[Gate-users] (Reproduce my problem)

[Atiq Ur Rahman]

Dear Users,
Anyone  who wants to reproduce my problem can directly go to google drive.
Here is the link to the problem.
https://drive.google.com/drive/folders/1r2LPzE7KLZX0-kfVTNaQyWADLgelVdR9?usp=sharing
Regards
Atiq

On Thu, Jul 8, 2021 at 4:05 AM Atiq Ur Rahman <atiqchep at gmail.com> wrote:

> Dear Gate users,
> I am trying to calculate the dose for the CT based Phantom (512x512x361
> matrix) using a proton beam. I read dicom images directly and define the HU
> to material conversion file.  I am using the vGate.8 virtual machine.
> *Problem:* If I define only three materials (vacuum, Air and
> TissueEquivalent ) the simulation gives output for 1000 primaries very fast
> in a couple of seconds and I can get the output. But if I define one extra
> material (any material, I have tried different materials) , let say
> (Vacuum, Air, TissueEquvalent, Liver)  the simulation runs for a very very
> long time even for 1 primary particle (Actually does not finish even in 10
> hours). Can you give me some suggestions to fix the problem. What is the
> possible cause of the problem? There seems to be something wrong with my
> approach. I have shared my code below.  I have 306 Dicom images put in a
> single directory.
> Definition of the HUToMat.txt
>
> -2000 -800   Vacuum
> -800  -40    Air
> -40    200   Blood
> 200    19000 TissueEquivalent
>
> #CODE
> /
>
> *control/execute mac/verbose.mac/gate/geometry/setMaterialDatabase
>  data/GateMaterials.db*
>
> *#WorldVolume*
>
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> */gate/world/setMaterial
> Vacuum/gate/world/geometry/setXLength           100
> cm/gate/world/geometry/setYLength           100
> cm/gate/world/geometry/setZLength           100
> cm/gate/world/daughters/name
> Pat/gate/world/daughters/insert
> box/gate/Pat/geometry/setXLength             32
> cm/gate/Pat/geometry/setYLength             32
> cm/gate/Pat/geometry/setZLength             32 cm*
>
> *#Daughter for DICOM*
>
>
> */gate/Pat/daughters/name
> Volume/gate/Pat/daughters/insert
>  ImageRegularParametrisedVolume #      ImageNestedParametrisedVolume *
>
> *#CoversionFile*
> */gate/Volume/geometry/setHUToMaterialFile       data/HUToMat.txt *
>
>
>
>
> */gate/Volume/geometry/setImage              New_CODE/data/dcm/1.dcm
> #/gate/Volume/placement/setRotationAxis          0 -1
> 0/gate/Volume/placement/setRotationAngle         90
> deg/gate/Volume/setSkipEqualMaterials   1*
>
>
> *#SIMPLEDOSEActor*
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> */gate/actor/addActor
> DoseActor  doseDistribution_text/gate/actor/doseDistribution_text/save
>
>  output/Dose_Map_Energy_MeV_1D_5material.root/gate/actor/doseDistribution_text/attachTo
>              Volume
> #PMMA_Block/gate/actor/doseDistribution_text/stepHitType
> random/gate/actor/doseDistribution_text/setSize               300 300 300
> mm/gate/actor/doseDistribution_text/setResolution         1280 1
> 1/gate/actor/doseDistribution_text/enableEdep
>  true/gate/actor/doseDistribution_text/enableUncertaintyEdep
> true/gate/actor/doseDistribution_text/enableDose
>  true/gate/actor/doseDistribution_text/enableUncertaintyDose
> true/gate/actor/doseDistribution_text/enableNumberOfHits    true*
>
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> *#PhysicsList/gate/physics/addPhysicsList
> QGSP_BIC_HP_EMZ#Cuts/gate/physics/Gamma/SetCutInRegion     world 10
> mm/gate/physics/Electron/SetCutInRegion    world 10
> mm/gate/physics/Positron/SetCutInRegion    world 10
> mm/gate/physics/Proton/SetCutInRegion       world 10
> mm/gate/physics/Gamma/SetCutInRegion     Pat 1
> mm/gate/physics/Electron/SetCutInRegion    Pat 1
> mm/gate/physics/Positron/SetCutInRegion    Pat 1
> mm/gate/physics/Proton/SetCutInRegion       Pat 1
> mm/gate/physics/SetMaxStepSizeInRegion    Pat 1
> mm/gate/physics/ActivateStepLimiter proton/gate/physics/displayCuts*
>
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> */gate/run/initialize/gate/random/setEngineName
> MersenneTwister/gate/random/setEngineSeed auto#Source/gate/source/addSource
> PBS PencilBeam/gate/source/PBS/setParticleType
> proton/gate/source/PBS/setEnergy 90 MeV/gate/source/PBS/setSigmaEnergy .88
> MeV/gate/source/PBS/setPosition 0 0 -36.5 cm /gate/source/PBS/setSigmaX 3.0
> mm /gate/source/PBS/setSigmaY 3.0 mm #/gate/source/PBS/setRotationAxis 0 1
> 0#/gate/source/PBS/setRotationAngle 90 deg/gate/source/PBS/setSigmaTheta 20
> mrad/gate/source/PBS/setSigmaPhi   20 mrad
> /gate/source/PBS/setEllipseXThetaEmittance 40 mm*mrad #40 mm*mrad,
> 2mm*mrad/gate/source/PBS/setEllipseYPhiEmittance   40 mm*mrad #40 mm*mrad,
> 2mm*mrad#positive-> converging beam; negative diverging
> beam/gate/source/PBS/setEllipseXThetaRotationNorm
> positive/gate/source/PBS/setEllipseYPhiRotationNorm
> positive/gate/application/setTotalNumberOfPrimaries 1000
> /gate/application/start*
>
> *I have dumped this file into single density (.mhd +.raw) format and tried
> to read it from a single density file but it has no difference in
> performance. Below is the information in the header file.*
>
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> *ObjectType = ImageNDims = 3BinaryData = TrueBinaryDataByteOrderMSB =
> FalseCompressedData = FalseTransformMatrix = 1 0 0 0 1 0 0 0 1Offset =
> -151.494 -36.6564 1115CenterOfRotation = 0 0 0ElementSpacing = 0.589844
> 0.589844 0.5DimSize = 512 512 361AnatomicalOrientation = ???ElementType =
> MET_FLOATElementDataFile = density-ffs-dcm_5mat.raw*
>
> *Please ask me any further details if you feel anything ambiguous.  Your
> suggestions and solutions are needed. Thank you in advance!*
> *Regards*
>
> *Atiq*
>
>
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