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<p>Hi Matthew,</p>
<p>I think we are narrowing this down. I created a new STL and
edited out one line doing attachment of STL data:</p>
<p><span lang="EN-US">#/gate/systems/cylindricalPET/layer0/attach
LSO</span></p>
<p><span lang="EN-US">It runs now without the seg fault. But it
will not create correct results as one need to attach this
geometry to the layer.</span></p>
<p><span lang="EN-US">Looks like we use slightly different versions
as I see different names. So I am attaching my .mac file and
the stl file used in it.</span></p>
<p><span lang="EN-US">Thank you!</span></p>
<p><span lang="EN-US">Sveta<br>
</span></p>
<div class="moz-cite-prefix">On 8/14/19 12:49 PM, Matthew Strugari
wrote:<br>
</div>
<blockquote type="cite"
cite="mid:9CE35302-3EED-4AD6-BEC8-42F05D57730B@dal.ca">
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<p class="MsoNormal"><span lang="EN-US">Hi again Sveta,<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">I created the lsobox
with the Blender software just to verify your geometry. Your
units appear to be in um rather than mm as previously
mentioned. Nonetheless, Gate fails to execute the macro file
past these lines when using the STL files: <o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"># A T T A
C H S Y S T E M
<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">/gate/systems/cylindricalPET/rsector/attach
head<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">/gate/systems/cylindricalPET/module/attach
block<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">/gate/systems/cylindricalPET/crystal/attach
crystal<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">/gate/systems/cylindricalPET/layer0/attach
LSOcrystal<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">/gate/systems/cylindricalPET/layer1/attach
BGO<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">I was able to visualize
the geometry without the SegFault after removing those
lines. I am unsure if this a bug in the cylindricalPET
system so I am hoping someone else can give some input on
this. Perhaps the commands to attach the system haved
changed (?) but I am really only familiar with the SPECThead
system.<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">I hope this helps.<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">Matthew<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<div style="border:none;border-top:solid #B5C4DF
1.0pt;padding:3.0pt 0cm 0cm 0cm">
<p class="MsoNormal"><b><span
style="font-size:12.0pt;color:black">From: </span></b><span
style="font-size:12.0pt;color:black">Gate-users
<a class="moz-txt-link-rfc2396E" href="mailto:gate-users-bounces@lists.opengatecollaboration.org"><gate-users-bounces@lists.opengatecollaboration.org></a>
on behalf of Matthew Strugari
<a class="moz-txt-link-rfc2396E" href="mailto:matthew.strugari@dal.ca"><matthew.strugari@dal.ca></a><br>
<b>Date: </b>Wednesday, August 14, 2019 at 3:12 PM<br>
<b>To: </b>"Svetlana G. Shasharina"
<a class="moz-txt-link-rfc2396E" href="mailto:sveta@txcorp.com"><sveta@txcorp.com></a><br>
<b>Cc: </b><a class="moz-txt-link-rfc2396E" href="mailto:gate-users@lists.opengatecollaboration.org">"gate-users@lists.opengatecollaboration.org"</a>
<a class="moz-txt-link-rfc2396E" href="mailto:gate-users@lists.opengatecollaboration.org"><gate-users@lists.opengatecollaboration.org></a><br>
<b>Subject: </b>Re: [Gate-users] STL file for detector<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
<p class="MsoNormal"><span lang="EN-US">Hi Svetlana,</span><o:p></o:p></p>
<p class="MsoNormal"><span lang="EN-US"> </span><o:p></o:p></p>
<p class="MsoNormal"><span lang="EN-US">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.</span><o:p></o:p></p>
<p class="MsoNormal"><span lang="EN-US"> </span><o:p></o:p></p>
<p class="MsoNormal"><span lang="EN-US">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?</span><o:p></o:p></p>
<p class="MsoNormal"><span lang="EN-US"> </span><o:p></o:p></p>
<p class="MsoNormal"><span lang="EN-US">Cheers,</span><o:p></o:p></p>
<p class="MsoNormal"><span lang="EN-US">Matthew</span><o:p></o:p></p>
<p class="MsoNormal"><span lang="EN-US"> </span><o:p></o:p></p>
<p class="MsoNormal"><span lang="EN-US"> </span><o:p></o:p></p>
<div style="border:none;border-top:solid #B5C4DF
1.0pt;padding:3.0pt 0cm 0cm 0cm">
<p class="MsoNormal"><b><span
style="font-size:12.0pt;color:black">From: </span></b><span
style="font-size:12.0pt;color:black">"Svetlana G.
