[REVIEW]: DIRECT: Deep Image REConstruction Toolkit

editorialbot commented 2 years ago

Submitting author: !--author-handle-->@georgeyiasemis@osorensen<!--end-editor-- Reviewers: @estenhl, @sairamgeethanath Archive: 10.5281/zenodo.6594702

Status

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Markdown: [![status](https://joss.theoj.org/papers/150119fd46692dad9448a26eca669a77/status.svg)](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

📝 Checklist for @estenhl

📝 Checklist for @sairamgeethanath

editorialbot commented 2 years ago

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:

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For example, to regenerate the paper pdf after making changes in the paper's md or bib files, type:

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editorialbot commented 2 years ago

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

editorialbot commented 2 years ago

Wordcount for paper.md is 1142

editorialbot commented 2 years ago

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

editorialbot commented 2 years ago

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

estenhl commented 2 years ago

Review checklist for @estenhl

Conflict of interest

[x] 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

[x] I confirm that I read and will adhere to the JOSS code of conduct.

General checks

[x] Repository: Is the source code for this software available at the https://github.com/NKI-AI/direct?
[x] License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
[x] 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?
[x] Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines

Functionality

[x] Installation: Does installation proceed as outlined in the documentation?
[x] Functionality: Have the functional claims of the software been confirmed?
[x] 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

[x] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
[x] Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
[x] Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
[x] Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
[x] Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?
[x] 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

[x] Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
[x] 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?
[x] State of the field: Do the authors describe how this software compares to other commonly-used packages?
[x] Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
[x] 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?

sairamgeethanath commented 2 years ago

@georgeyiasemis - Could you please let me know if there is a way for me to access the Docker image?

georgeyiasemis commented 2 years ago

Hi @sairamgeethanath this is it: https://github.com/NKI-AI/direct/tree/main/docker

sairamgeethanath commented 2 years ago

@georgeyiasemis Many thanks! If it is not any trouble, could you also please fix the broken link on your documentation page?

estenhl commented 2 years ago

@editorialbot commands

editorialbot commented 2 years ago

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

osorensen commented 2 years ago

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.

sairamgeethanath commented 2 years ago

@osorensen I will get this done the week after ISMRM (13th May).

osorensen commented 2 years ago

Thanks @sairamgeethanath!

sairamgeethanath commented 2 years ago

Review checklist for @sairamgeethanath

Conflict of interest

[x] 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

[x] I confirm that I read and will adhere to the JOSS code of conduct.

General checks

[x] Repository: Is the source code for this software available at the https://github.com/NKI-AI/direct?
[x] License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
[x] 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?
[x] Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines

Functionality

[x] Installation: Does installation proceed as outlined in the documentation?
[x] Functionality: Have the functional claims of the software been confirmed?
[x] 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

[x] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
[x] Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
[x] Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
[x] Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
[x] Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?
[x] 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

[x] Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
[x] 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?
[x] State of the field: Do the authors describe how this software compares to other commonly-used packages?
[x] Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
[x] 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?

sairamgeethanath commented 2 years ago

@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 commented 2 years ago

@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 commented 2 years ago

@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!

sairamgeethanath commented 2 years ago

I will test it by the end of the week.

Best, Sairam

On Mon, May 16, 2022 at 1:53 PM George Yiasemis @.***> wrote:

@georgeyiasemis https://github.com/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 https://github.com/NKI-AI/direct/issues/191 that @estenhl https://github.com/estenhl and I both reported? I will then check off the remaining items.

@sairamgeethanath https://github.com/sairamgeethanath The docker issue is fixed!

— Reply to this email directly, view it on GitHub https://github.com/openjournals/joss-reviews/issues/4278#issuecomment-1127965616, or unsubscribe https://github.com/notifications/unsubscribe-auth/AHLQWAJVPXWAG7NWP33B7ZTVKKDRNANCNFSM5R4FGQRA . You are receiving this because you were mentioned.Message ID: @.***>

-- Sairam Geethanath, Ph.D. “There are plenty of compelling reasons to push MRI to be more powerful, but that’s one facet of advancing the field. Another is delivering it to the world.”

sairamgeethanath commented 2 years ago

@georgeyiasemis I have checked off my list.

sairamgeethanath commented 2 years ago

Review checklist for @sairamgeethanath

Conflict of interest

[x] 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

[x] I confirm that I read and will adhere to the JOSS code of conduct.

General checks

[x] Repository: Is the source code for this software available at the https://github.com/NKI-AI/direct?
[x] License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
[x] 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?
[x] Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines

Functionality

[x] Installation: Does installation proceed as outlined in the documentation?
[x] Functionality: Have the functional claims of the software been confirmed?
[x] 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

[x] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
[x] Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
[x] Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
[x] Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
[x] Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?
[x] 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

[x] Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
[x] 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?
[x] State of the field: Do the authors describe how this software compares to other commonly-used packages?
[x] Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
[x] 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?

osorensen commented 2 years ago

@editorialbot generate pdf

editorialbot commented 2 years ago

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

osorensen commented 2 years ago

@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.

osorensen commented 2 years ago

@editorialbot check references

editorialbot commented 2 years ago

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

georgeyiasemis commented 2 years ago

@editorialbot generate pdf

editorialbot commented 2 years ago

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

georgeyiasemis commented 2 years ago

Comments fixed https://github.com/NKI-AI/direct/issues/205

editorialbot commented 2 years ago

Paper is not ready for acceptance yet, the archive is missing

osorensen commented 2 years ago

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 commented 2 years ago

@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.

[x] Make a tagged release of your software, and list the version tag of the archived version here (v1.0.1).
[x] Archive the reviewed software in Zenodo or a similar service (e.g., figshare, an institutional repository) (https://zenodo.org/record/6594702#.YpTPCmjMJL8)
[x] 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.
[x] Please list the DOI of the archived version here. (DOI: 10.5281/zenodo.6594702)

georgeyiasemis commented 2 years ago

Hi @osorensen I have completed the checklist

osorensen commented 2 years ago

@editorialbot set version v1.0.1

editorialbot commented 2 years ago

I'm sorry human, I don't understand that. You can see what commands I support by typing:

@editorialbot commands

osorensen commented 2 years ago

@editorialbot commands

editorialbot commented 2 years ago

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
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# 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

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osorensen commented 2 years ago

@editorialbot set v1.0.1 as version

editorialbot commented 2 years ago

Done! version is now v1.0.1

osorensen commented 2 years ago

@editorialbot set 10.5281/zenodo.6594702 as archive

editorialbot commented 2 years ago

Done! Archive is now 10.5281/zenodo.6594702

osorensen commented 2 years ago

@editorialbot recommend-accept

editorialbot commented 2 years ago

Attempting dry run of processing paper acceptance...

editorialbot commented 2 years ago

:wave: @openjournals/joss-eics, this paper is ready to be accepted and published.

Check final proof :point_right: https://github.com/openjournals/joss-papers/pull/3241

If the paper PDF and the deposit XML files look good in https://github.com/openjournals/joss-papers/pull/3241, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

editorialbot commented 2 years ago

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

georgeyiasemis commented 2 years ago

@editorialbot check references

editorialbot commented 2 years ago

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

georgeyiasemis commented 2 years ago

@editorialbot generate pdf

editorialbot commented 2 years ago

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

danielskatz commented 2 years ago

@editorialbot recommend-accept

openjournals / joss-reviews