<div class="gmail_quote">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 <div class="gmail_quote">Den 3 oktober 2009 18.34 skrev Marcin Balcerzyk <<a href="mailto:m.balcerzyk@pluri.ucm.es" target="_blank">m.balcerzyk@pluri.ucm.es</a>>:<div> <div></div><div class="h5"> <blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"> <div link="blue" vlink="purple" lang="EN-US"> <div> 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 <a href="http://webdav.nencki.gov.pl/mbalcerzyk/Albira/MYRIAD3DReader.exe" target="_blank">http://webdav.nencki.gov.pl/mbalcerzyk/Albira/MYRIAD3DReader.exe</a> 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 <div style="border-style: solid none none; border-color: rgb(181, 196, 223) -moz-use-text-color -moz-use-text-color; border-width: 1pt medium medium; padding: 3pt 0in 0in;"> From: Ida Häggström [mailto:<a href="mailto:ida.haggstrom@gmail.com" target="_blank">ida.haggstrom@gmail.com</a>] Sent: Friday, October 02, 2009 12:42 PM To: gate-users Cc: <a href="mailto:m.balcerzyk@pluri.ucm.es" target="_blank">m.balcerzyk@pluri.ucm.es</a>; <a href="mailto:gate.stute@gmail.com" target="_blank">gate.stute@gmail.com</a>; <a href="mailto:rehfeld@imnc.in2p3.fr" target="_blank">rehfeld@imnc.in2p3.fr</a> Subject: Possibly a bug in GATE geometry check? </div><div><div></div><div> 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 </div></div></div> </div> </blockquote></div></div></div> </div>