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<p class="MsoNormal"><span lang="EN-US">Hi Xinjie,<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">In any geometry definition, it is important to follow these three rules when
<a href="https://opengate.readthedocs.io/en/latest/defining_a_geometry.html?highlight=daughter#building-a-volume">
building a volume</a>:<o:p></o:p></span></p>
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<li class="MsoListParagraph" style="margin-left:0cm;mso-list:l0 level1 lfo1"><span lang="EN-US">A volume which is located inside another must be its daughter<o:p></o:p></span></li><li class="MsoListParagraph" style="margin-left:0cm;mso-list:l0 level1 lfo1"><span lang="EN-US">A daughter must be fully included in its mother<o:p></o:p></span></li><li class="MsoListParagraph" style="margin-left:0cm;mso-list:l0 level1 lfo1"><span lang="EN-US">Volumes must not overlap.<o:p></o:p></span></li></ul>
<p class="MsoNormal"><span lang="EN-US">This may require you to get creative with daughter definitions in order to obtain a final geometry representing your physical setup.
<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">Your geometry does not satisfy these points based on the issues that I previously outlined. If part of your geometry requires polyethylene with a height of 800mm, I would start by defining that size as your mother volume.
You can add on a daughter volume if you need a specific 100 mm region to be replaced with air.
<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">Consider, for example, that you define a mother polyethylene cylinder with a radius of 3.2 mm. Next, you define a daughter cylinder of air with a radius r of 2.4 <= r(mm) < 3.2 and within that daughter, you define a daughter
cylinder of water with a radius of 0 <= r(mm) < 1.6. The remaining volume between 1.6 <= r(mm) < 2.4 will remain as polyethylene (i.e. there’s no need to redefine a daughter of polyethylene with those dimensions). Try to use that approach when defining your
nested phantoms.<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">Hth,<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>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
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<p class="MsoNormal" style="margin-bottom:12.0pt"><b><span style="font-size:12.0pt;color:black">From:
</span></b><span style="font-size:12.0pt;color:black">Xinjie Cao <xinjie.cao@stonybrook.edu><br>
<b>Date: </b>Monday, January 18, 2021 at 13:08<br>
<b>To: </b>Matthew Strugari <matthew.strugari@dal.ca><br>
<b>Cc: </b>gate-users@lists.opengatecollaboration.org <gate-users@lists.opengatecollaboration.org><br>
<b>Subject: </b>Re: [Gate-users] Weird Phantom Warning<o:p></o:p></span></p>
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<p class="MsoNormal" style="line-height:12.0pt;mso-line-height-rule:exactly"><b><span style="font-size:9.0pt;font-family:"Arial",sans-serif;color:white">CAUTION:</span></b><span style="font-size:9.0pt;font-family:"Arial",sans-serif;color:white"> The Sender
of this email is not from within Dalhousie.<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="color:white">Hi Matthew, </span><o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">Thanks for your remind, how about setting the phantom 3 as the world daughter too to avoid that violation? Because that 800 mm length is according to the NEMA standard, so I am guessing better keep it if it could be solved.<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">For the phantom 3 configuration, I think it is necessary. There is actually an air gap between the inner plastic tube and the outer 200 mm diameter plastic shell according to the standard I believe.<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">Best,<o:p></o:p></p>
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<p class="MsoNormal">Xinjie<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">On Mon, Jan 18, 2021 at 11:58 AM Matthew Strugari <<a href="mailto:matthew.strugari@dal.ca">matthew.strugari@dal.ca</a>> wrote:<o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span lang="EN-US">Hi Xinjie,</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span lang="EN-US"> </span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span lang="EN-US">It looks like you have issues with overlapping geometries. You could try nesting phantom4 within phantom3 and nest phantom3 within phantom2. Also, is the height
of phantom3 correct at 800mm? This does not fit within your parent volume of phantom1.</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span lang="EN-US"> </span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span lang="EN-US">Alternatively, is phantom3 even required? It looks like you’re reinserting polystyrene after voiding the region with air in phantom2. This could be avoided by
setting Rmin to 2.4mm in phantom2.</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span lang="EN-US"> </span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span lang="EN-US">Regards,</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span lang="EN-US">Matthew</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span lang="EN-US"> </span><o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;margin-bottom:12.0pt"><b><span style="font-size:12.0pt;color:black">From:
