[PRE REVIEW]: RT-utils: A Minimal Python Library for RT-struct Manipulation #7056

editorialbot · 2024-07-30T08:04:48Z

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

Status

Status badge code:

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Markdown: [![status](https://joss.theoj.org/papers/7eb925046a71e235658070b87ac1f301/status.svg)](https://joss.theoj.org/papers/7eb925046a71e235658070b87ac1f301)

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The text was updated successfully, but these errors were encountered:

editorialbot · 2024-07-30T08:04:50Z

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 · 2024-07-30T08:05:05Z

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 · 2024-07-30T08:05:09Z

Paper file info:

📄 Wordcount for paper.md is 1723

✅ The paper includes a Statement of need section

editorialbot · 2024-07-30T08:05:11Z

License info:

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

editorialbot · 2024-07-30T08:05:21Z

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

editorialbot · 2024-07-30T08:05:28Z

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 · 2024-07-30T08:12:19Z

@editorialbot query scope

editorialbot · 2024-07-30T08:12:20Z

Submission flagged for editorial review.

Kevin-Mattheus-Moerman · 2024-07-30T08:16:08Z

@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 ☝️ 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.
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.
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 · 2024-08-02T07:56:17Z

@qurit-frizi 👋

Kevin-Mattheus-Moerman · 2024-08-26T08:50:38Z

@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 · 2024-08-26T16:06:35Z

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

qurit-frizi · 2024-08-28T21:54:15Z

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

qurit-frizi · 2024-08-30T22:57:25Z

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

Kevin-Mattheus-Moerman · 2024-09-16T09:27:47Z

@editorialbot generate pdf

editorialbot · 2024-09-16T09:28:22Z

⚠️ An error happened when generating the pdf.

Kevin-Mattheus-Moerman · 2024-09-16T09:29:14Z

@editorialbot check references

editorialbot · 2024-09-16T09:29:33Z

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 · 2024-09-16T09:33:32Z

@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? ☝️

Kevin-Mattheus-Moerman · 2024-09-16T09:34:37Z

@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 · 2024-09-16T09:35:14Z

@editorialbot invite @adamltyson as editor

editorialbot · 2024-09-16T09:35:17Z

Invitation to edit this submission sent!

Kevin-Mattheus-Moerman · 2024-09-16T12:31:06Z

@editorialbot invite @csoneson as editor

editorialbot · 2024-09-16T12:31:09Z

Invitation to edit this submission sent!

editorialbot · 2024-10-07T10:11:04Z

Five most similar historical JOSS papers:

adrt: approximate discrete Radon transform for Python
Submitting author: @karlotness
Handling editor: @diehlpk (Active)
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Similarity score: 0.7007

CleanX: A Python library for data cleaning of large sets of radiology images
Submitting author: @drcandacemakedamoore
Handling editor: @cMadan (Retired)
Reviewers: @henrykironde, @anki-xyz
Similarity score: 0.6808

MRdataset : A unified and user-friendly interface to medical imaging datasets
Submitting author: @sinhaharsh
Handling editor: @mstimberg (Active)
Reviewers: @htwangtw, @djmannion
Similarity score: 0.6713

Pylinac: Image analysis for routine quality assurance in radiotherapy
Submitting author: @jrkerns
Handling editor: @kellyrowland (Active)
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Similarity score: 0.6600

Volume Segmantics: A Python Package for Semantic Segmentation of Volumetric Data Using Pre-trained PyTorch Deep Learning
Models
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Handling editor: @osorensen (Active)
Reviewers: @jingpengw, @estenhl
Similarity score: 0.6585

⚠️ 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 · 2024-10-07T10:29:24Z

@editorialbot check references

editorialbot · 2024-10-07T10:29:43Z

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 · 2024-10-07T11:26:37Z

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.

adamltyson · 2024-10-07T11:37:05Z

Hi @Astarakee, @SimoneBendazzoli93, @xtie97, @pchlap, @suyashkumar would you be able to review this submission to JOSS?

If you haven't reviewed for JOSS before, we carry out our checklist-driven reviews here in GitHub issues following these guidelines. If you have any questions, let me know.

pchlap · 2024-10-07T15:51:30Z

Hi @adamltyson, this is great. Yes I'd be more than happy to review this submission.

suyashkumar · 2024-10-07T19:31:08Z

@adamltyson if you need another reviewer, I'm happy to help out.

xtie97 · 2024-10-07T19:48:25Z

@adamltyson Yes, I would be happy to review this submission if it is still needed

qurit-frizi · 2024-10-09T00:25:03Z

@adamltyson I think all the issues are resolved.

