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[PRE REVIEW]: PulPy: A Python Toolkit for MRI RF and Gradient Pulse Design #6482

Closed editorialbot closed 6 months ago

editorialbot commented 7 months ago

Submitting author: !--author-handle-->@jonbmartin<!--end-author-handle-- (Jonathan Martin) Repository: https://github.com/jonbmartin/pulpy Branch with paper.md (empty if default branch): Version: v1.8.1 Editor: !--editor-->@emdupre<!--end-editor-- Reviewers: @bwheelz36, @curtcorum Managing EiC: Kevin M. Moerman

Status

status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/98b588bb86f4842aa218c0c123ec5516"><img src="https://joss.theoj.org/papers/98b588bb86f4842aa218c0c123ec5516/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/98b588bb86f4842aa218c0c123ec5516/status.svg)](https://joss.theoj.org/papers/98b588bb86f4842aa218c0c123ec5516)

Author instructions

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

@jonbmartin 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

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editorialbot commented 7 months 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 7 months ago

Software report:

github.com/AlDanial/cloc v 1.90  T=0.04 s (1010.3 files/s, 154129.0 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          29           1013           1304           3003
TeX                              1              1              0            432
Markdown                         1             21              0             89
reStructuredText                 5             67            134             65
YAML                             2             12             24             41
TOML                             1              2              0             20
make                             1              4              6             10
Bourne Shell                     1              0              0              7
-------------------------------------------------------------------------------
SUM:                            41           1120           1468           3667
-------------------------------------------------------------------------------

Commit count by author:

   119  jonbmartin
     8  Jonathan Martin
editorialbot commented 7 months ago 
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1109/42.75611 is OK
- 10.1002/mrm.26235 is OK
- 10.1002/MRM.29686 is OK
- 10.1038/s42256-021-00411-1 is OK
- 10.1002/MRM.21013 is OK
- 10.1016/0022-2364(89)90265-5 is OK
- 10.1006/JMRE.2001.2340 is OK
- 10.1002/MRM.23152 is OK
- 10.1109/TMI.2008.922699 is OK
- 10.1002/MRM.10493 is OK
- 10.3390/BIOENGINEERING10020158 is OK
- 10.1109/TMI.2022.3161875 is OK
- 10.21105/JOSS.01725 is OK
- 10.1145/2833157.2833162 is OK
- 10.1002/MRM.20978 is OK
- 10.1002/MRM.26235 is OK
- 10.1002/MRM.22406 is OK
- 10.1002/MRM.29294 is OK
- 10.1002/MRM.29271 is OK

MISSING DOIs

- 10.1016/j.jmr.2008.06.010 may be a valid DOI for title: Multiband excitation pulses for hyperpolarized 13C...
- 10.1002/mrm.27411 may be a valid DOI for title: Multiband RF pulse design for realistic gradient p...
- No DOI given, and none found for title: Michigan Image Reconstruction Toolbox
- No DOI given, and none found for title: Adjustment and Basic Imaging Sequences for the Ope...
- 10.1117/12.3008456 may be a valid DOI for title: AniRes2D: Anisotropic Residual-enhanced Diffusion ...
- No DOI given, and none found for title: NMR Imaging in Biomedicine
- No DOI given, and none found for title: Selective complex pulse design by optimal control ...
- No DOI given, and none found for title: Advanced Normalization Tools (ANTS)
- No DOI given, and none found for title: SigPy: A Python Package for High Performance Itera...
- No DOI given, and none found for title: Berkeley Advanced Reconstruction Toolbox
- No DOI given, and none found for title: Quantitative MRI made easy with qMRLab
- No DOI given, and none found for title: MARIE a MATLAB-based open source software for the ...
- No DOI given, and none found for title: SigPy.RF: Comprehensive Open-Source RF Pulse Desig...
- No DOI given, and none found for title: OCRA : a low-cost, open-source FPGA-based MRI cons...

