[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
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.opengatecollaboration.org/pipermail/gate-users/attachments/20190814/4e86a889/attachment.html>
More information about the Gate-users
mailing list