adamltyson · 2024-10-15T11:35:27Z

@editorialbot check references

editorialbot · 2024-10-15T11:35:44Z

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

✅ OK DOIs

- 10.1016/j.prro.2021.02.003 is OK
- 10.48550/arXiv.2211.02701 is OK
- 10.1016/j.mri.2012.05.001 is OK
- 10.1158/0008-5472.can-18-0125 is OK
- 10.1016/j.cmpb.2021.106236 is OK
- 10.1038/s41598-023-41475-w is OK
- 10.1016/j.jmir.2024.101745 is OK

🟡 SKIP DOIs

- None

❌ MISSING DOIs

- None

❌ INVALID DOIs

- 10.21105/joss.04675 is INVALID

editorialbot · 2024-10-15T11:35:57Z

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

✅ OK DOIs

- 10.1016/j.prro.2021.02.003 is OK
- 10.48550/arXiv.2211.02701 is OK
- 10.1016/j.mri.2012.05.001 is OK
- 10.1158/0008-5472.can-18-0125 is OK
- 10.1016/j.cmpb.2021.106236 is OK
- 10.1038/s41598-023-41475-w is OK
- 10.1016/j.jmir.2024.101745 is OK

🟡 SKIP DOIs

- None

❌ MISSING DOIs

- None

❌ INVALID DOIs

- 10.21105/joss.04675 is INVALID

adamltyson · 2024-10-15T11:36:16Z

@editorialbot generate pdf

adamltyson · 2024-10-15T11:37:28Z

Thanks @pchlap, @suyashkumar, @xtie97, much appreciated!

adamltyson · 2024-10-15T11:37:44Z

@editorialbot add @pchlap as reviewer

editorialbot · 2024-10-15T11:37:46Z

@pchlap added to the reviewers list!

editorialbot · 2024-10-15T11:37:46Z

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

adamltyson · 2024-10-15T11:37:58Z

@editorialbot add @suyashkumar as reviewer

editorialbot · 2024-10-15T11:37:59Z

@suyashkumar added to the reviewers list!

adamltyson · 2024-10-15T11:38:08Z

@editorialbot add @xtie97 as reviewer

editorialbot · 2024-10-15T11:38:10Z

@xtie97 added to the reviewers list!

editorialbot · 2024-10-15T11:38:31Z

Five most similar historical JOSS papers:

adrt: approximate discrete Radon transform for Python
Submitting author: @karlotness
Handling editor: @diehlpk (Active)
Reviewers: @zhangjy-ge, @fruzsinaagocs
Similarity score: 0.7067

CleanX: A Python library for data cleaning of large sets of radiology images
Submitting author: @drcandacemakedamoore
Handling editor: @cMadan (Retired)
Reviewers: @henrykironde, @anki-xyz
Similarity score: 0.6834

MRdataset : A unified and user-friendly interface to medical imaging datasets
Submitting author: @sinhaharsh
Handling editor: @mstimberg (Active)
Reviewers: @htwangtw, @djmannion
Similarity score: 0.6745

PATATO: a Python photoacoustic tomography analysis toolkit
Submitting author: @tomelse
Handling editor: @AoifeHughes (Retired)
Reviewers: @MengjieSHI, @ASK-DataScience
Similarity score: 0.6613

Pylinac: Image analysis for routine quality assurance in radiotherapy
Submitting author: @jrkerns
Handling editor: @kellyrowland (Active)
Reviewers: @ProfLeao, @SimonBiggs
Similarity score: 0.6601

⚠️ 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 · 2024-10-15T12:42:20Z

We're just waiting for the bot to start the review issue, then I will post some links to the review criteria, and each reviewer can create their reviewer checklists.

In the meantime, @qurit-frizi, could you see if you can fix the Invalid DOI above?

I also noticed that the paper is over the recommended 250-1000 words. Would you be able to cut down the length of the text?

adamltyson · 2024-10-15T12:42:54Z

@editorialbot start review

adamltyson · 2024-10-16T07:33:04Z

@editorialbot start review

editorialbot · 2024-10-16T07:33:07Z

OK, I've started the review over in #7361.

editorialbot added pre-review Track: 2 (BCM) Biomedical Engineering, Biosciences, Chemistry, and Materials labels Jul 30, 2024

editorialbot added Python TeX labels Jul 30, 2024

editorialbot added the query-scope Submissions of uncertain scope for JOSS label Jul 30, 2024

Kevin-Mattheus-Moerman removed the query-scope Submissions of uncertain scope for JOSS label Sep 16, 2024

editorialbot assigned pchlap Oct 15, 2024

editorialbot assigned suyashkumar Oct 15, 2024

editorialbot assigned xtie97 Oct 15, 2024

editorialbot closed this as completed Oct 16, 2024

[PRE REVIEW]: RT-utils: A Minimal Python Library for RT-struct Manipulation #7056

[PRE REVIEW]: RT-utils: A Minimal Python Library for RT-struct Manipulation #7056

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