Shasharina" <a class="moz-txt-link-rfc2396E" href="mailto:sveta@txcorp.com"><sveta@txcorp.com></a><br>
<b>Date: </b>Wednesday, August 14, 2019 at 1:20 PM<br>
<b>To: </b>Matthew Strugari
<a class="moz-txt-link-rfc2396E" href="mailto:matthew.strugari@dal.ca"><matthew.strugari@dal.ca></a><br>
<b>Cc: </b><a class="moz-txt-link-rfc2396E" href="mailto:gate-users@lists.opengatecollaboration.org">"gate-users@lists.opengatecollaboration.org"</a>
<a class="moz-txt-link-rfc2396E" href="mailto:gate-users@lists.opengatecollaboration.org"><gate-users@lists.opengatecollaboration.org></a>, Peter
Neilson <a class="moz-txt-link-rfc2396E" href="mailto:neilson@txcorp.com"><neilson@txcorp.com></a><br>
<b>Subject: </b>Re: [Gate-users] STL file for detector</span><o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"> <o:p></o:p></p>
</div>
<p>Hi everybody,<o:p></o:p></p>
<p>I tried to run the kidney example under:<o:p></o:p></p>
<p>GateContrib-master/misc/geometry_STL/kidneys and got the
following error:<o:p></o:p></p>
<p>Core-0] Initialization of geometry<br>
[G4-cerr] STL file corrupted: number of facets do not
correspond to file size.<br>
^Z<br>
[2]+ Stopped Gate mac/main.mac<o:p></o:p></p>
<p>I am getting the same message for the Suzanne example.<o:p></o:p></p>
<p>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:<o:p></o:p></p>
<p># LSO layer<br>
/gate/crystal/daughters/name LSO<br>
#/gate/crystal/daughters/insert box<br>
/gate/crystal/daughters/insert tessellated<br>
/gate/LSO/placement/setTranslation -0.75 0.0 0.0 cm<br>
/gate/LSO/geometry/setPathToSTLFile lsobox.stl<br>
#/gate/LSO/geometry/setXLength 15 mm<br>
#/gate/LSO/geometry/setYLength 3.0 mm<br>
#/gate/LSO/geometry/setZLength 3.8 mm<br>
/gate/LSO/setMaterial LSO<br>
/gate/LSO/vis/setColor red<o:p></o:p></p>
<p>This example does not run anymore (it does when it uses the
original box) and I am getting:<o:p></o:p></p>
<p>I/O warning : failed to load external entity
"./Materials.xml"<br>
I/O warning: Discard the previous warning if your simulation
doesn't transport OPTICAL PHOTONS.
<br>
Otherwise, please copy the ./Materials.xml file from the
gate-source directory in the directory where you run your main
macro.<br>
I/O warning : failed to load external entity "./Materials.xml"<br>
I/O warning: Discard the previous warning if your simulation
doesn't transport OPTICAL PHOTONS.
<br>
Otherwise, please copy the ./Materials.xml file from the
gate-source directory in the directory where you run your main
macro.<br>
I/O warning : failed to load external entity "./Materials.xml"<br>
I/O warning: Discard the previous warning if your simulation
doesn't transport OPTICAL PHOTONS.
<br>
Otherwise, please copy the ./Materials.xml file from the
gate-source directory in the directory where you run your main
macro.<br>
I/O warning : failed to load external entity "./Materials.xml"<br>
I/O warning: Discard the previous warning if your simulation
doesn't transport OPTICAL PHOTONS.
