[REVIEW]: DIRECT: Deep Image REConstruction Toolkit
Closed this issue · 65 comments
Submitting author: @georgeyiasemis (George Yiasemis)
Repository: https://github.com/NKI-AI/direct
Branch with paper.md (empty if default branch): joss-submission
Version: v1.0.1
Editor: @osorensen
Reviewers: @estenhl, @sairamgeethanath
Archive: 10.5281/zenodo.6594702
Status
Status badge code:
HTML: <a href="https://joss.theoj.org/papers/150119fd46692dad9448a26eca669a77"><img src="https://joss.theoj.org/papers/150119fd46692dad9448a26eca669a77/status.svg"></a>
Markdown: [](https://joss.theoj.org/papers/150119fd46692dad9448a26eca669a77)
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
@estenhl & @sairamgeethanath, 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 @osorensen 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
Hello humans, I'm @editorialbot, a robot that can help you with some common editorial tasks.
For a list of things I can do to help you, just type:
@editorialbot commands
For example, to regenerate the paper pdf after making changes in the paper's md or bib files, type:
@editorialbot generate pdf
Software report:
github.com/AlDanial/cloc v 1.88 T=0.43 s (451.4 files/s, 69344.1 lines/s)
-------------------------------------------------------------------------------
Language files blank comment code
-------------------------------------------------------------------------------
Python 131 3454 4081 12136
SVG 2 0 0 5849
YAML 26 22 37 1955
reStructuredText 21 276 514 318
Markdown 6 81 0 316
TeX 1 15 0 161
make 2 27 6 80
TOML 1 9 4 49
Dockerfile 1 15 7 45
DOS Batch 1 8 1 27
-------------------------------------------------------------------------------
SUM: 192 3907 4650 20936
-------------------------------------------------------------------------------
gitinspector failed to run statistical information for the repository
Wordcount for paper.md is 1142
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):
OK DOIs
- 10.1109/tmi.2021.3075856 is OK
- 10.1007/978-3-030-59713-9_7 is OK
- 10.1016/j.media.2019.01.005 is OK
- 10.1109/tmi.2018.2799231 is OK
- 10.1002/mrm.27201 is OK
- 10.1109/cvpr46437.2021.00523 is OK
- 10.1088/0031-9155/52/7/r01 is OK
- 10.1109/TIT.2006.871582 is OK
MISSING DOIs
- None
INVALID DOIs
- None
Review checklist for @estenhl
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/NKI-AI/direct?
- License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
- Contribution and authorship: Has the submitting author (@georgeyiasemis) 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
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 and who the target audience is?
- 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?
@georgeyiasemis - Could you please let me know if there is a way for me to access the Docker image?
@georgeyiasemis Many thanks! If it is not any trouble, could you also please fix the broken link on your documentation page?
@editorialbot commands
Hello @estenhl, here are the things you can ask me to do:
# List all available commands
@editorialbot commands
# Get a list of all editors's GitHub handles
@editorialbot list editors
# Check the references of the paper for missing DOIs
@editorialbot check references
# Perform checks on the repository
@editorialbot check repository
# Adds a checklist for the reviewer using this command
@editorialbot generate my checklist
# Set a value for branch
@editorialbot set joss-paper as branch
# Generates the pdf paper
@editorialbot generate pdf
# Get a link to the complete list of reviewers
@editorialbot list reviewers
Thanks for completing your review checklist @estenhl!
@sairamgeethanath, could you please update us on how it is going with your review? Please let me know if there is anything I can help with.
@osorensen I will get this done the week after ISMRM (13th May).
Thanks @sairamgeethanath!
Review checklist for @sairamgeethanath
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/NKI-AI/direct?
- License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
- Contribution and authorship: Has the submitting author (@georgeyiasemis) 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
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 and who the target audience is?
- 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?
@georgeyiasemis Great job on the package! I thoroughly enjoyed playing with it for a while. However, I could not get your docker to work.Can you please close the Docker issue that @estenhl and I both reported? I will then check off the remaining items.
@georgeyiasemis Great job on the package! I thoroughly enjoyed playing with it for a while. However, I could not get your docker to work.Can you please close the Docker issue that @estenhl and I both reported? I will then check off the remaining items.
