[REVIEW]: open_iA: A tool for processing and visual analysis of industrial computed tomography datasets #1185

whedon · 2019-01-17T22:58:26Z

Submitting author: @codeling (Bernhard Fröhler)
Repository: https://github.com/3dct/open_iA
Version: 2019.03
Editor: @katyhuff
Reviewer: @trallard, @behollister
Archive: 10.5281/zenodo.2591999

Status

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Reviewer instructions & questions

@trallard & @behollister, please carry out your review in this issue by updating the checklist below. If you cannot edit the checklist please:

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The reviewer guidelines are available here: https://joss.theoj.org/about#reviewer_guidelines. Any questions/concerns please let @katyhuff know.

✨ Please try and complete your review in the next two weeks ✨

Review checklist for @trallard

Conflict of interest

As the reviewer I confirm that I have read the JOSS conflict of interest policy and that there are no conflicts of interest for me to review this work.

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 repository url?
License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
Version: 2019.03
Authorship: Has the submitting author (@codeling) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?

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 function 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

Authors: Does the paper.md file include a list of authors with their affiliations?
A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
References: Do all archival references that should have a DOI list one (e.g., papers, datasets, software)?

Review checklist for @behollister

Conflict of interest

As the reviewer I confirm that I have read the JOSS conflict of interest policy and that there are no conflicts of interest for me to review this work.

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 repository url?
License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
Version: 2019.03
Authorship: Has the submitting author (@codeling) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?

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 function 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

Authors: Does the paper.md file include a list of authors with their affiliations?
A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
References: Do all archival references that should have a DOI list one (e.g., papers, datasets, software)?

The text was updated successfully, but these errors were encountered:

whedon · 2019-01-17T22:58:29Z

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @trallard, it looks like you're currently assigned as the reviewer for this paper 🎉.

⭐ Important ⭐

If you haven't already, you should seriously consider unsubscribing from GitHub notifications for this (https://github.com/openjournals/joss-reviews) repository. As a reviewer, you're probably currently watching this repository which means for GitHub's default behaviour you will receive notifications (emails) for all reviews 😿

To fix this do the following two things:

Set yourself as 'Not watching' https://github.com/openjournals/joss-reviews:

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For a list of things I can do to help you, just type:

@whedon commands

whedon · 2019-01-17T22:58:30Z

Attempting PDF compilation. Reticulating splines etc...

whedon · 2019-01-17T22:58:54Z

👉 Check article proof 📄 👈

codeling · 2019-01-28T16:54:22Z

@whedon generate pdf

whedon · 2019-01-28T16:54:24Z

Attempting PDF compilation. Reticulating splines etc...

whedon · 2019-01-28T16:55:02Z

👉 Check article proof 📄 👈

behollister · 2019-02-03T22:14:14Z

@trallard, I'm currently using Linux Build instructions to verify manual installation. Mostly looks okay.

However, I can't verify Windows Build, as I don't have access to a Windows system.

Will it be possible for you or @katyhuff to verify building / installation on Windows?

katyhuff · 2019-02-03T23:30:04Z

I don't have a windows machine either. I can see about setting up a VM, but generally, confirming installation on the reviewer's platform is sufficient for the purpose of a JOSS review.

trallard · 2019-02-04T16:26:55Z

I can conduct my review on a Windows machine 😁 if needed but if this works on Linux I would say it satisfies the installation requirements

behollister · 2019-02-06T02:14:46Z

Currently having issues with various itk header files during compilation. One example:

[ 40%] Building CXX object modules/CMakeFiles/Segmentation.dir/Segmentation/iAWatershedSegmentation.cpp.o
In file included from /home/brad/JOSS/workspace/src/Toolkit/FuzzyCMeans/itkFCMClassifierInitializationImageFilter.h:21:0,
from /home/brad/JOSS/workspace/src/modules/Segmentation/iAFuzzyCMeans.cpp:23:
/home/brad/JOSS/workspace/src/Toolkit/FuzzyCMeans/itkFuzzyClassifierInitializationImageFilter.h:31:10: fatal error: itkMultiThreader.h: No such file or directory
#include "itkMultiThreader.h"

behollister · 2019-02-06T02:19:15Z

ITK_DIR points to /bin-4.13-itk, as directed per build instructions.

"Set ITK_DIR: /workspace/ITK/bin-4.13.0"

Will see about setting path to header files as needed for Linux build...

codeling · 2019-02-06T13:49:43Z

I don't have an immediate idea where this error could come from; the include paths should be set up properly by cmake, which doesn't seem to be the case here. As we have tested it mostly on Debian/Ubuntu-based distributions so far, one possible source of problems I could imagine is the Linux distribution - which one are you on?
The CMake configuration, generation and build of ITK/VTK succeeded?
Also the CMake configuration and generation of open_iA, no errors or warnings there?
Edit: One more thing - it's not explicitly noted in the build descriptions, but you are required to keep the ITK/VTK source directories. Alternatively you could probably install the ITK/VTK libraries to some third location, and then use these install locations as ITK_DIR/VTK_DIR, though we haven't really experimented much with this yet.

behollister · 2019-02-07T19:16:15Z

I'm using 18.04.1 LTS. ITK / VTK compiled fine per the instructions.