<br>
Otherwise, please copy the ./Materials.xml file from the
gate-source directory in the directory where you run your main
macro.<br>
<br>
*** Break *** illegal instruction<br>
[/usr/lib/system/libsystem_platform.dylib] _sigtramp (no debug
info)<br>
[<unknown binary>] (no debug info)<br>
[/opt/contrib-appleclang/gate-8.2/bin/Gate]
GateSystemComponent::SetCreator(GateVVolume*) (no debug info)<br>
[/opt/contrib-appleclang/geant4-sersh/lib/libG4intercoms.dylib]
G4UIcommand::DoIt(G4String) (no debug info)<br>
[/opt/contrib-appleclang/geant4-sersh/lib/libG4intercoms.dylib]
G4UImanager::ApplyCommand(char const*) (no debug info)<br>
[/opt/contrib-appleclang/geant4-sersh/lib/libG4intercoms.dylib]
G4UIbatch::ExecCommand(G4String const&) (no debug info)<br>
[/opt/contrib-appleclang/geant4-sersh/lib/libG4intercoms.dylib]
G4UIbatch::SessionStart() (no debug info)<br>
[/opt/contrib-appleclang/geant4-sersh/lib/libG4intercoms.dylib]
G4UImanager::ExecuteMacroFile(char const*) (no debug info)<br>
[/opt/contrib-appleclang/geant4-sersh/lib/libG4intercoms.dylib]
G4UIcontrolMessenger::SetNewValue(G4UIcommand*, G4String) (no
debug info)<br>
[/opt/contrib-appleclang/geant4-sersh/lib/libG4intercoms.dylib]
G4UIcommand::DoIt(G4String) (no debug info)<br>
[/opt/contrib-appleclang/geant4-sersh/lib/libG4intercoms.dylib]
G4UImanager::ApplyCommand(char const*) (no debug info)<br>
[/opt/contrib-appleclang/gate-8.2/bin/Gate] main (no debug
info)<br>
[/usr/lib/system/libdyld.dylib] start (no debug info)<br>
[<unknown binary>] (no debug info)<br>
[LSO::IsValidAttachmentRequest]:<br>
The volume creator ('?sveta@bladerunner/.../PET$ <o:p></o:p></p>
<p>Does anybody have a working example with STL geometry?<o:p></o:p></p>
<p>Thank you,<o:p></o:p></p>
<p>Svetlana<o:p></o:p></p>
<div>
<p class="MsoNormal">On 8/8/19 5:09 PM, Matthew Strugari
wrote:<o:p></o:p></p>
</div>
<blockquote style="margin-top:5.0pt;margin-bottom:5.0pt">
<div>
<p class="MsoNormal">Hi Svetlana, <o:p></o:p></p>
<div>
<p class="MsoNormal"> <o:p></o:p></p>
</div>
<div>
<p class="MsoNormal">Take a look at the section <span
style="font-size:13.5pt">How to build a "tessellated"
volume on the wiki page </span><a
href="http://wiki.opengatecollaboration.org/index.php/Users_Guide:Defining_a_geometry"
moz-do-not-send="true">http://wiki.opengatecollaboration.org/index.php/Users_Guide:Defining_a_geometry</a>.
The sample code is from the GateContrib GitHub
repository as outlined on the wiki.<br>
<br>
Cheers,<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal">Matthew<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"> <o:p></o:p></p>
</div>
<div>
<p class="MsoNormal">--<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal">Matthew Strugari<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal">Biomedical Translational Imaging
Centre - BIOTIC,<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal">5890 University Ave, <o:p></o:p></p>
</div>
<div>
<p class="MsoNormal">Halifax, NS, B3K 6R8<o:p></o:p></p>
<div>
<p class="MsoNormal"> <o:p></o:p></p>
</div>
<div>
<p class="MsoNormal" style="margin-bottom:12.0pt"><br>
On Aug 8, 2019, at 6:28 PM, Svetlana G. Shasharina
<<a href="mailto:sveta@txcorp.com"
moz-do-not-send="true">sveta@txcorp.com</a>>
wrote:<o:p></o:p></p>
</div>
<blockquote style="margin-top:5.0pt;margin-bottom:5.0pt">
<div>
<p class="MsoNormal">Hello,<br>
<br>
Is there a way to use an STL file for the detector
geometry?<br>
<br>
Thank you,<br>
<br>
Sveta<br>
<br>
-- <br>
Svetlana Shasharina | <a
href="mailto:sveta@txcorp.com"
moz-do-not-send="true">
sveta@txcorp.com</a><br>
Vice-President of Computational Infrastructure |
Tech-X Corporation<br>
<br>
_______________________________________________<br>
Gate-users mailing list<br>
<a
href="mailto:Gate-users@lists.opengatecollaboration.org"
moz-do-not-send="true">Gate-users@lists.opengatecollaboration.org</a><br>
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href="http://lists.opengatecollaboration.org/mailman/listinfo/gate-users"
moz-do-not-send="true">http://lists.opengatecollaboration.org/mailman/listinfo/gate-users</a><o:p></o:p></p>
</div>
</blockquote>
</div>
</div>
</blockquote>
<pre>-- <o:p></o:p></pre>
<pre>Svetlana Shasharina | <a href="mailto:sveta@txcorp.com" moz-do-not-send="true">sveta@txcorp.com</a><o:p></o:p></pre>
<pre>Vice-President of Computational Infrastructure | Tech-X Corporation <o:p></o:p></pre>
</div>
</blockquote>
<pre class="moz-signature" cols="72">--
Svetlana Shasharina | <a class="moz-txt-link-abbreviated" href="mailto:sveta@txcorp.com">sveta@txcorp.com</a>
Vice-President of Computational Infrastructure | Tech-X Corporation </pre>
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