[Gate-users] Fixed Forced Detection Actor

Triltsch, Nicolas nicolas.triltsch at tum.de
Wed Nov 30 13:30:53 CET 2016 

Hey David and Simon,

The libRTK in my case is located 
/usr/local/bin/RTK-1.3.0-install/lib/libRTK.so . If I set the 
LD_LIBRARY_PATH, Gate is starting. But after do a testrun with 
FixedForcedDetection Actor, it states the following:
"===========================================================
There was a crash.
This is the entire stack trace of all threads:
===========================================================
#0  0x00007f096571751b in __GI___waitpid (pid=20648, stat_loc=stat_loc
entry=0x7ffdb4477b40, options=options
entry=0) at ../sysdeps/unix/sysv/linux/waitpid.c:29
#1  0x00007f0965690fbb in do_system (line=<optimized out>) at 
../sysdeps/posix/system.c:148
#2  0x00007f096d69ddd4 in TUnixSystem::StackTrace() () from 
/usr/lib/x86_64-linux-gnu/libCore.so.5.34
#3  0x00007f096d6a003c in TUnixSystem::DispatchSignals(ESignals) () from 
/usr/lib/x86_64-linux-gnu/libCore.so.5.34
#4  <signal handler called>
#5  0x000000000353d050 in ?? ()
#6  0x00007f096b20b582 in itk::(anonymous 
namespace)::CleanUpObjectFactory::~CleanUpObjectFactory() () from 
/usr/local/bin/RTK-1.3.0-install/lib/libRTK.so
#7  0x00007f096568636a in __cxa_finalize (d=0x7f096bd2ec40) at 
cxa_finalize.c:56
#8  0x00007f096b158e43 in __do_global_dtors_aux () from 
/usr/local/bin/RTK-1.3.0-install/lib/libRTK.so
#9  0x00007ffdb447a810 in ?? ()
#10 0x00007f096f2dac17 in _dl_fini () at dl-fini.c:235
==========================================================="