INVALID DOIs

- 10.1007/S10334-023-01134-7/FIGURES/8 is INVALID
- 10.1002/(SICI)1522-2594(199911)42:5 is INVALID
editorialbot commented 7 months ago

Paper file info:

📄 Wordcount for paper.md is 1352

✅ The paper includes a Statement of need section

editorialbot commented 7 months ago

License info:

🟡 License found: GNU General Public License v3.0 (Check here for OSI approval)

editorialbot commented 7 months ago

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

Kevin-Mattheus-Moerman commented 7 months ago

@jonbmartin thanks for this submission to JOSS. I am the AEiC for this track and here to help process initial steps. Could you have a look at the above DOI analysis? Perhaps you can address some of these potentially missing ones? You can call @editorialbot check references to check them again, and use @editorialbot generate pdf to update the draft paper.

Kevin-Mattheus-Moerman commented 7 months ago

@AoifeHughes do you think you could help edit this one? Thanks!

Kevin-Mattheus-Moerman commented 7 months ago

@editorialbot invite @AoifeHughes as editor

editorialbot commented 7 months ago

Invitation to edit this submission sent!

Kevin-Mattheus-Moerman commented 7 months ago

@jonbmartin thanks for this submission. I am a little worried about wether this work is in scope for JOSS in terms of our "substantial scholarly effort criteria", in particular in relation to:

As a rule of thumb, JOSS’ minimum allowable contribution should represent not less than three months of work for an individual.

This work appears to have been created by a single contributor/author, within about ~1 month. There are no forks/issues/PR's from others, and only you are listed under stars/watching. I'll trigger a scope check now by the editorial board, so they can help have a look. However, it would be great if you could comment on the above, thanks.

jonbmartin commented 7 months ago

Hi @Kevin-Mattheus-Moerman, thank you for taking a look at our work. The vast majority of the code base was originally developed by the listed authors in two separate github projects, SigPy and SigPy.RF. The code contributions are primarily documented here: https://github.com/jonbmartin/sigpy-rf/graphs/contributors.

Development took place over several years, beginning in 2019. Upon conference with the authors in late 2023, we felt that the pulse design tools had matured enough and were distinct enough from the mission of SigPy to be a stand-alone Python package, so I migrated that code to the new PulPy project. However, the code base represents the work of a number of individuals over many years, and between the two previous projects has received over 300 stars! We have not previously published anything relating to the pulse design tools outside of a conference abstract, and so felt it was time to describe them in JOSS.

This is described in the manuscript, but I would appreciate it if you or the reviewers have any suggestions on how to make this more clear to the users.

editorialbot commented 7 months ago

I'm sorry human, I don't understand that. You can see what commands I support by typing:

@editorialbot commands

jonbmartin commented 7 months ago

@editorialbot commands

editorialbot commented 7 months ago

Hello @jonbmartin, here are the things you can ask me to do:


# List all available commands
@editorialbot commands

# Get a list of all editors's GitHub handles
@editorialbot list editors

# Adds a checklist for the reviewer using this command
@editorialbot generate my checklist

# Set a value for branch
@editorialbot set joss-paper as branch

# Run checks and provide information on the repository and the paper file
@editorialbot check repository

# Check the references of the paper for missing DOIs
@editorialbot check references

# Generates the pdf paper
@editorialbot generate pdf

# Generates a LaTeX preprint file
@editorialbot generate preprint

# Get a link to the complete list of reviewers
@editorialbot list reviewers
jonbmartin commented 7 months ago

@editorialbot check references

editorialbot commented 7 months ago 
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1016/j.jmr.2008.06.010 is OK
- 10.1002/mrm.27411 is OK
- 10.1007/s10334-023-01134-7 is OK
- 10.1109/42.75611 is OK
- 10.1002/mrm.26235 is OK
- 10.1002/MRM.29686 is OK
- 10.1117/12.3008456 is OK
- 10.1038/s42256-021-00411-1 is OK
- 10.1002/MRM.21013 is OK
- 10.1016/0022-2364(89)90265-5 is OK
- 10.1007/BF02797382 is OK
- 10.1006/JMRE.2001.2340 is OK
- 10.1002/MRM.23152 is OK
- 10.1109/TMI.2008.922699 is OK
- 10.1002/MRM.10493 is OK
- 10.3390/BIOENGINEERING10020158 is OK
- 10.1109/TMI.2022.3161875 is OK
- 10.21105/JOSS.01725 is OK
- 10.1145/2833157.2833162 is OK
- 10.1002/MRM.20978 is OK
- 10.1002/MRM.26235 is OK
- 10.1002/MRM.22406 is OK
- 10.1002/MRM.29294 is OK
- 10.1002/MRM.29271 is OK

