e}on V. E.}, + year = {2020}, + month = jan, + journal = {Monthly Notices of the Royal Astronomical Society}, + volume = {491}, + pages = {1398--1407}, + url = {http://adsabs.harvard.edu/abs/2020MNRAS.491.1398G}, + urldate = {2020-11-05}, + abstract = {Interferometry of the cosmic 21-cm signal is set to revolutionize our understanding of the epoch of reionization (EoR) and the cosmic dawn (CD). The culmination of ongoing efforts will be the upcoming Square Kilometre Array (SKA), which will provide tomography of the 21-cm signal from the first billion years of our Universe. Using a galaxy formation model informed by high-z luminosity functions, here we forecast the accuracy with which the first phase of SKA-low (SKA1-low) can constrain the properties of the unseen galaxies driving the astrophysics of the EoR and CD. We consider three observing strategies: (I) deep (1000 h on a single field); (II) medium-deep (100 h on 10 independent fields); and (III) shallow (10 h on 100 independent fields). Using the 21-cm power spectrum as a summary statistic, and conservatively only using the 21-cm signal above the foreground wedge, we predict that all three observing strategies should recover astrophysical parameters to a fractional precision of {$\sim$}0.1-10 per cent. The reionization history is recovered to an uncertainty of {$\Delta$}z {$\lessequivlnt$} 0.1 (1{$\sigma$}) for the bulk of its duration. The medium-deep strategy, balancing thermal noise against cosmic variance, results in the tightest constraints, slightly outperforming the deep strategy. The shallow observational strategy performs the worst, with up to an {$\sim$}10-60 per cent increase in the recovered uncertainty. We note, however, that non-Gaussian summary statistics, tomography, as well as unbiased foreground removal would likely favour the deep strategy.}, + keywords = {cosmology: theory,dark ages,diffuse radiation,early Universe,first stars,galaxies: high-redshift,intergalactic medium,reionization}, + annotation = {13 citations (Inspire/DOI) [2022-06-01]}, + file = {C\:\\Users\\steve\\Zotero\\storage\\HLLD7IG9\\Greig et al. - 2020 - Reionization and cosmic dawn astrophysics from the.pdf;C\:\\Users\\steve\\Zotero\\storage\\PPRUCZ3T\\abstract.html}, + doi = {10.1093/mnras/stz3138} +} + + +@article{Parsons2012, + title = {A {{Per-baseline}}, {{Delay-spectrum Technique}} for {{Accessing}} the 21 Cm {{Cosmic Reionization Signature}}}, + author = {Parsons, Aaron R. and Pober, Jonathan C. and Aguirre, James E. and Carilli, Christopher L. and Jacobs, Daniel C. and Moore, David F.}, + year = {2012}, + journal = {The Astrophysical Journal}, + volume = {756}, + number = {2}, + pages = {165}, + issn = {0004-637X}, + url = {http://stacks.iop.org/0004-637X/756/i=2/a=165}, + urldate = {2018-03-28}, + abstract = {A critical challenge in measuring the power spectrum of 21 cm emission from cosmic reionization is compensating for the frequency dependence of an interferometer's sampling pattern, which can cause smooth-spectrum foregrounds to appear unsmooth and degrade the separation between foregrounds and the target signal. In this paper, we present an approach to foreground removal that explicitly accounts for this frequency dependence. We apply the delay transformation introduced in Parsons \& Backer to each baseline of an interferometer to concentrate smooth-spectrum foregrounds within the bounds of the maximum geometric delays physically realizable on that baseline. By focusing on delay modes that correspond to image-domain regions beyond the horizon, we show that it is possible to avoid the bulk of smooth-spectrum foregrounds. We map the point-spread function of delay modes to k -space, showing that delay modes that are uncorrupted by foregrounds also represent samples of the three-dimensional power spectrum, and can be used to constrain cosmic reionization. Because it uses only spectral smoothness to differentiate foregrounds from the targeted 21 cm signature, this per-baseline analysis approach relies on spectrally and spatially smooth instrumental responses for foreground removal. For sufficient levels of instrumental smoothness relative to the brightness of interfering foregrounds, this technique substantially reduces the level of calibration previously thought necessary to detect 21 cm reionization. As a result, this approach places fewer constraints on antenna configuration within an array, and in particular, facilitates the adoption of configurations that are optimized for power-spectrum sensitivity. Under these assumptions, we demonstrate the potential for the Precision Array for Probing the Epoch of Reionization (PAPER) to detect 21 cm reionization at an amplitude of 10 mK 2 near k 0.2 h Mpc {\textendash}1 with 132 dipoles in 7 months of observing.