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<p style="margin-top:0;margin-bottom:0">Hi Sebastien,</p>
<p style="margin-top:0;margin-bottom:0">Thank you for your kind response. The code block you pointed was quite helpful. (For reference to others, line 64-103:
<a href="https://github.com/OpenGATE/Gate/blob/develop/source/digits_hits/src/GateReadout.cc" class="OWAAutoLink" id="LPlnk272518" previewremoved="true">
https://github.com/OpenGATE/Gate/blob/develop/source/digits_hits/src/GateReadout.cc</a> )</p>
<p style="margin-top:0;margin-bottom:0"><br>
</p>
<p style="margin-top:0;margin-bottom:0">I want to make it clear, you wrote "<font size="2"><span style="font-size:11pt;">« TakeEnergyWinner » works on the crystal level component</span></font>"</p>
<p style="margin-top:0;margin-bottom:0"><br>
</p>
<p style="margin-top:0;margin-bottom:0">Did you actually mean "<font size="2"><span style="font-size:11pt;"> « TakeEnergyCentroid » works <<One level above>> the crystal level component</span></font>" ?</p>
<p style="margin-top:0;margin-bottom:0"></p>
<p style="margin-top:0;margin-bottom:0"><br>
</p>
<p style="margin-top:0;margin-bottom:0">That is what I understand from line 101-102:</p>
<div><span class="pl-c"><span class="pl-c">----------- line 101-102 -----------<br>
</span></span></div>
<div><span class="pl-c"><span class="pl-c">//</span> Now force m_depth to be right above the crystal depth</span>
<br>
</div>
<div>m_depth = m_crystalDepth - <span class="pl-c1">1</span>;</div>
<div>-----------------------------------------<br>
</div>
<p></p>
<p style="margin-top:0;margin-bottom:0"><br>
</p>
<p style="margin-top:0;margin-bottom:0">Or, did you really mean "<font size="2"><span style="font-size:11pt;">« TakeEnergyWinner » works on the crystal level component</span></font>", so, setDepth has nothing to do with
<font size="2"><span style="font-size:11pt;">« TakeEnergyCentroid »</span></font>, I need to leave it as "4", which is the crystal level.<br>
</p>
<p style="margin-top:0;margin-bottom:0"><br>
</p>
<div>When working with "TakeEnergyCentroid", I will set the "setDepth" to 4, since it crashes otherwise. But I want to make sure that it is not effecting my results.</div>
<div><br>
</div>
<div><font size="2"><span style="font-size:11pt;">Thank you,<br>
Kutalmis Akpinar<br>
University of Central Florida, Computer Science, PhD candidate</span></font></div>
<div><br>
</div>
<div><br>
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<div id="divRplyFwdMsg" dir="ltr"><font style="font-size:11pt" face="Calibri, sans-serif" color="#000000"><b>From:</b> Gate-users <gate-users-bounces@lists.opengatecollaboration.org> on behalf of gate-users-request@lists.opengatecollaboration.org <gate-users-request@lists.opengatecollaboration.org><br>
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Today's Topics:<br>
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1. Re: SetDepth on TakeEnergyCentroid (JAN Sebastien)<br>
<br>
<br>
----------------------------------------------------------------------<br>
<br>
Message: 1<br>
Date: Mon, 18 Feb 2019 08:30:37 +0000<br>
From: JAN Sebastien <sebastien.jan@cea.fr><br>
To: Kutalmis Akpinar <kutalmis@knights.ucf.edu>,<br>
"gate-users@lists.opengatecollaboration.org"<br>
<gate-users@lists.opengatecollaboration.org><br>
Subject: Re: [Gate-users] SetDepth on TakeEnergyCentroid<br>
Message-ID:<br>
<63BD57EF92283749A0D90EC01273552C38B0FC55@EXDAG0-A1.intra.cea.fr><br>
Content-Type: text/plain; charset="iso-8859-1"<br>
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Hi,<br>
<br>
