[PRE REVIEW]: RT-utils: A Minimal Python Library for RT-struct Manipulation

[editorialbot]

Submitting author: !--author-handle-->@qurit-frizi<!--end-author-handle-- (Fereshteh Yousefi Rizi) Repository: https://github.com/qurit/rt-utils Branch with paper.md (empty if default branch): development Version: V1.2.0 Editor: !--editor-->@adamltyson<!--end-editor-- Reviewers: @pchlap, @suyashkumar, @xtie97 Managing EiC: Kevin M. Moerman

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Author instructions

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

@qurit-frizi 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.

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[editorialbot]

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[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.90  T=0.02 s (990.1 files/s, 98130.4 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          13            294            130            925
Markdown                         2             58              0            203
TeX                              1              9              0            118
YAML                             2              7              2             38
-------------------------------------------------------------------------------
SUM:                            18            368            132           1284
-------------------------------------------------------------------------------

Commit count by author:

   119  Asim Shrestha
    27  Adam Watkins
     9  Adam
     8  Fereshteh Yousefirizi
     5  Zhack47
     4  ThomasBudd
     4  zhack47
     3  Adam Zyzik
     3  Pedro Esquinas
     2  Carlos F. Uribe
     2  Pedro
     2  Robin Hegering
     2  asim-shrestha
     2  igorhlx
     1  Maxence Larose
     1  Phillip Chlap
     1  Samuel Ouellet
     1  Tom Roberts

[editorialbot]

Paper file info:

📄 Wordcount for paper.md is 1723

✅ The paper includes a Statement of need section

[editorialbot]

License info:

✅ License found: MIT License (Valid open source OSI approved license)

[editorialbot]

:warning: An error happened when generating the pdf. Author (Arman Rahmim) is missing affiliation.

[editorialbot]

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

OK DOIs

- None

MISSING DOIs

- 10.1016/j.mri.2012.05.001 may be a valid DOI for title: 3D Slicer as an image computing platform for the Q...
- No DOI given, and none found for title: Project MONAI
- 10.1016/j.cmpb.2021.106236 may be a valid DOI for title: TorchIO: A Python library for efficient loading, p...
- 10.1016/j.prro.2021.02.003 may be a valid DOI for title: Simple Python Module for Conversions Between DICOM...
- 10.2139/ssrn.4251277 may be a valid DOI for title: PyRaDiSe: A Python package for DICOM-RT-based auto...
- 10.1038/s41598-023-41475-w may be a valid DOI for title: Sensitivity of standardised radiomics algorithms t...
- No DOI given, and none found for title: The Image Biomarker Standardization Initiative: St...
- No DOI given, and none found for title: Federated testing of AI techniques: Towards sharin...
- 10.1158/0008-5472.can-18-0125 may be a valid DOI for title: LIFEx: A Freeware for Radiomic Feature Calculation...

INVALID DOIs

- None

[Kevin-Mattheus-Moerman]

@editorialbot query scope

[editorialbot]

Submission flagged for editorial review.

[Kevin-Mattheus-Moerman]

@qurit-frizi Dear author, thanks for this submission. I am the AEiC on this track and here to help process the initial steps. Before we proceed, please can you have a look at the following points:

• [ ] Please check the above error message for the paper compilation. It looks like you need to fix the affiliations.
• [ ] Please study the above reference check :point_up: and see if you can address any of the reported potential DOI issues. You can add/amend DOI entries in your .bib file, and call @editorialbot check references here to check them again.
• [x] Can you confirm this project includes automated testing? If not these need to be added and clearly linked to in both the documentation and also the readme.
• [x] Your project appears to lack contributing guidelines at the moment. Please work to add these and to mention/link to them in your README. You could for instance create a CONTRIBUTING.md file (see here for some examples: https://contributing.md/example/).

Note I have just added the query-scope label, to trigger a scope review by the editorial board. This is because of the relatively small size of the project. During this scope review we'll determine if the functionality offered is extensive enough and if the project conforms to our substantial scholarly effort criteria. The scope review should take about 2 weeks to complete.

[Kevin-Mattheus-Moerman]

@qurit-frizi :wave:

[Kevin-Mattheus-Moerman]

@qurit-frizi can you please respond to the above queries? It is important as an author that you respond to editor/reviewer queries in a timely manor. If we do not hear back by Friday August 30th we'll assume you are no longer interest and will proceed to reject this submission.

[qurit-frizi]

Sure I am addressing the mentioned issue. @Kevin-Mattheus-Moerman

[qurit-frizi]

@Kevin-Mattheus-Moerman I addressed the queries about the affiliation, and the DOI of the rereferences. This project includes automated testing.

[qurit-frizi]

@Kevin-Mattheus-Moerman CONTRIBUTING.md was now added to the readme in the development branch

[Kevin-Mattheus-Moerman]

@editorialbot generate pdf

[editorialbot]

:warning: An error happened when generating the pdf.

[Kevin-Mattheus-Moerman]

@editorialbot check references

[editorialbot]

Checking the BibTeX entries failed with the following error:

Failed to parse BibTeX on value "doi" (NAME) ["@", #<BibTeX::Entry >, {:title=>["{3D} Slicer as an image computing platform for the Quantitative Imaging Network"], :author=>["Fedorov, Andriy and Beichel, Reinhard and Kalpathy-Cramer, Jayashree and Finet, Julien and Fillion-Robin, Jean-Christophe and Pujol, Sonia and Bauer, Christian and Jennings, Dominique and Fennessy, Fiona and Sonka, Milan and Buatti, John and Aylward, Stephen and Miller, James V and Pieper, Steve and Kikinis, Ron"], :journal=>["Magn. Reson. Imaging"], :publisher=>["Elsevier"], :volume=>"30", :number=>"9", :pages=>["1323--1341"], :month=>[:nov], :year=>"2012", :language=>["en"]}]

[Kevin-Mattheus-Moerman]

@qurit-frizi the above paper compilation error appears to relate to this .bib file error, and in particular your first reference to 3D slicer. Can you check your .bib file? Perhaps the dot at the end of this doi should be remove? i.e. doi = {10.1016/j.mri.2012.05.001.} should be doi = {10.1016/j.mri.2012.05.001}?

