[Gate-users] STL file for detector

Svetlana G. Shasharina sveta at txcorp.com
Wed Aug 14 21:25:15 CEST 2019


Hi Matthew,

I think we are narrowing this down.  I created a new STL and edited out 
one line doing attachment of STL data:

#/gate/systems/cylindricalPET/layer0/attach LSO

It runs now without the seg fault.  But it will not create correct 
results as one need to attach this geometry to the layer.

Looks like we use slightly different versions as I see different names.  
So I am attaching my .mac file and the stl file used in it.

Thank you!

Sveta

On 8/14/19 12:49 PM, Matthew Strugari wrote:
>
> Hi again Sveta,
>
> I created the lsobox with the Blender software just to verify your 
> geometry. Your units appear to be in um rather than mm as previously 
> mentioned. Nonetheless, Gate fails to execute the macro file past 
> these lines when using the STL files:
>
> #              A T T A C H    S Y S T E M
>
> /gate/systems/cylindricalPET/rsector/attach head
>
> /gate/systems/cylindricalPET/module/attach block
>
> /gate/systems/cylindricalPET/crystal/attach crystal
>
> /gate/systems/cylindricalPET/layer0/attach LSOcrystal
>
> /gate/systems/cylindricalPET/layer1/attach BGO
>
> I was able to visualize the geometry without the SegFault after 
> removing those lines. I am unsure if this a bug in the cylindricalPET 
> system so I am hoping someone else can give some input on this. 
> Perhaps the commands to attach the system haved changed (?) but I am 
> really only familiar with the SPECThead system.
>
> I hope this helps.
>
> Matthew
>
> *From: *Gate-users 
> <gate-users-bounces at lists.opengatecollaboration.org> on behalf of 
> Matthew Strugari <matthew.strugari at dal.ca>
> *Date: *Wednesday, August 14, 2019 at 3:12 PM
> *To: *"Svetlana G. Shasharina" <sveta at txcorp.com>
> *Cc: *"gate-users at lists.opengatecollaboration.org" 
> <gate-users at lists.opengatecollaboration.org>
> *Subject: *Re: [Gate-users] STL file for detector
>
> Hi Svetlana,
>
> I cannot speak to the examples without testing them myself. However, 
> when using your STL files, the first warning suggests that the 
> Materials.xml file is not located in the folder where you are 
> executing “Gate PET_CYlindricalPet_System.mac”. You can copy the .xml 
> files into your directory or use softlinks to reference the location 
> of the .xml files in order to avoid different versions of the 
> materials/surface files should you make any edits.
>
> When loading your STL files, I also receive the SegFault but I suspect 
> that the problem is due to your STL files. When I load the lsobox STL 
> files into Slicer 3D, the long axis has a length of 0.15 mm rather 
> than the desired 15 mm. What program did you use to create your STL 
> files and have you verified their dimensions and orientations for 
> loading directly into Gate?
>
> Cheers,
>
> Matthew
>
> *From: *"Svetlana G. Shasharina" <sveta at txcorp.com>
> *Date: *Wednesday, August 14, 2019 at 1:20 PM
> *To: *Matthew Strugari <matthew.strugari at dal.ca>
> *Cc: *"gate-users at lists.opengatecollaboration.org" 
> <gate-users at lists.opengatecollaboration.org>, Peter Neilson 
> <neilson at txcorp.com>
> *Subject: *Re: [Gate-users] STL file for detector
>
> Hi everybody,
>
> I tried to run the kidney example under:
>
> GateContrib-master/misc/geometry_STL/kidneys and got the following error:
>
> Core-0] Initialization of geometry
> [G4-cerr] STL file corrupted: number of facets do not correspond to 
> file size.
> ^Z
> [2]+  Stopped                 Gate mac/main.mac
>
> I am getting the same message for the Suzanne example.
>
> Next I tried to use STL files (binary and asci STLs attached) instead 
> of the "LSO" box in 
> GateContrib-master/imaging/PET/PET_CylindricalPET_System.mac by doing 
> the following editing:
>
> #       LSO layer
> /gate/crystal/daughters/name                  LSO
> #/gate/crystal/daughters/insert                box
> /gate/crystal/daughters/insert                tessellated
> /gate/LSO/placement/setTranslation            -0.75 0.0 0.0 cm
> /gate/LSO/geometry/setPathToSTLFile            lsobox.stl
> #/gate/LSO/geometry/setXLength                 15 mm
> #/gate/LSO/geometry/setYLength                 3.0 mm
> #/gate/LSO/geometry/setZLength                 3.8 mm
> /gate/LSO/setMaterial                         LSO
> /gate/LSO/vis/setColor                        red
>
> This example does not run anymore (it does when it uses the original 
