[PRE REVIEW]: Pointcloud: Implementation of point clouds as graphs in the 3-d plant modeling platform GroIMP

[editorialbot]

Submitting author: @pomme-abricot (Gaetan Heidsieck)
Repository: https://gitlab.com/grogra/groimp-plugins/Pointcloud
Branch with paper.md (empty if default branch):
Version: v1.8
Editor: @willgearty
Reviewers: @UniCornXZC, @Abinashbunty
Managing EiC: Kristen Thyng

Status

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Markdown: [![status](https://joss.theoj.org/papers/45b3300852254ed2873fd58cd3c5869f/status.svg)](https://joss.theoj.org/papers/45b3300852254ed2873fd58cd3c5869f)

Author instructions

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

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[editorialbot]

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

✅ OK DOIs

- 10.3390/rs5020491 is OK
- 10.4149/cai_2017_6_1492 is OK

🟡 SKIP DOIs

- No DOI given, and none found for title: Design and implementation of a graph grammar based...
- No DOI given, and none found for title: Testing the capacity of an oil palm FSPM to simula...
- No DOI given, and none found for title: Reconstructing plant architecture from 3D laser sc...

❌ MISSING DOIs

- 10.1270/jsbbs.21074 may be a valid DOI for title: 3D modeling and reconstruction of plants and trees...

❌ INVALID DOIs

- https://doi.org/10.1016/j.compag.2021.106240 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.1016/j.jag.2023.103557 is INVALID because of 'https://doi.org/' prefix

[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.98  T=0.07 s (888.3 files/s, 156821.9 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Java                            43           1008           2080           6580
XML                              8             30             26            594
Markdown                         2             61              0            126
Maven                            1             12              0            106
JSON                             1              1              0             96
TeX                              1             10              0             74
Properties                       1             19              0             62
Lua                              1              5              0             29
INI                              3              0              0             16
YAML                             1              0              0             11
-------------------------------------------------------------------------------
SUM:                            62           1146           2106           7694
-------------------------------------------------------------------------------

Commit count by author:

   107	Gaetan Heidsieck
    12	Tim Oberländer
     9	Hundertmark Nico
     7	Tim
     1	gaetan heidsieck

[editorialbot]

Paper file info:

📄 Wordcount for paper.md is 1112

✅ The paper includes a Statement of need section

[editorialbot]

License info:

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

[editorialbot]

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

[editorialbot]

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[kthyng]

Hi @pomme-abricot and thanks for your submission! I am looking for some specific items to make sure your submission fits our requirements at a high level (not at the more detailed review level) before moving on to finding an editor or putting this on our waitlist if no relevant editors are available. I'll comment over time as I have a chance to go through them:

• OSI-approved license
• Installation instructions
• Documentation exists at all
• Tests of some sort
• Check paper (make sure compiles, read through, check for length 250-1000 words)
• Substantial scholarly effort
• Clear research application

In the meantime, please take a look at the comments above ⬆️ from the editorialbot to address any DOI, license, or paper issues if you're able (there may not be any), or suggest reviewers. For reviewers, please suggest 5 reviewers from the database listed above or your own (non-conflicted) extended network. Their github handles are most useful to receive but please don't use "@" to reference them since it will prematurely ping them.

[kthyng]

@pomme-abricot I recommend changing the title of this to something more descriptive at a high level and with less jargon. Until looking at your paper (and even through the readme) multiple of us couldn't tell even what track this submission should properly be in.

[pomme-abricot]

Hello @kthyng, thank you for your suggestion. I changed the title to : "Implementation of point clouds as graphs in the 3-d plant modeling platform GroIMP".

I also fixed the DOI issues.

[kthyng]

@pomme-abricot

• is there a non-manual way to install?
• Are there docs beyond the readme?
• are there function doc strings?
• Do you have tests or some way to verify software output?
• Do you have examples?

[pomme-abricot]

Hello @kthyng ,

• The software GroIMP can be installed with installers for Windows, MAC, and debian (https://download.grogra.de/). It still requires Java >= 17 to run.
• There is a dokuwiki for GroIMP, and some specific pages for both the plugin and the examples presented (https://wiki.grogra.de/doku.php?id=groimp-platform:pointcloud)
• Both GroIMP and the presented plugin have a Javadoc available at https://javadoc.grogra.de/pointcloud/module-summary.html
• We test the code by running the examples
• There are two examples (presented in the paper) embedded in GroIMP by default. They are available from the example explorer of GroIMP. They are also presented in the wiki (https://wiki.grogra.de/doku.php?id=tutorials:using-mesh-clouds-as-organ)

[kthyng]

@pomme-abricot I should add that you should also include the name of your package in the title. Typical syntax would be "pointcloud: [your title]".