After I installed the ITK / VTK builds, CMake picked up those locations. When the open_iA build failed, I switched ITK_DIR to the ITK build directory (then re-ran cmake after a 'make clean').

Best that I start anew, following instructions exactly. Also, I've found that reconfig sometimes fails. Cleaning out the previous build often fixes issues.

Will work through this again on Friday. Thank you for the suggestions. Sorry for any unnecessary delays.

codeling · 2019-02-08T09:45:23Z

What we've been thinking about for some time is providing a "superbuild", i.e. a CMake project that gathers, configures and builds all the required libraries for open_iA. I'm currently trying to put something together in that direction. This should make it easier to set up a working build environment.
Maybe you want to wait on that; though I'm not sure when exactly I will be able to provide this superbuild.

codeling · 2019-02-08T17:57:45Z

There is a somewhat working version of a superbuild available now, see https://github.com/3dct/open_iA-superbuild ; so far we have tested it only on Ubuntu 18.04.1 and 18.10, it should simplify the build procedure significantly! Hope this helps.

behollister · 2019-02-08T18:57:18Z

I'll give it another try before Monday as well. Btw, the Blender project provides a "superbuild" script. You might use that as a starting point.

See:
https://developer.blender.org/diffusion/B/browse/master/build_files/build_environment/install_deps.sh

behollister · 2019-02-08T18:59:27Z

There is a somewhat working version of a superbuild available now, see https://github.com/3dct/open_iA-superbuild ; so far we have tested it only on Ubuntu 18.04.1 and 18.10, it should simplify the build procedure significantly! Hope this helps.

Yes, this should be helpful. Will try it soon!

trallard · 2019-02-11T13:33:20Z

Hi just dropping by, I will pause this review on my side and resume on the 19th of February. I will aim to get it all completed within that week

behollister · 2019-02-20T20:37:54Z

Somewhat delayed recently due to circumstances. I have an opportunity this Thursday / Saturday to finish the review on my end, in its entirety.

behollister · 2019-02-21T21:57:41Z

Superbuild works fine on my system. Trying to verify functionality now...

@codeling, is there an automated test suite & data for each area of functionality claimed in https://github.com/3dct/open_iA/wiki/User-Guide? I don't see this provided as a script in the source tree, or any installation of sample data.

@katyhuff, what degree of coverage is needed for testing functionality? For example, each use case for a given data set could itself be tested with each file type supported:
https://github.com/3dct/open_iA/wiki/File-Formats

codeling · 2019-02-22T11:53:19Z

At this point, we only have limited automated tests available for some library functions.
See the iASimpleTester, used in tests of the iAStringHelper and in two tests in the RandomWalker module.

We were planning to include more tests but haven't found the time to do so yet.

The existing tests are run as part of our daily (Mon-Fri) CDash build. Its latest results are available here.

Since we recently added the possibility to run filters in the modules via command line, we are planning to add tests for all filters and file formats there.

Most of our visual analytics tools are heavily GUI- and interaction-based.
We do provide test datasets for most of them on our Releases page (the TestDatasets-2018.12.zip attached to our latest release 2018.12).
We currently however do not test these automatically, but would be very glad about pointers how we can easily achieve that!

behollister · 2019-02-27T00:05:41Z

I have completed my review. See checklist.
@katyhuff, @trallard, and @codeling, please let me know if you have any questions or concerns.

katyhuff · 2019-02-27T15:03:45Z

Sorry for the delay in responding to your question, @behollister .

what degree of coverage is needed for testing functionality? For example, each use case for a given data set could itself be tested with each file type supported: https://github.com/3dct/open_iA/wiki/File-Formats

Generally speaking, my approach to this is to assess whether the scientific functionality of the work is demonstrated and confimed by the tests, so full coverage is certainly not required, but test coverage should confirm the capability claims of the work.

Anyway -- thanks for conducting your review @behollister !

katyhuff · 2019-02-27T15:04:57Z

@trallard : I know you estimated review completion around this time. I hope that's still the target timeline! Thank you!

katyhuff · 2019-03-07T14:21:38Z

@whedon generate pdf

katyhuff · 2019-03-21T12:35:00Z

@whedon accept

whedon · 2019-03-21T12:35:03Z

Attempting dry run of processing paper acceptance...

codeling · 2019-03-21T12:35:28Z

sorry for the delay in responding - am still on vacation

Ah yes forgot that - sorry for bothering you on vacation!

I think this can be accepted with the DOI including your interleaved changes, as they seem mostly minor. I'll move forward with that.

