[PRE REVIEW]: IRXCT: Iterative Reconstruction and visualization application for X-ray Computed Tomography #1588

whedon · Jul 21, 2019

Submitting author: @dntrinca (D Narcis Trinca)
Repository: https://github.com/dntrinca/IRXCT
Version: 1.0
Editor: @usethedata
Reviewer: Pending

Author instructions

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

@dntrinca if you have any suggestions for potential reviewers then please mention them here in this thread. In addition, this list of people have already agreed to review for JOSS and may be suitable for this submission.

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 · Jul 21, 2019

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks.

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

What happens now?

This submission is currently in a pre-review state which means we are waiting for an editor to be assigned and for them to find some reviewers for your submission. This may take anything between a few hours to a couple of weeks. Thanks for your patience 😸

You can help the editor by looking at this list of potential reviewers to identify individuals who might be able to review your submission (please start at the bottom of the list). Also, feel free to suggest individuals who are not on this list by mentioning their GitHub handles here.

whedon · Jul 21, 2019

Attempting PDF compilation. Reticulating splines etc...

whedon · Jul 21, 2019

PDF failed to compile for issue #1588 with the following error:

Can't find any papers to compile :-(

danielskatz · Jul 21, 2019

@dntrinca - this submission has some problems - the source code being in a zip file is one. We expect to see the software in a version control repository (eg github) but in a way that the software can be updated via pull requests and changes - a zip file doesn't really work for that.

danielskatz · Jul 21, 2019

@whedon generate pdf

whedon · Jul 21, 2019

Attempting PDF compilation. Reticulating splines etc...

whedon · Jul 21, 2019

PDF failed to compile for issue #1588 with the following error:

/app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-5a9319b684e6/lib/whedon.rb:115:in check_fields': Paper YAML header is missing expected fields: affiliations (RuntimeError) from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-5a9319b684e6/lib/whedon.rb:80:in initialize'
from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-5a9319b684e6/lib/whedon/processor.rb:36:in new' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-5a9319b684e6/lib/whedon/processor.rb:36:in set_paper'
from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-5a9319b684e6/bin/whedon:55:in prepare' from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.3/lib/thor/command.rb:27:in run'
from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.3/lib/thor/invocation.rb:126:in invoke_command' from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.3/lib/thor.rb:387:in dispatch'
from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.3/lib/thor/base.rb:466:in start' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-5a9319b684e6/bin/whedon:116:in <top (required)>'
from /app/vendor/bundle/ruby/2.4.0/bin/whedon:23:in load' from /app/vendor/bundle/ruby/2.4.0/bin/whedon:23:in

'

danielskatz · Jul 21, 2019

Also, please follow the example paper to use affiliations correctly - they need to be marked as integer indexes in the authors section, then these indexes need to be used in the affiliations section.

Once you have made changes, please feel free to enter @whedon generate pdf here as a new comment in this issue to try to build the paper again.

dntrinca · Jul 22, 2019

Dear Daniel Skatz,

I just made the necessary corrections you have mentioned.

Best,
D Narcis

dntrinca · Jul 22, 2019

@whedon generate pdf

whedon · Jul 22, 2019

Attempting PDF compilation. Reticulating splines etc...

whedon · Jul 22, 2019

PDF failed to compile for issue #1588 with the following error:

Error reading bibliography ./paper.bib (line 24, column 3):
unexpected "j"
expecting space or "}"
Error running filter pandoc-citeproc:
Filter returned error status 1
Looks like we failed to compile the PDF

dntrinca · Jul 22, 2019

@whedon generate pdf

whedon · Jul 22, 2019

Attempting PDF compilation. Reticulating splines etc...

whedon · Jul 22, 2019

PDF failed to compile for issue #1588 with the following error:

Error reading bibliography ./paper.bib (line 29, column 1):
unexpected "@"
expecting space, ",", white space or "}"
Error running filter pandoc-citeproc:
Filter returned error status 1
Looks like we failed to compile the PDF

dntrinca · Jul 22, 2019

@whedon generate pdf

whedon · Jul 22, 2019

Attempting PDF compilation. Reticulating splines etc...

whedon · Jul 22, 2019

👉 Check article proof 📄 👈

dntrinca · Jul 22, 2019

Dear Daniel S Katz,

Sorry for mispelling your name in a previous reply.

