[REVIEW]: MorphoMetriX: a photogrammetric measurement GUI for morphometric analysis of megafauna #1825

whedon · 2019-10-21T21:07:17Z

Submitting author: @wingtorres (Walter Torres)
Repository: https://github.com/wingtorres/morphometrix
Version: v1.0.2
Editor: @Kevin-Mattheus-Moerman
Reviewer: @isaacvandor, @bw4sz
Archive: 10.5281/zenodo.3606865

Status

Status badge code:

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Markdown: [![status](https://joss.theoj.org/papers/716faddf06d43b06f4c8a5e890fb23d1/status.svg)](https://joss.theoj.org/papers/716faddf06d43b06f4c8a5e890fb23d1)

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

@isaacvandor & @bw4sz, please carry out your review in this issue by updating the checklist below. If you cannot edit the checklist please:

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✨ Please try and complete your review in the next two weeks ✨

Review checklist for @isaacvandor

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.

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General checks

Repository: Is the source code for this software available at the repository url?
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Contribution and authorship: Has the submitting author (@wingtorres) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?

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 @bw4sz

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 (@wingtorres) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?

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?

The text was updated successfully, but these errors were encountered:

whedon · 2019-10-21T21:07:20Z

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @isaacvandor, @bw4sz it looks like you're currently assigned to review this paper 🎉.

⭐ Important ⭐

If you haven't already, you should seriously consider unsubscribing from GitHub notifications for this (https://github.com/openjournals/joss-reviews) repository. As a reviewer, you're probably currently watching this repository which means for GitHub's default behaviour you will receive notifications (emails) for all reviews 😿

To fix this do the following two things:

Set yourself as 'Not watching' https://github.com/openjournals/joss-reviews:

You may also like to change your default settings for this watching repositories in your GitHub profile here: https://github.com/settings/notifications

For a list of things I can do to help you, just type:

@whedon commands

For example, to regenerate the paper pdf after making changes in the paper's md or bib files, type:

@whedon generate pdf

whedon · 2019-10-21T21:07:21Z

Attempting PDF compilation. Reticulating splines etc...

whedon · 2019-10-21T21:07:52Z

👉 Check article proof 📄 👈

isaacvandor · 2019-10-22T00:33:26Z

@Kevin-Mattheus-Moerman I've completed my review and there doesn't seem to be anything impeding acceptance. I did open an issue in the target repo with a feature enhancement I think could help, but that certainly shouldn't stop the rest of the review process.

Updating with link to issue filed in target repo: Issue #1: Allow user to change size of width lines/dots

Kevin-Mattheus-Moerman · 2019-10-22T09:13:55Z

@isaacvandor thanks. Can you mention/link to that issue here so we have a record of it? Thanks a lot for your help!

Kevin-Mattheus-Moerman · 2019-10-22T09:14:44Z

@bw4sz this is where the review takes place. The check boxes at the top guide you through the process. Let me know if you have questions.

bw4sz · 2019-10-22T18:43:24Z

@patrickcgray throw me some sample whale images to play with here?

bw4sz · 2019-10-22T18:45:13Z

grabbing and testing with some data from https://github.com/patrickcgray/cetacean_photogram

bw4sz · 2019-10-22T19:35:22Z

testing with this image looks good.

bw4sz · 2019-10-22T19:41:33Z

added a small idea wingtorres/morphometrix#2

kthyng · 2019-10-22T21:47:14Z

What a cool picture to get in my email from github notifications!

patrickcgray · 2019-10-25T02:07:55Z

Hey Ben, Late in replying but I'm happy to provide more imagery as needed, should be plenty in that DataDryad repo as you likely saw! Cheers, Patrick

…

On Tue, Oct 22, 2019 at 5:47 PM Kristen Thyng ***@***.***> wrote: What a cool picture to get in my email from github notifications! — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#1825?email_source=notifications&email_token=AATBWRNRYBGLVYYC7TNBSALQP5YGNA5CNFSM4JDFFDV2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEB7KHBI#issuecomment-545170309>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AATBWRJO6244OKEWWRMPKZ3QP5YGNANCNFSM4JDFFDVQ> .

-- Patrick Clifton Gray <http://patrickgray.me/> PhD Student Marine Robotics and Remote Sensing Lab <http://sites.nicholas.duke.edu/uas/> Duke University, Nicholas School of the Environment Computer Science '14, University of North Carolina

Kevin-Mattheus-Moerman · 2019-11-01T11:39:34Z

@wingtorres can you work on adding community guidelines?