</span></b><span style="font-size:12.0pt;color:black">Gate-users <<a href="mailto:gate-users-bounces@lists.opengatecollaboration.org" target="_blank">gate-users-bounces@lists.opengatecollaboration.org</a>> on behalf of Xinjie Cao <<a href="mailto:xinjie.cao@stonybrook.edu" target="_blank">xinjie.cao@stonybrook.edu</a>><br>
<b>Date: </b>Monday, January 18, 2021 at 12:38<br>
<b>To: </b><a href="mailto:gate-users@lists.opengatecollaboration.org" target="_blank">gate-users@lists.opengatecollaboration.org</a> <<a href="mailto:gate-users@lists.opengatecollaboration.org" target="_blank">gate-users@lists.opengatecollaboration.org</a>><br>
<b>Subject: </b>[Gate-users] Weird Phantom Warning</span><o:p></o:p></p>
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<b><span style="font-size:9.0pt;font-family:"Arial",sans-serif;color:white">CAUTION:</span></b><span style="font-size:9.0pt;font-family:"Arial",sans-serif;color:white"> The Sender of this email is not from within Dalhousie.</span><o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="color:white">Dear GATE users,
</span><o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">I am simulating the count rate performance of some PET scanners, while I found an interesting warning/error when I made a change to the phantom configuration.<o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><b>With the following simplified phantom configuration, both single thread or cluster tool can run the macro well:</b><o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">#==========================<br>
# P H A N T O M<br>
#==========================<br>
<br>
/gate/world/daughters/name phantom1<br>
/gate/world/daughters/insert cylinder<br>
/gate/phantom1/placement/setTranslation 0.0 0.0 0.0 mm<br>
/gate/phantom1/geometry/setRmax 101.5 mm<br>
/gate/phantom1/geometry/setHeight 700 mm<br>
/gate/phantom1/setMaterial Polyethylene<br>
/gate/phantom1/attachPhantomSD<br>
<br>
/gate/phantom1/daughters/name phantom2<br>
/gate/phantom1/daughters/insert cylinder<br>
/gate/phantom2/placement/setTranslation 0.0 -45.0 0.0 mm<br>
/gate/phantom2/geometry/setRmax 3.2 mm<br>
/gate/phantom2/geometry/setHeight 700 mm<br>
/gate/phantom2/setMaterial Air<br>
/gate/phantom2/attachPhantomSD<o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><b>While when I added two more daughter phantoms inside the previous outer shell volume as followed</b>,<o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">#===========================<br>
# P H A N T O M<br>
#===========================<br>
<br>
/gate/world/daughters/name phantom1<br>
/gate/world/daughters/insert cylinder<br>
/gate/phantom1/placement/setTranslation 0.0 0.0 0.0 mm<br>
/gate/phantom1/geometry/setRmax 101.5 mm<br>
/gate/phantom1/geometry/setHeight 700 mm<br>
/gate/phantom1/setMaterial Polyethylene<br>
/gate/phantom1/attachPhantomSD<br>
<br>
/gate/phantom1/daughters/name phantom2<br>
/gate/phantom1/daughters/insert cylinder<br>
/gate/phantom2/placement/setTranslation 0.0 -45.0 0.0 mm<br>
/gate/phantom2/geometry/setRmax 3.2 mm<br>
/gate/phantom2/geometry/setHeight 700 mm<br>
/gate/phantom2/setMaterial Air<br>
/gate/phantom2/attachPhantomSD<br>
<br>
/gate/phantom1/daughters/name phantom3<br>
/gate/phantom1/daughters/insert cylinder<br>
/gate/phantom3/placement/setTranslation 0.0 -45.0 0.0 mm<br>
/gate/phantom3/geometry/setRmax 2.4 mm<br>
/gate/phantom3/geometry/setRmin 1.6 mm<br>
/gate/phantom3/geometry/setHeight 800 mm<br>
/gate/phantom3/setMaterial Polyethylene<br>
/gate/phantom3/attachPhantomSD<br>
<br>
/gate/phantom1/daughters/name phantom4<br>
/gate/phantom1/daughters/insert cylinder<br>
/gate/phantom4/placement/setTranslation 0.0 -45.0 0.0 mm<br>
/gate/phantom4/geometry/setRmax 1.6 mm<br>
/gate/phantom4/geometry/setHeight 700 mm<br>
/gate/phantom4/setMaterial Water<br>
/gate/phantom4/attachPhantomSD<o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><b>the GATE feedbacked a warning/error like this,</b><o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">*** Break *** segmentation violation<br>
<br>
===========================================================<br>
There was a crash.<br>
This is the entire stack trace of all threads:<br>
===========================================================<br>
#0 0x00007f563c6d146c in waitpid () at /lib64/libc.so.6<br>
#1 0x00007f563c64ef62 in do_system () at /lib64/libc.so.6<br>
#2 0x00007f564b4c70c4 in TUnixSystem::StackTrace() () at /home/goldan/GATE/root/lib/libCore.so.6.18<br>
#3 0x00007f564b4c97fc in TUnixSystem::DispatchSignals(ESignals) () at /home/goldan/GATE/root/lib/libCore.so.6.18<br>
#4 0x00007f56471f4630 in <signal handler called> () at /lib64/libpthread.so.0<br>
#5 0x0000000000000040 in ()<br>
#6 0x00000000008e2658 in GateMaterialDatabase::~GateMaterialDatabase() ()<br>
#7 0x000000000087a8e6 in GateDetectorConstruction::~GateDetectorConstruction() ()<br>
#8 0x00007f564423a1e6 in G4RunManager::DeleteUserInitializations() (this=this<br>
entry=0x32997c0) at /home/goldan/GATE/geant4.10.05.p01/source/run/src/G4RunManager.cc:236<br>
#9 0x00007f564423ae75 in G4RunManager::~G4RunManager() (this=0x32997c0, __in_chrg=<optimized out>) at /home/goldan/GATE/geant4.10.05.p01/source/run/src/G4RunManager.cc:211<br>
#10 0x0000000000830e19 in GateRunManager::~GateRunManager() ()<br>
