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<div dir="ltr">Dear Gate users;<br>
<br>
I am simulating a PET system. I am trying to use "TakeEnergyCentroid" policy on digitizers. I am having difficulty to set the depth since the program crashes.<br>
<br>
<div>In manuel, it says: “If the energy centroid policy is used, the depth is forced to be at the level just above the crystal level, whatever the system used.”</div>
<div><br>
</div>
<div>This is how my levels are (Please see the "describe" output as below.):</div>
<div>cylindricalPET (level 0)<br>
</div>
<div>rsector (level 1)<br>
</div>
<div>submodule (level 3)<br>
</div>
<div>crystal (level 4)<br>
</div>
<div>lyso (level 5)</div>
<div><br>
</div>
<div>I also intend to use level 3, submodule, which is just above the crystal level. According to document, this should be by default. This should happen when I remove the line:</div>
<div>
<div>/gate/digitizer/Singles/<wbr>readout/setDepth 3 <br>
</div>
<div><br>
</div>
<div>However, it crashes if I remove setDepth. (Please see the "Crash Report" as below)<br>
</div>
<div><br>
</div>
<div>If I put the line and set it to 3, it also crashes the same way.<br>
</div>
<div><br>
</div>
<div>It does work when I set it to 4 or 5 though, but this is not what is intended. I also found this similar case from 2015, they mentioned as possible bug:
<br>
</div>
<div><br>
</div>
<div><a href="http://lists.opengatecollaboration.org/pipermail/gate-users/2015-June/008490.html" target="_blank" data-saferedirecturl="https://www.google.com/url?q=http://lists.opengatecollaboration.org/pipermail/gate-users/2015-June/008490.html&source=gmail&ust=1550544608234000&usg=AFQjCNHGW66S8403uq-YUe798NzVRpTVlA" id="LPlnk375465" class="OWAAutoLink" previewremoved="true">http://lists.<wbr>opengatecollaboration.org/<wbr>pipermail/gate-users/2015-<wbr>June/008490.html</a></div>
<div><br>
</div>
<div>The way that TakeEnergyCentroid works with setDepths is inconsistent with the document. I don't know the cause of the crash. When I simulate it with setDepth 4 or 5, is it performing what document describes? If it bypasses setDepth as described, why it
does not work with setDepth=3, which should be the level that it is working?</div>
<div><br>
</div>
<div>Is this a known problem? Is there a solution to it? If there is a bug, I can help you debug or re-create it as well. I am using Gate 8.1.<br>
</div>
<div><br>
</div>
<div>Thank you,</div>
<div>Kutalmis Akpinar<br>
</div>
<div>University of Central Florida, Computer Science, PhD candidate<br>
</div>
<div><br>
</div>
<div><br>
</div>
</div>
<div><br>
</div>
<div>*********************** This is my describe output ******************************<wbr>****<br>
</div>
<div>==========================<br>
</div>
<div>GATE object: 'systems/cylindricalPET'<br>
Components:<br>
<br>
GATE object: 'systems/cylindricalPET/base'<br>
Attached to volume: cylindricalPET<br>
Nb of children: 1<br>
<br>
GATE object: 'systems/cylindricalPET/<wbr>rsector'<br>
Attached to volume: cpi_module<br>
Nb of children: 1<br>
<br>
GATE object: 'systems/cylindricalPET/<wbr>module'<br>
Attached to volume: ---<br>
Nb of children: 1<br>
<br>
GATE object: 'systems/cylindricalPET/<wbr>submodule'<br>
Attached to volume: cpi_block<br>
Nb of children: 1<br>
<br>
GATE object: 'systems/cylindricalPET/<wbr>crystal'<br>
