[REVIEW]: ScatteringOptics.jl: An Interstellar Scattering Framework in the Julia Programming Language #6354
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@Edenhofer, @tomkimpson — This is the review thread for the paper. All of our correspondence will happen here from now on. Thanks again for agreeing to participate! 👉 Please read the "Reviewer instructions & questions" in the first comment above, and generate your checklists by commenting The JOSS review is different from most other journals. Our goal is to work with the authors to help them meet our criteria instead of merely passing judgment on the submission. As such, the reviewers are encouraged to submit issues and pull requests on the software repository. When doing so, please mention We aim for the review process to be completed within about 4-6 weeks but please try to make a start ahead of this as JOSS reviews are by their nature iterative and any early feedback you may be able to provide to the author will be very helpful in meeting this schedule. Please get your review started as soon as possible! |
Review checklist for @EdenhoferConflict of interest
Code of Conduct
General checks
Functionality
Documentation
Software paper
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I would like to request a COI waiver for my review of ScatteringOptics.jl (#6354) regarding Paul Tiede, who is a co-author of said paper. I've been at the Center for Astrophysics | Harvard & Smithsonian, Paul's employer, for about half a year in 2023 and have had two extended conversations with Paul about Gaussian processes, a subject unrelated to the submission. Since we work on very different topics in astrophysics, have never collaborated, and haven't interacted regularly, I believe I can evaluate the submission impartially. |
PaperThe paper is well written, summarizes the need for the software well, and focuses on the essential mathematics. However, as a non-expert in the field of radio astronomy, I think that the mathematics discussed should be more closely tied to what ScatteringOptics.jl provides. In particular, it is not clear to me how the equation after l70 and the equation after l74 are related. I probably am missing something, but I thought the scattering is performed in image space and only Minor notes
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@Edenhofer — Thanks for bringing this up! Given the weak nature of this potential COI, I'm happy for you to continue with the review, having noted this context. @annatartaglia — If you or any of your co-authors have any concerns about this at all please reach out to me here or over email (my address should be easy to find!). Thanks all!! |
Review checklist for @tomkimpsonConflict of interest
Code of Conduct
General checks
Functionality
Documentation
Software paper
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The package is useful and the accompanying paper is well-written. It was nice to learn about the use of Julia by the EHT collaboration. I have some general comments below. I will review the code itself separately and open any issues as needed.
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Apologies for the delay in my response–I have been busy with graduate admissions visits the past few weeks. We would like to thank the referees (@Edenhofer @tomkimpson) for their constructive comments. We are in the process of carefully going through each review and revising the paper and repository accordingly. I will respond to individual comments as we revise. Thanks for your patience! |
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@annatartaglia — Thanks for your previous update! I wanted to check in here to make sure that this is still on your radar. Let us know how things are going. Thanks! |
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@annatartaglia — Any updates here? Please let us know what your timeline looks like for the next steps. If I don't hear from you in the next 2 weeks, I'll assume that this review has been abandoned, and reject the submission, so just let me know how things are going ASAP! |
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We are very sorry for the delay in revising the submission. As @annatartaglia already wrote, we found the referee's suggestions constructive, and have been revising the repository and its documentation. As I wrote to you separately, the revision has been unexpectedly taking longer because the process collides with on-going Anna's career transition. I would appreciate if you can provide us with a few months of an extension to complete the revision. Also, as an author, I'm very sorry that I didn't respond --- I didn't receive a notification and I should have answered promptly if I did. Please include me when you reach out to us for the next time. |
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@kazuakiyama, @annatartaglia — Thanks for the update! I can "pause" this submission if it will be a few months before you can return to the review. Otherwise, please update here even with small changes - unlike other journals, we don't require a serial review process where you respond to all comments in one go. Please feel free to iterate interactively! Let me know what your realistic timeline looks like and we'll work with that. Thanks! |
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@kazuakiyama, @annatartaglia — Please let me know when you'll be able to get back to this review. If you don't think you'll be able to get to it in the next few weeks, we're going to need to reject the submission because we can't just sit on it for such a long time. Please let me know how you would like to proceed and if I don't hear back from you in the next week I will reject the submission. Thanks! |
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Dear Dan,
Thanks for the contact. We were about to reach out to you because @annatartaglia was now fully coming back to work. We have been working on the revision, and will fully revise the documentation and the entire package within few weeks. Do you think it is possible to set the deadline to 4 weeks from now, Monday, November 4th?
