[Gate-users] TPS Pencil Beam Source setting

jbaran jbaran at ifj.edu.pl
Tue May 19 12:17:13 CEST 2020 

Dear Hui Zhang,

maybe this is trivial (I am sorry if I write obvious things), but I want 
to clarify it. Whenever you change the source code of GATE you have to 
recompile it. Assuming you have GATE ver.8.2, you have to go to the 
directory gate_v8.2-build 
(https://opengate.readthedocs.io/en/latest/compilation_instructions.html#compilation-instructions-label 
this is for GATE 9.0 but the procedure is very similar) and run again 
commands:

make -jN (N is the number of processor(s) in your PC)
make install

you don't have to build it from the scratch and run commands like ccmake 
and others, just two commands will be enough (I belive only 'make 
install' would be sufficient but run both just to be sure). Due to the 
fact you changed just one file the compilation will be very fast not as 
it was in case of first compilation.

If you did that already, could you please provide example 2D dose 
distribution images?

Jakub


On 2020-05-19 11:54, 张晖 wrote:
> Dear Jakub,
> The attachment is the percentage depth dose distribution in water box.
> I just changed the default values on true in
> GateSourceTPSPencilBeam.cc file,and run my code again. Did you mean
> reinstall the Gate 8.2?
> 
> 
> > -----原始邮件-----
> > 发件人: jbaran <jbaran at ifj.edu.pl>
> > 发送时间: 2020-05-19 17:29:00 (星期二)
> > 收件人: "张晖" <zhanghui at impcas.ac.cn>
> > 抄送: gate-users at lists.opengatecollaboration.org
> > 主题: Re: [Gate-users] TPS Pencil Beam Source setting
> >
> > Dear Hui Zhang,
> >
> > just to check, did you recompile the GATE once again? Could you 
> please
> > explain if the differences are in spatial distribution or the 
> spatial
> > distribution of the doses is consistent and the differences are in 
> the
> > values?
> >
> > Jakub
> >
> >
> > On 2020-05-19 11:13, 张晖 wrote:
> > >> Dear Jakub
> > >> I used Gate 8.2 for simulation.In
> GateSourceTPSPencilBeam.cc, the beam
> > >> is divergent by default, and I have changed the default 
> values on
> > >> true. However, it dosen't work in my case.
> > >> #=====================================================
> > >> # BEAMS
> > >> #=====================================================
> > >> /gate/source/addSource PBS TPSPencilBeam
> > >> /gate/source/PBS/setParticleType GenericIon
> > >> /gate/source/PBS/setIonProperties 6 12 6 0
> > >> /gate/source/PBS/setTestFlag false
> > >> /gate/source/PBS/setPlan data/PlanDescriptionToGATE.txt
> > >> #/gate/source/PBS/setNotAllowedFieldID 1
> > >> #/gate/source/PBS/setNotAllowedFieldID 2
> > >> /gate/source/PBS/setFlatGenerationFlag false
> > >> /gate/source/PBS/setSpotIntensityAsNbIons true
> > >> /gate/source/PBS/setSortedSpotGenerationFlag false
> > >> /gate/source/PBS/setSigmaEnergyInMeVFlag false
> > >> /gate/source/PBS/setSourceDescriptionFile
> data/Source-Properties.txt
> > >> /gate/source/PBS/setBeamConvergence true
> > >>
> > >> This is my part of code in main.mac file.
> > >>
> > >>
> > >> > -----原始邮件-----
> > >> > 发件人: jbaran <jakub.baran at ifj.edu.pl>
> > >> > 发送时间: 2020-05-19 16:34:13 (星期二)
> > >> > 收件人: "张晖" <zhanghui at impcas.ac.cn>
> > >> > 抄送: gate-users at lists.opengatecollaboration.org
> > >> > 主题: Re: [Gate-users] TPS Pencil Beam Source setting
> > >> >
> > >> > Dear Hui Zhang,
> > >> >
> > >> > I am not sure which version of GATE you are using
> but from my
> > >> experience
> > >> > it seems that when you are using Pencil Beam source
> you are able
> > >> to set
> > >> > if your beam is divergent or convergent and you are 
> using
> > >> convergent
> > >> > beam from what I see in your souce code. In case of
> TPS source
> > >> the beam
> > >> > is divergent by default
> > >> >
> > >>
> (https://github.com/OpenGATE/Gate/blob/develop/source/physics/src/GateSourceTPSPencilBeam.cc
> > >> > - lines: 60 and 61), for sure in GATE 8.2 and 9.0
