[Gate-users] Error
Khalid Hussain
khalidhussain1134 at gmail.com
Sun Nov 7 13:56:36 CET 2021
Hi Deniz,
Sorry, It might be tough to further help you with the thyroid dose, as I
don't have experience with the dose.
Many experts are on the Gate list and hopefully will help you.
On Sun, Nov 7, 2021 at 5:37 PM Deniz Erkal <dnzrklfzk at gmail.com> wrote:
> Hello, you have made the changes you requested, but cannot receive data
> for thyroid and nasofarengeal.What do you think might be the reason for
> this?
>
> Khalid Hussain <khalidhussain1134 at gmail.com>, 7 Kas 2021 Paz, 12:19
> tarihinde şunu yazdı:
>
>> Dear Erkal,
>>
>> Sorry for the late reply, as I was sick and today came back to my
>> workplace.
>> There was a little problem, probably in the
>>
>> /gate/application/start
>> which I replaced with
>> /gate/application/startDAQ
>> Please see the attached zip file. Now it working
>>
>> Please change the material with the one that you defined in material db
>> file.
>>
>> I have changed the material to Breast just for checking.
>> Now it running.
>>
>> Now its running.
>>
>>
>> On Thu, Nov 4, 2021 at 10:35 PM Deniz Erkal <dnzrklfzk at gmail.com> wrote:
>>
>>> #-------------------oooooOOOOO00000OOOOOooooo---------------------#
>>>
>>> # Example of Carbon beam in water tank. Output is a 3D dose
>>> # distribution map (with associated uncertainty) and map of producted
>>> # C11.
>>>
>>> #-------------------oooooOOOOO00000OOOOOooooo---------------------#
>>>
>>>
>>> #=====================================================
>>> # VERBOSE and VISUALISATION
>>> #=====================================================
>>>
>>> /control/execute mac/verbose.mac
>>>
>>> # to use the visualisation :
>>> # - uncomment the following line
>>> # - use Gate --qt
>>> # - in the interface, type /control/execute mac/main.mac
>>> #/control/execute mac/visu.mac
>>>
>>>
>>> #=====================================================
>>> # GEOMETRY
>>> #=====================================================
>>>
>>> /gate/geometry/setMaterialDatabase data/GateMaterials.db
>>>
>>> # WORLD
>>> /gate/world/setMaterial Air
>>> /gate/world/geometry/setXLength 2.0 m
>>> /gate/world/geometry/setYLength 2.0 m
>>> /gate/world/geometry/setZLength 2.0 m
>>>
>>> # BrainSphere
>>> /gate/world/daughters/name BrainSphere
>>> /gate/world/daughters/insert ellipsoid
>>> /gate/BrainSphere/setMaterial Brain
>>> /gate/BrainSphere/geometry/setXLength 6.58 cm
>>> /gate/BrainSphere/geometry/setYLength 8.57 cm
>>> /gate/BrainSphere/geometry/setZLength 5.73 cm
>>> /gate/BrainSphere/placement/setTranslation 0 0 0 cm
>>> /gate/BrainSphere/placement/setRotationAxis 0 1 0
>>> /gate/BrainSphere/placement/setRotationAngle 90 deg
>>> /gate/BrainSphere/vis/setVisible 1
>>> /gate/BrainSphere/vis/setColor white
>>>
>>>
>>> # UpperSpine
>>> /gate/world/daughters/name UpperSpine
>>> /gate/world/daughters/insert eltub
>>> /gate/UpperSpine/setMaterial SpineBone
>>> /gate/UpperSpine/geometry/setLong 2.45 cm
>>> /gate/UpperSpine/geometry/setShort 1.73 cm
>>> /gate/UpperSpine/geometry/setHeight 5 cm
>>> /gate/UpperSpine/placement/setRotationAxis 0 1 0
>>> /gate/UpperSpine/placement/setRotationAngle 90 deg
>>> /gate/UpperSpine/vis/setVisible 1
>>> /gate/UpperSpine/vis/setColor yellow
>>>
>>> # Thyroid
>>> /gate/world/daughters/name Thyroid
>>> /gate/world/daughters/insert cylinder
>>> /gate/Thyroid/setMaterial Thyroid
>>> /gate/Thyroid/geometry/setRmin 0.83 cm
>>> /gate/Thyroid/geometry/setRmax 1.85 cm
>>> /gate/Thyroid/geometry/setHeight 4.50 cm
>>> /gate/Thyroid/geometry/setPhiStart 0 deg
>>> /gate/Thyroid/geometry/setDeltaPhi 360 deg
>>> /gate/Thyroid/placement/setTranslation 0 -3 13 cm
>>> /gate/Thyroid/placement/setRotationAxis 0 1 0
>>> /gate/Thyroid/placement/setRotationAngle 90 deg
>>> /gate/Thyroid/vis/setVisible 1
>>> /gate/Thyroid/vis/setColor blue
>>>
>>> # Nazofarengeal
>>> /gate/world/daughters/name Nazofarengeal
>>> /gate/world/daughters/insert cylinder
