search

openjournals / joss-reviews

Reviews for the Journal of Open Source Software
Creative Commons Zero v1.0 Universal
725 stars 38 forks source link

[PRE REVIEW]: LCOI: Local crystalline orientation identifier using mask fitting implemented in MATLAB #7378

Open editorialbot opened 1 month ago

editorialbot commented 1 month ago

Submitting author: !--author-handle-->@SnirMeiri<!--end-author-handle-- (Snir Meiri) Repository: https://github.com/SnirMeiri/LCOI_local_crystalline_orientation_identifier Branch with paper.md (empty if default branch): Version: v1.0.0 Editor: !--editor-->@rkurchin<!--end-editor-- Reviewers: Pending Managing EiC: Kevin M. Moerman

Status

status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/225ad32dfcf25fe5417f6fe2d7349dd0"><img src="https://joss.theoj.org/papers/225ad32dfcf25fe5417f6fe2d7349dd0/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/225ad32dfcf25fe5417f6fe2d7349dd0/status.svg)](https://joss.theoj.org/papers/225ad32dfcf25fe5417f6fe2d7349dd0)

Author instructions

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

@SnirMeiri if you have any suggestions for potential reviewers then please mention them here in this thread (without tagging them with an @). You can search the list of people that have already agreed to review and may be suitable for this submission.

Editor instructions

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

@editorialbot commands
editorialbot commented 1 month ago

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

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

@editorialbot commands

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

@editorialbot generate pdf
editorialbot commented 1 month ago

Software report:

github.com/AlDanial/cloc v 1.90  T=0.06 s (251.0 files/s, 129307.9 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
MATLAB                           8            466            879           5620
Markdown                         3             61              0            102
TeX                              1              3              0             39
YAML                             2              3              5             33
-------------------------------------------------------------------------------
SUM:                            14            533            884           5794
-------------------------------------------------------------------------------

Commit count by author:

   164  Snir Meiri
     4  SnirMeiri
editorialbot commented 1 month ago 
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

✅ OK DOIs

- 10.1107/S160057671501167X is OK
- 10.1002/crat.201100125 is OK
- 10.1063/1.4774084 is OK

🟡 SKIP DOIs

- None

❌ MISSING DOIs

- 10.2172/4457192 may be a valid DOI for title: Angle Calculations for 3-and 4-Circle X-ray and Ne...

❌ INVALID DOIs

- None
editorialbot commented 1 month ago

Paper file info:

📄 Wordcount for paper.md is 605

✅ The paper includes a Statement of need section

editorialbot commented 1 month ago

License info:

🟡 License found: Other (Check here for OSI approval)

editorialbot commented 1 month ago

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

editorialbot commented 1 month ago

Five most similar historical JOSS papers:

Reel1.0 - A visualization tool for evaluating powder diffraction refinements Submitting author: @fgjorup Handling editor: @rkurchin (Active) Reviewers: @cmbiwer, @mikapfl Similarity score: 0.7142

PXO (Poly-XTAL Operations): MATLAB Codebase to Generate, Analyse and Export Complex 2D Spatio-Temporally Gradient Grain Structures Submitting author: @SunilAnandatheertha Handling editor: @Kevin-Mattheus-Moerman (Active) Reviewers: @yangbai90, @ksyang2013, @littlelazy6 Similarity score: 0.6922

Ising_OPV v4.0: Experimental Tomography Data Import, Interpretation, and Analysis Submitting author: @MikeHeiber Handling editor: @katyhuff (Retired) Reviewers: @myousefi2016, @stuartcampbell, @mdoucet Similarity score: 0.6847

Dark-field X-ray microscopy visualization Submitting author: @trygvrad Handling editor: @jgostick (Active) Reviewers: @taw10, @marcocamma Similarity score: 0.6795

LiberTEM: Software platform for scalable multidimensional data processing in transmission electron microscopy Submitting author: @uellue Handling editor: @majensen (Active) Reviewers: @alvarolopez, @fedorov Similarity score: 0.6757

⚠️ Note to editors: If these papers look like they might be a good match, click through to the review issue for that paper and invite one or more of the authors before considering asking the reviewers of these papers to review again for JOSS.

arfon commented 1 week ago

@SnirMeiri - thanks for your submission to JOSS. We're currently managing a large backlog of submissions and the editor most appropriate for your area is already rather busy.

