[Gate-users] Fixed Forced Detection Actor
Simon Rit
simon.rit at creatis.insa-lyon.fr
Wed Nov 30 14:48:33 CET 2016
It still not clear to me, did you delete RTK-1.3.0-build after the
install? If not, then (1) I don't understand why it does not find
librtk and (2) your LD_LIBRARY_PATH should point to
/usr/local/bin/RTK-1.3.0-build/lib
If you want to use your installed directory, you should have in Gate
RTK_DIR:PATH=/usr/local//bin/RTK-1.3.0-install/lib/cmake/RTK-1.3/
Simon
On Wed, Nov 30, 2016 at 2:36 PM, Triltsch, Nicolas
<nicolas.triltsch at tum.de> wrote:
> Hey,
>
> This is what I found in my CMakeCache.txt file:
>
> //The directory containing RTKConfig.cmake. This is either the
> // root of the build tree, or PREFIX/lib for an installation.
> RTK_DIR:PATH=/usr/local/bin/RTK-1.3.0-build
>
> Which should be correct!
>
> In the first installation of ITK and RTK I didn't change in ccmake the
> option CMAKE_INSTALL_PREFIX. The second time I compiled ITK and RTK, I
> changed CMAKE_INSTALL_PREFIX=/usr/local/bin/RTK-1.3.0-install (a
> installation folder I created). Additionally I created I folder
> RTK-1.3.0-build for starting ccmake ../RTK-1.3.0 and compiling the source
> code.
>
> Do you think there could be the error?
>
> Nico
>
>
> On 11/30/2016 01:35 PM, Simon Rit wrote:
>>
>> 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
>>>>>>>>
>>>>>>>> _______________________________________________
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>>>>>>>> <mailto:Gate-users at lists.opengatecollaboration.org>
>>>>>>>>
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>>>>>>>>
>>>>>>>> <http://lists.opengatecollaboration.org/mailman/listinfo/gate-users>
>>>>>>>>
>>>>>>>>
>>>>>>
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