[REVIEW]: mednoise: a python package for medical image processing

[whedon]

Submitting author: @ravibandaru-lab (Ravi Bandaru) Repository: https://github.com/mednoise/mednoise Version: v.1.2.4 Editor: @osorensen Reviewer: @kasbohm, @ethanknights Archive: Pending

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Review checklist for @kasbohm

✨ Important: Please do not use the Convert to issue functionality when working through this checklist, instead, please open any new issues associated with your review in the software repository associated with the submission. ✨

Conflict of interest

• [x] I confirm that I have read the JOSS conflict of interest (COI) policy and that: I have no COIs with reviewing this work or that any perceived COIs have been waived by JOSS for the purpose of this review.

Code of Conduct

• [x] I confirm that I read and will adhere to the JOSS code of conduct.

General checks

• [x] Repository: Is the source code for this software available at the repository url?
• [x] License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
• [x] Contribution and authorship: Has the submitting author (@ravibandaru-lab) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
• [ ] Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines

Functionality

• [ ] Installation: Does installation proceed as outlined in the documentation?
• [ ] Functionality: Have the functional claims of the software been confirmed?
• [ ] Performance: If there are any performance claims of the software, have they been confirmed? (If there are no claims, please check off this item.)

Documentation

• [ ] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
• [ ] Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
• [ ] Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
• [ ] Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
• [ ] Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?
• [ ] Community guidelines: Are there clear guidelines for third parties wishing to 1) Contribute to the software 2) Report issues or problems with the software 3) Seek support

Software paper

• [ ] Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
• [ ] A statement of need: Does the paper have a section titled 'Statement of Need' that clearly states what problems the software is designed to solve and who the target audience is?
• [ ] State of the field: Do the authors describe how this software compares to other commonly-used packages?
• [ ] Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
• [ ] References: Is the list of references complete, and is everything cited appropriately that should be cited (e.g., papers, datasets, software)? Do references in the text use the proper citation syntax?

Review checklist for @ethanknights

✨ Important: Please do not use the Convert to issue functionality when working through this checklist, instead, please open any new issues associated with your review in the software repository associated with the submission. ✨

Conflict of interest

• [ ] I confirm that I have read the JOSS conflict of interest (COI) policy and that: I have no COIs with reviewing this work or that any perceived COIs have been waived by JOSS for the purpose of this review.

Code of Conduct

• [ ] I confirm that I read and will adhere to the JOSS code of conduct.

General checks

• [ ] Repository: Is the source code for this software available at the repository url?
• [ ] License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
• [ ] Contribution and authorship: Has the submitting author (@ravibandaru-lab) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
• [ ] Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines

Functionality

• [ ] Installation: Does installation proceed as outlined in the documentation?
• [ ] Functionality: Have the functional claims of the software been confirmed?
• [ ] Performance: If there are any performance claims of the software, have they been confirmed? (If there are no claims, please check off this item.)

Documentation

• [ ] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
• [ ] Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
• [ ] Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
• [ ] Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
• [ ] Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?
• [ ] Community guidelines: Are there clear guidelines for third parties wishing to 1) Contribute to the software 2) Report issues or problems with the software 3) Seek support

Software paper

• [ ] Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
• [ ] A statement of need: Does the paper have a section titled 'Statement of Need' that clearly states what problems the software is designed to solve and who the target audience is?
• [ ] State of the field: Do the authors describe how this software compares to other commonly-used packages?
• [ ] Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
• [ ] References: Is the list of references complete, and is everything cited appropriately that should be cited (e.g., papers, datasets, software)? Do references in the text use the proper citation syntax?

[whedon]

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @kasbohm, @ethanknights it looks like you're currently assigned to review this paper :tada:.

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[whedon]

Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1016/j.media.2020.101759 is OK
- 10.1038/s41586-020-2649-2 is OK
- 10.12688/f1000research.29032.1 is OK
- 10.5281/zenodo.5043456 is OK
- 10.1016/j.zemedi.2018.11.002 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[whedon]

Wordcount for paper.md is 737

[whedon]

Software report (experimental):

github.com/AlDanial/cloc v 1.88  T=0.08 s (167.7 files/s, 39064.9 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                           9            447           1099           1510
Markdown                         2             32              0             74
TeX                              1              0              0             70
YAML                             1              2              3             19
TOML                             1              0              0              6
-------------------------------------------------------------------------------
SUM:                            14            481           1102           1679
-------------------------------------------------------------------------------

Statistical information for the repository '239126222a9a1a05aba9e912' was
gathered on 2021/08/10.
The following historical commit information, by author, was found:

Author                     Commits    Insertions      Deletions    % of changes
Ravi Bandaru                    31          6005           2952          100.00

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
Ravi Bandaru               3056           50.9          0.2                3.99

[whedon]

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

[osorensen]

@ethanknights and @kasbohm thanks for agreeing to review this submission! The guidelines and checklist above should get you started, but please ask me in this thread if I can be of further help in the process.