Here is some more information on this:
https://help.github.com/en/github/site-policy/github-community-guidelines

Also here is a link to one of my projects. There I link to contributing guidelines in a CONTRIBUTING.md file in the README.md, which is an approach I recommend.
https://github.com/gibbonCode/GIBBON

If you imagine your contributors community will grow I also recommend adding a CODE_OF_CONDUCT.mdfile too (e.g. based on this template: https://www.contributor-covenant.org/).

Kevin-Mattheus-Moerman · 2019-11-01T11:40:42Z

@wingtorres can you work on the issues raised by the reviewers? https://github.com/wingtorres/morphometrix/issues

wingtorres · 2019-11-15T18:19:55Z

@Kevin-Mattheus-Moerman Sorry to be out of touch! I've been a bit swamped recently, but I have some time blocked out end of next week to incorporate the reviewers suggestions and add the community guidelines. Thanks!

danielskatz · 2019-12-05T10:00:05Z

👋 @wingtorres - Have you made progress on this?

wingtorres · 2019-12-15T21:41:50Z

@danielskatz Yes finally! I have updated the code to address @bw4sz 's suggestion and in regards to @isaacvandor 's thoughts I have at least pointed to where users can customize their version of the code in lieu of adding a preferences menu to modify the GUI cosmetics (although we may want to do this down the line, I believe the code will be useful to people without it for now). @Kevin-Mattheus-Moerman thank you for your suggestion to include the contribute and code of conduct files - I have added those as well. Thanks y'all! Let me know what else needs to be done.

wingtorres · 2019-12-15T21:50:32Z

@whedon generate pdf

whedon · 2019-12-15T21:50:35Z

Attempting PDF compilation. Reticulating splines etc...

whedon · 2019-12-15T21:51:12Z

👉 Check article proof 📄 👈

Kevin-Mattheus-Moerman · 2019-12-16T10:52:59Z

@isaacvandor, @bw4sz are you happy with the changes implemented? I see all boxes are ticked. Are you happy to recommend acceptance for this work? Thanks!

Kevin-Mattheus-Moerman · 2019-12-16T10:57:56Z

@wingtorres thanks for adding community guidelines. One note on your CONTRIBUTING.md file (https://github.com/wingtorres/morphometrix/blob/master/CONTRIBUTING.md). It appears it was copied from my own project's file I referred to. Please review the variable naming section since I changed that to suit my project (MATLAB syntax for mesh data handling). Perhaps yours should instead refer to some Python coding style (perhaps check what other major Python projects use there).

wingtorres · 2019-12-16T13:39:14Z

You are totally right that's embarrassing :D, sorry I should have paid closer attention. I'm a bit new to Python, but I try to adhere to the PEP-008 standards so I'll post a link to that.

Kevin-Mattheus-Moerman · 2019-12-26T09:09:22Z

@isaacvandor, @bw4sz are you happy with the changes implemented? I see all boxes are ticked. Are you happy to recommend acceptance for this work? Thanks!

@isaacvandor, @bw4sz ☝️ Thanks again for your help!

Kevin-Mattheus-Moerman · 2019-12-26T09:10:20Z

@whedon generate pdf

wingtorres · 2020-01-15T19:26:21Z

@whedon generate pdf

whedon · 2020-01-15T19:26:55Z

👉 Check article proof 📄 👈

wingtorres · 2020-01-15T19:27:06Z

@whedon check references

whedon · 2020-01-15T19:27:31Z

Reference check summary:

OK DOIs

- 10.1007/BF00233083 is OK
- 10.1038/s41559-018-0534-2 is OK
- 10.1371/journal.pone.0017686 is OK
- 10.1139/z85-345 is OK
- 10.1111/1365-2435.12200 is OK
- 10.3354/meps12522 is OK
- 10.1139/z98-195 is OK
- 10.3354/meps09675 is OK
- 10.1146/annurev-marine-010318-095323 is OK
- 10.3389/fmars.2017.00366 is OK
- 10.1139/cjz-2014-0311 is OK
- 10.1002/ajp.1350300207 is OK
- 10.1111/j.1748-7692.2009.00288.x is OK
- 10.1111/mms.12527 is OK
- 10.1038/nmeth.2089 is OK
- 10.1126/science.290.5497.1695b is OK
- 10.1002/ecs2.1468 is OK
- 10.1139/juvs-2015-0020 is OK