For now, we will need to waitlist this paper and process it as the queue reduces. Thanks for your patience!

rkurchin commented 1 week ago

@editorialbot add me as editor

🤚 I can take this one!

editorialbot commented 1 week ago

Assigned! @rkurchin is now the editor

rkurchin commented 1 week ago

👋 @larsenkg and/or @caldarolamartin, would you be willing to review this submission for JOSS? We carry out our checklist-driven reviews here in GitHub issues and follow these guidelines: https://joss.readthedocs.io/en/latest/review_criteria.html

rkurchin commented 4 days ago

👋 @fgjorup and/or @uellue, would you be willing to review this submission for JOSS? We carry out our checklist-driven reviews here in GitHub issues and follow these guidelines: https://joss.readthedocs.io/en/latest/review_criteria.html

uellue commented 2 days ago

Hi @rkurchin, hi @SnirMeiri, I don't have access to Matlab. Does the software work in Octave? If yes, I could review this.

caldarolamartin commented 2 days ago

Hi

Unfortunately I do not have time at this point.

Best regards, Martin

Martin Caldarola

On Wed, 13 Nov 2024, 16:33 Rachel Kurchin, @.***> wrote:

👋 @larsenkg https://github.com/larsenkg and/or @caldarolamartin https://github.com/caldarolamartin, would you be willing to review this submission for JOSS? We carry out our checklist-driven reviews here in GitHub issues and follow these guidelines: https://joss.readthedocs.io/en/latest/review_criteria.html

— Reply to this email directly, view it on GitHub https://github.com/openjournals/joss-reviews/issues/7378#issuecomment-2473961314, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAUGZKQXIZFOL5DUZFLQMR32ANWMHAVCNFSM6AAAAABQIRXAICVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDINZTHE3DCMZRGQ . You are receiving this because you were mentioned.Message ID: @.***>

rkurchin commented 1 day ago

👋 @aazocar and/or @larsenkg, would you be willing to review this submission for JOSS? We carry out our checklist-driven reviews here in GitHub issues and follow these guidelines: https://joss.readthedocs.io/en/latest/review_criteria.html

SnirMeiri commented 1 day ago

Hi @uellue, thanks for your answer. I have no experience with Octave but since the application itself is written as a MATLAB application (.mlapp file) I am not sure it will be able to run on Octave. I have tried to run it on the Octave online compiler and it did not compile. Should the desktop version of Octave be able to run the file although the online version is not able to do so?

uellue commented 1 day ago

@SnirMeiri with neither Matlab nor Octave I have much experience. I tried installing the Matlab runtime and running the mlapp file, but couldn't figure out how. To confirm, running it in the App Designer as described in the documentation is the only way? IMO it is unfortunate when an open source application depends so strongly on a runtime that is not easily accessible for everyone.

Long story short, I won't be able to review this submission because I currently can't run the software. It would be much better in general if the application runs stand-alone without purchasing a Matlab license and if the documentation explains how to do that.

fgjorup commented 1 day ago

Hi @SnirMeiri and @rkurchin. I tried to download the repo and run the app through App Designer (Matlab 2022b). While the UI opens, the functions does not work. I don't see any installers, there is no guide in the readme, and I am not sufficiently proficient in matlab to troubleshoot myself.

SnirMeiri commented 1 day ago

Hi @fgjorup. Do you have the Image Processing toolbox and the Parallel Computation toolbox installed? These are the only toolboxes needed which are not defaults in MATLAB. It is mentioned in the installation section in the readme file in github but not in the paper.md file. Should paper file have an installation section? If you do have these toolboxes installed and the functions still don't work I will try and see what might have happened but I have tried running it through different computers and MATLAB versions and it worked.

SnirMeiri commented 1 day ago

@uellue Thanks for your suggestions. Unfortunately as for now the application only runs through MATLAB. It was first written for internal use and only after our experimental collaborators have mentioned they believe it will be useful for other research groups that we have decided to adjust it for more general use and make it public. I will try to see if I can make it a stand-alone application.

fgjorup commented 1 day ago

Hi @fgjorup. Do you have the Image Processing toolbox and the Parallel Computation toolbox installed? These are the only toolboxes needed which are not defaults in MATLAB. It is mentioned in the installation section in the readme file in github but not in the paper.md file. Should paper file have an installation section? If you do have these toolboxes installed and the functions still don't work I will try and see what might have happened but I have tried running it through different computers and MATLAB versions and it worked.

I just tried installing the two toolboxes, unfortunately my university has a very strict data policy, so I cannot install software through external programs (matlab). Had it been python it would have been another story. I am afraid I won't be able to serve as reviewer.

-Frederik