[REVIEW]: 3dfier: automatic reconstruction of 3D city models

[whedon]

Submitting author: @hugoledoux (Hugo Ledoux)
Repository: https://github.com/tudelft3d/3dfier
Version: v1.3.1
Editor: @arfon
Reviewer: @GANys, @chenkianwee
Archive: 10.5281/zenodo.4461324

⚠️ JOSS reduced service mode ⚠️

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Status

Status badge code:

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Markdown: [![status](https://joss.theoj.org/papers/53cc45eaa9fbdc70f02e042bd433da87/status.svg)](https://joss.theoj.org/papers/53cc45eaa9fbdc70f02e042bd433da87)

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

@GANys & @chenkianwee, please carry out your review in this issue by updating the checklist below. If you cannot edit the checklist please:

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Review checklist for @GANys

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 repository url?
• License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
• Contribution and authorship: Has the submitting author (@hugoledoux) 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

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: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
• 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?

Review checklist for @chenkianwee

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 repository url?
• License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
• Contribution and authorship: Has the submitting author (@hugoledoux) 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

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: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
• 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?

[whedon]

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @GANys, @chenkianwee it looks like you're currently assigned to review this paper 🎉.

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[whedon]

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

OK DOIs

- 10.1016/j.buildenv.2014.04.013 is OK
- 10.1080/13658810701739039 is OK
- 10.4236/jep.2013.47081  is OK
- j.compenvurbsys.2011.02.001 is OK
- 10.14358/PERS.79.2.147 is OK
- 10.1186/s40965-019-0064-0 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[whedon]

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

[arfon]

@GANys, @chenkianwee - This is the review thread for the paper. All of our communications will happen here from now on.

Please read the "Reviewer instructions & questions" in the first comment above.

Both reviewers have checklists at the top of this thread (in that first comment) with the JOSS requirements. As you go over the submission, please check any items that you feel have been satisfied. There are also links to the JOSS reviewer guidelines.

The JOSS review is different from most other journals. Our goal is to work with the authors to help them meet our criteria instead of merely passing judgment on the submission. As such, the reviewers are encouraged to submit issues and pull requests on the software repository. When doing so, please mention #2866 so that a link is created to this thread (and I can keep an eye on what is happening). Please also feel free to comment and ask questions on this thread. In my experience, it is better to post comments/questions/suggestions as you come across them instead of waiting until you've reviewed the entire package.

We aim for the review process to be completed within about 4-6 weeks but please make a start well ahead of this as JOSS reviews are by their nature iterative and any early feedback you may be able to provide to the author will be very helpful in meeting this schedule.

[hugoledoux]

@arfon the Fig1 in my paper is very small, which is weird because the original .png is rather large (1500px X 346px). I couldn't find a way to make it use the width of the page. Possible?

[arfon]

@hugoledoux - I think you can force a specific size, e.g. ![](file.jpg){ width=50% }. Can you try experimenting with syntax like that?

[GANys]

@arfon Just a question about the following point :

Performance: If there are any performance claims of the software, have they been confirmed? (If there are no claims, please check off this item.)

Authors claim that "A simple model can be created even using a laptop with less RAM and slower CPU.". My tests confirm the statement but does it correspond to the performance check box requirements? Or should it be a normative benchmark?

[whedon]

👋 @chenkianwee, please update us on how your review is going.

[whedon]

👋 @GANys, please update us on how your review is going.

[GANys]

I have finished testing 3Dfier and reading the software paper. I hava some comments. Here is my point-by-point list of comments in regard of the review checklist :

Community Guidelines: besides the common GitHub community standards and tools, I don't see any framework or guidelines for people to contribute.
State of the field: 3Dfier is kind of unique. I don't see any package or solution that provide such an output. Some FME Workbench could for instance perform something comparable but this is completely out of the Open Source community.

Besides the performance related question, I don't have any remaining comment on the checklist.

But, about the paper, I have quick remarks:

• A point is lacking at the end of the sentence [...] different software. at the end of the Summary.
• The resulting surface aims at being error-free. This sentence does not do justice to the actual outputs of the programme. The main advantage of 3Dfier is that output objects are discrete. "Resulting surface" might means that the output is a common mesh. The result goes far away from it, in a good manner I mean.
• This point is somehow related to the second, but it does not seem obvious that 2D input information should not be contiguous. Hence, the result will not be contiguous in this case but 3Dfier still propose a solution.
  It is important to make this clear, all the more so because that the explanation of the "stitch" processing looks to work vertically form Figure 2. Moreover, Figure 2 does not leave a choice on the continuity of the 2D dataset.

Finally, 3Dfier is a state of the art software that improves the creation and thus the usability of consistent 3D City Models. It is used in research since several years and continues to improve.

@hugoledoux Here is an up.