Thanks a lot @sairamgeethanath 👍 ! Yes we will do that!
@georgeyiasemis Great job on the package! I thoroughly enjoyed playing with it for a while. However, I could not get your docker to work.Can you please close the Docker issue that @estenhl and I both reported? I will then check off the remaining items.
@sairamgeethanath The docker issue is fixed!
@georgeyiasemis I have checked off my list.
Review checklist for @sairamgeethanath
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/NKI-AI/direct?
- License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
- Contribution and authorship: Has the submitting author (@georgeyiasemis) 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
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 and who the target audience is?
- 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?
@editorialbot generate pdf
@georgeyiasemis, the reviewers have now completed their checklists. I will now read through the paper, and get back to you if I have any suggested changes.
In the meantime, could you:
- Make a tagged release of your software, and list the version tag of the archived version here.
- Archive the reviewed software in Zenodo or a similar service (e.g., figshare, an institutional repository)
- Check the archival deposit (e.g., in Zenodo) has the correct metadata. This includes the title (should match the paper title) and author list (make sure the list is correct and people who only made a small fix are not on it). You may also add the authors' ORCID.
- Please list the DOI of the archived version here.
@editorialbot check references
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):
OK DOIs
- 10.1117/12.2609876 is OK
- 10.1109/tmi.2021.3075856 is OK
- 10.1007/978-3-030-59713-9_7 is OK
- 10.1016/j.media.2019.01.005 is OK
- 10.1109/tmi.2018.2799231 is OK
- 10.1002/mrm.27201 is OK
- 10.1109/cvpr46437.2021.00523 is OK
- 10.1088/0031-9155/52/7/r01 is OK
- 10.1109/TIT.2006.871582 is OK
- 10.1002/mrm.21391 is OK
- 10.1109/TIT.2005.862083 is OK
- 10.1002/mrm.10171 is OK
- 10.1002/(sici)1522-2594(199911)42:5<952::aid-mrm16>3.0.co;2-s is OK
- 10.1109/msp.2019.2950640 is OK
- 10.48550/ARXIV.2109.08618 is OK
MISSING DOIs
- None
INVALID DOIs
- None
@editorialbot generate pdf
Comments fixed NKI-AI/direct#205
Paper is not ready for acceptance yet, the archive is missing
Thanks @georgeyiasemis. Please also
@georgeyiasemis, the reviewers have now completed their checklists. I will now read through the paper, and get back to you if I have any suggested changes.
In the meantime, could you:
- Make a tagged release of your software, and list the version tag of the archived version here.
- Archive the reviewed software in Zenodo or a similar service (e.g., figshare, an institutional repository)
- Check the archival deposit (e.g., in Zenodo) has the correct metadata. This includes the title (should match the paper title) and author list (make sure the list is correct and people who only made a small fix are not on it). You may also add the authors' ORCID.
- Please list the DOI of the archived version here.
Thanks @georgeyiasemis. If you also complete these tasks I can move forward with recommending acceptance.
@georgeyiasemis, the reviewers have now completed their checklists. I will now read through the paper, and get back to you if I have any suggested changes.
- Make a tagged release of your software, and list the version tag of the archived version here (v1.0.1).
- Archive the reviewed software in Zenodo or a similar service (e.g., figshare, an institutional repository) (https://zenodo.org/record/6594702#.YpTPCmjMJL8)
- Check the archival deposit (e.g., in Zenodo) has the correct metadata. This includes the title (should match the paper title) and author list (make sure the list is correct and people who only made a small fix are not on it). You may also add the authors' ORCID.
