[REVIEW]: atems: Analysis tools for TEM images of carbonaceous particles

[editorialbot]

Submitting author: @tsipkens (Timothy A. Sipkens)
Repository: https://github.com/tsipkens/atems
Branch with paper.md (empty if default branch):
Version: v1.2
Editor: @diazrenata
Reviewers: @jonbmartin, @tytell
Archive: Pending

Status

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Markdown: [![status](https://joss.theoj.org/papers/a720aa990aac5807797d97a01da5a6b4/status.svg)](https://joss.theoj.org/papers/a720aa990aac5807797d97a01da5a6b4)

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

@jonbmartin & @tytell, 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 @diazrenata 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 @jonbmartin

📝 Checklist for @tytell

[editorialbot]

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[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.88  T=0.12 s (729.5 files/s, 66513.7 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
MATLAB                          59           1530           1867           2856
XML                              6              0              0            664
Markdown                         6            261              0            421
TeX                              1             17              0            165
Python                           2             47             37             96
JSON                             8              0              0             71
YAML                             4              5              4             64
Bourne Shell                     1              1              5              2
SVG                              2              0              0              2
-------------------------------------------------------------------------------
SUM:                            89           1861           1913           4341
-------------------------------------------------------------------------------


gitinspector failed to run statistical information for the repository

[editorialbot]

Wordcount for paper.md is 1002

[editorialbot]

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

OK DOIs

- 10.1016/j.jaerosci.2017.10.002 is OK
- 10.1016/j.jaerosci.2020.105699 is OK
- 10.1016/j.powtec.2021.04.026 is OK
- 10.1016/j.jaerosci.2023.106211 is OK
- 10.1080/02786826.2014.932896 is OK
- 10.1080/02786826.2014.955565 is OK
- 10.1016/j.powtec.2016.03.027 is OK
- 10.4271/2015-01-1991 is OK
- 10.1038/nmeth.2089 is OK
- 10.1016/j.jaerosci.2019.105470 is OK
- 10.1016/j.powtec.2014.04.040 is OK
- 10.1016/j.fuel.2020.118478 is OK
- 10.1016/j.jaerosci.2019.105448 is OK
- 10.1080/02786826.2020.1758623 is OK
- 10.1016/j.powtec.2019.02.003 is OK
- 10.1021/es501809b is OK
- 10.1016/j.combustflame.2019.03.018 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[editorialbot]

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

[jonbmartin]

Review checklist for @jonbmartin

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/tsipkens/atems?
• 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 (@tsipkens) 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?

[jonbmartin]

I have completed my review and I am satisfied with both the software toolbox and the package describing it, and believe they are appropriate for publication in JOSS. The MATLAB functions seem robust - I tried to add a few different types of noise to the images before segmentation and processing and got what seemed like satisfactory results every time.

The GUI interface (documented in main_0.m) built as a MATLAB app is very nice and clean, and a flexible addition to the automatic tools. However it is a little bit difficult to use. I found myself struggling to use the slider to specify 'threshold relative to Otsu' - allowing users to input a specific number than rely on a slider could help a bit. I also had some trouble with tools.load_imgs(), I believe as a linux user. I was able to run the command without arguments succesfully, but could never get it to succesfully accept a string input as the file path. Wasn't able to fully troubleshoot.

The paper is very well written, as is the documentation that was developed. I think that overall this is an excellent product and highly recommend publication.

[diazrenata]

@jonbmartin thank you very much! @tsipkens, the two points raised (the somewhat finicky slider, and the question about running tools.load_imgs() with a string input) seem fairly minor, but do you have any thoughts in response?

[tsipkens]

Yes, I will! Hopefully I can get around to posting them shortly.

[tytell]

Review checklist for @tytell

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/tsipkens/atems?
• 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 (@tsipkens) 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?

[tsipkens]

@diazrenata. Some changes have been made to the code in response to @jonbmartin's recommendations.

The GUI interface (documented in main_0.m) built as a MATLAB app is very nice and clean, and a flexible addition to the automatic tools. However, it is a little bit difficult to use. I found myself struggling to use the slider to specify 'threshold relative to Otsu' - allowing users to input a specific number rather than rely on a slider could help a bit.

