<div dir="ltr">Hello Alex, <div> </div><div>pull-request #23 is now merged, thanks again. I will ask for a configuration in the <a href="http://my.cdash.org/index.php?project=GATE">dashboard</a> to be compiled daily with cxx11 enabled. </div><div> </div><div>David</div><div class="gmail_extra"> <div class="gmail_quote">On Thu, May 28, 2015 at 3:14 PM, Alex Vergara Gil <<a href="mailto:alexvergaragil@gmail.com" target="_blank">alexvergaragil@gmail.com</a>> wrote: <blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Dear David On pull request <a href="https://github.com/OpenGATE/Gate/pull/23" target="_blank">https://github.com/OpenGATE/Gate/pull/23</a> I added both the changes to make Gate c++11 compatible and the fix of the mentioned bug. Regards Alex <div class="HOEnZb"><div class="h5"> 2015-05-28 8:13 GMT-04:00, Alex Vergara Gil <<a href="mailto:alexvergaragil@gmail.com">alexvergaragil@gmail.com</a>>: > Dear David > > There is another things, code 'elegancy' lead to some specific > enhances that must be taken in consideration: > > 1. Indentation: helps to read better the code so bugs and unnecessary > sentences raise from all their hidden places, specially when you make > automatic indentation. > 2. changing from i++ to ++i as I explain leads to optimization of code > since it avoid a whole extra step at each call. > 3. Using std::vector functionalities lead to code enhancement since it > use a really optimized method for travel among lists. > 4. Using structured vectors is a security enhancement since you can no > longer create vector from different sizes, avoiding to not initialize > some of them and the corresponding segmentation fault when calling. > > I know there are a bunch of changes, but I can run all my macros with > them, decreasing a little the memory consumption, increasing a little > the histories per second and finally when I look now at the code it > seems made in modern times ;) > > Regards > Alex > > 2015-05-28 7:24 GMT-04:00, Alex Vergara Gil <<a href="mailto:alexvergaragil@gmail.com">alexvergaragil@gmail.com</a>>: >> Hello David >> >> As I said on github, you can create a testing branch so I can still >> contribute with great amount of changes and user can test them and >> report bugs, this will not affect Gate at all and we all be happy ;) >> >> Regards >> Alex >> >> 2015-05-28 2:11 GMT-04:00, David Sarrut >> <<a href="mailto:David.Sarrut@creatis.insa-lyon.fr">David.Sarrut@creatis.insa-lyon.fr</a>>: >>> Hello Alex, >>> >>> as said on github (see <a href="https://github.com/OpenGATE/Gate/issues/22" target="_blank">https://github.com/OpenGATE/Gate/issues/22</a>), >>> could >>> you please provide a separate pull-request for this issue, *without* >>> replacement of std::vector -> please keep it simple. Even if the code is >>> not so good, I acknowledge that ;) refrain to changing it to be more >>> 'elegant' as it could lead to unexpected issues. >>> >>> dont get me wrong, I really appreciate your contribution, but we need to >>> ensure to not break something ... >>> >>> thanks, >>> David >>> >>> On Tue, May 26, 2015 at 2:02 PM, Alex Vergara Gil >>> <<a href="mailto:alexvergaragil@gmail.com">alexvergaragil@gmail.com</a>> >>> wrote: >>> >>>> Dear David >>>> >>>> Indeed, doing that replace solved the bug, not only for range >>>> translator but also for hounsfield translator, in