- Please list the DOI of the archived version here. (DOI: 10.5281/zenodo.6594702)
Hi @osorensen I have completed the checklist
@editorialbot set version v1.0.1
I'm sorry human, I don't understand that. You can see what commands I support by typing:
@editorialbot commands
@editorialbot commands
Hello @osorensen, here are the things you can ask me to do:
# List all available commands
@editorialbot commands
# Add to this issue's reviewers list
@editorialbot add @username as reviewer
# Remove from this issue's reviewers list
@editorialbot remove @username from reviewers
# Get a list of all editors's GitHub handles
@editorialbot list editors
# Assign a user as the editor of this submission
@editorialbot assign @username as editor
# Remove the editor assigned to this submission
@editorialbot remove editor
# Remind an author or reviewer to return to a review after a
# certain period of time (supported units days and weeks)
@editorialbot remind @reviewer in 2 weeks
# Check the references of the paper for missing DOIs
@editorialbot check references
# Perform checks on the repository
@editorialbot check repository
# Adds a checklist for the reviewer using this command
@editorialbot generate my checklist
# Set a value for version
@editorialbot set v1.0.0 as version
# Set a value for archive
@editorialbot set 10.21105/zenodo.12345 as archive
# Set a value for branch
@editorialbot set joss-paper as branch
# Generates the pdf paper
@editorialbot generate pdf
# Recommends the submission for acceptance
@editorialbot recommend-accept
# Flag submission with questionable scope
@editorialbot query scope
# Get a link to the complete list of reviewers
@editorialbot list reviewers
# Open the review issue
@editorialbot start review
@editorialbot set v1.0.1 as version
Done! version is now v1.0.1
@editorialbot set 10.5281/zenodo.6594702 as archive
Done! Archive is now 10.5281/zenodo.6594702
@editorialbot recommend-accept
Attempting dry run of processing paper acceptance...
👋 @openjournals/joss-eics, this paper is ready to be accepted and published.
Check final proof 👉 openjournals/joss-papers#3241
If the paper PDF and the deposit XML files look good in openjournals/joss-papers#3241, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):
OK DOIs
- 10.1117/12.2609876 is OK
- 10.1109/tmi.2021.3075856 is OK
- 10.1007/978-3-030-59713-9_7 is OK
- 10.1016/j.media.2019.01.005 is OK
- 10.1109/tmi.2018.2799231 is OK
- 10.1002/mrm.27201 is OK
- 10.1109/cvpr46437.2021.00523 is OK
- 10.1088/0031-9155/52/7/r01 is OK
- 10.1109/TIT.2006.871582 is OK
- 10.1002/mrm.21391 is OK
- 10.1109/TIT.2005.862083 is OK
- 10.1002/mrm.10171 is OK
- 10.1002/(sici)1522-2594(199911)42:5<952::aid-mrm16>3.0.co;2-s is OK
- 10.1109/msp.2019.2950640 is OK
- 10.48550/ARXIV.2109.08618 is OK
MISSING DOIs
- Errored finding suggestions for "Multi-Coil MRI Reconstruction Challenge – Assessin...", please try later
- Errored finding suggestions for "i-RIM applied to the fastMRI challenge", please try later
- Errored finding suggestions for "fastMRI: An Open Dataset and Benchmarks for Accele...", please try later
- Errored finding suggestions for "Recurrent Variational Network: A Deep Learning Inv...", please try later
INVALID DOIs
- None
@editorialbot check references
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):
OK DOIs
- 10.1117/12.2609876 is OK
- 10.1109/tmi.2021.3075856 is OK
- 10.48550/ARXIV.2011.07952 is OK
- 10.48550/ARXIV.1910.08952 is OK
- 10.1007/978-3-030-59713-9_7 is OK
- 10.1016/j.media.2019.01.005 is OK
- 10.1109/tmi.2018.2799231 is OK
- 10.1002/mrm.27201 is OK
- 10.1109/cvpr46437.2021.00523 is OK
- 10.48550/ARXIV.1811.08839 is OK
- 10.48550/ARXIV.2111.09639 is OK
- 10.1088/0031-9155/52/7/r01 is OK
- 10.1109/TIT.2006.871582 is OK
- 10.1002/mrm.21391 is OK
- 10.1109/TIT.2005.862083 is OK
- 10.1002/mrm.10171 is OK
- 10.1002/(sici)1522-2594(199911)42:5<952::aid-mrm16>3.0.co;2-s is OK
- 10.1109/msp.2019.2950640 is OK
- 10.48550/ARXIV.2109.08618 is OK
MISSING DOIs
- None
INVALID DOIs
- None
@editorialbot generate pdf
@editorialbot recommend-accept
Attempting dry run of processing paper acceptance...