This policy « TakeEnergyWinner » works on the crystal level component.<br>
For details, you can check the code :<br>
Source/digits_hist/src/GateReadout.cc<br>
Line 64 -> 103<br>
<br>
Cheers<br>
Seb<br>
<br>
De : Gate-users <gate-users-bounces@lists.opengatecollaboration.org> De la part de Kutalmis Akpinar<br>
Envoyé : lundi 18 février 2019 03:59<br>
À : gate-users@lists.opengatecollaboration.org<br>
Objet : [Gate-users] SetDepth on TakeEnergyCentroid<br>
<br>
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>
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."<br>
<br>
This is how my levels are (Please see the "describe" output as below.):<br>
cylindricalPET (level 0)<br>
rsector (level 1)<br>
submodule (level 3)<br>
crystal (level 4)<br>
lyso (level 5)<br>
<br>
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:<br>
/gate/digitizer/Singles/readout/setDepth 3<br>
<br>
However, it crashes if I remove setDepth. (Please see the "Crash Report" as below)<br>
<br>
If I put the line and set it to 3, it also crashes the same way.<br>
<br>
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>
<br>
<a href="https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Flists.opengatecollaboration.org%2Fpipermail%2Fgate-users%2F2015-June%2F008490.html&data=02%7C01%7Ckutalmis%40knights.ucf.edu%7Cef55085f893049d8f38808d6957b65f7%7C5b16e18278b3412c919668342689eeb7%7C0%7C0%7C636860754559076595&sdata=qafGvRcGb8StEV0nOOLYtKswWcOrTiRIncIvoK1ww14%3D&reserved=0" id="LPlnk926362" class="OWAAutoLink" previewremoved="true">https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Flists.opengatecollaboration.org%2Fpipermail%2Fgate-users%2F2015-June%2F008490.html&data=02%7C01%7Ckutalmis%40knights.ucf.edu%7Cef55085f893049d8f38808d6957b65f7%7C5b16e18278b3412c919668342689eeb7%7C0%7C0%7C636860754559076595&sdata=qafGvRcGb8StEV0nOOLYtKswWcOrTiRIncIvoK1ww14%3D&reserved=0</a><br>
<br>
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?<br>
<br>
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>
<br>
Thank you,<br>
Kutalmis Akpinar<br>
University of Central Florida, Computer Science, PhD candidate<br>
<br>
<br>
<br>
*********************** This is my describe output **********************************<br>
==========================<br>
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/rsector'<br>
Attached to volume: cpi_module<br>
Nb of children: 1<br>
<br>
GATE object: 'systems/cylindricalPET/module'<br>
Attached to volume: ---<br>
Nb of children: 1<br>
<br>
GATE object: 'systems/cylindricalPET/submodule'<br>
Attached to volume: cpi_block<br>
Nb of children: 1<br>
<br>
GATE object: 'systems/cylindricalPET/crystal'<br>
Attached to volume: cpi_crystal<br>
Nb of children: 4<br>
<br>
GATE object: 'systems/cylindricalPET/layer0'<br>
Attached to volume: cpi_lyso<br>
Nb of children: 0<br>
<br>
GATE object: 'systems/cylindricalPET/layer1'<br>
Attached to volume: ---<br>
Nb of children: 0<br>
<br>
GATE object: 'systems/cylindricalPET/layer2'<br>
Attached to volume: ---<br>
Nb of children: 0<br>
<br>
GATE object: 'systems/cylindricalPET/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>
==================================<br>
<br>
<br>
<br>
************************************Crash Report:***********************************<br>
<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>
===========================================================<br>
There was a crash.<br>
This is the entire stack trace of all threads:<br>
===========================================================<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/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/root_v6.14.06/lib/libCore.so<br>
