<div dir="ltr"><div><div><div>Hi,<br><br></div>The optical photon simulation works with the Surfaces.xml file. The problem was the position of the initialization. It must be defined after adding the processes.<br><br></div>Thank you very much Vesna<br></div>Ilker<br></div><div class="gmail_extra"><br><div class="gmail_quote">2015-07-16 9:19 GMT-04:00 ilker ozsahin <span dir="ltr"><<a href="mailto:ilkerozsahin@gmail.com" target="_blank">ilkerozsahin@gmail.com</a>></span>:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr"><div>Ok, of course How can I add an answer on the mailing list? I thought this was in there already?<br><br></div>Also, what about the Materials.xml? Do you have any idea?<br></div><div class="HOEnZb"><div class="h5"><div class="gmail_extra"><br><div class="gmail_quote">2015-07-16 9:12 GMT-04:00 Vesna Cuplov <span dir="ltr"><<a href="mailto:vesna.cuplov@gmail.com" target="_blank">vesna.cuplov@gmail.com</a>></span>:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr"><div><div><div><div>Hi,<br><br></div>Oh yes, sometimes it's a silly issue like the position of the initialisation. I'm glad you figured this out.<br></div>Could you please add an answer on the mailing list so everyone knows that it works :)<br><br></div>thank you<span><font color="#888888"><br></font></span></div><span><font color="#888888">vesna<br><br></font></span></div><div class="gmail_extra"><span><br clear="all"><div><div><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div><div><div><div><div><span style="color:rgb(7,55,99)"><span style="font-family:tahoma,sans-serif"><span style="color:rgb(0,0,0)"><span style="background-color:rgb(255,255,255)">Vesna Cuplov<br>Laboratoire Imagerie Moléculaire In Vivo (IMIV)<br>UMR 1023 Inserm/CEA/Université Paris Sud - ERL 9218 CNRS<br>CEA/I2BM/Service Hospitalier Frédéric Joliot<br>4 place du Général Leclerc<br>91400 Orsay</span></span><br></span></span></div></div></div></div></div><span style="color:rgb(7,55,99)"><span style="font-family:tahoma,sans-serif"></span></span><div><div><div><div><span style="color:rgb(12,52,61)"><font face="Calibri,Arial,Helvetica,sans-serif" size="3"><span style="font-size:12pt"></span></font><span style="font-family:tahoma,sans-serif"><a href="http://v-cuplov.net" target="_blank">http://v-cuplov.net</a></span></span><br></div></div></div></div></div></div></div></div></div></div></div></div></div>
<br></span><div><div><div class="gmail_quote">On Thu, Jul 16, 2015 at 3:08 PM, ilker ozsahin <span dir="ltr"><<a href="mailto:ilkerozsahin@gmail.com" target="_blank">ilkerozsahin@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr"><div><div>Please see the output attached, now it has optical processes and it seems it works. <br></div>I enabled and initialized the processList after addProcess. That was the silly problem I guess, sorry. Thanks a lot, this conversation really helps to my understanding.<br><br></div>The macro is little complicated actually, but path is correct, because when I put a material that is in GateMaterials.db but not in Materials.xml, it work. I have both material files in the same directory.<br><br>I can send the macro anyway after arranging, if it will help for the Materials.xml<br><br><div><div><br><br></div></div></div><div><div><div class="gmail_extra"><br><div class="gmail_quote">2015-07-16 8:55 GMT-04:00 Vesna Cuplov <span dir="ltr"><<a href="mailto:vesna.cuplov@gmail.com" target="_blank">vesna.cuplov@gmail.com</a>></span>:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr"><div>Do you give the right path of the GateMaterials.db ?<br><br></div>If you have a simple macro, could you send it to me?<br></div><div class="gmail_extra"><span><br clear="all"><div><div><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div><div><div><div><div><span style="color:rgb(7,55,99)"><span style="font-family:tahoma,sans-serif"><span style="color:rgb(0,0,0)"><span style="background-color:rgb(255,255,255)">Vesna Cuplov<br>Laboratoire Imagerie Moléculaire In Vivo (IMIV)<br>UMR 1023 Inserm/CEA/Université Paris Sud - ERL 9218 CNRS<br>CEA/I2BM/Service Hospitalier Frédéric Joliot<br>4 place du Général Leclerc<br>91400 Orsay</span></span><br></span></span></div></div></div></div></div><span style="color:rgb(7,55,99)"><span style="font-family:tahoma,sans-serif"></span></span><div><div><div><div><span style="color:rgb(12,52,61)"><font face="Calibri,Arial,Helvetica,sans-serif" size="3"><span style="font-size:12pt"></span></font><span style="font-family:tahoma,sans-serif"><a href="http://v-cuplov.net" target="_blank">http://v-cuplov.net</a></span></span><br></div></div></div></div></div></div></div></div></div></div></div></div></div>
<br></span><div><div><div class="gmail_quote">On Thu, Jul 16, 2015 at 2:37 PM, ilker ozsahin <span dir="ltr"><<a href="mailto:ilkerozsahin@gmail.com" target="_blank">ilkerozsahin@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr">Well, maybe we can understand the problem through the Materials.xml. <br>What can you say about Materials.xml? Since we see the output gives something like ABSLENGTH, RINDEX, FASTCOMPONENT, etc., maybe it means I use optical processes? Also when I use Epoxy as a material which is defined in the Materials.xml, it says:<br><br>
<p class="MsoNormal">/usr/local/gate6.2/gate_v6.2/source/geometry/src/GateMaterialDatabase.cc
(l.132): GateMaterialDatabase: could not find the definition for material
'Epoxy' in material files</p><p class="MsoNormal"><br></p><p class="MsoNormal">but if I use BGO which is also defined in the Materials.xml, it works and gives its properties from that file.<br></p><p class="MsoNormal"><br></p><p class="MsoNormal"><br></p>
</div><div class="gmail_extra"><br><div class="gmail_quote">2015-07-16 1:52 GMT-04:00 Vesna Cuplov <span dir="ltr"><<a href="mailto:vesna.cuplov@gmail.com" target="_blank">vesna.cuplov@gmail.com</a>></span>:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr"><div>no. If you use optical processes the code knows that it needs to look at these xml files.<br></div>I am sure that you do not actually use optical processes at all. Did you see the output.txt? These processes are not enabled. <br></div><div class="gmail_extra"><span><br clear="all"><div><div><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div><div><div><div><div><span style="color:rgb(7,55,99)"><span style="font-family:tahoma,sans-serif"><span style="color:rgb(0,0,0)"><span style="background-color:rgb(255,255,255)">Vesna Cuplov<br>Laboratoire Imagerie Moléculaire In Vivo (IMIV)<br>UMR 1023 Inserm/CEA/Université Paris Sud - ERL 9218 CNRS<br>CEA/I2BM/Service Hospitalier Frédéric Joliot<br>4 place du Général Leclerc<br>91400 Orsay</span></span><br></span></span></div></div></div></div></div><span style="color:rgb(7,55,99)"><span style="font-family:tahoma,sans-serif"></span></span><div><div><div><div><span style="color:rgb(12,52,61)"><font face="Calibri,Arial,Helvetica,sans-serif" size="3"><span style="font-size:12pt"></span></font><span style="font-family:tahoma,sans-serif"><a href="http://v-cuplov.net" target="_blank">http://v-cuplov.net</a></span></span><br></div></div></div></div></div></div></div></div></div></div></div></div></div>
<br></span><div><div><div class="gmail_quote">On Wed, Jul 15, 2015 at 6:48 PM, ilker ozsahin <span dir="ltr"><<a href="mailto:ilkerozsahin@gmail.com" target="_blank">ilkerozsahin@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr">So, there is not any command to point the xml file, isnt there?<br></div><div><div><div class="gmail_extra"><br><div class="gmail_quote">2015-07-15 12:32 GMT-04:00 ilker ozsahin <span dir="ltr"><<a href="mailto:ilkerozsahin@gmail.com" target="_blank">ilkerozsahin@gmail.com</a>></span>:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr"><div>I have<span><br><br>
<p class="MsoNormal">/gate/physics/addProcess OpticalAbsorption</p>
<p class="MsoNormal">/gate/physics/addProcess OpticalRayleigh</p>
<p class="MsoNormal">/gate/physics/addProcess OpticalBoundary</p>
<br></span></div>in my macro.<br><br><br></div><div><div><div class="gmail_extra"><br><div class="gmail_quote">2015-07-15 12:30 GMT-04:00 Vesna Cuplov <span dir="ltr"><<a href="mailto:vesna.cuplov@gmail.com" target="_blank">vesna.cuplov@gmail.com</a>></span>:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr"><div><div>I don't see any physics process related to optical photons?<br><br></div><div>You need some of these otherwise you're not doing anything to the photons.... The OpticalBoundary process is important in case you look at physics of optical photons through surfaces. <br></div><br>/gate/physics/addProcess OpticalAbsorption<br>/gate/physics/addProcess OpticalRayleigh<br>/gate/physics/addProcess OpticalBoundary<br>/gate/physics/addProcess OpticalMie<span><font color="#888888"><br><br><br></font></span></div><span><font color="#888888">vesna<br><div><br></div></font></span></div><div class="gmail_extra"><span><br clear="all"><div><div><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div><div><div><div><div><span style="color:rgb(7,55,99)"><span style="font-family:tahoma,sans-serif"><span style="color:rgb(0,0,0)"><span style="background-color:rgb(255,255,255)">Vesna Cuplov<br>Laboratoire Imagerie Moléculaire In Vivo (IMIV)<br>UMR 1023 Inserm/CEA/Université Paris Sud - ERL 9218 CNRS<br>CEA/I2BM/Service Hospitalier Frédéric Joliot<br>4 place du Général Leclerc<br>91400 Orsay</span></span><br></span></span></div></div></div></div></div><span style="color:rgb(7,55,99)"><span style="font-family:tahoma,sans-serif"></span></span><div><div><div><div><span style="color:rgb(12,52,61)"><font face="Calibri,Arial,Helvetica,sans-serif" size="3"><span style="font-size:12pt"></span></font><span style="font-family:tahoma,sans-serif"><a href="http://v-cuplov.net" target="_blank">http://v-cuplov.net</a></span></span><br></div></div></div></div></div></div></div></div></div></div></div></div></div>
<br></span><div><div><div class="gmail_quote">On Wed, Jul 15, 2015 at 6:21 PM, ilker ozsahin <span dir="ltr"><<a href="mailto:ilkerozsahin@gmail.com" target="_blank">ilkerozsahin@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr"><div>Attached please find the output. I also attached the one with uncommented inserting the surface name and type, the output2 <br></div></div><div><div><div class="gmail_extra"><br><div class="gmail_quote">2015-07-15 12:11 GMT-04:00 Vesna Cuplov <span dir="ltr"><<a href="mailto:vesna.cuplov@gmail.com" target="_blank">vesna.cuplov@gmail.com</a>></span>:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr"><div><div><div><div><div>maybe your macro points to an other xml file, but not the one you are modifying?<br></div>I usually point to the entire path in my macro.<br><br></div>Could you run Gate like this:<br><br></div>Gate yourmacro.mac &> output.txt <br><br></div>and send me the output.txt ?<span><font color="#888888"><br><br></font></span></div><span><font color="#888888">vesna<br><br></font></span></div><div class="gmail_extra"><span><br clear="all"><div><div><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div><div><div><div><div><span style="color:rgb(7,55,99)"><span style="font-family:tahoma,sans-serif"><span style="color:rgb(0,0,0)"><span style="background-color:rgb(255,255,255)">Vesna Cuplov<br>Laboratoire Imagerie Moléculaire In Vivo (IMIV)<br>UMR 1023 Inserm/CEA/Université Paris Sud - ERL 9218 CNRS<br>CEA/I2BM/Service Hospitalier Frédéric Joliot<br>4 place du Général Leclerc<br>91400 Orsay</span></span><br></span></span></div></div></div></div></div><span style="color:rgb(7,55,99)"><span style="font-family:tahoma,sans-serif"></span></span><div><div><div><div><span style="color:rgb(12,52,61)"><font face="Calibri,Arial,Helvetica,sans-serif" size="3"><span style="font-size:12pt"></span></font><span style="font-family:tahoma,sans-serif"><a href="http://v-cuplov.net" target="_blank">http://v-cuplov.net</a></span></span><br></div></div></div></div></div></div></div></div></div></div></div></div></div>