my pull request are >>>> the necessary changes with a bunch of code enhacements (basically a >>>> lot of replacements to use std::vector functionalities). >>>> >>>> Look now at one of my results on a phantom compared with FLUKA. >>>> >>>> Regards >>>> Alex >>>> >>>> 2015-05-26 3:32 GMT-04:00, David Sarrut >>>> <<a href="mailto:David.Sarrut@creatis.insa-lyon.fr">David.Sarrut@creatis.insa-lyon.fr</a> >>>> >: >>>> > Hello Alex, >>>> > >>>> > I looked at your coments on the range translator and indeed, there is >>>> > a >>>> > bug. Could you please test if replacing the line >>>> > if(r2> pImage->GetOutsideValue()+1){ >>>> > with >>>> > if(r2>= pImage->GetOutsideValue()+1){ >>>> > >>>> > solve the issue ? >>>> > >>>> > Thanks you indeed to propose me to be coauthor of the paper, but I >>>> > really >>>> > did nothing to this work, so I cannot accept, this is not fair ;) >>>> > >>>> > I am however interested to read the draft if possible. >>>> > >>>> > As journal, I can suggest maybe : <a href="http://jnm.snmjournals.org" target="_blank">http://jnm.snmjournals.org</a> or >>>> > <a href="http://www.springer.com/medicine/nuclear+medicine/journal/259" target="_blank">http://www.springer.com/medicine/nuclear+medicine/journal/259</a> >>>> > >>>> > David >>>> > >>>> > >>>> > >>>> > On Thu, May 21, 2015 at 1:34 PM, Alex Vergara Gil >>>> > <<a href="mailto:alexvergaragil@gmail.com">alexvergaragil@gmail.com</a>> >>>> > wrote: >>>> > >>>> >> Dear David >>>> >> >>>> >> I think I have solved the bug, I ran several tests and I think >>>> >> results >>>> >> are fine now for both range and hounsfield translators. >>>> >> >>>> >> Next days I will be writing my results. If you want I will send you >>>> >> the draft I will prepare so you can coauthor the paper, is there a >>>> >> magazine you may recommended? >>>> >> >>>> >> Suggested title: "Using Gate for Molecular Radiotherapy Dosimetry on >>>> >> clinical environments" >>>> >> >>>> >> Regards >>>> >> Alex >>>> >> >>>> >> 2015-05-20 1:12 GMT-04:00, David Sarrut >>>> >> <<a href="mailto:David.Sarrut@creatis.insa-lyon.fr">David.Sarrut@creatis.insa-lyon.fr</a> >>>> >> >: >>>> >> > Hello Alex, >>>> >> > >>>> >> > I will study this issue probably next week, >>>> >> > >>>> >> > thanks again for reporting, >>>> >> > David >>>> >> > >>>> >> > On Tue, May 19, 2015 at 10:49 PM, Alex Vergara Gil >>>> >> > <<a href="mailto:alexvergaragil@gmail.com">alexvergaragil@gmail.com</a> >>>> >> >> wrote: >>>> >> > >>>> >> >> Dear David >>>> >> >> >>>> >> >> I have modified my macros and now I have a good patient dose >>>> >> >> image, >>>> so >>>> >> >> I think Hounsfield Translator is free of bugs, I will try to put >>>> >> >> Air >>>> >> >> as first segmentation material to see whats happens, but in the >>>> >> >> way >>>> >> >> I >>>> >> >> am seeing this Hounsfield is far better approach for the problem. >>>> >> >> >>>> >> >> I will update my templates to achieve this macro and when is >>>> >> >> ready >>>> >> >> I >>>> >> >> will publish my results. >>>> >> >> On issue #18 I put all my progress, This image was obtained with >>>> >> >> geant4 10.1.1 + gate with all modifications of pull request #21 >>>> >> >> applied. >>>> >> >> >>>> >> >> Regards >>>> >> >> Alex >>>> >> >> >>>> >> >> 2015-05-19 14:29 GMT-04:00, Alex Vergara Gil < >>>> <a