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):
OK DOIs
- 10.1117/12.2609876 is OK
- 10.1109/tmi.2021.3075856 is OK
- 10.48550/ARXIV.2011.07952 is OK
- 10.48550/ARXIV.1910.08952 is OK
- 10.1007/978-3-030-59713-9_7 is OK
- 10.1016/j.media.2019.01.005 is OK
- 10.1109/tmi.2018.2799231 is OK
- 10.1002/mrm.27201 is OK
- 10.1109/cvpr46437.2021.00523 is OK
- 10.48550/ARXIV.1811.08839 is OK
- 10.48550/ARXIV.2111.09639 is OK
- 10.1088/0031-9155/52/7/r01 is OK
- 10.1109/TIT.2006.871582 is OK
- 10.1002/mrm.21391 is OK
- 10.1109/TIT.2005.862083 is OK
- 10.1002/mrm.10171 is OK
- 10.1002/(sici)1522-2594(199911)42:5<952::aid-mrm16>3.0.co;2-s is OK
- 10.1109/msp.2019.2950640 is OK
- 10.48550/ARXIV.2109.08618 is OK
MISSING DOIs
- None
INVALID DOIs
- None
👋 @openjournals/joss-eics, this paper is ready to be accepted and published.
Check final proof 👉 openjournals/joss-papers#3244
If the paper PDF and the deposit XML files look good in openjournals/joss-papers#3244, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept
👋 @georgeyiasemis - I'm the AEiC on duty this week, and I have a few small changes for the paper before we publish it. Please merge NKI-AI/direct#206 or let me know what you disagree with.
👋 @georgeyiasemis - I'm the AEiC on duty this week, and I have a few small changes for the paper before we publish it. Please merge NKI-AI/direct#206 or let me know what you disagree with.
Hi @danielskatz. Thanks for that. Merged it !
@editorialbot recommend-accept
Attempting dry run of processing paper acceptance...
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):
OK DOIs
- 10.1117/12.2609876 is OK
- 10.1109/tmi.2021.3075856 is OK
- 10.48550/ARXIV.2011.07952 is OK
- 10.48550/ARXIV.1910.08952 is OK
- 10.1007/978-3-030-59713-9_7 is OK
- 10.1016/j.media.2019.01.005 is OK
- 10.1109/tmi.2018.2799231 is OK
- 10.1002/mrm.27201 is OK
- 10.1109/cvpr46437.2021.00523 is OK
- 10.48550/ARXIV.1811.08839 is OK
- 10.48550/ARXIV.2111.09639 is OK
- 10.1088/0031-9155/52/7/r01 is OK
- 10.1109/TIT.2006.871582 is OK
- 10.1002/mrm.21391 is OK
- 10.1109/TIT.2005.862083 is OK
- 10.1002/mrm.10171 is OK
- 10.1002/(sici)1522-2594(199911)42:5<952::aid-mrm16>3.0.co;2-s is OK
- 10.1109/msp.2019.2950640 is OK
- 10.48550/ARXIV.2109.08618 is OK
MISSING DOIs
- None
INVALID DOIs
- None
👋 @openjournals/joss-eics, this paper is ready to be accepted and published.
Check final proof 👉 openjournals/joss-papers#3247
If the paper PDF and the deposit XML files look good in openjournals/joss-papers#3247, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept
@editorialbot accept
Doing it live! Attempting automated processing of paper acceptance...
🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦
🚨🚨🚨 THIS IS NOT A DRILL, YOU HAVE JUST ACCEPTED A PAPER INTO JOSS! 🚨🚨🚨
Here's what you must now do:
- Check final PDF and Crossref metadata that was deposited 👉 openjournals/joss-papers#3248
- Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.04278
- If everything looks good, then close this review issue.
- Party like you just published a paper! 🎉🌈🦄💃👻🤘
Any issues? Notify your editorial technical team...
Congratulations to @georgeyiasemis (George Yiasemis) and co-authors!!
And thanks to @estenhl and @sairamgeethanath for reviewing, and @osorensen for editing!
We couldn't do this without you
🎉🎉🎉 Congratulations on your paper acceptance! 🎉🎉🎉
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[](https://doi.org/10.21105/joss.04278)
HTML:
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reStructuredText:
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:target: https://doi.org/10.21105/joss.04278
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