#11 0x000000000050198f in main ()<br>
===========================================================<br>
<br>
<br>
The lines below might hint at the cause of the crash.<br>
You may get help by asking at the ROOT forum <a href="http://root.cern.ch/forum" target="_blank">
http://root.cern.ch/forum</a><br>
Only if you are really convinced it is a bug in ROOT then please submit a<br>
report at <a href="http://root.cern.ch/bugs" target="_blank">http://root.cern.ch/bugs</a> Please post the ENTIRE stack trace<br>
from above as an attachment in addition to anything else<br>
that might help us fixing this issue.<br>
===========================================================<br>
#5 0x0000000000000040 in ()<br>
#6 0x00000000008e2658 in GateMaterialDatabase::~GateMaterialDatabase() ()<br>
#7 0x000000000087a8e6 in GateDetectorConstruction::~GateDetectorConstruction() ()<br>
#8 0x00007f564423a1e6 in G4RunManager::DeleteUserInitializations() (this=this<br>
entry=0x32997c0) at /home/goldan/GATE/geant4.10.05.p01/source/run/src/G4RunManager.cc:236<br>
#9 0x00007f564423ae75 in G4RunManager::~G4RunManager() (this=0x32997c0, __in_chrg=<optimized out>) at /home/goldan/GATE/geant4.10.05.p01/source/run/src/G4RunManager.cc:211<br>
#10 0x0000000000830e19 in GateRunManager::~GateRunManager() ()<br>
#11 0x000000000050198f in main ()<br>
===========================================================<br>
<br>
<br>
WARNING - Attempt to delete the physical volume store while geometry closed !<br>
WARNING - Attempt to delete the logical volume store while geometry closed !<br>
WARNING - Attempt to delete the solid store while geometry closed !<br>
WARNING - Attempt to delete the region store while geometry closed !<o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><b>The cluster tool could run the macro with added phantom configuration well with no warning/error, so I am not sure where the wrong with it or whether it has an</b>
<b>influence on the simulation result. I probably have seen </b>a<b> similar issue when I used CASToR for reconstruction so I am guessing it is related to ROOT?</b><o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><b>Did anyone ever meet this issue before? Any reply will be highly appreciated! Thanks!</b><o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">Best,<o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">Xinjie<o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">-- <o:p></o:p></p>
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<p class="MsoNormal"><b><span style="color:black">....................................................</span></b><o:p></o:p></p>
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<p class="MsoNormal"><b><span style="font-size:10.0pt;font-family:"Arial Black",sans-serif;color:#990000">Xinjie Cao</span></b><o:p></o:p></p>
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<p class="MsoNormal"><b><span style="font-size:7.5pt;font-family:"Arial Black",sans-serif">M.E. / Ph.D. Candidate</span></b><o:p></o:p></p>
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<p class="MsoNormal"><b><span style="font-size:7.5pt;font-family:"Arial Black",sans-serif">Research Project Assistant</span></b><o:p></o:p></p>
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<p class="MsoNormal"><b><span style="font-size:7.5pt;font-family:"Arial Black",sans-serif">Department of Electrical and Computer Engineering & Radiology </span></b><o:p></o:p></p>
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<p class="MsoNormal"><b><span style="font-size:7.5pt;font-family:"Arial Black",sans-serif">Novel Medical Imaging Technologies Lab</span></b><o:p></o:p></p>
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<p class="MsoNormal"><b><span style="font-size:7.5pt;font-family:"Arial Black",sans-serif">Health Science Center Level 8</span></b><o:p></o:p></p>
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<p class="MsoNormal"><b><span style="font-size:7.5pt;font-family:"Arial Black",sans-serif">Stony Brook, NY 11794-8460 </span></b><o:p></o:p></p>
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<p class="MsoNormal"><b><span style="font-size:7.5pt;font-family:"Arial Black",sans-serif">Tel: +1 (631)202-9445</span></b><o:p></o:p></p>
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<p class="MsoNormal"><a href="https://you.stonybrook.edu/goldan/people/" target="_blank">you.stonybrook.edu/goldan/people/</a><o:p></o:p></p>
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<p class="MsoNormal"><b><span style="font-size:7.5pt;font-family:"Arial Black",sans-serif">email:
</span></b><span style="font-size:7.5pt;font-family:"Arial Black",sans-serif"><a href="mailto:xinjie.cao@stonybrook.edu" target="_blank"><b>xinjie.cao@stonybroo</b>k.edu</a></span><o:p></o:p></p>
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<img border="0" width="200" height="33" style="width:2.0833in;height:.3437in" id="_x0000_i1025" src="https://drive.google.com/a/stonybrook.edu/uc?id=17TB1Ha3enD8HC5e_Ez238vpeBF92aCgH&export=download"><o:p></o:p></p>
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<p class="MsoNormal">It is prohibited to distribute or publish the files attached to any other people unless you get permission from the writer himself. All rights reserved.<o:p></o:p></p>
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