>>> /gate/Nazofarengeal/setMaterial Nazofarengeal
>>> #/gate/Nazofarengeal/setMaterial G4_WATER
>>> /gate/Nazofarengeal/geometry/setRmin 4.00 cm
>>> /gate/Nazofarengeal/geometry/setRmax 4.50 cm
>>> /gate/Nazofarengeal/geometry/setHeight 3.00 cm
>>> /gate/Nazofarengeal/geometry/setPhiStart 0 deg
>>> /gate/Nazofarengeal/geometry/setDeltaPhi 180 deg
>>> /gate/Nazofarengeal/placement/setTranslation 0 0 4.50 cm
>>> /gate/Nazofarengeal/placement/setRotationAxis 0 1 0
>>> /gate/Nazofarengeal/placement/setRotationAngle 90 deg
>>> /gate/Nazofarengeal/vis/setVisible 1
>>> /gate/Nazofarengeal/vis/setColor green
>>>
>>>
>>> #=====================================================
>>> # PHYSICS
>>> #=====================================================
>>>
>>> /gate/physics/addPhysicsList QGSP_BERT_HP_EMY
>>>
>>> /gate/physics/displayCuts
>>> /gate/physics/print output/physics.txt
>>>
>>> #=====================================================
>>> # CUTS
>>> #=====================================================
>>>
>>> /gate/physics/Gamma/SetCutInRegion world 1 mm
>>> /gate/physics/Electron/SetCutInRegion world 1 mm
>>> /gate/physics/Positron/SetCutInRegion world 1 mm
>>>
>>> #/gate/physics/Gamma/SetCutInRegion target 0.1 mm
>>> #/gate/physics/Electron/SetCutInRegion target 0.1 mm
>>> #/gate/physics/Positron/SetCutInRegion target 0.1 mm
>>>
>>> /gate/physics/SetMaxStepSizeInRegion world 1 mm
>>> /gate/physics/ActivateStepLimiter proton
>>> /gate/physics/ActivateStepLimiter deuteron
>>> /gate/physics/ActivateStepLimiter triton
>>> /gate/physics/ActivateStepLimiter alpha
>>> /gate/physics/ActivateStepLimiter GenericIon
>>>
>>> /gate/physics/ActivateStepLimiter proton
>>> /gate/physics/ActivateStepLimiter e-
>>>
>>> # Verbose physic list (uncomment to display)
>>> /gate/physics/displayCuts
>>> /gate/physics/processList Enabled
>>> # /gate/physics/processList Initialized
>>>
>>> #=====================================================
>>> # OUTPUT - DETECTOR
>>> #=====================================================
>>>
>>> /gate/actor/addActor SimulationStatisticActor stat
>>> /gate/actor/stat/save output/stat.txt
>>> /gate/actor/stat/saveEveryNSeconds 20
>>>
>>> # ----------------------------------------------------
>>> # the following actor stores 3D distributions of
>>> # dose/edep/uncertainty/nbHit into files (mhd image file format)
>>>
>>> /gate/actor/addActor ProductionAndStoppingActor carbonMap
>>> /gate/actor/carbonMap/save output1/C11.root
>>> /gate/actor/carbonMap/attachTo BrainSphere
>>> /gate/actor/carbonMap/stepHitType random
>>> /gate/actor/carbonMap/setVoxelSize 4 4 4 mm
>>> /gate/actor/carbonMap/addFilter particleFilter
>>> /gate/actor/carbonMap/particleFilter/addParticle C11
>>> /gate/actor/carbonMap/saveEveryNSeconds 20
>>>
>>> ### A simple linac with backup X,Y and MLC
>>> #/gate/geometry/setMaterialDatabase data/PreciseMaterials.db
>>> #/control/execute mac/precise_Linac.mac
>>>
>>> /gate/actor/addActor DoseActor
>>> doseDistribution
>>> /gate/actor/doseDistribution/save output1/IDD-C11.root
>>> /gate/actor/doseDistribution/attachTo BrainSphere
>>> /gate/actor/doseDistribution/stepHitType random
>>> /gate/actor/doseDistribution/setVoxelSize 1.00 1.00 1.00 cm
>>> /gate/actor/doseDistribution/setPosition 0 0 0 cm
>>> /gate/actor/doseDistribution/saveEveryNSeconds 20
>>> #/gate/actor/doseDistribution/addFilter particleFilter
>>> #/gate/actor/doseDistribution/particleFilter/addParticle C11
>>> /gate/actor/doseDistribution/enableEdep true
>>> /gate/actor/doseDistribution/enableUncertaintyEdep false
>>> /gate/actor/doseDistribution/enableDose true
>>> /gate/actor/doseDistribution/enableUncertaintyDose false
>>> /gate/actor/doseDistribution/enableNumberOfHits false
>>>
>>> /gate/actor/addActor DoseActor
>>> doseDistribution3
>>> /gate/actor/doseDistribution3/save
>>> output1/IDD-Thyroid.root
>>> /gate/actor/doseDistribution3/attachTo Thyroid
>>> /gate/actor/doseDistribution3/stepHitType random