Best,
D Narcis

danielskatz · Jul 22, 2019

Please carefully proofread your submission, and add DOIs to the bib entries for papers that have DOIs, again following the example in the JOSS documentation.

danielskatz · Jul 22, 2019

👋 @usethedata - would you be willing to edit this submission?

dntrinca · Jul 22, 2019

@whedon generate pdf

whedon · Jul 22, 2019

Attempting PDF compilation. Reticulating splines etc...

whedon · Jul 22, 2019

👉 Check article proof 📄 👈

dntrinca · Jul 22, 2019

@whedon generate pdf

whedon · Jul 22, 2019

Attempting PDF compilation. Reticulating splines etc...

whedon · Jul 22, 2019

👉 Check article proof 📄 👈

dntrinca · Jul 22, 2019

@whedon generate pdf

whedon · Jul 30, 2019

Attempting PDF compilation. Reticulating splines etc...

whedon · Jul 30, 2019

👉 Check article proof 📄 👈

dntrinca · Jul 30, 2019

@whedon generate pdf

whedon · Jul 30, 2019

Attempting PDF compilation. Reticulating splines etc...

whedon · Jul 30, 2019

👉 Check article proof 📄 👈

dntrinca · Jul 30, 2019

@whedon generate pdf

whedon · Jul 30, 2019

Attempting PDF compilation. Reticulating splines etc...

whedon · Jul 30, 2019

👉 Check article proof 📄 👈

dntrinca · Jul 30, 2019

@whedon generate pdf

whedon · Jul 30, 2019

Attempting PDF compilation. Reticulating splines etc...

whedon · Jul 30, 2019

PDF failed to compile for issue #1588 with the following error:

Error reading bibliography ./paper.bib (line 62, column 1):
unexpected end of input
expecting space, ",", white space or "}"
Error running filter pandoc-citeproc:
Filter returned error status 1
Looks like we failed to compile the PDF

dntrinca · Jul 30, 2019

@whedon generate pdf

whedon · Jul 30, 2019

Attempting PDF compilation. Reticulating splines etc...

whedon · Jul 30, 2019

👉 Check article proof 📄 👈

dntrinca · Jul 30, 2019

@whedon generate pdf

whedon · Jul 30, 2019

Attempting PDF compilation. Reticulating splines etc...

whedon · Jul 30, 2019

👉 Check article proof 📄 👈

dntrinca · Jul 30, 2019

@usethedata , I just finished the necessary additions; let me know if this is OK..Best, D Narcis

usethedata · Aug 4, 2019

@dntrinca My apologies for being less responsive than I should. It's been a crazy week. I'll go over things and start working on getting reviewers.

dntrinca · Aug 5, 2019

@usethedata Dear Bruce, That is very good, I am looking forward to hear from you soon. Best, D Narcis

usethedata · Aug 26, 2019

@brechmos @martlj @rlizzo Would a couple of you be willing to review this JOSS submission?

brechmos · Aug 27, 2019

Typically I would be more than happy to, but I do not have access to a Windows machine and have never done Windows programming. Given that, I would find it hard to do a proper review of the code and software. :/ Sorry.

dntrinca · Sep 10, 2019

@usethedata Dear Bruce, Did you find any reviewers ? I know it might be hard to find, as most of the scientific codes are in Matlab in general..But myself I wrote in Visual C++ to do a real Windows application, professionally written, and which does not require anything to be installed on a Windows system..

Given the situation, do you think it is a priority to review the code ? The submission has a step-by step manual that shows all the functionalities if it is followed properly..

Best, and let me know when you have some news..
D Narcis

martlj · Sep 11, 2019

Hi, apologies for the slow reply. Medical CT is a bit outside of my usual domain and I don't use Windows either so I'm not best placed to give a thorough review of this I'm afraid.

dntrinca · Sep 13, 2019

@abhishekbajpayee @rlizzo @casperdcl Hello, is any of you willing to review this submission concerning a Windows program for tomography reconstruction? Best Regards, D Narcis

dntrinca · Sep 16, 2019

@usethedata @danielskatz Hello, with this message I want to tell you that I withdraw my work from this journal..

danielskatz · Sep 16, 2019

I'm sorry to hear this, and that we didn't do a better job with this review.

casperdcl · Sep 16, 2019

yes sorry I work more in PET and PET-MRI, and also prefer avoiding windows and avoiding matlab.

whedon added the pre-review label Jul 21, 2019

whedon added the TeX label Jul 21, 2019

danielskatz added the withdrawn label Sep 16, 2019

danielskatz closed this Sep 16, 2019

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[PRE REVIEW]: IRXCT: Iterative Reconstruction and visualization application for X-ray Computed Tomography #1588

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whedon commented Jul 21, 2019 •

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