[Gate-users] Gat exercices - photon beam, dose in water - only 0 values as output

Tue Dec 14 13:05:04 CET 2021

Dear gate users, 

I'm still stuck on the same problem (the output has only 0 values) and I'm wondering if it could be linked with a problem of dose calculation algorithm? 
Does someone understand the following sentence in 8.2.3.2 in [ http://www.opengatecollaboration.org/ | http://www.opengatecollaboration.org/ ] 

> If the size of the image voxel is smaller than the size of the dosel of the
> DoseActor it can lead to undesired results.

I'm ok with the dosel of the DoseActor , but what does image voxel here exaclty mean? 

I will also look at matplotlib for analysing my code, but still it does not explain why the visualization with Gate works but the output files opened with ImageJ have only 0 values... 

If someone has an idea what could be the problem, thank you very much for your help! 

Sarah Blind 

----- Le 13 Déc 21, à 16:29, Musajoya Joya <musajoyajoya at gmail.com> a écrit : 

> Dear friends,

> I have the same problem. I am trying to do dynamic intensity-modulated
> brachytherapy. The movement and the radiation emission visualization look ok
> but the actors do not record any dose even with 200 million particles. I use
> the output format of .mhd and or .txt, but for both the dose is zero. what
> would be the reason(s)? Doseactors score the dose even when
> /gate/application/noGlobalOutput is active in static mode.
> Please any GATE expert has a look at my code and point out the problem.
> PLEASE HELP!!
> #=====================================================
> # PHYSICS
> #=====================================================
> /gate/physics/addPhysicsList emstandard_opt3
> /gate/physics/Gamma/SetCutInRegion world 10 mm
> /gate/physics/Electron/SetCutInRegion world 10 mm
> /gate/physics/Positron/SetCutInRegion world 10 mm
> #/gate/physics/Gamma/SetCutInRegion sc4 0.1 mm
> #/gate/physics/Electron/SetCutInRegion sc4 1 m
> /gate/physics/displayCuts
> #=====================================================
> # DETECTORS
> #=====================================================
> ### Target ##############
> /gate/actor/addActor DoseActor targetdose
> /gate/actor/targetdose/attachTo vaginatarget
> /gate/actor/targetdose/stepHitType random
> /gate/actor/targetdose/setVoxelSize 2 2 2 mm
> /gate/actor/targetdose/save output/target/targetdose.txt
> /gate/actor/targetdose/saveEveryNSeconds 60
> /gate/actor/targetdose/enableDose true
> /gate/actor/targetdose/enableUncertaintyDose true
> /gate/actor/targetdose/enableSquaredDose true

> # filter
> /gate/actor/targetdose/addFilter energyFilter
> /gate/actor/targetdose/energyFilter/setEmin 0.01 MeV
> /gate/actor/targetdose/energyFilter/setEmax 2.5 MeV
> #=====================================================
> #rotation
> #=====================================================
> /gate/outerlayer/moves/insert rotation
> /gate/outerlayer/rotation/setSpeed 1 deg/s
> /gate/outerlayer/rotation/setAxis 0 0 -1
> /gate/outerlayer/placement/setRotationAngle 90 deg

> /gate/application/setTimeSlice 1. s
> /gate/application/setTimeStart 0. s
> /gate/application/setTimeStop 90. s
> #/gate/application/startDAQ
> #=====================================================
> # INITIALISATION
> #=====================================================
> /gate/run/initialize
> #=====================================================
> # BEAMS
> #=====================================================
> #Description of co-60 source
> /gate/source/addSource co60s gps
> /gate/source/co60s/gps/particle gamma
> /gate/source/co60s/gps/energytype UserSpectrum
> /gate/source/co60s/gps/setSpectrumFile data/co60spectrum.txt
> /gate/source/co60s/gps/hist/type energy
> /gate/source/co60s/attachTo sourceSeed
> /gate/source/co60s/gps/type Volume
> /gate/source/co60s/gps/shape Cylinder
> /gate/source/co60s/gps/radius 0.025 cm
> /gate/source/co60s/gps/halfz 0.175 cm
> #/gate/source/co60s/gps/centre 0.85 0.0 11 cm
> /gate/source/co60s/gps/ang/type iso
> /gate/source/co60s/visualize 10000 red 5
> /gate/source/list
> #=====================================================
> # START BEAMS
> #=====================================================
> /gate/random/setEngineName MersenneTwister
> /gate/random/setEngineSeed auto
> /gate/application/setTotalNumberOfPrimaries 10000000
> /gate/application/start