> and I pressume
> > >> for all
> > >> > of GATE versions is the case but you have to check
> it with your
> > >> version.
> > >> > In my case I just change the default values on true
> (lines: 60
> > >> and 61)
> > >> > and recompile GATE once again. Please let us know
> if it works in
> > >> your
> > >> > case.
> > >> >
> > >> > All the best,
> > >> > Jakub
> > >> >
> > >> >
> > >> >
> > >> > On 2020-05-19 10:19, 张晖 wrote:
> > >> > > Dear Gate Users:
> > >> > >
> > >> > >  I previously used Pencil Beam Source to 
> simulate
> > >> single-energy pencil
> > >> > > beam for carbon-ion therapy. The features of
> the pencil beam
> > >> source
> > >> > > such as spot size, divergence and beam 
> emittance were
> > >> defined as
> > >> > > follows: 3 mm spot size in both x and y
> directions, 4 mrad
> > >> divergence
> > >> > > and 15 mm·mrad beam emittance. The energy
> spread was set to
> > >> 0.1% of
> > >> > > the respective energy. Except for dipole 
> scanning
> > >> magnets,vacuum pipe
> > >> > > and window, main and sub-dose monitors, a 
> multi-strip
> > >> ionization
> > >> > > chamber (IC) and a mini ridge filter were
> modeled in my MC
> > >> > > simulations. The source position was located 
> before the
> > >> vacuum window
> > >> > > and a water box was located at isocenter.
> > >> > >
> > >> > >  #################Pencil Beam
> > >> > > Source########################################
> > >> > >
> > >> > >  # SOURCE PBS
> > >> > > /gate/source/addSource C12 PencilBeam
> > >> > >
> > >> > > #particle type
> > >> > > /gate/source/C12/setParticleType GenericIon
> > >> > > /gate/source/C12/setIonProperties 6 12 6 0
> > >> > >
> > >> > > #energy spectrum
> > >> > > /gate/source/C12/setEnergy 2687.52 MeV
> > >> > > /gate/source/C12/setSigmaEnergy 2.68752 MeV
> > >> > >
> > >> > > #position
> > >> > > /gate/source/C12/setPosition 0 0 -1.4059 m
> > >> > >
> > >> > > # spot size
> > >> > > /gate/source/C12/setSigmaX 3 mm
> > >> > > /gate/source/C12/setSigmaY 3 mm
> > >> > >
> > >> > > #divergence
> > >> > > /gate/source/C12/setSigmaTheta 4 mrad
> > >> > > /gate/source/C12/setSigmaPhi 4 mrad
> > >> > >
> > >> > > #emittance
> > >> > > /gate/source/C12/setEllipseXThetaEmittance 15 
> mm*mrad
> > >> > > /gate/source/C12/setEllipseYPhiEmittance 15 
> mm*mrad
> > >> > >
> > >> > > #positive-> converging beam; negative 
> diverging beam
> > >> > > /gate/source/C12/setEllipseXThetaRotationNorm 
> positive
> > >> > > /gate/source/C12/setEllipseYPhiRotationNorm 
> positive
> > >> > >
> > >> > >  Now, I want to use TPS Pencil Beam Source to 
> simulate
> > >> realistic
> > >> > > treatment plan for carbon ion therapy. In
> > >> Source-properties.txt file,
> > >> > > it contains 8 polynomial equations, each
> equation being a
> > >> function of
> > >> > > the energy at the nozzle entrance.
> > >> > >
> > >> > >  #################TPS Pencil Beam
> > >> > >
> > >> 
> Source-Source-properties########################################
> > >> > >
> > >> > >  # Source properties
> > >> > >
> > >> > > # Nozzle exit to Isocenter distance
> > >> > > 1405.9
> > >> > > # SMX to Isocenter distance
> > >> > > 4000
> > >> > > # SMY to Isocenter distance
> > >> > > 4000
> > >> > >
> > >> > > # ENERGY
> > >> > > # mean energy
> > >> > > # polynomial order
> > >> > > 1
> > >> > > # polynomial parameters (highest to lowest)
> > >> > > 1
> > >> > > 0
> > >> > >
> > >> > > # energy spread
> > >> > > # polynomial order
> > >> > > percent
> > >> > > 1
> > >> > > # polynomial parameters (highest to lowest)
> > >> > > 0.001
> > >> > > 0
> > >> > >
> > >> > > # SPOT x y theta phi
> > >> > > # x
> > >> > > # polynomial order
> > >> > > 1
> > >> > > # polynomial parameters
> > >> > > 0
> > >> > > 3
> > >> > > # Theta
> > >> > > # polynomial order
> > >> > > 1
> > >> > > # polynomial parameters
> > >> > > 0
> > >> > > 0.004
> > >> > > # y