#3 0x00007ff77fd7b9a3 in TUnixSystem::DispatchSignals(ESignals) () from /home/cpi/Installations/ROOT/root_v6.14.06/lib/libCore.so<br>
#4 <signal handler called><br>
#5 0x0000000000b33fd1 in GateObjectStore::FindVolumeCreator(G4VPhysicalVolume*) ()<br>
#6 0x00000000006a1b03 in GateVolumeSelector::GateVolumeSelector(G4VPhysicalVolume*) ()<br>
#7 0x000000000086cf10 in GatePulse::ChangeVolumeIDAndOutputVolumeIDValue(unsigned long, int) ()<br>
#8 0x0000000000999bcb in GateReadout::ProcessPulseList(GatePulseList const*) ()<br>
#9 0x0000000000a68edb in GatePulseProcessorChain::ProcessPulseList() ()<br>
#10 0x00000000008226f4 in GateDigitizer::Digitize() ()<br>
#11 0x000000000096fff7 in GateOutputMgr::RecordEndOfEvent(G4Event const*) ()<br>
#12 0x00000000009f8299 in GateEventAction::EndOfEventAction(G4Event const*) ()<br>
#13 0x00007ff77cef8dd7 in G4EventManager::DoProcessing(G4Event*) () from /home/cpi/Installations/GEANT4/geant4.10.04.p02-install/lib/libG4event.so<br>
#14 0x00007ff77d1932a5 in G4RunManager::ProcessOneEvent(int) () from /home/cpi/Installations/GEANT4/geant4.10.04.p02-install/lib/libG4run.so<br>
#15 0x00007ff77d1912d3 in G4RunManager::DoEventLoop(int, char const*, int) [clone .localalias.94] () from /home/cpi/Installations/GEANT4/geant4.10.04.p02-install/lib/libG4run.so<br>
#16 0x00007ff77d19150b in G4RunManager::BeamOn(int, char const*, int) () from /home/cpi/Installations/GEANT4/geant4.10.04.p02-install/lib/libG4run.so<br>
#17 0x0000000000bc8d7c in GateApplicationMgr::StartDAQ() ()<br>
#18 0x0000000000b6f720 in GateApplicationMgrMessenger::SetNewValue(G4UIcommand*, G4String) ()<br>
#19 0x00007ff779e03fac in G4UIcommand::DoIt(G4String) () from /home/cpi/Installations/GEANT4/geant4.10.04.p02-install/lib/libG4intercoms.so<br>
#20 0x00007ff779e20261 in G4UImanager::ApplyCommand(char const*) () from /home/cpi/Installations/GEANT4/geant4.10.04.p02-install/lib/libG4intercoms.so<br>
#21 0x00007ff779deddd7 in G4UIbatch::ExecCommand(G4String const&) () from /home/cpi/Installations/GEANT4/geant4.10.04.p02-install/lib/libG4intercoms.so<br>
#22 0x00007ff779defbae in G4UIbatch::SessionStart() () from /home/cpi/Installations/GEANT4/geant4.10.04.p02-install/lib/libG4intercoms.so<br>
#23 0x00007ff779e21242 in G4UImanager::ExecuteMacroFile(char const*) () from /home/cpi/Installations/GEANT4/geant4.10.04.p02-install/lib/libG4intercoms.so<br>
#24 0x00007ff779e0e689 in G4UIcontrolMessenger::SetNewValue(G4UIcommand*, G4String) () from /home/cpi/Installations/GEANT4/geant4.10.04.p02-install/lib/libG4intercoms.so<br>
#25 0x00007ff779e03fac in G4UIcommand::DoIt(G4String) () from /home/cpi/Installations/GEANT4/geant4.10.04.p02-install/lib/libG4intercoms.so<br>
#26 0x00007ff779e20261 in G4UImanager::ApplyCommand(char const*) () from /home/cpi/Installations/GEANT4/geant4.10.04.p02-install/lib/libG4intercoms.so<br>
#27 0x0000000000632365 in main ()<br>
===========================================================<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="https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Froot.cern.ch%2Fforum&data=02%7C01%7Ckutalmis%40knights.ucf.edu%7Cef55085f893049d8f38808d6957b65f7%7C5b16e18278b3412c919668342689eeb7%7C0%7C0%7C636860754559076595&sdata=zo7Xfwy08MBi9t4FDVAMa6hybkMHzJhRru%2BoeLi3PN4%3D&reserved=0" id="LPlnk938246" class="OWAAutoLink" previewremoved="true">
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Only if you are really convinced it is a bug in ROOT then please submit a<br>
