[Gate-users] Problems with installation of ECAT7 library

[Ida Häggström]

Hello and thanks for your reply!
Unfortunately I've tried just that, but no success. I get errors when I try
and compile GATE. Actually the compilation seems OK (libgate.so,
GateVObjectMove.d, GateVolumeID.d etc are created in my
gate/tmp/Linux-g++/Gate folder ), it is the linking stage that doesn't
work... I have added the path to that folder to both PATH and
LD_LIBRARY_PATH. I still get:

Linking Gate ...
./tmp/Linux-g++/Gate/libGate.so: undefined reference to `GateVObjectMove::
PushMyPlacements(CLHEP::HepRotation const&, CLHEP::Hep3Vector const&,
double)'
./tmp/Linux-g++/Gate/libGate.so: undefined reference to `GateVolumeID::
MoveToBottomVolumeFrame(CLHEP::Hep3Vector, int) const'
./tmp/Linux-g++/Gate/libGate.so: undefined reference to
`GateToASCII::GateToASCII(G4String const&, GateOutputMgr*, DigiMode)'
...
./tmp/Linux-g++/Gate/libGate.so: undefined reference to
`GateToRoot::GetPHData(ComptonRayleighData&)'
./tmp/Linux-g++/Gate/libGate.so: undefined reference to
`GateTrack::GetTrackID()'
collect2: ld returned 1 exit status
make: *** [bin/Linux-g++/Gate] Error 1

Does anyone else know what could be the problem? Maybe something with my
installation of ECAT7?

thanks!
Ida

Den 10 september 2009 10.28 skrev Jan Mickelle Maratas <jmmaratas at gmail.com>
:

