[Gate-users] Weird Phantom Warning
Xinjie Cao
xinjie.cao at stonybrook.edu
Tue Jan 19 05:14:19 CET 2021
Hi Matthew,
I tested another phantom configuration with some modification based on
the before version. While the same error/warning showed again once I
changed the phantom 3 material from the air to water, is there any rule
about the material setting?
/gate/world/daughters/name phantom1
/gate/world/daughters/insert cylinder
/gate/phantom1/placement/setTranslation 0.0 0.0 0.0 mm
/gate/phantom1/geometry/setRmax 101.5 mm
/gate/phantom1/geometry/setHeight 700 mm
/gate/phantom1/setMaterial Polyethylene
/gate/phantom1/attachPhantomSD
/gate/phantom1/daughters/name phantom2
/gate/phantom1/daughters/insert cylinder
/gate/phantom2/placement/setTranslation 0.0 -45.0 0.0 mm
/gate/phantom2/geometry/setRmax 3.2 mm
/gate/phantom2/geometry/setRmin 2.4 mm
/gate/phantom2/geometry/setHeight 700 mm
/gate/phantom2/setMaterial Air
/gate/phantom2/attachPhantomSD
/gate/phantom1/daughters/name phantom3
/gate/phantom1/daughters/insert cylinder
/gate/phantom3/placement/setTranslation 0.0 -45.0 0.0 mm
/gate/phantom3/geometry/setRmax 1.6 mm
/gate/phantom3/geometry/setHeight 700 mm
/gate/phantom3/setMaterial Air
/gate/phantom3/attachPhantomSD
Best,
Xinjie
On Mon, Jan 18, 2021 at 3:16 PM Matthew Strugari <matthew.strugari at dal.ca>
wrote:
> You should always set the model dimensions to be exactly equal to the
> physical dimensions for accurate modelling. From there, check to make sure
> you do not have any overlapping geometries with the command
> “/geometry/test/run” in your macro following “/gate/run/initialize”. If you
> do have overlapping geometries, GATE will tell you what is overlapping,
> where it’s overlapping, and by how much.
>
>
>
> In some cases of exact dimensions, I found that abutting geometries
> required trimming by 1um to avoid overlap warnings, but they are just
> warnings and should not restrict the simulation from running. I trimmed
> them for peace of mind.
>
>
>
> Best,
>
> Matthew
>
>
>
> *From: *Xinjie Cao <xinjie.cao at stonybrook.edu>
> *Date: *Monday, January 18, 2021 at 15:40
> *To: *Matthew Strugari <matthew.strugari at dal.ca>
> *Cc: *gate-users at lists.opengatecollaboration.org <
> gate-users at lists.opengatecollaboration.org>
> *Subject: *Re: [Gate-users] Weird Phantom Warning
>
> *CAUTION:* The Sender of this email is not from within Dalhousie.
>
> Hi Matthew,
>
>
>
> Thanks! I think I get your point now. One more question about the detailed
> size of the daughter volume. As for the example you presented in the last
> email, If the mother cylinder is with a 3.2 mm radius, what is the actual
> radius should I define for the following daughter cylinder? Rmax is 3.2 or
> 3.199 (some number that is very close to 3.2) considering the overlap? Or
> it doesn't matter?
>
>
>
> Best,
>
> Xinjie
>
>
>
> On Mon, Jan 18, 2021 at 1:59 PM Matthew Strugari <matthew.strugari at dal.ca>
> wrote:
>
> Hi Xinjie,
>
>
>
> In any geometry definition, it is important to follow these three rules
> when building a volume
> <https://opengate.readthedocs.io/en/latest/defining_a_geometry.html?highlight=daughter#building-a-volume>
> :
>
> - A volume which is located inside another must be its daughter
> - A daughter must be fully included in its mother
> - Volumes must not overlap.
>
> This may require you to get creative with daughter definitions in order to
> obtain a final geometry representing your physical setup.
