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[PRE REVIEW]: MIRP: A Python package for standardised radiomics #6345

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editorialbot opened this issue Feb 12, 2024 · 35 comments
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[PRE REVIEW]: MIRP: A Python package for standardised radiomics #6345

editorialbot opened this issue Feb 12, 2024 · 35 comments
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@surajpaib @emdupre @Matthew-Jennings @drcandacemakedamoore @theanega
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pre-review Python Track: 2 (BCM) Biomedical Engineering, Biosciences, Chemistry, and Materials

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editorialbot commented Feb 12, 2024 •
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Submitting author: @alexzwanenburg (Alex Zwanenburg)
Repository: https://github.com/oncoray/mirp
Branch with paper.md (empty if default branch): paper
Version: v2.1.0
Editor: @emdupre
Reviewers: @surajpaib, @Matthew-Jennings, @drcandacemakedamoore, @theanega
Managing EiC: Kevin M. Moerman

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status

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HTML: <a href="https://joss.theoj.org/papers/165c85b1ecad891550a21b12c8b2e577"><img src="https://joss.theoj.org/papers/165c85b1ecad891550a21b12c8b2e577/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/165c85b1ecad891550a21b12c8b2e577/status.svg)](https://joss.theoj.org/papers/165c85b1ecad891550a21b12c8b2e577)

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

@alexzwanenburg 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:

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@editorialbot editorialbot added pre-review Track: 2 (BCM) Biomedical Engineering, Biosciences, Chemistry, and Materials labels Feb 12, 2024
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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

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

OK DOIs

- 10.1038/s41571-022-00707-0 is OK
- 10.1038/nrclinonc.2016.162 is OK
- 10.1148/radiol.2020191145 is OK
- 10.1038/s41598-017-13448-3 is OK
- 10.1038/s41598-018-36938-4 is OK
- 10.1038/s41598-022-13967-8 is OK
- 10.1148/radiol.211604 is OK
- 10.1148/radiol.231319 is OK
- 10.1038/nrclinonc.2017.141 is OK
- 10.1038/s41467-023-44591-3 is OK

MISSING DOIs

- None

INVALID DOIs

- None

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Software report:

github.com/AlDanial/cloc v 1.88  T=1.10 s (163.4 files/s, 48171.1 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                         104           5692           4648          19852
HTML                            25           1334             75           7703
Markdown                        12           1193              0           5535
SVG                              2              1              1           2996
JavaScript                      12            131            221            880
CSS                              4            190             35            779
reStructuredText                 7            169            159            351
XML                              4              0            336            256
TeX                              1             19              0            236
R                                1             25              8             77
YAML                             3              6              4             57
TOML                             1              5              0             47
DOS Batch                        2              8              1             28
make                             1              4              7              9
Bourne Shell                     1              0              0              1
-------------------------------------------------------------------------------
SUM:                           180           8777           5495          38807
-------------------------------------------------------------------------------


gitinspector failed to run statistical information for the repository

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Wordcount for paper.md is 1025

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👉📄 Download article proof 📄 View article proof on GitHub 📄 👈

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Five most similar historical JOSS papers:

mrivis: Medical image visualization library for neuroscience in python
Submitting author: @raamana
Handling editor: @arokem (Retired)
Reviewers: @miykael
Similarity score: 0.8356

PyMedPhys: A community effort to develop an open, Python-based standard library for medical physics applications
Submitting author: @Matthew-Jennings
Handling editor: @osorensen (Active)
Reviewers: @ProfLeao, @gbaltz
Similarity score: 0.8329

libfmp: A Python Package for Fundamentals of Music Processing
Submitting author: @fzalkow
Handling editor: @arfon (Active)
Reviewers: @brunaw, @expectopatronum
Similarity score: 0.8267

CleanX: A Python library for data cleaning of large sets of radiology images
Submitting author: @drcandacemakedamoore
Handling editor: @cMadan (Active)
Reviewers: @henrykironde, @anki-xyz
Similarity score: 0.8245

PoreSpy: A Python Toolkit for Quantitative Analysis of Porous Media Images
Submitting author: @jgostick
Handling editor: @usethedata (Retired)
Reviewers: @yxqd, @cr458
Similarity score: 0.8196

⚠️ 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.