Attached to volume: cpi_crystal<br>
Nb of children: 4<br>
<br>
GATE object: 'systems/cylindricalPET/<wbr>layer0'<br>
Attached to volume: cpi_lyso<br>
Nb of children: 0<br>
<br>
GATE object: 'systems/cylindricalPET/<wbr>layer1'<br>
Attached to volume: ---<br>
Nb of children: 0<br>
<br>
GATE object: 'systems/cylindricalPET/<wbr>layer2'<br>
Attached to volume: ---<br>
Nb of children: 0<br>
<br>
GATE object: 'systems/cylindricalPET/<wbr>layer3'<br>
Attached to volume: ---<br>
Nb of children: 0<br>
geometrical design type: 1<br>
ring diameter: 83.2 cm <br>
rsector axial pitch: 0 fm <br>
rsector azimuthal pitch: 8.18182 degree<br>
rsector tangential size: 5.674 cm <br>
rsector axial size: 17.114 cm <br>
module axial size: 17.114 cm <br>
module tangential size: 5.674 cm <br>
module axial pitch: 0 fm <br>
module tangential pitch: 0 fm <br>
submodule axial size: 5.674 cm <br>
submodule tangential size: 5.674 cm <br>
submodule axial pitch: 5.72 cm <br>
submodule tangential pitch: 0 fm <br>
crystal radial size: 1.5 cm <br>
crystal axial size: 4 mm <br>
crystal tangential size: 4 mm <br>
crystal axial pitch: 4.05692 mm <br>
crystal tangential pitch: 4.05692 mm <br>
layer0 radial size: 1.5 cm <br>
in layer0 interaction length: 7.5 mm <br>
Axial nb of rsectors: 1<br>
Azimuthal nb of rsectors: 44<br>
Axial nb of modules: 1<br>
Tangential nb of modules: 1<br>
Axial nb of submodules: 3<br>
Tangential nb of submodules: 1<br>
Axial nb of crystals: 14<br>
Tangential nb of crystals: 14<br>
Radial nb of layers: 1<br>
</div>
==============================<wbr>====<br>
<br>
<br>
<br>
******************************<wbr>******Crash Report:***********************<wbr>************</div>
<br>
*** Break *** segmentation violation<br>
[Acquisition-0] <br>
[Acquisition-0] ============= Source initialization =============<br>
[Acquisition-0] <br>
[Acquisition-0] ============= Acquisition starts! =============<br>
[Acquisition-0] Simulation start time = 0 sec<br>
[Acquisition-0] Simulation end time = 250 sec<br>
[Acquisition-0] Simulation will have = 1 run(s)<br>
[Acquisition-0] Slice 0 from 0 to 250 s [slice=250 s]<br>
<br>
<br>
<br>
==============================<wbr>=============================<br>
There was a crash.<br>
This is the entire stack trace of all threads:<br>
==============================<wbr>=============================<br>
#0 0x00007ff778b3307a in __GI___waitpid (pid=32153, stat_loc=stat_loc<br>
entry=0x7ffd9872e9c0, options=options<br>
entry=0) at ../sysdeps/unix/sysv/linux/<wbr>waitpid.c:29<br>
#1 0x00007ff778aabfbb in do_system (line=<optimized out>) at ../sysdeps/posix/system.c:148<br>
#2 0x00007ff77fd790d2 in TUnixSystem::StackTrace() () from /home/cpi/Installations/ROOT/<wbr>root_v6.14.06/lib/libCore.so<br>
#3 0x00007ff77fd7b9a3 in TUnixSystem::DispatchSignals(<wbr>ESignals) () from /home/cpi/Installations/ROOT/<wbr>root_v6.14.06/lib/libCore.so<br>
#4 <signal handler called><br>
#5 0x0000000000b33fd1 in GateObjectStore::<wbr>FindVolumeCreator(<wbr>G4VPhysicalVolume*) ()<br>
#6 0x00000000006a1b03 in GateVolumeSelector::<wbr>GateVolumeSelector(<wbr>G4VPhysicalVolume*) ()<br>
#7 0x000000000086cf10 in GatePulse::<wbr>ChangeVolumeIDAndOutputVolumeI<wbr>DValue(unsigned long, int) ()<br>
#8 0x0000000000999bcb in GateReadout::ProcessPulseList(<wbr>GatePulseList const*) ()<br>
