ImportError: No module named radiomics about slicerradiomics HOT 7 CLOSED

@gregsharp long time no see!

I assume you built using the superbuild approach - can you confirm? Did pyradiomics build as well? Were there any errors?

It is not clear what is the linux-related issue we are experiencing, it might be specific to the dashboard. I can try build/install on linux on Monday when I am back in the office. I am not sure I tried that.

from slicerradiomics.

@gregsharp I tried on linux, and I see what you mean. I can't figure out myself how to set up the extra directories so that it can find the dependency python packages! I think it is supposed to somehow configure the launcher with the extra paths, but I don't know how it works.

@jcfr here is what I tried (to be as close to the dashboard process as possible):

1. Build SlicerRadiomics and then make package in inner-build
2. Add <package>/lib/python2.7/site-packages and <package>/lib/Slicer-4.7/qt-scripted-modules in Application settings > Modules extra paths.

This does not work - I cannot import the radiomics package. Do you know what is going on?

Dashboard behavior is different today http://slicer.cdash.org/viewBuildError.php?buildid=1080469 from what we had before in #16. I did not have that problem when I did build+package on my Ubuntu.

from slicerradiomics.

In a nutshell, it would be difficult to have a systematic way of inferring the python path based only on the scripted module path.

Manually setting the PYTHONPATH allows to address the reported problem. for example:

$ SlicerRadiomics_BUILD_DIR=/home/jcfr/Projects/SlicerRadiomics-Release
$ PYTHONPATH=$SlicerRadiomics_BUILD_DIR/python-pyradiomics-install/lib/python2.7/site-packages \
  ./Slicer --additional-module-path $SlicerRadiomics_BUILD_DIR/inner-build/lib/Slicer-4.7/qt-scripted-modules/

Number of registered modules: 141 
Enabling C extensions
Number of instantiated modules: 141 
Number of loaded modules: 141 
Switch to module:  "Welcome"
[...]

from slicerradiomics.

Thank you! I will update the user guide

from slicerradiomics.

Update:

@fedorov The following is a general solution for any extension:

build_dir=/home/jcfr/Projects/SlicerRadiomics-Release/inner-build/

./Slicer \
  --launcher-additional-settings $build_dir/AdditionalLauncherSettings.ini \
  --additional-module-path $build_dir

from slicerradiomics.

I will update the user guide

@fedorov The referenced topic should do it

from slicerradiomics.

Greg, let us know if this resolved your problems. Sorry for the delay addressing this issue.

from slicerradiomics.