> Kind Regards

> Musa Joya

> Ph.D. candidate in Medical Physics

> Tehran University of Medical Sciences

> Tehran, Iran &

> Lecturer of Medical Physics

> Kabul University of Medical Sciences

> Kabul, Afghanistan

> Mobile and Telegram & WhatsApp: +989381560693

> On Mon, 13 Dec 2021 at 17:43, Sarah Blind < [
> mailto:sarah.blind at univ-lorraine.fr | sarah.blind at univ-lorraine.fr ] > wrote:

>> Yes !

>> ----- Le 13 Déc 21, à 14:40, Matthew Strugari < [ mailto:matthew.strugari at dal.ca
>> | matthew.strugari at dal.ca ] > a écrit :

>>> Did you increase your number of primaries from 1?

>>> Matthew

>>>> On Dec 13, 2021, at 9:00 AM, Sarah Blind < [ mailto:sarah.blind at univ-lorraine.fr
>>>> | sarah.blind at univ-lorraine.fr ] > wrote:

>>>> CAUTION: The Sender of this email is not from within Dalhousie.
>>>> I still have the same problem even without /gate/application/noGlobalOutput ...

>>>> ----- Le 13 Déc 21, à 13:43, Matthew Strugari < [ mailto:matthew.strugari at dal.ca
>>>> | matthew.strugari at dal.ca ] > a écrit :

>>>>> Hi Sarah,

>>>>> You have the output disabled. Remove /gate/application/noGlobalOutput from your
>>>>> macro and try again.

>>>>> Best,
>>>>> Matthew

>>>>>> On Dec 13, 2021, at 6:19 AM, Sarah Blind < [ mailto:sarah.blind at univ-lorraine.fr
>>>>>> | sarah.blind at univ-lorraine.fr ] > wrote:

>>>>>> CAUTION: The Sender of this email is not from within Dalhousie.
>>>>>> Dear Gate users,

>>>>>> I am trying to follow the exercices (1 and 2) of [
>>>>>> https://davidsarrut.pages.in2p3.fr/gate-exercices-site/docs/welcome/ |
>>>>>> https://davidsarrut.pages.in2p3.fr/gate-exercices-site/docs/welcome/ ] .
>>>>>> When I open the output files (with ImageJ) I obtain only 0 values.
>>>>>> Does anyone have any idea why those dose distribution values are all zero?

>>>>>>> # Visualization
>>>>>>> /vis/open OGLIQt
>>>>>>> /vis/drawVolume
>>>>>>> /vis/viewer/flush
>>>>>>> /tracking/storeTrajectory 1
>>>>>>> /vis/scene/add/trajectories
>>>>>>> /vis/scene/endOfEventAction accumulate
>>>>>>> /vis/modeling/trajectories/create/drawByParticleID

>>>>>>> /gate/geometry/setMaterialDatabase ../data/GateMaterials.db

>>>>>>> # World
>>>>>>> /gate/world/geometry/setXLength 1 m
>>>>>>> /gate/world/geometry/setYLength 1 m
>>>>>>> /gate/world/geometry/setZLength 1 m
>>>>>>> /gate/world/setMaterial Air

>>>>>>> # Water Box
>>>>>>> /gate/world/daughters/name waterbox
>>>>>>> /gate/world/daughters/insert box
>>>>>>> /gate/waterbox/geometry/setXLength 40 cm
>>>>>>> /gate/waterbox/geometry/setYLength 40 cm
>>>>>>> /gate/waterbox/geometry/setZLength 40 cm
>>>>>>> /gate/waterbox/placement/setTranslation 0 0 25 cm
>>>>>>> /gate/waterbox/setMaterial Water
>>>>>>> /gate/waterbox/vis/setVisible 1
>>>>>>> /gate/waterbox/vis/setColor blue

