[Gate-users] Crosstalk and coincidence window

Devin VanElburg vanelbud at tbh.net
Tue May 12 18:21:38 CEST 2015 

Hello again,

I have determined my problem with the coincidence window command. The /gate/digitizer/Coincidences branch is not available until the proper system has been defined. I was attempting to simulate a two-plate PET scan, but had my system defined with systemType scanner. I just created a cylinder volume and used a ring repeater, but repeated the ring twice. Once I changed my systemType to cylindricalPET and attached the daughter volumes as required, I was able to set the coincidence window.

I'm still curious about my crosstalk question I posted previously, though. 

Now I have a different issue. When reading the root files, the leaves in the Hits and Singles branches are all filled, but my leaves for my Coincidences and delay branches are all empty. I can't figure out why. When I run the benchPET macro and PET example macro, it's all there.

I am simulating two plates of LYSO crystals with a point source of backtoback 511keV gamma rays. I made the emission angles of the source to be concentrated over the plates. I know this works because I'm getting plenty of entries in my Hits and Singles output branches. It's just the Coincidence and delay that I'm having trouble with. I made my phantom a sphere of water for now. Here is my code so far:


### databases
/gate/geometry/setMaterialDatabase /home/djvanel/GateMaterials.db
/gate/physics/addPhysicsList QGSP_BERT_EMV

### world
/gate/world/geometry/setXLength 100. cm
/gate/world/geometry/setYLength 100. cm
/gate/world/geometry/setZLength 100. cm
/gate/world/setMaterial Air

### visual
/vis/open OGLSX
/vis/drawVolume
/vis/viewer/set/viewpointThetaPhi 15 30
/vis/scene/add/axes
#/tracking/storeTrajectory 1
#/vis/scene/add/trajectories
/vis/scene/endOfEventAction accumulate
#/vis/viewer/zoom 1.5
/gate/world/vis/setVisible false

### cylinder
/gate/world/daughters/name cylindricalPET
#/gate/world/daughters/systemType cylindricalPET
/gate/world/daughters/insert cylinder
/gate/cylindricalPET/setMaterial Air
/gate/cylindricalPET/geometry/setRmin 6. cm
/gate/cylindricalPET/geometry/setRmax 15. cm
/gate/cylindricalPET/geometry/setHeight 25. cm
/gate/cylindricalPET/vis/forceWireframe
/gate/cylindricalPET/vis/setColor white
/gate/geometry/rebuild

### board
/gate/cylindricalPET/daughters/name board
/gate/cylindricalPET/daughters/insert box
/gate/board/geometry/setXLength 2. cm
/gate/board/geometry/setYLength 20. cm
/gate/board/geometry/setZLength 20. cm
/gate/board/vis/forceWireframe
/gate/board/vis/setColor white
/gate/board/placement/setTranslation 10. 0. 0. cm
/gate/geometry/rebuild

### box1
/gate/board/daughters/name box1
/gate/board/daughters/insert box
/gate/box1/geometry/setXLength 2. cm
/gate/box1/geometry/setYLength 5. cm
/gate/box1/geometry/setZLength 5. cm
/gate/box1/setMaterial Air
/gate/box1/vis/forceWireframe
/gate/box1/vis/setColor red
/gate/geometry/rebuild

### pixel
/gate/box1/daughters/name pixel
/gate/box1/daughters/insert box
/gate/pixel/geometry/setXLength 2. cm
/gate/pixel/geometry/setYLength 1. cm
/gate/pixel/geometry/setZLength 1. cm
/gate/pixel/setMaterial Air
/gate/pixel/vis/forceWireframe
/gate/pixel/vis/setColor red
/gate/geometry/rebuild

### crystal
/gate/pixel/daughters/name crystal
/gate/pixel/daughters/insert box
/gate/crystal/geometry/setXLength 2. cm
/gate/crystal/geometry/setYLength 1. cm
/gate/crystal/geometry/setZLength 1. cm
/gate/crystal/setMaterial LYSO
/gate/crystal/vis/forceSolid
/gate/crystal/vis/setColor green
/gate/geometry/rebuild

### repeat pixel
/gate/pixel/repeaters/insert cubicArray
/gate/pixel/cubicArray/setRepeatNumberY 5
/gate/pixel/cubicArray/setRepeatNumberZ 5
/gate/pixel/cubicArray/setRepeatVector 0. 1. 1. cm
/gate/geometry/rebuild

### repeat box
/gate/box1/repeaters/insert cubicArray
/gate/box1/cubicArray/setRepeatNumberY 4
/gate/box1/cubicArray/setRepeatNumberZ 4
/gate/box1/cubicArray/setRepeatVector 0. 5. 5. cm
/gate/geometry/rebuild

