[Gate-users] SetDepth on TakeEnergyCentroid
Kutalmis Akpinar
kutalmis at knights.ucf.edu
Mon Feb 18 21:02:49 CET 2019
Hi Sebastien,
Thank you for your kind response. The code block you pointed was quite helpful. (For reference to others, line 64-103: https://github.com/OpenGATE/Gate/blob/develop/source/digits_hits/src/GateReadout.cc )
I want to make it clear, you wrote "« TakeEnergyWinner » works on the crystal level component"
Did you actually mean " « TakeEnergyCentroid » works <<One level above>> the crystal level component" ?
That is what I understand from line 101-102:
----------- line 101-102 -----------
// Now force m_depth to be right above the crystal depth
m_depth = m_crystalDepth - 1;
-----------------------------------------
Or, did you really mean "« TakeEnergyWinner » works on the crystal level component", so, setDepth has nothing to do with « TakeEnergyCentroid », I need to leave it as "4", which is the crystal level.
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.
Thank you,
Kutalmis Akpinar
University of Central Florida, Computer Science, PhD candidate
________________________________
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Today's Topics:
1. Re: SetDepth on TakeEnergyCentroid (JAN Sebastien)
----------------------------------------------------------------------
Message: 1
Date: Mon, 18 Feb 2019 08:30:37 +0000
From: JAN Sebastien <sebastien.jan at cea.fr>
To: Kutalmis Akpinar <kutalmis at knights.ucf.edu>,
"gate-users at lists.opengatecollaboration.org"
<gate-users at lists.opengatecollaboration.org>
Subject: Re: [Gate-users] SetDepth on TakeEnergyCentroid
Message-ID:
<63BD57EF92283749A0D90EC01273552C38B0FC55 at EXDAG0-A1.intra.cea.fr>
Content-Type: text/plain; charset="iso-8859-1"
Hi,
This policy « TakeEnergyWinner » works on the crystal level component.
For details, you can check the code :
Source/digits_hist/src/GateReadout.cc
Line 64 -> 103
Cheers
Seb
De : Gate-users <gate-users-bounces at lists.opengatecollaboration.org> De la part de Kutalmis Akpinar
Envoyé : lundi 18 février 2019 03:59
À : gate-users at lists.opengatecollaboration.org
Objet : [Gate-users] SetDepth on TakeEnergyCentroid
Dear Gate users;
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.
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."
This is how my levels are (Please see the "describe" output as below.):
cylindricalPET (level 0)
rsector (level 1)
submodule (level 3)
crystal (level 4)
lyso (level 5)
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:
/gate/digitizer/Singles/readout/setDepth 3
However, it crashes if I remove setDepth. (Please see the "Crash Report" as below)
If I put the line and set it to 3, it also crashes the same way.
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:
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
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?
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.
Thank you,
Kutalmis Akpinar
University of Central Florida, Computer Science, PhD candidate
*********************** This is my describe output **********************************
==========================
GATE object: 'systems/cylindricalPET'
Components:
GATE object: 'systems/cylindricalPET/base'
Attached to volume: cylindricalPET
Nb of children: 1
GATE object: 'systems/cylindricalPET/rsector'
Attached to volume: cpi_module
Nb of children: 1
GATE object: 'systems/cylindricalPET/module'
Attached to volume: ---
Nb of children: 1
GATE object: 'systems/cylindricalPET/submodule'
Attached to volume: cpi_block
Nb of children: 1
GATE object: 'systems/cylindricalPET/crystal'
Attached to volume: cpi_crystal
Nb of children: 4
GATE object: 'systems/cylindricalPET/layer0'
Attached to volume: cpi_lyso
Nb of children: 0
GATE object: 'systems/cylindricalPET/layer1'
Attached to volume: ---
Nb of children: 0
GATE object: 'systems/cylindricalPET/layer2'
Attached to volume: ---
Nb of children: 0
GATE object: 'systems/cylindricalPET/layer3'
Attached to volume: ---
Nb of children: 0
geometrical design type: 1
ring diameter: 83.2 cm
rsector axial pitch: 0 fm
rsector azimuthal pitch: 8.18182 degree
rsector tangential size: 5.674 cm
rsector axial size: 17.114 cm
module axial size: 17.114 cm
module tangential size: 5.674 cm
module axial pitch: 0 fm
module tangential pitch: 0 fm
submodule axial size: 5.674 cm
submodule tangential size: 5.674 cm
submodule axial pitch: 5.72 cm
submodule tangential pitch: 0 fm
crystal radial size: 1.5 cm
crystal axial size: 4 mm
crystal tangential size: 4 mm
crystal axial pitch: 4.05692 mm
crystal tangential pitch: 4.05692 mm
layer0 radial size: 1.5 cm
in layer0 interaction length: 7.5 mm
Axial nb of rsectors: 1
Azimuthal nb of rsectors: 44
Axial nb of modules: 1
Tangential nb of modules: 1
Axial nb of submodules: 3
Tangential nb of submodules: 1
Axial nb of crystals: 14
Tangential nb of crystals: 14
Radial nb of layers: 1
==================================
************************************Crash Report:***********************************
*** Break *** segmentation violation
[Acquisition-0]
[Acquisition-0] ============= Source initialization =============
[Acquisition-0]
[Acquisition-0] ============= Acquisition starts! =============
[Acquisition-0] Simulation start time = 0 sec
[Acquisition-0] Simulation end time = 250 sec
[Acquisition-0] Simulation will have = 1 run(s)
[Acquisition-0] Slice 0 from 0 to 250 s [slice=250 s]
===========================================================
There was a crash.