@openjournals/dev is this indeed the error? :point_up:

[Kevin-Mattheus-Moerman]

@qurit-frizi I have just removed the query-scope label as this submission as passed our initial scope check. Apologies that it took longer than usual. I will now proceed to find a handling editor for this submission.

[Kevin-Mattheus-Moerman]

@editorialbot invite @adamltyson as editor

[editorialbot]

Invitation to edit this submission sent!

[Kevin-Mattheus-Moerman]

@editorialbot invite @csoneson as editor

[editorialbot]

Invitation to edit this submission sent!

[Kevin-Mattheus-Moerman]

@csoneson just inviting you too since I think @adamltyson is at his max already in terms of handling submissions. Are you able to help as editor perhaps?

[adamltyson]

@Kevin-Mattheus-Moerman I can take this on. I think my other submissions will be in review for a while!

[adamltyson]

@editorialbot assign @adamltyson as editor

[editorialbot]

Assigned! @adamltyson is now the editor

[adamltyson]

Hi @qurit-frizi, I'll take over the submission from now on.

I won't start the review until the paper compiles properly. When you get the time, could you take a look at @Kevin-Mattheus-Moerman's comment above and see if this fixes the issue.

In the mean time, we may as well get started finding reviewers. Would you be able to recommend appropriate reviewers for this submission? You can use the list of potential reviewers to help. Please provide a list, but don't tag them (with @) so they aren't notified unnecessarily.

Thanks!

[qurit-frizi]

@adamltyson The appropriate reviewers could be: Astarakee, SimoneBendazzoli93, xtie97, AI-thecoder, Phillip Chlap, suyashkumar

[qurit-frizi]

@qurit-frizi the above paper compilation error appears to relate to this .bib file error, and in particular your first reference to 3D slicer. Can you check your .bib file? Perhaps the dot at the end of this doi should be remove? i.e. doi = {10.1016/j.mri.2012.05.001.} should be doi = {10.1016/j.mri.2012.05.001}?

@openjournals/dev is this indeed the error? ☝️

@adamltyson this issue is resolved.

[adamltyson]

@editorialbot generate pdf

[adamltyson]

@editorialbot check references

[editorialbot]

:warning: An error happened when generating the pdf.

[editorialbot]

Checking the BibTeX entries failed with the following error:

Failed to parse BibTeX on value "doi" (NAME) ["@", #<BibTeX::Entry >, {:title=>["{3D} Slicer as an image computing platform for the Quantitative Imaging Network"], :author=>["Fedorov, Andriy and Beichel, Reinhard and Kalpathy-Cramer, Jayashree and Finet, Julien and Fillion-Robin, Jean-Christophe and Pujol, Sonia and Bauer, Christian and Jennings, Dominique and Fennessy, Fiona and Sonka, Milan and Buatti, John and Aylward, Stephen and Miller, James V and Pieper, Steve and Kikinis, Ron"], :journal=>["Magn. Reson. Imaging"], :publisher=>["Elsevier"], :volume=>"30", :number=>"9", :pages=>["1323--1341"], :month=>[:nov], :year=>"2012", :language=>["en"]}]

[adamltyson]

Hi @qurit-frizi,

The paper building is still failing. Taking a look at the bib file, some parts of each entry seem to be missing a comma at the end of the line (e.g. language in the 3D slicer entry). Could you correct these and we'll try again?

[xuanxu]

Merging this PR should fix the error

[qurit-frizi]

@adamltyson I think it is good now!

[adamltyson]

@editorialbot generate pdf

[adamltyson]

@editorialbot check references

[editorialbot]

Checking the BibTeX entries failed with the following error:

Lexical or syntactical errors: 

@ARTICLE{Rufenacht2023-astitle={PyRaDiSe}: A Python package for {DICOM}-{RT}-based auto-segmentation pipeline construction and {DICOM}-{RT} data conversion,author=R\{u}fenacht,EliasandKamath,AmithandSuter,YannickandPoel,RobertandErmi\

[editorialbot]

:warning: An error happened when generating the pdf.

[adamltyson]

Hi @qurit-frizi,

There still seems to be issues compiling the paper. Could you ensure that it compiles locally then we can try again here?

Thanks!

[qurit-frizi]

It was compiled correctly and worked. @adamltyson

[adamltyson]

@editorialbot generate pdf

[editorialbot]

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

[editorialbot]

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⚠️ 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.

[adamltyson]

@editorialbot check references

[editorialbot]

Checking the BibTeX entries failed with the following error:

Lexical or syntactical errors: 

@ARTICLE{Rufenacht2023-astitle={PyRaDiSe}: A Python package for {DICOM}-{RT}-based auto-segmentation pipeline construction and {DICOM}-{RT} data conversion,author=R\{u}fenacht,EliasandKamath,AmithandSuter,YannickandPoel,RobertandErmi\

[adamltyson]

Thanks @qurit-frizi, the paper looks good now. Would you mind seeing if you can fix the one outstanding BibTeX issue? If you don't know where the problem lies, let me know and I'll see if someone from JOSS can help.