[Gate-users] Positron range measurement
David Boersma
david.boersma at physics.uu.se
Thu Sep 1 09:42:10 CEST 2016
Hi Rukiah,
Welcome to GATE!
Which program did you use to "open" the MyOutputFile.root file?
For me the usual way to explore the contents of a new root file is to
start "root" from the command line and then at the first root prompt I
type: "new TBrowser;" (followed by enter/return). A ROOT file browser
should open up, in which you should be able to navigate (in the left
tab) to your root file. Click on it see its contents. A root file can
contain all kinds of objects, but usually you are interested in "trees"
or "ntuples" (tabulated data), and "histograms" (1D/2D/3D distributions).
ROOT is a huge humongous program/framework, put together over decades by
a pack of crazy hacking particle physicists affiliated with CERN. See
the ROOT web page (root.cern.ch) for documentation, in particular the
User Guide. It can be intimidating, especially if you are not a
programmer. But don't be afraid, you only need to learn a very small
part of ROOT in order to be able to do most of the things that you'll
need when working with GATE output. There are many tutorials on the web
to teach you the basics of ROOT trees and histograms.
Good luck!
David
Den 01/09/2016 kl. 02:35, skrev nini latiff:
> Hi everyone,
>
> I am Rukiah. I am new with this GATE. Currently I working to measure
> positron range. I already put my tracklength actor so that I can obtain
> positron range output. When I run the macrofile below, visualization is
> good. However, I can not open the MyOutputFile.root as the message says
> 'failed to read the file type data'. Please help regarding this matter
> as I have no background in programming. Thank you.
>
>
> #=====================================================
> # VISUALISATION
> #=====================================================
>
>
> #/vis/disable
>
> /vis/open OGLS
> /vis/viewer/set/viewpointThetaPhi 60 60
> /vis/viewer/zoom 1.0
> /vis/drawVolume
> /vis/scene/add/trajectories
>
>
> /control/execute Verbose.mac
>
>
> #=====================================================
> # GEOMETRY
> #=====================================================
>
>
> /gate/geometry/setMaterialDatabase GateMaterials.db
>
>
> #
> # W O R L D
> #
> /gate/world/geometry/setXLength 40. cm
> /gate/world/geometry/setYLength 40. cm
> /gate/world/geometry/setZLength 40. cm
> #-------------------oooooOOOOO00000OOOOOooooo---------------------#
> # #
> # D E F I N I T I O N A N D D E S C R I T I O N #
> # O F Y O U R P H A N T O M #
> # #
> #-------------------oooooOOOOO00000OOOOOooooo---------------------#
>
>
> /gate/world/daughters/name phantom
> /gate/world/daughters/insert cylinder
> /gate/phantom/setMaterial Water
> /gate/phantom/vis/forceWireframe
> /gate/phantom/vis/setColor red
> /gate/phantom/geometry/setRmax 5 cm
> /gate/phantom/geometry/setHeight 10 cm
> /gate/phantom/attachPhantomSD
>
> #=====================================================
> # PHYSICS
> #=====================================================
> #/gate/physics/addProcess PhotoElectric
> #/gate/physics/processes/PhotoElectric/setModel StandardModells
>
> #/gate/physics/addProcess Compton
> #/gate/physics/processes/Compton/setModel StandardModel
>
> #/gate/physics/addProcess RayleighScattering
> #/gate/physics/processes/RayleighScattering/setModel PenelopeModel
>
> #/gate/physics/addProcess ElectronIonisation
> #/gate/physics/processes/ElectronIonisation/setModel StandardModel e-
> #/gate/physics/processes/ElectronIonisation/setModel StandardModel e+
>
> #/gate/physics/addProcess Bremsstrahlung
> #/gate/physics/processes/Bremsstrahlung/setModel StandardModel e-
> #/gate/physics/processes/Bremsstrahlung/setModel StandardModel e+
>
> /gate/physics/addProcess PositronAnnihilation
>
> #/gate/physics/addProcess MultipleScattering e+