This is the entire stack trace of all threads:
===========================================================
#0 0x00007ff778b3307a in __GI___waitpid (pid=32153, stat_loc=stat_loc
entry=0x7ffd9872e9c0, options=options
entry=0) at ../sysdeps/unix/sysv/linux/waitpid.c:29
#1 0x00007ff778aabfbb in do_system (line=<optimized out>) at ../sysdeps/posix/system.c:148
#2 0x00007ff77fd790d2 in TUnixSystem::StackTrace() () from /home/cpi/Installations/ROOT/root_v6.14.06/lib/libCore.so
#3 0x00007ff77fd7b9a3 in TUnixSystem::DispatchSignals(ESignals) () from /home/cpi/Installations/ROOT/root_v6.14.06/lib/libCore.so
#4 <signal handler called>
#5 0x0000000000b33fd1 in GateObjectStore::FindVolumeCreator(G4VPhysicalVolume*) ()
#6 0x00000000006a1b03 in GateVolumeSelector::GateVolumeSelector(G4VPhysicalVolume*) ()
#7 0x000000000086cf10 in GatePulse::ChangeVolumeIDAndOutputVolumeIDValue(unsigned long, int) ()
#8 0x0000000000999bcb in GateReadout::ProcessPulseList(GatePulseList const*) ()
#9 0x0000000000a68edb in GatePulseProcessorChain::ProcessPulseList() ()
#10 0x00000000008226f4 in GateDigitizer::Digitize() ()
#11 0x000000000096fff7 in GateOutputMgr::RecordEndOfEvent(G4Event const*) ()
#12 0x00000000009f8299 in GateEventAction::EndOfEventAction(G4Event const*) ()
#13 0x00007ff77cef8dd7 in G4EventManager::DoProcessing(G4Event*) () from /home/cpi/Installations/GEANT4/geant4.10.04.p02-install/lib/libG4event.so
#14 0x00007ff77d1932a5 in G4RunManager::ProcessOneEvent(int) () from /home/cpi/Installations/GEANT4/geant4.10.04.p02-install/lib/libG4run.so
#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
#16 0x00007ff77d19150b in G4RunManager::BeamOn(int, char const*, int) () from /home/cpi/Installations/GEANT4/geant4.10.04.p02-install/lib/libG4run.so
#17 0x0000000000bc8d7c in GateApplicationMgr::StartDAQ() ()
#18 0x0000000000b6f720 in GateApplicationMgrMessenger::SetNewValue(G4UIcommand*, G4String) ()
#19 0x00007ff779e03fac in G4UIcommand::DoIt(G4String) () from /home/cpi/Installations/GEANT4/geant4.10.04.p02-install/lib/libG4intercoms.so
#20 0x00007ff779e20261 in G4UImanager::ApplyCommand(char const*) () from /home/cpi/Installations/GEANT4/geant4.10.04.p02-install/lib/libG4intercoms.so
#21 0x00007ff779deddd7 in G4UIbatch::ExecCommand(G4String const&) () from /home/cpi/Installations/GEANT4/geant4.10.04.p02-install/lib/libG4intercoms.so
#22 0x00007ff779defbae in G4UIbatch::SessionStart() () from /home/cpi/Installations/GEANT4/geant4.10.04.p02-install/lib/libG4intercoms.so
#23 0x00007ff779e21242 in G4UImanager::ExecuteMacroFile(char const*) () from /home/cpi/Installations/GEANT4/geant4.10.04.p02-install/lib/libG4intercoms.so
#24 0x00007ff779e0e689 in G4UIcontrolMessenger::SetNewValue(G4UIcommand*, G4String) () from /home/cpi/Installations/GEANT4/geant4.10.04.p02-install/lib/libG4intercoms.so
#25 0x00007ff779e03fac in G4UIcommand::DoIt(G4String) () from /home/cpi/Installations/GEANT4/geant4.10.04.p02-install/lib/libG4intercoms.so
#26 0x00007ff779e20261 in G4UImanager::ApplyCommand(char const*) () from /home/cpi/Installations/GEANT4/geant4.10.04.p02-install/lib/libG4intercoms.so
#27 0x0000000000632365 in main ()
===========================================================
The lines below might hint at the cause of the crash.