>
>
>
> Your geometry does not satisfy these points based on the issues that I
> previously outlined. If part of your geometry requires polyethylene with a
> height of 800mm, I would start by defining that size as your mother volume.
> You can add on a daughter volume if you need a specific 100 mm region to be
> replaced with air.
>
>
>
> Consider, for example, that you define a mother polyethylene cylinder with
> a radius of 3.2 mm. Next, you define a daughter cylinder of air with a
> radius r of 2.4 <= r(mm) < 3.2 and within that daughter, you define a
> daughter cylinder of water with a radius of 0 <= r(mm) < 1.6. The remaining
> volume between 1.6 <= r(mm) < 2.4 will remain as polyethylene (i.e. there’s
> no need to redefine a daughter of polyethylene with those dimensions). Try
> to use that approach when defining your nested phantoms.
>
>
>
> Hth,
>
> Matthew
>
>
>
>
>
> *From: *Xinjie Cao <xinjie.cao at stonybrook.edu>
> *Date: *Monday, January 18, 2021 at 13:08
> *To: *Matthew Strugari <matthew.strugari at dal.ca>
> *Cc: *gate-users at lists.opengatecollaboration.org <
> gate-users at lists.opengatecollaboration.org>
> *Subject: *Re: [Gate-users] Weird Phantom Warning
>
> *CAUTION:* The Sender of this email is not from within Dalhousie.
>
> Hi Matthew,
>
>
>
> Thanks for your remind, how about setting the phantom 3 as the world
> daughter too to avoid that violation? Because that 800 mm length is
> according to the NEMA standard, so I am guessing better keep it if it could
> be solved.
>
>
>
> For the phantom 3 configuration, I think it is necessary. There is
> actually an air gap between the inner plastic tube and the outer 200 mm
> diameter plastic shell according to the standard I believe.
>
>
>
> Best,
>
> Xinjie
>
>
>
> On Mon, Jan 18, 2021 at 11:58 AM Matthew Strugari <matthew.strugari at dal.ca>
> wrote:
>
> Hi Xinjie,
>
>
>
> It looks like you have issues with overlapping geometries. You could try
> nesting phantom4 within phantom3 and nest phantom3 within phantom2. Also,
> is the height of phantom3 correct at 800mm? This does not fit within your
> parent volume of phantom1.
>
>
>
> Alternatively, is phantom3 even required? It looks like you’re reinserting
> polystyrene after voiding the region with air in phantom2. This could be
> avoided by setting Rmin to 2.4mm in phantom2.
>
>
>
> Regards,
>
> Matthew
>
>
>
> *From: *Gate-users <gate-users-bounces at lists.opengatecollaboration.org>
> on behalf of Xinjie Cao <xinjie.cao at stonybrook.edu>
> *Date: *Monday, January 18, 2021 at 12:38
> *To: *gate-users at lists.opengatecollaboration.org <
> gate-users at lists.opengatecollaboration.org>
> *Subject: *[Gate-users] Weird Phantom Warning
>
> *CAUTION:* The Sender of this email is not from within Dalhousie.
>
> Dear GATE users,
>
>
>
> I am simulating the count rate performance of some PET scanners, while I
> found an interesting warning/error when I made a change to the phantom
> configuration.