>
> Hi,
>
>
> I once tried and succeeded in using PET_Ecat_System.mac.
> I set the following environment variables before installing GATE:
>
>     export ECAT7_HOME=/home/soft/ecat7          # (ECAT7 Home location)
>     export GATE_USE_ECAT7=1
>
> Reinstalled GATE and now the PET_Ecat_System.mac
> runs with no problem.
>
> Hope it helps!
>
>
> Best regards,
>
> Mike
> --
>
>
>
>
> 2009/9/9 Ida Häggström <ida.haggstrom at radfys.umu.se>
>
>> Hi again!
>> I made a little typo in my commands previously... It SHOULD be
>>
>> > cd <...>/gate/ECAT
>> > make -f Makefile.unix
>> > rm *.o
>>
>> > mkdir <...>/gate/ECAT
>> > mkdir <...>/gate/ECAT/lib
>>
>>
>> > mkdir <...>/gate/ECAT/lib/Linux-g++
>> > mkdir <...>/gate/ECAT/include
>>
>> Cheers!
>> Ida
>>
>> Den 9 september 2009 15.21 skrev Ida Häggström <
>> ida.haggstrom at radfys.umu.se>:
>>
>> Hi all!
>>> I've successfully installed and run GATE for a week or so now when I
>>> decided I probably need the ECAT7 output as well.. (I omitted that the first
>>> time I installed GATE). Anyway, I've installed the package according to the
>>> guide at "http://cc.in2p3.fr/docenligne/674/en". I've thus run
>>>
>>> > cd <...>/gate/ECAT
>>> > make -f Makefile.unix
>>> > rm *.o
>>>
>>>
>>> > mkdir <...>/gate/gate_v5.0.0/ECAT
>>> > mkdir <...>/gate/gate_v5.0.0/ECAT/lib
>>>
>>>
>>> > mkdir <...>/gate/gate_v5.0.0/ECAT/lib/Linux-g++
>>> > mkdir <...>/gate/gate_v5.0.0/ECAT/include
>>>
>>>
>>> After this I copy the files "matrix.h" and "machine_indep.h" into the
>>> ECAT/include directory and I copy the file "libecat.a" into
>>> ECAT/lib/Linux-g++.
>>>
>>> I found on a previous thread that it was best to completely recompile
>>> GATE, with make clean and all... so I remove and reinstall GATE (note that I
>>> have NOT set the ECAT7_HOME variable yet!):
>>>
>>> > cd <...>/gate/gate_v_5.0.0
>>>
>>>
>>> > make clean (I also remove the tmp directory)
>>> > make
>>>
>>> After successful GATE compilation I set
>>>
>>>
>>>
>>> > export ECAT7_HOME=<...>/gate/ECAT
>>>
>>> I try and run the example PET_Ecat_System.mac in GATE, with default sinogram and ecat7 output, but it seems the ECAT7 library isn't found or something:
>>>
>>>
>>> ....
>>> GATE object:        'digitizer/finalCoinc'
>>>
>>>
>>>
>>> Is enabled?         Yes
>>> Nb of elements:     0
>>> Attached to:        'digitizer'
>>> Output:             'finalCoinc'
>>> ***** COMMAND NOT FOUND </gate/output/sinogram/StoreDelayed> *****
>>>
>>> ***** Batch is interupted!! *****
>>>
>>>
>>>
>>> Graphics systems deleted.
>>> Visualization Manager deleting...
>>> GateRTPhantomMgr deleting...
>>> [ida at localhost example_PET_Scanner]$
>>> ....
>>>
>>>
>>>
>>> If I remove the sinogram output and only use ecat7 output I instead get
>>>
>>> ...
>>>
>>>
>>> ***** COMMAND NOT FOUND </gate/output/ecat7/enable> *****
>>> ....
>>>
>>>
>>> When I try to compile GATE with the ECAT7_HOME variable set BEFORE
>>> compilation I don't get a successful linking:
>>> ....
>>> Creating shared library tmp/Linux-g++/Gate/libGate.so ...
>>> Creating/replacing object files in ./tmp/Linux-g++/Gate/libGate.a ...
>>> ar: creating ./tmp/Linux-g++/Gate/libGate.a
>>> Compiling Gate.cc ...
>>> Using global libraries ...
>>> Linking Gate ...
>>> ./tmp/Linux-g++/Gate/libGate.so: undefined reference to
>>> `GateVObjectMove::PushMyPlacements(CLHEP::HepRotation const&,
>>> CLHEP::Hep3Vector const&, double)'
>>> ./tmp/Linux-g++/Gate/libGate.so: undefined reference to `GateVolumeID::
>>> MoveToBottomVolumeFrame(CLHEP::Hep3Vector, int) const'
>>> ./tmp/Linux-g++/Gate/libGate.so: undefined reference to
>>> `GateToASCII::GateToASCII(G4String const&, GateOutputMgr*, DigiMode)'
>>> ...
>>> ./tmp/Linux-g++/Gate/libGate.so: undefined reference to
>>> `GateToRoot::GetPHData(ComptonRayleighData&)'
>>> ./tmp/Linux-g++/Gate/libGate.so: undefined reference to
>>> `GateTrack::GetTrackID()'
>>> collect2: ld returned 1 exit status
>>> make: *** [bin/Linux-g++/Gate] Error 1
>>> ....
>>>
>>> My question is do you set the ECAT7_HOME variable before or after GATE
>>> compilation, and how do you get GATE to enable to ECAT7 output?
>>> Thanks in advance!
>>>  /Ida
>>>
>>
>>
>> _______________________________________________
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>> Gate-users at lists.healthgrid.org
>> http://lists.healthgrid.org/mailman/listinfo/gate-users
>>
>>
>
>
> --
> #################################################################
>   Computational High Energy Physics Laboratory, Physics Department,
>   College of Science and Mathematics, MSU - Iligan Institute of Technology
>   A. Bonifacio Ave., Tibanga, 9200 Iligan City, Philippines
>   E-mail: jmmaratas at gmail.com, jmmaratas at physics.msuiit.edu.ph
> #################################################################
>
>
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