[PRE REVIEW]: PyOrthanc: A Python Interface for Orthanc DICOM Servers

[editorialbot]

Submitting author: @gacou54 (Gabriel Couture)
Repository: https://github.com/gacou54/pyorthanc
Branch with paper.md (empty if default branch): joss
Version: v1.18.0
Editor: @sappelhoff
Reviewers: @sinhaharsh, @jrkerns, @devnums
Managing EiC: Kevin M. Moerman

Status

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[editorialbot]

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

✅ OK DOIs

- None

🟡 SKIP DOIs

- No DOI given, and none found for title: Digital Imaging and Communications in Medicine (DI...
- No DOI given, and none found for title: HTTPX: A next-generation HTTP client for Python
- No DOI given, and none found for title: simple-openapi-client: OpenAPI Python client gener...

❌ MISSING DOIs

- 10.1007/s10278-018-0082-y may be a valid DOI for title: The Orthanc Ecosystem for Medical Imaging

❌ INVALID DOIs

- None

[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.90  T=0.25 s (196.4 files/s, 98734.2 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          34           4159          11810           8103
Markdown                         2             73              0            226
YAML                             2              3              0             43
TeX                              1              3              0             31
DOS Batch                        1              8              1             26
reStructuredText                 4             13             40             23
JSON                             2              0              0             19
TOML                             1              3              0             18
make                             1              4              6              9
Dockerfile                       1              5              0              7
-------------------------------------------------------------------------------
SUM:                            49           4271          11857           8505
-------------------------------------------------------------------------------

Commit count by author:

   205	Gabriel Couture
     6	Yannick Lemaréchal
     1	Justin Hamel

[editorialbot]

Paper file info:

📄 Wordcount for paper.md is 718

✅ The paper includes a Statement of need section

[editorialbot]

License info:

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

[editorialbot]

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

[editorialbot]

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[gacou54]

@editorialbot check references

[editorialbot]

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

✅ OK DOIs

- 10.1007/s10278-018-0082-y is OK

🟡 SKIP DOIs

- No DOI given, and none found for title: Digital Imaging and Communications in Medicine (DI...
- No DOI given, and none found for title: HTTPX: A next-generation HTTP client for Python
- No DOI given, and none found for title: simple-openapi-client: OpenAPI Python client gener...

❌ MISSING DOIs

- None

❌ INVALID DOIs

- None

[Kevin-Mattheus-Moerman]

@gacou54 Dear author, thanks for this submission. I am the AEiC on this track and here to help process the initial steps. For the moment I have waitlisted this submission, since all editors in this domain are currently unfortunately preoccupied with other submissions.

[Kevin-Mattheus-Moerman]

@srmnitc is this submission something you can help edit? It may not be your core topic, but I was wondering if you could help given your work on research data management and workflows.

[Kevin-Mattheus-Moerman]

@editorialbot invite @srmnitc as editor

[editorialbot]

Invitation to edit this submission sent!

[gacou54]

Thanks @Kevin-Mattheus-Moerman , pyorthanc doesn't have much domain logic. It's mainly a wrapper to communicate with Orthanc's REST API (Orthanc is an open-source medical images server) with utility functions. So I think anyone with Python + REST API knowledge could review it.

pyorthanc is already used by many, so (I hope :) ) the library has proven its relevance and deserves publication.

[Kevin-Mattheus-Moerman]

@gacou54 thanks for your comments. Although I'm convinced this represents a significant piece of work, that is no doubt very useful, I am a little worried if this work is in scope for JOSS, e.g. our guidelines say “Minor utility” packages, including “thin” API clients, and single-function packages are not acceptable. Although this submission seems substantial enough in terms of number of lines of code (so not very thin), can it arguably be defined as a wrapper/single-function utility package?

JOSS publishes "research software", i.e. software that is used for scientific research. A good check for JOSS scope is to image if one would feel the need to cite this work when used in such scientific research. There is typically no need to cite a utility tool but one would cite something that would influence the scientific findings directly. So can you help sketch a scenario where people would use your software in scientific research and where people would feel the need to cite your package because it influences the scientific findings/conclusions? Has this work been used and cited in scientific research papers already?

Any clarification on the above would be very helpful to understand if this represents research software. Thanks.

[gacou54]

I understand the issue you raised. PyOrthanc is used in several research projects and is an important element in medical imaging data management projects.

PyOrthanc is typically used upstream in anonymization and data transfer flows, and downstream for complex data management and queries. On our side, we are working on a medical imaging platform dedicated to AI and other algorithms in research (https://paradim.science/), and we orchestrate the data with PyOrthanc.

One of the reasons why we would like to publish in JOSS is that we often see that PyOrthanc is used at scientific conferences for medical imaging projects and we would like people to cite our work.

We will rely on your judgment on its publication value. While it is true that PyOrthanc is a fancy wrapper with several utility functions, its main purpose and the reason we created this tool is to support medical image research. In our opinion, PyOrthanc is a real asset for many medical imaging data management endeavors.

[Kevin-Mattheus-Moerman]

@gacou54 thanks for answering my question. I think I am happy to proceed.