>>> /gate/actor/doseDistribution/setVoxelSize 1.00 1.00 1.00 cm
>>> /gate/actor/doseDistribution3/setPosition 0 0 0 cm
>>> /gate/actor/doseDistribution3/saveEveryNSeconds 20
>>> #/gate/actor/doseDistribution3/addFilter
>>> particleFilter
>>> #/gate/actor/doseDistribution3/particleFilter/addParticle C11
>>> /gate/actor/doseDistribution3/enableEdep true
>>> /gate/actor/doseDistribution3/enableUncertaintyEdep false
>>> /gate/actor/doseDistribution3/enableDose true
>>> /gate/actor/doseDistribution3/enableUncertaintyDose true
>>> /gate/actor/doseDistribution3/enableNumberOfHits false
>>>
>>> /gate/actor/addActor DoseActor doseNazo
>>> /gate/actor/doseNazo/save output1/IDD-Nazofarengeal.root
>>> /gate/actor/doseNazo/attachTo Nazofarengeal
>>> /gate/actor/doseNazo/stepHitType random
>>> /gate/actor/doseNazo/setVoxelSize 1.00 1.00 1.00 cm
>>> /gate/actor/doseNazo/setPosition 0 0 0 cm
>>> /gate/actor/doseNazo/saveEveryNSeconds 20
>>> #/gate/actor/doseNazo/addFilter particleFilter
>>> #/gate/actor/doseNazo/particleFilter/addParticle C11
>>> /gate/actor/doseNazo/enableEdep true
>>> /gate/actor/doseNazo/enableUncertaintyEdep false
>>> /gate/actor/doseNazo/enableDose true
>>> /gate/actor/doseNazo/enableUncertaintyDose false
>>> /gate/actor/doseNazo/enableNumberOfHits false
>>>
>>> /gate/actor/addActor SecondaryProductionActor Secondaries
>>> /gate/actor/Secondaries/save secondary-list.root
>>> /gate/actor/Secondaries/attachTo BrainSphere
>>>
>>> #=====================================================
>>> # INITIALISATION
>>> #=====================================================
>>>
>>> /gate/run/initialize
>>>
>>> #=====================================================
>>> # BEAMS
>>> #=====================================================
>>>
>>> # Carbon 12 beam
>>> /gate/source/addSource C12 gps
>>> /gate/source/C12/gps/particle ion
>>> /gate/source/C12/gps/ion 6 12
>>> /gate/source/C12/gps/ene/type Mono
>>> /gate/source/C12/gps/ene/mono 2314.24 MeV
>>> /gate/source/C12/gps/pos/type Beam
>>> /gate/source/C12/gps/pos/shape Circle
>>> /gate/source/C12/gps/pos/sigma_x 2.0 mm
>>> /gate/source/C12/gps/pos/sigma_y 2.0 mm
>>> /gate/source/C12/gps/ang/type beam2d
>>> /gate/source/C12/gps/ang/sigma_x 0 deg
>>> /gate/source/C12/gps/ang/sigma_y 0 deg
>>> /gate/source/C12/gps/pos/centre 0.0 0.0 4.5 cm
>>>
>>> # Proton beam
>>> #/gate/source/addSource prot gps
>>> #/gate/source/prot/gps/particle proton
>>> #/gate/source/prot/gps/ene/type Gauss
>>> #/gate/source/prot/gps/ene/mono 150 MeV
>>> #/gate/source/prot/gps/ene/sigma 10. MeV
>>> #/gate/source/prot/gps/ang/type cos
>>> #/gate/source/prot/gps/ang/type beam1d
>>> #/gate/source/prot/gps/ang/sigma_r 0. deg
>>> #/gate/source/prot/gps/pos/type Beam
>>> #/gate/source/prot/gps/pos/shape Circle
>>> #/gate/source/prot/gps/pos/centre 0. 0. 30. cm
>>> #/gate/source/prot/gps/pos/radius 3. mm
>>> #/gate/source/prot/gps/pos/sigma_r 0.2 mm
>>>
>>> #/gate/source/addSource mybeam LinacBeam
>>> #/gate/source/mybeam/setSourceFromPhaseSpaceFilename data/linac-beam.root
>>> #/gate/source/mybeam/attachTo linacPhSPlane
>>> #/gate/source/mybeam/setMaxLeafDistanceAccordingToTime
>>> data/precise_BeamSource.rmax
>>>
>>> #=====================================================
>>> # START BEAMS
>>> #=====================================================
>>>
>>> /gate/random/setEngineName MersenneTwister
>>> /gate/random/setEngineSeed auto
>>> /gate/application/setTotalNumberOfPrimaries 100
>>> /gate/application/start
>>>
>>> Khalid Hussain <khalidhussain1134 at gmail.com>, 4 Kas 2021 Per, 20:31
>>> tarihinde şunu yazdı:
>>>
>>>> Yes please I will check your email and guide you as per the best of my
>>>> knowledge.
>>>>
>>>> On Thu, Nov 4, 2021, 10:28 PM Deniz Erkal <dnzrklfzk at gmail.com> wrote:
>>>>
>>>>> Hello, there is an error in the codes I wrote. Can't receive data, can
>>>>> you help me with this?
>>>>>
>>>>>
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