[Gate-users] R: Positron range measurement
nini latiff
katoshka_7880 at yahoo.com
Mon Sep 26 07:47:58 CEST 2016
Hi Ottavia,
Thank you for your help. Now I can get the coordinates of annihilation points in x, y and z. However, I wondering is the coordinate relative to the origin of positron emission or location of the source?
About other outputs printed in the screen during the simulation such as Step#, KinE which is kinetic energy, dE (MeV), StepLength and TrackLength.
Is the Step# shows the number of the process before it is annihilated? Most of Step# value is 1 and sometimes 2. Is 1 shows positron being annihilated straight away after emitted from the nucleus (1 steps) ; is 2 indicates positron went through 1. being emitted and 2. positronium formation before being annihilated (2 steps)?
The value for KinE is 0 and sometimes 1 MeV and dE = 0 MeV. Is that mean 0 MeV is transferred during annihilation process?
I understand that Track is formed from series of Step. Is TrackLength meaning the positron range for that particular location/coordinate?
Thank you. RukiahPhD candidateUniversity of SydneyAustralia
On Friday, September 9, 2016 7:49 PM, Ottavia Bertolli <ottavia.bertolli at gmail.com> wrote:
Hi Rukhia,
I had to collect the positron range annihilation coordinates as well for project some years ago.What I suggest you should do is the following:
- when you define the verbosity, put the following command:
/tracking/verbose 2
as this will print on screen all the output of the simulation.
- when you then run your code, do it in the following way:
Gate your_code.mac | grep "phantom_phys annihil" > output.txt
and this will write in output.txt all the lines that contain an annihilation event, that is defined by "phantom_phys annihil"
- to then extract the coordinates of the annihilation points do the following:
sed 's/phantom_phys annihil/0/g;s/G4/0/g;s/\[//g;s/\]//g' output.txt > coordinates.txt
and this will extract from output.txt the (x,y,z) coordinates and write them in coordinates.txt.The result of all this is therefore to have a file (coordinates.txt) which is made up of three columns that correspond to the (x,y,z) of all the annihilation events generated in your simulation.
I hope this helps.
OttaviaPhD studentUniversity College LondonUnited Kingdom
2016-09-09 1:05 GMT+01:00 nini latiff <katoshka_7880 at yahoo.com>:
Hi Andrea,
Thank you very much for your reply.I did follow your suggestion to use Prod and Stop actor to measure positron range. I put commands
#============================= ===================
#Production and stopping particle position Actor
#============================= ===================
/gate/actor/addActor ProductionAndStoppingActor MyActor
/gate/actor/MyActor/save cuba
/gate/actor/MyActor/attachTo phantom
/gate/actor/MyActor/ setResolution 10 10 100
/gate/actor/MyActor/ stepHitType post
#============================= ======
#Filter on particle type (beta)
#============================= ======
/gate/actor/ ProductionAndStoppingActor /addFilter particleFilter
/gate/actor/ ProductionAndStoppingActor /particleFilter/addParticle beta My volume name is 'phantom'. However, it seems no output at all. It was like not recording the physics process which is 'positron annihilation'. I just get the output of Hits, Singles and Coincidence only which is information from the scanner only. I also concerned whether the output file name of actor should be the same as the output file name in setup-root file?
# S E T U P - R O O T F I L E
/gate/output/root/enable
/gate/output/root/setFileName cubajaya
/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
Please advise. Thank you very much.
RukiahPhD candidateUniversity of SydneyAustralia
On Saturday, September 3, 2016 3:04 AM, andrea.colantuono <andrea.colantuono at studenti.polito.it> wrote:
Hi Rukiah!To get the positron range, usually I use the actor "production and stop particle position" with the filter on the beta particles. In this way I found easy the visualize the stop position of positrons with TBrowser of ROOT.
Inviato da smartphone Samsung Galaxy.
-------- Messaggio originale --------Da: nini latiff <katoshka_7880 at yahoo.com> Data: 01/09/16 02:35 (GMT+01:00) A: gate-users at lists.opengatecollaboration.org Oggetto: [Gate-users] Positron range measurement
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
RukiahPhD CandidateThe University of SydneyAustralia
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