[arfon]

Authors claim that "A simple model can be created even using a laptop with less RAM and slower CPU.". My tests confirm the statement but does it correspond to the performance check box requirements? Or should it be a normative benchmark?

Apologies for missing this earlier @GANys. I think you can check this off based on your test here.

[arfon]

👋 @chenkianwee - just checking in here to see how you're getting along here?

[chenkianwee]

Sorry for the delay, been busy, will work on the review today

[chenkianwee]

I have issue installing the binary version of 3dfier on my windows machine. This is the error I am getting. Am I suppose to install something before running the windows.zip file?

[chenkianwee]

I got it fix adter downloading necessary Visual studio packages

[chenkianwee]

I have followed the example here (http://tudelft3d.github.io/3dfier/first_run.html). I successfully generated the 3D geometry. However, the mesh that was generated are overlapping as shown in the image below. The terrain and side of the buildings have overlapping surfaces, which is not as described in the paper.

[chenkianwee]

3Dfier is a useful piece of software, especially in the built environment field, where the creation of 3D data is essential for running certain analyses and simulations (e.g. solar, airflow simulation). I see it as a much-needed software that can extend existing 2D GIS tools to generate 3D data for the built environment field.

Community Guidelines: I do not see any guideline or framework for contributing to the project. However, I feel the software is well-managed and there is sufficient documentation for interested parties to extend the software. Considering the software is a standalone cmd tool. It could potentially be a useful module where it could be easily included in other projects for 3Dfying 2D GIS data. So rather than be extended, I think this software is useful for other projects that require 3D generation functionality.

State of the field: There is no mention of the state of the field, there are existing commercial tools that offer similar functionality such as FME and ArcGIS software. They are definitely not in the realm of open-source, but I think it will be useful to mention tools of similar functionality regardless of whether they are proprietary or open-source.

There are still some minor issues with the software, e.g. with the installations and the overlapping surfaces shown in my previous comments. I hope the authors are able to fix those. Once addressed, I recommend the publication of the paper.

[hugoledoux]

Thanks for comments @GANys, sorry for delay in responding.

Community Guidelines: besides the common GitHub community standards and tools, I don't see any framework or guidelines for people to contribute.

You are right, I forgot to add this! tudelft3d/3dfier@0af1ef4

State of the field: 3Dfier is kind of unique. I don't see any package or solution that provide such an output. Some FME Workbench could for instance perform something comparable but this is completely out of the Open Source community.

If you see comments below from @chenkianwee he says FME and others could do the same. I somewhat disagree but it's a good point to mention. In short, you can extruse buildings and other other features/objects, but the stitching part that aims obtaining topologically clean data is not possible.

I'll add 1-2 sentence in the paper
update: done tudelft3d/3dfier@e351e5a

[hugoledoux]

I got it fix adter downloading necessary Visual studio packages

Should this be added in the installation tutorial though? Maybe we had this all along and never noticed?

[hugoledoux]

I have followed the example here (http://tudelft3d.github.io/3dfier/first_run.html). I successfully generated the 3D geometry. However, the mesh that was generated are overlapping as shown in the image below. The terrain and side of the buildings have overlapping surfaces, which is not as described in the paper.

Is this in the dataset given in the folder example_data/*? If yes, where is it? And more importantly, it's possible that there's a gap there between the terrain and the building, I would be very surprise they overlap?

[hugoledoux]

Community Guidelines: I do not see any guideline or framework for contributing to the project. However, I feel the software is well-managed and there is sufficient documentation for interested parties to extend the software. Considering the software is a standalone cmd tool. It could potentially be a useful module where it could be easily included in other projects for 3Dfying 2D GIS data. So rather than be extended, I think this software is useful for other projects that require 3D generation functionality.

I would agree with this, extending it is somewhat cumbersome, but it's possible. Would you say it would be better if I rephrased the paper as such?

State of the field: There is no mention of the state of the field, there are existing commercial tools that offer similar functionality such as FME and ArcGIS software. They are definitely not in the realm of open-source, but I think it will be useful to mention tools of similar functionality regardless of whether they are proprietary or open-source.

tudelft3d/3dfier@e351e5a

There are still some minor issues with the software, e.g. with the installations and the overlapping surfaces shown in my previous comments. I hope the authors are able to fix those. Once addressed, I recommend the publication of the paper.

Thanks. Overlap == we aim at avoiding those, and I'd like to know the location then I'll check. We don't guarantee clean 3D output, only if you have clean 2D then can you get sensible 3D output. Garbage in? Garbage out...