You may get help by asking at the ROOT forum 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
Only if you are really convinced it is a bug in ROOT then please submit a
report at 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 Please post the ENTIRE stack trace
from above as an attachment in addition to anything else
that might help us fixing this issue.
===========================================================
#5 0x0000000000b33fd1 in GateObjectStore::FindVolumeCreator(G4VPhysicalVolume*) ()
#6 0x00000000006a1b03 in GateVolumeSelector::GateVolumeSelector(G4VPhysicalVolume*) ()
#7 0x000000000086cf10 in GatePulse::ChangeVolumeIDAndOutputVolumeIDValue(unsigned long, int) ()
#8 0x0000000000999bcb in GateReadout::ProcessPulseList(GatePulseList const*) ()
#9 0x0000000000a68edb in GatePulseProcessorChain::ProcessPulseList() ()
#10 0x00000000008226f4 in GateDigitizer::Digitize() ()
#11 0x000000000096fff7 in GateOutputMgr::RecordEndOfEvent(G4Event const*) ()
#12 0x00000000009f8299 in GateEventAction::EndOfEventAction(G4Event const*) ()
#13 0x00007ff77cef8dd7 in G4EventManager::DoProcessing(G4Event*) () from /home/cpi/Installations/GEANT4/geant4.10.04.p02-install/lib/libG4event.so
#14 0x00007ff77d1932a5 in G4RunManager::ProcessOneEvent(int) () from /home/cpi/Installations/GEANT4/geant4.10.04.p02-install/lib/libG4run.so
#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
#16 0x00007ff77d19150b in G4RunManager::BeamOn(int, char const*, int) () from /home/cpi/Installations/GEANT4/geant4.10.04.p02-install/lib/libG4run.so
#17 0x0000000000bc8d7c in GateApplicationMgr::StartDAQ() ()
#18 0x0000000000b6f720 in GateApplicationMgrMessenger::SetNewValue(G4UIcommand*, G4String) ()
#19 0x00007ff779e03fac in G4UIcommand::DoIt(G4String) () from /home/cpi/Installations/GEANT4/geant4.10.04.p02-install/lib/libG4intercoms.so
#20 0x00007ff779e20261 in G4UImanager::ApplyCommand(char const*) () from /home/cpi/Installations/GEANT4/geant4.10.04.p02-install/lib/libG4intercoms.so
#21 0x00007ff779deddd7 in G4UIbatch::ExecCommand(G4String const&) () from /home/cpi/Installations/GEANT4/geant4.10.04.p02-install/lib/libG4intercoms.so
#22 0x00007ff779defbae in G4UIbatch::SessionStart() () from /home/cpi/Installations/GEANT4/geant4.10.04.p02-install/lib/libG4intercoms.so
#23 0x00007ff779e21242 in G4UImanager::ExecuteMacroFile(char const*) () from /home/cpi/Installations/GEANT4/geant4.10.04.p02-install/lib/libG4intercoms.so
#24 0x00007ff779e0e689 in G4UIcontrolMessenger::SetNewValue(G4UIcommand*, G4String) () from /home/cpi/Installations/GEANT4/geant4.10.04.p02-install/lib/libG4intercoms.so
#25 0x00007ff779e03fac in G4UIcommand::DoIt(G4String) () from /home/cpi/Installations/GEANT4/geant4.10.04.p02-install/lib/libG4intercoms.so
#26 0x00007ff779e20261 in G4UImanager::ApplyCommand(char const*) () from /home/cpi/Installations/GEANT4/geant4.10.04.p02-install/lib/libG4intercoms.so
#27 0x0000000000632365 in main ()
===========================================================
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