Maybe I should compile RTK again and save the library under /usr/lib?
Nico

On 11/30/2016 01:18 PM, Simon Rit wrote:
> Hi,
> I agree with everything pointed out by David. I have checked that
> compiling RTK with dynamic libraries did work and it does so I'm not
> sure what has happened on your side but it should find libRTK if you
> haven't moved it after compilation.
> Simon
>
> On Wed, Nov 30, 2016 at 11:59 AM, David Boersma
> <david.boersma at physics.uu.se> wrote:
>> Hi Nicolas,
>>
>> Den 30/11/2016 kl. 11:48, skrev Triltsch, Nicolas:
>>> Hey Simon,
>>>
>>> I compiled everything again and there were no more errors:) But if I
>>> start Gate it states the following:
>>>
>>> /"Gate: error while loading shared libraries: libRTK.so: cannot open
>>> shared object file: No such file or directory"/
>>>
>>> Why does it not find the libraries?
>>
>> Where is libRTK.so installed on your system?
>>
>> If it is in some standard directory, like /usr/lib, then it should just be
>> found without any extra actions. So I assume that you installed it somewhere
>> else. Do not move libraries around after installing (because sometimes their
>> paths are hardcoded inside the libraries and other code).
>>
>> Let's say the libRTK.so is installed in /A/B/C/lib, then you could try
>>
>> export LD_LIBRARY_PATH=/A/B/C/lib:$LD_LIBRARY_PATH
>>
>> Then try running Gate again. Or run "ldd Gate" to inspect the list of
>> libraries that the runtime linker is finding (or not finding) for it.
>>
>> (If you are on MacOSX, then you need to set DYLD_LIBRARY_PATH instead, and
>> instead of "ldd" you run "otool -L".)
>>
>> HTH,
>> /DavidB
>>
>>
>>> Cheers, Nico
>>>
>>> On 11/29/2016 10:09 PM, Simon Rit wrote:
>>>> Hi,
>>>> I'm not sure what happened. Did you maybe update ITK without
>>>> recompiling it? Anyway, I'd suggest to recompile ITK, RTK and Gate (in
>>>> this order). Sorry for the trouble, I know these dependencies are a
>>>> bit inconvenient.
>>>> Simon
>>>>
>>>> On Tue, Nov 29, 2016 at 2:06 PM, Triltsch, Nicolas
>>>> <nicolas.triltsch at tum.de <mailto:nicolas.triltsch at tum.de>> wrote:
>>>>
>>>>      Hey Simon,
>>>>
>>>>      I followed your two changes 1) and 3) and after that I compiled
>>>>      Gate again, in order to make the changes valid. But now I get an
>>>>      error message when compiling gate_v7.2, which says:
>>>>
>>>>      "/
>>>>      /
>>>>
>>>>      /make[2]: *** No rule to make target
>>>>
>>>> '/usr/local/bin/InsightToolkit-4.10.1/InsightToolkit-4.10.1-build/lib/libITKReview-4.10.so.1',
>>>>      needed by 'Gate'.  Stop.//
>>>>      //make[2]: *** Waiting for unfinished jobs....//
>>>>      //[100%] Building CXX object
>>>>
>>>> CMakeFiles/Gate.dir/source/externals/clhep/src/CLHEP/RandomObjects/RandomVector.cc.o//
>>>>      //CMakeFiles/Makefile2:67: recipe for target
>>>>      'CMakeFiles/Gate.dir/all' failed//
>>>>      //make[1]: *** [CMakeFiles/Gate.dir/all] Error 2//
>>>>      //Makefile:127: recipe for target 'all' failed//
>>>>      //make: *** [all] Error 2/
>>>>
>>>>      "
>>>>
>>>>      Honestly, I have no idea what to do. I think it has something to
>>>>      do with the ITK package, but I don't know why. If you have an idea
>>>>      that would be great, as my Gate is not running any more:/ If I
>>>>      type 'Gate' in the terminal, it says now:
>>>>
>>>>      "
>>>>
>>>>      /Gate: error while loading shared libraries:
>>>>      libITKIOBMP-4.10.so.1: cannot open shared object file: No such
>>>>      file or directory/
>>>>
>>>>      "
>>>>
>>>>      Thanks in advance!
>>>>
>>>>      Nico
>>>>
>>>>
>>>>
>>>>      On 11/28/2016 03:57 PM, Simon Rit wrote:
>>>>>      Hi,
>>>>>
>>>>>      On Mon, Nov 28, 2016 at 2:00 PM, Triltsch, Nicolas
>>>>>      <nicolas.triltsch at tum.de <mailto:nicolas.triltsch at tum.de>> wrote:
>>>>>
>>>>>          Hey everyone,
>>>>>
>>>>>          I have three questions concerning the fixed forced detection
>>>>>          actor(ffda):
>>>>>
>>>>>          1) As output one can generate e.g. primary.mha, compton.mha,
>>>>>          rayleigh.mha and total.mha images. In the GATE wiki it
>>>>>          states, that primary + compton + rayleigh = total. But if I
>>>>>          compare the two images they are different! Why? (total.mha
>>>>>          image was flatfield corrected by default; primary, compton
>>>>>          and rayleigh weren't, so I used the flatField.mha to correct
>>>>>          them before the comparison with total.mha)
>>>>>
>>>>>       I checked and there is a bug in the total filename. However, it
>>>>>      does not use the flat field but rather one step was forgotten
>>>>>      (accounting for the total number of particles in the simulation).
>>>>>      I must admit that I never use that output in practice, hence the
>>>>>      bug. This fix
>>>>>
>>>>> <https://github.com/OpenGATE/Gate/commit/988f886133ee741eeca692df027e7786e025c7bc>
>>>>>      should correct that.
>>>>>
>>>>>
>>>>>          2) For the ffda the source needs to be focused. Why is that
>>>>>          necessary?
>>>>>
>>>>>      Because ffda uses RTK <http://openrtk.org/> for deterministic
>>>>>      computation and RTK is working for point sources.
>>>>>
>>>>>
>>>>>          3) One output image is called secondary.mha. First, I thought
>>>>>          this image would represent secondary scatter events. But in
>>>>>          the GATE wiki it says that secondary = compton + rayleigh. Is
>>>>>          their a way to obtain a secondary scatter (multiple scatter)
>>>>>          image?
>>>>>
>>>>>      It used to be possible but I think we have removed it to
>>>>>      "minimize" the number of options. You can try (but I don't
>>>>>      guarantee it works) to add a line in the code, e.g. around line
>>>>>      57 of GateFixedForcedDetectionActor.cc:
>>>>>      mPerOrderImagesBaseName="order";
>>>>>      It will then create an image of the form
>>>>>      "orderRayleigh0004_order02.mha" for the second order of the
>>>>>      rayleigh projection number 4.
>>>>>      Simon
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>          I would appreciate any help!
>>>>>
>>>>>          Nico
>>>>>
>>>>>          _______________________________________________
>>>>>          Gate-users mailing list
>>>>>          Gate-users at lists.opengatecollaboration.org
>>>>>          <mailto:Gate-users at lists.opengatecollaboration.org>
>>>>>
>>>>> http://lists.opengatecollaboration.org/mailman/listinfo/gate-users
>>>>>
>>>>> <http://lists.opengatecollaboration.org/mailman/listinfo/gate-users>
>>>>>
>>>>>
>>>>
>>>
>>>
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