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[REVIEW]: atems: Analysis tools for TEM images of carbonaceous particles #6416

Open editorialbot opened 4 months ago

editorialbot commented 4 months ago

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

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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:

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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 commented 4 months ago

Hello humans, I'm @editorialbot, a robot that can help you with some common editorial tasks.

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editorialbot commented 4 months ago 
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 commented 4 months ago

Wordcount for paper.md is 1002

editorialbot commented 4 months ago 
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 commented 4 months ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

jonbmartin commented 4 months ago

Review checklist for @jonbmartin

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

jonbmartin commented 3 months ago

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 commented 3 months ago

@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 commented 3 months ago

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

tytell commented 3 months ago

Review checklist for @tytell

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

tsipkens commented 2 months ago

@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 commented 2 months ago

@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 commented 2 months ago

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

  1. Run main_kmeans.m. Works

  2. Run main_auto.m. Works

  3. 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

  4. 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.

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

  6. 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(...).

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

tsipkens commented 2 months ago

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

diazrenata commented 2 months ago

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

tsipkens commented 2 months ago

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

tsipkens commented 2 months ago

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.

crvernon commented 1 month ago

:wave: @diazrenata - could you check in on this one? It looks like it is almost ready for your review. Thanks!

diazrenata commented 1 month ago

Thanks @crvernon! @tytell and @jonbmartin - based on @tsipkens's responses to your comments, do you consider your reviews complete? (It looks like it to me, but I'd just like to confirm as I move forward!)

tytell commented 1 month ago

Yes - that seems to be sufficient to me.

Eric On May 28, 2024, 10:32 AM -0400, Renata Diaz @.***>, wrote:

Thanks @crvernonhttps://github.com/crvernon! @tytellhttps://github.com/tytell and @jonbmartinhttps://github.com/jonbmartin - based on @tsipkenshttps://github.com/tsipkens's responses to your comments, do you consider your reviews complete? (It looks like it to me, but I'd just like to confirm as I move forward!)

— Reply to this email directly, view it on GitHubhttps://github.com/openjournals/joss-reviews/issues/6416#issuecomment-2135378268, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AA3LX2VHN6VQTU3R53VDMWTZESIODAVCNFSM6AAAAABD3BULLKVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDCMZVGM3TQMRWHA. You are receiving this because you were mentioned.Message ID: @.***>

diazrenata commented 1 month ago

@editorialbot generate pdf

diazrenata commented 1 month ago

@editorialbot check references

editorialbot commented 1 month ago 
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

- No DOI given, and none found for title: Flame and smoke characterization in reduced gravit...

INVALID DOIs

- None
editorialbot commented 1 month ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

diazrenata commented 1 month ago

@tsipkens Typo on line 73: "These including" should be "These include".

tsipkens commented 1 month ago

@diazrenata I have committed a fix for this typo to the master branch of the repository. Thanks for catching it.

diazrenata commented 1 month ago

@jonbmartin Just checking in to see if you could confirm that you consider your review complete?

diazrenata commented 1 week ago

@jonbmartin - just re-upping the above - are we good to go as far as your review is concerned?