MISSING DOIs

- No DOI given, and none found for title: Michigan Image Reconstruction Toolbox
- No DOI given, and none found for title: Adjustment and Basic Imaging Sequences for the Ope...
- No DOI given, and none found for title: Selective complex pulse design by optimal control ...
- No DOI given, and none found for title: Advanced Normalization Tools (ANTS)
- No DOI given, and none found for title: SigPy: A Python Package for High Performance Itera...
- No DOI given, and none found for title: Berkeley Advanced Reconstruction Toolbox
- No DOI given, and none found for title: Quantitative MRI made easy with qMRLab
- No DOI given, and none found for title: MARIE a MATLAB-based open source software for the ...
- No DOI given, and none found for title: SigPy.RF: Comprehensive Open-Source RF Pulse Desig...
- No DOI given, and none found for title: OCRA : a low-cost, open-source FPGA-based MRI cons...

INVALID DOIs

- 10.1002/MRM. is INVALID
jonbmartin commented 7 months ago

@editorialbot check references

editorialbot commented 7 months ago 
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1016/j.jmr.2008.06.010 is OK
- 10.1002/mrm.27411 is OK
- 10.1007/s10334-023-01134-7 is OK
- 10.1109/42.75611 is OK
- 10.1002/mrm.26235 is OK
- 10.1002/MRM.29686 is OK
- 10.1117/12.3008456 is OK
- 10.1038/s42256-021-00411-1 is OK
- 10.1002/MRM.21013 is OK
- 10.1016/0022-2364(89)90265-5 is OK
- 10.1007/BF02797382 is OK
- 10.1006/JMRE.2001.2340 is OK
- 10.1002/MRM.23152 is OK
- 10.1109/TMI.2008.922699 is OK
- 10.1002/MRM.10493 is OK
- 10.3390/BIOENGINEERING10020158 is OK
- 10.1109/TMI.2022.3161875 is OK
- 10.21105/JOSS.01725 is OK
- 10.1145/2833157.2833162 is OK
- 10.1002/MRM.20978 is OK
- 10.1002/MRM.26235 is OK
- 10.1002/MRM.22406 is OK
- 10.1002/MRM.29294 is OK
- 10.1002/MRM.29271 is OK

MISSING DOIs

- No DOI given, and none found for title: Michigan Image Reconstruction Toolbox
- No DOI given, and none found for title: Adjustment and Basic Imaging Sequences for the Ope...
- No DOI given, and none found for title: Selective complex pulse design by optimal control ...
- No DOI given, and none found for title: Advanced Normalization Tools (ANTS)
- No DOI given, and none found for title: SigPy: A Python Package for High Performance Itera...
- No DOI given, and none found for title: Berkeley Advanced Reconstruction Toolbox
- No DOI given, and none found for title: Quantitative MRI made easy with qMRLab
- No DOI given, and none found for title: MARIE a MATLAB-based open source software for the ...
- No DOI given, and none found for title: SigPy.RF: Comprehensive Open-Source RF Pulse Desig...
- No DOI given, and none found for title: OCRA : a low-cost, open-source FPGA-based MRI cons...

INVALID DOIs

- https://doi.org/10.1002/(SICI)1522-2594(199911)42:5<952::AID-MRM16>3.0.CO;2-S is INVALID because of 'https://doi.org/' prefix
jonbmartin commented 7 months ago

Added DOI's to those papers missing them, and fixed invalid DOIs. Remaining references without DOI's are either A) conference proceedings for which none have been created, B) software toolboxes for which none have been created. The long invalid DOI with https:// prefix does resolve correctly when entered into the DOI database at doi.org; this is for an old paper which uses SICI referencing convetion. I have removed the https:// prefix and this now works.

