Joss-reviews: [PRE REVIEW]: ivadomed: A Medical Imaging Deep Learning Toolbox
Submitting author: @charleygros (Charley Gros)
Repository: https://github.com/ivadomed/ivadomed
Version: 2.5.0
Editor: @cMadan
Reviewer: Pending
Managing EiC: Kristen Thyng
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Author instructions
Thanks for submitting your paper to JOSS @charleygros. Currently, there isn't an JOSS editor assigned to your paper.
The author's suggestion for the handling editor is @arokem.
@charleygros 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).
Editor instructions
The JOSS submission bot @whedon is here to help you find and assign reviewers and start the main review. To find out what @whedon can do for you type:
@whedon commands
whedon
All 18 comments
Hello human, I'm @whedon, a robot that can help you with some common editorial tasks.
:warning: JOSS reduced service mode :warning:
Due to the challenges of the COVID-19 pandemic, JOSS is currently operating in a "reduced service mode". You can read more about what that means in our blog post.
For a list of things I can do to help you, just type:
@whedon commands
For example, to regenerate the paper pdf after making changes in the paper's md or bib files, type:
@whedon generate pdf
Software report (experimental):
github.com/AlDanial/cloc v 1.84 T=0.62 s (191.8 files/s, 32063.7 lines/s)
-------------------------------------------------------------------------------
Language files blank comment code
-------------------------------------------------------------------------------
Python 65 2884 3510 9196
JSON 13 2 0 1076
reStructuredText 18 563 273 1068
TeX 1 29 0 283
Markdown 6 127 0 273
Bourne Shell 8 75 131 220
YAML 4 15 14 84
DOS Batch 1 8 1 26
make 1 5 7 13
CSS 1 0 1 4
RobotFramework 1 0 0 2
-------------------------------------------------------------------------------
SUM: 119 3708 3937 12245
-------------------------------------------------------------------------------
Statistical information for the repository '1a28f68744d0d8badfad9ab2' was
gathered on 2020/11/11.
The following historical commit information, by author, was found:
Author Commits Insertions Deletions % of changes
Alexandru Jora 7 12 29 0.06
AnBucquet 83 2553 1221 5.66
BUCQUET Anthime 3 11 2 0.02
Christian S. Perone 8 527 20 0.82
Julien Cohen-Adad 40 745 310 1.58
Lucas Rouhier 33 144 139 0.42
Nick 2 11 23 0.05
Olivier 25 121 127 0.37
Olivier Vincent 35 339 148 0.73
Valentine-LL 7 15 18 0.05
ValentineLL 27 521 218 1.11
andreanne-lemay 563 10581 6911 26.24
bsauty 1 1 1 0.00
charleygros 1415 21212 12583 50.69
lrouhier 132 4060 2131 9.29
olivier 62 948 617 2.35
olix86 16 318 57 0.56
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
Alexandru Jora 8 66.7 4.4 0.00
AnBucquet 771 30.2 9.9 10.89
Christian S. Perone 90 17.1 11.1 2.22
Julien Cohen-Adad 488 65.5 7.9 35.86
Nick 10 90.9 6.8 100.00
Olivier 278 229.8 7.7 10.79
Olivier Vincent 2 0.6 12.4 0.00
Valentine-LL 7 46.7 15.3 28.57
ValentineLL 206 39.5 16.6 8.25
andreanne-lemay 4359 41.2 4.9 7.18
charleygros 6344 29.9 6.1 12.97
lrouhier 2765 68.1 2.2 9.69
olix86 262 82.4 2.9 9.16
PDF failed to compile for issue #2836 with the following error:
ORCID looks malformed
/app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-54ca145bf448/lib/whedon.rb:155:in block in check_orcids': Problem with ORCID (XX) for Lucas Rouhier (RuntimeError)
from /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-54ca145bf448/lib/whedon.rb:153:ineach'
from /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-54ca145bf448/lib/whedon.rb:153:in check_orcids'
from /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-54ca145bf448/lib/whedon.rb:90:ininitialize'
from /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-54ca145bf448/lib/whedon/processor.rb:38:in new'
from /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-54ca145bf448/lib/whedon/processor.rb:38:inset_paper'
from /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-54ca145bf448/bin/whedon:58:in prepare'
from /app/vendor/bundle/ruby/2.6.0/gems/thor-0.20.3/lib/thor/command.rb:27:inrun'
from /app/vendor/bundle/ruby/2.6.0/gems/thor-0.20.3/lib/thor/invocation.rb:126:in invoke_command'
