[REVIEW]: LiGuard: A GUI-powered Python Framework for Processing Point-Cloud Data

[editorialbot]

Submitting author: @m-shahbaz-kharal (Muhammad Shahbaz )
Repository: https://github.com/m-shahbaz-kharal/LiGuard-JOSS
Branch with paper.md (empty if default branch): main
Version: v1.0.0
Editor: @hugoledoux
Reviewers: @chenzhaiyu, @tgoelles
Archive: Pending

Status

Status badge code:

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Markdown: [![status](https://joss.theoj.org/papers/f57d8cdafbb47f64891ce84685b4cd05/status.svg)](https://joss.theoj.org/papers/f57d8cdafbb47f64891ce84685b4cd05)

Reviewers and authors:

Please avoid lengthy details of difficulties in the review thread. Instead, please create a new issue in the target repository and link to those issues (especially acceptance-blockers) by leaving comments in the review thread below. (For completists: if the target issue tracker is also on GitHub, linking the review thread in the issue or vice versa will create corresponding breadcrumb trails in the link target.)

Reviewer instructions & questions

@chenzhaiyu & @tgoelles, your review will be checklist based. Each of you will have a separate checklist that you should update when carrying out your review.
First of all you need to run this command in a separate comment to create the checklist:

@editorialbot generate my checklist

The reviewer guidelines are available here: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html. Any questions/concerns please let @hugoledoux know.

✨ Please start on your review when you are able, and be sure to complete your review in the next six weeks, at the very latest ✨

Checklists

📝 Checklist for @chenzhaiyu

📝 Checklist for @tgoelles

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[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.90  T=0.04 s (1576.2 files/s, 132499.0 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          44            766           1278           1992
reStructuredText                11            162            139            514
Markdown                         5             61              0            365
YAML                             4             25              5            167
TeX                              1             10              0             93
DOS Batch                        1              8              1             26
make                             1              4              7              9
-------------------------------------------------------------------------------
SUM:                            67           1036           1430           3166
-------------------------------------------------------------------------------

Commit count by author:

     1	m-shahbaz-kharal

[editorialbot]

Paper file info:

📄 Wordcount for paper.md is 806

✅ 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]

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

OK DOIs

- 10.21105/joss.03471 is OK
- 10.21105/joss.00990 is OK
- 10.1109/MCSE.2007.55 is OK

MISSING DOIs

- 10.1109/icra.2011.5980567 may be a valid DOI for title: 3D is here: Point Cloud Library (PCL)
- No DOI given, and none found for title: Open3D: A Modern Library for 3D Data Processing
- No DOI given, and none found for title: Laspy
- No DOI given, and none found for title: pyntcloud
- No DOI given, and none found for title: The OpenCV Library
- 10.1177/0278364913491297 may be a valid DOI for title: Vision meets robotics: The kitti dataset
- No DOI given, and none found for title: OpenPCDet: An Open-source Toolbox for 3D Object De...
- No DOI given, and none found for title: MMDetection3D: OpenMMLab next-generation platform ...

INVALID DOIs

- None

[chenzhaiyu]

Review checklist for @chenzhaiyu

Conflict of interest

• I confirm that I have read the JOSS conflict of interest (COI) policy and that: I have no COIs with reviewing this work or that any perceived COIs have been waived by JOSS for the purpose of this review.

Code of Conduct

• I confirm that I read and will adhere to the JOSS code of conduct.

General checks

• Repository: Is the source code for this software available at the https://github.com/m-shahbaz-kharal/LiGuard-JOSS?
• License: Does the repository contain a plain-text LICENSE or COPYING file with the contents of an OSI approved software license?
• Contribution and authorship: Has the submitting author (@m-shahbaz-kharal) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
• Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines
• Data sharing: If the paper contains original data, data are accessible to the reviewers. If the paper contains no original data, please check this item.
• Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
• Human and animal research: If the paper contains original data research on humans subjects or animals, does it comply with JOSS's human participants research policy and/or animal research policy? If the paper contains no such data, please check this item.

Functionality

• Installation: Does installation proceed as outlined in the documentation?
• Functionality: Have the functional claims of the software been confirmed?
• Performance: If there are any performance claims of the software, have they been confirmed? (If there are no claims, please check off this item.)

Documentation

• A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
• Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
• Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
• Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
• Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?
• Community guidelines: Are there clear guidelines for third parties wishing to 1) Contribute to the software 2) Report issues or problems with the software 3) Seek support

Software paper

• Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
• A statement of need: Does the paper have a section titled 'Statement of need' that clearly states what problems the software is designed to solve, who the target audience is, and its relation to other work?
• State of the field: Do the authors describe how this software compares to other commonly-used packages?
• Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
• References: Is the list of references complete, and is everything cited appropriately that should be cited (e.g., papers, datasets, software)? Do references in the text use the proper citation syntax?