The GUI was amended accordingly, adding a numerical field in addition to the slider.

I also had some trouble with tools.load_imgs(), I believe as a Linux user. I was able to run the command without arguments successfully, but could never get it to successfully accept a string input as the file path. Wasn't able to fully troubleshoot.

It is unclear as to the source of this issue. There is a reasonable chance this is related to the use of Linux. The CircleCI workflow still compiles, though this uses a weblink as an input. A note about potential issues for Linux users has been added to the README. The load_imgs function was also amended to take file names in addition to a folder, which could present another potential source for error.

[tsipkens]

@diazrenata. I have also addressed the issue that @tytell raised against the repository, namely an error in the README that did not match one of the sample scripts.

[tytell]

I have completed my review. As far as I can tell, the software does what it claims to do. My expertise is mainly in image analysis, and so I cannot address the specifics of analysis as it relates to soot or carbonaceous particles. The analysis is based on what seems to be a community need and seems based in existing literature. The paper is clear and well written and the scripts are documented and seem to run as described.

Here are a few notes and comments. I've added a few more minor issues to the repository.

1. Run main_b.m: Works

2. Run tools.write_json(Aggs, 'test.json');. Fails with

Error using jsonencode
Unable to encode objects of class logical as JSON-formatted text.
Error in tools.write_json (line 9)
t0 = jsonencode(var); % generate json text using built-in function

I think this is a Matlab version incompatibility. Here is my Matlab version info:

MATLAB Version: 9.14.0.2254940 (R2023a) Update 2
Operating System: macOS Version: 12.6.9 Build: 21G726
Java Version: Java 1.8.0_202-b08 with Oracle Corporation Java HotSpot(TM) 64-Bit Server VM mixed mode

3. Run main_kmeans.m. Works

4. Run main_auto.m. Works

5. Run main_0.m. Suggestions:

• Change "more particles or add to existing particles" button to be labeled something like "Interactive tool to adjust thresholding"
• Adjusting the "slider" does not seem to offer any feedback on how it is changing the threshold. That makes it very hard to judge whether the change is sufficient. I suggest overlying a color that shows the thresholded region.
• I'm not sure if I'm doing it incorrectly, but every time I adjust the slider, I get a black image afterward, suggesting that the threshold is incorrect
• There does not seem to be a way to go back in the steps. That would be helpful
• Now I see that "Add (to) aggregates" button is sort of like a "start over" option. It is unclear what that actually does

6. Several of the functions (main_kmeans and the final section of main_0 after agg.analyze_binary) occasionally crash Matlab on my computer. The program locks up entirely and I have to force quit. I can't determine why.

7. Run img_binary = agg.seg_slider_orig(imgs). Works

8. README refers to agg.seg_otsu_rb_orig(...) and agg.seg_otsu_rb(...). There aren't these functions in the agg directory. I think these should be agg.seg_otsu_orig(...) and agg.seg_otsu(...).

9. README refers to pp.kook*(...). I think this should be pp.hough_kook*.

[tsipkens]

@tytell Thanks for the thorough review. I will work to address some of these issues at my earliest convenience.

[diazrenata]

@tsipkens 👋 Just checking in to see how revisions are going!

[tsipkens]

I made a bunch more progress today, I hope to finish with a larger response soon. Thank you for the reminder.

[tsipkens]

Thanks to @tytell for the useful feedback. Brief responses to the review below:

1. The JSON encoding error has been resolved (related to encoding a sparse logical, which is not supported by JSON).

2. For main_0, the button for refining the threshold has been changed as suggested. Help buttons have also been added to the GUI (including why the thresholding may be failing), in addition to adding a text field for the slider related to the previous review. Color has been added to the overlay for the thresholding/slider step.

3. MATLAB locking up on occasion for some scripts could not be replicated and may be related to the use of EDM sizing on macOS. A note to this effect has been added to the README.

4. The reviewer is right, the README has been updated to contain correct references to the seg_otsu and kook methods.

All corresponding issues against the repository have been closed with comments.