href="mailto:alexvergaragil@gmail.com">alexvergaragil@gmail.com</a> >>>> >> >: >>>> >> >> > Dear David >>>> >> >> > >>>> >> >> > I am trying to move my workflow to Hounsfield converter, since >>>> >> >> > I >>>> can >>>> >> >> > get the range translator to work properly (In Patient Phantom 2 >>>> >> >> > you >>>> >> >> > may see that a material - Muscle - is taken as air). Up to now >>>> >> >> > I >>>> >> >> > have >>>> >> >> > successfully ran a voxelized physical phantom as you may see in >>>> >> >> > the >>>> >> >> > image (cylinder phantom 1), but when using a patient phantom >>>> >> >> > thing >>>> >> >> > goes really odd! Somehow geometry are no longer rendered >>>> >> >> > correctly >>>> >> >> > (patient phantom 1). I am trying to check what is wrong with >>>> >> >> > the >>>> >> >> > images but I see no errors, even the density map I export from >>>> >> >> > gate >>>> >> >> > is >>>> >> >> > fine (patient density phantom 1). I also see no relative >>>> differences >>>> >> >> > between the cylinder and patient macros, except for the image >>>> >> >> > properties. >>>> >> >> > >>>> >> >> > Regards >>>> >> >> > Alex >>>> >> >> > >>>> >> >> >>>> >> > >>>> >> > >>>> >> > >>>> >> > -- >>>> >> > David Sarrut, Phd >>>> >> > Directeur de recherche CNRS >>>> >> > CREATIS, UMR CNRS 5220, Inserm U 1044 >>>> >> > Centre de lutte contre le cancer Léon Bérard >>>> >> > 28 rue Laënnec, 69373 Lyon cedex 08 >>>> >> > Tel : <a href="tel:04%2078%2078%2051%2051" value="+33478785151">04 78 78 51 51</a> / <a href="tel:06%2074%2072%2005%2042" value="+33674720542">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> >>>> >> > _________________________________ >>>> >> > "2 + 2 = 5, for extremely large values of 2" >>>> >> > _________________________________ >>>> >> > >>>> >> >>>> > >>>> > >>>> > >>>> > -- >>>> > David Sarrut, Phd >>>> > Directeur de recherche CNRS >>>> > CREATIS, UMR CNRS 5220, Inserm U 1044 >>>> > Centre de lutte contre le cancer Léon Bérard >>>> > 28 rue Laënnec, 69373 Lyon cedex 08 >>>> > Tel : 04 78 78 51 51 / 06 74 72 05 42 >>>> > <a href="http://www.creatis.insa-lyon.fr/~dsarrut" target="_blank">http://www.creatis.insa-lyon.fr/~dsarrut</a> >>>> > _________________________________ >>>> > "2 + 2 = 5, for extremely large values of 2" >>>> > _________________________________ >>>> > >>>> >>> >>> >>> >>> -- >>> David Sarrut, Phd >>> Directeur de recherche CNRS >>> CREATIS, UMR CNRS 5220, Inserm U 1044 >>> Centre de lutte contre le cancer Léon Bérard >>> 28 rue Laënnec, 69373 Lyon cedex 08 >>> Tel : 04 78 78 51 51 / 06 74 72 05 42 >>> <a href="http://www.creatis.insa-lyon.fr/~dsarrut" target="_blank">http://www.creatis.insa-lyon.fr/~dsarrut</a> >>> _________________________________ >>> "2 + 2 = 5, for extremely large values of 2" >>> _________________________________ >>> >> > </div></div></blockquote></div> <div> </div>-- <div class="gmail_signature"><div dir="ltr">David Sarrut, Phd Directeur de recherche CNRS CREATIS, UMR CNRS 5220, Inserm U 1044<div>Centre de lutte contre le cancer Léon Bérard 28 rue Laënnec, 69373 Lyon cedex 08 Tel : 04 78 78 51 51 / 06 74 72 05 42 <a href="http://www.creatis.insa-lyon.fr/~dsarrut" target="_blank">http://www.creatis.insa-lyon.fr/~dsarrut</a> _________________________________</div><div> "2 + 2 = 5, for extremely large values of 2" _________________________________</div></div></div> </div></div>