The software GroIMP can be installed with installers for Windows, MAC, and debian (https://download.grogra.de/). It still requires Java >= 17 to run.

I can't see the pages either because they are down or more likely they are blocked on this work machine. To clarify, you seem to be saying that the larger software package that you library is based on has installers (great). What is the current installation setup for your actual library?

I'll trust your docs are there since I can't look at those pages.

[pomme-abricot]

@kthyng , the download pages are sometimes blocked by anti-malwares such as windows defender... Additionally there was a typo in one of the wiki links which I corrected.

The plugin is indeed part of a bigger software. It is included by default in the latest release of that software. Thus, it should not require any additional installation.
There is however two possible ways to install the plugin in the software: using the plugin manager which will download and install it automatically, or manually compiling it from the sources.
The instructions are described in the readme on the gitlab page.

[kthyng]

@pomme-abricot Ok, thanks. Do you want to update your title?

[pomme-abricot]

@kthyng I just did. Thank you for the suggestion.

[kthyng]

@editorialbot generate pdf

[editorialbot]

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

[kthyng]

We have a backlog of submissions so I will add this to our waitlist. Thanks for your patience.

[kthyng]

@hugoledoux Can you edit this submission?

[kthyng]

@editorialbot invite @hugoledoux as editor

[editorialbot]

Invitation to edit this submission sent!

[hugoledoux]

I'll have to refuse for the moment: I bought a new house and everything is exploding at the moment with the construction so I cannot really take another one... sorry, in 2-3w hopefully it's better!

[kthyng]

Ok got it! Good luck with your move!

[kthyng]

@willgearty Can you edit this submission?

[kthyng]

@editorialbot invite @willgearty as editor

[editorialbot]

Invitation to edit this submission sent!

[willgearty]

Sure!

[willgearty]

@editorialbot assign @willgearty as editor

[editorialbot]

Assigned! @willgearty is now the editor

[willgearty]

@pomme-abricot could you please suggest 5 reviewers from our reviewer database or your own (non-conflicted) extended network? Their github handles are most useful to receive but please don't use "@" to reference them since it will prematurely ping them.

[pomme-abricot]

Hello, the fields of application for the presented library and the software it is part of, include: complex graph rewriting, plant analyses and simulation, functional modeling, light simulation.
Perhaps the following people would be interested (in no particular order):

• Rémi VEZY (VEZY)
• Vissarion Fisikopoulos (vissarion)
• Abhishek Tiwari (abhishektiwari)
• Timothée Poisot (tpoisot)
• Dr. Brad Hollister (behollister )

[willgearty]

👋 @behollister & @VEZY, 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

[willgearty]

👋 @behollister @VEZY @sebastian-raubach @UniCornXZC, 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.

[willgearty]

@pomme-abricot sorry for the delay. I've sent emails to some of the above potential reviewers, hopefully they'll respond!

[VEZY]

Hi @willgearty, I apologize for the delay. I've been very busy and will be until May 5th. I hope you find other reviewers by then, but if not, I'll take care of it after the 5th (just remind me please).

[willgearty]

@VEZY thanks for the response (and apologies for my own delay). @behollister has also offered to review around the end of April/start of May. I'll continue to look for other reviewers who can conduct their review sooner, but if I can't find anyone, I'd appreciate you both reviewing this submission once you're available.

[willgearty]

@editorialbot add @UniCornXZC as reviewer

[editorialbot]

@UniCornXZC added to the reviewers list!

[willgearty]

👋 @martinmodrak @Abinashbunty, would either 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

[Abinashbunty]

@willgearty Yeah sure. I am available for review. Thank you!

[willgearty]

@editorialbot add @Abinashbunty as reviewer

Great, thanks @Abinashbunty!

[editorialbot]

@Abinashbunty added to the reviewers list!

[willgearty]

@editorialbot start review

[editorialbot]

OK, I've started the review over in #8062.

[martinmodrak]

@willgearty This is a bit outside of my expertise and I already have another JOSS review pending, so unfortunately, I won't be able to review this.

[willgearty]

No worries, thanks for quick response @martinmodrak!