[Gate-users] TPS Pencil Beam Source setting
jbaran
jbaran at ifj.edu.pl
Thu May 21 22:40:46 CEST 2020
Dear Loic,
many thanks for your answear. I was not so explicit in my explanations
as you in previous emails. Regarding your comment about te
setBeamConvergence option, I completely missed that somehow (I have no
idea why) during the beam model preparation and this is the reason why I
change the source code. You are right, thanks for claryfing and
indicating that option.
All the best,
Jakub
On 2020-05-20 09:58, Grevillot Loic wrote:
> Dear both,
>
> I was having a short look at your discussion and I do not exactly get
> your issue, but I would like to provide a few hints if it may help:
>
> 1. In the TPS source, one can set the following option to true
> or false, depending if you want the beam to be diverging or
> converging:
>
> o /gate/source/PBS/setBeamConvergence true (or false)
>
> o If you use this option, I do not understand why you would need to
> change the source code or recompile? Just use the setBeamConvergence
> option.
>
> o For a more detailed understanding of the TPS source, you can run
> the validation tests provided in the GATE-RTion folder [1] of the
> GitContrib repository of GATE
>
> 2. If despite changing this option, the beam is always
> diverging, it may simply be that you define your beam properties at
> the waist position… then in that case the beam can only diverge.
>
> o
>
> Hope this helps?
>
> Best,
>
> Loïc
>
> -----Original Message-----
> From: Gate-users
> [mailto:gate-users-bounces at lists.opengatecollaboration.org] On Behalf
> Of jbaran
> Sent: Dienstag, 19. Mai 2020 12:17
> To: 张晖 <zhanghui at impcas.ac.cn>
> Cc: gate-users at lists.opengatecollaboration.org
> Subject: Re: [Gate-users] TPS Pencil Beam Source setting
>
> 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://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fopengate.readthedocs.io%2Fen%2Flatest%2Fcompilation_instructions.html%23compilation-instructions-label&data=02%7C01%7Cloic.grevillot%40medaustron.at%7C7689c7e6677d4cbf737908d7fbdde75d%7Cadb749e06dfd4f6fbea8cd9f8e0c9b89%7C0%7C0%7C637254802831509937&sdata=phmMjoqNL9dXmsyN0zzMkFvqzDJjZ8NHMK%2BT2I5J98Y%3D&reserved=0
> [2]
>
> 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://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgit
> [3]
>
>>
> hub.com%2FOpenGATE%2FGate%2Fblob%2Fdevelop%2Fsource%2Fphysics%2Fsrc%2F
>
>
>>
> GateSourceTPSPencilBeam.cc&data=02%7C01%7Cloic.grevillot%40medaust
>
>
>>
> ron.at%7C7689c7e6677d4cbf737908d7fbdde75d%7Cadb749e06dfd4f6fbea8cd9f8e
>
>
>>
> 0c9b89%7C0%7C0%7C637254802831519922&sdata=YQQt8kRb6F9Xf%2BYiVkouea
>
>
>> 6hf%2BUO0ErAb6eZ0%2FWswZM%3D&reserved=0
>
>> > >> > - 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
>
>> > >> > >
>
>> > >>
>
>>
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>
>> > >>
>
>> > >>
>
>> > >> ------------------------------ > >> 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
>
>> > >>
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>>
>
>> ------------------------------
>
>> 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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> Links:
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