> #/gate/physics/addProcess MultipleScattering e-
>
> /gate/physics/processList Enabled
> /gate/physics/processList Initialized
>
> /gate/run/initialize
> #=====================================================
> # CUTS
> #=====================================================
>
> #/gate/physics/Gamma/SetCutInRegion crystal 1.0 cm
> #/gate/physics/Electron/SetCutInRegion crystal 1.0 cm
> #/gate/physics/Positron/SetCutInRegion crystal 1.0 cm
>
>
> #/gate/physics/Gamma/SetCutInRegion phantom 0.1 mm
> #/gate/physics/Electron/SetCutInRegion phantom 0.1 mm
> /gate/physics/Positron/SetCutInRegion phantom 10 cm
>
> /gate/physics/SetMaxStepSizeInRegion phantom 1 cm
>
> #TrackLengthActor
>
> /gate/actor/addActor TrackLengthActor MyActor
> /gate/actor/MyActor/save MyOutputFile.root
> /gate/actor/MyActor/setLmin 0 mm
> /gate/actor/MyActor/setLmax 10 cm
> /gate/actor/MyActor/setNumberOfBins 200
>
> #-------------------oooooOOOOO00000OOOOOooooo---------------------#
> # #
> # D E F I N I T I O N O F #
> # Y O U R V E R B O S I T Y L E V E L #
> # #
> #-------------------oooooOOOOO00000OOOOOooooo---------------------#
>
> /control/execute Verbose.mac
>
> #=====================================================
> # INITIALISATION
> #=====================================================
>
> /gate/run/initialize
>
> #-------------------oooooOOOOO00000OOOOOooooo---------------------#
> # #
> # D E F I N I T I O N O F #
> # Y O U R O U T P U T F I L E #
> # #
> #-------------------oooooOOOOO00000OOOOOooooo---------------------#
>
>
> # R A N D O M
>
> # JamesRandom Ranlux64 MersenneTwister
> /gate/random/setEngineName JamesRandom
> #/gate/random/setEngineSeed default
> #/gate/random/setEngineSeed auto
> #/gate/random/setEngineSeed 123456789
> /gate/random/setEngineSeed default
> #/gate/random/resetEngineFrom fileName
> /gate/random/verbose 1
>
>
> # S E T U P - R O O T F I L E
> /gate/output/root/enable
> /gate/output/root/setFileName MySimu
> /gate/output/root/setRootSinglesAdderFlag 1
> /gate/output/root/setRootSinglesReadoutFlag 1
> /gate/output/root/setRootHitFlag 1
> /gate/output/root/setRootSinglesFlag 1
> /gate/output/root/setRootCoincidencesFlag 1
>
> #-------------------oooooOOOOO00000OOOOOooooo---------------------#
> # #
> # P O S I T R O N E M I S S I O N S O U R C E #
> # #
> # Ga-68 #
> # #
> # NB : In this example, each isotope source is generated #
> # in a sphere placed at the center of the FOV. #
> # The sphere radius is set at 0.5 cm. #
> # #
> #-------------------oooooOOOOO00000OOOOOooooo---------------------#
>
> #
> # For Ga68
> #
>
> /gate/source/addSource sourceGa68
> /gate/source/sourceGa68/setActivity 10. becquerel
> /gate/source/sourceGa68/gps/particle e+
> /gate/source/sourceGa68/setForcedUnstableFlag true
> /gate/source/sourceGa68/gps/energytype Ga68
> /gate/source/sourceGa68/setForcedHalfLife 6586 s
> /gate/source/sourceGa68/gps/type Volume
> /gate/source/sourceGa68/gps/shape Sphere
> /gate/source/sourceGa68/gps/radius 0.01 mm
> /gate/source/sourceGa68/gps/centre 0. 0. 0. cm
> /gate/source/sourceGa68/vis/setColor red
> /gate/source/sourceGa68/gps/confine NULL
> /gate/source/sourceGa68/gps/angtype iso
>
>
>
> /gate/source/list
> #-------------------oooooOOOOO00000OOOOOooooo---------------------#
> # #
> # S T A R T A C Q U I S I T I O N #
> # T I M E P A R A M E T E R S #
> # #
> #-------------------oooooOOOOO00000OOOOOooooo---------------------#
>
> #
> # EXPERIMENT
> #
> /gate/application/setTimeSlice 120. s
> /gate/application/setTimeStart 0. s
> /gate/application/setTimeStop 240. s
>
> #
> # LET'S RUN THE SIMULATION!
> #
> /gate/application/startDAQ
> #/gate/output/allowNoOutput
>
>
>
> Rukiah
> PhD Candidate
> The University of Sydney
> Australia
>
> */_
> _/*
>
>
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>
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