[Gate-users] Using IAEA phase spaces

[germano.russo at i-seecomputing.com]

I should have succeeded in submitting the pull request. I have attached
there a few plots of a test I made with a 10x10 cm field.

BR,
Germano


On Thu, 4 Jun 2015 11:14:57 +0200, David Sarrut
<David.Sarrut at creatis.insa-lyon.fr> wrote:
> 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
>> >> _______________________________________________
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>> >> Gate-users at lists.opengatecollaboration.org
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>> >>
>>
>>