Kevin-Mattheus-Moerman commented 7 months ago

@jonbmartin thanks for those comments. The board has decided this may be in scope for JOSS. I will search for a handling editor.

Kevin-Mattheus-Moerman commented 7 months ago

@editorialbot invite @emdupre as editor

editorialbot commented 7 months ago

Invitation to edit this submission sent!

emdupre commented 7 months ago

👋 Happy to take this, @Kevin-Mattheus-Moerman !

emdupre commented 7 months ago

@editorialbot assign @emdupre as editor

editorialbot commented 7 months ago

Assigned! @emdupre is now the editor

emdupre commented 7 months ago

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

If you have suggestions for potential reviewers, please let me know by listing their names or GitHub handles (without the @, so they don't receive a notification) here.

You can suggest reviewers from any relevant project, though we often recommend starting with this database of people who have already agreed to review for JOSS.

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.

jonbmartin commented 7 months ago

Hi @emdupre, thank you for the editorial assistance.

I will suggest the following JOSS reviewers:

mathieuboudreau tomelse bwheelz36 spinicist rmarkello

emdupre commented 7 months ago

Thank you, @jonbmartin !

I'll review these suggestions and make invitations shortly, including my own recommendations. I'll update this thread with that outreach !

emdupre commented 7 months ago

👋 Hi @spinicist, @bwheelz36, @curtcorum,

Would you be willing to review PulPy: A Python Toolkit for MRI RF and Gradient Pulse Design 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.06482/joss.06482/10.21105.joss.06482.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 !

curtcorum commented 7 months ago

@emdupre I can do it with the clock starting in two weeks if that works?

bwheelz36 commented 7 months ago

Hi @emdupre Yes, this sounds really interesting :-)

spinicist commented 7 months ago

Apologies, I have too much on including another review but looks like you have two volunteers now?

emdupre commented 7 months ago

I can do it with the clock starting in two weeks if that works?

Thank you, @curtcorum ! I will aim to identify reviewers with sooner availability but will plan to circle back to you next week, if that sounds reasonable to you.

Yes, this sounds really interesting :-)

Thank you, @bwheelz36 ! I'll add you as a reviewer on this submission now.

Apologies, I have too much on including another review but looks like you have two volunteers now?

Thank you for letting me know, @spinicist ! Please feel free to mute this issue so that you don't receive any additional pings.

emdupre commented 7 months ago

@editorialbot add @bwheelz36 as reviewer

editorialbot commented 7 months ago

@bwheelz36 added to the reviewers list!

emdupre commented 7 months ago

👋 Hi @kerkelae, @imr-framework,

Would you be willing to review PulPy: A Python Toolkit for MRI RF and Gradient Pulse Design 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.06482/joss.06482/10.21105.joss.06482.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 !

curtcorum commented 7 months ago

@emdupre

That works for me.

emdupre commented 6 months ago

👋 Hi @curtcorum ! Are you still available to review this submission for PulPy ? Thank you for considering !

curtcorum commented 6 months ago

@emdupre Sure, your welcome and looking forward to it!

emdupre commented 6 months ago

Thank you, @curtcorum ! I'll go ahead and add you as a reviewer on this issue now.

@bwheelz36, please let me know if you will not be able to review, given the delayed timeline. If I don't hear from you (or @kerkelae and @imr-framework) within the next day, I'll assume that we're OK to move forward as-is !

Thank you all for considering !

emdupre commented 6 months ago

@editorialbot add @curtcorum as reviewer

editorialbot commented 6 months ago

@curtcorum added to the reviewers list!

emdupre commented 6 months ago

Given that we have a sufficient number of reviewers, I'll go ahead and open a dedicated review issue 🚀

Thank you again !

emdupre commented 6 months ago

@editorialbot start review

editorialbot commented 6 months ago

OK, I've started the review over in https://github.com/openjournals/joss-reviews/issues/6586.