[Gate-users] STL file for detector

Svetlana G. Shasharina sveta at txcorp.com
Wed Aug 14 20:50:23 CEST 2019


Hi Matthew,

I copied Materials.xml into PET directory.

Nice catch about the units in our STL file!  We use meters when create 
STL...  So I did 2 things wrong here: I should have had 0.015 for m and 
since GATE expects mm, I should use dimensions 15x3x3.8.  I recreated 
the STL file and still get the seg fault in this example.

But I succeeded in just adding an STL phantom and now can see it!

Thank you,

Sveta



On 8/14/19 12:12 PM, Matthew Strugari wrote:
>
> 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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