[Gate-users] Possibly a bug in GATE geometry check?

[Ida Häggström]

Dear Marcin,
here are all files in a zip file! I removed the directory structure, so the
files need only be in the same directory. CameraTest.mac is a copy of the
benchmarkPET camera setup, with some slight modifications to get rid of
geometry test errors. I for example changed

/gate/module/geometry/setYLength 8 cm
/gate/module/geometry/setZLength 10 cm

to

/gate/module/geometry/setYLength 7.999999 cm
/gate/module/geometry/setZLength 9.999999 cm


Regarding the warnings about the materials, I have some added posts in my
"GateMaterials.db", such as

Spleen: d=1.06 g/cm3 ; n=9
        +el: name=Hydrogen  ; f=0.103
        +el: name=Carbon    ; f=0.113
        +el: name=Nitrogen  ; f=0.032
        +el: name=Oxygen    ; f=0.741
        +el: name=Sodium    ; f=0.001
        +el: name=Phosphor  ; f=0.003
        +el: name=Sulfur    ; f=0.002
        +el: name=Chlorine  ; f=0.002
        +el: name=Potassium ; f=0.003

and more... These new materials are not added in my "Materials.xml" however
(only the defaults, LSO, Air and Epoxy are defined here). I added the .db
file in the zip-file as well, just in case.

Thanks!
Ida

Den 3 oktober 2009 18.34 skrev Marcin Balcerzyk <m.balcerzyk at pluri.ucm.es>:

 Dear Ida.
>
>
>
> I tried to run your Main.mac on my Gate 5 for Windows, but there is no
> CameraTest.mac in what you provided. Could you send it? Visu.mac is in your
> example, I guess. ZIP the required files with directory structure, as you
> use subdirectories in your MAC.
>
>
>
> My experience with Gate is that it gives very unexpected stupid errors. For
> example in ver. 3.0.0 I could not specify longer filenames then 8 characters
> for root files. So if you cannot use visualization OGLSX, don’t use it!.
> There is one which worked for me, when I did not have OpenGL system:
> VRML2FILE – it creates WRL files whenever you visualize the thing. Use your
> viewer of choice, in case you do not have, use
> http://webdav.nencki.gov.pl/mbalcerzyk/Albira/MYRIAD3DReader.exe with 1
> year free license. I have seen weird things in WRL files, like intermediate
> shapes of Gate which should not exist.
>
>
>
> I would put all files in the current directory of your simulation, where
> you invoke Gate, as it seems for me, there is sparking between Gate and
> GEANT4.
>
>
>
> I got the following message from Gate 5, with CameraTest.mac missing (which
> is weird enough already) from your Main.mac:
>
>
>
> PreInit> /control/execute Main.mac
>
> ***** Can not open a macro file <CameraTest.mac>
>
>    GateMaterialDatabase: did not load properties table for material
> 'Vacuum'.
>
>      This is only a problem when OPTICAL PHOTONS are transported in this
> materia
>
> l.'
>
> GateGeometryVoxelTabulatedTranslator::ReadFile : fileName:
> testPhantom/range.dat
>
>
>
> nTotCol: 1
>
>   imageValue: 1241208  material: , visible true, rgba(0.5,0,0,1)
>
>    GateMDBFile::ReadItem: I could not find the item '' in section
> [Materials] of
>
>  the material database.
>
>    GateMaterialDatabase: could not download the definition for ''
>
> GateMaterialDatabase: failed to read the material '' in the database file!
>
>
>
> GateSourceVoxelImageReader::ReadFile : fileName:
> testPhantom/smallVoxelPhantom.d
>
> at
>
> nx ny nz: 2002806303 0 2002807037
>
>
>
> This application has requested the Runtime to terminate it in an unusual
> way.
>
> Please contact the application's support team for more information.
>
>
>
> C:\Users\mbalcerzyk\Documents\...   \BugExample>
>
>
>
> Marcin Balcerzyk
>
>
>
> *From:* Ida Häggström [mailto:ida.haggstrom at gmail.com]
> *Sent:* Friday, October 02, 2009 12:42 PM
> *To:* gate-users
> *Cc:* m.balcerzyk at pluri.ucm.es; gate.stute at gmail.com;
> rehfeld at imnc.in2p3.fr
> *Subject:* Possibly a bug in GATE geometry check?
>
>
>
> Dear all,
>
> I've recently posted some questions regarding segmentation violations,
> geometry test errors and voxelized phantoms. I've experienced a lot of
> problems with getting a proper run from GATE, and I've spent many hours
> (piuh!) troubleshooting! =) Anyway, I discovered something that I'm not sure
> is a bug in GATE or if it's my code that is erroneous...
>
> I run a geometry check as I initialize my run, to check that there are no
> geometry overlaps etc since I believe this can cause segmentation violations
> which aborts the entire run.
> -------------
> /run/initialize
> /geometry/test/recursive_test
> -------------
> I usually keep the visualization disabled since this saves a lot of time
> for longer runs:
> -------------
> /vis/disable
> -------------
>  I noticed that I get errors regarding my voxelized phantom (overshooting
> daughter volume) which I don't think should be there (emphasis on THINK!).
> When I turn the visualization ON however, the errors disappear and I only
> get results like:
> ----------
> GeomTest: no daughter volume extending outside mother detected.
> GeomTest: no overlapping daughters detected.
> ---------
> from the geometry check. My visualization macro is very simple:
> ----------
> # Visualization.mac
> /vis/open OGLSX
> /vis/viewer/reset
> /vis/drawView 45 45
> /vis/viewer/zoom 2
> /vis/viewer/set/style surface
> /vis/drawVolume
> /tracking/storeTrajectory 1
> /vis/scene/endOfEventAction accumulate
> /vis/viewer/update
> ------------
> and I don't think the visualization should have anything to do with the
> geometry setup at all?(!) Can this be a GATE bug? Note that the only thing I
> change in my main macro is changing "/vis/disable" to
> ----------
> #/vis/disable
> /control/execute Visualization.mac
> ----------
> and I get no errors. I've also tried to disable all visualization of the
> phantom (in the range.dat file, setting visualization to "false") but this
> has no affect on the run results (no matter if I have the main visualization
> on or off).
>
> I have attached my main macro, GATE run output log, voxelized phantom macro
> with related .dat files and a screenshot of my setup with camera and
> phantom.
>
> Please, if anyone has any idea what could cause these problems, please let
> me know! I'm really running out of ideas... =) It's not a good option to
> always have to run with visualization on for longer runs...
> Thanks!
> Ida
>
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