>>>>>>> # aluminium box
>>>>>>> /gate/world/daughters/name alubox
>>>>>>> /gate/world/daughters/insert box
>>>>>>> /gate/alubox/geometry/setXLength 5 cm
>>>>>>> /gate/alubox/geometry/setYLength 5 cm
>>>>>>> /gate/alubox/geometry/setZLength 5 cm
>>>>>>> /gate/alubox/placement/setTranslation 0 0 15 cm
>>>>>>> /gate/alubox/setMaterial Aluminium
>>>>>>> /gate/alubox/vis/setVisible 1
>>>>>>> /gate/alubox/vis/setColor yellow

>>>>>>> #=========
>>>>>>> # PHYSICS
>>>>>>> #=========

>>>>>>> /gate/physics/addPhysicsList emstandard_opt3

>>>>>>> /gate/physics/Gamma/SetCutInRegion world 10 mm
>>>>>>> /gate/physics/Electron/SetCutInRegion world 10 mm
>>>>>>> /gate/physics/Positron/SetCutInRegion world 10 mm

>>>>>>> /gate/physics/Gamma/SetCutInRegion waterbox 0.01 mm
>>>>>>> /gate/physics/Electron/SetCutInRegion waterbox 0.01 mm
>>>>>>> /gate/physics/Positron/SetCutInRegion waterbox 0.01 mm

>>>>>>> /gate/physics/displayCuts

>>>>>>> #===========
>>>>>>> # DETECTORS
>>>>>>> #===========

>>>>>>> /gate/actor/addActor DoseActor depthdose
>>>>>>> /gate/actor/depthdose/save output/gamma-depth.txt
>>>>>>> /gate/actor/depthdose/attachTo waterbox
>>>>>>> /gate/actor/depthdose/stepHitType random
>>>>>>> /gate/actor/depthdose/setPosition 0 0 0 cm
>>>>>>> /gate/actor/depthdose/setResolution 1 1 100
>>>>>>> /gate/actor/depthdose/saveEveryNSeconds 60
>>>>>>> /gate/actor/depthdose/enableEdep true
>>>>>>> /gate/actor/depthdose/enableUncertaintyEdep true
>>>>>>> /gate/actor/depthdose/enableDose true
>>>>>>> /gate/actor/depthdose/enableUncertaintyDose true
>>>>>>> /gate/actor/depthdose/enableNumberOfHits true

>>>>>>> /gate/actor/addActor DoseActor doseprofile
>>>>>>> /gate/actor/doseprofile/save output/gamma-profile.txt
>>>>>>> /gate/actor/doseprofile/attachTo waterbox
>>>>>>> /gate/actor/doseprofile/stepHitType random
>>>>>>> /gate/actor/doseprofile/setPosition 0 0 4 cm
>>>>>>> /gate/actor/doseprofile/setResolution 100 1 1
>>>>>>> /gate/actor/doseprofile/setSize 5 40 40 cm
>>>>>>> /gate/actor/doseprofile/saveEveryNSeconds 60
>>>>>>> /gate/actor/doseprofile/enableEdep true
>>>>>>> /gate/actor/doseprofile/enableUncertaintyEdep true
>>>>>>> /gate/actor/doseprofile/enableDose true
>>>>>>> /gate/actor/doseprofile/enableUncertaintyDose true
>>>>>>> /gate/actor/doseprofile/enableNumberOfHits true

>>>>>>> /gate/actor/addActor SimulationStatisticActor stat
>>>>>>> /gate/actor/stat/save output/gamma-stat.txt
>>>>>>> /gate/actor/stat/saveEveryNSeconds 60

>>>>>>> /gate/actor/addActor DoseActor doseDistribution3D_1
>>>>>>> /gate/actor/doseDistribution3D_1/save output/doseDistribution3D_1.hdr
>>>>>>> /gate/actor/doseDistribution3D_1/attachTo waterbox
>>>>>>> /gate/actor/doseDistribution3D_1/stepHitType random
>>>>>>> /gate/actor/doseDistribution3D_1/setPosition 0.0 0.0 0.0 um
>>>>>>> /gate/actor/doseDistribution3D_1/setSize 40.0 40.0 40.0 um
>>>>>>> /gate/actor/doseDistribution3D_1/setResolution 200 200 200
>>>>>>> /gate/actor/doseDistribution3D_1/enableDose true
>>>>>>> /gate/actor/doseDistribution3D_1/saveEveryNSeconds 60

