[Gate-users] Simulate a beam with spaced bunches in GATE
David Sarrut
David.Sarrut at creatis.insa-lyon.fr
Mon Apr 29 08:00:20 CEST 2013
Hello Salvatore,
I haven't got the time to look at in detail, but this is true that
phase-space dose not store runID, eventID, and that, in that case, the time
is no taken into account with the source.
I think the best solution for your problem is to write a new type of
source. That should not be too difficult (even if it requires some times),
starting from a new class inheriting from GateVSource. You will need also
to slightly modify GateSourceMgr (in function AddSource) to enable your new
source type. Maybe instead of a new source type, you can alternatively add
timing option to the GPS source type. I am convinced that it could be
useful to other too.
Another alternative option, simpler but maybe not as useful, could be to
add RunID and EvenID branch in the phase space. I attached to this mail a
new version of the PhaseSpaceActor that store eventID and runID. You can
try it (without any guarantee) by adding the files in the src/include
folders of the digits_hits folder.
Sincerely,
David
On Mon, Apr 22, 2013 at 5:58 PM, Salvatore Di Guida <
salvatore.di.guida at cern.ch> wrote:
> Dear GATE users and developers,
> since I have been using the framework for few weeks, I apologize for my
> misunderstandings and mistakes.
> I have simulated the detector I am working on as two water boxes
> (equivalent to gas detectors), two plastic scintillator boxes plus a
> scanner system made up of 30 plastic scintillators. I have attached one
> phase space to each water box (in order to describe the incoming particles
> from the source and from the first box, respectively), to the air box
> between the water boxes (in order to look at the particles outgoing the
> first water box) and to the air box between the second water fox and the
> first scintillator (in order to look at the particles outgoing the second
> water box). Moreover, I have defined a proton pencil beam source: I have
> implemented it both via G4 GeneralParticleSource and using the PencilBeam
> template in GATE.
> If you like, you can check the geometry and the sources in details in the
> archive I am attaching to this mail: there you can find the macros I am
> using. I am working with GATE 6.1 on vGATE 2.0.
> The output I want to retrieve is, for each proton, the x and y position in
> each water box, and the energy deposition in each level of the scanner
> system.
> In my first attempt, I simply created the geometry, the source, and the
> digitizer system, and launched the simulation with 1000 primaries,
> producing ROOT files as output. My idea was to distinguish the incoming
> protons by the (runID, eventID) pair: unfortunately, the phase space does
> not store this piece of information [1].
> Then, since both the phase space and the scanner keep time information, my
> next attempt was to calculate the coincidences of each proton in the water
> boxes and in the first scintillator: in this way, I could mark the protons
> propagating outside the scanner with the same (runID, eventID) pair
> established inside it. Unfortunately, both sources generate all the protons
> at t = 0, so it is impossible to get an adequate result via coincidence
> computations [2].
> Next, I tried to overcome this issue using time slices in Data
> Acquisition: I defined 1000 time slices, where each slice has a time
> duration larger than the time of flight of the proton, so that I had one
> primary per slice, and the association between data in water and data in
> the scanner could be quite easy. Unfortunately, when the second time slice
> starts, GATE crashes with a segmentation violation with both the PencilBeam
> source and with GPS source (even when I tried to set
> GeneralParticleSource::number or setActivity in GATE). Debugging with gdb
> did not help.
>
> My question is: is there a way in GATE to produce a beam source where a
> given number of protons are grouped in bunches spaced by a given time
> interval (say: 100 protons-per-bunch, bunches spaced by 100 ms).
>
> Thanks in advance for your help!
>
> Salvatore
>
> [1]
> $ root -l
> root [] TFile* gem0RootFile =
> TFile::Open("GEM0PHS_1000primaries_perfectPBS.root")
> root [] TTree* gem0PhaseSpaceTree = (TTree*) gem0RootFile->Get(
> "PhaseSpace" )
> root [] phaseSpaceTree->Print()
>
> [2] the source is 0.05 mm far from the phase space, which is at the origin
> of the world; so, all protons enter the water box associated to the phase
> space at t > 0:
> root [] TFile* gem0RootFile =
> TFile::Open("GEM0PHS_1000primaries_perfectPBS.root")
> root [] TTree* gem0PhaseSpaceTree = (TTree*) gem0RootFile->Get(
> "PhaseSpace" )
> root [] gem0PhaseSpaceTree->Scan( "ParticleName:Time:X:Y:Z:dX:dY:dZ:Ekine"
> )
>
> ************************************************************************************************************************
> * Row * ParticleN * Time * X * Y * Z *
> dX * dY * dZ * Ekine *
>
> ************************************************************************************************************************
> * 0 * proton * 0.0003519 * 0 * 0 * 0 *
> -2.63e-08 * 2.610e-08 * 1 * 100 *
> * 1 * proton * 0.0003519 * 0 * 0 * 0 *
> 2.421e-08 * 9.183e-11 * 1 * 100 *
> * 2 * proton * 0.0003519 * 0 * 0 * 0 *
> 1.011e-09 * 2.843e-09 * 1 * 100 *
> * 3 * proton * 0.0003519 * 0 * 0 * 0 *
> -5.11e-09 * 7.478e-10 * 1 * 100 *
> * 4 * proton * 0.0003519 * 0 * 0 * 0 *
> 2.031e-08 * -2.61e-08 * 1 * 100 *
> * 5 * proton * 0.0003519 * 0 * 0 * 0 *
> 2.153e-08 * 9.473e-09 * 1 * 100 *
> ...
> And here it is how the ROOT file for the phase space between the two water
> boxes look like: there is a very slight difference in timing between
> protons...
> root [] TFile* gemSpacingRootFile =
> TFile::Open("GEMSpacingPHS_1000primaries_perfectPBS.root")
> root [] TTree* gemSpacingPhaseSpaceTree = (TTree*)
> gemSpacingRootFile->Get( "PhaseSpace" )
> root [] gemSpacingPhaseSpaceTree->Scan(
> "ParticleName:Time:X:Y:Z:dX:dY:dZ:Ekine" )
>
> ************************************************************************************************************************
> * Row * ParticleN * Time * X * Y * Z *
> dX * dY * dZ * Ekine *
>
> ************************************************************************************************************************
> * 0 * proton * 0.0194233 * 0.0030443 * -0.001321 * 2.7000000 *
> 0.0042755 * -0.001657 * 0.9999895 * 98.147529 *
> * 1 * proton * 0.0194286 * -0.002575 * 0.0078605 * 2.7000000 *
> -0.002732 * 0.0060394 * 0.9999780 * 97.927230 *
> * 2 * proton * 0.0194189 * 0.0081350 * -0.003375 * 2.7000000 *
> 0.0061967 * -0.000981 * 0.9999803 * 98.123619 *
> * 3 * proton * 0.0194209 * 0.0102742 * -0.006316 * 2.7000000 *
> -0.002067 * -0.004013 * 0.9999898 * 97.984443 *
> * 4 * proton * 0.0194191 * -0.007278 * 0.0019697 * 2.7000000 *
> -0.005616 * 0.0024906 * 0.9999811 * 98.163551 *
> ...
>
> _______________________________________________
> Gate-users mailing list
> Gate-users at lists.opengatecollaboration.org
> http://lists.opengatecollaboration.org/mailman/listinfo/gate-users
>
--
David Sarrut, Phd
Chargé 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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