}, + langid = {english}, + annotation = {178 citations (Inspire/DOI) [2022-06-01]}, + doi = {10.1088/0004-637X/756/2/165} +} + +@article{Pober2013, + title = {The {{Baryon Acoustic Oscillation Broadband}} and {{Broad-beam Array}}: {{Design Overview}} and {{Sensitivity Forecasts}}}, + shorttitle = {The {{Baryon Acoustic Oscillation Broadband}} and {{Broad-beam Array}}}, + author = {Pober, Jonathan C. and Parsons, Aaron R. and DeBoer, David R. and McDonald, Patrick and McQuinn, Matthew and Aguirre, James E. and Ali, Zaki and Bradley, Richard F. and Chang, Tzu-Ching and Morales, Miguel F.}, + year = {2013}, + month = mar, + journal = {The Astronomical Journal}, + volume = {145}, + pages = {65}, + issn = {0004-6256}, + url = {http://adsabs.harvard.edu/abs/2013AJ....145...65P}, + urldate = {2019-01-09}, + abstract = {This work describes a new instrument optimized for a detection of the neutral hydrogen 21 cm power spectrum between redshifts of 0.5 and 1.5: the Baryon Acoustic Oscillation Broadband and Broad-beam (BAOBAB) array. BAOBAB will build on the efforts of a first generation of 21 cm experiments that are targeting a detection of the signal from the Epoch of Reionization at z {\textasciitilde} 10. At z {\textasciitilde} 1, the emission from neutral hydrogen in self-shielded overdense halos also presents an accessible signal, since the dominant, synchrotron foreground emission is considerably fainter than at redshift 10. The principle science driver for these observations are baryon acoustic oscillations in the matter power spectrum which have the potential to act as a standard ruler and constrain the nature of dark energy. BAOBAB will fully correlate dual-polarization antenna tiles over the 600-900 MHz band with a frequency resolution of 300 kHz and a system temperature of 50 K. The number of antennas will grow in staged deployments, and reconfigurations of the array will allow for both traditional imaging and high power spectrum sensitivity operations. We present calculations of the power spectrum sensitivity for various array sizes, with a 35 element array measuring the cosmic neutral hydrogen fraction as a function of redshift, and a 132 element system detecting the BAO features in the power spectrum, yielding a 1.8\% error on the z {\textasciitilde} 1 distance scale, and, in turn, significant improvements to constraints on the dark energy equation of state over an unprecedented range of redshifts from {\textasciitilde}0.5 to 1.5.}, + keywords = {cosmological parameters,distance scale,instrumentation: interferometers,large-scale structure of universe,techniques: interferometric}, + annotation = {107 citations (Inspire/DOI) [2022-06-01]}, + doi = {10.1088/0004-6256/145/3/65} +} + +@article{Pober2014, + title = {What {{Next-generation}} 21 Cm {{Power Spectrum Measurements}} Can {{Teach}} Us {{About}} the {{Epoch}} of {{Reionization}}}, + author = {Pober, Jonathan C. and Liu, Adrian and Dillon, Joshua S. and Aguirre, James E. and Bowman, Judd D. and Bradley, Richard F. and Carilli, Chris L. and DeBoer, David R. and Hewitt, Jacqueline N. and Jacobs, Daniel C. and McQuinn, Matthew and Morales, Miguel F. and Parsons, Aaron R. and Tegmark, Max and Werthimer, Dan J.