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[PRE REVIEW]: SenAOReFoc: A Closed-Loop Sensorbased Adaptive Optics and Remote Focusing Control Software #4023

Closed whedon closed 2 years ago

whedon commented 2 years ago

Submitting author: @jiahecui (Jiahe Cui) Repository: https://github.com/jiahecui/SenAOReFoc Version: v1.0.0 Editor: @diehlpk Reviewers: @abhilash12iec002 , @JackTyson, @alvesjnr Managing EiC: Arfon Smith

:warning: JOSS reduced service mode :warning:

Due to the challenges of the COVID-19 pandemic, JOSS is currently operating in a "reduced service mode". You can read more about what that means in our blog post.

Status

status

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Markdown: [![status](https://joss.theoj.org/papers/c0c5c8e06b379c4ac5374b261241068d/status.svg)](https://joss.theoj.org/papers/c0c5c8e06b379c4ac5374b261241068d)

Author instructions

Thanks for submitting your paper to JOSS @jiahecui. Currently, there isn't an JOSS editor assigned to your paper.

The author's suggestion for the handling editor is @jni.

@jiahecui if you have any suggestions for potential reviewers then please mention them here in this thread (without tagging them with an @). In addition, this list of people have already agreed to review for JOSS and may be suitable for this submission (please start at the bottom of the list).

Editor instructions

The JOSS submission bot @whedon is here to help you find and assign reviewers and start the main review. To find out what @whedon can do for you type:

@whedon commands
whedon commented 2 years ago

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks.

:warning: JOSS reduced service mode :warning:

Due to the challenges of the COVID-19 pandemic, JOSS is currently operating in a "reduced service mode". You can read more about what that means in our blog post.

For a list of things I can do to help you, just type:

@whedon commands

For example, to regenerate the paper pdf after making changes in the paper's md or bib files, type:

@whedon generate pdf
whedon commented 2 years ago

Wordcount for paper.md is 1615

whedon commented 2 years ago 
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1038/lsa.2014.46 is OK
- 10.1038/nn.4358 is OK
- 10.1364/OE.401117 is OK
- 10.1364/OE.27.031316 is OK
- 10.1364/OE.25.004368 is OK
- 10.1364/OE.26.001655 is OK
- 10.1364/OE.23.026208 is OK
- 10.5281/zenodo.3885508 is OK
- 10.1364/OE.442025 is OK
- 10.1364/BOE.8.004369 is OK
- 10.1364/AOPT.2005.AThB4 is OK
- 10.1111/j.1365-2966.2004.08524.x is OK
- 10.1364/OL.26.000746 is OK
- 10.1097/OPX.0b013e3181ff9a8b is OK
- 10.1098/rsta.2007.0013 is OK
- 10.1038/nmeth.4218 is OK
- 10.3928/1081-597X-20010901-13 is OK

MISSING DOIs

- 10.1364/boda.2021.dth2a.2 may be a valid DOI for title: Remote-Focussing for Volumetric Imaging in a Contactless and Label-Free Neurosurgical Microscope
- 10.1117/12.2054470 may be a valid DOI for title: Object-oriented Matlab adaptive optics toolbox
- 10.1146/annurev.aa.31.090193.000305 may be a valid DOI for title: Adaptive optics for astronomy: principles, performance, and applications

INVALID DOIs

- None
whedon commented 2 years ago 
Software report (experimental):

github.com/AlDanial/cloc v 1.88  T=0.24 s (210.3 files/s, 81868.8 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          43           3134           4702           8803
Qt                               2              0              0           1474
Markdown                         2            165              0            763
TeX                              1             21              0            241
YAML                             1             12              0             82
JSON                             1              0              0             70
-------------------------------------------------------------------------------
SUM:                            50           3332           4702          11433
-------------------------------------------------------------------------------

Statistical information for the repository 'cf2651fd48f43136d981d7e9' was
gathered on 2021/12/21.
The following historical commit information, by author, was found:

Author                     Commits    Insertions      Deletions    % of changes
Jiahe Cui                      203       1380249        1369584           99.68
jiahecui                        55          7430           1470            0.32

Below are the number of rows from each author that have survived and are still
intact in the current revision:

Author                     Rows      Stability          Age       % in comments
Jiahe Cui                 16639            1.2          9.7               10.30
whedon commented 2 years ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

jiahecui commented 2 years ago

Suggestion for potential reviewers: caldarolamartin, jonatanalvelid

arfon commented 2 years ago

:wave: @jiahecui – many thanks for your submission to JOSS. While I look for an editor to handle your submission if you want to fix the DOIs (noting that Whedon's suggestions are not always right), you can, then use the following commands (one at a time, as the first line of a new comment) to regenerate the PDF and check the references.