>
>
>
> *With the following simplified phantom configuration, both single thread
> or cluster tool can run the macro well:*
>
> #==========================
> # P H A N T O M
> #==========================
>
> /gate/world/daughters/name phantom1
> /gate/world/daughters/insert cylinder
> /gate/phantom1/placement/setTranslation 0.0 0.0 0.0 mm
> /gate/phantom1/geometry/setRmax 101.5 mm
> /gate/phantom1/geometry/setHeight 700 mm
> /gate/phantom1/setMaterial Polyethylene
> /gate/phantom1/attachPhantomSD
>
> /gate/phantom1/daughters/name phantom2
> /gate/phantom1/daughters/insert cylinder
> /gate/phantom2/placement/setTranslation 0.0 -45.0 0.0 mm
> /gate/phantom2/geometry/setRmax 3.2 mm
> /gate/phantom2/geometry/setHeight 700 mm
> /gate/phantom2/setMaterial Air
> /gate/phantom2/attachPhantomSD
>
>
>
> *While when I added two more daughter phantoms inside the previous outer
> shell volume as followed*,
>
>
>
> #===========================
> # P H A N T O M
> #===========================
>
> /gate/world/daughters/name phantom1
> /gate/world/daughters/insert cylinder
> /gate/phantom1/placement/setTranslation 0.0 0.0 0.0 mm
> /gate/phantom1/geometry/setRmax 101.5 mm
> /gate/phantom1/geometry/setHeight 700 mm
> /gate/phantom1/setMaterial Polyethylene
> /gate/phantom1/attachPhantomSD
>
> /gate/phantom1/daughters/name phantom2
> /gate/phantom1/daughters/insert cylinder
> /gate/phantom2/placement/setTranslation 0.0 -45.0 0.0 mm
> /gate/phantom2/geometry/setRmax 3.2 mm
> /gate/phantom2/geometry/setHeight 700 mm
> /gate/phantom2/setMaterial Air
> /gate/phantom2/attachPhantomSD
>
> /gate/phantom1/daughters/name phantom3
> /gate/phantom1/daughters/insert cylinder
> /gate/phantom3/placement/setTranslation 0.0 -45.0 0.0 mm
> /gate/phantom3/geometry/setRmax 2.4 mm
> /gate/phantom3/geometry/setRmin 1.6 mm
> /gate/phantom3/geometry/setHeight 800 mm
> /gate/phantom3/setMaterial Polyethylene
> /gate/phantom3/attachPhantomSD
>
> /gate/phantom1/daughters/name phantom4
> /gate/phantom1/daughters/insert cylinder
> /gate/phantom4/placement/setTranslation 0.0 -45.0 0.0 mm
> /gate/phantom4/geometry/setRmax 1.6 mm
> /gate/phantom4/geometry/setHeight 700 mm
> /gate/phantom4/setMaterial Water
> /gate/phantom4/attachPhantomSD
>
>
>
> *the GATE feedbacked a warning/error like this,*
>
>
>
> *** Break *** segmentation violation
>
> ===========================================================
> There was a crash.
> This is the entire stack trace of all threads:
> ===========================================================
> #0 0x00007f563c6d146c in waitpid () at /lib64/libc.so.6
> #1 0x00007f563c64ef62 in do_system () at /lib64/libc.so.6
> #2 0x00007f564b4c70c4 in TUnixSystem::StackTrace() () at
> /home/goldan/GATE/root/lib/libCore.so.6.18
> #3 0x00007f564b4c97fc in TUnixSystem::DispatchSignals(ESignals) () at
> /home/goldan/GATE/root/lib/libCore.so.6.18
> #4 0x00007f56471f4630 in <signal handler called> () at
> /lib64/libpthread.so.0
> #5 0x0000000000000040 in ()
> #6 0x00000000008e2658 in GateMaterialDatabase::~GateMaterialDatabase() ()
> #7 0x000000000087a8e6 in
> GateDetectorConstruction::~GateDetectorConstruction() ()
> #8 0x00007f564423a1e6 in G4RunManager::DeleteUserInitializations()
> (this=this
> entry=0x32997c0) at
> /home/goldan/GATE/geant4.10.05.p01/source/run/src/G4RunManager.cc:236
> #9 0x00007f564423ae75 in G4RunManager::~G4RunManager() (this=0x32997c0,
> __in_chrg=<optimized out>) at
> /home/goldan/GATE/geant4.10.05.p01/source/run/src/G4RunManager.cc:211
> #10 0x0000000000830e19 in GateRunManager::~GateRunManager() ()
> #11 0x000000000050198f in main ()
> ===========================================================
>
>
> The lines below might hint at the cause of the crash.
> You may get help by asking at the ROOT forum http://root.cern.ch/forum
> Only if you are really convinced it is a bug in ROOT then please submit a
> report at http://root.cern.ch/bugs Please post the ENTIRE stack trace
> from above as an attachment in addition to anything else
> that might help us fixing this issue.