}, + year = {2014}, + month = feb, + journal = {The Astrophysical Journal}, + volume = {782}, + pages = {66}, + issn = {0004-637X}, + url = {http://adsabs.harvard.edu/abs/2014ApJ...782...66P}, + urldate = {2018-03-28}, + abstract = {A number of experiments are currently working toward a measurement of the 21 cm signal from the epoch of reionization (EoR). Whether or not these experiments deliver a detection of cosmological emission, their limited sensitivity will prevent them from providing detailed information about the astrophysics of reionization. In this work, we consider what types of measurements will be enabled by the next generation of larger 21 cm EoR telescopes. To calculate the type of constraints that will be possible with such arrays, we use simple models for the instrument, foreground emission, and the reionization history. We focus primarily on an instrument modeled after the {\textasciitilde}0.1 km2 collecting area Hydrogen Epoch of Reionization Array concept design and parameterize the uncertainties with regard to foreground emission by considering different limits to the recently described "wedge" footprint in k space. Uncertainties in the reionization history are accounted for using a series of simulations that vary the ionizing efficiency and minimum virial temperature of the galaxies responsible for reionization, as well as the mean free path of ionizing photons through the intergalactic medium. Given various combinations of models, we consider the significance of the possible power spectrum detections, the ability to trace the power spectrum evolution versus redshift, the detectability of salient power spectrum features, and the achievable level of quantitative constraints on astrophysical parameters. Ultimately, we find that 0.1 km2 of collecting area is enough to ensure a very high significance (gsim 30{$\sigma$}) detection of the reionization power spectrum in even the most pessimistic scenarios. This sensitivity should allow for meaningful constraints on the reionization history and astrophysical parameters, especially if foreground subtraction techniques can be improved and successfully implemented.}, + keywords = {dark ages,first stars,reionization,techniques: interferometric}, + annotation = {217 citations (Inspire/DOI) [2022-06-01]}, + doi = {10.1088/0004-637X/782/2/66} +} + +@article{Pritchard2015, + title = {Cosmology from {{EoR}}/{{Cosmic Dawn}} with the {{SKA}}}, + author = {Pritchard, J. and Ichiki, K. and Mesinger, A. and Metcalf, R. B. and Pourtsidou, A. and Santos, M. and Abdalla, F. B. and Chang, T. C. and Chen, X. and Weller, J. and Zaroubi, S.}, + year = {2015}, + month = apr, + journal = {AASKA14}, + pages = {12}, + url = {https://ui.adsabs.harvard.edu/abs/2015aska.confE..12P/abstract}, + urldate = {2019-11-01}, + abstract = {The SKA will build upon early detections of the EoR by precursor instruments, such as MWA, PAPER, and LOFAR, and planned instruments, such as HERA, to make the first high signal-to-noise measurements of fluctuations in the 21 cm brightness temperature from both reionization and the cosmic dawn. This will allow both imaging and statistical maps of the 21cm signal at redshifts z = 6 - 27 and constrain the underlying cosmology and evolution of the density field. This era includes nearly 60\% of the (in principle) observable volume of the Universe and many more linear modes than the CMB, presenting an opportunity for SKA to usher in a new level of precision cosmology. This optimistic picture is complicated by the need to understand and remove the effect of astrophysics, so that systematics rather than statistics will limit constraints. This chapter describes the cosmological, as opposed to astrophysical, information available to SKA. Key areas for discussion include: cosmological parameters constraints using 21cm fluctuations as a tracer of the density field; lensing of the 21cm signal, constraints on heating via exotic physics such as decaying or annihilating dark matter; impact of fundamental physics such as non-Gaussianity or warm dark matter on the source population; and constraints on the bulk flows arising from the decoupling of baryons and photons at z = 1000. The chapter explores the path to separating cosmology from astrophysics, for example via velocity space distortions and separation in redshift. We discuss new opportunities for extracting cosmology made possible by the sensitivity of SKA Phase 1 and explores the advances achievable with SKA2.