[Gate-users] [Gate] Fix the use of IAEA phase space files (#34)

[David Sarrut]

thanks Kris,

I will change to probably for std::int32_t. But does it require to compile
with cxx11 ?

David

On Tue, Jun 9, 2015 at 12:58 PM, Kris Thielemans <
kris.f.thielemans at gmail.com> wrote:

> Hi
>
>
>
> A quick comment on the following:
>
> ----------
>
> *things seem to be outdated, for instance in the "GateIAEAConfig.h" the*
>
> *definition 'typedef long IAEA_I32' must be replaced with 'typedef
> intIAEA_I32' in order to conform to the current "*.IAEAphsp" file format.
>
> -----------
>
>
>
> 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.
>
>
>
> Kris
>
> *From:* gate-users-bounces at lists.opengatecollaboration.org [mailto:
> gate-users-bounces at lists.opengatecollaboration.org] *On Behalf Of *David
> Sarrut
> *Sent:* 09 June 2015 00:57
> *To:* gate-users; germano.russo at i-seecomputing.com
> *Subject:* Re: [Gate-users] [Gate] Fix the use of IAEA phase space files
> (#34)
>
>
>
> Hello Germano Russo,
>
>
>
> 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.
>
>
>
> More details : https://github.com/OpenGATE/Gate/pull/34
>
>
>
> Sincerely,
>
> David
>
>
>
> On Mon, Jun 8, 2015 at 10:32 AM, germanorusso <notifications at github.com>
> wrote:
>
> I recently tried to use as source an IAEA phase space, specifically the
> one named "VarianClinaciX_6MV_10x10_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 3 bugs
> for which I propose a correction in the 'fixIAEAphspSource' branch.
>
> 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.
> Somethings seem to be outdated, for instance in the "GateIAEAConfig.h"
> thedefinition 'typedef long IAEA_I32' must be replaced with 'typedef
> intIAEA_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 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 ("
> https://www-nds.iaea.org/phsp/photon1/VarianClinaciX_6MV_PHSPdoc_Gothenburg.pdf
> ").
>
> [image: Image removed by sender. comparisonpdd]
> <https://cloud.githubusercontent.com/assets/8522577/8030667/fed03d40-0dc8-11e5-8a51-90eae801a36d.png>
>
> [image: Image removed by sender. comparisonxprofiles]
> <https://cloud.githubusercontent.com/assets/8522577/8030686/28bccb3c-0dc9-11e5-9075-8756f6952043.png>
>
> [image: Image removed by sender. comparisonyprofiles]
> <https://cloud.githubusercontent.com/assets/8522577/8030692/2e0595f6-0dc9-11e5-8da2-ed4992dd8c9b.png>
> ------------------------------
> You can view, comment on, or merge this pull request online at:
>
>   https://github.com/OpenGATE/Gate/pull/34
> Commit Summary
>
> · Reversed type of IAEA_I32 to int, according with the current IAEA
> setting.
>
> · 1) In the function 'GateSourcePhaseSpace::OpenIAEAFile()' the call
> File Changes
>
> · *M* source/general/include/GateIAEAConfig.h
> <https://github.com/OpenGATE/Gate/pull/34/files#diff-0> (5)
>
> · *M* source/physics/src/GateSourcePhaseSpace.cc
> <https://github.com/OpenGATE/Gate/pull/34/files#diff-1> (5)
> Patch Links:
>
> · https://github.com/OpenGATE/Gate/pull/34.patch
>
> · https://github.com/OpenGATE/Gate/pull/34.diff
>
> —
> Reply to this email directly or view it on GitHub
> <https://github.com/OpenGATE/Gate/pull/34>.[image: Image removed by
> sender.]
>
>
>
>
>
> --
>
> 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"
> _________________________________
>



-- 
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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