[tgoelles]

Review checklist for @tgoelles

Conflict of interest

• I confirm that I have read the JOSS conflict of interest (COI) policy and that: I have no COIs with reviewing this work or that any perceived COIs have been waived by JOSS for the purpose of this review.

Code of Conduct

• I confirm that I read and will adhere to the JOSS code of conduct.

General checks

• Repository: Is the source code for this software available at the https://github.com/m-shahbaz-kharal/LiGuard-JOSS?
• License: Does the repository contain a plain-text LICENSE or COPYING file with the contents of an OSI approved software license?
• Contribution and authorship: Has the submitting author (@m-shahbaz-kharal) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
• Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines
• Data sharing: If the paper contains original data, data are accessible to the reviewers. If the paper contains no original data, please check this item.
• Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
• Human and animal research: If the paper contains original data research on humans subjects or animals, does it comply with JOSS's human participants research policy and/or animal research policy? If the paper contains no such data, please check this item.

Functionality

• Installation: Does installation proceed as outlined in the documentation?
• Functionality: Have the functional claims of the software been confirmed?
• Performance: If there are any performance claims of the software, have they been confirmed? (If there are no claims, please check off this item.)

Documentation

• A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
• Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
• Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
• Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
• Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?
• Community guidelines: Are there clear guidelines for third parties wishing to 1) Contribute to the software 2) Report issues or problems with the software 3) Seek support

Software paper

• Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
• A statement of need: Does the paper have a section titled 'Statement of need' that clearly states what problems the software is designed to solve, who the target audience is, and its relation to other work?
• State of the field: Do the authors describe how this software compares to other commonly-used packages?
• Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
• References: Is the list of references complete, and is everything cited appropriately that should be cited (e.g., papers, datasets, software)? Do references in the text use the proper citation syntax?

[hugoledoux]

@chenzhaiyu @tgoelles just a small reminder not to forget this review

[tgoelles]

Mine can be found here: m-shahbaz-kharal/LiGuard-JOSS#1
I can not checkoff all the points. See my reasoning in my review there.

[chenzhaiyu]

I will complete my review by next week.

[hugoledoux]

I missed this @tgoelles sorry. I think it's better if the review is here but this is fine.

I agree with most of @tgoelles points, and while the 2nd reviewer will do his review next week, I am interested in hearing about the main point raised:

1. what is the novelty and also a comparison to PDAL and ROS should be provided
2. I now notice that the commits are indeed less than optimal. If it was in a private repo, making it public is one click. I am slightly worried that the repo has "-JOSS" in its name. Is it because the "real" repo will stay private?

Actually, the authors recommend "reject" but this is not really how JOSS proceeds. We aim at bringing the submission to a certain standard that we deem accepted, in this case when all the checklists can be checked.

[chenzhaiyu]

The authors present a Python GUI for processing LiDAR data, optionally accompanying imagery. They claim the contribution user-friendly with five sub-modules for IO, configuration, inter-process data sharing, data processing, and visualization.

General Concerns

1. I am not sure if the magnitude of scholarly contribution is above the bar. This concerns both the commit history and lines of code. In my opinion the code appears to be largely boilerplate on top of existing libraries.
2. Although the paper does reference Open3D and OpenCV (line 44). It would be more appropriate to state clearly the diference from existing libs (not limited to the two), highlighting the authors' unique contributions rather than making broad claims.

Paper

3. The authors emphasize multiple times GUI to contrast their contribution from other software. I support @tgoelles's point that it is important to discuss and conceptually compare other GUI-based software to provide context.
4. I find the claim of extensible (line 28) not sufficiently substantiated as much as the other ones.
5. Currently, the paper includes only one conceptual figure. Given that the GUI is the primary focus of the software presentation, incorporating visual elements would probably help.

Documentation

6. The README sections could be made more user-friendly by including self-contained examples. As it stands, one must read through the lengthy documentation to get started with the software. A concise example at the beginning would help. The current example usage is too conceptual and less ideal.
7. Documentation for modules and functions is incomplete and almost broken in formatting. E.g., https://m-shahbaz-kharal.github.io/LiGuard-JOSS/algo.html.
8. While automated tests seem to be present, their usage is undocumented.
9. If example data can be provided, users would be able to quickly test the software. Without such data I could only follow the README until opening-the-pipeline-config-file, and thus could not confirm the functional claims beyond that point.