@whedon generate pdf @whedon check references

arfon commented 2 years ago

@whedon invite @jni as editor

:wave: @jni – would you be able to edit this submission for JOSS? Many thanks!

whedon commented 2 years ago

@jni has been invited to edit this submission.

jiahecui commented 2 years ago

@whedon generate pdf

whedon commented 2 years ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

jiahecui commented 2 years ago

@whedon check references

whedon commented 2 years ago 
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1038/lsa.2014.46 is OK
- 10.1038/nn.4358 is OK
- 10.1364/OE.401117 is OK
- 10.1364/OE.27.031316 is OK
- 10.1364/OE.25.004368 is OK
- 10.1364/OE.26.001655 is OK
- 10.1364/OE.23.026208 is OK
- 10.5281/zenodo.3885508 is OK
- 10.1364/boda.2021.dth2a.2 is OK
- 10.1364/OE.442025 is OK
- 10.1364/BOE.8.004369 is OK
- 10.1364/AOPT.2005.AThB4 is OK
- 10.1111/j.1365-2966.2004.08524.x is OK
- 10.1117/12.2054470 is OK
- 10.1364/OL.26.000746 is OK
- 10.1146/annurev.aa.31.090193.000305 is OK
- 10.1097/OPX.0b013e3181ff9a8b is OK
- 10.1098/rsta.2007.0013 is OK
- 10.1038/nmeth.4218 is OK
- 10.3928/1081-597X-20010901-13 is OK

MISSING DOIs

- None

INVALID DOIs

- None
kthyng commented 2 years ago

@whedon assign @diehlpk as editor

whedon commented 2 years ago

OK, the editor is @diehlpk

diehlpk commented 2 years ago

@jiahecui would be great if you could recommend some reviewers?

jiahecui commented 2 years ago

Hello and thank you for agreeing to be editor! Suggestion for potential reviewers: caldarolamartin, jonatanalvelid.

diehlpk commented 2 years ago

Hi @caldarolamartin and @jonatanalvelid would you be interested in reviewing this paper?

diehlpk commented 2 years ago

Hi @dvanic or @sfuxy or @jodemaey or @abhilash12iec002 would you be interested in reviewing this paper?

dvanic commented 2 years ago

@diehlpk: sorry, it's too far outside my area of expertise 😓

jonatanalvelid commented 2 years ago

Hi @diehlpk, thank you for considering me, but I am unfortunately not available to review currently. I hope I will be considered again in the future and will happily review then, and thanks for your understanding.

Best, Jonatan

abhilash12iec002 commented 2 years ago

Yes, I can review the said paper.

Best,

Abhilash Singh PhD Scholar, 1810302 Fluvial Geomorphology and Remote Sensing Lab, Department of EES, AB-2, Lab-10, Indian Institute of Science Education and Research Bhopal mobile: +91-9990674147 @. www.abhilashsingh.net @.>

On Tue, Jan 11, 2022 at 1:29 PM Jonatan Alvelid @.***> wrote:

Hi @diehlpk https://github.com/diehlpk, thank you for considering me, but I am unfortunately not available to review currently. I hope I will be considered again in the future and will happily review then, and thanks for your understanding.

Best, Jonatan

— Reply to this email directly, view it on GitHub https://github.com/openjournals/joss-reviews/issues/4023#issuecomment-1009685900, or unsubscribe https://github.com/notifications/unsubscribe-auth/ALFVGVBVTTS67XANNVAWWGDUVPPN7ANCNFSM5KQVAYHA . Triage notifications on the go with GitHub Mobile for iOS https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Android https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub.

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jodemaey commented 2 years ago

Hi,

Same as @dvanic comment for me, it is way outside of my area of expertise.