> box) and I am getting:
>
> I/O warning : failed to load external entity "./Materials.xml"
> I/O warning: Discard the previous warning if your simulation doesn't 
> transport OPTICAL PHOTONS.
> Otherwise, please copy the ./Materials.xml file from the gate-source 
> directory in the directory where you run your main macro.
> I/O warning : failed to load external entity "./Materials.xml"
> I/O warning: Discard the previous warning if your simulation doesn't 
> transport OPTICAL PHOTONS.
> Otherwise, please copy the ./Materials.xml file from the gate-source 
> directory in the directory where you run your main macro.
> I/O warning : failed to load external entity "./Materials.xml"
> I/O warning: Discard the previous warning if your simulation doesn't 
> transport OPTICAL PHOTONS.
> Otherwise, please copy the ./Materials.xml file from the gate-source 
> directory in the directory where you run your main macro.
> I/O warning : failed to load external entity "./Materials.xml"
> I/O warning: Discard the previous warning if your simulation doesn't 
> transport OPTICAL PHOTONS.
> Otherwise, please copy the ./Materials.xml file from the gate-source 
> directory in the directory where you run your main macro.
>
>  *** Break *** illegal instruction
> [/usr/lib/system/libsystem_platform.dylib] _sigtramp (no debug info)
> [<unknown binary>] (no debug info)
> [/opt/contrib-appleclang/gate-8.2/bin/Gate] 
> GateSystemComponent::SetCreator(GateVVolume*) (no debug info)
> [/opt/contrib-appleclang/geant4-sersh/lib/libG4intercoms.dylib] 
> G4UIcommand::DoIt(G4String) (no debug info)
> [/opt/contrib-appleclang/geant4-sersh/lib/libG4intercoms.dylib] 
> G4UImanager::ApplyCommand(char const*) (no debug info)
> [/opt/contrib-appleclang/geant4-sersh/lib/libG4intercoms.dylib] 
> G4UIbatch::ExecCommand(G4String const&) (no debug info)
> [/opt/contrib-appleclang/geant4-sersh/lib/libG4intercoms.dylib] 
> G4UIbatch::SessionStart() (no debug info)
> [/opt/contrib-appleclang/geant4-sersh/lib/libG4intercoms.dylib] 
> G4UImanager::ExecuteMacroFile(char const*) (no debug info)
> [/opt/contrib-appleclang/geant4-sersh/lib/libG4intercoms.dylib] 
> G4UIcontrolMessenger::SetNewValue(G4UIcommand*, G4String) (no debug info)
> [/opt/contrib-appleclang/geant4-sersh/lib/libG4intercoms.dylib] 
> G4UIcommand::DoIt(G4String) (no debug info)
> [/opt/contrib-appleclang/geant4-sersh/lib/libG4intercoms.dylib] 
> G4UImanager::ApplyCommand(char const*) (no debug info)
> [/opt/contrib-appleclang/gate-8.2/bin/Gate] main (no debug info)
> [/usr/lib/system/libdyld.dylib] start (no debug info)
> [<unknown binary>] (no debug info)
> [LSO::IsValidAttachmentRequest]:
>     The volume creator ('?sveta at bladerunner/.../PET$
>
> Does anybody have a working example with STL geometry?
>
> Thank you,
>
> Svetlana
>
> On 8/8/19 5:09 PM, Matthew Strugari wrote:
>
>     Hi Svetlana,
>
>     Take a look at the section How to build a "tessellated" volume on
>     the wiki page
>     http://wiki.opengatecollaboration.org/index.php/Users_Guide:Defining_a_geometry.
>     The sample code is from the GateContrib GitHub repository as
>     outlined on the wiki.
>
>     Cheers,
>
>     Matthew
>
>     --
>
>     Matthew Strugari
>
>     Biomedical Translational Imaging Centre - BIOTIC,
>
>     5890 University Ave,
>
>     Halifax, NS, B3K 6R8
>
>
>     On Aug 8, 2019, at 6:28 PM, Svetlana G. Shasharina
>     <sveta at txcorp.com <mailto:sveta at txcorp.com>> wrote:
>
>         Hello,
>
>         Is there a way to use an STL file for the detector geometry?
>
>         Thank you,
>
>         Sveta
>
>         -- 
>         Svetlana Shasharina                            |
>         sveta at txcorp.com <mailto:sveta at txcorp.com>
>         Vice-President of Computational Infrastructure | Tech-X
>         Corporation
>
>         _______________________________________________
>         Gate-users mailing list
>         Gate-users at lists.opengatecollaboration.org
>         <mailto:Gate-users at lists.opengatecollaboration.org>
>         http://lists.opengatecollaboration.org/mailman/listinfo/gate-users
>
> -- 
> Svetlana Shasharina                            |sveta at txcorp.com  <mailto:sveta at txcorp.com>
> Vice-President of Computational Infrastructure | Tech-X Corporation

-- 
Svetlana Shasharina                            | sveta at txcorp.com
Vice-President of Computational Infrastructure | Tech-X Corporation

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