[whedon]

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

OK DOIs

- 10.1016/j.buildenv.2014.04.013 is OK
- 10.1080/13658810701739039 is OK
- 10.4236/jep.2013.47081  is OK
- j.compenvurbsys.2011.02.001 is OK
- 10.14358/PERS.79.2.147 is OK
- 10.1186/s40965-019-0064-0 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[whedon]

PDF failed to compile for issue #2866 with the following error:

/app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-92346a0773a4/lib/whedon/bibtex_parser.rb:82:in doi_citation': undefined method encode' for nil:NilClass (NoMethodError)
from /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-92346a0773a4/lib/whedon/bibtex_parser.rb:64:in make_citation' from /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-92346a0773a4/lib/whedon/bibtex_parser.rb:50:in block in generate_citations'
from /app/vendor/bundle/ruby/2.6.0/gems/bibtex-ruby-5.1.6/lib/bibtex/bibliography.rb:149:in each' from /app/vendor/bundle/ruby/2.6.0/gems/bibtex-ruby-5.1.6/lib/bibtex/bibliography.rb:149:in each'
from /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-92346a0773a4/lib/whedon/bibtex_parser.rb:43:in generate_citations' from /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-92346a0773a4/lib/whedon/compilers.rb:248:in crossref_from_markdown'
from /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-92346a0773a4/lib/whedon/compilers.rb:21:in generate_crossref' from /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-92346a0773a4/lib/whedon/processor.rb:100:in compile'
from /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-92346a0773a4/bin/whedon:88:in compile' from /app/vendor/bundle/ruby/2.6.0/gems/thor-0.20.3/lib/thor/command.rb:27:in run'
from /app/vendor/bundle/ruby/2.6.0/gems/thor-0.20.3/lib/thor/invocation.rb:126:in invoke_command' from /app/vendor/bundle/ruby/2.6.0/gems/thor-0.20.3/lib/thor.rb:387:in dispatch'
from /app/vendor/bundle/ruby/2.6.0/gems/thor-0.20.3/lib/thor/base.rb:466:in start' from /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-92346a0773a4/bin/whedon:131:in <top (required)>'
from /app/vendor/bundle/ruby/2.6.0/bin/whedon:23:in load' from /app/vendor/bundle/ruby/2.6.0/bin/whedon:23:in

'

[arfon]

@hugoledoux - can you merge this PR? There's an issue with one of your DOIs: tudelft3d/3dfier#124

[hugoledoux]

done.

I should re-issue/update v1.3.1 now, right?

[arfon]

I should re-issue/update v1.3.1 now, right?

No, we don't need an update for something as small as this.

[arfon]

@whedon accept

[whedon]

Attempting dry run of processing paper acceptance...

[whedon]

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

OK DOIs

- 10.1016/j.buildenv.2014.04.013 is OK
- 10.1080/13658810701739039 is OK
- 10.4236/jep.2013.47081  is OK
- 10.1016/j.compenvurbsys.2011.02.001 is OK
- 10.14358/PERS.79.2.147 is OK
- 10.1186/s40965-019-0064-0 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[whedon]

👋 @openjournals/joss-eics, this paper is ready to be accepted and published.

Check final proof 👉 openjournals/joss-papers#2050

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#2050, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true

[arfon]

One more small set of changes @hugoledoux: tudelft3d/3dfier#125

[arfon]

@whedon accept

[whedon]

Attempting dry run of processing paper acceptance...

[whedon]

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

OK DOIs

- 10.1016/j.buildenv.2014.04.013 is OK
- 10.1080/13658810701739039 is OK
- 10.4236/jep.2013.47081  is OK
- 10.1016/j.compenvurbsys.2011.02.001 is OK
- 10.14358/PERS.79.2.147 is OK
- 10.1186/s40965-019-0064-0 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[whedon]

👋 @openjournals/joss-eics, this paper is ready to be accepted and published.

Check final proof 👉 openjournals/joss-papers#2051

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#2051, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true

[arfon]

@whedon accept deposit=true

[whedon]

Doing it live! Attempting automated processing of paper acceptance...

[whedon]

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

[whedon]

🚨🚨🚨 THIS IS NOT A DRILL, YOU HAVE JUST ACCEPTED A PAPER INTO JOSS! 🚨🚨🚨

Here's what you must now do:

0. Check final PDF and Crossref metadata that was deposited 👉 Creating pull request for 10.21105.joss.02866 joss-papers#2052
1. Wait a couple of minutes to verify that the paper DOI resolves https://doi.org/10.21105/joss.02866
2. If everything looks good, then close this review issue.
3. Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

[arfon]

@GANys, @chenkianwee - many thanks for your reviews here. JOSS relies upon the volunteer efforts of folks like yourself and we simply wouldn't be able to do this without you! ✨

@hugoledoux - your paper is now accepted into JOSS ⚡🚀💥

[whedon]

🎉🎉🎉 Congratulations on your paper acceptance! 🎉🎉🎉

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