MISSING DOIs

- https://doi.org/10.2307/1374074 may be missing for title: Southern Blue and Fin Whales

INVALID DOIs

- 10.1641/0006-3568(2003)053[0210:WAS]2.0.CO;2 is INVALID

wingtorres · 2020-01-15T19:33:31Z

The missing DOI is for a paper that was published in 1929 so it does not have one as far as we can tell. I'm not sure what to do about the invalid DOI though...it should link to the article below. https://academic.oup.com/bioscience/article/53/3/210/251944

arfon · 2020-01-15T20:05:14Z

I'm not sure what to do about the invalid DOI though...it should link to the article below. https://academic.oup.com/bioscience/article/53/3/210/251944

I think you can ignore this. The URL library we're using for Whedon doesn't like https://doi.org/10.1641/0006-3568(2003)053[0210:WAS]2.0.CO;2 (it's a pretty unusual URL) but it looks like it resolves.

whedon · 2020-01-15T20:37:43Z

Reference check summary:

OK DOIs

- 10.1007/BF00233083 is OK
- 10.1038/s41559-018-0534-2 is OK
- 10.1371/journal.pone.0017686 is OK
- 10.1139/z85-345 is OK
- 10.1111/1365-2435.12200 is OK
- 10.3354/meps12522 is OK
- 10.1139/z98-195 is OK
- 10.3354/meps09675 is OK
- 10.1146/annurev-marine-010318-095323 is OK
- 10.3389/fmars.2017.00366 is OK
- 10.1139/cjz-2014-0311 is OK
- 10.1002/ajp.1350300207 is OK
- 10.1111/j.1748-7692.2009.00288.x is OK
- 10.1111/mms.12527 is OK
- 10.1038/nmeth.2089 is OK
- 10.1126/science.290.5497.1695b is OK
- 10.1002/ecs2.1468 is OK
- 10.1139/juvs-2015-0020 is OK

MISSING DOIs

- https://doi.org/10.2307/1374074 may be missing for title: Southern Blue and Fin Whales

INVALID DOIs

- 10.1641/0006-3568(2003)053[0210:WAS]2.0.CO;2 is INVALID

kyleniemeyer · 2020-01-15T21:41:57Z

Hi @wingtorres, looks like the references are fine, but I have just a few typographic issues to resolve:

Can you remove the period at the end of the title?
in a number of places, you are missing commas after "i.e." and "e.g."
in the 4th paragraph, there are some inconsistencies in some citation formatting; you can use these syntax options for in-text citations:

- `@author:2001`  ->  "Author et al. (2001)"
- `[@author:2001]` -> "(Author et al., 2001)"
- `[@author1:2001; @author2:2001]` -> "(Author1 et al., 2001; Author2 et al., 2002)"

Otherwise, it is well written, thanks!

wingtorres · 2020-01-15T22:55:24Z

@whedon generate pdf

whedon · 2020-01-15T22:56:47Z

👉 Check article proof 📄 👈

wingtorres · 2020-01-15T22:58:09Z

@kyleniemeyer thank you for the typographic edits! Just made the changes you suggested and generated a new proof.

kyleniemeyer · 2020-01-16T00:17:52Z

@whedon accept

whedon · 2020-01-16T00:17:55Z

Attempting dry run of processing paper acceptance...

whedon · 2020-01-16T00:18:18Z

Reference check summary:

OK DOIs

- 10.1007/BF00233083 is OK
- 10.1038/s41559-018-0534-2 is OK
- 10.1371/journal.pone.0017686 is OK
- 10.1139/z85-345 is OK
- 10.1111/1365-2435.12200 is OK
- 10.3354/meps12522 is OK
- 10.1139/z98-195 is OK
- 10.3354/meps09675 is OK
- 10.1146/annurev-marine-010318-095323 is OK
- 10.3389/fmars.2017.00366 is OK
- 10.1139/cjz-2014-0311 is OK
- 10.1002/ajp.1350300207 is OK
- 10.1111/j.1748-7692.2009.00288.x is OK
- 10.1111/mms.12527 is OK
- 10.1038/nmeth.2089 is OK
- 10.1126/science.290.5497.1695b is OK
- 10.1002/ecs2.1468 is OK
- 10.1139/juvs-2015-0020 is OK

MISSING DOIs

- https://doi.org/10.2307/1374074 may be missing for title: Southern Blue and Fin Whales

