<div dir="ltr"><div>Hi Maxime, </div><div><br></div>Thanks for your prompt reply. I see your point on "_phys". In the new document for v9.0, there is a "_phys" appending to cold_area in <div><div>"<i>/gate/source/number1/gps/Forbid cold_area_phys</i>". However, in the document for v8.0, there is no such a "_phys". I tried that, even though the GATE did not throw any error, but it did not solve the problem either. <br></div></div><div><br></div><div>I also thought about the third hack you put forward. It works for simple geometries, like the one, a single annulus source. However, I am overwhelmed with moving NEMA body phantom. I wish there is someone who has tried this before and could share their thoughts. The reason why I feel it is hard to move NEMA body phantom and its sources is that some sources may dump many volumes to form the desired shape. I try to break them into pieces and see if I can successfully move them together. </div><div><br></div><div>Thank you very much. </div><div><br></div><div>Zhengzhi</div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Thu, Apr 2, 2020 at 11:13 AM Maxime Toussaint <<a href="mailto:Maxime.Toussaint@usherbrooke.ca" target="_blank">Maxime.Toussaint@usherbrooke.ca</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
<div dir="ltr">
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Greetings,</div>
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<br>
</div>
<div style="font-family:Calibri,Arial,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0);background-color:rgb(255,255,255)">
No problemo about the (attempt to) help.<br>
</div>
<div style="font-family:Calibri,Arial,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0);background-color:rgb(255,255,255)">
<br>
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For the first part, I was refering to section 6.1.8 in [1], named "Defining a cold source". I have no idea if the "_phys" is required or if it is an error in the wiki.<br>
</div>
<div style="font-family:Calibri,Arial,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0);background-color:rgb(255,255,255)">
<br>
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<div style="font-family:Calibri,Arial,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0);background-color:rgb(255,255,255)">
For the second part, my bad. I assumed that an annulus was a 3D object from your message. I was wrong and it explains why you are not using it. We can define a hollowed cylinder geometry, so I had assumed that we could do the same with a source. You could stack
a couple of annulus source but I hope you won't need to ressort to that!</div>
<div style="font-family:Calibri,Arial,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0);background-color:rgb(255,255,255)">
<br>
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<div style="font-family:Calibri,Arial,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0);background-color:rgb(255,255,255)">
I still do not have an idea about the problem you highlighted, but another hack would be to create a voxelized version of that phantom.
<br>
</div>
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<br>
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A third hack: if you are only doing one translation: extend, in the motion axis, your cold cylinder height to the full domain of position and do not apply motion on it. Thus, if the "forbid" command work but it cannot be moved, it should be okay.<br>
</div>
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<br>
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Well, let's hope that a Gate Master will have a more pratical answer than those 3 hacks!<br>
</div>
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<div style="font-family:Calibri,Arial,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0);background-color:rgb(255,255,255)">
Have a nice day,</div>
<div style="font-family:Calibri,Arial,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0);background-color:rgb(255,255,255)">
Maxime Toussaint<br>
</div>
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[1] <a href="https://opengate.readthedocs.io/en/latest/source_and_particle_management.html#id12" id="gmail-m_-4251898087851316977gmail-m_-4057135874682295304LPNoLP612005" target="_blank">
https://opengate.readthedocs.io/en/latest/source_and_particle_management.html#id12</a><br>
</div>
<br>
<div id="gmail-m_-4251898087851316977gmail-m_-4057135874682295304appendonsend"></div>
<hr style="display:inline-block;width:98%">
<div id="gmail-m_-4251898087851316977gmail-m_-4057135874682295304divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" style="font-size:11pt" color="#000000"><b>De :</b> Zhengzhi Liu <<a href="mailto:zliu36@stanford.edu" target="_blank">zliu36@stanford.edu</a>><br>
<b>Envoyé :</b> 2 avril 2020 13:32<br>
<b>À :</b> Maxime Toussaint <Maxime.Toussaint@USherbrooke.ca><br>