>>>>>>> #=============
>>>>>>> # INITIALISATION
>>>>>>> #==============

>>>>>>> /gate/run/initialize

>>>>>>> #================
>>>>>>> # BEAMS / SOURCE
>>>>>>> #================

>>>>>>> /gate/source/addSource mybeam gps
>>>>>>> /gate/source/mybeam/gps/particle gamma
>>>>>>> /gate/source/mybeam/gps/pos/type Beam
>>>>>>> /gate/source/mybeam/gps/pos/rot1 1 1 1
>>>>>>> #/gate/source/mybeam/gps/pos/rot2 0 0 0
>>>>>>> /gate/source/mybeam/gps/pos/shape Circle
>>>>>>> /gate/source/mybeam/gps/pos/centre 0 0 0 mm
>>>>>>> /gate/source/mybeam/gps/pos/sigma_x 3 mm
>>>>>>> /gate/source/mybeam/gps/pos/sigma_y 3 mm
>>>>>>> /gate/source/mybeam/gps/ene/mono 10 MeV
>>>>>>> /gate/source/mybeam/gps/ene/type Gauss
>>>>>>> /gate/source/mybeam/gps/ene/sigma 1.0 MeV
>>>>>>> /gate/source/mybeam/gps/direction 0 0 1

>>>>>>> #=============
>>>>>>> # START BEAMS
>>>>>>> #=============

>>>>>>> /gate/random/setEngineName MersenneTwister
>>>>>>> /gate/random/setEngineSeed auto

>>>>>>> /gate/application/noGlobalOutput
>>>>>>> /gate/application/setTotalNumberOfPrimaries 1
>>>>>>> /gate/application/start

>>>>>> Many thanks for your help,

>>>>>> Sarah Blind
>>>>>> _______________________________________________
>>>>>> Gate-users mailing list
>>>>>> [ mailto:Gate-users at lists.opengatecollaboration.org |
>>>>>> Gate-users at lists.opengatecollaboration.org ]
>>>>>> [ http://lists.opengatecollaboration.org/mailman/listinfo/gate-users |
>>>>>> http://lists.opengatecollaboration.org/mailman/listinfo/gate-users ]

>>>> --
>>>> Sarah Blind
>>>> Ingénieure de recherche - CNRS
>>>> Centre de Recherche en Automatique de Nancy (CRAN)
>>>> Département Biologie, Signaux et Systèmes en Cancérologie et Neurosciences
>>>> (BioSiS)
>>>> Site de la faculté de médecine
>>>> 9, Avenue de la Forêt de Haye
>>>> 54505 Vandoeuvre les Nancy
>>>> Tél : 03.72.74.61.13

>> --
>> Sarah Blind
>> Ingénieure de recherche - CNRS
>> Centre de Recherche en Automatique de Nancy (CRAN)
>> Département Biologie, Signaux et Systèmes en Cancérologie et Neurosciences
>> (BioSiS)
>> Site de la faculté de médecine
>> 9, Avenue de la Forêt de Haye
>> 54505 Vandoeuvre les Nancy
>> Tél : 03.72.74.61.13
>> _______________________________________________
>> Gate-users mailing list
>> [ mailto:Gate-users at lists.opengatecollaboration.org |
>> Gate-users at lists.opengatecollaboration.org ]
>> [ http://lists.opengatecollaboration.org/mailman/listinfo/gate-users |
>> http://lists.opengatecollaboration.org/mailman/listinfo/gate-users ]

-- 
Sarah Blind 
Ingénieure de recherche - CNRS 
Centre de Recherche en Automatique de Nancy (CRAN) 
Département Biologie, Signaux et Systèmes en Cancérologie et Neurosciences (BioSiS) 
Site de la faculté de médecine 
9, Avenue de la Forêt de Haye 
54505 Vandoeuvre les Nancy 
Tél : 03.72.74.61.13 
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