#9 0x0000000000a68edb in GatePulseProcessorChain::<wbr>ProcessPulseList() ()<br>
#10 0x00000000008226f4 in GateDigitizer::Digitize() ()<br>
#11 0x000000000096fff7 in GateOutputMgr::<wbr>RecordEndOfEvent(G4Event const*) ()<br>
#12 0x00000000009f8299 in GateEventAction::<wbr>EndOfEventAction(G4Event const*) ()<br>
#13 0x00007ff77cef8dd7 in G4EventManager::DoProcessing(<wbr>G4Event*) () from /home/cpi/Installations/<wbr>GEANT4/geant4.10.04.p02-<wbr>install/lib/libG4event.so<br>
#14 0x00007ff77d1932a5 in G4RunManager::ProcessOneEvent(<wbr>int) () from /home/cpi/Installations/<wbr>GEANT4/geant4.10.04.p02-<wbr>install/lib/libG4run.so<br>
#15 0x00007ff77d1912d3 in G4RunManager::DoEventLoop(int, char const*, int) [clone .localalias.94] () from /home/cpi/Installations/<wbr>GEANT4/geant4.10.04.p02-<wbr>install/lib/libG4run.so<br>
#16 0x00007ff77d19150b in G4RunManager::BeamOn(int, char const*, int) () from /home/cpi/Installations/<wbr>GEANT4/geant4.10.04.p02-<wbr>install/lib/libG4run.so<br>
#17 0x0000000000bc8d7c in GateApplicationMgr::StartDAQ() ()<br>
#18 0x0000000000b6f720 in GateApplicationMgrMessenger::<wbr>SetNewValue(G4UIcommand*, G4String) ()<br>
#19 0x00007ff779e03fac in G4UIcommand::DoIt(G4String) () from /home/cpi/Installations/<wbr>GEANT4/geant4.10.04.p02-<wbr>install/lib/libG4intercoms.so<br>
#20 0x00007ff779e20261 in G4UImanager::ApplyCommand(char const*) () from /home/cpi/Installations/<wbr>GEANT4/geant4.10.04.p02-<wbr>install/lib/libG4intercoms.so<br>
#21 0x00007ff779deddd7 in G4UIbatch::ExecCommand(<wbr>G4String const&) () from /home/cpi/Installations/<wbr>GEANT4/geant4.10.04.p02-<wbr>install/lib/libG4intercoms.so<br>
#22 0x00007ff779defbae in G4UIbatch::SessionStart() () from /home/cpi/Installations/<wbr>GEANT4/geant4.10.04.p02-<wbr>install/lib/libG4intercoms.so<br>
#23 0x00007ff779e21242 in G4UImanager::ExecuteMacroFile(<wbr>char const*) () from /home/cpi/Installations/<wbr>GEANT4/geant4.10.04.p02-<wbr>install/lib/libG4intercoms.so<br>
#24 0x00007ff779e0e689 in G4UIcontrolMessenger::<wbr>SetNewValue(G4UIcommand*, G4String) () from /home/cpi/Installations/<wbr>GEANT4/geant4.10.04.p02-<wbr>install/lib/libG4intercoms.so<br>
#25 0x00007ff779e03fac in G4UIcommand::DoIt(G4String) () from /home/cpi/Installations/<wbr>GEANT4/geant4.10.04.p02-<wbr>install/lib/libG4intercoms.so<br>
#26 0x00007ff779e20261 in G4UImanager::ApplyCommand(char const*) () from /home/cpi/Installations/<wbr>GEANT4/geant4.10.04.p02-<wbr>install/lib/libG4intercoms.so<br>
#27 0x0000000000632365 in main ()<br>
==============================<wbr>=============================<br>
<br>
<br>
The lines below might hint at the cause of the crash.<br>
You may get help by asking at the ROOT forum <a href="http://root.cern.ch/forum" target="_blank" data-saferedirecturl="https://www.google.com/url?q=http://root.cern.ch/forum&source=gmail&ust=1550544608235000&usg=AFQjCNHrQCsrTTi8vdjZ7OV-iErta_dE2g" id="LPlnk359530" class="OWAAutoLink" previewremoved="true">
http://root.cern.ch/forum</a><br>
Only if you are really convinced it is a bug in ROOT then please submit a<br>
report at <a href="http://root.cern.ch/bugs" target="_blank" data-saferedirecturl="https://www.google.com/url?q=http://root.cern.ch/bugs&source=gmail&ust=1550544608235000&usg=AFQjCNGkYni0aw-WA8bh-HceEUk_02IgpQ" id="LPlnk851884" class="OWAAutoLink" previewremoved="true">