Great, thanks!

whedon · 2019-03-21T12:35:29Z

Check final proof 👉 openjournals/joss-papers#569

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#569, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true

whedon · 2019-03-21T12:35:38Z


OK DOIs

- 10.1111/cgf.12896 is OK
- 10.1109/TVCG.2010.214 is OK
- 10.1109/PACIFICVIS.2015.7156377 is OK
- 10.1109/TVCG.2016.2582158 is OK
- 10.1016/j.cag.2015.04.001 is OK
- 10.1109/PacificVis.2014.52 is OK
- 10.1111/cgf.12895 is OK
- 10.1109/TVCG.2013.177 is OK
- 10.1109/VAST.2016.7883516 is OK
- 10.1111/cgf.12365 is OK
- 10.1109/TVCG.2018.2864510 is OK

MISSING DOIs

- None

INVALID DOIs

- None

katyhuff · 2019-03-21T12:40:30Z

Thanks @codeling for your submission, patience, and cooperation with the process!

Thank you @trallard and @behollister for your detailed reviews!

This paper should be ready to accept @openjournals/joss-eics - over to you!

ooo · 2019-03-21T12:40:32Z

👋 Hey @katyhuff...

Letting you know, @trallard is currently OOO until Sunday, April 7th 2019. ❤️

arfon · 2019-03-21T12:45:16Z

@whedon accept

whedon · 2019-03-21T12:45:18Z

Attempting dry run of processing paper acceptance...

whedon · 2019-03-21T12:45:27Z


OK DOIs

- 10.1111/cgf.12896 is OK
- 10.1109/TVCG.2010.214 is OK
- 10.1109/PACIFICVIS.2015.7156377 is OK
- 10.1109/TVCG.2016.2582158 is OK
- 10.1016/j.cag.2015.04.001 is OK
- 10.1109/PacificVis.2014.52 is OK
- 10.1111/cgf.12895 is OK
- 10.1109/TVCG.2013.177 is OK
- 10.1109/VAST.2016.7883516 is OK
- 10.1111/cgf.12365 is OK
- 10.1109/TVCG.2018.2864510 is OK

MISSING DOIs

- None

INVALID DOIs

- None

whedon · 2019-03-21T12:45:47Z

Check final proof 👉 openjournals/joss-papers#570

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#570, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true

arfon · 2019-03-21T12:47:09Z

@whedon accept deposit=true

whedon · 2019-03-21T12:47:13Z

Doing it live! Attempting automated processing of paper acceptance...

whedon · 2019-03-21T12:47:47Z

🚨🚨🚨 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 👉 Creating pull request for 10.21105.joss.01185 joss-papers#571
Wait a couple of minutes to verify that the paper DOI resolves https://doi.org/10.21105/joss.01185
If everything looks good, then close this review issue.
Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? notify your editorial technical team...

arfon · 2019-03-21T12:50:12Z

@trallard, @behollister - many thanks for your reviews here and to @katyhuff for editing this submission ✨

@codeling - your paper is now accepted into JOSS ⚡🚀💥

ooo · 2019-03-21T12:50:15Z

👋 Hey @arfon...

Letting you know, @trallard is currently OOO until Sunday, April 7th 2019. ❤️

whedon · 2019-03-21T12:50:15Z

🎉🎉🎉 Congratulations on your paper acceptance! 🎉🎉🎉

If you would like to include a link to your paper from your README use the following code snippets:

Markdown:
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HTML:
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  <img src="http://joss.theoj.org/papers/10.21105/joss.01185/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: http://joss.theoj.org/papers/10.21105/joss.01185/status.svg
   :target: https://doi.org/10.21105/joss.01185

This is how it will look in your documentation:

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whedon assigned katyhuff Jan 17, 2019

whedon added the review label Jan 17, 2019

whedon mentioned this issue Jan 17, 2019

[PRE REVIEW]: open_iA: A tool for processing and visual analysis of industrial computed tomography datasets #1139

Closed

This was referenced Jan 28, 2019

[JOSS REVIEW] Statement of need 3dct/open_iA#31

Closed

[JOSS REVIEW] Install instructions 3dct/open_iA#32

Closed

whedon added the accepted label Mar 21, 2019

arfon closed this as completed Mar 21, 2019

whedon added published Papers published in JOSS recommend-accept Papers recommended for acceptance in JOSS. labels Mar 2, 2020

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[REVIEW]: open_iA: A tool for processing and visual analysis of industrial computed tomography datasets #1185

[REVIEW]: open_iA: A tool for processing and visual analysis of industrial computed tomography datasets #1185

Comments

whedon commented Jan 17, 2019 • edited Loading

Status

Reviewer instructions & questions

Review checklist for @trallard

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

Review checklist for @behollister

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

whedon commented Jan 17, 2019

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codeling commented Jan 28, 2019

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behollister commented Feb 3, 2019

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