[Gate-users] Weird Phantom Warning
Xinjie Cao
xinjie.cao at stonybrook.edu
Tue Jan 19 16:01:15 CET 2021
Hi Matthew,
Same error, the error/warning disappears only when I change the phantom 3
material from water to air.
Best,
Xinjie
On Tue, Jan 19, 2021 at 7:18 AM Matthew Strugari <matthew.strugari at dal.ca>
wrote:
> What happens when you define phantom 3 as the daughter of phantom 2? It’s
> still defined as the daughter of phantom 1.
>
> Matthew
>
> On Jan 19, 2021, at 12:14 AM, Xinjie Cao <xinjie.cao at stonybrook.edu>
> wrote:
>
>
>
> CAUTION: The Sender of this email is not from within Dalhousie.
> 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.
>
>
--
*....................................................*
*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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