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

[editorialbot]

Submitting author: @ZappyMan (Elliott Chimienti)
Repository: https://github.com/ZappyMan/MorphoMetriX
Branch with paper.md (empty if default branch): master
Version: v.2.0.0
Editor: Pending
Reviewers: Pending
Managing EiC: Kevin M. Moerman

Status

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[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.88  T=0.02 s (501.2 files/s, 81146.0 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                           2            190            121            947
TeX                              1             15              0            210
Markdown                         5             73              0            161
YAML                             3              6              5             53
-------------------------------------------------------------------------------
SUM:                            11            284            126           1371
-------------------------------------------------------------------------------


gitinspector failed to run statistical information for the repository

[editorialbot]

Wordcount for paper.md is 1144

[editorialbot]

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

OK DOIs

- 10.21105/joss.01825 is OK
- 10.21105/joss.02328 is OK
- 10.1242/jeb.224196 is OK
- 10.3354/meps13638 is OK
- 10.3354/meps13814 is OK
- 10.3389/fmars.2021.749943 is OK
- 10.1002/rse2.258 is OK
- 10.1111/2041-210X.13962 is OK
- 10.1093/iob/obac038 is OK
- 10.3389/fmars.2022.1036860 is OK
- 10.1038/s41559-023-01993-2 is OK
- 10.1098/rsos.230452 is OK
- 10.1098/rsos.220724 is OK
- 10.1242/jeb.243224 is OK

MISSING DOIs

- 10.3389/fmars.2022.867258 may be a valid DOI for title: Range-Wide Comparison of Gray Whale Body Condition Reveals Contrasting Sub-Population Health Characteristics and Vulnerability to Environmental Change

INVALID DOIs

- None

[editorialbot]

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

[Kevin-Mattheus-Moerman]

@ZappyMan, thanks for this submission. I am the AEiC for this track and here to help process initial steps.

Since you are seeking a "new version paper" (former version was published in JOSS and was reviewed here: #1825) could you please provide a list of all the major changes since that version? It would help if you could leave a detailed post here highlighting the developments since that published version. You can include links to issues addressed and/or links to new docs/files/code where appropriate. The more evidence you can provide, that the changes made are significant enough to justify a new JOSS paper, the better. Thanks.

[ZappyMan]

@Kevin-Mattheus-Moerman thanks for the quick response. Below is a comprehensive list of major changes since version 1:

Features

• Widths measurement functionality has been replaced with draggable crosshairs. This new feature enables users to easily adjust and edit width points, whereas in v1 width points could only be clicked on each line and users were unable to edit and adjust the points. This saves significant time measuring: MovingEllipse class, line 1088
• Controls for width crosshair size and color have been added to help users customize based on the lighting and contrast of the image and size of the subject in the frame: Issue 17
• CSV output has been reformatted for improved interpretability and usability with CollatriX
• CSV output now contains both metric and pixel measurements
• Implemented side-bias functionality for width measuring when visibility is poor. This new feature helps increase the number of measurable images that would otherwise be excluded, thus improving the sample sizes for analyses: Issue 15
• Added width side labels for bias functionality
• Added Windows and Universal2 MacOS distributions in release, greatly improving user-friendly downloading and installation: Issue 10
• Replaced built-in manual viewer with button that redirects user to online version
• Reimplemented undo functionality to support new graphics items: Line 409
• Implemented crash catching and logging for issue reporting: Crash catcher, Line 1213
• Added MorphoMetriX logo to GUI: Logo
• Changed default camera values
• Fixed errors related to diagonal length measurements, as well as Bezier curves fitted to two points: Issue 7

Stability

• Fixed issue with cursor not returning to normal after angle calculation
• Fixed crash on export with angle or area measurements: Issue 14
• Switched GUI frameworks from PyQt6 to PySide6 for Universal2 distribution support
• Fixed issue with widths button re-enabling self
• Fixed errors related to diagonal length measurements, as well as Bezier curves fitted to two points:
• Refactored undo functionality for improved stability: Issue 18

Contributors
Lastly, a major change to MorphoMetriX from the published v1, is the team. I have taken over leadership of development from wingtorres as I led all the software updates for v2 and now manage the repository and will handle issues moving forwards. Cbirdferrer has also been added as a contributor.

[Kevin-Mattheus-Moerman]

@ZappyMan thanks for that information. I will now consult the editorial board on this and we will get back to you with a verdict.

Notes to editors:

• This authors seek the review/publication of a new version of their software. Their previous version was reviewed/accepted, see: [REVIEW]: MorphoMetriX: a photogrammetric measurement GUI for morphometric analysis of megafauna #1825
• It looks like the authors forked the old version which has the following cloc output:

-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                           2            156            153            741
TeX                              1             23              0            226
Markdown                         5            105              0            196
YAML                             2              5              1             34
CSV                              1              0              0             16
-------------------------------------------------------------------------------
SUM:                            11            289            154           1213
-------------------------------------------------------------------------------

• One of the authors @ZappyMan has provided a list of changes since this published version ☝️
• The new version has the following cloc output:

github.com/AlDanial/cloc v 1.88  T=0.02 s (501.2 files/s, 81146.0 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                           2            190            121            947
TeX                              1             15              0            210
Markdown                         5             73              0            161
YAML                             3              6              5             53
-------------------------------------------------------------------------------
SUM:                            11            284            126           1371

• As such only ~200 LOC were added (keeping in mind that LOC added do not tell a complete story of course, i.e. line deletion/code simplification/shortening can be very important).
• From the above comments from the author, it looks like most changes relate to improvements to the look/performance/easy-of-use of the GUI, or treat minor bugs. It looks to me like only the following point addresses a "scientific functionality" change/improvement

• Implemented side-bias functionality for width measuring when visibility is poor. This new feature helps increase the number of measurable images that would otherwise be excluded, thus improving the sample sizes for analyses

@ZappyMan, if you feel I've misrepresented your summary, feel free to elaborate on more changes that relate to scientific functionality/outcomes.

[Kevin-Mattheus-Moerman]

@editorialbot query scope

[editorialbot]

Submission flagged for editorial review.

[Kevin-Mattheus-Moerman]

@ZappyMan the editorial board has studied you submission, and the differences with the previously published version. Unfortunately the changes made to this new version are not seen here as sufficient to justify a new JOSS paper. The key thing we would look for in this case is significant changes of the scientific functionality/performance.

We will now proceed to reject this submission. Note though that this conclusion does not mean this work (and the enhancements made) are of a poor quality or not useful, it merely means that the enhancements proposed are not deemed significant enough to warrant a new paper.

Note we would welcome any future (re)submissions that are of a more substantial nature.

[Kevin-Mattheus-Moerman]

@editorialbot reject

[editorialbot]

Paper rejected.