}, + langid = {english}, + keywords = {⛔ No DOI found}, + file = {C:\Users\steve\Zotero\storage\IAI3LAY6\abstract.html}, + doi = {10.22323/1.215.0012} +} + +@article{Robitaille2013, + title = {Astropy: {{A}} Community {{Python}} Package for Astronomy}, + author = {Robitaille, Thomas P. and Tollerud, Erik J. and Greenfield, Perry and Droettboom, Michael and Bray, Erik and Aldcroft, Tom and Davis, Matt and Ginsburg, Adam and {Price-Whelan}, Adrian M. and Kerzendorf, Wolfgang E. and Conley, Alexander and Crighton, Neil and Barbary, Kyle and Muna, Demitri and Ferguson, Henry and Grollier, Fr{\'e}d{\'e}ric and Parikh, Madhura M. and Nair, Prasanth H. and G{\"u}nther, Hans M. and Deil, Christoph and Woillez, Julien and Conseil, Simon and Kramer, Roban and Turner, James E. H. and Singer, Leo and Fox, Ryan and Weaver, Benjamin A. and Zabalza, Victor and Edwards, Zachary I. and Azalee Bostroem, K. and Burke, D. J. and Casey, Andrew R. and Crawford, Steven M. and Dencheva, Nadia and Ely, Justin and Jenness, Tim and Labrie, Kathleen and Lim, Pey Lian and Pierfederici, Francesco and Pontzen, Andrew and Ptak, Andy and Refsdal, Brian and Servillat, Mathieu and Streicher, Ole}, + year = {2013}, + month = sep, + journal = {Astronomy \& Astrophysics}, + volume = {558}, + pages = {A33-A33}, + url = {http://www.aanda.org/articles/aa/full_html/2013/10/aa22068-13/aa22068-13.html}, + langid = {english}, + annotation = {1763 citations (Inspire/DOI) [2022-06-01]}, + doi = {10.1051/0004-6361/201322068} +} + +@article{lofar, + title = {{{LOFAR}}: {{The LOw-Frequency ARray}}}, + author = {{van Haarlem}, M. P. and Wise, M. W. and Gunst, A. W. and Heald, G. and McKean, J. P. and Hessels, J. W. T. and {de Bruyn}, A. G. and Nijboer, R. and Swinbank, J. and Fallows, R. and Brentjens, M. and Nelles, A. and Beck, R. and Falcke, H. and Fender, R. and H{\"o}randel, J. and Koopmans, L. V. E. and Mann, G. and Miley, G. and R{\"o}ttgering, H. and Stappers, B. W. and Wijers, R. A. M. J. and Zaroubi, S. and van den Akker, M. and Alexov, A. and Anderson, J. E. and Anderson, K. and {van Ardenne}, A. and Arts, M. and Asgekar, A. and Avruch, I. M. and Batejat, F. and B{\"a}hren, L. and Bell, M. E. and Bell, M. R. and {van Bemmel}, I. and Bennema, P. and Bentum, M. J. and Bernardi, G. and Best, P. and B{\^i}rzan, L. and Bonafede, A. and Boonstra, A. -J. and Braun, R. and Bregman, J. and Breitling, F. and {van de Brink}, R. H. and Broderick, J. and Broekema, P. C. and Brouw, W. N. and Br{\"u}ggen, M. and Butcher, H. R. and {van Cappellen}, W. and Ciardi, B. and Coenen, T. and Conway, J. and Coolen, A. and Corstanje, A. and Damstra, S. and Davies, O. and Deller, A. T. and Dettmar, R. -J. and {van Diepen}, G. and Dijkstra, K. and Donker, P. and Doorduin, A. and Dromer, J. and Drost, M. and {van Duin}, A. and Eisl{\"o}ffel, J. and {van Enst}, J. and Ferrari, C. and Frieswijk, W. and Gankema, H. and Garrett, M. A. and {de Gasperin}, F. and Gerbers, M. and {de Geus}, E. and Grie{\ss}meier, J. -M. and Grit, T. and Gruppen, P. and Hamaker, J. P. and Hassall, T. and Hoeft, M. and Holties, H. and Horneffer, A. and {van der Horst}, A. and {van Houwelingen}, A. and Huijgen, A. and Iacobelli, M. and Intema, H. and Jackson, N. and Jelic, V. and {de Jong}, A. and Juette, E. and Kant, D. and Karastergiou, A. and Koers, A. and Kollen, H. and Kondratiev, V. I. and Kooistra, E. and Koopman, Y. and Koster, A. and Kuniyoshi, M. and Kramer, M. and Kuper, G. and Lambropoulos, P. and Law, C. and {van Leeuwen}, J. and Lemaitre, J. and Loose, M. and Maat, P. and Macario, G. and Markoff, S. and Masters, J. and {McKay-Bukowski}, D. and Meijering, H. and Meulman, H. and Mevius, M. and Middelberg, E. and Millenaar, R. and {Miller-Jones}, J. C. A. and Mohan, R. N. and Mol, J. D. and Morawietz, J. and Morganti, R. and Mulcahy, D. D. and Mulder, E. and Munk, H. and Nieuwenhuis, L. and {van Nieuwpoort}, R. and Noordam, J. E. and Norden, M. and Noutsos, A. and Offringa, A. R. and Olofsson, H. and Omar, A. and Orr{\'u}, E. and Overeem, R. and Paas, H. and {Pandey-Pommier}, M. and Pandey, V. N. and Pizzo, R. and Polatidis, A. and Rafferty, D. and Rawlings, S. and Reich, W. and {de Reijer}, J. -P. and Reitsma, J. and Renting, A. and Riemers, P. and Rol, E. and Romein, J. W. and Roosjen, J. and Ruiter, M. and Scaife, A. and {van der Schaaf}, K. and Scheers, B. and Schellart, P. and Schoenmakers, A. and Schoonderbeek, G. and Serylak, M. and Shulevski, A. and Sluman, J. and Smirnov, O. and Sobey, C. and Spreeuw, H. and Steinmetz, M. and Sterks, C. G. M. and Stiepel, H. -J. and Stuurwold, K. and Tagger, M. and Tang, Y. and Tasse, C. and Thomas, I. and Thoudam, S. and Toribio, M. C. and {van der Tol}, B. and Usov, O. and {van Veelen}, M. and {van der Veen}, A. -J. and {ter Veen}, S. and Verbiest, J. P. W. and Vermeulen, R. and Vermaas, N. and Vocks, C. and Vogt, C. and {de Vos}, M. and {van der Wal}, E. and {van Weeren}, R. and Weggemans, H. and Weltevrede, P. and White, S. and Wijnholds, S. J. and Wilhelmsson, T. and Wucknitz, O. and Yatawatta, S. and Zarka, P. and Zensus, A. and {van Zwieten}, J.