[Gate-users] Fixed Forced Detection Actor

Triltsch, Nicolas nicolas.triltsch at tum.de
Wed Nov 30 18:17:19 CET 2016


Hey everyone,

Gate is working again!:) I deleted ITK, RTK and gate, compiled 
everything from the beginning and it works now!

Thanks guys,

Nico


On 11/30/2016 02:48 PM, Simon Rit wrote:
> 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
>>>>>>>>>
>>>>>>>>>            _______________________________________________
>>>>>>>>>            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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