Again thank you very much for your patience. Please let us know if this doesn’t work or you have any questions about the paper.
Thanks, Kazu
… On Oct 5, 2024, at 10:28 AM, Dan Foreman-Mackey ***@***.***> wrote:
@kazuakiyama <https://github.com/kazuakiyama>, @annatartaglia <https://github.com/annatartaglia> — Please let me know when you'll be able to get back to this review. If you don't think you'll be able to get to it in the next few weeks, we're going to need to reject the submission because we can't just sit on it for such a long time. Please let me know how you would like to proceed and if I don't hear back from you in the next week I will reject the submission. Thanks!
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Thanks for the update - sounds good! But, like I've mentioned several times now, please don't plan on just revising in one go. It's much more useful to iterate on JOSS reviews! Please start responding to GitHub issues and on this thread ASAP rather than waiting for a complete revision. That's not the best use of anyone's time. |
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On behalf of the authors, I resubmit our JOSS paper here. We have fully revised the package, its documentation, and our JOSS manuscript according to many helpful and constructive comments made by @Edenhofer and @tomkimpson. The package also has other major updates to support the latest Comrade.jl’s ecosystem, which is not related to the previous review. You can find the revised paper PDF here. The revised documentation can be found here. The corresponding package can be found in the tag joss_v2 of the branch For your reference, you can compare them with the documentation at the time of the first submission (here) as well as the package with the tag In the following replies, we will describe our point-to-point answer to the referee comments by each reviewer. We believe the paper and package now meet the standard of the JOSS. Please let us know if you have any questions or suggestions for our revision and replies below. Responses to the report by @Edenhofer
We are, unfortunately, limited by the number of words allowed for a JOSS paper (250-1000). Because the mathematics used in our package are so extensive, it is not possible to include all of it in the paper. In the revision, instead, we have significantly extended the texts in our documentation. See ``Brief Introduction to Interstellar Scattering’’ in the updated documentation.
To clarify your initial question–the l74 equation is the l70 equation represented in Fourier “visibility” space. The exponential term in l74 is the Fourier space transformation of our scattering kernel ‘G’. Scattering is easier to handle in the Fourier domain due to the nature of Radio Interferometric measurements. The kernel is well described in this space. We have added a line clarifying this (l71). This is also now clarified in ``Brief Introduction to Interstellar Scattering’’ in the updated documentation.
This is correct. ScatteringOptics.jl produces a sky model of Comrade.jl for the scattering kernel, described analytically in Fourier space. Comrade.jl provides a powerful tool kit to compute the kernel on the image domain through FFT, and blur arbitral sky models with this kernel. For instance, this allows users to see the kernel also in the image domain using the standard Comrade.jl’s function.
Thanks for pointing this out. Indeed, there is no strong reason to put r on \phi. \phi_r(r) has been replaced to \phi(r) in the paper.
The structure function is a measure of second-order phase changes in the phase screen at different locations. A complete description of the mathematics involved in calculating the structure function can be found in this paper: https://arxiv.org/abs/1805.01242. Due to constraints on the length of our paper, it is not possible to detail all of the mathematics of scattering. We have added further explanation of this function in the documentation ``Brief Introduction to Interstellar Scattering’’.
Our previous clarifications have answered this question — the scattering kernel relates to the structure function in Fourier space, and the structure function itself depends on \phi. It is also now explained in the documentation. Please see ``Brief Introduction to Interstellar Scattering’’.
The definition is now in l65.
This refers to the distance between the earth and the scattering material. We have added that clarification.
Yes, refer to the above notes.
This FITS file is now included in the tutorial. Also, the tutorial now fixed the random number generator so that the results will be reproducible.
