Windows installation for Slicer Radiomics not working

[JoostJM]

When installing SlicerRadiomics from extension manager, installation works, however, the module cannot be loaded due to an error with the pyYAML library. When you comment out import pykwalify in featureextractor.py (in the installed site-packages), module loads fine and works without issue (pykwalify not needed in slicer extension)

[pieper]

Until this is fixed, the file to change:

C:/Users/username/AppData/Roaming/NA-MIC/Extensions-revision/SlicerRadiomics/lib/site-packages/radiomics/featureextractor.py

Where revision is something like 26083 depending on the nightly version of Slicer.

Line 9 should be changed from:

import pykwalify.core

to:

# import pykwalify.core

[pieper]

See user discussion here: https://discourse.slicer.org/t/qunatitative-features-with-eeterogeneitycad/518/8

[pieper]

@JoostJM was this issue fixed by d0a77c?

[JoostJM]

@pieper, d0a77c presents a temporary workaround. Additionally, that fix won't take effect until the extension is rebuilt and repackaged.

[fedorov]

Joost, the extension is rebuilt and packaged automatically on each source code update.

[pieper]

I just tested the current nightly build on windows (2017-07-16) and confirmed that the Radiomics extension is working as expected. So the workaround is in place but the underlying issue remains.

[jcfr]

Now #16 is fixed, I will address this next week.

[JoostJM]

@jcfr, what is the status of this issue?

[jcfr]

Thanks for the note. I will follow up later today or tomorrow.

…

On Nov 13, 2017 10:14 AM, "Joost van Griethuysen" ***@***.***> wrote: @jcfr <https://github.com/jcfr>, what is the status of this issue? — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#23 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AANXo3NgnR67o1cW-yYqfKf_Wt9pG8r4ks5s2Fy7gaJpZM4N578T> .

[renjiliang]

I have installed radiomics extension，but the following bug was always appeared. How to resolve the problem?

File "C:/Users/Administrator/AppData/Roaming/NA-MIC/Extensions-26309/SlicerRadiomics/lib/Slicer-4.7/qt-scripted-modules/SlicerRadiomics.py", line 535, in run
enabledImageTypes)
File "C:/Users/Administrator/AppData/Roaming/NA-MIC/Extensions-26309/SlicerRadiomics/lib/Slicer-4.7/qt-scripted-modules/SlicerRadiomics.py", line 448, in calculateFeatures
extractor.disableAllImagesTypes()

[renjiliang]

I did not find import "pykwalify.core" in file featureextractor

[JoostJM]

@renjiliang, That's correct, pykwalify.core is currently disabled due to this issue. We are working on a fix. The error you received is unrelated and due to a typo bug in the SlicerRadiomics Code. I corrected this just now in 8c4ffc7. This change will be incorporated in tonights nightly build of slicer, so to fix it, reinstall the latest nightly of slicer tomorrow, or apply the fix yourself in the SlicerRadiomics python file, which is located somewhere in C:\Users\<USER>\AppData\Roaming\NA-MIC\Extensions-26442\SlicerRadiomics\Lib\Slicer-4.7\qt-scripted-modules (It is possible that the extensions number is different, but the NA-MIC folder contains all your installed Slicer Extensions, including SlicerRadiomics).

[fedorov]

It looks like now build is failing because a warning is interpreted as an error:

http://slicer.cdash.org/viewBuildError.php?buildid=1148769

  D:\D\N\Slicer-1-build\python-install\Lib\site-packages\pip\commands\install.py:194: UserWarning: 
  Disabling all use of wheels due to the use of --build-options / --global-options / --install-options.

[jcfr]

Yes.

I have been working on address this, it will be fixed later today.

[jcfr]

Extension now available on all platform: http://slicer.cdash.org/index.php?project=Slicer4&filtercount=1&showfilters=1&field1=buildname&compare1=63&value1=Radiomics

After releasing Slicer 4.8.1, it will also be available with the stable release.