[Gate-users] TPS Pencil Beam Source setting
张晖
zhanghui at impcas.ac.cn
Mon May 25 04:11:01 CEST 2020
Dear Jakub,
Thanks for your advice! I have done as you said, but it dose not work. Now I doubt that my parameter settings in TPS Pencil Beam Source simulation might be wrong. From my experience, different parameters of energy spread and optical settings could influence the results,such as the ratio between the Bragg peak and plateau, and the longitudinal broadening. Do you have some suggestions about this aspect?
Best regard
Hui Zhang
> -----原始邮件-----
> 发件人: jbaran <jbaran at ifj.edu.pl>
> 发送时间: 2020-05-22 04:40:46 (星期五)
> 收件人: "Grevillot Loic" <loic.grevillot at medaustron.at>
> 抄送: "张晖" <zhanghui at impcas.ac.cn>, gate-users at lists.opengatecollaboration.org
> 主题: Re: [Gate-users] TPS Pencil Beam Source setting
>
> 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
> >
> >> > >> > >
> >
> >> > >>
> >
> >>
> > https://eur03.safelinks.protection.outlook.com/?url=http%3A%2F%2Flists
> > [4]
> >
> >>
> > .opengatecollaboration.org%2Fmailman%2Flistinfo%2Fgate-users&data=
> >
> >
> >>
> > 02%7C01%7Cloic.grevillot%40medaustron.at%7C7689c7e6677d4cbf737908d7fbd
> >
> >
> >>
> > de75d%7Cadb749e06dfd4f6fbea8cd9f8e0c9b89%7C0%7C0%7C637254802831519922&
> >
> >
> >>
> > amp;sdata=oItkB5U0cTnuuyVWvjCg0MF%2FRr%2B%2FZzCJ7Bn5BdcXKhs%3D&res
> >
> >
> >> erved=0
> >
> >> > >>
> >
> >> > >>
> >
> >> > >> ------------------------------ > >> 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
> >
> >> > >>
> >
> >>
> > https://eur03.safelinks.protection.outlook.com/?url=http%3A%2F%2Flists
> > [4]
> >
> >>
> > .opengatecollaboration.org%2Fmailman%2Flistinfo%2Fgate-users&data=
> >
> >
> >>
> > 02%7C01%7Cloic.grevillot%40medaustron.at%7C7689c7e6677d4cbf737908d7fbd
> >
> >
> >>
> > de75d%7Cadb749e06dfd4f6fbea8cd9f8e0c9b89%7C0%7C0%7C637254802831519922&
> >
> >
> >>
> > amp;sdata=oItkB5U0cTnuuyVWvjCg0MF%2FRr%2B%2FZzCJ7Bn5BdcXKhs%3D&res
> >
> >
> >> erved=0
> >
> >>
> >
> >>
> >
> >> ------------------------------
> >
> >> Zhang HuiUniversity of Chinese Academy of Sciences Institute of
> > Modern
> >
> >> Physics </zhanghui at impcas.ac.cn></jbaran at ifj.edu.pl>
> >
> > _______________________________________________
> >
> > Gate-users mailing list
> >
> > Gate-users at lists.opengatecollaboration.org
> >
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> > [5]
> >
> > DISCLAIMER:
> > Please notice our E-Mail Disclaimer
> > http://www.medaustron.at/email-disclaimer/ [6]
> >
> >
> > Links:
> > ------
> > [1]
> > https://github.com/OpenGATE/GateContrib/tree/master/GATE-RTion/TPSPencilBeamSource
> > [2]
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------------------------------
Zhang HuiUniversity of Chinese Academy of Sciences
Institute of Modern Physics
</zhanghui at impcas.ac.cn></zhanghui at impcas.ac.cn></loic.grevillot at medaustron.at></jbaran at ifj.edu.pl>
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