[whedon]

:wave: @ethanknights, please update us on how your review is going (this is an automated reminder).

[whedon]

:wave: @kasbohm, please update us on how your review is going (this is an automated reminder).

[osorensen]

@ethanknights and @kasbohm, how is it going with your reviews? If you have any particular issues or suggestions, please feel free to eleborate here or start an issue in the source repository.

[osorensen]

Dear @ravibandaru-lab After reading through the paper once more, and testing the submitted software, I am not sure whether the software is within the scope of JOSS. I will therefore pause this review for now, and discuss with the other JOSS editors' whether the submission is within scope.

In particular, whereas the submitted manuscript describes that 'mednoise' contains several algorithms for analyzing medical imaging data, I have not been able to find any demonstrations of such algorithms in the source repository.

[osorensen]

@kasbohm and @ethanknights, I pause this review for now, and will get back to you in due time.

[ravibandaru-lab]

Hello @osorensen!

Hopefully I can clear up some misconceptions/misunderstandings surrounding mednoise.

mednoise is not a tool to analyze medical imaging data. I've read over my paper once more to make sure that I didn't make any claims to mednoise's functionality as tool to analyze medical imaging data. mednoise is simply a tool to process medical images to improve the accuracy of ML and DL models (by removing noise/unneccesary features).

I did, however, make claims and demonstrations to mednoise's algorithms. At the time of submission to this journal, mednoise has three algorithms: hotspot, branch, and manual. The source code for these algorithms are present in my source directory as branch.py, hotspot.py, and manual.py. I've linked them below, as well as their associated testcases below.

• Manual Algorithm Source Code - https://github.com/mednoise/mednoise/blob/main/src/mednoise/manual.py

• Hotspot Algorithm Source Code - https://github.com/mednoise/mednoise/blob/main/src/mednoise/hotspot.py

• Branch Algorithm Source Code - https://github.com/mednoise/mednoise/blob/main/src/mednoise/branch.py

• Manual Algorithm Testcases - https://github.com/mednoise/mednoise/blob/main/tests/tests_manual.py

• Hotspot Algorithm Testcases - https://github.com/mednoise/mednoise/blob/main/tests/tests_hotspot.py

• Branch Algorithm Testcases - https://github.com/mednoise/mednoise/blob/main/tests/tests_branch.py

I've also included a description of the functionality of these algorithms in my documentation here: https://mednoise.github.io/documentation/api_reference/explanation.html. You can also learn more about the algorithms by viewing the API usage guide for them here: https://mednoise.github.io/documentation/api_reference/usage.html

Finally, I've included a sample input and output of the branch algorithm in my paper, which hopefully shows exactly what mednoise does.

Let me know if there is anything else you would like clarification on. Hopefully we can resolve this issue soon.

[osorensen]

Thanks for explaining @ravibandaru-lab. I will bring it on to the other editors, and you can expect to hear back from us in a week or two.

[kthyng]

Hi @ravibandaru-lab! Thanks for your submission. Unfortunately, the editorial board has determined that this submission is not currently in scope primarily due to not passing the substantial scholarly effort bar and confusion around what exactly the package does. We do, however, encourage you to improve your work over time and consider submitting it again in the future after more development.

Here is some specific feedback:

• Include explicit references to peer-reviewed publications for the algorithms implemented in the work
• Include examples showing the package being used to show what the software can do in a real life example
• There was a feeling of a disconnect between the scope as described in the paper and docs and in the included functionality -- e.g. the described methods seem concentrated on 2D images like ultrasounds, while the description is medical imaging more broadly ? so even with more development I'd think linking those two would be important !
• There is a lot of duplicated code: Every function in the all.py file also exists (copied) in one of the other files. This matters because it isn't a good coding practice (easy to make errors when you need to update that copied code!), but also it artificially inflates the lines of code in the package.
• The terminology was found to be confusing, which obfuscates the true value/intent of the package.
• It doesn't install because it declares Python standard library components as dependencies in the setup.cfg (they can be left off the dependencies list).

[kthyng]

@whedon reject

[whedon]

Paper rejected.

[kthyng]

I just realized that I forgot to acknowledge our reviewers @kasbohm and @ethanknights! (Usually the scope checks happen before there are reviewers.) Thank you for being willing to review this submission and for your time.

[kasbohm]

Thanks @kthyng!