This is fixed now.
This is fixed as well, thanks! Response to the issues posted by @Edenhofer We made public responses to each of the issues posted by @Edenhofer. See below. Response to the referee report by @tomkimpson
Yes, this is true. The current Python and this new Julia implementation are both based on the theoretical discovery and framework by Blandford & Narayan 1985 (MNRAS, 213, 591) and later modernized by Johnson & Narayan 2016 (ApJ, 826, 170), which has been the community standard for almost a decade. When the measurements are obtained within a timescale longer than the diffractive timescale (often seconds or shorter), the refractive scattering effects can be accurately estimated through a simplified, semi-analytic geometrical optics framework. This works for the vast majority of radio interferometric observations. This allows a significant acceleration to simulate refractive scattering effects compared to full numerical models (e.g. Johnson & Gwinn 2015, ApJ, 805, 180), which are much slower and in addition have an issue with numerical accuracy. We didn’t mention it because the full numerical model of Johnson & Gwinn 2015 has not been publicly released and was quickly replaced within a year by the framework of this package.
We implemented all models in the literature, but yes it is indeed straightforward for interested users to implement their own scattering models. We have added a new documentation page ``Define Your Own Scattering Model’’.
This FITS file is now included in the tutorial. Also, the tutorial now fixed the random number generator so that the results will be reproducible.
See the answer to the GitHub issue (here).
We have added the ColPrac guideline to the readme page. |
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👋 @openjournals/aass-eics, this paper is ready to be accepted and published. Check final proof 👉📄 Download article If the paper PDF and the deposit XML files look good in openjournals/joss-papers#6339, then you can now move forward with accepting the submission by compiling again with the command |
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@Edenhofer, @tomkimpson — Many thanks for your reviews here! JOSS relies upon the volunteer effort of people like you and we simply wouldn't be able to do this without you!! @annatartaglia — Your paper has now been handed off to the track EiC who may have some final edits, before handling the final processing. |
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I'm having a first look at this now. @tomkimpson, on the basis of this comment of yours, above, I've gone ahead and ticked off everything in your review checklist. @annatartaglia, there a few things to address in the current metadata:
I intend to give the paper a closer look in the next few days, after which I'll probably propose some changes in a pull request. |
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Hi @warrickball, I've made all the requested amendments to the paper and Zenodo. Let me know if it looks good, or if more changes are needed. Additionally, let me know if we should make a patch release (v0.1.10) to the repository and update the Zenodo accordingly. Thanks! |
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Hi @annatartaglia, I've proposed what I hope are some final changes in a pull request. Once those are merged (presuming they're all okay), I'll give the publication pipeline another test run to check the relevant metadata (e.g. author affiliations) is also correctly updated. All the archive metadata looks good now. Changes to the paper don't require a new archive. |
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Hi @warrickball, thanks for making those changes; I've just merged the pull request. |
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👋 @openjournals/aass-eics, this paper is ready to be accepted and published. Check final proof 👉📄 Download article If the paper PDF and the deposit XML files look good in openjournals/joss-papers#6369, then you can now move forward with accepting the submission by compiling again with the command |
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@editorialbot accept |
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Fantastic! Thank you very much @dfm for managing the entire process as the editor, @Edenhofer & @tomkimpson for constructive reviews, and @warrickball for careful proofing! I am very excited to have the first JOSS paper for @annatartaglia and myself! |
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I'll echo @kazuakiyama's thanks to @Edenhofer & @tomkimpson for reviewing and @dfm for editing! JOSS simply wouldn't be possible without its community of volunteers. Congratulations @annatartaglia & @kazuakiyama, your paper has been published in JOSS! |
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Submitting author: @annatartaglia (Anna Tartaglia)
Repository: https://github.com/EHTJulia/ScatteringOptics.jl
Branch with paper.md (empty if default branch):
Version: v0.1.9
Editor: @dfm
Reviewers: @Edenhofer, @tomkimpson
Archive: 10.5281/zenodo.14552842
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