[Gate-users] Fixed Forced Detection Actor

Simon Rit simon.rit at creatis.insa-lyon.fr
Wed Nov 30 13:35:42 CET 2016 

I don't know what's going on but the fact that you have to change
LD_LIBRARY_PATH is very suspicious. I would check in the
CMakeCache.txt of your Gate compilation directory what is the value of
RTK_DIR. It seems to me that you might have mixed several versions of
RTK.
Simon

On Wed, Nov 30, 2016 at 1:30 PM, Triltsch, Nicolas
<nicolas.triltsch at tum.de> wrote:
>
> 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>
>>>>>>
>>>>>>
>>>>>
>>>>
>>>>
>>>> _______________________________________________
>>>> Gate-users mailing list
>>>> Gate-users at lists.opengatecollaboration.org
>>>> http://lists.opengatecollaboration.org/mailman/listinfo/gate-users
>>>>
>>> _______________________________________________
>>> Gate-users mailing list
>>> Gate-users at lists.opengatecollaboration.org
>>> http://lists.opengatecollaboration.org/mailman/listinfo/gate-users
>>
>> _______________________________________________
>> Gate-users mailing list
>> Gate-users at lists.opengatecollaboration.org
>> http://lists.opengatecollaboration.org/mailman/listinfo/gate-users
>
>

More information about the Gate-users mailing list