INVALID DOIs

- 10.1641/0006-3568(2003)053[0210:WAS]2.0.CO;2 is INVALID

whedon · 2020-01-16T00:18:35Z

Check final proof 👉 openjournals/joss-papers#1222

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#1222, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true

kyleniemeyer · 2020-01-16T00:19:03Z

@whedon accept deposit=true

whedon · 2020-01-16T00:19:07Z

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

whedon · 2020-01-16T00:19:56Z

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

whedon · 2020-01-16T00:19:57Z

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

Here's what you must now do:

Check final PDF and Crossref metadata that was deposited 👉 Creating pull request for 10.21105.joss.01825 joss-papers#1223
Wait a couple of minutes to verify that the paper DOI resolves https://doi.org/10.21105/joss.01825
If everything looks good, then close this review issue.
Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? notify your editorial technical team...

kyleniemeyer · 2020-01-16T00:22:17Z

Congrats on your article's publication in JOSS @wingtorres!

Many thanks to @isaacvandor and @bw4sz for reviewing this submission, and @Kevin-Mattheus-Moerman for editing.

whedon · 2020-01-16T00:22:20Z

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

If you would like to include a link to your paper from your README use the following code snippets:

Markdown:
[![DOI](https://joss.theoj.org/papers/10.21105/joss.01825/status.svg)](https://doi.org/10.21105/joss.01825)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.01825">
  <img src="https://joss.theoj.org/papers/10.21105/joss.01825/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.01825/status.svg
   :target: https://doi.org/10.21105/joss.01825

This is how it will look in your documentation:

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whedon added the review label Oct 21, 2019

whedon assigned Kevin-Mattheus-Moerman Oct 21, 2019

whedon mentioned this issue Oct 21, 2019

[PRE REVIEW]: MorphoMetriX: a photogrammetric measurement GUI for morphometric analysis of megafauna #1691

Closed

whedon assigned bw4sz and isaacvandor Oct 22, 2019

whedon added the accepted label Jan 16, 2020

kyleniemeyer closed this as completed Jan 16, 2020

Kevin-Mattheus-Moerman mentioned this issue Feb 1, 2020

[PRE REVIEW]: Using drones to quantify the length of marine animals #2056

Closed

whedon added published Papers published in JOSS recommend-accept Papers recommended for acceptance in JOSS. labels Mar 2, 2020

Kevin-Mattheus-Moerman mentioned this issue Mar 4, 2020

[PRE REVIEW]: DetecTree: Tree detection from aerial imagery in Python #2143

Closed

Kevin-Mattheus-Moerman mentioned this issue Feb 20, 2021

[PRE REVIEW]: WhaleMap: a tool to collate and display whale survey results in near real-time #3047

Closed

Kevin-Mattheus-Moerman mentioned this issue Aug 1, 2023

[PRE REVIEW]: MorphoMetriX version 2: updates to the photogrammetric analysis software #5714

Closed

editorialbot mentioned this issue Sep 25, 2024

[PRE REVIEW]: respdetect: A Matlab tool for detecting breath events from whale biologger data #7282

Closed

[REVIEW]: MorphoMetriX: a photogrammetric measurement GUI for morphometric analysis of megafauna #1825

[REVIEW]: MorphoMetriX: a photogrammetric measurement GUI for morphometric analysis of megafauna #1825

Comments

whedon commented Oct 21, 2019 • edited Loading

Status

Reviewer instructions & questions

Review checklist for @isaacvandor

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

Review checklist for @bw4sz

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

whedon commented Oct 21, 2019

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whedon commented Oct 21, 2019

isaacvandor commented Oct 22, 2019 • edited Loading

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bw4sz commented Oct 22, 2019

bw4sz commented Oct 22, 2019

kthyng commented Oct 22, 2019

patrickcgray commented Oct 25, 2019 via email

Kevin-Mattheus-Moerman commented Nov 1, 2019

Kevin-Mattheus-Moerman commented Nov 1, 2019

wingtorres commented Nov 15, 2019

danielskatz commented Dec 5, 2019

wingtorres commented Dec 15, 2019

wingtorres commented Dec 15, 2019

whedon commented Dec 15, 2019

whedon commented Dec 15, 2019

Kevin-Mattheus-Moerman commented Dec 16, 2019

Kevin-Mattheus-Moerman commented Dec 16, 2019

wingtorres commented Dec 16, 2019

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wingtorres commented Jan 15, 2020

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arfon commented Jan 15, 2020

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whedon commented Oct 21, 2019 •

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