<b>Cc :</b> gate-users <<a href="mailto:gate-users@lists.opengatecollaboration.org" target="_blank">gate-users@lists.opengatecollaboration.org</a>><br>
<b>Objet :</b> Re: [Gate-users] Movement of source with cold_area</font>
<div> </div>
</div>
<div>
<div dir="ltr">Hi Maxime,
<div><br>
</div>
<div>Thank you very much for scrutinizing my code and providing suggestions. </div>
<div><br>
</div>
<blockquote style="margin:0px 0px 0px 40px;border:none;padding:0px">
<div>You said I "didn't add the '_phys' part on the object name when using the forbid command" and I "didn't follow that part of the wiki example". First, which wiki example were you referring to? Secondly, it looks like '_phys' is only used in the old way
of moving source as stated <a href="https://can01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fopengate.readthedocs.io%2Fen%2Flatest%2Fsource_and_particle_management.html%23movement-of-a-source&data=02%7C01%7CMaxime.Toussaint%40usherbrooke.ca%7C35185c3a8f24483b35ba08d7d72c097c%7C3a5a8744593545f99423b32c3a5de082%7C0%7C0%7C637214457128673504&sdata=8ZrcE8%2BkKwESK9WZpKJddbbwZtrcX5kT0HfzGh4tOm0%3D&reserved=0" target="_blank">
here</a> in the user manual. For creating a source with Forbid, I have not seen people appending '_phys' to their object name. </div>
<div><br>
</div>
<div>Yes, it looks like the GATE is capable of creating an <a href="https://can01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fopengate.readthedocs.io%2Fen%2Flatest%2Fsource_and_particle_management.html%23defining-the-shape-of-the-source&data=02%7C01%7CMaxime.Toussaint%40usherbrooke.ca%7C35185c3a8f24483b35ba08d7d72c097c%7C3a5a8744593545f99423b32c3a5de082%7C0%7C0%7C637214457128673504&sdata=q7R6sS30whSJ8vD7VIsiUxZGyt3h6xfvDD%2FPPz0gccI%3D&reserved=0" target="_blank">annulus
source</a>, however, literally, it is a ring source, as it does support adding <i>
halfz</i> to its definition. Thus it has no thickness. I also am not sure which wiki example you were referring to. </div>
</blockquote>
<div><br>
</div>
<div>What I am trying to achieve is to move the <a href="https://can01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.spect.com%2Fpub%2FNEMA_IEC_Body_Phantom_Set.pdf&data=02%7C01%7CMaxime.Toussaint%40usherbrooke.ca%7C35185c3a8f24483b35ba08d7d72c097c%7C3a5a8744593545f99423b32c3a5de082%7C0%7C0%7C637214457128683499&sdata=PUrUjK11X8vc9OyWqSthSAZtjknf7uLiQO6v5rcFTDc%3D&reserved=0" target="_blank">NEMA
IEC Body Phantom</a> with the source in my simulated PET system along axial direction back and forth. The definition of the source is a little bit complicated, it uses many cold_area. Thus, I started with a simplistic case where there is only a source created
with cold_area. However, after the movement, the annulus didn't maintain its shape. If I can't get this simple case work, I don't see any chance to move the NEMA phantom and source correctly. </div>
<div><br>
</div>
<div>I think sincerely thank you for your great contribution to GATE development and helping me and others. </div>
<div><br>
</div>
<div>Zhengzhi </div>
<div><br>
</div>
<div><br>
</div>
</div>
<br>
<div>
<div dir="ltr">On Thu, Apr 2, 2020 at 6:43 AM Maxime Toussaint <<a href="mailto:Maxime.Toussaint@usherbrooke.ca" target="_blank">Maxime.Toussaint@usherbrooke.ca</a>> wrote:<br>
</div>
<blockquote style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
<div dir="ltr">
<div style="font-family:Calibri,Arial,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0);background-color:rgb(255,255,255)">
Greetings,</div>
<div style="font-family:Calibri,Arial,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0);background-color:rgb(255,255,255)">
<br>
</div>
<div style="font-family:Calibri,Arial,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0);background-color:rgb(255,255,255)">
I do not know why the approach you used did not work. The only difference I have found between your code and the example shown in the wiki, is that you didn't add the "_phys" part on the object name when using the forbid command. Is there a reason for why you
didn't follow that part of the wiki example?</div>
<div style="font-family:Calibri,Arial,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0);background-color:rgb(255,255,255)">
<br>
</div>
<div style="font-family:Calibri,Arial,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0);background-color:rgb(255,255,255)">
Also, from my understanding, you want an <span style="font-size:15px;color:rgb(0,0,0);background-color:rgb(255,255,255);display:inline">
annulus</span> source. Why don't you directly define one as shown in the wiki? Is there a particularity in your case that make it invalid?</div>
<div style="font-family:Calibri,Arial,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0);background-color:rgb(255,255,255)">
<br>
</div>
<div style="font-family:Calibri,Arial,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0);background-color:rgb(255,255,255)">