}, + year = {2013}, + month = may, + journal = {Astronomy \& Astrophysics}, + volume = {556}, + pages = {53}, + url = {http://arxiv.org/abs/1305.3550}, + abstract = {LOFAR, the LOw-Frequency ARray, is a new-generation radio interferometer constructed in the north of the Netherlands and across europe. Utilizing a novel phased-array design, LOFAR covers the largely unexplored low-frequency range from 10-240 MHz and provides a number of unique observing capabilities. Spreading out from a core located near the village of Exloo in the northeast of the Netherlands, a total of 40 LOFAR stations are nearing completion. A further five stations have been deployed throughout Germany, and one station has been built in each of France, Sweden, and the UK. Digital beam-forming techniques make the LOFAR system agile and allow for rapid repointing of the telescope as well as the potential for multiple simultaneous observations. With its dense core array and long interferometric baselines, LOFAR achieves unparalleled sensitivity and angular resolution in the low-frequency radio regime. The LOFAR facilities are jointly operated by the International LOFAR Telescope (ILT) foundation, as an observatory open to the global astronomical community. LOFAR is one of the first radio observatories to feature automated processing pipelines to deliver fully calibrated science products to its user community. LOFAR's new capabilities, techniques and modus operandi make it an important pathfinder for the Square Kilometre Array (SKA). We give an overview of the LOFAR instrument, its major hardware and software components, and the core science objectives that have driven its design. In addition, we present a selection of new results from the commissioning phase of this new radio observatory.}, + keywords = {dark ages,first stars,instrumentation: interferometers,radio continuum: general,radio lines: general,reionization,telescopes}, + annotation = {755 citations (Inspire/arXiv) [2022-06-01] 755 citations (Inspire/DOI) [2022-06-01]}, + doi = {10.1051/0004-6361/201220873} +} +@article{Trott2016a, + title = {Exploring the Evolution of {{Reionisation}} Using a Wavelet Transform and the Light Cone Effect}, + author = {Trott, Cathryn M.}, + year = {2016}, + month = sep, + journal = {Monthly Notices of the Royal Astronomical Society}, + volume = {461}, + number = {1}, + pages = {126--135}, + issn = {0035-8711}, + url = {http://adsabs.harvard.edu/abs/2016MNRAS.461..126T}, + abstract = {The Cosmic Dawn and Epoch of Reionization, during which collapsed structures produce the first ionizing photons and proceed to reionize the intergalactic medium, span a large range in redshift (z {\texttildelow} 30-6) and time (tage {\texttildelow} 0.1-1.0 Gyr). Exploration of these epochs using the redshifted 21 cm emission line from neutral hydrogen is currently limited to statistical detection and estimation metrics (e.g. the power spectrum) due to the weakness of the signal. Brightness temperature fluctuations in the line-of-sight dimension are probed by observing the emission line at different frequencies, and their structure is used as a primary discriminant between the cosmological signal and contaminating foreground extragalactic and Galactic continuum emission. Evolution of the signal over the observing bandwidth leads to the `line cone effect' whereby the H I structures at the start and end of the observing band are not statistically consistent, yielding a biased estimate of the signal power, and potential reduction in signal detectability. We implement a wavelet transform to wide bandwidth radio interferometry experiments to probe the local statistical properties of the signal. We show that use of the wavelet transform yields estimates with improved estimation performance, compared with the standard Fourier Transform over a fixed bandwidth. With the suite of current and future large bandwidth reionization experiments, such as with the 300 MHz instantaneous bandwidth of the Square Kilometre Array, a transform that retains local information will be important.