Sorry,

Jonathan

diehlpk commented 2 years ago

@whedon assign @abhilash12iec002 as reviewer

whedon commented 2 years ago

OK, @abhilash12iec002 is now a reviewer

diehlpk commented 2 years ago

@jiahecui would be great if you could recommend more reviewers?

abhilash12iec002 commented 2 years ago

@jiahecui Please find my comments below; I have read the complete article, “SenAOReFoc: A Closed-Loop Sensorbased Adaptive Optics and Remote Focusing Control Software” with full consideration. The title is short and sufficient. The summary part is nicely written in a very concise way. In the statement of need section, there exists a scope of improvement. For example; “The functionality of the software has also been tested on different operating systems (Windows/macOS/Linux) for sake of generality.” For this line, a concluding remark on the performance on each platform must be added. Also, the lines from 71 to 73 must be explained in detail. I think these two points are very crucial points and a good set of motivation for this software. I am very much satisfied with the Example usage section. Apart from reading the article, I have spent a good chunk of time using the SenAOReFoc package in the due course of this review. I am satisfied with the functionality of this software.

Overall, the submitted manuscript is well written, and ably demonstrates the community requirement for this open-source tool. I recommend publication after incorporating the suggestions discussed above.

diehlpk commented 2 years ago

@whedon start review

whedon commented 2 years ago

OK, I've started the review over in https://github.com/openjournals/joss-reviews/issues/4075.

diehlpk commented 2 years ago

@abhilash12iec002 That was quick. I started the review in #4075, and please check the checkboxes there.

jiahecui commented 2 years ago

@diehlpk Sure no problem, I suggest JackTyson, caldarolamartin, alvesjnr, aquilesC. Thank you very much!

jiahecui commented 2 years ago

@jiahecui Please find my comments below; I have read the complete article, “SenAOReFoc: A Closed-Loop Sensorbased Adaptive Optics and Remote Focusing Control Software” with full consideration. The title is short and sufficient. The summary part is nicely written in a very concise way. In the statement of need section, there exists a scope of improvement. For example; “The functionality of the software has also been tested on different operating systems (Windows/macOS/Linux) for sake of generality.” For this line, a concluding remark on the performance on each platform must be added. Also, the lines from 71 to 73 must be explained in detail. I think these two points are very crucial points and a good set of motivation for this software. I am very much satisfied with the Example usage section. Apart from reading the article, I have spent a good chunk of time using the SenAOReFoc package in the due course of this review. I am satisfied with the functionality of this software.

Overall, the submitted manuscript is well written, and ably demonstrates the community requirement for this open-source tool. I recommend publication after incorporating the suggestions discussed above.

@abhilash12iec002 Thank you very much for the thorough review and detailed comments. Your time is greatly appreciated! We will make the revisions as soon as possible!

abhilash12iec002 commented 2 years ago

@jiahecui Thanks and Good luck!

diehlpk commented 2 years ago

Hi @JackTyson, @caldarolamartin, @alvesjnr, @aquilesC would you be interested in reviewing this paper?

aquilesC commented 2 years ago

Thanks for the invite! I am wrapping up another review here on JOSS and with zero bandwidth to take up another one.

JackTyson commented 2 years ago

Hi @diehlpk, yes, this area sits within my expertise and I would be happy to review.

diehlpk commented 2 years ago

@whedon add @JackTyson as reviewer

whedon commented 2 years ago

OK, @JackTyson is now a reviewer

alvesjnr commented 2 years ago

Hi,

I would be happy to review.

On Thu, Jan 20, 2022, 17:29 Patrick Diehl @.***> wrote:

Hi @JackTyson https://github.com/JackTyson, @caldarolamartin https://github.com/caldarolamartin, @alvesjnr https://github.com/alvesjnr, @aquilesC https://github.com/aquilesC would you be interested in reviewing this paper?

— Reply to this email directly, view it on GitHub https://github.com/openjournals/joss-reviews/issues/4023#issuecomment-1017687110, or unsubscribe https://github.com/notifications/unsubscribe-auth/AABXQCAZAPX6DXXZ3LCIE6LUXAZ7BANCNFSM5KQVAYHA . Triage notifications on the go with GitHub Mobile for iOS https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Android https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub.

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diehlpk commented 2 years ago

@whedon add @alvesjnr as reviewer

whedon commented 2 years ago

OK, @alvesjnr is now a reviewer