http://root.cern.ch/bugs</a> Please post the ENTIRE stack trace<br>
from above as an attachment in addition to anything else<br>
that might help us fixing this issue.<br>
==============================<wbr>=============================<br>
#5 0x0000000000b33fd1 in GateObjectStore::<wbr>FindVolumeCreator(<wbr>G4VPhysicalVolume*) ()<br>
#6 0x00000000006a1b03 in GateVolumeSelector::<wbr>GateVolumeSelector(<wbr>G4VPhysicalVolume*) ()<br>
#7 0x000000000086cf10 in GatePulse::<wbr>ChangeVolumeIDAndOutputVolumeI<wbr>DValue(unsigned long, int) ()<br>
#8 0x0000000000999bcb in GateReadout::ProcessPulseList(<wbr>GatePulseList const*) ()<br>
#9 0x0000000000a68edb in GatePulseProcessorChain::<wbr>ProcessPulseList() ()<br>
#10 0x00000000008226f4 in GateDigitizer::Digitize() ()<br>
#11 0x000000000096fff7 in GateOutputMgr::<wbr>RecordEndOfEvent(G4Event const*) ()<br>
#12 0x00000000009f8299 in GateEventAction::<wbr>EndOfEventAction(G4Event const*) ()<br>
#13 0x00007ff77cef8dd7 in G4EventManager::DoProcessing(<wbr>G4Event*) () from /home/cpi/Installations/<wbr>GEANT4/geant4.10.04.p02-<wbr>install/lib/libG4event.so<br>
#14 0x00007ff77d1932a5 in G4RunManager::ProcessOneEvent(<wbr>int) () from /home/cpi/Installations/<wbr>GEANT4/geant4.10.04.p02-<wbr>install/lib/libG4run.so<br>
#15 0x00007ff77d1912d3 in G4RunManager::DoEventLoop(int, char const*, int) [clone .localalias.94] () from /home/cpi/Installations/<wbr>GEANT4/geant4.10.04.p02-<wbr>install/lib/libG4run.so<br>
#16 0x00007ff77d19150b in G4RunManager::BeamOn(int, char const*, int) () from /home/cpi/Installations/<wbr>GEANT4/geant4.10.04.p02-<wbr>install/lib/libG4run.so<br>
#17 0x0000000000bc8d7c in GateApplicationMgr::StartDAQ() ()<br>
#18 0x0000000000b6f720 in GateApplicationMgrMessenger::<wbr>SetNewValue(G4UIcommand*, G4String) ()<br>
#19 0x00007ff779e03fac in G4UIcommand::DoIt(G4String) () from /home/cpi/Installations/<wbr>GEANT4/geant4.10.04.p02-<wbr>install/lib/libG4intercoms.so<br>
#20 0x00007ff779e20261 in G4UImanager::ApplyCommand(char const*) () from /home/cpi/Installations/<wbr>GEANT4/geant4.10.04.p02-<wbr>install/lib/libG4intercoms.so<br>
#21 0x00007ff779deddd7 in G4UIbatch::ExecCommand(<wbr>G4String const&) () from /home/cpi/Installations/<wbr>GEANT4/geant4.10.04.p02-<wbr>install/lib/libG4intercoms.so<br>
#22 0x00007ff779defbae in G4UIbatch::SessionStart() () from /home/cpi/Installations/<wbr>GEANT4/geant4.10.04.p02-<wbr>install/lib/libG4intercoms.so<br>
#23 0x00007ff779e21242 in G4UImanager::ExecuteMacroFile(<wbr>char const*) () from /home/cpi/Installations/<wbr>GEANT4/geant4.10.04.p02-<wbr>install/lib/libG4intercoms.so<br>
#24 0x00007ff779e0e689 in G4UIcontrolMessenger::<wbr>SetNewValue(G4UIcommand*, G4String) () from /home/cpi/Installations/<wbr>GEANT4/geant4.10.04.p02-<wbr>install/lib/libG4intercoms.so<br>
#25 0x00007ff779e03fac in G4UIcommand::DoIt(G4String) () from /home/cpi/Installations/<wbr>GEANT4/geant4.10.04.p02-<wbr>install/lib/libG4intercoms.so<br>
#26 0x00007ff779e20261 in G4UImanager::ApplyCommand(char const*) () from /home/cpi/Installations/<wbr>GEANT4/geant4.10.04.p02-<wbr>install/lib/libG4intercoms.so<br>
#27 0x0000000000632365 in main ()<br>
==============================<wbr>=============================</div>
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