[m-shahbaz-kharal]

Hi, I believe all the reviews are submitted as the assigned reviewers (@chenzhaiyu and @tgoelles) have submitted their responses; please inform me if that is not correct. In the following the response to the reviews is submitted.

Dear Reviewers,

Thanks for a thorough review. The submitted comments/recommendations/decisions helped us a lot in understanding the process of publication in JOSS more clearly, and more importantly, it has helped us see the potential issues in both the paper and the code/repository. The issues discussed in the reviews primarily included incomprehensive statement-of-need, missing references and comparisons to some similar libraries, broader (than evident) claims, improper tests and documentation, and a lack of enough commit history. Based on the comment from @hugoledoux ("We aim at bringing the submission to a certain standard that we deem accepted, in this case when all the checklists can be checked."), it seems like the submission can be improved and eventually published if it checks all the requirements; please inform us if that is not the case for this submission.

While it may take us sometime before all the raised points/concerns are covered/fixed, some quick comments are provided in the following to answer some of those questions.

• Commit History: This repository is a trimmed-down version of our original project LiGuard-GUI that is kept private as it contains some under-research algorithms that are (implemented using LiGuard but) are not published yet. Since it is not confirmed, as of the moment, if and when those algorithms are going to be made available, we created this repo and added only the files required to run the software. However, since the commit history is required for the JOSS review process, the reviewers (@hugoledoux, @chenzhaiyu, @tgoelles) are being added as collaborators to that repo so the commit history can be reviewed.
• Tests: The test-cases written for this repo are only meant to test if the signatures and return types of custom functions are being followed correctly and not necessarily the definition/logic of those functions. Therefore, the software may still crash, even if the tests doesn't show an error; in that case, the logs may be checked to figure out the errors.
• Comparison to ROS: The comparison to ROS is deliberately not added for this project as it seems to us that it is not an apple-to-apple comparison. ROS is a meta-operating system whereas LiGuard is focused only on processing point-cloud (and accompanying image) data. Therefore, a reference to it will be added for completeness purpose but since ROS and LiGuard serve a different purpose, a detailed comparison seems unnecessary.
• Supported File-Types: Please note that, for lidar, supported file-types include .bin, npy, .ply, and .pcd (most of these are supported by Open3D so those are supported by extension) and for images imread function of OpenCV is used so all supported image file-types supported by OpenCV are also supported in our software (by extension).
• Segmentation Fault: The software is tested only Windows 11 using Python 3.10.0 and although our docs say that it should run as far as the dependencies are installed but as @tgoelles pointed out that's not the case. So, for now, the only environment it should be tested on is Windows 10 with Python 3.10.0 (we'll reflect this statement in the docs). Also, we'll update docs as more operating systems are tested.

Summary of Future Updates

1. Updates in Paper: Based on the reviews, a major re-writing of the paper is needed. So, although the title and basics of the submission may remain similar, an improved version of the paper.md will be submitted that'll include a comprehensive statement-of-need, missed references, revised claims, novelty statement(s), and comparison to related SOTA packages.

2. Updates in Repository: Following are the major planned updates to the repo:

   • Quick-Start Guide: A few example datasets and yaml configuration-files will be added to allow quick trying of various features of LiGuard.
   • Documentation Breakdown and Improvements: The documentation will be broken down to multiple sub-docs to allow easy navigation.
   • Installation Package: The software will be bundled as python package to allow easier installation.

Note: The updates will be posted and informed in this thread in the same order as given in Summary of Future Updates above. Please let us know if anything is still missing/unaccounted from our side regarding the review process.

Thanks.

[hugoledoux]

Sorry for taking so long to getting back to this. A few answers and comments:

• yes that's the idea that you get the chance to improve your submission so that eventually when the reviewers and myself think it fulfils the JOSS criteria, it can be accepted.
• my invite for your private repo expired, sorry. Could you reinvite me?
• however, why not keeping the not-published algos in a develop branch and have the main part in the main branch? I would find that simpler to be honest, also for you.
• Comparison to ROS: perhaps a full comparison is not necessary, but since a knowledgeable reviewer thought that there is a link you could explain why it is different, and how? And what are the similarities?
• it seems both reviewers couldn't run your software, this is worrying for JOSS. You need to dive into this and try your software with other OSes than Windows
• Comparison to PDAL: will you add this?
• what is missing is simple demos to run, with data (as @chenzhaiyu points out)

So I suggest you improve the software, the docs, and the paper. And then you let us know here what changes you've made, and then we can continue the review.

How long do you reckon it will take you?