Have a nice day,</div>
<div style="font-family:Calibri,Arial,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0);background-color:rgb(255,255,255)">
Maxime Toussaint</div>
<div style="font-family:Calibri,Arial,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0);background-color:rgb(255,255,255)">
<br>
</div>
<div style="font-family:Calibri,Arial,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0);background-color:rgb(255,255,255)">
<br>
</div>
<div id="gmail-m_-4251898087851316977gmail-m_-4057135874682295304x_gmail-m_-4102621443068267093appendonsend"></div>
<hr style="display:inline-block;width:98%">
<div id="gmail-m_-4251898087851316977gmail-m_-4057135874682295304x_gmail-m_-4102621443068267093divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" color="#000000" style="font-size:11pt"><b>De :</b> Gate-users <<a href="mailto:gate-users-bounces@lists.opengatecollaboration.org" target="_blank">gate-users-bounces@lists.opengatecollaboration.org</a>>
de la part de Zhengzhi Liu <<a href="mailto:zliu36@stanford.edu" target="_blank">zliu36@stanford.edu</a>><br>
<b>Envoyé :</b> 1 avril 2020 18:23<br>
<b>À :</b> gate-users <<a href="mailto:gate-users@lists.opengatecollaboration.org" target="_blank">gate-users@lists.opengatecollaboration.org</a>><br>
<b>Objet :</b> [Gate-users] Movement of source with cold_area</font>
<div> </div>
</div>
<div>
<div dir="ltr">Dear Gate users,<br>
<div><br>
</div>
<div>I am trying to move NEMA IQ phantom with the source along the axial direction back and forth to simulate a real experiment that we have done. I started with a much simpler case where there is only an annulus phantom with an annulus source in the simulated
PET system. Phantom as a volume is very easy to be translated. According to the user manual, to move a source, the source had better be attached to a volume. For common source without cold_area, it works very well. However, I found it did not work in the
case where the source is determined by a volume and a cold_area (which is also a volume), such as the annulus source. Could anyone teach me how to do so if it is possible?</div>
<div><br>
</div>
<div>Following is my code, I moved the phantom and cold_area simultaneously, whether or not I attached the source to phantom, after the translation, GATE did not return an annulus source rather a cylindrical source same as the phantom as shown in the attached
screenshot. <br>
</div>
<div><br>
</div>
<div>phantom.mac<br>
</div>
<div>#=====================================================<br>
# WATER PHANTOM<br>
#=====================================================<br>
/gate/world/daughters/name Normal_AP<br>
/gate/world/daughters/insert cylinder<br>
/gate/Normal_AP/geometry/setRmax 30.051 cm<br>
/gate/Normal_AP/geometry/setRmin 30.0 cm<br>
/gate/Normal_AP/geometry/setHeight 6 cm<br>
/gate/Normal_AP/placement/setTranslation 0.0 0.0 0.0 cm<br>
/gate/Normal_AP/moves/insert genericMove<br>
/gate/Normal_AP/genericMove/setPlacementsFilename ./macros/phantomMovement0.placements<br>
/gate/Normal_AP/setMaterial Water<br>
/gate/Normal_AP/vis/forceSolid<br>
/gate/Normal_AP/vis/setColor white<br>
/gate/Normal_AP/vis/setVisible 1<br>
<br>
/gate/world/daughters/name cold_area<br>
/gate/world/daughters/insert cylinder<br>
/gate/cold_area/geometry/setRmax 30.00 cm<br>
/gate/cold_area/geometry/setHeight 6 cm<br>
/gate/cold_area/placement/setTranslation 0.0 0.0 0.0 cm<br>
/gate/cold_area/moves/insert genericMove<br>
/gate/cold_area/genericMove/setPlacementsFilename ./macros/phantomMovement0.placements<br>
/gate/cold_area/setMaterial Air<br>
/gate/cold_area/vis/forceWireframe<br>
/gate/cold_area/vis/setColor white</div>
<div><br>
</div>
<div><br>
</div>
<div>source.mac<br>
</div>
<div>#=====================================================<br>
# FASTER PRODUCTION MODULE FOR GE-68 ISOTOPES<br>
#=====================================================<br>
/gate/source/addSource Ge68<br>
/gate/source/Ge68/setActivity 37000 Bq #1. uci<br>
/gate/source/Ge68/gps/particle gamma<br>
/gate/source/Ge68/setType backtoback<br>
/gate/source/Ge68/gps/type Volume<br>
/gate/source/Ge68/gps/shape Cylinder<br>
/gate/source/Ge68/gps/radius 30.051 cm<br>
/gate/source/Ge68/gps/halfz 3 cm<br>
/gate/source/Ge68/gps/centre 0. 0. 0. cm<br>
#/gate/source/Ge68/attachTo Normal_AP<br>
/gate/source/Ge68/gps/energytype Mono<br>
/gate/source/Ge68/gps/monoenergy 0.511 MeV<br>
/gate/source/Ge68/gps/angtype iso<br>
/gate/source/Ge68/setForcedUnstableFlag false<br>
#/gate/source/Ge68/setForcedHalfLife 6586 s<br>
/gate/source/Ge68/gps/Forbid cold_area<br>
/gate/source/Ge68/dump 1<br>
<br>
/gate/source/list</div>
<div><br>
</div>
<div><br>
</div>
<div>Thanks a lot for your reading and any help.</div>
<div>Sincerely,</div>
<div>Zhengzhi </div>
<div><br>
</div>
</div>
</div>
</div>
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