}, + keywords = {Astrophysics - Cosmology and Nongalactic Astrophysics,Astrophysics - Instrumentation and Methods for Astrophysics,dark ages,first stars,methods: statistical,reionization,techniques: interferometric}, + annotation = {11 citations (Inspire/DOI) [2022-06-01]}, + file = {C:\Users\steve\Zotero\storage\XVE36E5M\1605.html}, + doi = {10.1093/mnras/stw1310} +} + +@ARTICLE{Schosser2024, + author = {{Schosser}, Benedikt and {Heneka}, Caroline and {Plehn}, Tilman}, + title = "{Optimal, fast, and robust inference of reionization-era cosmology with the 21cmPIE-INN}", + journal = {arXiv e-prints}, + keywords = {Astrophysics - Cosmology and Nongalactic Astrophysics, Astrophysics - Astrophysics of Galaxies, Astrophysics - Instrumentation and Methods for Astrophysics, High Energy Physics - Phenomenology}, + year = 2024, + month = jan, + eid = {arXiv:2401.04174}, + pages = {arXiv:2401.04174}, + doi = {10.48550/arXiv.2401.04174}, +archivePrefix = {arXiv}, + eprint = {2401.04174}, + primaryClass = {astro-ph.CO}, + adsurl = {https://ui.adsabs.harvard.edu/abs/2024arXiv240104174S}, + adsnote = {Provided by the SAO/NASA Astrophysics Data System} +} + +@ARTICLE{Liu2020, + author = {{Liu}, Adrian and {Shaw}, J. Richard}, + title = "{Data Analysis for Precision 21 cm Cosmology}", + journal = {\pasp}, + keywords = {dark ages, reionization, first stars, methods: statistical, techniques: interferometric, Astrophysics - Instrumentation and Methods for Astrophysics, Astrophysics - Cosmology and Nongalactic Astrophysics}, + year = 2020, + month = jun, + volume = {132}, + number = {1012}, + eid = {062001}, + pages = {062001}, + doi = {10.1088/1538-3873/ab5bfd}, +archivePrefix = {arXiv}, + eprint = {1907.08211}, + primaryClass = {astro-ph.IM}, + adsurl = {https://ui.adsabs.harvard.edu/abs/2020PASP..132f2001L}, + adsnote = {Provided by the SAO/NASA Astrophysics Data System} +} + +@ARTICLE{jwst, + author = {{Castellano}, Marco and {Fontana}, Adriano and {Treu}, Tommaso and {Santini}, Paola and {Merlin}, Emiliano and {Leethochawalit}, Nicha and {Trenti}, Michele and {Vanzella}, Eros and {Mestric}, Uros and {Bonchi}, Andrea and {Belfiori}, Davide and {Nonino}, Mario and {Paris}, Diego and {Polenta}, Gianluca and {Roberts-Borsani}, Guido and {Boyett}, Kristan and {Brada{\v{c}}}, Maru{\v{s}}a and {Calabr{\`o}}, Antonello and {Glazebrook}, Karl and {Grillo}, Claudio and {Mascia}, Sara and {Mason}, Charlotte and {Mercurio}, Amata and {Morishita}, Takahiro and {Nanayakkara}, Themiya and {Pentericci}, Laura and {Rosati}, Piero and {Vulcani}, Benedetta and {Wang}, Xin and {Yang}, Lilan}, + title = "{Early Results from GLASS-JWST. III. Galaxy Candidates at z 9-15}", + journal = {\apjl}, + keywords = {Reionization, 1383, Astrophysics - Astrophysics of Galaxies}, + year = 2022, + month = oct, + volume = {938}, + number = {2}, + eid = {L15}, + pages = {L15}, + doi = {10.3847/2041-8213/ac94d0}, +archivePrefix = {arXiv}, + eprint = {2207.09436}, + primaryClass = {astro-ph.GA}, + adsurl = {https://ui.adsabs.harvard.edu/abs/2022ApJ...938L..15C}, + adsnote = {Provided by the SAO/NASA Astrophysics Data System} +} + +@ARTICLE{Munoz2022, + author = {{Mu{\~n}oz}, Julian B. and {Qin}, Yuxiang and {Mesinger}, Andrei and {Murray}, Steven G. and {Greig}, Bradley and {Mason}, Charlotte}, + title = "{The impact of the first galaxies on cosmic dawn and reionization}", + journal = {\mnras}, + keywords = {galaxies: high-redshift, intergalactic medium, cosmology: theory, dark ages, reionization, first stars, diffuse radiation, Astrophysics - Cosmology and Nongalactic Astrophysics, Astrophysics - Astrophysics of Galaxies}, + year = 2022, + month = apr, + volume = {511}, + number = {3}, + pages = {3657-3681}, + doi = {10.1093/mnras/stac185}, +archivePrefix = {arXiv}, + eprint = {2110.13919}, + primaryClass = {astro-ph.CO}, + adsurl = {https://ui.adsabs.harvard.edu/abs/2022MNRAS.511.3657M}, + adsnote = {Provided by the SAO/NASA Astrophysics Data System} +} + + +@article{Murray2020, + doi = {10.21105/joss.02582}, + url = {https://doi.org/10.21105/joss.02582}, + year = {2020}, + publisher = {The Open Journal}, + volume = {5}, + number = {54}, + pages = {2582}, + author = {Steven G. Murray and Bradley Greig and Andrei Mesinger and Julian B. Muñoz and Yuxiang Qin and Jaehong Park and Catherine A. Watkinson}, + title = {21cmFAST v3: A Python-integrated C code for generating 3D realizations of the cosmic 21cm signal.