[Gate-users] How do you get the deposited energy for each layer or crystal in a separate output/tree?

David Leibold D.Leibold at tudelft.nl
Mon May 30 08:13:00 CEST 2022

Dear Paul,

have you tried accessing the componentID, volumeID, pixelID etc. stored in the root tree? These variables should enable you to figure out in which element of your system an event was registered.

Best regards,

On 25 May2022, at 15:01, Klever, Paul <paul.klever at alumni.fh-aachen.de<mailto:paul.klever at alumni.fh-aachen.de>> wrote:

Dear Users,

I am currently working on a cylindrical PET system with heterostructured scintillators. At first I am designing a one block detector and want to get a proper readout done before creating a whole scanner.
Goal of this is to simulate a couple of materials and calculate their CTRs. My problem is that eventhough I assigned the two different layers as separate sensitive detectors, I only get one root tree for the energy deposited in the singles tree.
I've tried it with one crystal for each layer, or with just one crystal for both layers. I've tried the DoseActor, but the created File seems to have as many entries as I define in the macro with the variable z in "/setResolution x y z", eventhough I dont have that many hits or singles. So I don't think thats a proper way to get the deposited energy for each layer.

There is not much to find about that topic, neither in the mailing list archive nor in the benchmarks.

I appreciate any advice.
Best regards

Paul K.

Here is my macro. I use Gate 9.1 with geant4-10-07. I've installed the precompiled version of Gate and recompiled it, to activate photons and surfaces.

# M A T E R I A L  F I L E

/gate/geometry/setMaterialDatabase          data/GateMaterials.db
/gate/geometry/setIonisationPotential EJ232 64.7 eV


# W O R L D

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


# S Y S T E M

/gate/world/daughters/name         cylindricalPET
/gate/world/daughters/systemType    cylindricalPET
/gate/world/daughters/insert box
/gate/cylindricalPET/setMaterial Air
/gate/cylindricalPET/geometry/setXLength 15 mm
/gate/cylindricalPET/geometry/setYLength 2.1 mm
/gate/cylindricalPET/geometry/setZLength 3. mm
/gate/cylindricalPET/placement/setTranslation 0 0 -1.5 mm
/gate/cylindricalPET/vis/setColor gray


# P H A N T O M


# R S E C T O R

/gate/cylindricalPET/daughters/name rsector
/gate/cylindricalPET/daughters/insert box
/gate/rsector/placement/setTranslation 0 0 0 mm
/gate/rsector/geometry/setXLength 15. mm
/gate/rsector/geometry/setYLength 2.1 mm
/gate/rsector/geometry/setZLength 3. mm
/gate/rsector/vis/setColor green


# M O D U L E

/gate/rsector/daughters/name module
/gate/rsector/daughters/insert box
/gate/module/placement/setTranslation 0 0 0 mm
/gate/module/geometry/setXLength 15. mm
/gate/module/geometry/setYLength 2.1 mm
/gate/module/geometry/setZLength 3. mm
/gate/module/vis/setColor blue


# C R Y S T A L 0

/gate/module/daughters/name crystal
/gate/module/daughters/insert box
/gate/crystal/geometry/setXLength 15. mm
/gate/crystal/geometry/setYLength 2.1 mm
/gate/crystal/geometry/setZLength 3. mm
/gate/crystal/placement/setTranslation 0 0. 0  mm
/gate/crystal/setMaterial Air
/gate/crystal/vis/setColor yellow
/gate/crystal/vis/setVisible false

# L A Y E R 0

/gate/crystal/daughters/name LYSO
/gate/crystal/daughters/insert box
/gate/LYSO/geometry/setXLength 15. mm
/gate/LYSO/geometry/setYLength 0.1 mm
/gate/LYSO/geometry/setZLength 3. mm
/gate/LYSO/placement/setTranslation 0 0 0 mm
/gate/LYSO/setMaterial LYSO
/gate/LYSO/vis/setColor yellow

# L A Y E R 1

/gate/crystal/daughters/name EJ232
/gate/crystal/daughters/insert box
/gate/EJ232/geometry/setXLength 15. mm
/gate/EJ232/geometry/setYLength 0.1 mm
/gate/EJ232/geometry/setZLength 3. mm
/gate/EJ232/placement/setTranslation 0 0 0 mm
/gate/EJ232/setMaterial EJ232
/gate/EJ232/vis/setColor red

# R E P E A T C R Y S T A L

/gate/LYSO/repeaters/insert cubicArray
/gate/LYSO/cubicArray/setRepeatNumberX 1
/gate/LYSO/cubicArray/setRepeatNumberY 11
/gate/LYSO/cubicArray/setRepeatNumberZ 1
/gate/LYSO/cubicArray/setRepeatVector 0. 0.2 0.  mm

/gate/EJ232/repeaters/insert cubicArray
/gate/EJ232/cubicArray/setRepeatNumberX 1
/gate/EJ232/cubicArray/setRepeatNumberY 10
/gate/EJ232/cubicArray/setRepeatNumberZ 1
/gate/EJ232/cubicArray/setRepeatVector 0. 0.2 0. mm


# R E P E A T  M O D U L E

#/gate/module/repeaters/insert linear
#/gate/module/linear/setRepeatNumber 33
#/gate/module/linear/setRepeatVector 0. 0. 3.01 mm

