[PRE REVIEW]: SPECTPSFToolbox: A Python Toolbox for SPECT Point Spread Function Modeling

[editorialbot]

Submitting author: @lukepolson (Lucas Polson)
Repository: https://github.com/PyTomography/SPECTPSFToolbox
Branch with paper.md (empty if default branch):
Version: v0.1.0
Editor: Pending
Reviewers: Pending
Managing EiC: Kevin M. Moerman

Status

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[editorialbot]

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

OK DOIs

- 10.1109/42.363108 is OK
- 10.1109/42.52985 is OK
- 10.1109/TNS.2002.998681 is OK
- 10.1109/NSSMIC.2006.354345 is OK
- 10.1088/1361-6560/aa6911 is OK
- 10.1088/1361-6560/aadac1 is OK
- 10.1109/TMI.2003.812251 is OK
- 10.1007/978-1-4614-7657-3_19 is OK
- 10.1109/NSS/MIC42677.2020.9507966 is OK
- 10.21037/atm-20-5988 is OK
- 10.1007/s00259-022-06092-1 is OK
- 10.1007/s00259-024-06681-2 is OK
- 10.1088/0031-9155/35/1/008 is OK
- 10.1088/0031-9155/43/4/021 is OK
- 10.1088/0031-9155/43/11/013 is OK
- 10.1088/0031-9155/25/6/003 is OK
- 10.1109/TNS.2002.1039547 is OK
- 10.1007/0-387-25444-7_1 is OK
- 10.2967/jnumed.124.267482 is OK

MISSING DOIs

- 10.1097/mnm.0000000000001675 may be a valid DOI for title: Anatomically guided reconstruction improves lesion...
- No DOI given, and none found for title: PyTomography: A Python Library for Quantitative Me...
- No DOI given, and none found for title: Foundations of Image Science
- No DOI given, and none found for title: Targeted α-therapy of metastatic castration-resist...
- No DOI given, and none found for title: Predictors of overall and disease-free survival in...
- No DOI given, and none found for title: First clinical results for PSMA-targeted α-therapy...
- No DOI given, and none found for title: Molecular imaging and biochemical response assessm...

INVALID DOIs

- https://doi.org/10.1016/0169-2607(89)90111-9 is INVALID because of 'https://doi.org/' prefix

[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.90  T=0.03 s (1038.8 files/s, 209643.2 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Jupyter Notebook                10              0           3043            861
Python                           7            196            518            856
TeX                              1             28              0            298
Markdown                         3             35              0             82
YAML                             2              5              0             44
TOML                             1              8              0             41
DOS Batch                        1              8              1             26
reStructuredText                 2             43            106             15
Bourne Shell                     2              3              2             14
make                             1              4              7              9
CSS                              1              0              0              3
-------------------------------------------------------------------------------
SUM:                            31            330           3677           2249
-------------------------------------------------------------------------------

Commit count by author:

    16	lukepolson
     1	Luke Polson

[editorialbot]

Paper file info:

📄 Wordcount for paper.md is 1874

✅ The paper includes a Statement of need section

[editorialbot]

License info:

✅ License found: MIT License (Valid open source OSI approved license)

[editorialbot]

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

[editorialbot]

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[Kevin-Mattheus-Moerman]

@editorialbot query scope

[editorialbot]

Submission flagged for editorial review.

[Kevin-Mattheus-Moerman]

@lukepolson Dear author, thanks for this re-submission (original pre-review here: #7067). I see some of the issues raised were addressed. I present a summary below.

Note also I have just added the query-scope label, to trigger a scope review by the editorial board. This is because of the relatively small size of the project. During this scope review we'll determine if the functionality offered is extensive enough and if the project conforms to our substantial scholarly effort criteria. The scope review should take about 2 weeks to complete. In the meantime, if you can continue to look at/work on the below that would be good.

Points raised at previous PRE-REVIEW:

• The submission is of a relatively small size (~717 lines of code appear to capture core functionality)

Still remains

• The contribution history appears to show less than 3 months of work. Although work could have occurred off line, it is typically a sign of low maturity as evident also by the lack of forks/issues/stars/follows and community engagement with the work.

