diff --git a/.github/workflows/draft-pdf.yml b/.github/workflows/draft-pdf.yml new file mode 100644 index 0000000000..682fe6ea9b --- /dev/null +++ b/.github/workflows/draft-pdf.yml @@ -0,0 +1,24 @@ +name: Draft PDF +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: paper.md + - name: Upload + uses: actions/upload-artifact@v3 + 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.pdf diff --git a/paper.bib b/paper.bib index 10b341d617..8bc17b6bd4 100644 --- a/paper.bib +++ b/paper.bib @@ -78,3 +78,57 @@ @ARTICLE{fhd adsnote = {Provided by the SAO/NASA Astrophysics Data System} url = {https://github.com/EoRImaging/FHD} } + +@TECHREPORT{ms, + author = {{Kemball}, A.~J. and {Wieringa}, M.~H.}, + title = "{MeasurementSet definition version 2.0}", + year = 2000, + month = jan, + file = {https://casa.nrao.edu/Memos/229.ps.gz}, + url = {https://casper.berkeley.edu/astrobaki/index.php/AIPY}} +} + +@TECHREPORT{ms, + author = {{Kemball}, A.~J. and {Wieringa}, M.~H.}, + title = "{MeasurementSet definition version 2.0}", + year = 2000, + month = jan, + file = {https://casa.nrao.edu/Memos/229.ps.gz}, + url = {https://casper.berkeley.edu/astrobaki/index.php/AIPY}} +} + +@TECHREPORT{mir, + author = {{Qi}, C.}, + title = "{The MIR Cookbook}", + year = 2022, + month = mar, + file = {https://lweb.cfa.harvard.edu/~cqi/mircook.pdf}, + url = {https://lweb.cfa.harvard.edu/~cqi/mircook.html}} +} + +@TECHREPORT{uvh5, + author = {{La Plante}, P. and {the pyuvdata team}}, + title = "{Memo: UVH5 file format}", + year = 2024, + month = apr, + file = {https://github.com/RadioAstronomySoftwareGroup/pyuvdata/blob/main/docs/references/uvh5_memo.pdf}, +} + +@ARTICLE{casa, + 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 = {\pasp}, + 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} +} diff --git a/paper.md b/paper.md index e514160263..0a129434ee 100644 --- a/paper.md +++ b/paper.md @@ -1,53 +1,90 @@ --- -title: 'pyuvdata: an interface for astronomical interferometeric datasets in python' +title: 'pyuvdata v3: an interface for astronomical interferometeric datasets in python' tags: - radio astronomy - uvfits - miriad authors: + - name: Garrett K. Keating + orcid: 0000-0002-3490-146X + affiliation: 1 - name: Bryna J. Hazelton orcid: 0000-0001-7532-645X - affiliation: 1, 2 + affiliation: 2, 3 + - name: Matthew Kolopanis + orcid: 0000-0002-2950-2974 + affiliation: 4 + - name: Steven Murray + orcid: 0000-0003-3059-3823 + affiliation: 4 + - name: Adam P. Beardsley + orcid: 0000-0001-9428-8233 + affiliation: 5 - name: Daniel C. Jacobs orcid: 0000-0002-0917-2269 affiliation: 3 + - name: Nicholas Kern + affiliation: 6 + orcid: 0000-0002-8211-1892 + - name: Adam Lanman + affiliation: 7 + orcid: 0000-0003-2116-3573 + - name: Paul La Plante + affiliation: 8 + orcid: 0000-0002-4693-0102 - name: Jonathan C. Pober orcid: 0000-0002-3492-0433 - affiliation: 4 - - name: Adam P. Beardsley - orcid: 0000-0001-9428-8233 - affiliation: 3 + affiliation: 9 + - name: Pyxie Star + orcid: XXXX-XXXX-XXXX-XXXX + affiliation: 2 affiliations: - - name: University of Washington, eScience Institute + - name: Center for Astrophysics | Harvard & Smithsonian index: 1 - - name: University of Washington, Physics Department + - name: University of Washington, eScience Institute index: 2 - - name: Arizona State University, School of Earth and Space Exploration + - name: University of Washington, Physics Department index: 3 - - name: Brown University, Physics Department + - name: Arizona State University, School of Earth and Space Exploration index: 4 -date: 22 November 2016 + - name: Winona State University, Physics Department + index: 5 + - name: Massachusetts Institute of Technology, Physics Department + index: 6 + - name: Kavli Institute of Astrophysics and Space Research + index: 7 + - name: University of Nevada, Las Vegas, Department of Computer Science + index: 8 + - name: Brown University, Physics Department + index: 9 +date: 2 July 2024 bibliography: paper.bib --- # Summary +pyuvdata is an open-source software package that seeks to do provide a well-documented, +feature-rich interface for many of the different data formats that exist within radio +interferometry, including support for reading and writing UVH5 [@uvh5], UVFITS +[@uvfits], MIRIAD [@miriad], and measurement set [@ms] visibility files; and reading of +FHD [@fhd] and MIR [@mir] visibility save files. Additionally, pyuvdata supports reading +and writing measurement set calibration tables, and reading of FHD calibration tables. +# Statement of Need There are several standard formats for astronomical interferometric data, but -converting between them in a stable and repeatable way has historically been -very challenging. This is partly because of subtle assumptions in the -implementations of the formats and the complexity of the mathematical -relationships between the different formats (e.g. drift mode vs phased data) -and partly because data analysis for individual telescopes -typically used just one of the standards along with the associated analysis -code. New low frequency instruments (e.g. MWA (http://www.mwatelescope.org/), -PAPER (http://eor.berkeley.edu/), HERA (http://reionization.org/)), -have required custom analysis and simulation software that rely on a range of -different file formats. pyuvdata was designed to facilitate interoperability -between these instruments and codes by providing high quality, well documented -conversion routines as well as an interface to interact with interferometric -data and simulations directly in python. +converting between them in a stable, repeatable way has historically been +challenging. This is partially due to conflicting assumptions and standards, giving +rise to significant (though sometimes subtle) differences between formats. +Interfacing with different data formats -- like one does when they convert from one +format to another -- thus requires careful accounting for the complex mathematical +relationships between both data and metadata to ensure proper data fidelity. This is +required both for leveraging existing community-favored tools that typically built +to interface with a specific data format, as well as analyses requiring bespoke tools +for specialized types of analyses and simulations leveraging data in a variety of +formats. -pyuvdata currently supports reading and writing uvfits [@uvfits] and -miriad [@miriad] files and reading FHD [@fhd] visibility save files. +pyuvdata has been designed to facilitate interoperability between different instruments +and codes by providing high quality, well documented conversion routines as well as an interface to interact with interferometric data and simulations directly in Python. Originally motivated to support new low frequency instruments (e.g. MWA (http://www.mwatelescope.org/), PAPER (http://eor.berkeley.edu/), HERA (http://reionization.org/)), +the capabilities of pyuvdata have been steadily expanded to support handling of data from +several telescopes, ranging from meter to submillimeter wavelengths. # References