}, + journal = {Journal of Open Source Software} +} + +@software{Mesinger2011, + author = {{Mesinger}, Andrei and {Furlanetto}, Steven and {Cen}, Renyue}, + title = "{21cmFAST: A Fast, Semi-Numerical Simulation of the High-Redshift 21-cm Signal}", + howpublished = {Astrophysics Source Code Library, record ascl:1102.023}, + year = 2011, + month = feb, + eid = {ascl:1102.023}, + adsurl = {https://ui.adsabs.harvard.edu/abs/2011ascl.soft02023M}, + adsnote = {Provided by the SAO/NASA Astrophysics Data System} +} diff --git a/joss-paper/paper.md b/joss-paper/paper.md new file mode 100644 index 0000000..2f76b67 --- /dev/null +++ b/joss-paper/paper.md @@ -0,0 +1,125 @@ +--- +title: '21cmSense v2: A modular, open-source 21 cm sensitivity calculator' +tags: + - Python + - astronomy + - 21 cm Cosmology +authors: + - name: Steven G. Murray + orcid: 0000-0003-3059-3823 + equal-contrib: true + affiliation: 1 # (Multiple affiliations must be quoted) + corresponding: true + - name: Jonathan Pober + equal-contrib: true # (This is how you can denote equal contributions between multiple authors) + affiliation: 2 + orcid: 0000-0002-3492-0433 + - name: Matthew Kolopanis + affiliation: 3 + orcid: 0000-0002-2950-2974 +affiliations: + - name: Scuola Normale Superiore, Italy + index: 1 + - name: Department of Physics, Brown University, Providence, RI, USA + index: 2 + - name: School of Earth and Space Exploration, Arizona State University, Tempe, AZ, USA + index: 3 +date: 18 January 2024 +bibliography: paper.bib +--- + +# Summary + +The 21cm line of neutral hydrogen is a powerful probe of the high-redshift +universe (Cosmic Dawn and the Epoch of Reionization), with an unprecedented potential to +inform us about key processes of early galaxy formation, the first stars and even +cosmology and structure formation [@Liu2020], via intensity mapping. +It is the subject of a number of current and upcoming +low-frequency radio experiments, including the MWA [@mwa], LOFAR [@lofar], HERA [@hera] +and the SKA [@Pritchard2015], which complement the detailed information concerning the +brightest sources in these early epochs from powerful optical and near-infrared telescopes +such as the JWST [@jwst]. + + +21cmSense is a Python package that provides a modular framework for calculating the +sensitivity of these experiments, in order to enhance the process of their design. +This paper presents version v2.0.0 of 21cmSense, which has been re-written from the ground up +to be more modular and extensible, and to provide a more user-friendly interface -- as +well as converting the well-used legacy package, presented in [@Pober2013,@Pober2014] from Python 2 to 3. + +21cmSense can compute sensitivity estimates for both map-making [@fhd] and +delay-spectrum [@Parsons2012] approaches to power-spectrum estimation. +The full sensitivity calculation is rather involved and +computationally expensive in its most general form, however 21cmSense uses a few +key assumptions to accelerate the calculation: + +1. Each baseline (pair of antennas) in the interferometer intrinsically measures a dense + blob of 2D spatial Fourier modes of the sky intensity distribution, centred at a + particular Fourier coordinate $(u,v)$ given by the displacement vector between the + antennas forming the baseline, and covering an area in this $(u,v)$-space that is given + by the Fourier-transform of the primary beam of the instrument. + The Fourier-space representation of the sky is thus + built up by collecting many baselines that cover the so-called "$(u,v)$-plane". + ``21cmSense`` approximates this process of synthesising many baselines by + nearest-grid-point interpolation onto a regular grid in the $(u,v)$-plane. + Furthermore, importantly the $(u,v)$-grid is chosen to have cells that are comparable + to the instrument's Fourier-space beam size, so that a particular baseline essentially + measures a single cell in the grid, and no more. + This maximizes resolution while keeping the covariance between