> ===========================================================
> #5 0x0000000000000040 in ()
> #6 0x00000000008e2658 in GateMaterialDatabase::~GateMaterialDatabase() ()
> #7 0x000000000087a8e6 in
> GateDetectorConstruction::~GateDetectorConstruction() ()
> #8 0x00007f564423a1e6 in G4RunManager::DeleteUserInitializations()
> (this=this
> entry=0x32997c0) at
> /home/goldan/GATE/geant4.10.05.p01/source/run/src/G4RunManager.cc:236
> #9 0x00007f564423ae75 in G4RunManager::~G4RunManager() (this=0x32997c0,
> __in_chrg=<optimized out>) at
> /home/goldan/GATE/geant4.10.05.p01/source/run/src/G4RunManager.cc:211
> #10 0x0000000000830e19 in GateRunManager::~GateRunManager() ()
> #11 0x000000000050198f in main ()
> ===========================================================
>
>
> WARNING - Attempt to delete the physical volume store while geometry
> closed !
> WARNING - Attempt to delete the logical volume store while geometry closed
> !
> WARNING - Attempt to delete the solid store while geometry closed !
> WARNING - Attempt to delete the region store while geometry closed !
>
>
>
> *The cluster tool could run the macro with added phantom configuration
> well with no warning/error, so I am not sure where the wrong with it or
> whether it has an* *influence on the simulation result. I probably have
> seen *a* similar issue when I used CASToR for reconstruction so I am
> guessing it is related to ROOT?*
>
>
>
> *Did anyone ever meet this issue before? Any reply will be highly
> appreciated! Thanks!*
>
>
>
> Best,
>
> Xinjie
>
>
>
>
>
>
> --
>
> *....................................................*
>
> *Xinjie Cao*
>
> *M.E. / Ph.D. Candidate*
>
> *Research Project Assistant*
>
> *Department of Electrical and Computer Engineering & Radiology *
>
> *Novel Medical Imaging Technologies Lab*
>
> *Health Science Center Level 8*
>
> *Stony Brook, NY 11794-8460 *
>
> *Tel: +1 (631)202-9445*
>
> you.stonybrook.edu/goldan/people/
>
> *email: **xinjie.cao at stonybroo*k.edu <xinjie.cao at stonybrook.edu>
>
>
>
>
>
> *....................................................*
>
> It is prohibited to distribute or publish the files attached to any other
> people unless you get permission from the writer himself. All rights
> reserved.
>
>
>
>
> --
>
> *....................................................*
>
> *Xinjie Cao*
>
> *M.E. / Ph.D. Candidate*
>
> *Research Project Assistant*
>
> *Department of Electrical and Computer Engineering & Radiology *
>
> *Novel Medical Imaging Technologies Lab*
>
> *Health Science Center Level 8*
>
> *Stony Brook, NY 11794-8460 *
>
> *Tel: +1 (631)202-9445*
>
> you.stonybrook.edu/goldan/people/
>
> *email: **xinjie.cao at stonybroo*k.edu <xinjie.cao at stonybrook.edu>
>
>
>
>
>
> *....................................................*
>
> It is prohibited to distribute or publish the files attached to any other
> people unless you get permission from the writer himself. All rights
> reserved.
>
--
*....................................................*
*Xinjie Cao*
*M.E. / Ph.D. Candidate*
*Research Project Assistant*
*Department of Electrical and Computer Engineering & Radiology *
*Novel Medical Imaging Technologies Lab*
*Health Science Center Level 8*
*Stony Brook, NY 11794-8460 *
*Tel: +1 (631)202-9445*
you.stonybrook.edu/goldan/people/
*email: **xinjie.cao at stonybroo*k.edu <xinjie.cao at stonybrook.edu>
*....................................................*
It is prohibited to distribute or publish the files attached to any other
people unless you get permission from the writer himself. All rights
reserved.
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