Partially addressed by explaining:

"while the repository is relatively new, it was built using prior code from the PyTomography (https://github.com/PyTomography/PyTomography) library, and has been in development offline for some time. The repository was made separate from PyTomography because we believe it forms an independent function in modeling of gamma camera resolution. "

• Your project appears to lack contributing guidelines at the moment. Please work to add these and to mention/link to them in your README. You could for instance create a CONTRIBUTING.md file (see here for some examples: https://contributing.md/example/).

Partially addressed, a basic file was added but is not linked to or mentioned in the README

• The project appears to lack dedicated documentation and automated testing (or at least the README does not link to them)

Potentially addressed assuming documentation covers all functionality.

• The README is too short and short include a brief description of the software, links to installation/getting started, documentation, testing, contributing guidelines etc (in addition since your project features imaging, some graphical examples/visualisations may be good to include). Here are three examples of more complete READMEs for Python projects:
  * https://github.com/sunpy/sunpy
  * https://github.com/astropy/astropy
  * https://github.com/paucablop/chemotools

README somewhat improved. The README is still very short and not like the example READMEs in that it does not link to contributing guidelines, does not mention/link to testing, does not mention/link to license, e.g. it should be more like this one: https://github.com/paucablop/chemotools.

Note that the above python projects also show examples of automated testing/continuous integration.

Potentially/partially addressed since the authors state they've:
"add[ed] a tests/ folder to the repository with some automated testing"

I have not reviewed your paper in detail but I can add the following about the paper:

• Please study the above paper compilation error, it looks like you need to fix the ORCID id for one author. Check our documentation on this too if needed.

Looks like this was addressed.

• Please study the above reference check ☝️ and see if you can address any of the reported potential DOI issues

Not completely addressed. Please study the above reference check ☝️ and see if you can address any of the reported potential DOI issues. You can add/amend DOI entries in your .bib file, and call @editorialbot check references here to check them again.

[lukepolson]

@editorialbot check references

[editorialbot]

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

OK DOIs

- 10.1109/42.363108 is OK
- 10.1109/42.52985 is OK
- 10.1016/0169-2607(89)90111-9 is OK
- 10.1109/TNS.2002.998681 is OK
- 10.1109/NSSMIC.2006.354345 is OK
- 10.1088/1361-6560/aa6911 is OK
- 10.1097/MNM.0000000000001675 is OK
- 10.1088/1361-6560/aadac1 is OK
- 10.1109/TMI.2003.812251 is OK
- 10.1007/978-1-4614-7657-3_19 is OK
- 10.48550/arXiv.2309.01977 is OK
- 10.1109/NSS/MIC42677.2020.9507966 is OK
- 10.21037/atm-20-5988 is OK
- 10.1117/1.1905634 is OK
- 10.2967/jnumed.117.203539 is OK
- 10.2967/jnumed.119.229229 is OK
- 10.2967/jnumed.120.251017 is OK
- 10.7150/thno.56211 is OK
- 10.1007/s00259-022-06092-1 is OK
- 10.1007/s00259-024-06681-2 is OK
- 10.1088/0031-9155/35/1/008 is OK
- 10.1088/0031-9155/43/4/021 is OK
- 10.1088/0031-9155/43/11/013 is OK
- 10.1088/0031-9155/25/6/003 is OK
- 10.1109/TNS.2002.1039547 is OK
- 10.1007/0-387-25444-7_1 is OK
- 10.2967/jnumed.124.267482 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[lukepolson]

@Kevin-Mattheus-Moerman I recently pushed to the library to enhance the README file and make it more like the other packages you've linked. I've also fixed the DOI issues, as seen above. Thanks again for the in depth recommendations in improving the library!!

[Kevin-Mattheus-Moerman]

@lukepolson thanks for this re-submission, and the efforts to improve this work prior to resubmission. Unfortunately, the second scope review by the JOSS editorial has once again concluded this work is out of scope. The small size and limited functionality of the package still cause this submission to not pass our substantial scholarly effort criterion, and the work is still deemed too immature at present.

We will now proceed to reject this submission.

One possible alternative to JOSS is to follow GitHub's guide on how to create a permanent archive and DOI for your software. This DOI can then be used by others to cite your work.

[Kevin-Mattheus-Moerman]

@editorialbot reject

[editorialbot]

Paper rejected.