cells small. + This removes the need for tracking the full covariance between cells, and also removes + the need to perform a beam convolution, which can be expensive. +2. We do not consider flagging of visibilities due to RFI and other systematics, which + can complicate the propagation of uncertainties. + +Some of the key new features introduced in this version of 21cmSense include: + +1. Simplified, modular library API: the calculation has been split into modules that can + be used independently (for example, a class defining the `Observatory`, the + `Observation` and the `Sensitivity`). These can be used interactively via Jupyter + [@jupyter] or other interactive interfaces for Python, or called as library functions + in other code. +2. Command-line interface: the library can be called from the command-line, allowing + for easy scripting and automation of sensitivity calculations. +3. More accurate cosmological calculations using `astropy` [@Robitaille2013; @astropy] +4. Improved documentation and examples, including a Jupyter notebook that walks through + the calculation step-by-step. +5. Generalization of the sensitivity calculation. The `Sensitivity` class is an abstract + class from which the sensitivity of differing summary statistics can be defined. + Currently, its only implementation is the `PowerSpectrum` class, which computes the + classic sensitivity of the power spectrum. However, the framework + can be extended to other summaries, for example wavelets [@Trott2016a]. +6. Improved speed: the new version of 21cmSense is significantly faster than the legacy + version, due to a number of vectorization improvements in the code. +7. Built-in profiles for several major experiments: MWA, HERA and SKA-1. These can be + used as-is, or as a starting point for defining a custom instrument. + +An example of the predicted sensitivity of the HERA experiment after a year's observation +at $z=8.5$ is shown in Figure \ref{sense}, corresponding to the sampling of the $(u,v)$-grid +shown in Figure \ref{uvsampling}. The sensivity here is a signal-to-noise, +assuming a signal magnitude computed using a semi-numerical model from the 21cmFAST +code [@Mesinger2011; @Murray2020], using parameters from [@Munoz2022]. +This figure also demonstrates that the new +21cmSense is capable of producing sensitivity predictions in the cylindrically-averaged +2D power spectrum space, which is helpful for upcoming experiments. + +![Sampling of the $(u,v)$-plane for the HERA experiment during a full year of observations.\label{uvsampling}](uv-sampling.pdf) + +![Predicted sensitivity of 1000 hours (one year) of HERA observations, as a function of perpendicular and line-of-sight fourier scale. The sensitivity is represented as the signal-to-noise on each $k$-mode, assuming a particular astrophysical model.\label{sense}](2dps.pdf) + +# Statement of need + +`21cmSense` provides a simple interface for computing the expected sensitivity of +radio interferometers that aim to measure the 21cm line of neutral hydrogen. +This field is growing rapidly, with a number of experiments currently underway or in +the planning stages. Historically, `21cmSense` has been a trusted tool for the design of +these experiments [@Pober2013; @Pober2014; @Greig2020] and for forecasting parameter +constraints [@Greig2015; @Greig2017; @Greig2018]. +This overhauled, modularized version of `21cmSense` provides a more user-friendly +interface, improved performance, and the extensibility required for the next generation, +as evidenced by its usage in the literature [@Brietman2024,@Schosser2024]. + +# Acknowledgements + +We acknowledge helpful conversations with Danny Jacobs. + +# References diff --git a/joss-paper/uv-sampling.pdf b/joss-paper/uv-sampling.pdf new file mode 100644 index 0000000..6b49e8b Binary files /dev/null and b/joss-paper/uv-sampling.pdf differ diff --git a/joss-paper/uv-sampling.png:Zone.Identifier b/joss-paper/uv-sampling.png:Zone.Identifier new file mode 100644 index 0000000..77c2b8a --- /dev/null +++ b/joss-paper/uv-sampling.png:Zone.Identifier @@ -0,0 +1,4 @@ +[ZoneTransfer] +ZoneId=3 +ReferrerUrl=https://21cmsense.readthedocs.io/en/latest/tutorials/getting_started.html +HostUrl=https://21cmsense.readthedocs.io/en/latest/_images/tutorials_getting_started_51_1.png