@alexzwanenburg
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Potential reviewers:

  • Olivia Prior Palomares (theanega)
  • Phil Chlap (pchlap)
  • Suraj Pai (surajpaib)
  • André Pedersen (andreped)

@alexzwanenburg
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R and Tex labels can be removed from this issue. The software is fully in Python.

@Kevin-Mattheus-Moerman
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@editorialbot invite @emdupre as editor

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Invitation to edit this submission sent!

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emdupre commented Feb 16, 2024

Thanks for the invitation, @Kevin-Mattheus-Moerman ! Happy to take this

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emdupre commented Feb 16, 2024

@editorialbot assign @emdupre as editor

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Assigned! @emdupre is now the editor

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emdupre commented Feb 16, 2024

👋 Hi @alexzwanenburg, and thanks for your submission to JOSS !

I see that you have suggested several potential reviewers, thank you !

I'll put together a list of folks to reach out to as reviewers based on these suggestions and my own recommendations. I'll update this thread with that outreach.

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emdupre commented Feb 16, 2024

👋 Hi @Matthew-Jennings, @surajpaib, @andreped,

Would you be willing to review MIRP: A Python package for standardised radiomics for JOSS (the Journal of Open Source Software)?

You can learn more about reviewing for JOSS -- including our conflict of interest policy -- here.

The review takes place on GitHub and focuses on the software and this short paper:
https://github.com/openjournals/joss-papers/blob/joss.06345/joss.06345/10.21105.joss.06345.pdf

If you're available to review this work within the next month—or six weeks, at most—please let me know and I'll add you as a reviewer.

Once I have sufficient reviewers I'll open a dedicated review issue.

Thank you for considering !

@andreped
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@emdupre I am busy finalizing my PhD atm, so I am unable to review this submission.

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emdupre commented Feb 19, 2024

Thank you for letting us know @andreped !

Please feel free to mute this issue so that you don't receive any additional pings. And best of luck with finishing up your degree !

@surajpaib
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@emdupre
Hi Elizabeth,
I'm happy to review this work.

@alexzwanenburg Thank you for the recommendation!

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emdupre commented Feb 19, 2024

Thank you, @surajpaib !

I'll add you as a reviewer on this issue now. Once we have a sufficient number of reviewers, I'll open a dedicated review issue 🚀

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emdupre commented Feb 19, 2024

@editorialbot add @surajpaib as reviewer

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@surajpaib added to the reviewers list!

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emdupre commented Feb 23, 2024 •
edited

👋 Hi @drcandacemakedamoore, @theanega, @Matthew-Jennings,

Would you be willing to review MIRP: A Python package for standardised radiomics for JOSS (the Journal of Open Source Software)?

You can learn more about reviewing for JOSS -- including our conflict of interest policy -- here.

The review takes place on GitHub and focuses on the software and this short paper:
https://github.com/openjournals/joss-papers/blob/joss.06345/joss.06345/10.21105.joss.06345.pdf

If you're available to review this work within the next month—or six weeks, at most—please let me know and I'll add you as a reviewer.

Once I have sufficient reviewers I'll open a dedicated review issue.

Thank you for considering !

@Matthew-Jennings
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Hi @emdupre. Sure! Happy to review. No conflicts of interest to disclose.

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emdupre commented Feb 23, 2024

Thank you, @Matthew-Jennings !

I'll add you as a reviewer on this issue now. Once we have a sufficient number of reviewers, I'll open a dedicated review issue 🚀

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emdupre commented Feb 23, 2024

@editorialbot add @Matthew-Jennings as reviewer

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@Matthew-Jennings added to the reviewers list!

@drcandacemakedamoore
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Hello @emdupre I will be happy to review the work.

@theanega
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theanega commented Feb 24, 2024 via email

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emdupre commented Feb 26, 2024

Thank you, @drcandacemakedamoore and @theanega ! I'll add you both as reviewers now.

We'll then have a sufficient number of reviewers, so I'll go ahead and open the dedicated review issue ! 🚀

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emdupre commented Feb 26, 2024

@editorialbot add @drcandacemakedamoore as reviewer

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@drcandacemakedamoore added to the reviewers list!

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emdupre commented Feb 26, 2024

@editorialbot add @theanega as reviewer

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@theanega added to the reviewers list!

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emdupre commented Feb 26, 2024

@editorialbot start review

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OK, I've started the review over in #6413.

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