[Gate-users] Using IAEA phase spaces

[David Sarrut]

your are almost there ! Just create your own copy (fork) of Gate repository
inside your github account, you will be able to push your branch onto this
copy.

Once completed, you will be able to create a pull-request from your Gate
repo to the official Gate repo.

sorry for this not so simple procedure, but is allows us to really follow
what happens.

ideally, a very simple simulation test (with a very small phase space!)
could be needed to ensure everything is and remains ok.

thanks,
David
PS: I put gate-users in copy to inform on how to do a pull-request.

On Thu, Jun 4, 2015 at 10:58 AM, <germano.russo at i-seecomputing.com> wrote:

> Dear David,
>
> I tried to do what you suggested, but I am not allowed to push my
> locally-created branch in the repository, so to proceed with a
> pull-request.
>
> Here is the procedure I followed:
>
>    git clone https://github.com/OpenGATE/Gate/
>
>    git checkout -b fixIAEAphspSource
>
>    vim Gate/source/general/include/GateIAEAConfig.h
>    vim Gate/source/physics/src/GateSourcePhaseSpace.cc
>
>    git commit Gate/source/general/include/GateIAEAConfig.h -m "..."
>    git commit Gate/source/physics/src/GateSourcePhaseSpace.cc -m "..."
>
>    git push origin fixIAEAphspSource
>
> The reply to the last command was:
>
>    Username for 'https://github.com': germanorusso
>    Password for 'https://germanorusso@github.com':
>    remote: Permission to OpenGATE/Gate.git denied to germanorusso.
>    fatal: unable to access 'https://github.com/OpenGATE/Gate/': The
> requested URL returned error: 403
>
> Since it is the first time for me to use GIT, I am probably missing
> something stupid.
>
> Thanks,
> Germano
>
>
>
>
> On Thu, 4 Jun 2015 07:14:28 +0200, David Sarrut
> <David.Sarrut at creatis.insa-lyon.fr> wrote:
> > Hello Germano,
> >
> > thank you very much for those inputs. There have been some
> considerations
> > about IAEA in Gate in the mailing list recently, you may want to have a
> > look.
> >
> > Regarding your suggestions, could you please propose a pull-request via
> the
> > Gate repository : https://github.com/OpenGATE/Gate so that we include
> the
> > corrections in the next release ?
> >
> > Basically :
> > - create a github account
> > - clone from the Gate develop branch
> > - commit your code modification in your branch
> > - submit pull-request
> >
> > thanks a lot !
> > David
> >
> >
> > On Wed, Jun 3, 2015 at 6:04 PM, <germano.russo at i-seecomputing.com>
> wrote:
> >
> >> Dear all,
> >>
> >> I recently tried to use as source an IAEA phase space, specifically the
> >> one named "VarianClinaciX_6MV_20x20_aboveMLC_w1.IAEAphsp" (downloadable
> >> from https://www-nds.iaea.org/phsp/photon1/), via the
> >> "/gate/source/[Source
> >> name]/addPhaseSpaceFile" macro command.
> >>
> >> The simulation (Gate 7.0) run smoothly, however I got meaningless
> >> results.
> >> Digging into the related Gate source code, I believe I found a few bugs
> >> which I report to you asking for confirmation.
> >>
> >>    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.
> >>
> >>    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.
> >>
> >>    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).
> >>
> >> After having applied these correction, I was able to obtain a
> reasonable
> >> output dose distribution.
> >> Could you please check the above and give me a feedback? Thanks!
> >>
> >> Kind regards,
> >>
> >> Germano Russo
> >> R&D I-See (Internet - Simulation Evaluation Envision) company
> >> _______________________________________________
> >> Gate-users mailing list
> >> Gate-users at lists.opengatecollaboration.org
> >> http://lists.opengatecollaboration.org/mailman/listinfo/gate-users
> >>
>
>


-- 
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
http://www.creatis.insa-lyon.fr/~dsarrut
_________________________________
 "2 + 2 = 5,  for extremely large values of 2"
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