[PRE REVIEW]: imea: A Python package for extracting 2D and 3D shape measurements from images

[whedon]

Submitting author: @nilskroell (Nils Kroell) Repository: https://git.rwth-aachen.de/ants/sensorlab/imea Version: v0.2.2 Editor: @mbobra Reviewers: @Atif-Anwer, @tuelwer Managing EiC: Daniel S. Katz

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Thanks for submitting your paper to JOSS @nilskroell. Currently, there isn't an JOSS editor assigned to your paper.

@nilskroell if you have any suggestions for potential reviewers then please mention them here in this thread (without tagging them with an @). In addition, this list of people have already agreed to review for JOSS and may be suitable for this submission (please start at the bottom of the list).

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[whedon]

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[whedon]

Software report (experimental):

github.com/AlDanial/cloc v 1.88  T=0.30 s (39.6 files/s, 13243.9 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                           7            557            752            890
Markdown                         2             66              0            197
TeX                              1             34              0            168
Jupyter Notebook                 2              0           1241            107
-------------------------------------------------------------------------------
SUM:                            12            657           1993           1362
-------------------------------------------------------------------------------

Statistical information for the repository 'a7e7eda1426829055c5a5940' was
gathered on 2021/02/27.
The following historical commit information, by author, was found:

Author                     Commits    Insertions      Deletions    % of changes
Nils Kroell                     49          3725           3565           76.36
nkroell                          3          2148            109           23.64

Below are the number of rows from each author that have survived and are still
intact in the current revision:

Author                     Rows      Stability          Age       % in comments
Nils Kroell                2199           59.0          0.1               12.73

[whedon]

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

OK DOIs

- 10.1016/j.mineng.2011.10.001 is OK
- 10.1016/j.wasman.2020.11.003 is OK
- 10.1016/j.ces.2013.02.043 is OK
- 10.1063/5.0002233 is OK
- 10.1109/IEMBS.2005.1617159 is OK
- 10.1016/s0165-0270(96)00080-5 is OK
- 10.1016/j.patrec.2017.08.022 is OK
- 10.1016/j.wasman.2020.09.033 is OK
- 10.7717/peerj.453 is OK
-  10.25080/Majora-92bf1922-00a is OK

MISSING DOIs

- None

INVALID DOIs

- None

[whedon]

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

[danielskatz]

👋 @nilskroell - Due to the relatively small size of this code, the JOSS editors will now examine if this submission meets the substantial scholarly effort criterion for review by JOSS.

[danielskatz]

@whedon query scope

[whedon]

Submission flagged for editorial review.

[nilskroell]

Hi @danielskatz, thanks for your fast reply!

To give you and the editorial board more context on the scholary effort that was required to develop imea, I would like to add the following four points, which are difficult to be discovered from the repository and LOC:

• A substantial scholary effort was applied by conducting a thorough literature review to identify and select all relevant shape measurements proposed and used in scientific literature.
• Determining 2D and 3D shape measurements of arbitrary shapes takes a lot of computational effort, as for example statistical lengths need to be determined at various rotation angles. A lot of time and effort has thus been invested to find and test the most computational efficient implementation. To ensure a clear structure and good maintainability, only the fastest and clearest implementations were integrated in imea.
• Instead of implementing all shape measurements from ground up, a lot of time and effort has been invested to identify existing implementations. Identified implementation has then been extensively tested on various shapes and evaluated. As a result, only the implementations from scikit-image and open-cv have been found suitable and are thus integrated in imea – saving additional LOC and making maintaining imea easier.
• In a previous project, I had invested a lot of effort in implementing various 3D shape measurements in MATLAB, which could then be reformulated for imea and implemented in a rather short time.

For our department and project partners, imea has already been extremely useful in extracting shape measurements in various projects in the short time since it was available for internal validation. Several research publications where imea was used for data extraction are already in preparation. An inclusion of imea into JOSS would help me a lot in making imea more visible for other researchers and citable in upcoming publications. I look forward to your decision. If you need any additional information – do not hesitate to ask me, I am happy to reply.

Best regards, Nils

[danielskatz]

This has passed the scope check

[danielskatz]

👋 @mbobra - would you be able to edit this submission?

[danielskatz]

@whedon invite @mbobra as editor

[whedon]

@mbobra has been invited to edit this submission.

[mbobra]

@whedon assign me as editor

[whedon]

OK, the editor is @mbobra

[mbobra]

@nilskroell Thank you for your submission! Please give me a week to find some reviewers (I am tied up until the day after tomorrow, but will search for reviewers after that).

If you have any suggested reviewers, please let me know here (you can give me the Github handle without @ mentioning them, e.g. mbobra instead of @mbobra).

[nilskroell]

@danielskatz : Thanks a lot for the fast decision. I'm glad that imea fits the scope of JOSS.

@mbobra : Thanks a lot for taking the time to edit this submission and the clear and fast communication.

Based on the provided list of potential reviewers I can suggest the following reviewers:

• tuelwer: expertise in image processing, machine learning, computer vision and data science
• macrocosme: expertise in image processing and visualization
• PingjunChen: expertise in biomedical image analysis and machine learning
• Atif-Anwer: expertise in image processing and computer vision
• lbugnon: expertise in image processing and machine learning

All suggested reviewers are familiar with Python, have currently no active reviews (as indicated in the list) and have at least one time reviewed for JOSS before. I also made sure, that none of them is working at the same university as I am and that the suggested reviewers come from different fields. However, there are many more potential reviewers with expertise in image processing & Python in the list which could be included. If you need more suggestions @mbobra feel free to contact me.

[Atif-Anwer]

Hi!

I've looked at the repo as well as the draft submission and I would be glad to review the submission. However before committing, I would like to ask about the deadline/timeline available for the review; since I am myself teaching this semester etc. I would hopefully be able to review it in a couple of weeks approximately; testing out the package and etc. If that is ok with JOSS's timeline, then I will be glad to formally accept as reviewer on the JOSS pre-review thread. (@mbobra I tried to reply to your email; but the server rejected my email as spam so I figured i'll post here directly)

[mbobra]

@Atif-Anwer Thank you so much for your reply (and persistence)! I'm sorry about the spam filter (I will look into it).

JOSS is operating on a reduced service mode (see here) so we're giving reviewers six weeks to complete their review. This is not a hard deadline, though, so if you need an additional week or so that's fine. Is this okay with you? If so, I'll go ahead and assign you as a reviewer.

[Atif-Anwer]

Six weeks is ample time. Ill be able to do it before that for sure. Thanks!

[mbobra]

@whedon assign @Atif-Anwer as reviewer

[whedon]

OK, @Atif-Anwer is now a reviewer

[mbobra]

@whedon add @tuelwer as reviewer

[whedon]

OK, @tuelwer is now a reviewer

[mbobra]

@whedon start review

[whedon]

OK, I've started the review over in https://github.com/openjournals/joss-reviews/issues/3091.

[mbobra]

@Atif-Anwer @tuelwer See you over in #3091 where the review will take place!