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

[editorialbot]

Submitting author: !--author-handle-->@gacou54<!--end-author-handle-- (Gabriel Couture) Repository: https://github.com/gacou54/pyorthanc Branch with paper.md (empty if default branch): joss Version: v1.18.0 Editor: Pending Reviewers: Pending Managing EiC: Kevin M. Moerman

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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]

: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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[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!