Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

X ray phase contrast #170

merged 26 commits into from Mar 14, 2018


None yet
3 participants
Copy link

SimonRit commented Mar 9, 2018

The intention of this code is two-fold:

Two additional features for FFT are included in this PR:

  • Parallel imaging for FFD but this requires to have compiled RTK with SimonRit/RTK@1325b71.
  • Binning of FFD output.

cenzhenjie and others added some commits May 26, 2016

* All changes in Geant4 are moved to Gate;
* Refraction effects work for hard coding refractive index value.
* cleanup;
* beautification.
 * xraylib is now integrated in the G4XrayBoundaryProcess;
 * xraylib can be enabled/disabled with the CMake option;
 * when xraylib is disabled, the G4XrayBoundaryProcess always uses 1 as refractive index which doesn't change the x-ray propagation direction.
- header gate added ;
- reference added.

- mShrinkFactor for two dimensions (x,y) ;
- binning works now for all outputs.
Merge remote-tracking branch 'origin/develop' into develop
 - Error when xraylib is not available ;
 - Delta map computation/Fresnel PCI can be disabled now.

@dsarrut dsarrut merged commit a7d518a into OpenGATE:develop Mar 14, 2018


This comment has been minimized.

Copy link

djboersma commented Mar 15, 2018

I think that the cmake error message for not finding xraylib needs to be clarified/corrected: adding a directory to PATH did not solve it for me. This is a problem for users who cannot install xraylib in /usr/local.

I tried this out. I installed xraylib in a non-standard directory (with ./configure --prefix=/home/boersma/Software/Installations/XRAYLIB). Then cmake tells me "xraylib not found! Please install xraylib and make it available in PATH". So I added /home/boersma/Software/Installations/XRAYLIB/bin to my PATH variable. That did not help at all. Adding /home/boersma/Software/Installations/XRAYLIB/lib64 to my LD_LIBRARY_PATH did not help either. I "solved" it eventually with this incantation:

ccmake \
-DLIBXRL_LIBRARY:FILEPATH=/home/boersma/Software/Installation/XRAYLIB/lib64/libxrl.a \
-DLIBXRL_INCLUDE_DIR:PATH=/home/boersma/Software/Installation/XRAYLIB/include/xraylib \

This made cmake happy and allowed a successful build of Gate. After adding the RTK library path to my LD_LIBRARY_PATH I could also run the imaging/CT/XRayRefraction example in GateContrib.

So I wonder what we should recommend to the users. Maybe urge them to install xraylib in the standard location. But users do not always have access to /usr/local, e.g. when they run their stuff on a university cluster, on which they need to install their own special stuff on a user directory, like above. Is there a more advanced/subtle way to guide "pkgconfig" to find my xraylib installation? If yes, maybe the cmake error message could include a hint to that?


This comment has been minimized.

Copy link

SimonRit commented Mar 15, 2018

I can't reproduce the problem on my MacOS. I don't know why but I have updated the error message.

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
You can’t perform that action at this time.
You signed in with another tab or window. Reload to refresh your session. You signed out in another tab or window. Reload to refresh your session.