> > >> > > # polynomial order
> > >> > > 1
> > >> > > # polynomial parameters
> > >> > > 0
> > >> > > 3
> > >> > > # Phi
> > >> > > # polynomial order
> > >> > > 1
> > >> > > # polynomial parameters
> > >> > > 0
> > >> > > 0.004
> > >> > >
> > >> > > # SPOT emmittances
> > >> > > # x-theta emmittance
> > >> > > # polynomial order
> > >> > > 1
> > >> > > # polynomial parameters
> > >> > > 0
> > >> > > 0.015
> > >> > > # y-phi emmittance
> > >> > > # polynomial order
> > >> > > 1
> > >> > > # polynomial parameters
> > >> > > 0
> > >> > > 0.015
> > >> > >
> > >> > >  #################TPS Pencil Beam
> > >> > >
> > >>
> Source-PlanDescriptionToGate########################################
> > >> > >
> > >> > >  #TREATMENT-PLAN-DESCRIPTION
> > >> > > #PlanName
> > >> > > IMPT
> > >> > > #NumberOfFractions            ***    CURRENTLY
> THIS VALUE IS
> > >> NOT USED
> > >> > >   ***
> > >> > > 1
> > >> > > ##FractionID                ***    CURRENTLY
> THIS VALUE IS
> > >> NOT USED
> > >> > > ***
> > >> > > 1
> > >> > > ##NumberOfFields
> > >> > > 1
> > >> > > ###FieldsID
> > >> > > 1
> > >> > >
> > >> > > #TotalMetersetWeightOfAllFields        ***
> CURRENTLY THIS
> > >> VALUE IS
> > >> > > NOT USED    ***
> > >> > > 662421
> > >> > >
> > >> > > #FIELD-DESCRIPTION
> > >> > > ###FieldID
> > >> > > 1
> > >> > > ###FinalCumulativeMeterSetWeight    ***
> CURRENTLY THIS
> > >> VALUE IS NOT
> > >> > > USED    ***
> > >> > > 336732
> > >> > > ###GantryAngle (in degrees)
> > >> > > 0
> > >> > > ###PatientSupportAngle            ***    
> CURRENTLY THIS
> > >> VALUE IS NOT
> > >> > > USED    ***
> > >> > > 0
> > >> > > ###IsocenterPosition            ***
> CURRENTLY THIS VALUE
> > >> IS NOT
> > >> > > USED    ***
> > >> > > 0 0 0
> > >> > > ###NumberOfControlPoints
> > >> > > 1
> > >> > >
> > >> > > #SPOTS-DESCRIPTION
> > >> > > ####ControlPointIndex
> > >> > > 0
> > >> > > ####SpotTunnedID            ***    CURRENTLY
> THIS VALUE IS
> > >> NOT USED
> > >> > > ***
> > >> > > 0
> > >> > > ####CumulativeMetersetWeight        ***
> CURRENTLY THIS
> > >> VALUE IS NOT
> > >> > > USED    ***
> > >> > > 0
> > >> > > ####Energy (MeV)
> > >> > > 2687.52
> > >> > > ####NbOfScannedSpots
> > >> > > 1
> > >> > > ####X Y Weight (spot position at isocenter in 
> mm, with
> > >> weight in MU
> > >> > > (default) or number of ions
> "setSpotIntensityAsNbIons true")
> > >> > > 0 0 100
> > >> > >
> > >> > >  I simulated the same energy beam in my
> > >> PlanDescriptionToGate.txt file
> > >> > > and the spot position is at isocenter.
> However, I find that
> > >> the dose
> > >> > > distributions with these two sources in water 
> box were
> > >> different. I'm
> > >> > > puzzled about the parameter settings in TPS 
> Pencil Beam
> > >> Source if I
> > >> > > want to make them consistent with those in 
> Pencil Beam
> > >> Source
> > >> > > settings. How can I do?
> > >> > >
> > >> > >  Best regards,
> > >> > >
> > >> > >  Hui Zhang
> > >> > >
> > >> > > -------------------------
> > >> > > _______________________________________________
> > >> > > Gate-users mailing list
> > >> > > Gate-users at lists.opengatecollaboration.org
> > >> > >
> > >> 
> http://lists.opengatecollaboration.org/mailman/listinfo/gate-users
> > >>
> > >>
> > >> ------------------------------
> > >> Zhang HuiUniversity of Chinese Academy of Sciences
> > >> Institute of Modern Physics
> > >> </zhanghui at impcas.ac.cn></jakub.baran at ifj.edu.pl>
> > >> _______________________________________________
> > >> Gate-users mailing list
> > >> Gate-users at lists.opengatecollaboration.org
> > >> 
> http://lists.opengatecollaboration.org/mailman/listinfo/gate-users
> 
> 
> ------------------------------
> Zhang HuiUniversity of Chinese Academy of Sciences
> Institute of Modern Physics
> </zhanghui at impcas.ac.cn></jbaran at ifj.edu.pl>

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