# R E P E A T  R S E C T O R

#/gate/rsector/repeaters/insert ring
#/gate/rsector/ring/setRepeatNumber 250

#/gate/cylindricalPET/placement/setRotationAxis 0 0 1


# A T T A C H S Y S T E M


/gate/systems/cylindricalPET/rsector/attach rsector
/gate/systems/cylindricalPET/module/attach module
/gate/systems/cylindricalPET/crystal/attach crystal
/gate/systems/cylindricalPET/layer0/attach LYSO
/gate/systems/cylindricalPET/layer1/attach EJ232

# A C T O R

/gate/actor/addActor DoseActor             MyActor0
/gate/actor/MyActor0/save                   EdepLYSO.txt
/gate/actor/MyActor0/attachTo               LYSO
/gate/actor/MyActor0/stepHitType            random
/gate/actor/MyActor0/setResolution          1 1 3000
/gate/actor/MyActor0/enableEdep             true
/gate/actor/MyActor0/enableDose          false

/gate/actor/addActor DoseActor             MyActor1
/gate/actor/MyActor1/save                   EdepEJ232.txt
/gate/actor/MyActor1/attachTo               EJ232
/gate/actor/MyActor1/stepHitType            random
/gate/actor/MyActor1/setResolution          1 1 3000
/gate/actor/MyActor1/enableEdep             true
/gate/actor/MyActor1/enableDose          false





# V I E W E R #
#/vis/open                     OGLSX

# set the view angle
#/vis/viewer/set/viewpointThetaPhi        45 45

# define the zoom factor
#/vis/viewer/zoom                    50.

# set the drawing style
#/vis/viewer/set/style                      wireframe
#/vis/viewer/set/style                surface

# tell the viewer to draw the volume

#/tracking/verbose 2

# The trajectories for each run should be drawn together
# don't store trajectories = 0; store trajectories = 1
#/tracking/storeTrajectory 1

# Requests viewer to refresh hits, tracks, etc., at end of event.
# Or to accumulate drawings. Detector remains or is redrawn.
#/vis/scene/endOfEventAction accumulate


/gate/physics/addPhysicsList emstandard_opt4
#/gate/physics/addPhysicsList emlivermore

/gate/physics/addProcess Scintillation
/gate/physics/addProcess OpticalAbsorption
/gate/physics/addProcess OpticalRayleigh
#/gate/physics/addProcess OpticalBoundary
#/gate/physics/addProcess OpticalMie
/gate/physics/addProcess OpticalWLS

#/gate/physics/addPhysicsList emlivermore
#/gate/physics/addProcess  Scintillation

#/gate/physics/addProcess RadioactiveDecay

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



/gate/LYSO/surfaces/name surface1
/gate/LYSO/surfaces/insert EJ232
/gate/LYSO/surfaces/surface1/setSurface perfect_apd

/gate/EJ232/surfaces/name surface2
/gate/EJ232/surfaces/insert LYSO
/gate/EJ232/surfaces/surface2/setSurface perfect_apd


/gate/digitizer/Singles/insert opticaladder
/gate/digitizer/Singles/insert readout
/gate/digitizer/Singles/readout/setDepth 4 #Crystal | "5" Layer

/gate/digitizer/Singles/insert blurring
/gate/digitizer/Singles/blurring/setEnergyOfReference 511. keV

#/gate/digitizer/verbose                 1

 # C O I N C I D E N C E

#/gate/digitizer/Coincidences/setWindow 4. ns
#/gate/digitizer/Coincidences/setOffset 0. ns
#/gate/digitizer/Coincidences/minSectorDifference 88

#/gate/digitizer/DelCoinc/addSource prompts
#/gate/digitizer/DelCoinc/addSource delayed

# D E F I N E  T H E  S O U R C E

# source: opticalPhoton

/gate/source/addSource                 Mysource gps
#/gate/source/Mysource/setType         backtoback
/gate/source/Mysource/gps/particle        gamma
/gate/source/Mysource/gps/pos/shape        Sphere
/gate/source/Mysource/gps/pos/radius    0.125 mm
/gate/source/Mysource/gps/pos/centre     0. 0. 10.125 mm
/gate/source/Mysource/gps/ene/type         Mono
/gate/source/Mysource/gps/ene/mono         511. keV
/gate/source/Mysource/setActivity         100000. Bq
/gate/source/Mysource/gps/ang/type        iso
#/gate/source/Mysource/gps/polarization     1 1 1

/gate/source/Mysource/gps/ang/mintheta     0 deg
/gate/source/Mysource/gps/ang/maxtheta     30 deg

/gate/source/Mysource/gps/ang/minphi     0 deg
/gate/source/Mysource/gps/ang/maxphi     360. deg

#  D A T A   O U T P U T

/gate/output/root/setFileName             LYSOEJ232CP1
#/gate/output/root/setRootSinglesAdderFlag 1
#/gate/output/root/setRootSinglesReadoutFlag 1
/gate/output/root/setRootHitFlag 1
/gate/output/root/setRootSinglesFlag 1
#/gate/output/root/setRootNtupleFlag 1
#/gate/output/root/setRootCoincidencesFlag 1
/gate/output/root/setRootOpticalFlag          1


#  R A N D O M   E N G I N E  A N D  S E E D
# JamesRandom
/gate/random/setEngineName                      JamesRandom
/gate/random/setEngineSeed auto
/gate/random/verbose                            0

#   M E A S U R E M E N T   S E T T I N G S

/gate/application/setTimeSlice   1 s
/gate/application/setTimeStart   0 s
/gate/application/setTimeStop    1 s


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