Dear John,<br><br>Thank you so much for your reply! I find it very strange too that the visualization enabled or disabled gives different results. The reason I started with this geometry check is that my GATE run is aborted and I can't figure out why. As I found errors in the geometry test, I figured that might be the root to by problems (I'm not sure about this however, but it's the best guess I have so far). <br>
<br>I've looked through the GATE users manual, but the only type of test I could find there was the one I'm using, i.e. "/geometry/test/recursive_test". I have built up my geometries step by step with the visaulization on, and everything looks OK in my eyes, i.e. no overlapping crystals, blocks, foils etc. Is there a better way you think to check the geometry? <br>
<br>I tried running a new voxelized phantom today, with visualization disabled. I got the error:<br>-------------------------------------------<br><span style="color: rgb(255, 0, 0);">GeomTest Error: Overshooting daughter volume</span><br style="color: rgb(255, 0, 0);">
<span style="color: rgb(255, 0, 0);"> The volume xcatPhantomVoxel_PVP[-1] appears to extend outside the mother volume xcatPhantom_P[1]</span><br style="color: rgb(255, 0, 0);"><span style="color: rgb(255, 0, 0);"> at the following points in global coordinates: (list truncated)</span><br>
.<br>.<br>.<br><br><span style="color: rgb(255, 0, 0);">970000 singles stored in LMF fileTime set to (s) 1</span><br style="color: rgb(255, 0, 0);"><span style="color: rgb(255, 0, 0);">1950000 singles stored in LMF fileTime set to (s) 2</span><br style="color: rgb(255, 0, 0);">
<span style="color: rgb(255, 0, 0);">2930000 singles stored in LMF fileTime set to (s) 3</span><br style="color: rgb(255, 0, 0);"><span style="color: rgb(255, 0, 0);">ERROR - G4PhantomParameterisation::GetReplicaNo()</span><br style="color: rgb(255, 0, 0);">
<span style="color: rgb(255, 0, 0);"> localPoint - (1.837206641,1.061885918,-0.07676457566) - is outside container solid: xcat_S</span><br style="color: rgb(255, 0, 0);"><br style="color: rgb(255, 0, 0);"><span style="color: rgb(255, 0, 0);">*** G4Exception : InvalidSetup</span><br style="color: rgb(255, 0, 0);">
<span style="color: rgb(255, 0, 0);"> issued by : G4PhantomParameterisation::GetReplicaNo()</span><br style="color: rgb(255, 0, 0);"><span style="color: rgb(255, 0, 0);">Point outside voxels!</span><br style="color: rgb(255, 0, 0);">
<span style="color: rgb(255, 0, 0);">*** Fatal Error In Argument *** core dump ***</span><br style="color: rgb(255, 0, 0);"><br style="color: rgb(255, 0, 0);"><span style="color: rgb(255, 0, 0);">*** G4Exception: Aborting execution ***</span><br style="color: rgb(255, 0, 0);">
<span style="color: rgb(255, 0, 0);">3530000 singles stored in LMF fileGatedied with signal 6</span><br>-----------------------------------------<br> I don't know how the voxels can extend outside the mother xcatPhantom. I only create the regular matrix xcatPhantom, and the voxels are created by the program. I get the same geometry error for the voxelized phantom I attached in the zip-file in the previous post. Anway, I figured the latter error that aborted the run is associated to the geometry check error. <br>
With visualization enabled, I don't get any geometry check errors, but the computer hangs after a while, before I arrive at the error point! I tried four times, same result. I guess the CPU gets overloaded or something with visualization enabled, I don't know. I really don't know how to proceed, cause I need to run these voxelized phantoms. <br>
<br>Sorry for making this post looonger and looonger, but I really have no clue what to do, or if I'm trying to solve the right problem. Thank you for your help!<br>Ida<br><br><div class="gmail_quote">Den 5 oktober 2009 15.25 skrev John Apostolakis <span dir="ltr"><<a href="mailto:john.apostolakis@cern.ch">john.apostolakis@cern.ch</a>></span>:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
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Dear Ida,<br>
<br>
I write from the perspective of a Geant4 developer - but the
observations should apply equally to any GATE application.<br>
<br>
- It is unexpected that using visualisation should change the result
of any geometry check.<br>
- The results of the recursive_test should be reasonably accurate;
that is at the limit of high statistics you should get a correct
answer, and using default number of trial lines you should get an
answer which does not vary from run to run.<br>
<br>
There is another method to check a Geant4 geometry, which involves
checking every volume which is positioned to see that it does not
overlap with a volume at the same level or protrude from its parent
volume. I am not certain whether this capability is exploited already
in Gate, in all or recent releases. <br>
<br>
Best regards,<br>
John A.<br>
<br>
Ida Häggström wrote:
<blockquote type="cite"><div><div></div><div class="h5">
<div class="gmail_quote">Dear all, <br>
<br>
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...<br>
<br>
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. <br>
<span style="color: rgb(51, 51, 255);">-------------<br>
/run/initialize</span><br style="color: rgb(51, 51, 255);">
<span style="color: rgb(51, 51, 255);">/geometry/test/recursive_test</span><br>
-------------<br>
I usually keep the visualization disabled since this saves a lot of
time for longer runs:<br>
<span style="color: rgb(51, 51, 255);">-------------<br>
/vis/disable</span><br>
-------------<br>
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:<br>
----------<br>
<span style="color: rgb(51, 51, 255);">GeomTest: no daughter volume
extending outside mother detected.</span><br style="color: rgb(51, 51, 255);">
<span style="color: rgb(51, 51, 255);">GeomTest: no overlapping
daughters detected.</span><br>
---------<br>
from the geometry check. My visualization macro is very simple:<br>
----------<br>
<span style="color: rgb(51, 51, 255);"># Visualization.mac</span><br>
<span style="color: rgb(51, 51, 255);">/vis/open OGLSX</span><br style="color: rgb(51, 51, 255);">
<span style="color: rgb(51, 51, 255);">/vis/viewer/reset</span><br style="color: rgb(51, 51, 255);">
<span style="color: rgb(51, 51, 255);">/vis/drawView 45 45</span><br style="color: rgb(51, 51, 255);">
<span style="color: rgb(51, 51, 255);">/vis/viewer/zoom 2</span><br style="color: rgb(51, 51, 255);">
<span style="color: rgb(51, 51, 255);">/vis/viewer/set/style surface</span><br style="color: rgb(51, 51, 255);">
<span style="color: rgb(51, 51, 255);">/vis/drawVolume</span><br style="color: rgb(51, 51, 255);">
<span style="color: rgb(51, 51, 255);">/tracking/storeTrajectory 1</span><br style="color: rgb(51, 51, 255);">
<span style="color: rgb(51, 51, 255);">/vis/scene/endOfEventAction
accumulate</span><br style="color: rgb(51, 51, 255);">
<span style="color: rgb(51, 51, 255);">/vis/viewer/update</span><br>
------------<br>
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<span style="color: rgb(0, 0, 0);"> </span><span style="color: rgb(51, 51, 255);"><span style="color: rgb(0, 0, 0);">"/vis/disable"
to</span><br>
----------<br>
#/vis/disable</span><br style="color: rgb(51, 51, 255);">
<span style="color: rgb(51, 51, 255);">/control/execute
Visualization.mac</span><br>
----------<br>
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).<br>
<br>
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.<br>
<br>
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...<br>
Thanks!<br>
<font color="#888888">Ida<br>
</font></div>
<br>
<br>
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