report at <a href="https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Froot.cern.ch%2Fbugs&data=02%7C01%7Ckutalmis%40knights.ucf.edu%7Cef55085f893049d8f38808d6957b65f7%7C5b16e18278b3412c919668342689eeb7%7C0%7C0%7C636860754559076595&sdata=wKwKMS7R%2FU7urMT%2FPBqkmwXoUd2EvYesuLuZoMpXEOg%3D&reserved=0" id="LPlnk58380" class="OWAAutoLink" previewremoved="true">
https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Froot.cern.ch%2Fbugs&data=02%7C01%7Ckutalmis%40knights.ucf.edu%7Cef55085f893049d8f38808d6957b65f7%7C5b16e18278b3412c919668342689eeb7%7C0%7C0%7C636860754559076595&sdata=wKwKMS7R%2FU7urMT%2FPBqkmwXoUd2EvYesuLuZoMpXEOg%3D&reserved=0</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>
===========================================================<br>
#5 0x0000000000b33fd1 in GateObjectStore::FindVolumeCreator(G4VPhysicalVolume*) ()<br>
#6 0x00000000006a1b03 in GateVolumeSelector::GateVolumeSelector(G4VPhysicalVolume*) ()<br>
#7 0x000000000086cf10 in GatePulse::ChangeVolumeIDAndOutputVolumeIDValue(unsigned long, int) ()<br>
#8 0x0000000000999bcb in GateReadout::ProcessPulseList(GatePulseList const*) ()<br>
#9 0x0000000000a68edb in GatePulseProcessorChain::ProcessPulseList() ()<br>
#10 0x00000000008226f4 in GateDigitizer::Digitize() ()<br>
#11 0x000000000096fff7 in GateOutputMgr::RecordEndOfEvent(G4Event const*) ()<br>
#12 0x00000000009f8299 in GateEventAction::EndOfEventAction(G4Event const*) ()<br>
#13 0x00007ff77cef8dd7 in G4EventManager::DoProcessing(G4Event*) () from /home/cpi/Installations/GEANT4/geant4.10.04.p02-install/lib/libG4event.so<br>
#14 0x00007ff77d1932a5 in G4RunManager::ProcessOneEvent(int) () from /home/cpi/Installations/GEANT4/geant4.10.04.p02-install/lib/libG4run.so<br>
#15 0x00007ff77d1912d3 in G4RunManager::DoEventLoop(int, char const*, int) [clone .localalias.94] () from /home/cpi/Installations/GEANT4/geant4.10.04.p02-install/lib/libG4run.so<br>
#16 0x00007ff77d19150b in G4RunManager::BeamOn(int, char const*, int) () from /home/cpi/Installations/GEANT4/geant4.10.04.p02-install/lib/libG4run.so<br>
#17 0x0000000000bc8d7c in GateApplicationMgr::StartDAQ() ()<br>
#18 0x0000000000b6f720 in GateApplicationMgrMessenger::SetNewValue(G4UIcommand*, G4String) ()<br>
#19 0x00007ff779e03fac in G4UIcommand::DoIt(G4String) () from /home/cpi/Installations/GEANT4/geant4.10.04.p02-install/lib/libG4intercoms.so<br>
#20 0x00007ff779e20261 in G4UImanager::ApplyCommand(char const*) () from /home/cpi/Installations/GEANT4/geant4.10.04.p02-install/lib/libG4intercoms.so<br>
#21 0x00007ff779deddd7 in G4UIbatch::ExecCommand(G4String const&) () from /home/cpi/Installations/GEANT4/geant4.10.04.p02-install/lib/libG4intercoms.so<br>
#22 0x00007ff779defbae in G4UIbatch::SessionStart() () from /home/cpi/Installations/GEANT4/geant4.10.04.p02-install/lib/libG4intercoms.so<br>
#23 0x00007ff779e21242 in G4UImanager::ExecuteMacroFile(char const*) () from /home/cpi/Installations/GEANT4/geant4.10.04.p02-install/lib/libG4intercoms.so<br>
#24 0x00007ff779e0e689 in G4UIcontrolMessenger::SetNewValue(G4UIcommand*, G4String) () from /home/cpi/Installations/GEANT4/geant4.10.04.p02-install/lib/libG4intercoms.so<br>
#25 0x00007ff779e03fac in G4UIcommand::DoIt(G4String) () from /home/cpi/Installations/GEANT4/geant4.10.04.p02-install/lib/libG4intercoms.so<br>
#26 0x00007ff779e20261 in G4UImanager::ApplyCommand(char const*) () from /home/cpi/Installations/GEANT4/geant4.10.04.p02-install/lib/libG4intercoms.so<br>
#27 0x0000000000632365 in main ()<br>
===========================================================<br>
<br>
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End of Gate-users Digest, Vol 153, Issue 16<br>
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