from /app/vendor/bundle/ruby/2.6.0/gems/thor-0.20.3/lib/thor.rb:387:indispatch'
from /app/vendor/bundle/ruby/2.6.0/gems/thor-0.20.3/lib/thor/base.rb:466:in start'
from /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-54ca145bf448/bin/whedon:131:inload'
from /app/vendor/bundle/ruby/2.6.0/bin/whedon:23:in
whedon
on 11 Nov 2020
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):
OK DOIs
- 10.1016/j.nicl.2018.03.029 is OK
- 10.1016/j.neuroimage.2018.09.081 is OK
- 10.14245/ns.1938396.198 is OK
- 10.1038/sdata.2016.44 is OK
- 10.1016/j.neucom.2019.01.103 is OK
- 10.1109/CVPR.2016.90 is OK
MISSING DOIs
- 10.1109/iccv.2019.00707 may be a valid DOI for title: Adaptive Wing Loss for Robust Face Alignment via Heatmap Regression
- 10.1007/978-3-030-00928-1_74 may be a valid DOI for title: Exploring Uncertainty Measures in Deep Networks for Multiple Sclerosis Lesion Detection and Segmentation
- 10.1007/978-3-319-46723-8_54 may be a valid DOI for title: Hemis: Hetero-modal image segmentation
- 10.1109/iccvw.2017.9 may be a valid DOI for title: Count-ception: Counting by Fully Convolutional Redundant Counting
- 10.1016/j.neuroimage.2018.11.042 may be a valid DOI for title: QuickNAT: A Fully Convolutional Network for Quick and Accurate Segmentation of Neuroanatomy
- 10.1109/3dv.2016.79 may be a valid DOI for title: V-net: Fully convolutional neural networks for volumetric medical image segmentation
- 10.1007/978-3-030-00931-1_70 may be a valid DOI for title: 3D segmentation with exponential logarithmic loss for highly unbalanced object sizes
INVALID DOIs
- None
@cMadan are you interested in editing this submission?
kthyng
on 11 Nov 2020
@whedon invite @cMadan as editor
kthyng
on 11 Nov 2020
@cMadan has been invited to edit this submission.
whedon
on 11 Nov 2020
@kthyng, sure, I can take this one.
cMadan
on 11 Nov 2020
@whedon assign @cMadan as editor
cMadan
on 11 Nov 2020
OK, the editor is @cMadan
whedon
on 11 Nov 2020
@charleygros, do you have any suggestions for reviewers? (See initial comment in this issue.)
It would also be great if you can add DOIs for articles that are currently missing them in the bib. See some suggestions earlier in this issue (but please double check!).
cMadan
on 11 Nov 2020
Many thanks @cMadan for accepting to be the editor for this submission!
And apologies for the delayed reply.
@charleygros, do you have any suggestions for reviewers? (See initial comment in this issue.)
Suggestions for reviewers from the provided list:
- rlizzo
- NMontanaBrown
- Bsingstad
- justusschock
- lbugnon
- esadr
- fernandoandreotti
It would also be great if you can add DOIs for articles that are currently missing them in the bib. See some suggestions earlier in this issue (but please double check!).
Sure, I'm happy do this ASAP and will keep you posted.
charleygros
on 15 Nov 2020
@whedon generate pdf
charleygros
on 15 Nov 2020
PDF failed to compile for issue #2836 with the following error:
Error reading bibliography file paper.bib:
(line 107, column 10):
unexpected ","
expecting white space
Looks like we failed to compile the PDF
whedon
on 15 Nov 2020
@whedon generate pdf
charleygros
on 15 Nov 2020
PDF failed to compile for issue #2836 with the following error:
[WARNING] Could not convert image '/tmp/tex2pdf.-02aca882a10b72c1/78fb38f212fa49029aff24c669a39648d9b4e68b.vs': Cannot load file
Jpeg Invalid marker used
PNG Invalid PNG file, signature broken
Bitmap Invalid Bitmap magic identifier
GIF Invalid Gif signature : 404: N
HDR Invalid radiance file signature
Tiff Invalid endian tag value
TGA not enough bytes
Error producing PDF.
! LaTeX Error: Cannot determine size of graphic in /tmp/tex2pdf.-02aca882a10b72
c1/78fb38f212fa49029aff24c669a39648d9b4e68b.vs (no BoundingBox).
See the LaTeX manual or LaTeX Companion for explanation.
Type H
...
l.398 ...b38f212fa49029aff24c669a39648d9b4e68b.vs}
Looks like we failed to compile the PDF
whedon
on 15 Nov 2020
@whedon generate pdf
charleygros
on 15 Nov 2020
:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:
whedon
on 15 Nov 2020
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Most helpful comment
:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left: