<html xmlns:v="urn:schemas-microsoft-com:vml" xmlns:o="urn:schemas-microsoft-com:office:office" xmlns:w="urn:schemas-microsoft-com:office:word" xmlns:m="http://schemas.microsoft.com/office/2004/12/omml" xmlns="http://www.w3.org/TR/REC-html40"><head><meta http-equiv=Content-Type content="text/html; charset=utf-8"><meta name=Generator content="Microsoft Word 15 (filtered medium)"><style></style></head><body lang=EN-GB link=blue vlink=purple><div class=WordSection1>Hi<o:p></o:p><o:p> </o:p>A quick comment on the following:<o:p></o:p>----------<o:p></o:p>things seem to be outdated, for instance in the "GateIAEAConfig.h" the definition 'typedef long IAEA_I32' must be replaced with 'typedef int IAEA_I32' in order to conform to the current ".IAEAphsp" file format.<o:p></o:p>-----------<o:p></o:p><o:p> </o:p>This change will be compiler/system/time dependent. I don’t know what the GATE policy is, but in STIR we use boost::int32_t. if you don’t care about older compilers, you should use std::int32_t (from <cstdint>) I guess.<o:p></o:p><a name="_MailEndCompose"><o:p> </o:p></a>Kris<o:p></o:p>From: gate-users-bounces@lists.opengatecollaboration.org [mailto:gate-users-bounces@lists.opengatecollaboration.org] On Behalf Of David Sarrut Sent: 09 June 2015 00:57 To: gate-users; germano.russo@i-seecomputing.com Subject: Re: [Gate-users] [Gate] Fix the use of IAEA phase space files (#34)<o:p></o:p><o:p> </o:p>Hello Germano Russo, <o:p></o:p><div><o:p> </o:p></div><div>thank you very much for your pull-request, it has been merged (develop branch). I think a lot of users will be happy to see IAEA phase space now corrected in Gate.<o:p></o:p></div><div><o:p> </o:p></div><div>More details : <a href="https://github.com/OpenGATE/Gate/pull/34">https://github.com/OpenGATE/Gate/pull/34</a><o:p></o:p></div><div><o:p> </o:p></div><div>Sincerely, <o:p></o:p></div><div>David<o:p></o:p></div><o:p> </o:p><div>On Mon, Jun 8, 2015 at 10:32 AM, germanorusso <<a href="mailto:notifications@github.com" target="_blank">notifications@github.com</a>> wrote:<o:p></o:p><blockquote style='border:none;border-left:solid #CCCCCC 1.0pt;padding:0cm 0cm 0cm 6.0pt;margin-left:4.8pt;margin-right:0cm'>I recently tried to use as source an IAEA phase space, specifically the one named "VarianClinaciX_6MV_10x10_w1.IAEAphsp" (downloadable from <a href="https://www-nds.iaea.org/phsp/photon1/" target="_blank">https://www-nds.iaea.org/phsp/photon1/</a>), via the "/gate/source/[Source name]/addPhaseSpaceFile" macro command.<o:p></o:p>The simulation (Gate 7.0) run smoothly, however I got meaningless results. Digging into the related Gate source code, I believe I found 3 bugs for which I propose a correction in the 'fixIAEAphspSource' branch.<o:p></o:p>1) In the function 'GateSourcePhaseSpace::OpenIAEAFile()' the call 'pIAEARecordType->initialize()' is placed after 'pIAEAReader->getRecordContents(pIAEARecordType)'. These two lines shall be swapped, otherwise the record contents information extracted form the IAEA header and stored in the the object pointed by pIAEARecordType is cleared by the initialisation operation.<o:p></o:p>2) The "GateIAEA" source files appear to be based on an old C++ implementation for handling phase spaces distributed by the IAEA. Some things seem to be outdated, for instance in the "GateIAEAConfig.h" the definition 'typedef long IAEA_I32' must be replaced with 'typedef int IAEA_I32' in order to conform to the current ".IAEAphsp" file format.<o:p></o:p>3) In the function 'GateSourcePhaseSpace::GenerateIAEAVertex()' the 'pIAEARecordType->w' variable seems to be misused in the expression 'dz *= pIAEARecordType->w'. The 'pIAEARecordType->w' variable contains the Z direction cosine of the particle, not just its sign. So it should rather be 'dz = pIAEARecordType->w'. Since the 'pIAEARecordType->w' variable is slightly smaller than 1, this mistake causes small errors in the normalisation of the momentum (and hence of the kinetic energy).<o:p></o:p>After having applied these correction, I was able to obtain an output dose distribution for the 10x10 cm field quite close to the experimental data reported in the documentation distributed by IAEA along with the IAEAphsp and IAEAheader files ("<a href="https://www-nds.iaea.org/phsp/photon1/VarianClinaciX_6MV_PHSPdoc_Gothenburg.pdf" target="_blank">https://www-nds.iaea.org/phsp/photon1/VarianClinaciX_6MV_PHSPdoc_Gothenburg.pdf</a>").<o:p></o:p><a href="https://cloud.githubusercontent.com/assets/8522577/8030667/fed03d40-0dc8-11e5-8a51-90eae801a36d.png" target="_blank"><img border=0 width=100 height=100 id="_x0000_i1045" src="cid:~WRD000.jpg" alt="Image removed by sender. comparisonpdd"></a><o:p></o:p><a href="https://cloud.githubusercontent.com/assets/8522577/8030686/28bccb3c-0dc9-11e5-9075-8756f6952043.png" target="_blank"><img border=0 width=100 height=100 id="_x0000_i1046" src="cid:~WRD000.jpg" alt="Image removed by sender. comparisonxprofiles"></a><o:p></o:p><a href="https://cloud.githubusercontent.com/assets/8522577/8030692/2e0595f6-0dc9-11e5-8da2-ed4992dd8c9b.png" target="_blank"><img border=0 width=100 height=100 id="_x0000_i1047" src="cid:~WRD000.jpg" alt="Image removed by sender. comparisonyprofiles"></a><o:p></o:p><div class=MsoNormal align=center style='margin-left:36.0pt;text-align:center'><hr size=3 width="100%" align=center></div><h4 style='margin-left:36.0pt'>You can view, comment on, or merge this pull request online at:<o:p></o:p></h4> <a href="https://github.com/OpenGATE/Gate/pull/34" target="_blank">https://github.com/OpenGATE/Gate/pull/34</a><o:p></o:p><h4 style='margin-left:36.0pt'>Commit Summary<o:p></o:p></h4><![if !supportLists]>· <![endif]>Reversed type of IAEA_I32 to int, according with the current IAEA setting.<o:p></o:p><![if !supportLists]>· <![endif]>1) In the function 'GateSourcePhaseSpace::OpenIAEAFile()' the call<o:p></o:p><h4 style='margin-left:36.0pt'>File Changes<o:p></o:p></h4><![if !supportLists]>· <![endif]>M <a href="https://github.com/OpenGATE/Gate/pull/34/files#diff-0" target="_blank">source/general/include/GateIAEAConfig.h</a> (5) <o:p></o:p><![if !supportLists]>· <![endif]>M <a href="https://github.com/OpenGATE/Gate/pull/34/files#diff-1" target="_blank">source/physics/src/GateSourcePhaseSpace.cc</a> (5) <o:p></o:p><h4 style='margin-left:36.0pt'>Patch Links:<o:p></o:p></h4><![if !supportLists]>· <![endif]><a href="https://github.com/OpenGATE/Gate/pull/34.patch" target="_blank">https://github.com/OpenGATE/Gate/pull/34.patch</a><o:p></o:p><![if !supportLists]>· <![endif]><a href="https://github.com/OpenGATE/Gate/pull/34.diff" target="_blank">https://github.com/OpenGATE/Gate/pull/34.diff</a><o:p></o:p>— Reply to this email directly or <a href="https://github.com/OpenGATE/Gate/pull/34" target="_blank">view it on GitHub</a>.<img border=0 width=1 height=1 id="_x0000_i1049" src="cid:image002.jpg@01D0A281.A215E850" alt="Image removed by sender."><o:p></o:p></blockquote></div> <o:p></o:p><div><o:p> </o:p></div>-- <o:p></o:p>David Sarrut, Phd Directeur de recherche CNRS CREATIS, UMR CNRS 5220, Inserm U 1044<o:p></o:p><div>Centre de lutte contre le cancer Léon Bérard 28 rue Laënnec, 69373 Lyon cedex 08 Tel : <a href="tel:04%2078%2078%2051%2051" target="_blank">04 78 78 51 51</a> / <a href="tel:06%2074%2072%2005%2042" target="_blank">06 74 72 05 42</a> <a href="http://www.creatis.insa-lyon.fr/~dsarrut" target="_blank">http://www.creatis.insa-lyon.fr/~dsarrut</a> _________________________________<o:p></o:p></div> "2 + 2 = 5, for extremely large values of 2" _________________________________<o:p></o:p></div></body></html>