### repeat board
/gate/board/repeaters/insert ring
/gate/board/ring/setRepeatNumber 2

### phantom
/gate/world/daughters/name phantom
/gate/world/daughters/insert sphere
/gate/phantom/geometry/setRmin 0. cm
/gate/phantom/geometry/setRmax 3. cm
/gate/phantom/setMaterial Water
/gate/phantom/vis/forceSolid
/gate/phantom/vis/setColor blue
/gate/geometry/rebuild

### system
/gate/systems/cylindricalPET/rsector/attach board
/gate/systems/cylindricalPET/module/attach box1
/gate/systems/cylindricalPET/crystal/attach pixel
/gate/systems/cylindricalPET/layer0/attach crystal
/gate/systems/cylindricalPET/describe

### attach layer SD
/gate/phantom/attachPhantomSD
/gate/crystal/attachCrystalSD


### physics
/gate/physics/addProcess PhotoElectric
/gate/physics/processes/PhotoElectric/setModel StandardModel

/gate/physics/addProcess Compton
/gate/physics/processes/Compton/setModel StandardModel

/gate/physics/addProcess RayleighScattering gamma
/gate/physics/processes/RayleighScattering/setModel PenelopeModel

/gate/physics/addProcess GammaConversion
/gate/physics/processes/GammaConversion/setModel StandardModel

/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 RadioactiveDecay

/gate/physics/addProcess eMultipleScattering
/gate/physics/processes/eMultipleScattering/setGeometricalStepLimiterType e- distanceToBoundary
/gate/physics/processes/eMultipleScattering/setGeometricalStepLimiterType e+ distanceToBoundary

/gate/physics/processList Enabled
/gate/physics/processList Initialized

### cut in regions
#/gate/physics/Gamma/SetCutInRegion world 10. cm
#/gate/physics/Gamma/SetCutInRegion phantom 5. mm
#/gate/physics/SetMaxStepSizeInRegion phantom 5. mm

### initialization
/gate/run/initialize

### digitizer
/gate/digitizer/Singles/insert adder
/gate/digitizer/Singles/insert readout
/gate/digitizer/Singles/readout/setPolicy TakeEnergyWinner
/gate/digitizer/Singles/readout/setDepth 1
/gate/digitizer/Singles/insert crystalblurring
/gate/digitizer/Singles/crystalblurring/setCrystalResolutionMin 0.15
/gate/digitizer/Singles/crystalblurring/setCrystalResolutionMax 0.35
/gate/digitizer/Singles/crystalblurring/setCrystalQE 0.9
/gate/digitizer/Singles/crystalblurring/setCrystalEnergyOfReference 511. keV
/gate/digitizer/Singles/insert thresholder
/gate/digitizer/Singles/thresholder/setThreshold 0. keV
/gate/digitizer/Singles/insert upholder
/gate/digitizer/Singles/upholder/setUphold 750. keV

/gate/digitizer/Coincidences/setWindow 50. ns
/gate/digitizer/Coincidences/minSectorDifference 2
/gate/digitizer/Coincidences/MultiplesPolicy takeWinnerOfGoods

/gate/digitizer/name delay
/gate/digitizer/insert coincidenceSorter
/gate/digitizer/delay/setWindow 50. ns
/gate/digitizer/delay/setOffset 500. ns
/gate/digitizer/delay/MultiplesPolicy takeWinnerOfGoods
/gate/digitizer/delay/setDepth 1

### source
/gate/source/addSource Gamma
/gate/source/Gamma/gps/centre 0. 0. 0. cm
/gate/source/Gamma/setActivity 100000. becquerel
/gate/source/Gamma/gps/particle gamma
/gate/source/Gamma/setType backtoback
/gate/source/Gamma/gps/energytype Mono
/gate/source/Gamma/gps/monoenergy 511. keV
/gate/source/Gamma/setForcedUnstableFlag true
/gate/source/Gamma/setForcedHalfLife 1000 s
/gate/source/Gamma/gps/angtype iso
/gate/source/Gamma/gps/mintheta 60. deg
/gate/source/Gamma/gps/maxtheta 120. deg
/gate/source/Gamma/gps/minphi 120. deg
/gate/source/Gamma/gps/maxphi 240. deg

### output
/gate/output/root/enable
/gate/output/root/setFileName dualplate
/gate/output/root/setRootHitFlag 1
/gate/output/root/setRootSinglesFlag 1
/gate/output/root/setRootNtupleFlag 1
/gate/output/root/setRootCoincidencesFlag 1
/gate/output/root/setRootdelayFlag 1

### random
# JamesRandom Ranlux64 MersenneTwister
/gate/random/setEngineName MersenneTwister
#/gate/random/setEngineSeed default
#/gate/random/setEngineSeed auto
/gate/random/setEngineSeed 123456789
#/gate/random/resetEngineFrom fileName
/gate/random/verbose 0

### simulation length
/gate/application/setTimeSlice 1 s
/gate/application/setTimeStart 0. s
/gate/application/setTimeStop 10 s



Any help is appreciated! Thank you
Devin Van Elburg

---------------
Physics w/ c/ Biomedical Physics
Lakehead University


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