<br></span><div><div><div class="gmail_quote">On Wed, Jul 15, 2015 at 5:59 PM, ilker ozsahin <span dir="ltr"><<a href="mailto:ilkerozsahin@gmail.com" target="_blank">ilkerozsahin@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr"><div>Hi,<br><br>Yes, It is, as well. <br>Also, when I remove the Surface.xml file from the directory, it works and I can see the optical photons anyway. Also even I put something like <br><br></div><div>/gate/coupling/surface/name teflonsurf<br></div><div>......insert<br></div><div>......rough<br><br></div><div>it runs without any errors.<span><font color="#888888"><br><br></font></span></div><span><font color="#888888"><div><br></div>Ilker <br></font></span></div><div><div><div class="gmail_extra"><br><div class="gmail_quote">2015-07-15 11:55 GMT-04:00 Vesna Cuplov <span dir="ltr"><<a href="mailto:vesna.cuplov@gmail.com" target="_blank">vesna.cuplov@gmail.com</a>></span>:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr"><div><div><div>Hi,<br><br></div>If you have no error then the Gate_use_optical is ON, otherwise it would have complained because without that boolean ON, you can not work with the optical photons. <br></div>What do you mean by 'it doesn't recognize the files'? You change some values and it doesn't make any difference in the output?<span><font color="#888888"><br><br></font></span></div><span><font color="#888888">vesna</font></span><div><div><br><div><div><br><br><br><br><div class="gmail_extra"><br><div class="gmail_quote">On Wed, Jul 15, 2015 at 5:49 PM, ilker ozsahin <span dir="ltr"><<a href="mailto:ilkerozsahin@gmail.com" target="_blank">ilkerozsahin@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr"><div><div><div>Hi,<br><br></div>There is no error. It just works without recognizing the files. <br>How can I enable it? It says uncomment this line<br></div><pre>export GATE_USE_OPTICAL=1 (in env_gate.sh)</pre>Where can I find it?<br><br></div>Thank you<br><div><div><div><div><br><br><br><br><pre><br></pre></div></div></div></div></div><div class="gmail_extra"><br><div class="gmail_quote">2015-07-15 11:36 GMT-04:00 Vesna Cuplov <span dir="ltr"><<a href="mailto:vesna.cuplov@gmail.com" target="_blank">vesna.cuplov@gmail.com</a>></span>:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr"><div><div><div>Hi,<br><br></div>Did you enable the use of optical photons in Gate: GATE_USE_OPTICAL = ON? <br></div>Could you send your error message? <br><br></div>vesna<br><br><div><div><div><br></div></div></div></div><div class="gmail_extra"><br clear="all"><div><div><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div><div><div><div><div><span style="color:rgb(7,55,99)"><span style="font-family:tahoma,sans-serif"><span style="color:rgb(0,0,0)"><span style="background-color:rgb(255,255,255)">Vesna Cuplov<br>Laboratoire Imagerie Moléculaire In Vivo (IMIV)<br>UMR 1023 Inserm/CEA/Université Paris Sud - ERL 9218 CNRS<br>CEA/I2BM/Service Hospitalier Frédéric Joliot<br>4 place du Général Leclerc<br>91400 Orsay</span></span><br></span></span></div></div></div></div></div><span style="color:rgb(7,55,99)"><span style="font-family:tahoma,sans-serif"></span></span><div><div><div><div><span style="color:rgb(12,52,61)"><font face="Calibri,Arial,Helvetica,sans-serif" size="3"><span style="font-size:12pt"></span></font><span style="font-family:tahoma,sans-serif"><a href="http://v-cuplov.net" target="_blank">http://v-cuplov.net</a></span></span><br></div></div></div></div></div></div></div></div></div></div></div></div></div>
<br><div class="gmail_quote"><div><div>On Wed, Jul 15, 2015 at 5:23 PM, ilker ozsahin <span dir="ltr"><<a href="mailto:ilkerozsahin@gmail.com" target="_blank">ilkerozsahin@gmail.com</a>></span> wrote:<br></div></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div><div><div dir="ltr"><div><div><div>Hi,<br><br></div>I have both Surface.xml and Materials.xml files in the directory where I run Gate but it does not recognize the files. Is there a command to execute those files? Anyone has ever managed to use and modify those files?<br><br></div>Thank you<span><font color="#888888"><br></font></span></div><span><font color="#888888">Ilker<br></font></span></div>
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