[Kevin-Mattheus-Moerman]

@srmnitc can you please help edit this submission if you feel it fits your background? Thanks!

[Kevin-Mattheus-Moerman]

@srmnitc and is this one you can help with too? Thanks!

[srmnitc]

@Kevin-Mattheus-Moerman this is unfortunately not in my wheelhouse. Ideally, I would like to pass this one.

[Kevin-Mattheus-Moerman]

@gacou54 apologies for the delays encountered so far. I am still looking for a handling editor however since all in this domain are busy handling other submission we will need to remain patient a bit longer.

[Kevin-Mattheus-Moerman]

@editorialbot invite @diehlpk as editor

[editorialbot]

Invitation to edit this submission sent!

[gacou54]

Hi @Kevin-Mattheus-Moerman, I understand, thanks for the follow-up!

[Kevin-Mattheus-Moerman]

@editorialbot invite @sappelhoff as editor

[editorialbot]

Invitation to edit this submission sent!

[Kevin-Mattheus-Moerman]

@sappelhoff I was wondering if you could help edit this submission? (I thought I could invite you, since one of the papers you are handling is about to be wrapped up).

[sappelhoff]

Hi @Kevin-Mattheus-Moerman, yes I am happy to take this on.

[sappelhoff]

@editorialbot assign @sappelhoff as editor

[editorialbot]

Assigned! @sappelhoff is now the editor

[sappelhoff]

@gacou54 do you have suggestions for potential reviewers? Please just have potential conflicts of interest in mind.

If not, I will consult the automatic suggestions from above, or will have a look at the JOSS reviewer database.

[gacou54]

Hi @sappelhoff ,

I don't have anyone in particular in mind. I think anyone who has handled DICOM (medical imaging) files as part of their job might have a good idea of ​​what's going on.

The suggestions here seem good to me :)

[sappelhoff]

👋 @jrkerns @matteocao @sinhaharsh @drcandacemakedamoore @devnums

would any of you be willing to review this submission for JOSS? We carry out our checklist-driven reviews here in GitHub issues and follow these guidelines: https://joss.readthedocs.io/en/latest/review_criteria.html

[sinhaharsh]

Thank you for the invitation. I would be happy to serve as a reviewer for this submission. On Nov 26, 2024, at 1:32 PM, Stefan Appelhoff ***@***.***> wrote: 👋 @jrkerns<https://github.com/jrkerns> @matteocao<https://github.com/matteocao> @sinhaharsh<https://github.com/sinhaharsh> @drcandacemakedamoore<https://github.com/drcandacemakedamoore> @devnums<https://github.com/devnums> would any of you be willing to review this submission for JOSS? We carry out our checklist-driven reviews here in GitHub issues and follow these guidelines: https://joss.readthedocs.io/en/latest/review_criteria.html — Reply to this email directly, view it on GitHub<#7236 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/ABPYHELHYFLEVO7HFX6J3IT2CS5DDAVCNFSM6AAAAABOJHT4S6VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDKMBRGY2TSNBYG4>. You are receiving this because you were mentioned.Message ID: ***@***.***>

[jrkerns]

Having personally used the library I'd be happy to review.

[drcandacemakedamoore]

Due to previous time commitments I would be unable to review until 2025. I am hoping you get enough reviewers before then.

[sappelhoff]

@editorialbot add @sinhaharsh as reviewer

[editorialbot]

@sinhaharsh added to the reviewers list!

[sappelhoff]

@editorialbot add @jrkerns as reviewer

[editorialbot]

@jrkerns added to the reviewers list!

[sappelhoff]

Thanks @sinhaharsh @jrkerns, and @drcandacemakedamoore for your swift replies!

And thanks @sinhaharsh and @jrkerns for volunteering!

@drcandacemakedamoore -- no worries. I hope we will find a third reviewer in the next week or so, but if not, then we can also proceed with @sinhaharsh and @jrkerns.

[sappelhoff]

I have reached out to @devnums @matteocao via email to see whether they would be interested to review this submission.

[matteocao]

Dear Stefan, Thank you for reaching out. Unfortunately this is a very intense working period and I would not have the time to review the submission. Apologies. Best regards, Matteo Il Lun 2 Dic 2024, 22:08 Stefan Appelhoff ***@***.***> ha scritto:

…

I have reached out to @devnums <https://github.com/devnums> @matteocao <https://github.com/matteocao> via email to see whether they would be interested to review this submission. — Reply to this email directly, view it on GitHub <#7236 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AJJEPHY2TMVD4E5VCVEEOKT2DTD6BAVCNFSM6AAAAABOJHT4S6VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDKMJSHA2DKOJYG4> . You are receiving this because you were mentioned.Message ID: ***@***.***>

[devnums]

Hi @sappelhoff I have received your email, I would be happy to review this paper. Thank you for inviting me.

[sappelhoff]

@editorialbot add @devnums as reviewer

[editorialbot]

@devnums added to the reviewers list!

[sappelhoff]

Thanks for the reply @devnums!

We have 3 reviewers now. I am going to start the proper review.

[sappelhoff]

@editorialbot start review

[editorialbot]

OK, I've started the review over in #7562.